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1. 26 C10 ASCIIZ 2 in 24 hours format e g 18 34 04 36 C72 ASCIIZ 2 username operator or Unknown or 0 108 C218 ASCIIZ 2 company name etc or Unknown or 0 326 c60 ASCIIZ 2 sample identification 386 C160 ASCIIZ 2 comment 546 C2 2 bytes of padding for alignment 548 14 goniometer model 0 unmeasured 0 Theta 2 Theta D5000 1 measured 2 active 1 Theta Theta D5000 2 D5000 matic M86 E01008 DIFFRACP S Raw Data File Format GADDS Software Reference Manual 3 AL Theta D5000 4 GADDS FRAMBO 2 17 4 circle 2 18 Small XYZ stage 2 5 SAXS 2 19 Large XYZ stage 2 6 SMART 2 20 1 4 circle 2 7 8 9 reserved 9999 unknown 10 Theta 2 Theta D5005 556 14 sample changer 11 Theta Theta D5005 0 None 12 reserved 1 40 position 13 AL Theta D5005 2 Y matic 20 Theta 2 Theta other 3 X Y matic 21 Theta Theta other 9999 unknown 22 Matic other 560 14 goniometer controller 23 AL Theta other 0 STD only 9999 unknown 1 STD TC 552 14 goniometer stage 2 STD FDC 0 Standard 3 STD FDC TC 1 Synchron rotation 16 GGCS 2 2 Rotation reflection 9999 unknown 3 Rotation transm
2. GB A EET Weak 75 Gavin avec Weak 85 Percentage of average pixel below which pixel is considered weak Lower criteria is used for edge at radius and higher criteria is used for center Assume linear function with respect to radius Go ieee eet Hot G6 oscar dace Hot Percentage of average pixel above which pixel is considered hot Lower criteria is used for center and higher criteria is used for edge at radius Assume linear function with respect to radius A ee ee ee eee Cluster 8 Number of adjacent neighbor pixels to be considered a cluster excludes bad pixel in question Clusters of questionable pixels at or above this size are flagged Range is 0 to 8 LOCAL 00000008 Local average Yes Check to calculate average pixel within a box of 15x15 for 512 frames 31x31 for 1024 frames or 63x63 for 2048 frames The cen ter 3x3 pixels are skipped as are the over flow rows Uncheck to use average pixel as a function of radius from center 115 125 M86 E01008 Process Routines GADDS Software Reference Manual 6 6 Process gt Spatial gt New Acquire data and generate a new spatial correction Menu Command Process gt Spatial gt New Accelerator none User Level 3 SLAM Syntax SPATIAL NEW 1 COUNTS lt n gt DISPLAY lt n gt REALTIME FILE lt s gt XENGEN THRESHOLD lt n gt SHUTTER This routine is used to collect a brass fiducial plate image at
3. M86 E01008 GADDS Software Reference Manual Project Management Routines 2 9 Project gt Overwrite defaults Overwrite the default configuration with the current settings Menu Command Project gt Overwrite defaults Accelerator None User Level 3 SLAM Syntax PROJECT MAKEDEF Use this command to define the system wide default settings for projects Typically your GADDS administrator will issue this command whenever he changes the goniometer stage or other hardware option Before issuing this command go through all menu options and define your default settings The most critical settings are located in the com mand e Edit gt Configure gt User settings e Edit gt Configure gt Admin settings e Collect gt Goniometer gt All commands Double check that these settings are correct After issuing the Project gt Overwrite defaults command the message appears Save the current configuration as default values for new copy edit reset to defaults option Click Yes to continue No to abort The pro gram will save current settings in the GADDS SYSTEM gaddsdef _nc system wide default configuration file Whenever the reset to defaults option is checked in a Project gt New gt Copy or gt Edit command these system wide defaults are read NOTE If your GADDS administrator frequently changes goniometer stages he may wish to cre ate a project for each stage with the appropriate
4. GADDS fixes omega at 345 for optical alignment on a 4 circle goniometer see the Collect gt Goniom gt Optical command In addition during data collection GADDS rotates phi back and forth by 170 every few frames to help reduce possible sample icing TEMP lt n gt 6 Current Temperature 1 Enter current temperature in degrees K 1 room temperature or unknown default value The Collect gt Goniometer gt Temper ature command see Section 5 28 can also be used to define this parameter XBEAM lt n gt Direct Beam X current value Unwarped X pixel coordinate 0 to frame size 1 of direct beam center at 2 Theta 0 in the Bruker coordinate convention with 0 0 at the lower left of a displayed frame It is important that you enter the correct value here before collecting frames that will be analyzed with the interactive cursor com mands used in conjunction with the spatial correction or for determination of crystal ori entation with the Reflection Array com mands These commands rely heavily on the value given for the beam center The value is stored in the output header of Bruker format frames and in output p4p files If you change the value of the FRAME SIZE field the beam center position will be scaled and converted to the new frame size convention the display will be updated when you tab out of the FRAMESIZE field NOTE If you save frames in raw warped mode this should be
5. Num integration steps 10 For the numerical integration algorithm input the number of integration steps along the radius The more integration steps the greater the accuracy but the longer the time for calculation A value of 10 seems to give sufficient accuracy MU lt N gt on eee Sample mucm 1 8 0 Enter sample mu in cm 1 RADIUS lt n gt Radius cm 0 03 Enter sample radius in cm M86 E01008 29 Process Routines GADDS Software Reference Manual 6 13 Process gt Corrections gt Plate Menu Command Process gt Corrections gt Plate Accelerator none User Level 2 SLAM Syntax CORRECTIONS PLATE 1 2 3 X lt n gt Y lt n gt Z lt n gt MU lt n gt THICKNESS lt n gt Calculates an absorption correction table based on a flat plate of infinite dimensions and a given thickness Thus the flat plate is larger than the incident beam in all directions for all orienta tions The sample vector is expressed in goniometer head coordinates where when the goniometer angles are all zero X direction of incident beam away from tube Y normal to X and Z and forms right handed coordinate system Z vertical direction up For speed considerations we will only calculate the absorption correction every 16 or 32 for 1K frames pixels along the detector Intermediate pixel corrections may be determined using linear extrapolation Both transmission and reflection c
6. PEAKS AUTO 1 FWHM n PEAKSIG n BKGDSIG n VERBOSE GRAPH SPLIT n amp FLAG n RATIO n 2 3 where the arguments are 1 CALIBRATION FILE Calibration file containing representative profile lineshapes BKGDSIG n BKGD Background significance used to determine regions containing peaks PEAKSIG n PEAK SIGNIFICANCE Peak significance to adding new peaks FWHM n INITIAL FWHM Initial FWHM is used to e Determine minimum size of region removes spurious background points e Capture tails of peaks by extending regions twice the FWHM e Attempt to resolve peaks with a FWHM 1 75 input as two overlapping peaks e Set initial FWHM of new peaks before refinement VERBOSE VERBOSE OUTPUT Y N Non verbose output lists only the resulting peak parame ters Verbose output lists regions refinements with standard deviations and the final peak parameter table GRAPH GRAPH PEAKS Y N Check the box to draw the resulting fitted peak profiles FLAG n NUMBER OF WAVELENGTHS Default 1 Flag 1 or 2 Determines the number of wavelengths present NOTE If the profile shapes contain a1 and a2 lines FLAG must be set to 1 SPLIT n ALPHA 1 ALPHA 2 SPLIT Default 0 0 Alpha 1 to alpha 2 split at true zero May be non zero for incident beam monochromator systems RATIO n ALPHA 1 ALPHA 2 RATIO Default 0 5 Alpha 1 alpha 2 intensity ratio 2 2THETA BEGIN Starting 20 for peak fitting 3 2THETA END
7. 0 085 7 54 E24 TAGUES crx idee a Pee ddd a T AORE ateee gnats a EE vets E dane 7 54 7 25 Analyze gt Pole Figure gt Texture AT Create Texture AT file from pole figure frame DIN ANY hte Seti d foe aad eae eee AAR ALS AE ERIN Pita lita bg Maden R EEE alta heb 7 55 A25 A AIQUMONIS eke net oe hdl ed HRA hee Red out gleaned be beac ated 7 55 7 26 Analyze gt Pole Figure gt popLA Create popLA data file from pole figure frame ASCII 7 56 TEGI Arguments 22 opted OROREN E Gila at ea Gein Beale 7 57 7 27 Analyze gt Pole Figure gt Orientate Calculate Hermans and White Spruiell Orientation MACOS esee ner a eee nde bee A eae be ed eee eed peka ee tawteees 7 58 L2FACAIQUMONIS ceed ond akin sacbit dads Adres EE bath Retna deal war enne ba RNA wed tans 7 59 7 28 Analyze gt Pole Figure gt Stein Plot Stein triangle using calculated Hermans indices 7 60 Tee TAGUES es ga IERE AIR eee E crig ane ade agate os Gene la Oe Vege eet eR it ns A a a 7 61 M86 E01008 4 04 ix Table of Contents GADDS Software Reference Manual 7 29 Analyze gt Pole Figure gt Normalize e Normalize pole image so random 100 counts 7 62 Peg TAJUME 28 erme e pee ead bathed sober a le sateen a UE a ee Hees 2 Salt eee 7 62 7 30 Analyze gt Pole Figure gt Contours Draw contour plot of pole figure 7 63 3031 Arguments icc ee vate Wak oh etl e Nek Peet eee ty Pa Paha ee oS 7 63 7 31 Analyze gt Pole Figure gt Surfac
8. 2 Use lower numbers to reduce the effects of upward creep where the ball can fit inside the peaks and produce background frames with some crystallinity intensity not removed M86 E01008 GADDS Software Reference Manual Analyze Routines 7 18 Analyze gt Pole Figure gt Scheme e Determine data collection scheme for pole figure Menu Command Analyze gt Pole Figure gt Scheme Accelerator None User Level 1 SLAM Syntax POLE_FIG SCHEME 1 DISTANCE lt n gt 2THETA1 lt n gt OMEGA1 lt n gt PHI1 lt n gt CHI1 lt n gt AX S1 lt n gt WIDTH1 lt n gt NUM1 lt n gt THETA11 lt n gt THETA21 lt n gt 2THETA2 lt n gt OMEGA2 lt n gt PHI2 lt n gt CHI2 lt n gt AXIS2 lt n gt WIDTH2 lt n gt NUM2 lt n gt THETA12 lt n gt THETA22 lt n gt 2THETA3 lt n gt OMEGA3 lt n gt PHI3 lt n gt CHI3 lt n gt AX IS38 lt n gt WIDTH3 lt n gt NUM3 lt n gt THETA13 lt n gt THETA23 lt n gt 2THETA4 lt n gt OMEGA4 lt n gt PHI4 lt n gt CHl4 lt n gt AX S4 lt n gt WIDTH4 lt n gt NUM4 lt n gt THETA14 lt n gt THETA24 lt n gt DIRECTION lt s gt MAPPING lt s gt REFLECTION X lt n gt Y lt n gt Z lt n gt Pole figure frames are stereographic projections of the pole density sphere where each pixel of the pole figure frame represents the pole density of crystallites possessing a particular orienta tion Pole maps of this kind are the preferred
9. A eee E pecs First frame map_0O_001 gfrm FRAME lt s gt To frame number 001 RUN lt S gt 008 To run number G These three parameters define the run series to process G2 aieea fees Map parameter Area Area integration area internal external full Peak 2theta Peak height Peak fwhm Peak area M86 E01008 Analyze Routines GADDS Software Reference Manual Biaxial Sigma 11 stress Biaxial Sigma 12 stress Biaxial Sigma 22 stress Biaxial Sigma ph stress Shear Sigma 11 stress Shear Sigma 12 stress Shear Sigma 22 stress Shear Sigma 13 stress Shear Sigma 23 stress Shear Sigma ph stress Triaxial Sigma 11 stress Triaxial Sigma 12 stress Triaxial Sigma 22 stress Triaxial Sigma 13 stress Triaxial Sigma 23 stress Triaxial Sigma 33 stress SLAM lt S gt blank This parameter is used in script mode It is the script command for the processing parameters dialog box In menu mode just leave this blank 7 76 M86 E01008 8 Peaks Routines 8 1 Peaks gt Mask gt Create Create a new active pixel mask for this frame Menu Command Peaks gt Mask gt Create Accelerator None User Level 1 SLAM Syntax MASK CREATE 1 FILTER BORDER lt n gt MASK CREATE is used to create a bitmask for defining active pixels This bitmask is used in INTEGRATE SMOOTH and PER_CRYSTAL commands The user should be aware the bitmask or the octagon mask are us
10. Due to the interactive nature of this com mand RSPACE cannot be executed in SLAM mode M86 E01008 Peaks Routines GADDS Software Reference Manual 8 28 Peaks gt Refl Array gt CDF Search e Search the CDF database for structure with specified unit cell Menu Command Peaks gt Refl Array gt CDF Search Accelerator None User Level 1 SLAM Syntax REFL_ARRAY CDF 1 2 3 4 5 6 7 8 FORMULA lt s gt TYPE lt s gt FILE lt s gt VERBOSE REFL_ARRAY CDF CDF Search on the sub menu lets you search the NIST Crystal Data File for any published lattice parameters that match the lattice parameters for your crystal Supports either the ICDD Crystal Data or the newer NIST Crystal Data 1999 database Before CDF search may be used the CDF index file must be generated by running saxi gadds32 indxtl exe INDXTL requires a couple of files as input SAXI CDCODE codens dat SAXISCDROM crystal dat And generates as output the index file SAXI CDF cryidx bin INDXTL takes a long time to run so be patient 8 28 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA estdes dtevesiveeess A Axis Length 10 0 Dake fico tees Sort B Axis Length 10 0 Ke E ETET C Axis Length 10 0 G4 A eee Alpha Cell Angle 90 0 AATA EEE EIES Beta Cell Angle 90 0 DO ere t Gamma Cell Angle 90 0 These are the 6 unit cell para
11. GADDS Software Reference Manual Edit Routines 4 8 Edit gt Contrast Change the screen brightness and contrast Menu Command Edit gt Contrast Accelerator Ctrl T User Level 1 SLAM Syntax CONTRAST LO lt n gt Hl lt n gt This command performs real time linear map ping of frame pixel values into the colors in the color lookup table currently loaded See Edit gt Colors for more about color lookup tables Based on the current mouse position or the specified LO and HI values if invoked from the command line Edit gt Contrast computes a lower and upper limit All pixel values at or below lower limit show up as lowest color in the color table for example black Those at or above upper limit appear as highest color for example white Pixel values in between are linearly mapped to colors in the table When you invoke this command from the menu or from the command line with no arguments you can change the lower and upper limit with the mouse or arrow keys Horizontal motion changes the width of the contrast window Motion to the left brings the lower and upper lim its closer together increasing contrast and motion to the right moves the upper and lower limits farther apart reducing contrast and increasing latitude Horizontal motion is thus analogous to a contrast control or choosing a type of film according to the desired latitude Vertical motion raises or lowers the upper and lower limits toget
12. GADDS Software Reference Manual Peaks Routines 8 27 Peaks gt Refl Array gt Rspace Reciprocal space viewing for interactive indexing Menu Command Peaks gt Refl Array gt RSpace Accelerator None User Level 1 SLAM Syntax REFL_ARRAY RSPACE Rspace command is designed to perform inter active indexing on an HKL list consisting of mul tiple domains These domains can be either the same structure with different orientations or dif ferent structures Rotate Use Rotate to view the HKL reflections in reciprocal space The idea is to rotate the view until the reciprocal space planes line up All reflections lining up on planes are from a single domain Zero all angles Rotate to initial position Sort of a return to starting point Set plane Select points on a plane These points are assigned to a group up to five groups may be used Typically used after rotating until reflections line up on planes Zoom in 2x Select new center of rotation the zoom by a factor of 2 Zoom out Zoom out by a factor of 2 Delete group Assigns all points of a group to the global group The reflections are not deleted so it reverses the effects of Set plane Write group Write a group to a file This file can be read under Refl_array Edit and then indexed Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses NONG 0 p
13. GOt ates E Scan Angle 9999 Starting scan angle for pattern prediction in degrees The special value 9999 the default directs the program to obtain the starting angle from the currently displayed frame The signed frame width and scan axis omega or phi are always obtained from the currently displayed frame The scan angle range covered by the predicted pattern will be from A1 to A2 calculated as follows FRAME_CENTER SCAN_ANGLE FRAME_WIDTH 2 A1 FRAME_CENTER SPREAD 2 A2 FRAME_CENTER SPREAD 2 M86 E01008 GADDS Software Reference Manual File Routines The OVERLAY option in File gt Display when set directs the program to draw an overlay automatically every time a frame is displayed The parameters given in the File gt Display gt HKLs input dialog are used for these automatic overlays as well Three types of marker characters are used to indicate the difference between the scan angle corresponding to the centroid of the displayed frame that is FRAME_CENTER above and the predicted scan angle of a reflection Predicted Scan Angle Marker Within scan range of the current frame Box Within scan range of a preceding frame Circle Within scan range of a subsequent frame Cross X The circle and cross can be thought of as the tip and tail of an arrow which points from the current frame to the predicted position assuming a stack of frames with earlier frames positioned in front of the scre
14. mouse button performs the same function when you re in the editing window Edit Edit displayed lines using mouse or cursor to move between lines UpPage Move up one page screen in list of reflec tions The PgUp key Prev on VAX per M86 E01008 GADDS Software Reference Manual Peaks Routines forms the same function when you re in the editing window DownPage Move down one page screen in list of reflections Note that you cannot move down past the end of the list The PgDn key Next on VAX performs the same function when you re in the editing window Top This moves you to the first line in the reflec tion array The key combination CTRL PgUp has the same effect when you re in the edit ing window Bottom This moves you to the last line in the reflec tion array The key combination CTRL PgDn has the same effect when you re in the edit ing window Write Writes all lines or selected lines to an ASCII file on disk for storage and future use If a range of lines has been highlighted with SELECT see below only the highlighted range is written to the file otherwise the entire array is written Read Appends lines from a disk file for example created by WRITE to the end of the array You can use the Cut and Paste functions to move the new lines elsewhere if necessary Select This function is used to highlight select a range of lines in the array permitting writing cutting
15. must begin in the first col umn of a line one directive per line A line with the character in the first column is taken as a comment and skipped unless it starts with the directive prefix Most of the directives need to be followed by a few parameters again in free for mat Some of the directives require you to spec ify X Y fractional coordinates The convention for these coordinates is that X Y 0 0 0 0 corre sponds to the lower left of the graph viewport and X Y 1 0 1 0 corresponds to the upper right When you use a directive the directive remains in effect for all remaining lines in the file unless superseded by another occurrence of the directive The directives are 1 A Writes a text string at specified X Y frac tional coordinates Requires the fractional X fractional Y and text string as parameters Example A 0 5 0 5 Your line of text here C Specifies X Y character size for subsequent annotation text Requires the X character size and Y character size as parameters Each size is specified as an integer from 1 M86 E01008 13 11 Utility Programs GADDS Software Reference Manual to 4 Example C 1 2 By default text is written in size 1 1 G Normally the plot is drawn with a dashed grid highlighting certain tic marks This directive lets you specify whether or not the grid is to be drawn Examples are G1 to enable drawing of the grid
16. 16 14 Flag word in DACO MP format 2048 continuous scan 8192 2theta fixed rocking curve 16384 chi range 20 14 Sample number in sample changer 0 manual insertion 24 R4 Two theta in degrees 28 R4 Theta for reflection 2theta alpha for transmission 32 R4 Alpha for reflection Beta start for transmission 36 R4 Beta start for reflection 0 0 for transmission 40 A32 Sample name 32 characters 72 R4 K alpha 1 wavelength 76 R4 K alpha 2 wavelength 0 0 if monochromator used 80 4R4 Background information for this range 2theta for low background measurement 1 none 2theta for high background measurement 1 none M86 E01008 TEXTURE AT Raw Data File Format GADDS Software Reference Manual intensity at low 2theta rescaled to measuring time per circle intensity at high 2theta 0 0 none Table E 2 Data Range Block Offset Format Field description 156 R4 Counts not counts sec 96 A32 Sample name extension charac ters 33 64 of sample name Additional ranges use this same format and are 128 R4 Linear absorption coefficient appended to the end of the first range thickness Table E 3 Measuring Parameters Block placed as trailer 132 14 Pointer to measuring parameters block block in this file 136 12 iW
17. 7 25 CIA APQUMOMS cust ee oR Gam red DEKO E thats eBid edule awh 2 Pale ed We 7 26 7 10 Analyze gt Graph gt Poster Interactively annotate displayed graph or frame 7 29 7 11 Analyze gt Graph gt HKL e Plot HKL curve profile through frames 00 7 33 Tik LAUMEI eera ote nour eee ars see mati a ee be Pe ea eae aed 7 33 7 12 Analyze gt Graph gt Psi e Plot Psi curve profile through frames 000005 7 34 CAN AUMENS eg iio ees o EARE EN EAA Geld elaine ay lo Dn ete ee eed Gos bee eo ee 7 34 7 13 Analyze gt Graph gt Write Write generated curve to file 0 000 eeeaee 7 35 7 14 Analyze gt Percent Crystal gt External e Amorphous region external from Bragg peak 7 35 PACA Arguments veto ee pei gels ane Oe eet kw ks eee eet Pda die aes 2 7 36 7 15 Analyze gt Percent Crystal gt Internal e Amorphous region surrounds Bragg peak 7 37 viii M86 E01008 4 04 GADDS Software Reference Manual Table of Contents TAS AGUES neti ane Seiad Mand we hited E hited Mach BN RNa oa eet ae aed 7 37 7 16 Analyze gt Percent Crystal gt Compton Define the incoherent scattering due to the Compton effect ssrt ees iaasa cette 7 39 LAG AQUMONTS ce soe ee 8 sate gece Macha etalk s abuse fat a Renee af eee 7 39 7 17 Analyze gt Percent Crystal gt Full e Calculate and use an amorphous background frame 7 40 LALA AIQUMONIS sei Balhae woke ibe Paratha elie ed nace doe leh tbe
18. 8 18 Peaks gt Refl Array gt LeastSq Determine orientation and refined cell parameters Menu Command Peaks gt Refl Array gt LeastSq Accelerator Ctrl L User Level 1 SLAM Syntax REFL_ARRAY LEASTSQ 1 2 3 4 5 6 7 DXC lt n gt DYC lt n gt DISTANCE lt n gt ROLL lt n gt YAW lt n gt U1 lt n gt U2 lt n gt U3 lt n gt HKLTOL lt n gt HALFWIDTH lt n gt MASK lt n gt PARNAME lt n gt REFL_ARRAY LEASTSQ determines and refines the crystallographic orientation matrix unit cell parameters and detector positional cor rections given a valid list of indexed x ray spots in the Reflection Array Its output contains the orientation matrix the refined parameters and their standard deviation refinement and agree ment statistics and a reflection by reflection list of observations versus least squares calculated values Usually the reflection array will have been popu lated through a previous REFL_ARRAY THRESHOLD or PICK followed by REFL_ARRAY AUTOINDExX to index the array then REFL_ARRAY BRAVAIS to determine the Bravais lattice and perform any required trans formation of HKL indices However all of this can be done only after you have a good spatial correction computed and accurate values for the detector distance and X Y beam center stored in the CONFIGURE EDIT input panel This leaves the array in a state where least squares can be performed The Reflection Array can hold
19. Cursor gt Vector starts running directly that is there are no dialog items to be filled in A rub ber band vector cursor appears in the detector frame area and can be dragged or resized by the mouse or keyboard arrow keys Several quantities described below related to the cur rently displayed frame at the cursor position are displayed in real time at the right of the image Pressing ENTER or releasing the left mouse button exits returning you to the menu Pressing ESC or clicking the right mouse button while dragging with the left button pressed toggles between position change mode and size change mode The vector origin remains anchored while the vector endpoint moves as the mouse is dragged When moving or sizing the cursor with the arrow keys you can press CTRL along with an arrow key to move in increments ten times larger than for the unmodified arrow key By providing arguments on the command line you can direct GADDS to compute the calcula tions once at one specified position after which control returns immediately to the command line The line weight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cursors Odd values are better than even ones since the extra thickness is then added symmetrically about the true cursor posi tion If
20. FILE lt filename gt will read up to eight 72 character title lines from an ASCII file and place these title strings into the eight TITLE lines in the frame header The for mat of the ASCII file is R lt single line of title information gt where R is the run number taken from the filename Repeat up to eight times for each run SAMPLE lt s gt Sample Name YLID Enter sample name to be stored in frame header If no name is specified the default name of Lysozyme will be entered NUMSAMPLE lt n gt Sample Number 0 Enter sample number to be stored in frame header The permitted range is from 0 to 32 767 with a default setting at 1 NAME lt Ss gt Job Name HKLFRAM Enter the base filename for the output frames The filenames for each series of output frames are generated by adding the series RUN see below window and an extension built from the series starting FRAME see below to the end of this base name For example if the Job Name is LYS the Run Number is 04 and the starting Frame Number is 000 assuming that the number of characters in a Run Number is set to 2 and number characters in a Frame Number is set to 3 in the CONFIGURE EDIT panel the data files are named in sequence as LYS04 000 LYS04 001 LYS04 002 etc See the description FRAME NAMING CONVENTIONS for more information The default name if none is specified is NEWFRAM The
21. FRAME INTERVAL lt n gt Contour Interval 16 Enter the contour interval M86 E01008 Analyze Routines GADDS Software Reference Manual 7 31 Analyze gt Pole Figure gt Surface e Draw 2D surface plot of pole figure Menu Command Analyze gt Pole Figure gt Surface Accelerator None User Level 1 SLAM Syntax POLE_FIG SURFACE 1 ROTATION lt n gt ELEVATION lt n gt COARSENESS lt n gt LOGSCALE Pole figures can be displayed in three methods 1 As frame images were each pixel is dis played by a color indicating it s intensity 2 Asacontour plot were lines of equal inten sity are drawn at given intervals 3 As a 3D surface plot where intensity is rep resented by height The surface algorithm is very susceptible to noise If the frame was not smoothed then a Process gt Smooth gt Convolve command is automatically suggested see Section 6 16 however in command mode only a warning is displayed Frame type is not SMOOTHED 7 31 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Gite es Input File FRAME Enter the input pole figure filename or FRAME ROTATION lt n gt Rotation 0 Enter the rotation angle ELEVATION lt n gt Elevation 30 Enter the elevation angle for viewing 3D plot COARSENESS lt n gt Coarseness 5 Enter the coarseness for drawing the sur
22. If the detector is set at negative swing angle omega 180 psi 2T 2 For example to set psi at 45 30 15 0 15 30 45 for iron 211 whose 2T 156 with the detector swinging negative the omega scan val ues are 57 72 87 102 117 132 147 M86 E01008 GADDS Software Reference Manual Analyze Routines 7 33 3 Data Processing with GADDS For GADDS software version 3 323 or above the stress function is added under the Analyze menu Follow these steps to process the data 1 Load the first frame 2 Select Stress under the Analyze menu 3 Inthe pop up windows several variables must be set Particularly 2theta start and 2theta end for the peak of interest with appropriate background Chi start and Chi end for the chi integration range The val ues should be 90 x x is normally set below 10 degrees Set to 5 degrees if not sure Normalize intensity use a default value of 3 Peak 2T input the estimated or pre determined 2T peak position This value is used to calculate psi tilt File name the processed data will be saved in DIFFRAC format into this filename 4 Check OK to start processing The 2 theta and Chi range can be redefined using the mouse for each of frame Click in the inte gration box for each frame 7 33 4 Stress Calculation DIFFRAC SSTRESS can open the data saved in the last step For data format compatibility reasons the p
23. Initial guess for the CORRECTION to the detector beam center X coordinate in pixels Zero is usually a good value See com ments for DXC above DISTANCE lt n gt Detector Distance Correc tion 0 0 Initial guess for the CORRECTION to the detector distance in CM Zero is usually a good value Valid range is 10 to 10 CM See comments for DXC above ROLL lt n gt Detector Roll Angle 0 0 Initial guess for the detector roll angle in degrees Zero is usually a good value Roll is defined as right handed rotation of the detector about the goniometer X axis the direct beam axis when the swing angle is zero At zero roll the detector Y axis is par allel to the goniometer Z axis Valid range is 60 to 60 degrees See comments for DXC above IYAWEEND nonen Detector Yaw Angle 0 0 Initial guess for the detector yaw angle in degrees Zero is usually a good value Yaw is defined as right handed rotation about the detector Y axis the vertical axis At zero yaw the detector X axis is parallel to but reversed in direction from the goniometer Y axis Valid range is 60 to 60 degrees See comments for DXC above M86 E01008 Peaks Routines GADDS Software Reference Manual U1 EKN nnana 1st U Matrix Eulerian Angle 0 0 Initial guess for the first Eulerian angle in degrees The Eulerian angles define the ori entation of the crystal axes relative to the goniometer XYZ axes when
24. MENUMODE PDF2 VIEW 1 NBS AIDS TYPE lt n gt PDF2 PRINT 1 2 NBS AIDS TYPE lt n gt CARD PDF2 DISPLAY 1 DASHED PDF2 SEARCH 1 MINERAL INORGANIC ORGANIC PDF2 CLEAR PER CRYSTAL EXTERNAL 1 2 3 4 5 6 7 8 COMPTON PER CRYSTAL INTERNAL 1 2 3 4 5 6 7 8 LINEAR COMPTON PER CRYSTAL COMPTON 1 SCALE lt n gt XSCALE lt n gt PER CRYSTAL FULL 1 DISPLAY lt n gt 2 RADIUS lt n gt POLE FIG SCHEME 1 POLE lt n gt DISTANCE lt n gt 2 2THETA lt n gt THETAl lt n gt OMEGA lt n gt THETA2 lt n gt PHI lt n gt CHI lt n gt AXIS lt n gt WIDTH lt n gt CLEAR 3 MAPPING lt s gt REFLECTION X lt n gt Y lt n gt Z lt n gt POLE FIG PROCESS 1 2 3 4 5 POLE lt n gt MAPPING lt s gt BACKGROUND 6 7 8 9 FIBERGEOM ABSORPTION lt s gt X lt n gt Y lt n gt Z lt n gt MU lt n gt RADIUS lt n gt NSTEPS lt n gt REFLECTION POLE FIG INTERPOLATE 1 DISPLAY lt n gt WIDTH lt n gt 2 POLE FIG TILT 1 DISPLAY lt n gt X lt n gt Y lt n gt 2 POLE FIG ROTATE 1 DISPLAY lt n gt 2 POLE FIG SYMMETRIZE 1 DISPLAY lt n gt 2 LAUE lt s gt POLE FIG INVERT 1 DISPLAY lt n gt 2 POLE FIG TEXTUREAT 1 TITLE lt n gt HKL lt n gt APPEND ALPHAINC lt n gt BETAINC lt n gt REFLECTION POLE FIG POPLA 1 TITLE lt n gt HKL lt n gt APPEND POLE FIG ORIENT 1 DISPLAY lt n gt 2 APPEND FILM HKL lt s gt POLE FIG S
25. Next are the five refined detector positional cor rections with the X and Y beam center correc tion in pixels the detector distance correction in CM and the angular corrections in degrees In this example our estimate of the X beam center was just a guess and was not very good as the result indicates Depending on the smallest inter spot separation on the input frames you may not be able to get away with this poor an estimate off by 4 pixels in your own data sets You should try to specify the beam center to bet ter than half the smallest center to center spot separation The refined Eulerian angles come next with the three values in order corresponding to U1 U2 and U3 in degrees A line containing overall refinement statistics fol lows with values of the starting and ending residual goodness of fit number of refinement cycles actually performed and a completion code The residuals give an indication of the amount of improvement made by the non linear refinement relative to the initial guesses com puted by the linear least squares Usually the residual improves by a factor of two or more The goodness of fit is relative to an estimated 0 2 pixel error in detector X Y position of a reflection centroid and an estimated 0 25 frame width error in scan angle If the goodness of fit is less than 1 0 the refinement is better overall than these nominal estimates values higher than 1 0 indicate that the fit is not as good
26. Sort all or part of array on a specified parameter 8 71 8 21 Arguments scape reek a heed Bald oe Cee alee hil Ane ad He s 8 72 8 22 Peaks gt Refl Array gt Transform Transform HKLs in array according to specified SKI MAK oo doin Pies Viale feet Te le a Si eee fae bad Ge bok dal be Me Abed ee 8 74 8 22 RAUMES i225 eee dienes head EA bend o esis Bena bas Weide BRN name a5 8 74 8 23 Peaks gt Refl Array gt Matrix Enter an orientation matrix e g from external program 8 76 8 23 1 AUMENS sevens cig ale gee seed a eet Wed ee nes en at ede es dae bees als 8 76 8 24 Peaks gt Refl Array gt Hcalc e Compute X Y and scan angle for specified HKL 8 78 8 24 TAUM erram errin ienna e wed a oats ale oe Male ule ls deena Daas 8 79 8 24 2 ACALC Outputs cnn woe tiewha ahah te se pets wes a Mie E E Mears lath Ho s 8 80 8 25 Peaks gt Refl Array gt Clear Erase the reflection array and current orientation matrix 8 81 8 25 1 ArQUMeENS nice iy eee we pola eee dete Neth e oad ee Wed E E 8 81 8 26 Peaks gt Refl Array gt Load Read in orientation matrix from existing p4p or _pr file 8 82 8 26 11 Arguments o ENE fe inns CEE EE yee ie ke ee ee ied Sea 8 82 8 27 Peaks gt Refl Array gt Rspace Reciprocal space viewing for interactive indexing 8 83 8 28 Peaks gt Refl Array gt CDF Search Search the CDF database for structure with Specified Unt eal erari E EEEN Sela wee eek TAE a weg ues aet
27. e Error messages e Angle Drive Shutter Laser Attenuator sta tuses Remotely you can send to NT e Command to start a program such as GADDS e Command to kill a program Command to reboot frame buffer Typically you can use TELNET to remotely and efficiently monitor data collection status Simply connect via winsockets modem or network to SMARTservice Then connect to the GADDS log file when you are just monitoring the log file GADDS may be running in either menu or com M86 E01008 Remote Operations SMARTservice GADDS Software Reference Manual mand mode You will see the last ten lines of the log file enough to easily determine whether GADDS is still running or stopped with an error condition New lines will display as they are received For more elaborate remote control of GADDS you must either write your own winsocket enabled program or modify a third party pack age such as EPICS LABVIEW or SPECS to send commands over winsockets Bruker does not supply any such winsocket enabled pro gram See the SMARTservice Software Manual for more details NOTE Bruker supplies PCAnywhere32 on our frame buffers for remote diagnostics by our ser vice department using either modems or a net work PCAnywhere32 allows the entire desktop of the frame buffer to be remotely controlled from another computer running PCAnywhere32 You can install the client version of PCAnywhere32 on another NT workstati
28. face plot LOGSCALE Logscale No Check to display using a logrithmic intensity scale M86 E01008 GADDS Software Reference Manual Analyze Routines 7 32 Analyze gt Pole Figure gt Fiber Take a cut through pole figure and display I versus tilt angle Menu Command Analyze gt Pole Figure gt Fiber Accelerator None User Level 1 SLAM Syntax POLE_FIG FIBERPLOT 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt Use this command to display a slice through the pole figure as an intensity versus alpha angle plot 7 32 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses NORMAL c lt gt Normalize Intensity 1 Normalize intensities O sum 1 avg STEPSIZE lt n gt Step Size 0 5 Enter step size for tilt angle axis in degrees GA E Tilt Start 0 0 Enter starting tilt angle in degrees Oe a kate Tilt End 90 0 Enter ending tilt angle in degrees i ee Beta 0 0 Enter beta of conic region in degrees G4 iia Height 0 Enter height of conic region Range 0 to 5 degrees M86 E01008 7 65 Analyze Routines GADDS Software Reference Manual 7 33 Analyze gt Stress gt Conventional e Process frame images into data file for STRESSP S package Menu Command Analyze gt Stress gt Conventional Accelerator None User Level 1 SLAM Syntax STRESS CONVENTIONAL 1 2 3
29. 0 Enter the text strings to be written to the out put file If your text contains slashes or more than ten separate blank delimited words enclose the text in double quotes OUT lt s gt Enter the name of the output file to receive the text APPEND If this qualifier is given the text gets appended to the output file if the file already exists otherwise a new output file is created to receive the text If this qualifier is omitted M86 E01008 SLAM Routines GADDS Software Reference Manual the output file is overwritten if it already exists WAIT lt n gt Enter a value to represent the number of seconds to wait after text is displayed The script will continue after this number of sec onds or when you press a key whichever occurs first The valid value range is 1 to 1 0x10 seconds A value of 1 will wait indefinitely until you press a key Example The following commands direct GADDS to dis play double height text in its image area then to wait for 16 seconds or a keyboard key before continuing echo out wrtext tmp C1 2 echo app out wrtext tmp A 1 75 In this example we determine echo app out wrtext tmp A 1 70 the structure of a small compound echo app out wrtext tmp A 1 65 the YLID C 11 H 10 N 2 S graph file quad 0 wrtext tmp wait 16 M86 E01008 GADDS Software Reference Manual SLAM Rout
30. 0 7 2 6 2 3 0010 256 9 196 0 0 4 21 21 2 9 0000 270 4 329 3 0 4 3 7 2 8 0010 234 9 128 2 0 8 21 21 3 0 0000 303 5 195 3 0 9 2 6 2 6 0011 200 4 128 1 0 4 23 22 3 3 0000 244 7 218 5 0 6 3 7 3 1 0010 296 8 353 0 0 2 17 18 2 6 0005 260 4 104 3 0 6 2 6 2 8 0010 132 4 380 0 0 8 26 23 3 9 0005 250 3 377 0 0 5 2 6 2 8 0010 325 7 53 4 0 8 11 15 2 3 0000 147 2 454 3 0 6 2 7 3 3 0010 304 2 262 2 0 5 13 16 2 6 0000 72 0 25 8 0 3 2 7 3 9 0010 303 9 217 5 0 7 12 16 2 6 0000 23 8 435 2 0 6 170 59 4 7 002C 290 0 424 7 0 9 11 15 2 5 0001 7 9 98 7 0 8 299 78 5 9 0025 257 5 173 6 0 8 12 16 2 9 0000 22 8 362 3 0 2 97 44 6 1 0021 106 4 219 3 0 7 18 19 5 1 0000 8 8 194 9 0 6 88 42 8 5 0020 210 6 173 7 0 8 14 17 3 3 0005 9 7 314 0 0 8 13 16 7 8 0020 315 9 217 4 0 4 10 14 2 5 0000 2 6 362 4 0 6 773 125 6 8 008C 106 7 264 7 0 5 16 18 5 1 0000 48 6 434 3 0 5 396 89 4 5 008C 316 2 239 9 0 3 8 13 2 5 0000 61 8 459 2 0 5 179 60 4 0 008C 210 8 218 8 0 2 11 15 3 4 0001 95 7 26 0 0 7 117 49 3 7 008C 234 9 151 0 0 2 10 14 3 1 0001 136 7 480 4 0 3 77 39 3 2 008C 60 6 407 7 0 9 13 16 4 6 0001 86 4 457 2 0 8 687 118 3 8 0085 182 7 2 8 0 5 9 13 2 9 0000 3 9 146 8 0 2 288 76 7 6 0085 269 6 150 3 0 7 8 13 2 8 0000 35 3 409 2 0 9 117 49 5 0 0081 316 3 262 0 0 3 7 12 2 5 0000 38 3 459 1 0 5 26 23 4 3 0080 436 9 191 6 0 2 4 9 2 0 0001 75 5 483 8 0 9 11 15 3 7 0081 157 7 426 6 0 8 9 14 3 4 0001 258 4 307 4 0 5 8 12 2 9 0000 328 4 217 5 0 2 6
31. 2 to 10 counts Smaller values make the displayed image look brighter larger values make look darker M86 E01008 File Routines GADDS Software Reference Manual 3 9 File gt Logfile Create a new log file and start recording Menu Command File gt Logfile File gt Logfile gt Enabled Accelerator None User Level 1 SLAM Syntax LOGFILE NEW 1 APPEND LOGFILE ON OFF The File gt LogFile commands are used to main tain a record of all of a user s interaction with the system This record is referred to as the log file or logfile Logfiles are standard ASCII text files that can be typed edited printed etc like any other text file When you start recording to a log file you have the option of appending to the file or overwriting it if it already exists The File gt LogFile gt Enabled command toggles the current state of recording to the log file If logging is enabled the command disables it If logging is disabled the command re enables it A check mark is displayed in the menu next to the File gt LogFile gt Enabled command if logging is currently enabled From the SLAM command line LOGFILE ON and LOGFILE OFF enable and disable scripting respectively The log file records each command issued along with its parameter values a date time stamp and any non graphic command output For example the cursor commands write the statistics at the final cursor position to the log
32. 4 NORMAL lt n gt STEPSIZE lt n gt 2THETA lt n gt 5 FILENAME lt s gt DIFFRAC SSTRESS is Windows NT based software designed for residual stress calcula tions This document describes the use of DIF FRAC SSTRESS to analyze residual stress data collected with a General Area Detector Dif fraction System GADDS 7 33 1 Hardware Requirement for Stress Measurements One of the following sample stages is required to perform stress measurements with GADDS XYZ Stage 1 4 Circle Eulerian Cradle at chi 90 posi tion Two Position Chi Stage at chi 90 position For all of the above stages the sample surface must face the operator when omega 0 and face the incident beam when omega 90 For stress tensor measurements phi rotation is required 7 33 2 Data Collection with GADDS Data can be collected either SingleRun with omega scan for normal stress measurements single phi phi 0 or MultiRun with omega scan for stress tensor measurements multiple phi e g phi 0 45 and 90 All frames must have the same file name and consecutive extension num bers For MultiRun it is required to set the same run number for all runs in the EditRuns menu The psi tilt is achieved by sample omega rota tion the so called iso inclination mode Use the following equations to determine omega scan angles where 2T is the estimated peak position If the detector is set at positive swing angle omega psi 2T 2
33. ENDRUN lt n gt MODE lt n gt ROTATE VIDEO OSCILLATE lt S gt AMPLITUDE lt n gt Additional SLAM Syntax for dual detector mode SNAME lt s gt NOTE As one cannot load the run list in com mand mode we recommend using the equiva lent SCAN SINGLERUN commands in script mode This command allows you to collect multiple scan series each containing one or more con tiguous frames of data starting at specified goni ometer setting angles Normally Collect gt Scan gt MultiRun stores frames as an unwarped image after applying the spatial correction table It also applies the flood field intensity uni formity corrections as the counts are received Before invoking Collect gt Scan gt MultiRun you must set the parameters that are unique from series to series See Section 5 31 Collect gt Scan gt EditRuns command for details on these settings and the generation of filenames Then use Collect gt Scan gt MultiRun to define those parameters that are the same for all the different scan series to be performed and start the scans When you invoke the command from the menu or the command line without arguments a dia log box appears where you can view edit the arguments described below as follows e press ENTER or click the OK button to start scanning e press ESC or click the Cancel button to return to the menu You can interrupt a scan as follows e press ESC to stop after finishing collect
34. Pressing ESC or the right mouse button in the editing window returns you to the REFL_ARRAY submenu When you sort on one of the HKL indices the program automatically performs secondary and tertiary sub sorts on the other two indices For example if you sort on H the program performs that sort then sorts on K for each H and on L for each K The result would look something like this HKL 001 002 Similarly if you sort on one of the scan angles sub sorts are performed on the other scan angles The sub sorts are performed in the fol lowing order Specified Secondary Tertiary Quaternary Sort Key Sort Sort Sort H K L None K L H None L H K None 2 Theta Omega Phi Chi Omega 2 Theta Phi Chi Phi 2 Theta Omega Chi Chi 2 Theta Omega Phi 8 21 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Piparra First Reflection 1 This is the Reflection Array line where you want the sort range to start The first line is numbered 1 For example if you want to sort only reflections 9 through 50 you would enter 9 as the 1 parameter 2 tiar Ra Last Reflection 512 This is the line where you want the sort range to end To continue the previous example if you want to sort only reflections 9 through 50 you would enter 50 in the LAST parameter 8 72 M86 E01008 GADDS Software Reference Manual Peaks Routines F
35. Sample Name Corundum NUMSAMPLE lt s gt Sample Number 0 DISPLAY lt n gt Max Display Counts 31 REAL TIME Real time Display Yes CLEAR 0805 Pre Clear Yes See Section 5 30 STARTRUN lt n gt Sequence of Starting Run 1 You can collect just a specified range of the scan series set up in the EDITRUNS array by using STARTRUN and ENDRUN STARTRUN specifies the first line number NOT the RUN in the EDITRUNS array for which data collection is to be performed The lines are numbered 1 50 The default is 1 and valid range is 1 to 50 ENDRUN lt n gt Sequence of Ending Run 9999 You can collect just a specified range of the scan series set up in the EDITRUNS array by using STARTRUN and ENDRUN ENDRUN specifies the line number NOT the RUN in the EDITRUNS array after which data collection is to be terminated The lines are numbered 1 50 The default is 9999 works the same as 50 and valid range is 1 to 32767 MODE lt n gt Mode Scan Oscillate Step Scan ROTATE 20008 Rotate Sample No NIDEO ee Capture Video Image no M86 E01008 Collect Routines GADDS Software Reference Manual OSCILLATE lt s gt Sample Osc None AMPLITUDE lt n gt Amplitude 0 0 See Section 5 30 AUTOZALIGN Auto Z Align No See Section 5 30 NOTE On failure the algorithm proceeds to the next target
36. The completion code is for diagnostic use by Bruker It is normally O if it is nonzero and the number of refinement cycles is listed as 20 it indicates that the solution might benefit from additional cycles of refinement In this situation negate the CONSTRAINT TYPE see descrip tion of the 1 argument and re rerun the least squares and the refinement will continue where it left off Other cases where the completion code is non zero indicate that no further improvement in the residual can be made even though some of the gradients are non zero and indicates that we ve probably underestimated the magnitude of round off errors in the compu M86 E01008 GADDS Software Reference Manual Peaks Routines tations the solution however should still be valid Please notify Bruker if you see many non zero completion codes Following the overall statistics is a reflection by reflection summary of the agreement for each reflection in the reflection array Each record consists of two lines the first containing the reflection as it s entered in the reflection array i e the observed values and the second containing the differences for HKL scan angle always converted into omega rotation and detector X Y with the sense OBSERVED CAL CULATED This output shows both those reflec tions included in the least squares and those not included for example reflections without the C flag set It also shows computed HKL indic
37. This is also an ASCII file that can be edited with notepad Any peak with L limit condition or missing standard deviation is rejected Typically peaks that are poorly refined have a large standard deviation and you may want to reject these peaks Delete any existing lt filename gt txt as these will be processed before the Ist file Finally restart the Stress command with the reprocess option checked 7 35 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA ETE 2theta start 154 5 Enter lower 2 theta of conic region degrees AEE 2theta end 157 5 Enter upper 2 theta of conic region degrees GB AAE EE Chi start 70 0 Enter lower chi of conic region degrees GAY EEPE ETE Chi end 110 0 Enter upper chi of conic region degrees NORMAL lt n gt Normalize intensity 3 Normalize intensities 0 sum 1 avg 2 arc 3 solid angle 4 bin 5 norm bin STEPSIZE lt n gt Step size 0 1 Enter the step size degrees NUMBER lt n gt of sub regions 15 Enter the number of sub regions to inte grate 2THETA lt n gt Peak 2T ord 156 0 Enter unstressed 2T or d for triaxial tensor calculations M86 E01008 Analyze Routines GADDS Software Reference Manual eE T E E Title TITLE Enter title string or TITLE to leave unchanged FILENAME lt s gt File name Ente
38. This latter display method has no effect on observed data rate If you re not sure whether real time display will affect the observed data rate signifi cantly at your current incident count rate check the late counts in the frame header of a representative frame with the FRAME_INFO command If the late counts are more than a few percent of the total counts your data collection will be more effi cient if real time display is turned off In gen eral you should be able to use real time display for set up and sample evaluation but you should disable it during collection of frame series which will be used as input to data reduction see the similar SCAN com mand display options While real time display is active you can change the upper display limit using the plus key to increase or the minus key to decrease the current limit by a factor of two The range is 7 to 524287 Modify the con trast using the left and right arrow keys Modify the brightness using the up and down keys Hold down the control key and an arrow to increase the change of contrast or brightness RESET lt n gt Reset Interval 0 This qualifier specifies the number of sec onds before repetitive auto clear of frame memory 0 do not clear The default value is 0 the range is from 1 to 65 535 seconds This parameter is useful in conjunction with real time display if you re looking for a change in intensity over time For instance if you r
39. User Level 2 SLAM Syntax PROJECT LOAD 1 not recom mended to use in SLAM mode Use this command to create a project from an existing configuration file You can click the browse button to search for an existing configu ration file Before the program creates and switches to the requested project the message appears Save the current configuration before changing projects Typically you click Yes as this is the safest option The program will create and switch to the requested project by loading that project s set tings clearing the frame buffer clearing the dis played frame and displaying the current project settings However if an error occurs the pro gram will display a message and restore the original project settings Next the program automatically generates a project name and adds the new project to the project database If the new project name already exists the message appears lt PROJECTO gt is already a project Replace it Click Yes to replace or No to generate a differ ent project name by incrementing the sample number 2 2 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses ST eaaa Configuration Filename Enter the full file specification of an existing configuration file The default is _nc which will invoke the file browser M86 E01008 GADDS Software Reference Manual Projec
40. You can enter time in decimal seconds or in the for mat HH MM SS SS where HH represents hours MM minutes and SS SS decimal seconds Valid values are 0 05 to 32 767 seconds The default value is 60 TITLE lt S gt 000 Title Scan frame Enter a title for the output frames 80 char acters maximum The default entry is the sample title from the Project gt New Copy Edit dialog box or Scan Frame If you invoked this command from the command line you must enclose any title containing blanks in double quotes FILE lt filename gt will read up to eight 72 character title lines from an ASCII file and place these title strings into the eight TITLE lines in the frame header The for mat of the ASCII file is R lt single line of title information gt where R is the run number taken from the filename Repeat up to eight times for each run SAMPLE lt s gt Sample Name dum Corun Enter sample name to be stored in frame header If no name is specified the default name of Corundum will be entered NUMSAMPLE lt s gt Sample Number 0 Enter sample number to be stored in frame header The permitted range is from 0 to 32 767 with a default setting at 0 NAME lt Ss gt Job Name NEWFRAM Enter the base filename for the output frames The filenames for each series of output frames are generated by adding the series RUN and an extension buil
41. acquired Otherwise these setting angles are left at their current position The default is Y checked On 0 0 systems this drives 01 and 02 to zero IPHI lt N gt oes Starting Phi 0 00 Enter starting phi for photo in degrees The allowed range is from 0 to 360 with a default setting of 0 M86 E01008 Collect Routines GADDS Software Reference Manual ICHI lt n gt 0cceeee Starting Chi 0 00 Enter goniometer chi for photo in degrees The allowed range is from 0 to 360 witha default setting of 0 DISPLAY lt n gt Mzx Displayed Counts 15 See Section 5 30 for an explanation of this argument REAL TIME Real time Display Yes See Section 5 30 for an explanation of this argument RESET lt n gt Reset Interval 0 This qualifier specifies the number of sec onds before repetitive auto clear of frame memory 0 do not clear The default value is 0 the range is from 1 to 65 535 seconds This parameter is useful in conjunction with real time display if you re looking for a change in intensity over time When you start collecting a rotation frame if you checked the option to zero 2 theta and omega GADDS drives the two angles to zero otherwise the goniometer 2 theta and omega setting angles stay at their current position Chi moves to the value specified on the input panel a 3 cir cle goniometer is fixed at chi 54 74 or chi 45 depending on the
42. administrator configuration settings Menu Command Edit gt Configure gt Admin set tings Accelerator None User Level 2 view 3 edit SLAM Syntax CONFIGURE ADMIN TARGET lt s gt WAVELENGTH lt n gt ALPHA1 lt n gt ALPHA2 lt n gt BETA lt n gt UNITS lt s gt KV lt n gt MA lt n gt STANDBYKV lt n gt STANDBYMA lt n gt STANDBYIDLETIME lt n gt STANDBYNOEXCLUDE MONOCHROMATOR lt s gt OFFSET lt n gt Edit gt Configure gt Admin settings displays a dialog box where you can view edit certain instrumental setup variables including the x ray source generator and optics Unless you are the GADDS Administrator all fields are only viewable To change a view only field see your GADDS Administrator Whenever a GADDS configuration file is read starting GADDS switching projects etc the program checks the Preferred generator set tings against the current settings and if different displays the message Warning Current high voltage generator settings are different than user values When you invoke a command from the menu or the command line without arguments a dialog box appears View or edit its contents or type text Then e Press ENTER or click the OK button to save your entry e Press ESC or click the Cancel button to return to the menu without saving your last entry 4 2 1 Arguments Each argument is listed below by its command line name followed by its dialog box p
43. all lines below this threshold will be ignored and thus not displayed DISTANCE lt n gt Sample to detector distance cm from frame header The default is read from the frame header This distance is measured from the sample to the front of the detector face and is read off the scale below the detector ANER NETEN Delta distance 0 05 Enter the interactive sensitivity for calibrat ing the detector distance in cm ANGLE lt n gt Detector swing angle from frame header Default from frame header Detector swing angle in degrees hie eee ee eee Delta angle 0 00 Enter the interactive sensitivity for calibrat ing the detector angle in degrees M86 E01008 Process Routines GADDS Software Reference Manual X eant Detector X center from frame header Default from frame header Detector X cen ter in pixels The origin is taken as lower left corner of frame IXEKND gt e Detector Y center from frame header Default from frame header Detector Y cen ter in pixels GA OE tate Delta XY 0 5 Enter the interactive sensitivity for calibrat ing the detector center in pixels Range 0 1 to 10 AUTO rerien Auto mode Y N No Enter Y to perform an automatic least squares fit of the calibration standard line s prior to allowing user manipulation of the detector parameters DELAY lt n gt 10 0 Delay before exiting routine useful in demo
44. command _Ix Contains the indexed fiducial spot positions can be used to restore a previously computed spatial correction when it is read in with the SPATIAL LOAD command _if Shows the spatial correction table used to transform pixel X Y coordi nates FROM raw to corrected values _it Shows the table which transforms cor rected coordinates TO raw coordi nates Both the _if and _it plot files are strictly infor mationalthe program doesn t require them since the information in them is automatically re generated from the _ix file by FRAMBO when SPATIAL LOAD is used and you can delete them if desired All three of the output files are by default created in the current frame directory set in the CON FIGURE EDIT panel 6 9 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses DF ETT Output Filename brass Enter the base filename for the output cor rection data By default all three output files _ix _if and _it as described above in the frame directory specified in the CON FIGURE EDIT input panel More specifi cally the filename you enter here is merged with the default filespec Frame_root _ix _if etc where Frame_root refers to the directory in the CONFIGURE EDIT panel See CONFIGURE EDIT for details on how M86 E01008 Process Routines GADDS Software Reference Manual filenames are merged The default na
45. default settings for each stage already preset Then when he switches stages he only needs to 1 Project gt Switch Switch to the project for the new goniometer stage for example Fixed Chi XYZstage XYZstageSTRESS Huber Cradle etc which have already been defined 2 Project gt Overwrite defaults Save these settings to the system wide defaults 2 9 1 Arguments 1 None Commands execute immediately after confirmation message M86 E01008 Project Management Routines GADDS Software Reference Manual 2 10 Project gt Exit Leave program and return to operating system Menu Command Project gt Exit Accelerator None User Level 1 SLAM Syntax EXIT After saving the current configuration this com mand terminates GADDS returning you to the operating system You may also exit GADDS by double clicking on the GADDS icon in the upper left clicking the application close button in the upper right corner pressing Alt F4 or with the QUIT command see Section 12 3 Quit but these methods do not save the current configu ration If you choose EXIT from the menu a box appears with OK and Cancel buttons and the message Save current configuration Are you sure Normally you want the program to save the cur rent settings press OK Occasionally you may wish to ignore your project session and start over press Cancel All settings are stored in the project s working directory in the file gad
46. gt Command Line menu item To return to menu mode from command line mode enter the fol lowing command at the prompt GADDS gt MENUMODE If you start GADDS with the LOCK qualifier all commands in the Level menu are disabled grayed including Special gt Command Line However SLAM command scripts can still be executed from the User menu For more information on command line and command file scripts see the GADDS User s Manual Scripts section 9 6 1 Arguments None Command executes immediately M86 E01008 Special Routines GADDS Software Reference Manual 9 7 Special gt System Suspend program and invoke the Command Prompt processor Menu Command Special gt System Accelerator None User Level 1 SLAM Syntax SYSTEM 1 Use the SYSTEM command to spawn either a single command or a session Spawning a sin gle command permits the execution of external programs such as a temperature controller soft ware without leaving the GADDS environment If the spawn command is non interactive it may even be used within a script file Spawning a session allows the execution of one or numerous programs in the native operating system command interpreter e g CMD EXE by temporarily returning you to that environ ment The GADDS software is kept resident in the operating system and when you are fin ished with the system level program s you can quickly return to the configuration existing when you select
47. gt Rotation Accelerator Ctrl Shft F4 User Level 1 SLAM Syntax SCAN ROTATION 1 TTZERO PHl lt n gt CHl lt n gt DISPLAY lt n gt REAL TIME RESET lt n gt Collect gt Scan gt Rotation allows you to collect a rotation photo of a sample or crystal by rotat ing the sample in phi while exposing it to the X ray beam When invoked from the menu or run from the command line without arguments Collect gt Scan gt Rotation displays a dialog box where you can view edit the arguments described below Pressing the ENTER key or clicking the OK button starts the operation Pressing ESC or Cancel button stops the operation and returns you to the menu You can interrupt the operation by pressing CTRL BREAK Upon interruption the goniome ter stays at the position where the rotation was interrupted 5 34 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses BA EO ERT Exposure Time 36 0 Enter the requested exposure time in sec onds The valid range is from X to 65535 seconds where the minimum is calculated from the maximum phi speed and the default value is 36 CLEAR oaeiae Pre Clear Yes See Section 5 30 for an explanation of this argument ATITZERO siini Zero 2 Theta Omega Y N No TTZERO aaa Zero Theta 1 Theta 2 Y N No If you check this option 2 theta and omega are driven to zero before the rotation is
48. gt Scan gt PickTargets e Manually drive and select target positions for MultiTarget list Menu Command Collect gt Scan gt PickTargets Accelerator Ctrl Shft F9 User Level 1 SLAM Syntax SCAN SELECTTARGETS SCAN SELECTTARGETS manually select XYZ target position s and automatically enter the selected target into the SCAN MULTITARGETS by appending the list When SELECTTARGETS is first entered the user has the option of either clearing the target list or appending to the existing target list Pre clear the existing target list Y N The video program should already be running in a separate window SELECTTARGETS will turn the video to live and turn the laser ON Manual speed ratios can be selected and the program enters manual mode The user then drives to a position where data collection is requested makes sure the laser is positioned within the video cross hairs then hits lt Ctrl G gt to exit manual mode The current sample position can be automatically entered into the target list Do you want to enter this position in the tar gets list Y N Additional targets may be selected before exiting SELECTTARGETS Do you want to enter more positions in the targets list Y N 5 40 1 Arguments None Command executes immediately This is an interactive command only M86 E01008 Collect Routines GADDS Software Reference Manual 5 41 Collect gt Scan gt GridTargets Set up grid for MultiTarge
49. lost axis position Heavy stages or samples will result in a slower reliable slew speed for the omega axis If you increase the speeds above the default please test the drives for reliability M86 E01008 Collect Routines GADDS Software Reference Manual 5 18 Collect gt Goniometer gt Zero Drive all angles to home position zero degrees Menu Command Collect gt Goniometer gt Zero Accelerator Ctrl Shift Z User Level 1 SLAM Syntax GONIOMETER ZERO Use this command to quickly drive the goniome ter to the zero position The zero position is defined as either e All angles to zero degrees non XYZ sys tems e XYZ angles to zero degrees e All angles to zero degrees except omega to 180 omega restricted by collision from 0 When invoked from the menu this command displays one of the following prompts in a Yes No message box DRIVE ALL AXES TO ZERO ARE YOU SURE DRIVE XYZ STAGE TO ZERO ARE YOU SURE DRIVE ALL AXES TO ZERO amp OMEGA to 180 ARE YOU SURE Pressing the Y key ENTER key or clicking the Yes button will drive all the goniometer axes to their zero position Pressing N the ESC or the No button will return you to the menu without driving the axes In command line mode the action is the same except that the program does not prompt before driving the axes to zero 5 18 1 Arguments None Command executes immediately after confirmation prompt M86 E0100
50. mand line name followed by its dialog box prompt in parentheses Of aatinene ans Width in pixels 2 Enter width in pixels of neighborhood to convolve M86 E01008 Process Routines GADDS Software Reference Manual 6 17 Process gt Calibrate Calibrate detector distance angle and center using a known standard Menu Command Process gt Calibrate Accelerator none User Level 1 SLAM Syntax CALIBRATE 1 MININT lt n gt DISTANCE lt n gt 2 ANGLE lt n gt 3 X lt n gt Y lt n gt 4 AUTO NOERASE DELAY lt n gt Precise detector position cannot be determined by visual methods but require taking a frame of a known standard and comparing the measured Debye Scherrer rings with the calculated lines based on various detector positional parame ters Detector distance swing angle and beam center are determined permitting accurate 2 theta and chi values from other routines such as INTEGRATE The calibration process requires a data frame s using a known standard sample Typically corundum quartz or silicon is used but in prac tice any material exhibiting high stability and extremely sharp diffraction lines can be used Also uses GADDS SYSTEM iprofile pro for defi nition of the lineshape function In interactive mode the standard d l file is superimposed over the collected data frame The user can move the detector position or the detector beam position using either the cursor keys or the
51. method for describing a material s texture The radius of the pole figure is called alpha and the azimuthal angle is called beta These angles are related to the sample orientation by alpha angle between reflecting plane and normal to the reference plane in the sample beta angle between the reference direc tion and the normal to the diffractometer direction Consider a polycrystalline textured specimen at a fixed orientation within an x ray beam The dif fracted rays from a particular hkl plane form a cone where the azimuthal intensity variation is related to the orientation of the sample about the incident x ray beam The intersection of this diffraction cone and an area detector form a cir cle of intensity data that maps to a great circle on the pole sphere By varying the sample ori entation to the incident beam this circle of data can map to other regions of the pole sphere Thus by measuring the distribution of diffracted rays at various sample positions the relative pole density at every point along the pole figure may be obtained M86 E01008 Analyze Routines GADDS Software Reference Manual 7 18 1 Scheme The complexity of the pole figure and the required precision will determine the number of frames that are necessary to collect Further complications arise whenever the area detector is off axis and only intersects a portion of the dif fracted cone To aid the diffractionist the data collection s
52. n results in a scale factor of t1 t2 and n results in a scale of t1 t2 where t1 and t2 are the respective acquisition times of frame 1 and frame 2 OFFSET lt n gt Offset 0 Offset to be added prior to clipping negative values to zero This corresponds to B in the equation given in the scale factor description above This allows you to quanti tatively assess signed differences between two frames The DIFFER LUT color table can be useful for viewing signed differences While the linear combination capability is useful primarily for background subtraction in general diffraction applications you can also use it to sum a series of frames to form an oscillation picture For example the fol lowing SLAM commands generated a sum of 8 myoglobin frames Note the increase in display level as the sum grows larger Make oscillation picture from 8 myoglobin frames LOAD LOAD LOAD LOAD LOAD LOAD LOAD swmyol SFRAME SFRAME SFRAME SFRAME SFRAME SFRAME 002 swmyol swmyol swmyol swmyol swmyol swmyol swmyol 004 005 006 007 008 009 DISPLAY 128 SCALE 1 0 OFFSET 0 0 DISPLAY 160 SCALE 1 0 OFFSET 0 0 DISPLAY 192 SCALE 1 0 OFFSET 0 0 DISPLAY 224 SCALE 1 0 OFFSET 0 0 003 DISPLAY 32 SCALE 1 0 OFFSET 0 0 DISPLAY 64 SCA DISPLAY 96 SCALE E 1 0 OFFSET 0 0 1 0 OFFSET 0 0 M86 E01008 GADDS Software Reference Manual File Routines LOGSC
53. or GO to disable drawing of the grid IL Sets plot axis limits overriding the auto scaling normally performed Requires four parameters Xmin Ymin Xmax Ymax cor responding to the lower X lower Y upper X and upper Y axis limits respectively If both the lower and upper limit for an axis are specified as zero autoscaling is restored for that axis The default limits are 0 0 0 0 meaning that auto scaling is performed on each axis When an axis is auto scaled a nice interval for tic marks is determined This interval is always 1 2 or 5 times some power of 10 Limits are then chosen which are integer multiples of this interval and which contain the range of values input for the axis being auto scaled An example of this directive is L0 0 100 0 This example specifies that the X axis will range from 0 to 100 and the Y will be auto scaled based on the range of the input Y values IM Specifies the character to be used as a Marker The Marker Character is plotted at each subsequent X Y point The marker character must immediately follow the direc tive that is it must be the fifth character on the line Examples are M to plot a at each input X Y position or M to dis able plotting of a character at each X Y posi tion IN Specifies that subsequent X Y points should be drawn as a new plot rather than added to the existing set of axes This directive requ
54. refined in the last ReflArray gt LeastSquares command These values will be correct for frames acquired in Bruker format frames in gen eral They will probably NOT be correct for XEN GEN 1 3 format frames because those frames do not contain the required setting angle infor mation If logging is turned on see the File gt LogFile command for more information the quantities computed for the final position of the cursor prior to exiting the command are written to the output logfile If scripting is enabled see File gt Script File a non interactive CURSOR command cor responding to the final cursor position is written to the output script file The SLAM command arguments are 1 The X coordinate of the lower left of the box in pixels The range is from 0 to framesize 1 default value is 256 2 The Y coordinate of the lower left of the box in pixels The range is from 0 to framesize 1 default value is 256 3 The width of the box in pixels The range is from 0 to framesize 1 default is 32 4 The height of the box in pixels The range is from 0 to framesize 1 default is 32 DELAY lt n gt Specifies a time interval in seconds to wait before erasing the cursor and returning con trol to the program This is for use in scripts where it is desirable for the cursor to remain M86 E01008 GADDS Software Reference Manual Analyze Routines on screen long enough for the user to dis cern its
55. sate for other sources of error such as inten sity fluctuation due to an unstable source FRAMES The number of frames to be acquired in this series Ensure that the generated filename of the last frame in the series is a valid file name with regard to the frame naming parameters in the Edit gt Configure gt User settings dialog TIME The accumulation time in seconds during which each frame is to be acquired You can enter time in decimal seconds or in the for mat HH MM SS SS where HH represents hours MM minutes and SS SS decimal seconds Valid values are 0 05 to 32 767 seconds When you invoke this command gt EditMulti GADDS displays a scrollable editing window listing all scan series currently in the corre sponding array You can add to delete from or reorganize the list as desired using the appropri ate screen editing functions see Section 1 5 Dialog Box and Keyboard Conventions When you invoke the multirun scan command Collect gt Scan gt MultiRun each series will be acquired in the order they appear in the corre sponding array GADDS generates output filena mes for each frame from the Job Name in the Collect gt Scan gt MultiRun dialog box GADDS also generates the Run Number given for the series in the array the starting Frame given for the series in the array the Frame being collected and the frame naming parameters defined in the Edit gt Configure gt User settings
56. stroms alpha beta gamma degrees The second line contains the rows of the 3 x 3 trans formation matrix which would transform the HKL indices from the input lattice to the lattice corre sponding to the solution The rows are sepa rated by slashes thus using the standard mathematical convention the nine elements on the third line are in the order T11 T12 T13 T21 T22 T23 T31 T32 T33 If you stack these rows above one another the first row on top the resulting matrix will pre multiply a column M86 E01008 Peaks Routines GADDS Software Reference Manual HKL vector in the input cell to give a column HKL vector in the new cell Example 8 4 Bravais Lattice Output for Myoglobin Test Data Sigmas for acceptance of any soln best soln Input lattice type P Input cell and standard deviations 92 865 91 946 46 174 89 264 89 442 59 640 340159 50 0 476 0 494 0 036 Number of solutions Sig A TRIGONAL P NO C AXIS SYMMETRY HEXAGONAL P C AXIS SYMMETRY 46 174 90 736 gt gt gt 1 2 98 91 906 1 00 1 00 0 00 ORTHORHOMBIC C 2 2 55 92 865 1 00 0 00 0 00 3 2 98 91 906 1 00 1 00 0 00 4 3 02 91 946 0 00 1 00 0 00 MONOCLINIC C 5 1 31 158 674 1 00 2 00 0 00 6 1 72 91 946 0 00 1 00 0 00 7 1 74 160 341 1 00 1 00 0 00 8 2 19 92 865 1 00 0 00 0 00 14 B Cc Alpha 91 946 0 00 1 00 0 00 158 674 46 174 90 527 1 00 2 00 0 00 160 341 46 174 89 255 1 00 1 00 0
57. the message appears Working directory already contains a con figuration file gadds _nc Choose a different directory or use the Project gt Load com mand The sample information parameters are all optional Enter what you know and leave the rest set to Before the program creates and switches to the requested project the message appears Save the current configuration before changing projects Typically you click Yes as this is the safest option The program will close any log and auto script files before creating and switching to the new project Closing last project s log file Closing last project s auto script M86 E01008 Project Management Routines GADDS Software Reference Manual New project defaults are taken from the system wide default file create by the Project gt Over write defaults command All crystal information is cleared reflection array list orientation matrix and face indices The new project is cre ated by clearing the frame buffer clearing the displayed frame displaying the project settings and setting all title requests in other menus to the sample title If the previous project had either the log or auto script enabled you will be prompted to restart those features Start append log file for new project Start append auto script file for new project 2 3 1 Arguments Each argument is listed below by its SLAM c
58. tial correction obtained by processing a brass fiducial plate image with the SPATIAL NEW PROCESS or LOAD command REFL_ARRAY THRESH OLD and PICK automatically set this flag and store the corrected X Y values if a spatial correction was in effect 8 66 M86 E01008 GADDS Software Reference Manual Peaks Routines when they were executed If this flag is absent REFL_ARRAY INDEX and LEASTSQ assume that the X Y val ues in this record are raw values and explicitly correct them in the course of their computations X Display angles in XSCANS conven tions with X Y at detector center instead of goniometer settings and X Y pixel location H K L The HKL crystallographic indices INDEX automatically computes these indices and stores them in the array BRAVAIS and TRANSFORM transform these indices among different unit cell possibilities and conventions If HKL indices are not available for a reflection LEASTSQ ignores it 2 THETA OMEGA PHI CHI The goniometer setting angles THRESH OLD and PICK automatically enter these values into the array based on the angles found in the frame headers If the C flag is set the scan angle omega or phi will typi cally be set to the intensity weighted cen troid value computed by THRESHOLD or PICK otherwise the scan angle is set to that corresponding to the frame on which the spot was located If angles are not avail able for a reflection INDEX and LEAST
59. triple of solutions for the three crystallographic axes derived from the three non coplanar axis vectors with best lowest figures of merit The shortest solutions with good integerness of cal culated HKL indices have the best figures of merit In addition to the solution number and length of each axis chosen the XYZ compo nents of each axis vector are displayed If the program was not able to find an accept able set of three solutions from its first group of trial solutions generated from a basis set con sisting of the three shortest non coplanar differ ence vector groups the output will contain the message RETRYING WITH NEXT SHORTEST VEC TOR followed by another listing of axis vector solu tions If you see this message even several occurrences of it followed by successful index ing it is no cause for concern If necessary the program continues to step through the differ ence vector groups generating trial solutions from a new basis set of three such groups until a solution is found or until the number of groups has been exhausted If this occurs the output will contain the lines INDEXING FAILED ON DIFFERENCE VECTORS RE TRYING WITH FIRST 100 FULL VEC TORS M86 E01008 Peaks Routines GADDS Software Reference Manual and a final attempt at indexing on the full vectors is made Following the axis vector solution a unit cell reduction by the method of Buerger is per formed The output contain
60. 0 Initial phi goniometer setting CHI lt n gt eeee Chi 0 0 Initial chi goniometer setting AXIS lt Nn gt ee Scan Axis 3 Goniometer axis for scanning 2 OM 3 PH 4 CH WIDTH lt np gt Frame Width 5 0 Step size of scan axis between frames M86 E01008 GADDS Software Reference Manual Analyze Routines CLEAR 00005 Pre Clear Y N Yes Y will clear both the screen display and any output file or SCAN MULTIRUN menu requests N will draw additional pole data onto previous SCHEME results and also append to any output file or the SCAN MULTIRUN list DIRECTION lt S gt Projection Direction 1 Enter projection direction of sphere 1 X beam 2 Y 3 Z Up MAPPING lt s gt Mapping Stereo Enter Stereo or Polar REFLECTION Reflection only Y N No Enter Y for reflection only mode All points from transmission through the sample are tossed out Requires sample vector to be entered XSEN gt araire Sample vector X 0 Enter sample vector in X direction on goni ometer head INZENS eek econo Sample vector Y 0 Enter sample vector in Y direction on goni ometer head Z RNS tesa Sample vector Z 1 Enter sample vector in Z direction on goni ometer head M86 E01008 Analyze Routines GADDS Software Reference Manual 7 19 Analyze gt Pole Figure gt Process e Process frames into pole figure image M
61. 0222 00 2054 424 45 b 00462 Fea PaEeG PEGE bea eG dea wee EAS 12 19 12 46 PEAKS SAVE 24256420 2 Seta beso Gene bas Lae ool he ey ieee ete 12 20 12 4 9 PEAKS SIMULA TE 3 23 peu hedda peti deci ayn Y alde de ca neitand y E 12 21 12 4 0 PEAKS VIEW oi Liuga pied tear beards amp ne AA eee hed E wed et 12 24 12 4 11 PEAKS ZOOM ieee fete baa Ye ads ehhh dak oo Pele wa Ke eet es 12 24 12 5 Rale molor erabe pete okieta eRe Ss Bee eae attend aegig eee eae 12 25 12 6 SPAWN ve peo re Kae nee ae ares ee Vee eh De aa oa ited oben wifes 12 25 12 07 Video LIVE oem aka a ae lt a Biba a Pee eRe eae AA eee th aa E Sv OA aL oe 12 26 12 8 VIdGO Fr6 Ze tages ise dn bead pe dee Chee A eed Dae deka eda e peta geek 12 26 12 9 Walt annaa e aa aE ae dard uma hace het eet snared aaa eae oat eee Ge Seen ates S 12 27 12 10 COMMENK yar resni a He e a Leagan E T e Waite ee aw aia R 12 27 12 11 execute scriptfile ringi ie oia ia aaa Aa eee 12 28 13 Utility Programs nies vei heraa ea eae a a e E oa a 13 1 13 1 FrmFix FRaMe header FIX up utility 2 00 ee 13 1 13 2 Frm2Frm FRaMe to FRaMe file format conversion utility 000 13 3 13 3 GADDSMAP GADDS MAPping program 60 060s 13 6 13 4 Indxtl e NIST index generator suau aaaea tees 13 6 13 5 Merge RAW file range merging utility 0 0 0 ee 13 8 13 6 PDFnoind PDF2 index generator 0 00 tee 13 10 xiv M86 E01008 4 04 GADDS Software Refere
62. 11 2 5 0001 73 4 432 3 0 7 10 14 4 2 0000 145 8 1 4 0 7 8 13 3 2 0000 59 9 312 0 0 5 11 15 6 0 0000 231 6 4 0 0 2 5 10 2 7 0001 307 2 126 6 0 4 4 9 2 5 0000 209 7 476 2 0 3 5 10 2 8 0000 292 0 262 0 0 9 4 9 2 7 0001 M86 E01008 8 27 Peaks Routines GADDS Software Reference Manual 8 15 Peaks gt Refl Array gt Pick Select spots from currently displayed frame to put in array Menu Command Peaks gt Refl Array gt Pick Accelerator None User Level 1 SLAM Syntax REFL_ARRAY PICK 1 2 3 4 START lt n gt QUADRANT lt n gt FRAME_HALFWIDTH lt n gt This option provides an interactive means for adding reflections to the array This is useful in cases where a known reflection has fallen below threshold during automatic picking or when you want to isolate specific reflections to see if there is a satellite or twinning in the sample This com mand is very similar to GRAPH ROCKING except that the computed 3D intensity weighted centroid coordinates and setting angles are entered into the Reflection Array on completion Before running REFL_ARRAY PICK a set of data frames must be collected with fixed step size in any angle a single frame is sufficient but the centroid in scan angle will not be precisely determined and the rocking curve will not be displayed Use the DISPLAY or LOAD com mand to display the central frame about which you want the rocking curve to be computed Then invoke
63. 2 3 DELAY lt n gt NOERASE GRAPH HKL draws a graph in the frame win dow or a specified quadrant called an hkl curve This graph shows integrated intensity in a specified rectangular area as a function of hkl position and requires that you have a contigu ous series of frames collected using SCAN HKL available for input 7 11 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses F EE ET 1st frame hkl01 000 The name of the first frame in the HKL scan series QUADRANT lt n gt Quadrant 0 This parameter specifies whether you want the graph to appear covering the entire data frame enter O or just one of the four quadrants enter 1 through 4 as appropri ate The default value is O full frame win dow Quadrants are 0 full window 1 lower left 2 lower right 3 upper left and 4 upper right Doosan ETE Width 32 The width of the box defining the region of interest in pixels The range is from 0 to 128 default value is 32 BB aires oe Height 32 The height of the box defining the region of interest in pixels The range is from 0 to 128 default value is 32 DELAY lt n gt 0 0 available in com mand mode only Specifies a time interval in seconds to wait before erasing the cursor and returning con trol to the program This is for use in scripts where it is desirable for the
64. 2 3 for explanations ICLEAR eeeeeeee Clear Crystal Info No Check to clear the crystal face list reflection array and orientation matrix Default is no I RESET penina Reset to Defaults No Check to reset program to default settings Default is no 2 8 M86 E01008 GADDS Software Reference Manual Project Management Routines 2 5 Project gt Edit Edit the current project settings Menu Command Project gt Edit Accelerator None User Level 1 SLAM Syntax PROJECT EDIT TITLE lt s gt FORMULA lt s gt MORPH lt s gt CCOL lt s gt DENSITY lt s gt DENSMETH lt s gt CLEAR RESET Use this command to modify the current project settings Because you are not creating a new project you cannot change the project s sample name sample number or working directory But you may change the sample s title and the sam ple information parameters reset defaults to system wide default settings and or clear the crystal information 2 5 1 Arguments Project gt New and Project gt Copy arguments apply here see Section 2 3 and Section 2 4 for explanations Defaults are current settings M86 E01008 Project Management Routines GADDS Software Reference Manual 2 6 Project gt Backup Backup all files in the specified project s directories Menu Command Project gt Backup Accelerator None User Level 2 SLAM Syntax PROJECT BACKUP 1 2 3 NOCALIB NOWORK Use t
65. 3 4 1 2 3 4 5 6 7 8 9 GRAPH FILE 1 QUADRANT lt n gt PRECLEAR NOCLEAR GRAPH VECTOR 1 2 3 4 QUADRANT lt n gt DELAY lt n gt NOERASE GRAPH ROCKING 1 2 3 4 QUADRANT lt n gt FRAME HALFWIDTH lt n gt DELAY lt n gt NOERASE GRAPH POSTER GRAPH HKL 1 QUADRANT lt n gt 2 3 DELAY lt n gt NOERASE GRAPH PSI 1 QUADRANT lt n gt 2 3 DELAY lt n gt NOERASE HELP HELP REFERENCE HELP USERGUIDE HELP ERRATA HELP MAP HELP RELNOTES NTEGRATE CHI 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt NTEGRATE 2THETA 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt NTEGRATE AREA 1 2 3 4 INTEGRATE SLICE 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt INTEGRATE WRITE 1 FILENAME lt n gt FORMAT lt n gt APPEND INTEGRATE CLEAR NTEGRATE RECTANGLE 1 2 3 4 VERTICAL NTEGRATE WRITE 1 FILENAME lt s gt FORMAT lt s gt APPEND SCALE lt n gt LEVEL1 LEVEL2 M86 E01008 SLAM Command Reference GADDS Software Reference Manual LEVEL3 LOAD 1 2 DISPLAY lt n gt SCALE lt n gt OFFSET lt n gt LOGSCALE USE_CONFIG LOGFILE NEW 1 APPEND LOGFILE ON OFF LOGFILE SCRNEW 1 APPEND LOGFILE SCRON SCROFF MAPPING 1 FRAME lt s gt RUN lt s gt 2 SLAM lt s gt MASK CREATE 1 FILTER BORDER lt n gt MASK SAVE 1 MASK READ 1 MASK VIEW 1 MASK EDIT interactive MASK OCTAGON 1 2 3 4 5 6 7 8
66. 5 6 5 7 Collect gt Detector gt X E vs X e Set PDC for X preamp calibration 5 6 SA TAIME r rare veudip iio aye A rE KEE E Wis wen tiene ERa Bie ad deny att aceite ee 5 6 5 8 Collect gt Detector gt Y E vs X e Set PDC for Y preamp calibration 5 7 So AQUMOMS iste ed a dateitala teas ae ae eee sed da be ee aed ake oe 5 7 5 9 Collect gt Detector gt Custom Enter values to be loaded into PDC setup registers 5 7 5 9 V ArQUIMEMIS rrn ea ERREEN ERE EEI a ieee AGES ws Sica tae ea en bapa a PGE on Boe 5 7 5 10 Collect gt Goniometer gt Drive e Move goniometer angles to specified positions 5 8 Sal Os CARQUMONIS erren TEREE ATEA A EART Hatta aed tind belt amp denen wae bebe 5 9 5 11 Collect gt Goniometer gt Manual Control goniometer from manual box 5 10 SIL ARGUMENTS idee uea eterna elie a he a aha tah ow een waded ai eae S 5 12 5 12 Collect gt Goniometer gt Optical e Perform check optical centering of sample 5 13 5312 AARQUMONIS iai oe td neha adhe aie weet eaten edi alates bu Wee a ANAE EATA 5 15 5 13 Collect gt Goniometer gt Flatsample Perform check flat sample plane on XYZ stage 5 15 SASS ARGUMENTS eiere arane e TEA GPRS Ae eee n a ee ced ety nee a 5 16 5 14 Collect gt Goniometer gt Update Enter observed goniometer angles 5 17 Sal4 AVALQUMONS e nen Shane haben a bree tied otal s doeen duped ae 5 18 5
67. 524287 Modify the con trast using the left and right arrow keys Modify the brightness using the up and down keys Holding the control key down in combination with any arrow key results in a greater change of contrast or brightness 70 M86 E01008 GADDS Software Reference Manual Collect Routines 5 37 Collect gt Scan gt CoupledScan Conventional 20 0 coupled scan Uses AD as a point detector Menu Command Collect gt Scan gt Coupled Scan Accelerator Ctrl Shft F7 User Level 1 SLAM Syntax SCAN COUPLED 1 2 3 WIDTH lt n gt SCANTIME lt n gt TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt n gt NAME lt s gt RUN lt s gt ROTATE X lt n gt Y lt n gt REAL TIME Perform a conventional 2T T coupled scan using a square portion of the area detector grid as a point detector The omega axis is always driven at half the rate of the 2 theta axis Scan Coupled performs a conventional 2T T coupled scan using a square portion of the area detector grid as a point detector The resulting scan data is displayed in 1D spectra not 2D frames The 1D spectra is saved as an addi tional range in a DIFFRAC AT file suitable for input into other software packages such as PROFILE S or EVA Data is collected from 2T start to 2T end You may collect in negative 2T space and in negative 2T direction The 1D spectrum is always stored in positive 2T direction If both start and end 2T positions are i
68. 606 10 00 1 001 28 00 28 00 90 00 54 74 2 0 300 435 10 00 2 001 28 00 28 00 180 00 54 74 2 0 300 230 10 00 3 001 28 00 28 00 0 00 54 74 2 0 300 50 10 00 M86 E01008 Collect Routines GADDS Software Reference Manual Each line of a run list defines one contiguous scan series When entering the individual run arguments keep in mind the following special considerations The RUN FRAME and FRAMES must conform to the frame naming parameters See Edit gt Configure gt User settings com mand The number of runs or lines must not exceed the maximum number of runs allowed by RUNCHARS and RUNBASE see Edit gt Configure gt User settings com mand The default maximum number of runs is 36 The absolute maximum is 51 All generated filenames must be valid and should not create duplicate names explained later in this section With these considerations in mind we recom mend that you always configure the frame nam ing conventions as follows For 36 or fewer runs set the Base of Run in the Edit gt Configure gt User settings dialog to base 36 which will prevent the run number from wrapping from 9 to 0 The Characters in Run should be 1 These are the default settings For greater than 36 runs you must set the Characters in Run in the Edit gt Config ure gt User settings dialog to 2 characters The Base of Run can be base 10 if you find it more conveni
69. At Zoom of 7 0 starting Z must be within 0 5 mm of true position SNAME lt s gt Slave Job Name NEWFRA2 Job name for frames collected on Slave frame buffer SRUN lt s gt Slave Run 0 Run number for frames collected on Slave frame buffer SFRAME lt s gt Slave Frame 000 Starting frame number for frames collected on Slave frame buffer M86 E01008 GADDS Software Reference Manual Collect Routines 5 31 Collect gt Scan gt EditRuns Edit parameters for MultiRun scans Menu Command Collect gt Scan gt EditRuns Accelerator Ctrl Shft F2 User Level 1 SLAM Syntax SCAN EDITRUNS interactive command only Use this command to create read or edit a run list often called an array of scans that you wish to acquire in multiple run fashion where one or more series of contiguous frames are collected without intervention Upon entering a Collect gt Scan gt EditRuns command GADDS displays a run list with cur rent settings A typical list follows Each run list is identical in format to that in ASTRO allowing you to transfer run lists between GADDS and ASTRO Use the READ button in the dialog box to import the run list written by ASTRO On ASTRO list with an extra DeltaD column only those lines with DeltaD 0 0 are read Typical run list Run Frame 2 Theta Omega Phi Chi Axis Width Frames Time 0 001 28 00 28 00 0 00 54 74 2 0 300
70. CALIBRATON FILE Filename for profile file deletes existing file 2 3 START LOW BKGD Low background start and end 20 4 5 START HIGH BKGD High background start and end 20 PEAKS PROFILE ADD When started from the command line PEAKS PROFILE ADD takes the following arguments PEAKS PROFILE ADD 1 2 3 4 5 where the arguments are 1 CALIBRATON FILE Filename for profile file to append or insert new profile 2 3 START LOW BKGD Low background start and end 20 4 5 START HIGH BKGD High background start and end 20 PEAKS PROFILE DELETE When started from the command line PEAKS PROFILE DELETE takes the following argu ments PEAKS PROFILE DELETE 1 2 where the arguments are 1 Filename of profile file 2 Profile number to delete profiles stored in ascending 2T order 12 18 M86 E01008 GADDS Software Reference Manual SLAM Routines 12 4 7 PEAKS REFINE PEAKS REFINE performs a least squares fit of all variable parameters Very accurate results can be obtained from user specified peaks When started from the command line PEAKS REFINE takes the following arguments PEAKS REFINE 1 VERBOSE GRAPH SPLIT n FLAG n RATIO n 2 3 where the arguments are 1 VERBOSE GRAPH FLAG n SPLIT n RATIO n 2 3 CALIBRATION FILE Calibration file containing representative profile lineshapes VERBOSE OUTPUT Y N Non verbose output lists the resulting peak
71. CONFIGURE EDIT panel item called Base of Run 2 If you have more than 36 runs in the array you MUST set the number of characters in the run number to at least 2 Note that for DOS compatible filenames this reduces the number of possible characters in the data set name Job ID in the SCAN panel to 6 8 characters for data set run number Set M86 E01008 GADDS Software Reference Manual Collect Routines this in the CONFIGURE EDIT panel item called Characters in Run In this case it should be OK to use base 10 run numbers if you find them more convenient 5 44 1 Arguments Each argument is listed below by its command line name followed by its input panel prompt in parentheses These arguments are the same as the similar singlerun type scans and are thus explained once in Section 5 30 See that section for explanations Slim cac as Frames 1 2THETA lt n gt 2 Theta 0 00 or THETA1 lt n gt Theta 1 0 00 OMEGA lt n gt Omega 0 00 or THETA2 lt n gt Theta 2 0 00 IPHI lt n gt 0 Phi 0 00 ICHl lt n gt onnan Chi 0 00 IAXIS lt N gt oo Scan Axis 2 WIDTH lt n gt Frame Widith 0 25 SCANTIME lt n gt Seconds Frame 1 00 See Section 5 30 DO vids TTT Job Name NEWFRAM See NAME lt s gt argument under Section 5 30 TITLE lt S gt 000 Title New frame SAMPLE lt s gt
72. COUNTS Value of pixel at circle center XY PIXEL X and Y coordinate of circle center range from 0 to framesize 1 with origin X 0 Y 0 being located at lower left of screen R PIXELS Radius of circle in pixels DEGREES Radius of circle in degrees 2 theta ANGSTRMS Radius of circle Angstroms The following output statistics are related to single crystal alignment based on the posi tion of a circle of reflections arising from a zero level layer LAYER A Spacing of planes normal to the beam axis in the case where the crystal is aligned so that the diffracted layer circles are centered on the direct beam M86 E01008 GADDS Software Reference Manual Analyze Routines SPINDLE Change required to phi axis position in degrees to move the diffracted layer circle to the beam center PARA ARC Change required to goniometer head arc which is parallel to the detector plane at 2 theta omega phi 0 0 0 in order to move the diffracted layer circle to the beam center PERP ARC Change required to goniometer head arc which is perpendicular to the detector plane at 2 theta omega phi 0 0 0 in order to move the diffracted layer circle to the beam center Pole figures are handled slightly differently On these frames the following output statistics are displayed on screen in real time and are also written to the logfile if applicable XY Pixel Coordinates of current pixel range f
73. Command Analyze gt Graph gt Poster Accelerator None User Level 1 SLAM Syntax GRAPH POSTER Analyze gt Annotate has several subcommands to produce hard copy plots and pictures suitable for poster presentation and publishing When you choose this command from the menu the program displays a right cascading submenu containing these subcommands When you invoke GRAPH POSTER from the command line no qualifiers are allowed a submenu of dia log buttons will appear and the program will wait until you ve made a selection GRAPH POSTER will execute only in interactive mode The subcommands are summarized in the fol lowing table Menu SLAM Description New NEW Start a new list of annota tions Edit EDIT Edit current annotations Clear CLEAR Clear annotations within rectangular region Save SAVE Save annotations to PLOTSO file Text TEXT Position text on screen Label LABEL Label spots peaks using d hkl TH 2T etc Arrow DRAW Draws an arrow pointer ARROW Box DRAW BOX Circle DRAW CIRCLE Dot DRAW DOT Line DRAW LINE Style DRAW Switches between solid and STYLE dashed line styles Draws a rectangular box Draws an ellipse Draws a single dot Draws a straight line Each subcommand is described below Menu Command Analyze gt Annotate gt New SLAM Syntax GRAPH POSTER NEW This command clears the annotation list in preparation for starting a new series of annotati
74. DIFFRAC 5000 files on which only ranges in the first series are accessible When started from the command line PEAKS LOAD takes the following arguments PEAKS LOAD 1 RANGE n QUADRANT n where the arguments are 1 INPUT FILENAME DIFFRAC AT v1 v2 DIFFRAC 5000 or PLOTSO file containing raw data The file format does not need to be specified PEAKS LOAD automatically determines which file format is being read RANGE n INPUT RANGE Scan range to read On DIFFRAC 5000 files only ranges in the first series can be accessed QUADRANT n DISPLAY QUADRANT Specifies the quadrant to display the raw data trace 0 full screen 1 4 respective quadrants 5 6 top or bottom half of screen 12 10 M86 E01008 GADDS Software Reference Manual SLAM Routines 12 4 4 PEAKS MANUAL MANUAL is used to interactively choose peaks and their parameters The most frequent use of MANUAL is to correct any shortcomings of PEAKS AUTO which is known to have difficul ties whenever the scan range begins or ends within a peak and with extremely complicated patterns with more than 15 overlapping peaks MANUAL lets you enter all peak and back ground data as well as variables which you wish to refine At least once after installation and before executing MANUAL you must run PEAKS PROFILE to generate the required peak profile s file These profile lineshapes are used to overlay the manually inserted peaks overtop the displ
75. Display gt Next File gt Display gt Previous Accelerator Ctrl RightArrow next Ctrl LeftArrow previous User Level 1 SLAM Syntax DISPLAY NEXT DISPLAY PREVIOUS When data frames have been collected as part of a set these commands provide a convenient means of specifying display of the data frame that comes either just before File gt Display gt Previous or just after File gt Display gt Next the one currently displayed The next or previous sequential name in a series of frames is com puted according to the frame naming parame ters set in the Edit gt Configure gt User settings dialog box see Section 4 1 Edit gt Configure gt User settings The items entered in the File gt Display input dia log box remain in effect for the duration of the File gt Display Next or File gt Display gt Previous subcommand including the display quadrant and autoincrement qualifiers If the specified quadrant is 1 4 and autoincrement is set suc cessive frames will be displayed cyclically in the different quadrants When invoked from the menu or when run from the command line File gt Display gt Next and File gt Display gt Previous start running immedi ately without prompting for additional input 3 2 1 Arguments None Command executes immediately M86 E01008 GADDS Software Reference Manual File Routines 3 3 File gt Display gt Movie and File gt Display gt Movie Repea
76. E01008 GADDS Software Reference Manual Process Routines 6 11 4 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses PTni Input Filename FRAME Enter filename for first input frame in series to process G2 AENEAN of Frames to Process 1 Enter consecutive frames to process PIi nans Output Filename NULL Enter filename for first output corrected frame MONOCHROMATOR lt n gt Mono 2T 26 6 Enter monochromator 2 theta 0 if filter AIRMU lt n gt Air Mu in Cm 1 0 01 Enter air absorption coefficient NOREVERSE Suppress Reverse Corr Y N No Enter Y to suppress reverse polarization correction M86 E01008 Process Routines GADDS Software Reference Manual 6 12 Process gt Corrections gt Fiber Menu Command Process gt Corrections gt Fiber Accelerator none User Level 2 SLAM Syntax CORRECTIONS FIBER 1 2 3 X lt n gt Y lt n gt Z lt n gt NSTEPS lt n gt MU lt n gt RADIUS lt n gt Calculates an absorption correction table based on a long fiber It is assumed that the fiber along its axis is longer than the diameter of the inci dent beam in all orientations In the directions perpendicular to the fiber axis the fiber is smaller than the diameter of the incident beam The sample vector is expressed in goniometer head coordinates where when the goniometer
77. E01008 GADDS Software Reference Manual Process Routines IMAGH lt N gt 00e Magnification of Corrected Frame 2 Enter the magnification factor of the correc tion table The default value is 1 the range is from 1 to 8 6 4 Process gt Flood gt Linear Reset to linear table i e no correction Menu Command Process gt Flood gt Linear Accelerator none User Level 2 SLAM Syntax FLOOD LINEAR Selecting FLOOD LINEAR with the LINEAR option from the FLOOD submenu or from the command line specifies that no flood field cali bration file will be used in subsequent data acquisition linear scaling of event positions The name of the current flood field correction is shown on the display in the current status area at the bottom right of the screen FLOOD LIN EAR updates this name to LINEAR Since you will in general obtain better data if a flood field correction is in effect the ADD SPATIAL NEW and SCAN commands will issue a warning if you start data collection with a linear flood field cor rection FLOOD LINEAR runs immediately without prompting for additional input 6 4 1 Arguments None Command executes immediately M86 E01008 Process Routines GADDS Software Reference Manual 6 5 Process gt Bad Pixels gt Process e Process flood image to determine bad pixels Menu Command Process gt Bad Pixels gt Process Accelerator none User Level 3 SLAM Syntax BADP
78. Ending 28 for peak fitting 12 8 M86 E01008 GADDS Software Reference Manual SLAM Routines 12 4 2 PEAKS CLEAR Full visual screen control is accomplished with CLEAR Screen text windows can be cleared Also the raw data trace the peak profiles or both can be cleared from any quadrant Addi tional options let you destroy raw or peak data from internal memory When started from the command line PEAKS CLEAR takes the following arguments PEAKS CLEAR 1 DATA_ SAVE TRACE SAVE PEAKS SAVE FIT_SAVE SCREEN_SAVE where the arguments are 1 SCREEN QUADRANT Quadrant to clear 1 none 0 full 1 4 respective quadrants 5 6 top or bottom half of screen DATA_SAVE PRESERVE RAW DATA Y N Check the box to preserve raw data in internal memory TRACE_SAVE PRESERVE RAW TRACE Y N Check the box to preserve graphic raw data trace PEAKS_SAVE PRESERVE PEAK DATA Y N Check the box to preserve peak parameters in internal memory FIT_SAVE PRESERVE PROFILES Y N Check the box to preserve graphic peak profiles SCREEN_SAVE PRESERVE TEXT SCREENS Y N Check the box to preserve text screens M86 E01008 12 9 SLAM Routines GADDS Software Reference Manual 12 4 3 PEAKS LOAD Raw data traces must be displayed with INTE GRATE or PEAKS LOAD which can read either a DIFFRAC AT v1 or v2 file DIFFRAC 5000 file ora PLOTSO file regardless of which computer platform is being operated GADDS can directly read
79. FIELD 5 VALUE 30 0 8 21 Peaks gt Refl Array gt Sort Sort all or part of array on a specified parameter Menu Command Peaks gt Refl Array gt Sort Accelerator None User Level 1 SLAM Syntax REFL_ARRAY SORT 1 2 FIELD N DESCENDING This command lets you sort the reflection array or a specified range of lines within the array in ascending or descending order The array may be sorted on any of the 12 Reflection Array col umns FLAGS H K L 2THETA OMEGA PHI CHI X Y INORM I SIGMA This provides a means for organizing the array in a manner more suitable for publication e g placing it in hkl order 001 002 003 or that will facilitate editing problem diagnosis etc When invoked with the SORT option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY SORT displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins the sort the ESC key or right mouse button returns you to the REFL_ARRAY submenu When sort ing starts the program displays the message M86 E01008 Peaks Routines GADDS Software Reference Manual SORTING on the bottom status line Sorting should be completed within a few seconds On completion the program displays the resulting array in an editing window for review identical to the REFL_ARRAY EDIT window see REFL_ARRAY EDIT
80. I table can be outputted as either 0 author s reported method original data as reported in literature 1 theta values in degrees 2 2 theta values in degrees 3 d spacings in Angstroms 4 sin theta 5 Q values ICARD 0000805 Card format No An alternative format is the standard JCPDS card image format where the output is simi lar to the pretty format but the d spacing table is positioned to the right of the name cell and comments boxes This output is in 128 column format If selected CARD will override the NBS AIDS switch M86 E01008 Special Routines GADDS Software Reference Manual 9 3 Special gt PDF2 gt Display Graph PDF2 card above frame image as Debye Scherrer rings Menu Command Special gt PDF2 gt Display Accelerator None User Level 1 SLAM Syntax PDF2 DISPLAY 1 DASHED PDF2 DISPLAY will draw the PDF pattern s d lines on top of any displayed frame image for quick pattern matching or verification 9 3 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Pils teresa eres PDF Number 33 1161 The PDF number is defined by a set number and a pattern number These numbers can be separated by a space a comma ora dash i e 33 1161 83 1161 or 33 1161 are all valid PDF numbers DASHED Dashed lines No Defines whether the PDF pat
81. If you leave slave mode first the master frame buffer will lose communication with the GGCS and become confused NOTE This command is not available on theta theta systems 5 46 1 Arguments None Command executes immediately after confirmation 5 47 Collect gt Add Accumulate an area detector frame Still frame Menu Command Collect gt Add Accelerator Ctrl Shft A User Level 1 SLAM Syntax ADD 1 CLEAR PATTERN COUNTS lt n gt DISPLAY lt n gt REAL TIME RESET lt n gt SHUTTER ATTENUATOR Collect gt Add allows you to collect a single still frame of data at a fixed goniometer position use any of the Collect gt Scan commands to collect multiple data frames The Collect gt Goniometer gt Manual command also lets you acquire a still frame while operating the goniom eter with the manual control box See Collect gt Goniometer gt Manual for details Data are Data are continuously acquired until a specified amount of time has elapsed or a specified num ber of counts is reached whichever occurs first You can optionally display the accumulated frame after it has been acquired or update the display immediately as each count is recorded referred to as real time display If you elect one of the display options ADD also updates the current frame status information displayed at the upper right of the screen M86 E01008 Collect Routines GADDS Software Reference Manual
82. Lanusei e so n a aie ee oud rh ak awe ee bale ek ee nk 3 8 3 5 File gt Display gt Next Run and File gt Display gt Prev Run 0000 e eee eee 3 9 3 6 File gt Display gt Movie Run and File gt Display gt Movie Run 2 005 3 10 3 7 File gt Load Read a frame from disk into frame accumulation memory 3 10 3 1 ALQUMOMS Msc see Ee es Ale dae eta le Bal ha ek seed tere as Oe PR eee 3 11 3 8 File gt Save Save a new detector frame to a disk file 0 0 c cee eee 3 14 3 8 1 Arguments sensiha eau tE taddbaad Hiei pee daeesh weenie tee beam O 3 15 3 9 File gt Logfile e Create a new log file and start recording 0 00 ceca eeaee 3 16 3 91 ArgQumentS e EOE eGcpees cota ed tae ede TOANE fed eats 3 18 3 10 File gt Scriptfile e Create a new script file and start recording 000000 3 19 i M86 E01008 4 04 GADDS Software Reference Manual Table of Contents IOT ArQUMeNIS eid arek AEAEE were a aie heme eerem Sued weet Ad Midna ea Be ee aes 3 19 3 11 File gt Print e Dump screen to printer device or file 0 cee eee 3 21 SAA TeAIQUMONIS a arn Sete Bae tle daa eG eka elated Wi bala Pare Ww Ae eee des 3 21 4 Edit ROUUNCS s2cicadrss c0 ek coed Pie den wae oon Ga tea Gad see bates 4 1 4 1 Edit gt Configure gt User settings Edit the current user configuration settings 4 1 4 1 1 Frame Naming Parameters 0 0 tees 4 1 4 1 2 Sample
83. No Check this option to write frame in XENGEN 1 3 format more correctly in the old PCS computer format The default is unchecked Bruker format Selects either a scan oscillate or stepping between frames of a series of the requested drive along the drive axis Perform sample oscillation 3 circle goniom eter only Normally scans are taken by continuously actually in 0 0005 deg steps driving the specified scan axis of the goni ometer as the data are accumulated This provides a very uniform distribution of col lection time versus scan angle as well as very good contiguity between successive frames If the MODE qualifier is set to oscil late the scan angle is driven back and forth between the starting position and starting position plus the frame width approximately once per second AN INTEGRAL NUMBER OF OSCILLATIONS IS ALWAYS PER FORMED IN THIS MODE the collection time per frame is adjusted as necessary to accommodate an integral number of 1 s oscillations The default is Scan In general oscillation is not recommended Drawbacks are that the ends of the scan range have anomalously high weight since the goniometer must stop and restart at the end of each oscillation and there may be some overlap or underlap of successive frames Oscillation can however compen sate for some sources of error such as M86 E01008 Collect Routines GADDS Software Reference Manual intensity fluctuation due
84. Omega 0 271 0 006 0 443 0 016 0 448 0 006 etc 1 00 25 ooo o 1 25 0 0 X 0 039 0 215 Phi 0 000 0 000 82 85 0 000 0 000 33 26 0 000 0 000 142 13 309 54 DQ SOs SES Sore Ss OOGO fo fo fo Inf Inf V Sig 112 97 83 8 44 M86 E01008 GADDS Software Reference Manual Peaks Routines 8 17 Peaks gt Refl Array gt Bravais Determine Bravais lattice and perform HKL transformations Menu Command Peaks gt Refl Array gt Bravais Accelerator Ctrl B User Level 1 SLAM Syntax REFL_ARRAY BRAVAIS 1 2 3 4 5 6 7 SIGA lt n gt SIGB lt n gt SIGC lt n gt SIGMA lt n gt SIGBEST lt n gt REFL_ARRAY BRAVAIS determines possible Bravais lattices corresponding to the specified input unit cell parameters and standard devia tions based strictly on the metric symmetry Possible solutions are ranked according to degree of symmetry and a goodness of fit The highest symmetry solution whose goodness of fit is better than an input threshold is flagged as the most likely solution You can accept that solution or one of the other possible solutions in which case the reflections in the Reflection Array will be automatically re indexed according to the selected unit cell Normally you will invoke this command immedi ately after autoindexing the Reflection Array with the REFL_ARRAY INDEX command REFL_ARRAY INDEX automatically stores its re
85. Overflow Table sin a a E cis iene he Hh Does Gee ia eo elt Soe ee T R Aa A 10 AA TAOS agaaa ES a dise et Mastin TER ERIRE oie R he a alive a ata T EA A EEE a A 11 Appendix B DIFFRAC 4S Raw Data File Format 0000eeeeee B 1 Appendix C DIFFRAC AT Raw Data File Format 0000ee ees C 1 Appendix D PLOTSO Raw Data File Format 22000c ee eeeeees D 1 Appendix E TEXTURE AT Raw Data File Format 222 005 E 1 Appendix F POPLA Data File Format 020 0c eeeeeee ee eeees F 1 M86 E01008 4 04 xv Table of Contents GADDS Software Reference Manual Appendix G SLAM Command Reference 220000ceeeeeeeeee G 1 Appendix H Remote Operations SMARTservice 000000es H 1 Appendix I Electronic Tracking of Instrument Configuration Changes Bruker Log Service 2 iis cseccee ec eee is dnvar en eee Ge eee l 1 xvi M86 E01008 4 04 1 General Information The GADDS Software Reference Manual is designed to supplement the GADDS User s Manual and the GADDS Administrator s Manual Information already contained in these manuals is not duplicated here See the GADDS User Manual for e General descriptions of the instrument goniometer stages generator etc e General operation of the instrument power up operation shut down etc e Theory of analysis e Geometry conventions e Typical applications of GADDS to solve common diffraction problems See the
86. Pernet et Select Project no default Enter the project s name to archive or use PROJECT for current project No default G2 S Archive Filename PROJECT Enter the filename for the file archive Default is project name he PE EEST Archive Directory GADDS FRAMES Enter the directory to store the file archive Default is GADDS FRAMES NOCALIB Exclude Calibration Files Yes Check to exclude all calibration files from the archive Default is yes M86 E01008 GADDS Software Reference Manual Project Management Routines NOWORK Exclude Work Files No Check to exclude all working directory files from the archive Default is no 2 7 Project gt Remove Remove a project from the project database Menu Command Project gt Remove Accelerator None User Level 2 SLAM Syntax PROJECT REMOVE 1 Use this command to remove the requested project from the project database but does not delete any data files A scrollable alphabetized list of all Known projects excluding the current project will appear Highlight the project of inter est and click OK The program will remove the requested project NOTE Because the configuration and data files were not deleted you could re add the project using the Project gt Load command 2 7 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses EE
87. Project gt New Edit Copy panel is defined as GADDS FRAMES you would need to enter only cor1 001 in the File gt Display gt New panel In order to allow users flexibility in working with multiple products on the same computer e g FRAMBO and GADDS GADDS supports pro gram specific logical names environment vari ables The program specific names are GADDS SYSTEM GADDS SYSDATA and GADDS FRAMES which serve the same pur pose as SAXI SYSTEM points to executables and help files SAXISSYSDATA points to color lookup table directory and SAXISFRAMES points to directory containing frame and plot data If the program specific name exists its translation is used If it does not exist the pro gram attempts to use the corresponding SAXI name thus the program remains compatible with earlier logical name setups GADDS recognizes the following logical names GADDS CALIB This variable translates to the directory which contains area detector calibration files such as flood field and spatial tables GADDS FRAMES This variable translates to the root directory which contains area detector frames cali bration files project files and 1D spectra raw files GADDS PROJECT This variable translates to the full pathname of the file to be used as the project data base for example D frames projects gadds prj GADDS SCRIPTS If present this optional variable translates to the name of the common scr
88. Routines logfile If scripting is enabled again see LOG FILE a non interactive GRAPH VECTOR com mand corresponding to the final cursor position is written to the output script file 7 8 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Sloe een X Origin 256 The X coordinate of the lower left of the box defining the region of interest in pixels The range is from 0 to framesize 1 default value is 256 G2 teen TEAS Y Origin 256 The Y coordinate of the lower left of the box defining the region of interest in pixels The range is from 0 to framesize 1 default value is 256 Oriel even tas X Length 32 The X length of the vector pixels The range is from O to framesize 1 default value is 32 DA seston ch tits Y Length 0 The Y length of the vector in pixels The range is from 0 to framesize 1 default value is 1 QUADRANT lt n gt Quadrant 0 This parameter specifies whether you want the graph to appear covering the entire data frame enter O or just one of the four quadrants enter 1 through 4 as appropri ate The default value is O full frame win dow Quadrants are 0 full window 1 lower left 2 lower right 3 upper left and 4 upper right DELAY lt n gt mand mode only 0 0 available in com Specifies a time interval in seconds to wait before erasing the
89. Routines GADDS Software Reference Manual 5 28 Collect gt Goniometer gt Temperature Watlow Series 988 Temperature Controller Menu Command Collect gt Goniometer gt Temperature Accelerator Ctrl Shift T User Level 1 SLAM Syntax GONIOMETER TEMP 1 RAMP lt n gt HOLD lt n gt WAIT Operate a temperature controller using the sec ondary COM port which defaults to COM2 but can be specified with the command line argu ment TCPORT where is the com port number 1 4 Currently supported temperature controllers are e Watlow Series 988 e AntonPAAR KHR e EuroTherm 800 series e EuroTherm 905 e DHS 900 DCS 350 Eurotherm 2600 2700 Connection to the TC is only established upon entering the GONIOMETER TEMP command and is always disconnected upon exiting this command This permits a more elaborate TC control program to be run from either the SYS TEM command or as a separate and indepen dent program task however the GONIMOETER TEMP command will not function if the TC port is already in use or allocated by another pro gram You must terminate any TC control pro gram before executing the GONIOMETER TEMP command All temperature parameters are stored in subse quently created frame headers You may over ride waiting for the either the ramp up to temperature the hold time or both with either the lt Enter gt or lt Lf button gt and the temperature parameters will still be stored in new
90. Software Reference Manual Example output follows 281 8 150 3 0 4 22 21 2 7 000C 107 0 287 4 0 7 32 26 5 0 000C Example 8 1 REFL_ARRAY THRESHOLD Output from 322 7 376 5 0 3 14 17 24 000C Eight Myoglobin Test Frames 155 1 79 3 0 6 10 14 3 5 000C 107 2 52 7 0 8 355 85 3 8 0005 141 2 173 6 0 8 369 86 4 2 0001 164 8 286 4 0 8 334 82 3 9 0001 83 4 287 8 0 2 325 81 5 5 0005 164 4 219 1 0 8 246 70 4 0 0005 117 8 173 3 0 1 230 68 4 6 0001 165 5 127 6 0 3 178 60 3 7 0000 175 7 196 5 0 1 177 60 3 8 0001 70 6 75 7 0 2 191 62 4 5 0005 143 7 53 8 0 1 135 52 3 5 0001 210 9 285 8 0 2 98 44 3 4 0001 167 7 378 3 0 5 99 45 3 5 0000 267 9 3 1 0 9 63 36 2 5 0001 224 1 330 9 0 3 84 41 3 2 0000 Reflection disposition found 133 on first or last frame 33 in X exclusion range 5 outside radius limit 10 outside res limits 0 lt I sigma threshold 0 orphan pixels 11 bifurcated 0 Total useable 107 centered for LS 26 Total unused 26 x Y Rot Inorm Sig D Code 134 1 4285 0 2 93 43 36 0001 82 9 S12 0 3 Bet TV iA 000C 210 3 196 4 0 3 85 41 34 0000 33 3 99 1 0 4 468 97 54 000C 263 7 400 4 0 7 56 34 27 0000 142 1 309 5 0 4 344 83 42 000C E E E E coger 82 9 196 2 0 6 379 87 5 6 000C 352 0 518 0 5 36 27 22 0000 130 0 127 2 0 6 285 76 41 000C Boana CoG Aas ROO 156 7 28 7 0 7 223 67 32 000C 82 9 1015 0 8 75 39 46 0000 164 6 264 0 0 7 228 68 4 0 0006 177 6 331 6 0
91. Sum pixels 2 Average pixel 3 Arc Length quick and dirty M86 E01008 Peaks Routines GADDS Software Reference Manual 4 Solid Angle 5 Bin Method 6 Normalized Bin preferred Methods 0 to 3 are described later They are quick and dirty methods In contrast the bin method produces the most accurate results although at a slower pace The bin method will produce narrower profiles FWHMs smoother spectra and improved relative intensities across the spectra Bins are determined by the start end and step size of the integration Say you requested the range 5 to 65 in 0 5 steps The first bin covers the range 4 75 to 5 25 the second bin covers 5 25 to 5 75 the last bin covers the range 64 75 to 65 25 The idea is to place all of the observed intensity within each bin range into that bin Each frame pixel covers one or more integration bins The intensity of the each frame pixel is divided into these integration bins using the fractional area as the weighting factor eq 1 The sum of all of the fractional areas for any given pixel must equal one eq 2 N h A lpn eq 1 n 1 M 1 0 2 Ani eq 2 i 1 Wherel Intensity i integration bin number n frame pixel number A fractional area N total number of frame pixels M total number of integration bins For speed considerations the frame pixels at the edges of the integration region are not han dled precisely For chi integration if
92. Y and Zobs and Zcalc are the observed and calculated scan angle for each spot The rel ative weights Wxy and Wz are determined according to Wxy 1 Exy and Wz 1 0 5 H where Exy is an estimate of the positional standard deviation of a reflection and H is the frame halfwidth specified here 0 25 of the frame width appears to be a fair esti mate for the expected rms error in scan angle A smaller value for the halfwidth will give more weight to the scan angle information a larger value gives it less weight The valid range is 0 001 to 9999 The scan angle information is very powerful in determining a correct solution and it is probably better for the value you enter here to be too low than too high The default is 0 125 correspond ing to 0 25 degree frames MASK lt n gt 05 Constraint Mask 0 Specifies that certain variables are to be held fixed in the non linear refinement The default value of 0 frees all variables allow ing the refinement to proceed normally and should be satisfactory in almost all cases The value you specify here is a decimal inte ger corresponding to a bit mask where a set bit fixes its assigned parameter and a clear bit frees the parameter The bit param eter assignments are Bit Value Parameter Detector X positional correction 0 1 1 2 Detector Y positional correction 2 4 Detector distance correction 3 8 Detector roll 4 16 Detector yaw 5 32 Unit cell axis l
93. _tm OSCILLATE lt s gt Sample Osc from resume _tm AMPLITUDE lt n gt Amplitude from resume _tm SNAME 06 Slave Job Name from resume _tm See Section 5 30 Section 5 31 and Section 5 32 AE A TEES ATI Frames from resume _tm Enter the number of frames remaining to be collected in the current scan series 2THETA lt n gt 2 Theta from resume _tm THETA1 lt n gt Theta1 from resume _tm Enter the detector swing angle in degrees at which the remaining frames in the current scan series are to be collected On 6 0 sys tems this is the 01 angle tube OMEGA lt n gt Omega from resume _tm THETA1 lt n gt Theta1 from resume _tm Enter the omega angle in degrees at which the goniometer will be positioned at the start of this frame series If you specify a scan axis number see AXIS lt n gt below of 2 M86 E01008 GADDS Software Reference Manual Collect Routines omega will be scanned as each frame is taken Otherwise omega remains fixed throughout the frame series On 6 0 sys tems this is the 02 angle detector PHI lt n gt eceeseeessee Phi Enter the phi angle in degrees at which the goniometer will be positioned at the start of this frame series If you specify a scan axis number see AXIS lt n gt below of 3 phi will be scanned as each frame is taken Other wise phi remains fixed throughout the fram
94. a frame and run least squares without the need for autoindexing When invoked with the MATRIX option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY MATRIX displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button installs the specified orientation matrix and returns you to the REFL_ARRAY submenu the ESC key or right mouse button returns you directly to the REFL_ARRAY submenu without updating the matrix When REFL_ARRAY MATRIX updates the ori entation matrix it also extracts the unit cell parameters from the matrix and places them in the REFL_ARRAY BRAVAIS and LEAST SQUARES input panels as defaults in the case of the LEASTSQUARES panel the Eulerian angle defaults are also extracted from the input matrix You can use this feature to compute the cell parameters and Eulerian angles corre sponding to a given orientation matrix 8 23 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Note that the element order on the input panel corresponds to the standard mathematical con vention e g 1 3 is 3 column on 1st row It has nothing to do with FORTRAN storage con ventions As entered the matrix will pre multiply a column HKL vector to give and column recip rocal lattice vector The matrix must conform to the com
95. a box to a specified value allowing you to edit the image with basic functions When you press BACKSPACE or DELETE on the extended middle keypad GADDS displays a dialog box where you can enter a value to set all pixels inside the box cur sor The default value is equal to the current M86 E01008 Analyze Routines GADDS Software Reference Manual background estimate based on pixel values around the box perimeter Pressing ESC or clicking the Cancel button exits without chang ing pixel values After editing the image you can use the SAVE command to write the image in edited form This function can be performed only interactively that is there is no way to clear the area in a box with command line commands By providing arguments on the command line you can direct GADDS to compute the box cal culations once at one specified position after which control returns immediately to the com mand line The line weight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cursors Odd values are better than even ones since the extra thickness is then added symmetrically about the true cursor posi tion Analyze gt Cursor gt Box can display HKL indices corresponding to the centroid position based on the current orientation matrix that is the one
96. a maximum of 512 reflections however determination of orien tation requires only a small fraction of this num ber Usually 25 reflections is the bare minimum you ll need with 50 100 reflections about opti mal While determination of orientation from just a few contiguous frames is possible for exam ple the FRAMBO and SADIE verification tests determine the orientation of a myoglobin crystal from eight contiguous frames you ll get much more precise cell parameters if you threshold a few frames taken 90 degrees or so in scan angle from the first set adding them to the Reflection Array prior to indexing The least squares can incorporate crystal sys tem constraints if desired By default the pro gram performs a quick linear least squares of the type used in the P3 program which deter mines unit cell parameters and orientation but doesn t refine any of the detector positional cor rections or apply constraints The result cou pled with guesses of zero for the small detector positional corrections is used as an initial guess for a nonlinear refinement which incorporates detector positional corrections and constraints While crystal system constraints are useful if you want to obtain the best unit cell parameters M86 E01008 GADDS Software Reference Manual Peaks Routines you should usually NOT use constraints to determine the matrix to be used for data collec tion or data reduction the unconstrained matrix
97. a solid line style to drawing the objects with a dashed line style The current style is displayed in the DRAW submenu title bar when using the SLAM command line This command will draw a single dot When selected a crosshair cursor is visible Posi tion the crosshairs at the position to draw the dot and press ENTER or the left mouse button A dot is drawn and the crosshairs will remain for positioning the next dot Pressing ESC or the right mouse button will return you to the menu Menu Command Analyze gt Annotate gt Line SLAM Syntax GRAPH POSTER DRAW LINE This command will draw a line segment between two points When selected a crosshair cursor is visible Position the crosshairs at the start of the line segment and anchor the line segment by pressing ENTER or the left mouse button The crosshairs will disappear and be replaced with a line segment between the anchored point and the current cursor position Posi tion the line segment end point and press ENTER or the left mouse button The line segment is drawn and a crosshair cursor appears for positioning the next line Press ing ESC or the right mouse button will return you to the menu 7 32 M86 E01008 GADDS Software Reference Manual Analyze Routines 7 11 Analyze gt Graph gt HKL e Plot HKL curve profile through frames Menu Command Analyze gt Graph gt HKL Accelerator None User Level 2 SLAM Syntax GRAPH HKL 1 QUAD RANT lt n gt
98. a specific detector distance and automatically compute and install a spatial cor rection for data subsequently collected at that distance This will be necessary when you col lect a new flood field whenever experimental parameters change e g the detector distance is moved or whenever the instrument has been modified e g the goniometer has been realigned etc Prior to running SPATIAL NEW make sure the correct value for the current sample to detector distance is entered in the CONFIGURE EDIT panel see CONFIGURE EDIT for more infor mation The correction is computed from a frame acquired with the brass fiducial plate fastened to the front of the detector face and with a reason ably uniformly radiating point source positioned at the center of the goniometer The supplied Fe source is good for this purpose You should acquire and compute a new spatial correction from such a frame before starting data collection on each new sample but AFTER acquiring and computing a new flood field correction see the description of the FLOOD command The sam ple to detector distance for this frame must be exactly the same as it will be for the frames col lected from the sample crystal Usually a fiducial plate frame with a time cutoff of about 30 min utes or a count cutoff of about 100 000 counts is adequate a rule of thumb which works well is to use the same collection time as for the flood field data plus 5 minutes but no
99. and a processing direction Both the sample and the pole projection must be defined as below Z M X N NOTE The crystallographic axes must be orthogonal We have only implemented the algorithm for orthorhombic symmetry and thus tetragonals and cubics For materials oriented uniaxially about a single processing direction such as would be the case for spun fibers one usually calculates Hermans orientation indices for each crystallographic axis with respect to that processing axis Herman s orientation indices are defined by 3 cos a 1 F X x eget 2 where X processing direction i e MD TD N x crystallographic direction M86 E01008 GADDS Software Reference Manual Analyze Routines a angle between above lt gt averaged over entire pole figure Table 7 1 Some limiting cases of orientation and their second moments and orientation indices Orientation Angle c z lt cos c z gt Fe z Chain axis is parallel 0 1 1 0 to the fiber axis Chain axis perpen 90 0 0 5 dicular to the fiber axis Chain axis oriented a random 1 3 0 0 random Equal bimodal orien 0 or 90 1 3 0 0 tation of chains Typically Herman s indices are plotted on a Stein triangle The three apexes of the triangle correspond to the crystallographic axis a b c being parallel to the z axis of the sample The edges of the triangle represent the orientation of a crystallogr
100. and press ENTER The box is drawn and a crosshairs cursor appears to position the next box When you are finished press ESC to return to the Poster menu M86 E01008 12 13 SLAM Routines GADDS Software Reference Manual PEAKS POSTER DRAW CIRCLE PEAKS POSTER DRAW CIRCLE is used to draw an ellipse When selected a crosshair cur sor appears To draw a circle 1 Use the mouse to position the crosshairs at the center of the ellipse and press ENTER to anchor this spot The crosshairs are replaced with an ellipse drawn with the cen ter anchored and the width and height selected from the cursor 2 Move the mouse until the width and height are correct and press ENTER The ellipse is drawn and a crosshairs cursor appears to position the ellipse center 3 When you are finished press ESC to return to the POSTER menu PEAKS POSTER DRAW DOT PEAKS POSTER DRAW DOT is used to draw a single dot When selected a crosshair cursor appears To draw a dot 1 Use the mouse to position the crosshairs at the point you want to draw the dot and press ENTER A dot is drawn and the crosshairs remain to position the next dot 2 When you are finished press ESC to return to the POSTER menu PEAKS POSTER DRAW LINE PEAKS POSTER DRAW LINE is used to draw a line segment between two points When selected a crosshairs cursor is visible To draw a line segment 1 Position the crosshairs at the start of the line segment to
101. angles are all zero X direction of incident beam away from tube Y normal to X amp Z and forms right handed coordinate system Z vertical direction up For speed considerations we will only calculate the absorption correction every 16 or 32 for 1K frames pixels along the detector Intermediate pixel corrections may be determined using linear extrapolation Divide the cross section of the fiber into little boxes of volume dV Let p path length to box q path length of diffracted beam a incident beam angle to normal b diffracted beam angle to normal u absorption coefficient Then the absorption formula is given by A y qe 0P ba dV 6 12 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses OT E ETT Input File FRAME Enter filename for first input frame in series to process n ARAE EENT ET dies Frames to Process 1 Enter consecutive frames to process e E E Output File NULL Enter filename for first output corrected frame M86 E01008 GADDS Software Reference Manual Process Routines KEATS aaen Sample vector X 1 VE NE Sample vector Y 0 EERE secchiteeniieatitin Sample vector Z 0 Input the coordinates in the goniometer head coordinate system of the vector which is along the fiber axis If the fiber axis points vertically the coordinates are 0 0 1 NSTEPS lt n gt
102. any output frames created in Bruker for mat and in output raw files It is also used by the interactive cursor commands and all the Peaks commands M86 E01008 GADDS Software Reference Manual Edit Routines UNITS lt S gt Units angstroms Enter the wavelength units as either Ang stroms conventional and US standard or nanometers new European standard The default value is Angstroms This value only affects displaying wavelengths within the GADDS program All wavelengths within data files are always stored in Angstroms IKVEKND gt onnan Preferred Settings Voltage 50 Enter the preferred X ray generator kV set ting default is 50 kV This value is stored in output p4p and raw files and in the header of output Bruker format frames If you use Goniom gt Generator to set the X ray gener ator voltage this value will default to the cur rent generator setting IMAH lt ND nnna Preferred Settings Current 40 Enter the preferred X ray generator milli amps setting default is 40 ma This value is stored in output p4p and raw files and in the header of output Bruker format frames If you use Goniom gt Generator to set the X ray generator current this value will default to the current generator setting STANDBYKV lt n gt Standby settings Voltage 20 Enter the standby X ray generator kV set ting default is 20 kV GADDS will automat ically reduce the generator settin
103. background trace in chi is smoothed using a three point average The background below the Bragg peak is determined by linear interpolation between the low and high back ground values 20 low end li x 20 low beg I 20 d20 If the background obtained for a certain value of sample inclination is higher than the measured intensity in the pole figure its subtraction would lead to a negative intensity in the pole figure This would be physically meaningless because there cannot be negative probability in the pole figure The background correction will simply replace any negative values with zero and dis play a warning message with the maximum neg ative value that was encountered Usually significant errors of this sort occur by the mis placement of the two theta values for integrating the background regions 20 high end La 7 20 d20 26 high beg _ Liow x i 20 pign F 26 rage L high x i 20 prag g 2B row 20 en 26 64 Loor xa ae y a 1 y M86 E01008 Analyze Routines GADDS Software Reference Manual 7 19 2 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 teenie teat 2theta start 24 5 Two theta start of Bragg peak region G2 raii 2theta end 26 5 Two theta end of Bragg peak region a EAE Chi start 0 0 Chi start of Bragg peak region a EEEE TEET Chi end 360 0 Chi end of Bragg
104. becomes much more robust with respect to noise see SMOOTH The 3D shape of the rolling ball is a half ellipsoid where both axes in the XY plane are identical and the negative intensity direction is irrelevant thus producing a half dome shape Figure 7 2 Depiction of why rolling ball filter is sensitive to noise M86 E01008 Analyze Routines GADDS Software Reference Manual 7 17 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 A AAE NS Input frame FRAME Enter name of input frame or frame DISPLAY lt n gt Max display counts 16 Enter counts corresponding to white AT Bkgd frame NULL Enter name of output background frame or null RADIUS lt n gt Radius 25 Enter the radius of the rolling ball in pixels This determines the size in the XY plane for the rolling ball Range is 1 to 50 You should determine the half width in pixels of the broadest feature in your frame images and use a value greater than that half width Remember that the broadest feature may consist of overlapping peaks use the half width of background to background of these overlapping peaks feature HEIGHT lt n gt HEIGHT 2 Enter the height of the rolling ball in pixels This determines the shape or flatness of the rolling ball in the intensity direction Range is O to 20 A rule of thumb is height lt radius
105. copying and pasting a specified range Pressing the F7 key has the same effect when you re in the editing window Cut This removes a selection from the array and places it in the paste buffer Use PASTE to reinsert the line s that were cut Pressing the F8 key has the same effect when you re in the editing window Store Makes a copy of the current selection this is the same as CUT but does not remove the selected text from the array and places it in the paste buffer Pressing the F9 key has the same effect when you re in the editing window Paste Inserts the contents of the paste buffer ahead of the current line Pressing the F10 key has the same effect when you re in the editing window If there aren t enough free lines in the array the paste will not be per formed M86 E01008 Peaks Routines GADDS Software Reference Manual The items in the Reflection Array have the fol lowing definition FLAGS The status of a reflection is indicated by a series of single character flags that are dis played in this field There are four possible flags having the following meanings The flags always appear in sorted order ACHS ACS AH etc with no intervening spaces If you re entering or changing the flags in the EDIT sub command you can enter the flags in a different order but make sure that there are no imbedded spaces A This reflection record includes the goniometer settings angles and the the X Y
106. correct distance M86 E01008 File Routines GADDS Software Reference Manual 3 8 File gt Save Save a new detector frame to a disk file Menu Command File gt Save Accelerator Ctrl S User Level 1 SLAM Syntax SAVE 1 TITLE lt s gt XENGEN DISPLAY lt n gt This command copies a data frame from the frame accumulation memory to a specified disk file disk for retention In the process it allows you to specify the file format and a title up to 72 characters to display with the data frame This title is stored in the output frame header The data to be saved must exist in the 32 bit frame accumulation memory A frame currently displayed as a result of a File gt Display File gt Load Collect Menu or Process gt Spatial gt New command can be saved A few commands will destroy the contents of the accumulation mem ory If you need to save a data frame do so before issuing one of these destructive com mands Edit gt Clear if data image memory is cleared Peaks gt Refl Array gt Threshold If you try to save data that has been overwritten by one of these commands the program dis plays a box with the message DETECTOR DATA NOT YET TAKEN OR OVERWRITTEN Because File gt Save allows you to write a frame in either Bruker or XENGEN 1 3 format you can use it to convert a frame from one format to the other For example you can use File gt Load to read in a Bruker format frame fol
107. corresponding to the current inten sity centroid are also outputted XUnwarped If a spatial correction is in use provides spatially corrected X coordinate of centroid of intensity otherwise this value will be iden tical to the raw coordinate YUnwarped If a spatial correction is in use provides spatially corrected raw Y coordinate of cen troid of intensity otherwise this value will be identical to the raw coordinate M86 E01008 Analyze Routines GADDS Software Reference Manual 7 7 Analyze gt Graph gt File Plot points from ASCII disk file Menu Command Analyze gt Graph gt File Accelerator Ctrl G User Level 1 SLAM Syntax GRAPH FILE 1 QUADRANT lt n gt PRECLEAR NOCLEAR This command plots X Y graphs from disk resi dent data The input data file must be in PLOTSO format as described in Appendix D Examples of PLOTSO format files generated by GADDS are _pj flood field projection intermedi ate data files _fl flood field corrections _ix spatial correction files _if raw to corrected spa tial maps and _it corrected to raw spatial maps When invoked from the menu or run from the command line without arguments Analyze gt Graph gt File displays a dialog box where you can view edit the arguments described below Pressing ENTER or clicking the OK button starts graphing the specified file Pressing ESC or the Cancel button returns you to the menu See PLOTSO file format S
108. cursor and returning con trol to the program This is for use in scripts where it is desirable for the cursor to remain on screen long enough for the user to dis cern its position NOERASE mand mode only No available in com Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor left from a NOERASE by reissuing the command with the same parameters The CLEAR com mand also provides a way to erase cursors left over from NOERASE options The following output statistics are displayed on screen in real time and are also written to the logfile if applicable M86 E01008 Analyze Routines GADDS Software Reference Manual OrigCnts Counts of pixel at vector origin EndpCnts Counts of pixel at vector endpoint X Origin X coordinate of origin in pixels Y Origin Y coordinate of origin in pixels X Endpt X coordinate of endpoint in pixels Y Endpt Y coordinate of endpoint in pixels X Midpt X coordinate of midpoint in pixels Y Midpt Y coordinate of midpoint in pixels D Pixel Length of vector in pixels D Deg Length of vector in degrees 2 theta D Angst Length of vector in Angstroms Chi Angle of the vector in degrees clockwise from X This chi convention is the same as that used on a 4 circle diffractometer i e if the vector origin is at the beam center an
109. cursor to remain on screen long enough for the user to dis cern its position NOERASE 0 No available in com mand mode only Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor left from a NOERASE by reissuing the command with the same parameters The CLEAR com mand also provides a way to erase cursors left over from NOERASE options M86 E01008 Analyze Routines GADDS Software Reference Manual 7 12 Analyze gt Graph gt Psi Plot Psi curve profile through frames Menu Command Analyze gt Graph gt Psi Accelerator None User Level 2 SLAM Syntax GRAPH PSI 1 QUADRANT lt n gt 2 3 DELAY lt n gt NOERASE GRAPH PSI draws a graph in the frame window or a specified quadrant called an psi curve This graph shows integrated intensity in a speci fied rectangular area as a function of psi angle and requires that you have a contiguous series of frames collected using SCAN PSI available for input 7 12 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses EET A ETA 1stframe psi01 000 The name of the first frame in the PSI scan series QUADRANT lt n gt Quadrant 0 This parameter specifies whether you want the graph to appear covering the entire data frame enter 0 or just one of
110. description of the method used to measure the density or enter Default is 9r 2 4 Project gt Copy Copy the current project to a new project Menu Command Project gt Copy Accelerator None User Level 1 SLAM Syntax PROJECT COPY CNAME lt s gt 1 TITLE lt s gt WORKDIR lt s gt FORMULA lt s gt MORPH lt s gt CCOL lt s gt DENSITY lt s gt DENSMETH lt s gt CLEAR RESET Use this command to create a new project using the current project settings as defaults You typi cally use this command when mounting a similar sample on the goniometer or repeating a collect and process operation on the same sample Project gt Copy differs from Project gt New see Section 2 3 in that e The project defaults can be taken from either the system wide defaults see Section 2 9 Project gt Overwrite defaults or from the current project settings by using the Clear switch e The crystal information may be either cleared or retained from the current project settings by using the Reset switch e The project information defaults to stay the same except that the sample number is M86 E01008 Project Management Routines GADDS Software Reference Manual incremented however you may override these defaults 2 4 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Project gt New argu ments also apply here see Section
111. drawn This graph is actually a GRAPH FILE of the plottable ASCII _ix spatial calibra tion file Dashed lines are drawn along the rows and columns of the indexed pattern If a line jumps from one row or column to another the holes have been mis indexed and the spatial calibration will not be valid If this happens use the CONTRAST command to check the quality of the fiducial plate frame If the frame looks OK you can try re processing it with SPATIAL PROCESS with a different I sigma level for thresholding spots from the image Another possibility is to acquire a fidu cial plate image for a longer period of time Usu ally mis indexing occurs because the I sigma threshold is set too low causing the program to interpret background as a spot The default threshold of 4 works well on brass plate images which contain 80 000 to 100 000 total counts If your image contains more counts you will prob ably have to raise the threshold accordingly for example if the image contains 1 000 000 counts i e about 10 times the nominal number increase the threshold by a factor of about sqrt 10 12 would be a good value in this case 6 6 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GT E A TEE Max Seconds 15 00 This is the maximum count time in sec onds The default value is 900 the range is from 1 to 65 535 seconds Times can be entered in dec
112. e Ka1 Ka2 R21 1 R21 588 R4 detector slit diffr side in degrees oea R8 primary wavelength in A Obs or nm 9999 0 unknown i e Ka1 592 14 secondary soller slit 632 R8 secondary wavelength in A Obs or nm i e Ka2 0 not present 640 R8 tertiary wavelength in A Obs or nm 1 present i e KB 1 2 deg 2 1 648 R8 intensity ratio of secondary to primary 2 4 deg 2 1 wavelength 3 other 2 1 656 C4 wavelength unit name 2 now always A 9999 unknown PEROFETA obs in RAW1 00 files both A or 596 14 thin film crit Wars ised 0 not present 660 R4 intensity ratio of tertiary to primary 1 present wavelength M86 E01008 B 3 DIFFRACP S Raw Data File Format GADDS Software Reference Manual 664 R4 total sample run time V where sample illumination in 9999 0 unknown obs mm 1 0 unknown 2 or Unkn for unknown 668 C44 reserved for expansion or fix for fixed 80 R8 anti slit start in degrees if antislit_code RAW_RANGE_HEADER 304 bytes of range fix header information that precedes every range in 9999 0 if not present a RAW file Similar to DIF_RANGE_HEADER but DIFFERENT 88 C8 anti slit code ASCIIZ V20 V6 u H y4 V2 fix Offset Code Description V where sample illumination in 0 14
113. executes immediately M86 E01008 File Routines GADDS Software Reference Manual 3 4 File gt Display gt HKLs Overlay predicted HKL pattern on the display Menu Command File gt Display gt HKLs Accelerator None User Level 2 SLAM Syntax DISPLAY HKL 1 2 3 These commands allow you to draw an overlay of predicted spot positions onto a displayed frame The OVERLAY option in File gt Display also allows you to automatically display the overlay every time a new frame is displayed The over lay is computed from the current orientation matrix from the last Peaks gt Refl Array gt LeastSq command and takes into account any lattice centering determined in Peaks gt Refl Array gt Bravais You can draw overlays on mag nified frames by entering the desired magnifica tion and center in the File gt Display dialog when the image is displayed the Edit gt Zoom com mand does not redraw or magnify graphic over lays 3 4 1 Arguments File gt Display gt HKLs draws an overlay on the currently displayed frame according to three input arguments Each argument is listed below by its SLAM command line name followed by its dialog box prompt in parentheses 1 ete E Spread 0 75 Width in degrees of the predicted pattern Default is 0 75 2 N Lineweight 1 Line thickness used for drawing the overlay markers The drawing routine will constrain the input value to be from 1 to 3 Default is
114. exits without updating the angles On successful completion the program also updates the cur rent goniometer angles displayed in the goniom eter status area at the lower right of the screen NOTE To change the settings of non controlla ble axes see the Collect gt Goniometer gt Fixed axes command Section 5 24 M86 E01008 Collect Routines GADDS Software Reference Manual 5 14 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses F EEEE 2 Theta A ETEO Theta1 The current 2 Theta swing angular reading from the goniometer to the nearest 0 5 degree On 8 0 systems this is the Theta1 tube axis A AAEE AETAT Omega G2 oiai Theta2 The current omega angular reading from the goniometer to the nearest 0 5 degree On 8 0 systems this is the Theta2 detector axis C e ate rte eases Phi The current phi angular reading from the goniometer to the nearest 0 5 degree CA th crs snes Chi The current chi angular reading from the goniometer to the nearest 0 5 degree leave this field alone if you re connected to a 4 cir cle goniometer Coco raan X The current X positional reading from the goniometer to the nearest 0 5 mm current value current value current value current value current value current value current value ne ae ee Y The current Y positional reading from the goniometer
115. factor Available normaliza tions are O none sums all active pixels 1 average pixel sum of pixels number of pixels 2 arc length sum of pixels arc length sum of arc lengths 3 solid angle sum of pixels solid angle sum of solid angle 4 bin method See Peaks gt Inte grate gt Chi for full description of this normal ization method STEPSIZE lt n gt Step size 0 1 The angle step width in degrees The default of 0 1 works well for frames taken at 7 cm Frames taken at 10 cm may need a smaller stepsize 8 12 M86 E01008 GADDS Software Reference Manual Peaks Routin es 8 9 Peaks gt Integrate gt Area Perform area integration in conic region gt integer Menu Command Peaks gt Integrate gt Area Accelerator None User Level 1 SLAM Syntax INTEGRATE AREA 1 2 3 4 Integrates total counts inside and on a user defined conic region Does not subtract out background 8 9 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GT EON EE 2 Theta Start 0 00 Enter lower 2 theta of conic region in degrees Valid range is 0 to 179 E ety 2 Theta End 30 00 Enter upper 2 theta of conic region in degrees Valid range is 1 to 180 3 E Chi Start 0 00 Enter lower chi of conic region in degrees Valid range is 360 to 180 ae aa ate aaas Chi End 860 00 Enter upper chi of co
116. fh led eed eet 7 42 7 18 Analyze gt Pole Figure gt Scheme Determine data collection scheme for pole figure 7 43 FAB AHSCHEMCG se es Some ewe ee Ae ta G athe E E E want ea eau 7 44 TAS ATQUMONIS 2m seedy oe eae edn apidert ern pat wR a datos Reh ele we eee a ane 7 44 7 19 Analyze gt Pole Figure gt Process Process frames into pole figure image 7 46 FAQ PIOCCSS acs nte ath sc hc siete abate Bale e dye ation de does esl wns Pea a ake a Soe ins 7 46 19 2 ARGUMENTS 2 25 6 oes yn a eed ee ee a a ide baa dP Pda ie een en eels 7 48 7 20 Analyze gt Pole Figure gt Interpolate Interpolate a processed pole figure image 7 50 L207 AMQuUMONS aprenan a ohawi de A bei Mie oels glee oe Peedi adiawdely es 7 50 7 21 Analyze gt Pole Figure gt Tilt Tilt pole figure about a new polar origin 7 51 241 APQUMONTS 2s Yeoman bene O ete Rs Mien pled ew eh aie anti dly 7 51 7 22 Analyze gt Pole Figure gt Rotate Rotate pole figure about beta azimuthal angle 7 52 E22 ACAIQUMONIS tit gaia bday teed we eae daa weeds yeu ee belle ead eed 7 52 7 23 Analyze gt Pole Figure gt Symmetrize e Symmetrize pole figure using various Laue symmetries 4 ec pals oie Ga eee ee be ete OE See Sede Hidde 2x gadis 7 53 Pea A AKQUMONIS wis a9 eee Sete Sei A ai tate Ankit eine a teat las bales wv ene aoa Slee sad 7 53 7 24 Analyze gt Pole Figure gt Invert Invert pole figure about x axis
117. followed by its dialog box prompt in parentheses ST ante iT eiye 2 Theta Start 0 00 Enter lower 2 theta of conic region in degrees Valid range is 0 to 179 2 circ cee 2 Theta End 30 00 Enter upper 2 theta of conic region in degrees Valid range is 1 to 180 SS iweseetedl densi se Chi Start 0 00 Enter lower chi of conic region in degrees Valid range is 360 to 180 4 tian ea Chi End 360 00 Enter upper chi of conic region in degrees Valid range is 180 to 360 NORMAL lt n gt Normalize intensity 5 When integrating pixels along a conic line segment each pixel may be weighted by a normalization factor Available normaliza tions are O none sums all active pixels 1 average pixel sum of pixels number of pixels 2 arc length sum of pixels arc length sum of arc lengths 3 solid angle sum of pixels solid angle sum of solid angle 4 bin method 5 normalized bin method See Peaks gt Integrate gt Chi for full description of this normalization method STEPSIZE lt n gt Step size 0 1 The angle step width in degrees The default of 0 1 works well for frames taken at 7 cm Frames taken at 10 cm may need a smaller stepsize M86 E01008 GADDS Software Reference Manual Peaks Routines 8 8 Peaks gt Integrate gt 2Theta Perform 2 theta integration in conic region gt F chi Menu Command Peaks gt Integrate gt 2theta Accelerator None Us
118. for amorphous region 5 Two Theta Begin for Crystalline Reg 6 Two Theta End for Crystalline Region 7 Chi Begin for Crystalline Region 60 8 Chi End for Crystalline Region 90 Defines conic region for crystalline region COMPTON Compton Scattering Y N No Enter Y to subtract the Compton scattering effect from the amorphous result The Compton scattering must be previously calculated using PER_CRYSTAL COMPTON M86 E01008 GADDS Software Reference Manual Analyze Routines 7 15 Analyze gt Percent Crystal gt Internal e Amorphous region surrounds Bragg peak Menu Command Analyze gt Percent Crystal gt Internal Accelerator None User Level 1 SLAM Syntax PER_CRYSTAL INTERNAL 1 2 3 4 5 6 7 8 LINEAR COMPTON PER_CRYSTAL provides a quick method to esti mate a percent crystallinity using frame data Frames must have air scatter and sample holder scattering effects subtracted out to obtain meaningful results Calculates percent crystallinity within a user defined region The user must specify both an amorphous region and an internal crystalline region Pixels along the 2 theta boundaries of the crystalline region are integrated to obtain a left and right background value The amorphous contribution under the crystalline region is assumed to be a linear function in 2 theta and constant in chi An alternate non linear background function i
119. gh oa a ee LS les leg tay 6 8 6 4 Process gt Flood gt Linear Reset to linear table i e no correction 44 6 9 DAT ANUME E ie aea EERIE EEN area EN dobar ean eal ds eae EEES debe ane 6 9 6 5 Process gt Bad Pixels gt Process Process flood image to determine bad pixels 6 10 6 5 1 Evaluation RedOne iiaa EREA A E EOE A AERE E A RETER RA O 6 10 05A Bad Pixel Criteria need here i te Ded EAEE E eee E Male etd wee AE 6 10 6 5 3 Rejection Criteria u eae 6 10 6 5 4 Arguments ae ae Oy eeu bee E OSE E ee edn a es ean E EA E KEROS 6 11 6 6 Process gt Spatial gt New Acquire data and generate a new spatial correction 6 12 6 624 AUMENS 2 4 kay te ed setts ted eae nee eee Gee he bed ee E 6 14 6 7 Process gt Spatial gt Load e Install a disk resident spatial correction 6 17 6 7 WV ATQUMENS oette terete E a hey eek dea ee he hs Pd Ee ate ed 6 18 6 8 Process gt Spatial gt Linear Revert to linear table i e no correction 6 19 6 8 TAUM tnd welt aden beh dale dle i e eadaee at bee ween OTEA 6 19 6 9 Process gt Spatial gt Process Compute correction from current LOADed brass plate fame sri y na eae Dig ta wy ein oes AA oo ed Ven ate od E ann 2x gids 6 20 6 91 AIQUMEINS rora eie oat de aude anh ee eat wa melee Alay lene a Rien Maen Blea 6 21 6 10 Process gt Spatial gt Unwarp Apply spatial correction and write unwarped output Mame SI oe See tues
120. gt PHI lt n gt CHl lt n gt AXIS lt n gt WIDTH lt n gt SCANTIME lt n gt 2 TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt s gt DISPLAY lt n gt REAL TIME CLEAR STARTRUN lt n gt ENDRUN lt n gt MODE lt n gt ROTATE VIDEO OSCILLATE lt s gt AMPLITUDE lt n gt AUTOZALIGN This command allows you to collect multiple sin gle scan series at different target positions on the same sample on systems equipped with an XYZ stage or multiple samples attached to the XYZ stage Normally Collect gt Scan gt MultiTar gets stores frames as an unwarped image after applying the spatial correction table It also applies the flood field intensity uniformity cor rections as the counts are received Before invoking Collect gt Scan gt MultiTargets you must set the parameters that are unique from series to series See Section 5 43 Collect gt Scan gt EditTargets Then use Collect gt Scan gt MultiTargets to define those parameters that are the same for all the different scan series to be performed and to start the scans When you invoke the command from the menu a dialog box appears where you can view edit the arguments described below as follows e press ENTER or click the OK button to start scanning e press ESC or click the Cancel button to return to the menu You can interrupt a scan as follows e press ESC to stop after finishing collecting the current frame soft abort e press
121. gt HIGHLIGHT lt n gt BORDER lt n gt GRAPH lt n gt CONTRAST LO lt n gt HI lt n gt CORRECTIONS LPA 1 2 3 MONOCHROMATOR lt n gt AIRMU lt n gt NOREVERSE CORRECTIONS FIBER 1 2 3 X lt n gt Y lt n gt Z lt n gt NSTEPS lt n gt MU lt n gt RADIUS lt n gt CORRECTIONS PLATE 1 2 3 X lt n gt Y lt n gt Z lt n gt MU lt n gt THICKNESS lt n gt M86 E01008 G 1 SLAM Command Reference GADDS Software Reference Manual CURSORS BOX 1 2 3 4 DELAY lt n gt NOERASE CURSORS CIRCLE 1 2 3 DELAY lt n gt NOERASE CURSORS PIXEL 1 2 DELAY lt n gt NOERASE DUMP CURSORS VECTOR 1 2 3 4 DELAY lt n gt NOERASE CURSORS CONIC 1 2 DELAY lt n gt NOERASE CURSORS RBOX 1 2 3 4 DELAY lt n gt NOERASE DETECTOR CU DETECTOR FE DETECTOR YVSX DETECTOR EVSE DETECTOR ADD 1 CLEAR PATTERN COUNTS lt n gt DISPLAY lt n gt SHUTTER DETECTOR DETRESET DETECTOR XEVSX DETECTOR YEVSX DETECTOR PDCCUSTOM 1 2 3 GRAPHICS SAVE ORIENTATION VIDEO OVERLAY NEXT PREVIOUS MOVIE MOVIE RMOVIE RMOVIE RNEXT RPREVIOUS HKL 1 2 3 SPLAY SPLAY SPLAY SPLAY SPLAY SPLAY SPLAY SPLAY DISPLAY We Rd RP A RG RD Y S e ECHO OUT lt s gt APPEND WAIT lt n gt 1 2 3 8 9 0 EXIT LOOD NEW 1 COUNTS lt n gt DISPLAY lt n gt REALTIME FILE lt s gt MAG
122. gt Spawn Section 9 8 GADDS PPF This variable if defined instructs GADDS to process pole figures in 1 0 resolution using bin integration and to create a partial pole figure ASCII file PDF2 IND This variable translates to the directory which contains the PDF2 index files These files should be copied from slow CDROM to the faster hard disk e g C PC PDF PDF2 KEY This variable translates to the directory which contains the PDF2 search indexes PDF2 S e g E PDF2 M86 E01008 GADDS Software Reference Manual General Information PDF2 PDF This variable translates to the directory which contains the PDF2 database file PDF2 DAT e g E PDF2 SAXISADMODEL Sets the combination of goniometer and controller assumed for instrument control purposes by GADDS The environment vari able SAXISADMODEL if defined must translate to P3X2000 for 4 circle systems X2000 for older 3 circle systems black Aztalan goniometer PLATFORM for 3 circle systems T 1 4 CIRCLE for 3 circle systems with quarter circle in transmission mode R 1 4 CIRCLE for 3 circle systems with quarter circle in reflection mode D8 for new D8 Discovery systems If SAXISADMODEL is not defined PLAT FORM 3 circle is assumed The model number given here is stored in the header of new frames saved in Bruker format SAXISNAMECHARS characters in NAME part of filename SAXI SRUNCHARS characters o
123. here otherwise press lt ENTER gt without supplying a filename and TOSAXII will explicitly prompt for the beam center coordi nates with the prompts BEAM X CENTER XENGEN COORDS BEAM Y CENTER XENGEN COORDS Supply the coordinates of the direct beam at swing angle of zero in the XENGEN convention 0 0 at upper right in a frame displayed with GADDS or VGADDS OUTPUT FILENAME Enter the full pathname to give the output data frame OUTPUT FRAME TITLE The text you supply here is written to the output SAXII frame header in the first title record and will be shown truncated to 20 characters on the screen when you display the output frame SAMPLE DETECTOR DISTANCE IN CM LE 0 TO USE CURRENT If you want to override the detector distance that exists in the input frame header enter the new value here otherwise just press lt ENTER gt SWING ANGLE DEG 9999 TO USE CUR RENT If you want to override the detector swing angle that exists in the input frame header enter the new value here otherwise just press lt ENTER gt 13 24 M86 E01008 A Area Detector Frame Format The Bruker format addresses issues of data portability speed of image I O and display and storage of all the data acquisition conditions required to reduce the data Header and over flow information are stored in portable ASCII rather than binary Critical data such as setting angles can thus be stored portably as format
124. image from top to bottom 7 24 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses aE ETET Input File input filename for pole figure or frame DISPLAY lt n gt Max Display Counts 2 Enter 0 for no display otherwise this item specifies the number of counts mapped into the maximum display memory value for frame example corresponding to white on the dis play The special value 1 directs the pro gram to pick a reasonable value by scanning through the pixels in the frame prior to display the special value 2 directs the program to use whatever setting is cur rently in effect The default value is 2 the allowed range is from 2 to 10 counts Smaller values make the displayed image look brighter larger values make look darker TANER Output File null Output filename to store inverted pole figure image or null M86 E01008 GADDS Software Reference Manual Analyze Routines 7 25 Analyze gt Pole Figure gt Texture AT Create Texture AT file from pole figure frame binary Menu Command Analyze gt Pole Figure gt TextureAT Accelerator None User Level 1 SLAM Syntax POLE_FIG TEXTUREAT 1 TITLE lt n gt HKL lt n gt APPEND ALPHAINC lt n gt BETAINC lt n gt REFLECTION Besides the storing of bitmapped images the pole figure may be exported in either TEX TURE AT file format or pop
125. in If you leave this item blank it is the same as enter ing a wildcard pattern Both filenames and patterns entered here are merged with the CONFIGURE EDIT frame directory se CONFIGURE EDIT for a description of how this is done De Aerts thes thee Frames to Process 7 Enter the number of consecutive frames to process It is not necessary to enter all frames in a series Try to pick number of frames and threshold that result in about 100 spots being written to the array CONTIG lt n gt Max Pixel Separation 1 Enter the maximum number of pixels of sep aration still considered contiguous within a given reflection Statistical fluctuations could cause a pixel within a reflection to drop below the threshold whereas its neighbors exceed the threshold Raising the value given here allows pixels to be considered part of the same reflection even if they are separated by below threshold pixels The default of 1 specifies that pixels must be contiguous and should be satisfactory for the vast majority of cases M86 E01008 Peaks Routines GADDS Software Reference Manual COUNTS lt n gt Raw Count Threshold 50 Process pixels that have counts equal to or greater than this value Try to pick a value that will place about 100 reflections in the array Note that a threshold that is low enough to accept background points as possible reflections can cause autoindexing to fail A quick way of dete
126. in effect the HKL indices corresponding to the intensity cen troid are also output M86 E01008 GADDS Software Reference Manual Analyze Routines XUNWARPED If a spatial correction is in use this provides spatially corrected X coordinate of centroid of intensity otherwise this value will be iden tical to the raw coordinate YUNWARPED If a spatial correction is in use this provides spatially corrected raw Y coordinate of cen troid of intensity otherwise this value will be identical to the raw coordinate M86 E01008 GADDS Software Reference Manual Analyze Routines 7 2 Analyze gt Cursors gt Circle e Display position and size of circular cursor Menu Command Analyze gt Cursors gt Circle Accelerator F6 User Level 1 SLAM Syntax CURSORS CIRCLE 1 2 3 DELAY lt n gt NOERASE When invoked from the menu or when run from the command line without arguments Analyze gt Cursor gt Circle starts running directly that is there are no dialog items to be filled in A circu lar cursor with a small crosshair at its center appears in the detector frame area and can be dragged or resized under control of the mouse and or keyboard arrow keys Several quantities described below related to the currently dis played frame at the cursor position are displayed in real time at the right of the image Pressing ENTER or releasing the left mouse button exits returning you to the menu Pressing ESC
127. left from a NOERASE by reissuing the command with the same parameters The CLEAR com mand also provides a way to erase cursors left over from NOERASE options The following output statistics are displayed on screen in real time and are also written to the logfile if applicable X Center X center of box in pixels range from 0 to framesize 1 with origin X 0 being located at lower left of screen Y Center Y center of box in pixels range from 0 to framesize 1 with origin Y 0 being located at lower left of screen Width Width of box in pixels Height Height of box in pixels TotalCts Sum of counts in rectangular box Integrated intensity minus background The background is computed as the aver age of the points on the perimeter of the box excluding all points which are more than three standard deviations above the mean M86 E01008 GADDS Software Reference Manual Analyze Routines Sigma l Standard deviation of integrated intensity I Sigmal Integrated intensity divided by its standard deviation Backgnd Average of points on perimeter of box excluding those points which are more than three standard deviations above the mean XCntroid Raw X coordinate of centroid of intensity YCntroid Raw Y coordinate of centroid of intensity Maximum Maximum pixel intensity in box Mean Average counts in box HKL If an orientation matrix is in effect the HKL indices
128. less than 15 minutes It is essential that the brass plate be properly fastened to the area detector face see figure in manual The flat side of the brass plate rests against the detector face the side with the counter sunk holes faces the sample Insert and tighten ALL the fastening screws to eliminate any small warpage in the fiducial plate Either remove the beam stop or make sure that the detector is swung out far enough that the beam stop will cast no shadow when you acquire the brass plate image Make sure that the Fe source is properly centered in the goni ometer and directly faces the area detector The name of the spatial correction currently in effect is displayed in the current status area at the lower right of the screen This correction is M86 E01008 GADDS Software Reference Manual Process Routines used by the CURSOR commands when they output HKL values and unwarped X Y coordi nates and by all the REFL_ARRAY commands which extract spots from a series of frames index the diffraction pattern and compute a least squares crystal orientation matrix SPATIAL NEW writes four output files all cre ated in the current frame directory set in CON FIGURE EDIT The first is written in a frame file format The other three output files are all ASCII files in PLOTSO format which can be displayed with the GRAPH FILE command __br File containing the brass plate frame suitable for input to da
129. logging is turned on see the File gt LogFile command for more information the quantities computed for the final position of the cursor prior to exiting the command are written to the output logfile If scripting is enabled see File gt Script File a non interactive CURSOR command cor responding to the final cursor position is written to the output script file The SLAM command arguments are 1 The X coordinate of the lower left of the vec tor in pixels The range is from 0 to frame size 1 default value is 256 M86 E01008 GADDS Software Reference Manual Analyze Routines 2 The Y coordinate of the lower left of the vec tor in pixels The range is from 0 to frame size 1 default value is 256 3 The X length of the vector pixels The range is from 0 to framesize 1 default value is 32 4 The Y length of the vector in pixels The range is from 0 to framesize 1 default value is 1 DELAY lt n gt Specifies a time interval in seconds to wait before erasing the cursor and returning con trol to the program This is for use in scripts where it is desirable for the cursor to remain on screen long enough for the user to dis cern its position NOERASE Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor left from a NOERASE by reissuing the command with the same parameters The Analyze g
130. lt n gt SHUTTER FLOOD LOAD 1 FLOOD REPROCESS 1 2 XMIN lt n gt YMIN lt n gt MAG lt n gt FLOOD LINEAR FRAME INFO 1 GONIOMETER MANUAL 1 2 3 4 5 6 7 8 Or GONIOMETER MANUAL 1 2 3 4 5 RATEMETER 1 RESET lt n gt SHUTTER GONIOMETER OPTICAL 1 2 3 4 5 6 7 8 1 2 3 4 REALTIME RESET lt n gt DISPLAY NEW 1 QUADRANT lt n gt LO lt n gt HI lt n gt X lt n gt Y lt n gt MAG lt n gt AUTOINCREMENT XMIN lt n gt YMIN lt n gt 5 GONIOMETER FLATSAMPLE Xl lt n gt Yl lt n gt Z1l lt n gt X2 lt n gt Y2 lt n gt Z2 lt n gt X3 lt n gt Y3 lt n gt Z3 lt n gt M86 E01008 GADDS Software Reference Manual SLAM Command Reference GONIOMETER UPDATE 1 2 3 4 5 6 7 8 9 1 2 3 4 GONIOMETER LIMITS 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 0 XMAX lt n gt XMIN lt n gt YMAX lt n gt YMIN lt n gt ZMAX lt n gt ZMIN lt n gt AMAX lt n gt AMIN lt n gt DMIN lt n gt DMAX lt n gt GONIOMETER EXTLIMITS GONIOMETER SPEEDS 1 2 3 4 5 6 7 8 9 1 2 3 1 2 GONIOMETER ZERO GONIOMETER ATTENUATOR GONIOMETER SHUTTER GONIOMETER LASER GONIOMETER GENERATOR 1 2 WAIT GONIOMETER FIXEDAXES 1 2 3 4 5 6 7 8 GONIOMETER HOME 1 2 GONIOMETER PARK GONIOMETER XYZ 1 2 3 4 GONIOMETER TEMP 1 RAMP lt n gt HOLD lt n gt WAIT GONIOMETER ENCODERS 1 2
131. lt s gt NUMSAMPLE lt n gt NAME lt s gt RUN lt s gt ROTATE X lt n gt Y lt n gt REALTIME SCAN ZONE 1 WIDTH lt n gt SCANTIME lt n gt DISPLAY lt n gt SCAN AXIAL 1 WIDTH lt n gt SCANTIME lt n gt DISPLAY lt n gt SCAN SELECTTARGETS SCAN GRIDTARGETS XBEG lt n gt XEND lt n gt XINC lt n gt YBEG lt n gt YEND lt n gt YINC lt n gt TRANSMISSION SCAN EDITTARGETS SCAN MULTITARGETS 1 2THETA lt n gt THETAl lt n gt OMEGA lt n gt THETA2 lt n gt PHI lt n gt CHI lt n gt AXIS lt n gt WIDTH lt n gt SCANTIME lt n gt 2 TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt s gt DISPLAY lt n gt REALTIME CLEAR STARTRUN lt n gt ENDRUN lt n gt MODE lt n gt ROTATE VIDEO SCAN MASTER 1 SEND_CONFIG SCAN SLAVE SHUTTER SMOOTH AVERAGE SMOOTH MEDIAN SMOOTH CONVOLVE 1 SPATIAL NEW 1 COUNTS lt n gt DISPLAY lt n gt REALTIME FILE lt s gt XENGEN THRESHOLD lt n gt SHUTTER SPATIAL LOAD 1 SPATIAL LINEAR SPATIAL PROCESS 1 THRESHOLD lt n gt SPATIAL UNWARP 1 2 3 NONORMALIZATION DISPLAY lt n gt XENGEN NOBEAMCENTER SPAWN STRESS CONVENTIONAL 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt 2THETA lt n gt 5 FILENAME lt s gt STRESS SCHEME2D 1 PEAK lt n gt DISTANCE lt n gt 2 2THETA lt n gt THETA1 lt n gt G 6 M86 E01008 GADDS Software Reference Manual SLAM Command Refere
132. n gt X lt n Y lt n gt Z lt n gt AUX lt n gt AX IS lt n gt WIDTH lt n gt SCANTIME lt n gt TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt n gt NAME lt s gt RUN lt s gt FRAMENO lt s gt DISPLAY lt n gt REAL TIME CLEAR OLDXENGEN MODE lt n gt ROTATE VIDEO OSCILLATE lt s gt AMPLITUDE lt n gt AUTOZALIGN Additional SLAM Syntax for dual detector mode SNAME lt s gt SRUN lt n gt SFRAME lt s gt Collect gt Scan gt SingleRun allows you to collect a scan series comprising one or more contigu ous frames of data starting at specified goniom eter setting angles Normally Collect gt SingleRun stores frames as an unwarped image after applying the spatial correction M86 E01008 Collect Routines GADDS Software Reference Manual table It also applies the flood field intensity uni formity correction as the counts are received When you invoke the command from the menu or the command line without arguments a dia log box appears where you can view edit the arguments described below as follows e press ENTER or click the OK button to start scanning e press ESC or click the Cancel button to return to the menu You can interrupt a scan as follows e press ESC to stop after finishing collecting the current frame e press CTRL BREAK to interrupt the scan e press CTRL S to temporarily stop after fin ishing collecting the current frame press CTRL Q to
133. nonnina Sample mu cm 1 131 22 Enter sample mu in cm 1 RADIUS lt n gt Radius Thickness cm 0 05 Enter sample radius for fibers or thickness for plates in cm NSTEPS lt n gt Num integration steps 10 Enter number of steps REFLECTION Reflection only Y N No Enter Y for reflection only mode All points from transmission through the sample are tossed out M86 E01008 Analyze Routines GADDS Software Reference Manual 7 20 Analyze gt Pole Figure gt Interpolate Interpolate a processed pole figure image Menu Command Analyze gt Pole Figure gt Inter polate Accelerator None User Level 1 SLAM Syntax POLE_FIG INTERPOLATE 1 DISPLAY lt n gt WIDTH lt n gt 2 Pole figures are displayed using a bitmapped image with each pixel location representing an alpha and beta sample orientation Mapped pix els have intensities of the pole density plus one while unmapped pixels possess the value of zero For better visualization of the pole figure image it is useful to interpolate a value for all the unmapped pixels 7 20 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses PT Input File FRAME Input filename for pole figure or frame DISPLAY lt n gt Max Display Counts 2 Enter 0 for no display otherwise this item specifies the number of counts mapped into the m
134. number of alpha scans in 1 8 points 2 12 points 3 20 points 4 32 points M86 E01008 TEXTURE AT Raw Data File Format GADDS Software Reference Manual 699 R4 absolute minimum of normalized 1094 130X reserved data computed by TEXD5 703 R4 absolute maximum of normalized data computed by TEXD5 707 12 diameter of pole figures for plotter in cm 709 12 number of copies for plotter 711 L1 must be 0 true data collection still in progress 712 8R4 x values for 8 pole figures in mm 744 8R4 y values for 8 pole figures in mm 776 14X unused 790 A64 sample name repeated 854 A32 data file name 886 R4 sample thickness 890 L1 true for a texture less sample 891 1X unused 892 R4 thichness of transmission sample 896 124X unused 1020 A32 name of TEX file used for mea surement 1052 12 number of pole figures in the file same as 615 1054 12 number of background positions in the file 1056 12 number of beta steps in the file 1058 12 number of beta steps in reflection mode 1060 12 number of beta steps in transmis sion mode 1062 8R4 2theta of pole figures same as 64 and 24 in range header E 4 M86 E01008 F POPLA Data File Format REF Kocks Kallend Wenk Rollett and Wright popLA Preferred Orientation Package Los Alamos LA CC 89 18 GTDA Oct 1995 popLA data files are s
135. of Detectors 1 Enter number of detectors to control not physical SEND_CONFIG Send Config No Check to update configuration on Slave frame buffer M86 E01008 Collect Routines GADDS Software Reference Manual 5 46 Collect gt Scan gt Slave e Place frame buffer into slave mode for dual detector system Menu Command Collect gt Scan gt Slave Accelerator None User Level 3 SLAM Syntax SCAN SLAVE SCAN SLAVE is used to place the frame buffer in slave mode That is a second frame buffer will take over all goniometer operations see SCAN MASTER The MASTER frame buffer is attached through COM2 while the GGCS is attached to COM1 Before entering SLAVE mode one should collect a flood field and fudi cial plate image as well as verify that the CON FIGURE EDIT menu is correct distance angle offset frame naming conventions detector cen ter etc NOTE Before running GADDS on the Master frame buffer the frame buffer which is attached to the GGCS MUST BE IN SLAVE MODE When invoked with the SLAVE option from the SCAN submenu the current bias and flood field settings are check then the user is prompted for confirmation Enter SLAVE mode are you sure Once in SLAVE mode all menus disappear and Frame buffer in SLAVE mode is printed in the message window The SLAVE keyboard is dead with the exception of the interrupt keys lt Ctrl C gt lt Ctrl F gt l
136. of the Reflec tion Array The output results from a rough linear least squares refinement of the reduced primi tive unit cell to the indexed full vectors It is simi lar to the output produced by REFL_ARRAY LEASTSQ although the refinement will not be as precise First are several tabular histograms showing the distribution of the unsigned differences between observed and calculated values of H K L scan angle always labeled OMEGA even if the scan angle was actually PHI and detector X Y posi tion In all cases the more closely bunched toward the left side of the histogram the differ ences are the better the refinement Scan angle differences are in degrees and X Y differences are in pixels Following the histograms are the overall average and rms differences for these same quantities H K L scan angle X and Y The myoglobin example shown below is a very good one Often the numbers are two or three times higher The AVG values indicate any sys tematic bias in the results Unlike the case for REFL_ARRAY LEASTSQ the AVG values will probably be significant here however if they are large compared with the corresponding RMS values you might suspect mis indexing or mis alignment of the system In such a case make M86 E01008 GADDS Software Reference Manual Peaks Routines sure you have a good spatial correction and cor rect estimates for the detector distance and beam center entered in the CONFIGURE EDIT pan
137. of the counts in a R4 field followed by several R8 fields Codes used are 12 16 bit integer 14 32 bit integer R4 32 bit real R8 64 bit real Cn ASCII character string of n bytes no null character Cn ASCIIZ character string of n bytes ends in null character 2 new field or value for RAW1 01 version files obs obsolete field or value for RAW1 00 version files M86 E01008 DIFFRACP S Raw Data File Format GADDS Software Reference Manual B 10 M86 E01008 C DIFFRAC AT Raw Data File Format Diffrac AT V1 raw data files are stored in a direct access binary file without any record delimina tors Record Format Field description 1 A4 RAW File identification text 2 14 Number of steps for this range 1 32767 3 R4 Measurement time per step 1 999 0 4 R4 Step size for this range in degrees 5 14 Flag word in DACO MP format meaningful bits are 1024 theta fixed 2048 continuous scan 8192 2theta fixed rocking curve 6 14 Sample number in sample changer 0 manual insertion 7 R4 Two theta start in degrees 1E6 unknown 8 R4 Theta start 1E6 unknown 9 R4 Chi start 1E6 unknown 10 R4 Phi start 1E6 unknown 11 18 8A4 Sample name 32 characters 19 R4 K alpha 1 wavelength 20 R4 K alpha 2 wavelength 0 0 if monochromator used 21 38 Unused 39 14 Number of ranges following this rang
138. of the first output frame in the series and will be incremented according to the frame naming parameters to form the extensions of subsequent frames DISPLAY lt n gt Max Display Counts 31 0 no display otherwise counts corre sponding to white on the display SAVE will optionally display the data being saved using this value as the upper display limit see DISPLAY NEW for more details The default value is 16 the allowed range is from 0 to 10 counts REAL TIME Real time Display Yes This qualifier when present displays data as it is being collected The display does require additional processing time and will limit the maximum rate at which counts can be accumulated If the MAX DISPLAYED COUNTS qualifier is given a non zero value the frame will be automatically displayed at the end of each scan if real time display is off This latter display method has no effect on observed data rate Unless your data rate is very low it is better NOT to use real time display in the course of a SCAN com mand even though the default here is Y While real time display is active you can change the upper display limit using the plus key to increase or the minus key to decrease the current limit by a factor of two the range is 7 to 524287 Modify the con trast using the left and right arrow keys Modify the brightness using the up and down keys Holding the control key down in combination with a
139. of the pole sphere Thus by measuring the distribution of diffracted rays at various sample positions the relative pole density at every point along the pole figure may be obtained 7 19 1 Process GADDS provides a quick processing of a series of frames to obtain pole figures at a specific two theta For each frame in the series a 2 theta integration is performed using the normalized bin method with the resulting chi trace mapped to a appropriate pixel locations on a pole figure frame Where multiple chi intensities map to the same pixel on the pole image the average intensity is used Likewise if multiple intensities from different data frames map to the same pixel on the pole image the average of the possibly averaged intensities is used The background correction is made by integrat ing background intensity values in the immedi ate vicinity of the Bragg angle Two background values are determined their angles being below M86 E01008 GADDS Software Reference Manual Analyze Routines and above the Bragg angle with the final back ground determined by linear extrapolation between the low and high background values It is important that the background intensity values are determined at a two theta value that avoids any Bragg peak intensity in all frames of the series For a particular Bragg angle the background intensity is determined by integrating a low and high background region in two theta Each resulting
140. on different x ray tubes anode e Collected at different temperatures e Collected at different generator voltage e Collected at different generator current e Collected using different step widths e Collected using overlapping step widths e Collected using different scan axes Other checks only produce warnings and the user must decide if the ranges are compatible e Collected on different dates e Collected by different users e Collected on different goniometer models e Collected on different goniometer stages e Collected at different detector distances e Collected for different step times e Collected using different scan types Syntax for command line MERGE B A S R filein raw R filein raw R merge out B Batch mode suppresses final Hit lt Return gt to continue message A Averages overlapped regions instead of using weighting factor M86 E01008 GADDS Software Reference Manual Utility Programs S Scales merged ranges to first using intensity fit scale factor R Merge specific ranges to inclusive Defaults to all ranges If is missing the ending range defaults to the first range and only one range is merged The location of the switch is important Placed after MERGE R specifies the default ranges for all input files When placed after a filename R specified the ranges only for that file and will overrid
141. or the right mouse button in the editing window or in the input panel returns you to the REFL_ARRAY submenu 8 20 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses BA EOR ET First Reflection 1 This is the line where you want the selection range to start Line numbers start at 1 For example if you want to modify only reflec tions 5 through 7 you would enter 5 in the FIRST REFLECTION parameter Default is 1 Valid range is 1 512 G2 eis syvheieancupiatines Last Reflection 512 This is the line where you want the range to end Line numbers start at 1 To continue the previous example if you want to modify only reflections 5 through 7 you would enter 7 in the LAST parameter Default is 1 Valid range is 1 512 M86 E01008 Peaks Routines GADDS Software Reference Manual FIE Fiel OMAN DOA FW YP LD lt n gt Field to Modify 1 Specify which field column you want to change You specify the field by its column number Default is 1 Valid range is 1 12 Field numbers are d Description Flags for example ACHSX H index K index L index 2 Theta setting swing angle Omega setting angle Phi setting angle Chi setting angle Detector X pixel coordinate Detector Y pixel coordinate Intensity Vsigma INALUE lt S gt New Value C Enter the value to which the entries
142. or the left mouse button during the wait period the program aborts the wait and pro ceeds This command is useful in scripts where you want to display a frame or text and have it remain visible for some minimum length of time The valid value range is 1 to 1 0x10 seconds WAIT will wait indefinitely if you specify a time value of 1 Syntax is WAIT 1 where 1 is the wait time in seconds as a real number 12 10 comment Menu Command None Accelerator None User Level Command SLAM Syntax any text string Use the command to add comment lines within a script file Simply place the character at the start of any line and follow it with your comment statement myscript slm created 26Mar98 by KLS Load first frame in series DISPLAY M86 E01008 12 27 SLAM Routines GADDS Software Reference Manual 12 11 execute script file Menu Command None but see UserTasks Accelerator None User Level Command SLAM Syntax filename p1 p2 p3 p4 p5 p6 p7 p8 p9 po Use the command to execute commands from a script file while in GADDS s command line mode You must specify the name of the script file immediately after the symbol By convention SLAM script files have the extension SIm and a sim extension is assumed if none is given in the command The program looks for a script file in three places current project direc tory system data directory see GADDS SYS DATA or co
143. or when run from the command line GONIOMETER LASER immediately tog gles the status of the hardware laser beam on those systems equipped with a laser 5 21 1 Arguments None Command executes immediately 5 30 M86 E01008 GADDS Software Reference Manual Collect Routines 5 22 Collect gt Goniometer gt Generator Control the high voltage generator kv and ma settings Menu Command Collect gt Goniometer gt Generator Accelerator Ctrl Shift G User Level 1 SLAM Syntax GONIOMETER GENERATOR 1 2 WAIT When invoked from the menu or when run from the command line without arguments Collect gt Goniometer gt Generator displays a dialog box where you can view edit the desired generator settings The values in the dialog default to the current generator settings When in the panel pressing the ENTER key or clicking the OK but ton sends the entered generator settings to the Bruker K710D generator Pressing ESC or click ing the Cancel button in the dialog returns you to the menu without changing the generator set tings The new generator settings are displayed in the goniometer status window 5 22 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Sienka anels kV Enter the desired kV setting for the X ray generator AEA mA Enter the desired mA setting for the X ray generator WAIT cs ccevsac cdeetess Wait Y
144. per seconds on scan frames Frames collected with fewer cps are automatically recollected up to 3 times This allows correcting stuck shutter problems The default is 25 cps This is automatically deactivated for frames of ten minutes or longer TIMEOUT lt n gt Auto Command Mode Timeout 10 Enter the number of seconds that you want the program to wait before proceeding when a prompt or output window displays in SLAM command line mode The default is 10 seconds and the valid input range is 0 to 1 000 000 seconds A value of 0 means no time out infinite wait NAMECHARS lt n gt Characters in Base Frame Name 28 The maximum number of characters which can be used in the base component of a frame filename The base component is defined as the filename after removing any node device directory extension and ver sion components NAMECHARS should be set to 8 for NT FAT filenames or 39 for NT enhanced FAT or NTFS or UNIX filena mes The default is 28 M86 E01008 Edit Routines GADDS Software Reference Manual RUNCHARS lt n gt Characters in Run 1 This is the number of characters to be appended to the Job Name as a Set Num ber or Run Number that is the number assigned to a series of frames taken at the same phi chi setting The Run Number is padded with leading zeros if needed to fill RUNCHARS characters it is not automati cally incremented within a scan series unless the Fr
145. pixel of rectangle bottom side Plener uneia Y end 510 Y pixel of rectangle top side 8 18 M86 E01008 GADDS Software Reference Manual Peaks Routines 8 14 Peaks gt Refl Array gt Threshold e Place spots threshold in a series of frames into the array Menu Command Peaks gt Refl Array gt Threshold Accelerator None User Level 1 SLAM Syntax REFL_ARRAY THRESHOLD 1 2 CON TIG lt n gt COUNTS lt n gt SIGMA lt NN gt XEXMIN lt n gt KEXMAX lt n gt RMAX lt n gt DMIN lt n gt DMAX lt n gt DBIAS lt n gt 3 4 5 6 7 8 This routine provides a means for automatically picking reflections from a series of data frames and placing them in the Reflection Array The algorithm provides control over selection factors such as intensity threshold and resolution range Spots entered into the array in this manner always have the A flag set and contain the goni ometer setting angles detector X Y position intensity normalized to 1 deg min and I sigma If the pixels above the threshold span more than one frame the computed scan angle centroid is more precise and the C flag is set for that reflection These centered reflections are especially suitable for autoindexing and least squares however if you can t find many reflec tions that span frames you can set the C flags manually with the REFL_ARRAY MODIFY com mand to force the autoindexing and least squares to use all the ref
146. position is to be computed Default is 0 and valid range is 9999 to 9999 Real values may be used they are not rounded to inte ger values prior to computing the position Eg n iaa L 2 Enter the L index of the reflection whose position is to be computed Default is 2 and valid range is 9999 to 9999 Real values may be used they are not rounded to inte ger values prior to computing the position EEE AET Scan Axis 2 Enter the axis number 2 for omega or 3 for phi of the axis whose position to place the specified HKL in the diffracting condition if possible is to be computed The values that you specify below for the other three goni ometer axes are kept fixed for the purposes of computation The value that you supply below for this scan axis makes no differ ence AE 2 Theta 0 00 Enter the detector swing angle in degrees at which the scan angle and detector X Y of the specified HKL reflection are to be com puted Default is zero and valid range is 360 to 9999 RNG ae ee Omega 0 00 Enter the omega goniometer angle in degrees at which the scan angle and detec tor X Y of the specified HKL reflection are to be computed If you ve specified a scan axis of 2 See above any valid value is OK here Default is zero and valid range is 360 to 9999 ieii eeit S Phi 0 00 Enter the phi goniometer angle in degrees at which the scan angle and detector X Y of M86 E01008 Peaks Routines GA
147. raw X pixel coordinate YBEAM lt n gt Direct Beam Y current value Unwarped Y pixel coordinate 0 to frame size 1 of direct beam center at 2 Theta 0 in the Bruker coordinate convention with 0 0 at the lower left of a displayed frame It is important that you enter the correct value M86 E01008 Edit Routines GADDS Software Reference Manual here before collecting frames that will be analyzed with the interactive cursor com mands used in conjunction with the spatial correction or for determination of crystal ori entation with the Reflection Array com mands These commands rely heavily on the value given for the beam center The value is stored in the output header of Bruker format frames and in output p4p files If you change the value of the FRAME SIZE field the beam center position will be scaled and converted to the new frame size convention the display will be updated when you tab out of the FRAMESIZE field NOTE If you save frames in raw warped mode this should be raw Y pixel coordinate FRAMESIZE lt n gt Size of Created Frames 1024 Enter the linear frame dimension 512 or 1024 for newly created frames Subsequent frames created by commands in the Collect menu will have this size If you change the value of the FRAMESIZE field the beam center position will be scaled and converted to the new frame size convention the dis play will be updated when you tab out of the FRA
148. resume NOTE Unlike the Collect gt Scan gt MultiRun command an interrupted SingleRun scan can not be restarted with the Collect gt Scan gt Resume command Instead the SingleRun parameters are automatically decremented after each frame is saved Thus you can simply reis sue a SingleRun command to resume where it left off Also Collect gt Scan gt SingleRun does not precheck the scan range for potential colli sion the way Collect gt Scan gt MultiRun does If you need these capabilities use Collect gt Scan gt MultiRun which can perform a single series if desired When you interrupt a scan with CTRL BREAK the goniometer returns to the starting scan angle of the current scan This repositioning is performed by backing up to the starting position minus one frame width or 0 5 maximum then driving forward to the starting position The same positioning technique is used when driv ing to the first scan in a new series which makes the positioning extremely repeatable but does require you to allow for an extra scan width at the beginning of the series when you re start ing close to the goniometer collision limits The current configuration is saved in the current default configuration file usually gadds _nc before starting the first scan which makes recovery easier in the event of a power failure etc The filename of the first frame is generated from the Job Name Run and Starting Frame listed b
149. run If the first or last frame in a run is outside the currently set limits the warn ing message PROBABLE COLLISION IN 1ST SCAN OF EDITTARGETS LINE lt line gt or PROBABLE COLLISION IN LAST SCAN OF EDITTARGETS LINE lt line gt is displayed where lt line gt represents the number of the line starting at 1 in the EDITRUNS array which produced the message You can choose to continue with the scans or quit to re edit the run list and try again The current configuration is saved in the current default configuration file usually GADDS _NC prior to starting the first scan This also makes recovery easier in the event of a power failure etc The filename of the first frame in each series in generated from the Job Name described below the Run and Frame specified for the series in the EDITTARGETS array and the frame naming parameters set in the CONFIGURE EDIT input panel Successive names are generated by incrementing the filename extension again according to the naming parameters in the CONFIGURE EDIT panel see CONFIGURE EDIT and the separate topic FRAME NAMING CONVENTIONS for more information Note that with 256 lines in the EDITTARGETS array it is possible to overflow a single character run number even in base 36 It is recommended that run numbers for the output frame files be set up as follows 1 Use base 36 0 9 A Z for run numbers to prevent them from wrapping from 9 to 0 Set this in the
150. s gt File name stress raw Enter output file name for RAW data M86 E01008 GADDS Software Reference Manual Analyze Routines 7 34 Analyze gt Stress gt Scheme 2D Menu Command Analyze gt Stress gt Scheme 2D Accelerator None User Level 1 SLAM Syntax STRESS SCHEME2D 1 PEAK lt n gt DISTANCE lt n gt 2 2THETA lt n gt I THETA1 lt n gt OMEGA lt n gt I THETA2 lt n gt PHl lt n gt CHl lt n gt AXIS lt n gt WIDTH lt n gt CLEAR Use this command to determine proper scan parameters when stress measurements are required and to determine which stress direc tions are properly determined 7 34 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Sana Output file NULL Output file for multirun scan listing SCAN will automatically update directly to the SCAN MULTIRUN menu NULL will skip this feature PEAK lt n gt Stress peak 156 0 2T or d spacing of desired stress peak DISTANCE lt n gt Distance 7 0 cm Detector distance in cm s AE a ites frames 36 Number of frames to collect 2THETA lt n gt THETA1 lt n gt 2Theta or Theta 135 0 deg Detector swing angle in degrees OMEGA lt n gt THETA2 lt n gt Omega or Theta2 0 0 deg PHI lt n gt 06 Phi 0 0 deg ICHl lt n gt 06 Chi 90 0 deg The sample positioning ang
151. scanned as follows 2 for omega scans 3 for phi scans 4 for chi 5 for X 6 for Y or 7 for Z N None C Coupled or T Tube on theta theta sys tems Note that while SAINT can reduce phi scans taken at any chi angle some data reduction programs KENGEN may not be able to reduce phi scan data unless it was taken at CHI 0 When using a restrictive data reduction package you must perform omega scans on both the Platform goniom eter and the older Aztalan black 3 axis 0 25 The scan width in degrees either positive or negative of each frame to be acquired Thus the starting scan angle for the Nth frame in the series where the first frame is N 0 is OMEGA N WIDTH if the axis above is 2 or PHI N WIDTH if the axis above is 3 where WIDTH OMEGA and PHI are the values given on the same line of the array The intensity within a frame is M86 E01008 GADDS Software Reference Manual Collect Routines uniformly distributed with respect to scan angle over the range WIDTH specified here unless 3 circle frames are taken by oscilla tion in which case the ends of the range have slightly higher weight and there may be some overlap or underlap of successive frames oscillation can however compen sate for other sources of error such as inten sity fluctuation due to an unstable source SCANTIME lt n gt Seconds Frame 1 00 00 The accumulation time in seconds during which each frame is to be acquired
152. setting before collecting the data Fe high bias is used by Flood and Spatial while Cu low bias is used for Scan commands 5 2 1 Arguments None Command executes immediately 5 3 Collect gt Detector gt Y vs X Set PDC for normal positional display Menu Command Collect gt Detector gt Y vs X Accelerator none User Level 1 SLAM Syntax DETECTOR YVSX Use this command to place the PDC and detec tor into normal X Y position display The action is performed immediately with no prompt for additional input 5 3 1 Arguments None Command executes immediately M86 E01008 GADDS Software Reference Manual Collect Routines 5 4 Collect gt Detector gt E vs E Set PDC for energy versus energy for bias calibration Menu Command Collect gt Detector gt E vs E Accelerator none User Level 1 SLAM Syntax DETECTOR EVSE Use this command to place the PDC and detec tor into energy versus energy for bias calibra tion The action is performed immediately with no prompt for additional input 5 4 1 Arguments None Command executes immediately 5 5 Collect gt Detector gt Add Accumulate a frame with temporary linear flood field Menu Command Collect gt Detector gt Add Accelerator none User Level 1 SLAM Syntax DETECTOR ADD 1 CLEAR PATTERN COUNTS lt n gt DISPLAY lt n gt REALTIME RESET lt n gt SHUTTER W Use this command to collect a single sti
153. specified angles positions During the drive the message appears on the bottom status line DRIVING PRESS ANY KEY TO STOP You can halt the drive by pressing a keyboard key for example ENTER or the space bar On completion the program updates the current goniometer angles displayed in the goniometer status area at the lower right of the screen Collect gt Goniometer gt Drive will try to drive any angle to the specified destination by the shortest path unless the collision limits specifically pre vent it from doing so In that case the longer path will be taken On 1 4 circle systems Col lect gt Goniometer gt Drive will drive around obstacles in omega chi space as defined by the Goniometer Extlimits command which may take several drives to reach the final destination M86 E01008 GADDS Software Reference Manual Collect Routines 5 10 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses DT OE E EET 2 Theta Saara ea e THETA1 Enter the destination 20 angle in degrees or the theta tube angle for 0 0 systems in degrees Default is current setting 2 areant orii Omega G2 enni ieiti ta THETA2 Enter the destination angle in degrees or the theta detector for 0 0 systems angle in degrees Default is current setting Ce OOO Phi Enter the destination angle in degrees Default is current setting GA OO Chi E
154. sr iiaa aS aad aca eed na Se eae Gee h oa tenths wave aat iani 1 20 2 Project Management Routines 200 c eee 2 1 2 1 Project gt Switch e Change to a different existing project 000 0 eee eee 2 3 21s ATQUIMOIIS lt 928 diye eed eg tee Le Se CaM aS ttre AAP DSS es ee oo lle a e ERN Si 2 3 2 2 Project gt Load Load a configuration file and create a new project 2 4 22 TAJUME 2290s de ea Sek wea hale Rew aoa Rs Beta eater See ne bees 2 4 2 3 Project gt New e Create a new project from scratch 000 cee eee ee 2 5 2 331 AT QUIMIOINS 22 diye Sek to Ade itt E ear tet RE A RA Ee td ETE 2 6 2 4 Project gt Copy Copy the current project to a new project 0 0 c eee eee 2 7 24 ALQUMONIS oros nid a es Gana ee ead E PG BRE aie el Eh he eee 2 8 2 5 Project gt Edit e Edit the current project settings 0 cece eee 2 9 M86 E01008 4 04 i Table of Contents GADDS Software Reference Manual 2 5 1 AIQUMOMIS sei LOE wld Wes oe WA AE a eae ats R Biden Se ee ee 2 9 2 6 Project gt Backup Backup all files in the specified project s directories 2 10 2 6 TAGME MS rra eee A inci nate da ete te ae Sean eee ead a ea hen Aik at 2 10 2 7 Project gt Remove e Remove a project from the project database 2 11 2 1 ALGUMOMS lt ane Sole alae E RA 5 Bataan Stud EEA EA Gia e wy bie A God ae 2 11 2 8 Project gt Delete Delete all projec
155. still read the correct values The default value is 0 the allowed range is from 255 to 65 535 Hl kis Upper Limit 63 The number of counts to be mapped to the highest display memory value currently 63 that is displayed frames are shown with 64 simultaneous colors Pixel values higher then the specified value are truncated to that value on display although the cursor commands will still read the correct values M86 E01008 GADDS Software Reference Manual File Routines The special value 1 causes the program to scan the pixel values in the frame and auto matically pick reasonable display limits and contrast settings based on the result The special value 2 directs the program to use whatever the previous limits were The default value is 1 the allowed range is from 2 to 1 000 000 KEENE onain X 256 X pixel coordinate to try to center in the specified quadrant The range is from 0 to 511 1023 or 2047 depending on the frame size the default value is 256 If the magnifi cation is small enough that centering the specified X in the quadrant would leave part of the quadrant blank the image is trans lated only far enough to place the edge of the frame at the edge of the quadrant INSEND sesssessesteeeseee Y 256 Y pixel coordinate to try to center in the specified quadrant The range is from 0 to 511 1023 or 2047 the default value is 256 If the magnification is small enough that cente
156. stroms The default value is based on the default target Cu and is set at 1 54056 A This value is automatically updated when the target is re entered if the target is one of the known types Cu Mo Ag Fe Cr or Co It is important that you update this entry whenever the source wavelength is changed The value is stored in the header of any output frames created in Bruker for mat and in output raw files It is also used by the interactive cursor commands all the Peaks commands and the Stress com mands stroms The default value is based on the default target Cu and is set at 1 54439 A This value is automatically updated when the target is re entered if the target is one of the known types Cu Mo Ag Fe Cr or Co It is important that you update this entry whenever the source wavelength is changed The value is stored in the header of any output frames created in Bruker for mat and in output raw files It is also used by the interactive cursor commands all the Peaks commands and the Stress com mands IBETAH lt n gt eee Beta 1 39222 Enter the Kb X ray wavelength in Ang stroms The default value is based on the default target Cu and is set at 1 39222 A This value is automatically updated when the target is re entered if the target is one of the known types Cu Mo Ag Fe Cr or Co It is important that you update this entry whenever the source wavelength is changed The value is stored in the header of
157. that is it requires no additional input A full window crosshair cur sor appears in the detector frame area and can be dragged under control of the mouse and or keyboard arrow keys Several quantities described below related to the currently dis played frame at the cursor position are dis played in real time to the right of the image Pressing ENTER or releasing the left mouse button exits returning you to the menu Pressing ESC or clicking the right mouse button while dragging with the left button pressed displays a pixel map of the numeric values in memory for a 17 x 17 pixel grid centered on the pixel under the crosshair In this display a box appears around the value for the pixel currently under neath the cursor Pressing any mouse or key board key returns to display of the data frame and the interactive crosshair cursor When dragging the cursor with the arrow keys you can press CTRL along with an arrow key to move in increments ten times larger than for the unmodified arrow key By providing arguments on the command line you can direct the cursor computations to be performed once at a single specified position after which control returns immediately to the command line The line weight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cu
158. the color of the line drawn around windows and panels as a 9 digit number in RRRGGGBBB format see above By default it is light cyan 064192200 GRAPH lt n gt Raw Graph Color 255255255 Specifies the color of the graphs drawn in the Peaks commands as a 9 digit number in RRRGGGBBB format see above By default it is white 255255255 OVERLAY lt n gt Peak Overlay Color 000255000 Specifies the color of the peak overlays drawn in the Peaks commands as a 9 digit number in RRRGGGBBB format see above By default it is green 000255000 MATCH1 lt n gt Match 1 Overlay Color 000255255 Specifies the color of the second graph drawn in the Peaks commands as a 9 digit number in RRRGGGBBB format see above By default it is cyan 000255255 M86 E01008 Edit Routines GADDS Software Reference Manual 4 7 Edit gt Clear Erase the data array and or the display screen Menu Command Edit gt Clear Accelerator Ctrl Del User Level 1 SLAM Syntax CLEAR 1 QUADRANT lt n gt GRAPHICS_SAVE IMAGE_SAVE Analyze gt Clear erases a specified region of the display and or frame buffer memory Clearing of the screen can be confined to just image data retaining any overlaid graphics or just graphic overlays retaining the underlying image When invoked from the menu or from the com mand line without arguments Analyze gt Clear displays a dialog box where you can view ed
159. the four quadrants enter 1 through 4 as appropri ate The default value is O full frame win dow Quadrants are 0 full window 1 lower left 2 lower right 3 upper left and 4 upper right ER ee SEO Width 32 The width of the box defining the region of interest in pixels The range is from 0 to 128 default value is 32 ee Pees Height 32 The height of the box defining the region of interest in pixels The range is from 0 to 128 default value is 32 DELAY lt n gt 0 0 available in com mand mode only Specifies a time interval in seconds to wait before erasing the cursor and returning con trol to the program This is for use in scripts where it is desirable for the cursor to remain on screen long enough for the user to dis cern its position NOERASE No available in com mand mode only Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor left from a NOERASE by reissuing the command with the same parameters The CLEAR com mand also provides a way to erase cursors left over from NOERASE options M86 E01008 GADDS Software Reference Manual Analyze Routines 7 13 Analyze gt Graph gt Write Write generated curve to file Menu Command Analyze gt Graph gt Write Accelerator None User Level 1 SLAM Syntax INTEGRATE WRITE 1 FILE
160. the goniometer angles have been driven to zero They define the unitary component of the orienta tion matrix i e they define the U matrix in Busing and Levy s terminology The first Eulerian angle is a rotation about Z analo gous to the omega angle on a 4 circle goni ometer the second is a rotation about X analogous to chi and the third is a rotation about Z analogous to phi Note that if the constraint type 1 is 1 9 the value you start with here doesn t matter since the pro gram will get the initial guesses for the Eule rian angles from the linear least squares This entry is updated with its refined value on exit Valid range is 360 to 360 degrees U2 lt N gt nnana 2nd U Matrix Eulerian Angle 0 0 Initial guess for the second Eulerian angle in degrees See comments for U1 above UBE lt N gt wceecceceeees 3rd U Matrix Eulerian Angle 0 0 Initial guess for the third Eulerian angle in degrees See comments for U1 above HKLTOL lt n gt Max Allowed HKL Deviation 0 25 When the least squares is begun a compar ison between the HKL values in the reflec tion array and HKL s computed based on the setting angles and detector X Y is made for each reflection Any reflection with a cal culated index which deviates from the value in the array by more than the tolerance specified here is removed from the least squares by clearing its H flag The following prompt is issued when any re
161. the script filename The script associated with the selected task is then executed Up to 10 parameters may be added to any user task and they are treated as replaceable parameters within the script file If no parameters are associ ated with the user task then the task begins executing immediately Instructions on modifying usertask ini file are found in the header of that file The following example corresponding to one section of the GADDS SYSDATA usertask ini file defines user task number 12 to execute the SLAM com mand script d frames scripts process slIm 12 menu My Collect help My favorite data collection process slam D frames scripts process prompt Filename Enter filename specifi cation prompt Title Enter title string M86 E01008 User Task Routines GADDS Software Reference Manual 10 2 M86 E01008 11 Help Routines 11 1 Help gt Software Reference e 11 1 1 Arguments Display Software Reference online None Command executes immediately documentation Menu Command Help gt Software Reference Accelerator None User Level Ctrl H SLAM Syntax HELP REFERENCE or HELP Spawns or displays the GADDS Software Refer ence Manual This is either a PDF document a windows help file or ASCII _TP files located in the GADDS SYSTEM directory The Acrobat reader must be installed to display PDF files M86 E01008 Help Routines GADDS Software Re
162. thse cite hg eae ad a ae eaves ate ee ooo at vit aves E aed ai TLE WRG Ava Sete 6 23 6 10 17 Arguments mere re idles cere ey oh ee einen Be peel ed eyed eae aaa 6 24 6 11 Process gt Corrections gt LPA 00000 i a aa aE Ko aa E a a a ata 6 26 61D LOPE nize es eai mea Patel Se a AA E AAE a ly fee be Va ot edad Beg 6 26 6 11 2 Polarization rese deve cd A Bale dese de eat eae eee o ate ae ead 6 26 6 11 3 Air and Faceplate Absorption 0 000 tees 6 26 Gl ASATQuMOeNtS mE Moiceech onus nS EE eae kt wale wp eases anblled aay weeded a EE 6 27 6 12 Process gt Corrections gt Fiber 0 000 e cette eee 6 28 6 12 1 ALGQUMENIS aesa an rE E ikaw arate Pameeeee E EE eae bed ea aah acd ed avs 6 28 6 13 Process gt Corrections gt Plate pa serei n aa teeta 6 30 BISTAGNE S aaae aE ace ok Sew ERN E AE E EEE OE a Athen aE ete Mast a eee ans 6 31 M86 E01008 4 04 vii Table of Contents GADDS Software Reference Manual 6 14 Process gt Smooth gt Average Smooth image with 3x3 boxcar average filter 6 32 6 14 1 Arguments wniirgode gota whee sts iat wea Pe ee Pe he he abe 6 32 6 15 Process gt Smooth gt Median Smooth image with 3x3 median filter 6 32 6 15 1 Arguments 24 pee eee be eE aia tates Peas E ee Pea eed 6 32 6 16 Process gt Smooth gt Convolve Smooth image by convolving with average Neighborhood erer 42 peal See ek fee eb ee a bt bea ee arieaa ly ee eden ee tad 6 33 6 16 41 Argu
163. to Detector Distance and Beam Center Measurement 4 4 2 Ao AGUES dee sop Be ave ces Gee ae ete Unrate anager Ged er EEA edie orn Deiat ee lta tae 4 3 4 2 Edit gt Configure gt Admin settings View edit the current administrator configuration SOUINGS eraan ted cuneate a ENA ends Sat ohn da Malach dae pi heat T MAS adele era eee 4 7 Ae TATUNE a wren TIA rege hed peas Mace i ake cap acer teat ead ae ean ree od 4 7 4 3 Edit gt Configure gt Read Read a new configuration from a disk file 4 10 4 3 1 ArQUMEMS ecccaecdavetigared eer enpe yas bet tas PES WEe ST pERAW EEE EEE YS 4 10 4 4 Edit gt Configure gt Write Save the current configuration to a disk file 4 11 AAT AUNES nea Gb eet ee Oo Gabe vin Abe te ae ele atte atts 4 11 4 5 Edit gt Configure gt Show model Display the current goniometer and controller type 4 12 A AAPQUMEMIS ese eicid ite t an peerage edna deed Goto a dey dos bees eh ae toe eae 4 12 4 6 Edit gt Configure gt Colors Edit the current color configuration settings 4 13 46 1 AUNES oc 2 r E ai bared Cat ay ee ee Re ee eet AE ee eae 4 14 4 7 Edit gt Clear Erase the data array and or the display screen 00000 cues 4 16 ArT A AKQUMEMS fcc ce elaine ed LEG A yee els bee Se EOS bee i a eed 4 16 4 8 Edit gt Contrast e Change the screen brightness and contrast 0000 caus 4 17 4 9 Edit gt Zoom Magnify a specif
164. to a file or printer with this func tion You can also move through the window contents with the page keys arrow keys or with mouse motion Pressing ESC or the right mouse button exits the output window continuing with the BRAVAIS sub command The output is described in more detail below After you exit the output window an input win dow appears requesting you to enter the solu tion number of the Bravais lattice you want to use with a default value corresponding to the solution labelled as best that solution is pre ceded in the output window by the characters gt gt gt If you enter a non zero solution number M86 E01008 GADDS Software Reference Manual Peaks Routines pressing the ENTER key or left mouse button selects the input solution number and re indexes the reflections in the Reflection Array to correspond to the selected Bravais lattice then returns to the REFL_ARRAY submenu with the LEASTSQ option highlighted since that s usu ally the next operation If you enter a solution number of zero and press ENTER or the left but ton the program returns to the submenu without re indexing the array Pressing ESC or the right mouse button in the input window returns you to the BRAVAIS scrollable output window for reviewing the output prior to selecting a solution If REFL BRAVAIS was invoked from the com mand line the output window is displayed sub ject to a 10 s timeout to allow command scri
165. to an unstable source and is therefore an option ROTATE 0 05 Rotate Sample No Perform sample rotation in phi When used in conjunction with MODE OSCILLATE an integer number of rotations are performed during each oscillation Use of both the MODE OSCILLATE and ROTATE argu ments are designed for micro diffraction applications where a random sample is desired NIDEO ee Capture Video Image No Capture vide image of sample with same name and TIF extension Requires a sys tem equipped with the video option The video capture program must be running in a separate window Only on dual detector systems are addi tional parameters for control of the Slave frame buffer OSCILLATE lt s gt Sample Osc None Select the axes to oscillate during data col lection Valid entries are None X XY XYZ RA YZ or RLS AMPLITUDE lt n gt Amplitude 0 0 Enter the half amplitude of the oscillations in range 0 to 25 mm Oscillation occurs between the starting position minus ampli tude and the starting position plus amplitude and uses a speed of half the maximum drive speed for that axis AUTOZALIGN Auto Z Align No Check Yes to perform automatic sample height alignment using laser spot imaging This feature requires VIDEO 1 3 02 or later If Zoom is 1 0 you must enter a starting Z value that is within 3 5 mm of the true sam ple height
166. to be tested for correspon dence with other lattices This item is auto matically filled in with the value from the M86 E01008 Peaks Routines GADDS Software Reference Manual reduced primitive cell when you run INDEX Default is 10 Valid input range is 1 to 2500 SS E eave Current B Axis Length 10 0 Specifies the B axis length in Angstroms of the input unit cell to be tested for correspon dence with other lattices This item is auto matically filled in with the value from the reduced primitive cell when you run INDEX Default is 10 Valid input range is 1 to 2500 4 re ciie ia Current C Axis Length 10 0 Specifies the C axis length in Angstroms of the input unit cell to be tested for correspon dence with other lattices This item is auto matically filled in with the value from the reduced primitive cell when you run INDEX Default is 10 Valid input range is 1 to 2500 PO el ete Current Alpha Cell Angle 90 0 Specifies the ALPHA unit cell angle in degrees of the input unit cell to be tested for correspondence with other lattices This item is automatically filled in with the value from the reduced primitive cell when you run INDEX Default is 90 Valid input range is 0 to 179 TOn Current Beta Cell Angle 90 0 Specifies the BETA unit cell angle in degrees of the input unit cell to be tested for correspondence with other lattices This item is automatically filled in with the value
167. to form a nor mal 512 x 512 output frame These arguments allow you to choose the detector bin at which the output frame origin is placed and to use a re binning factor less than 32 to effectively mag nify a smaller detector region to cover the whole 512 x 512 output frame For example MAG 2 results in re binning by 16 1 instead of 32 1 In general this feature is useful only for special M86 E01008 Process Routines GADDS Software Reference Manual e g non crystallographic applications and these settings should be left at their defaults When invoked with the REPROCESS option from the FLOOD submenu or when run from the command line without arguments FLOOD REPROCESS displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins computation installation of the new flood field correction the ESC key or right mouse button returns you to the FLOOD submenu 6 3 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses n E E Input Projection File name normal _fi Enter the filename for input projection data _PJ The default file is NORMAL _PJ By convention these files reside in the frame directory specified in the CONFIGURE EDIT input panel The filename you specify here is merged with the default specification Frame_root _pj before the program a
168. to trailer info COMPRES 57 1 Cc Compression scheme ID if any Such as NONE LINEAR 58 1 Cc Linear scale offset for pixel values typically 1 0 0 0 PHD 59 1 2R Discriminator Pulse height settings PREAMP 60 1 R Preamp gain setting CORRECT 61 1 Cc Flood table correction filename WARPFIL 62 1 C Brass plate correction filename A 6 M86 E01008 GADDS Software Reference Manual Area Detector Frame Format WAVELEN 63 1 8 3R Wavelengths average a1 a2 8 4R 8 Adds beta wavelength MAXXY 64 2 2R X Y pixel of maximum counts AXIS 65 3 Int Scan axis 1 4 for 2 theta omega phi chi Default is 2 ENDING 66 3 4R Actual goniometer angles at end of frame DETPAR 67 68 4 6R Detector position corrections dX dY dDist Pitch Roll Yaw LUT 69 4 Cc Recommended display lookup table DISPLIM 70 4 2R Recommended display limits PROGRAM 71 4 C Name and version of program writing frame such as GADDS for WNT V4 0 07 ROTATE 72 5 Int Nonzero if acquired by rotation of phi during scan BITMASK 73 5 C File name of active pixel mask associated with this frame or NULL OCTMASK 74 75 5 8lnt Octagon mask parameters to use if BITMASK null ESDCELL 76 77 7 6R Unit cell parameter standard deviations M86 E01008 A 7 Area Detector Frame Format GADDS Software Reference Manual DETTYPE 78 7 C Detector type MULTIWIRE default CCD PXL small CCD CCD PXL 2
169. trackball On a fully calibrated frame the calculated Debye Sherrer lines will precisely center over the lines in the data frame Toggling between the calibration of the detector distance and the swing angle and the calibration of the detector center is performed by pressing the C key As an aid during interactive calibra tion the detector distance swing angle and cen ter are continuously displayed and updated on the screen To align the detector center move the calibration lines until a calculated and a measured Debye ring exhibit the same center This is most easily accomplished with an on axis data frame if the data frame is off axis it can still be done by examining the offset at the extreme top and bot tom of the display To align the detector distance use the cursor keys to expand or contract the calibration lines To align the swing angle use the cursor keys to shift left or right the calibration lines When cor rectly calibrated all calculated Debye rings will be precisely centered over the corresponding lines in the data frame Upon exiting CALIBRATE the detector parame ter offsets are stored in the frame header Gen eral GADDS users cannot change the calibration and must inform their administrator if the calibration is off If the user is an administra tor this message appears Update configura M86 E01008 GADDS Software Reference Manual Process Routines tion with new distance and be
170. trial A B and C axis solutions A trial axis vector is accepted only if its length is in the range AX MAX 1 FCELL 0 01 to AX 1 FCELL where AX is one of the lengths specified above for AAX BAX or CAX The allowed input range is 0 0 2 0 and the default value is 0 75 If you know the axis lengths enter them as AAX BAX CAX make FCELL small for example 0 1 otherwise make the best guesses you can You can use the CURSORS VECTOR and CURSORS CIR CLE commands to derive approximate unit cell axis lengths SIGA lt N gt 0 Cell Angle Deviation 0 1 Specifies the fractional range of cell angles which will be accepted for trial solutions when a known unit cell is assumed This value is used ONLY when assuming a known unit cell if ASSUME KNOWN UNIT CELL is specified as N on the input panel or NOREDUCE is absent in command line mode this value is ignored A trial cell angle is accepted only if its length is in the range ANGLE MAX 1 FCELL 0 01 to ANGLE 1 FCELL where ANGLE is one of the lengths specified above for U1 U2 or U3 The allowed input range is 0 0 2 0 and the default value is 0 1 NOREDUCE Assume Known Unit Cell Y N No If specified as Y on the input panel or as NOREDUCE in command line mode this qualifier suppresses the normal computa tion of the reduced primitive cell Instead the program attempts to find a solutions only for the input A B C A
171. type and phi moves to the starting angle specified on the input panel After these goniometer movements GADDS opens the shutter performs a full rotation of phi while acquiring a frame The shutter closes once the exposure has been completed then GADDS displays the unwarped frame The speed of rotation depends on the collection time requested in the input panel The requested time adjusts as needed to make a full phi rota tion Since the maximum rotation speed is 3600 degrees minute for Platform 24 seconds is the shortest actual rotation exposure time 600 degrees minute for P4 36 seconds A rotation photo taken at a detector swing angle 2 theta setting angle of zero provides the best method for estimating the direct beam center Usually you ll need a strongly diffracting crystal to see a good pattern The rotation photo will contain a center of symmetry at the direct beam position You can place the origin and endpoint of a vector cursor see Analyze gt Cursor gt Vec tor on two spots related by the center of sym metry and obtain the direct beam coordinates from the displayed vector midpoint values M86 E01008 GADDS Software Reference Manual Collect Routines 5 35 Collect gt Scan gt HKL e Reciprocal space scan from starting HKL to ending HKL Menu Command Collect gt Scan gt HKL Accelerator Ctrl Shft F5 User Level 1 SLAM Syntax SCAN HKL 1 2 3 SCANTIME lt n gt TITLE lt s gt SA
172. values don t correspond to your current experimental setup run CONFIG URE EDIT and correct them before acquiring the brass plate data These values are stored in the output frame header and are used in subse quent processing for example in the spatial correction If you don t supply the correct values you may not be able to auto index your frames without a lot of extra effort Since collected data are of higher quality when a flood field correction is made the message M86 E01008 Process Routines GADDS Software Reference Manual WARNING NO FLOOD FIELD CORREC TION CONTINUE is displayed on the bottom status line in the case where SPATIAL NEW is run with no current active flood field correction When acquisition of the fiducial plate image begins the progress message COLLECTING SPATIAL CALIBRATION DATA is displayed on the bottom status line After the fiducial plate image has been acquired SPATIAL NEW automatically pro cesses it to extract positions of the spots and based on the known positions of the corre sponding holes in the fiducial plate computes a new spatial correction In the course of process ing the data it must index the rows and columns curved due to the pincushion distortion of fidu cial spots in order to match each spot with a hole of known position on the fiducial plate When the indexing is complete a graphic map of the fiducial spot positions extracted from the frame is
173. wait before eras ing the cursor and returning control to the program This is for use in scripts where it is desirable for the cursor to remain on screen long enough for the user to discern its position NOERASE Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor left from a NOERASE by reissuing the command with the same parameters The Analyze gt Clear command is another way to erase cursors left over from NOERASE options DUMP Displays a 17x17 numeric pixel dump at the specified position If a keyboard or mouse event doesn t occur within the time out value set in the Edit gt Config dialog the display times out and control is returned to the com mand line If logging is enabled a copy of the pixel dump is also written to the logfile The following output statistics are displayed on screen in real time and are also written to the logfile if applicable for non pole figures XY PIXEL X and Y coordinates of current pixel range from 0 to framesize 1 with origin 0 0 being located at lower left of screen COUNTS Counts at current pixel XUNWARPED If a spatial correction is in use provides spatially corrected X coordinate of current pixel otherwise this value will be identical to the raw coordinate M86 E01008 GADDS Software Reference Manual Analyze Routines YUNWARPED If a spati
174. with REFL_ARRAY LEASTSQ prior to executing this command In general there are two solutions Depending on the angle between the scan axis and recipro cal lattice vector the setting angles you specify for the non scan axes and the current detector distance one both or none of the solutions may be observable The program displays the results in a scrollable output window When invoked with the HCALC option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY HCALC displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button solves for the positions at which the specified HKL can be observed the ESC key or right mouse button returns you directly to the REFL_ARRAY sub menu Following a successful computation a scrolling output window is displayed containing the resulting output text If logging is enabled see LOGFILE the contents of this window are also written to the logfile When viewing the out put pressing ENTER or the left mouse button displays a pop up menu of options including export of ASCII data for example the contents of the window could be sent to a file or printer with this function You can also move through the window contents with the page keys arrow keys or with mouse motion Pressing ESC or the right mouse button exits the output window returning you to the REFL_ARRAY submenu The o
175. 0 00 1000 00 1000 00 1000 00 3600 00 600 0 1600 0 1600 0 1600 0 300 0 1000 0 allowable speeds are read from the DEVICE INI configuration file Table 5 6 PLATFORM beige Multi Axes Systems Parameter 1 2 3 4 5 6 7 8 Dialog Box Prompt 2 THETA SPEED OMEGA SPEED PHI SPEED CHI SPEED X SPEED Y SPEED Z SPEED AUX SPEED Default 600 00 600 00 3600 00 600 0 150 0 150 0 150 0 50 0 Maximum Allowable 1000 00 1000 00 3600 00 600 0 1600 0 1600 0 1600 0 300 0 Table 5 7 PLATFORM beige 3 Circle Systems Parameter 1 2 3 Dialog Box Prompt 2 THETA SPEED OMEGA SPEED PHI SPEED Default 1000 00 1000 00 3600 00 Maximum Allowable 1000 00 1000 00 3600 00 M86 E01008 GADDS Software Reference Manual Collect Routines Table 5 8 4 Circle Systems Parameter Dialog Box Default Prompt 1 2 THETA 234 375 OMEGA SPEED 2 PHI CHI 600 00 SPEED Maximum Allowable 600 00 600 00 Table 5 9 Older Aztalan black 3 Circle Systems Parameter Dialog Box Default Prompt 1 2 THETA 150 00 SPEED 2 OMEGA PHI 600 00 SPEED I CAUTION Maximum Allowable 150 00 600 00 Although the software s valid range for speeds is up to the Maximum Allowable values specified above increasing the slew speeds to above what the goniometer can handle will result in
176. 0 1 75 2 00 2 25 inf X 2 4 0 0 0 0 0 0 o 0 Y 25 1 0 0 0 0 0 0 o o0 H K L Omega X Y AVG 0 000 0 000 0 000 0 000 0 000 0 000 RMS 0 012 0 006 0 006 0 014 0 147 0 137 Detector corrections X Cen Y Cen Dist Roll Yaw 4 530 0 531 0 201 0 200 0 003 Eulerian angles 95 154 178 930 37 169 Nonlinear refinement StartingRes FinalRes GOF Cycles Code 6 49567E 01 2 76423E 01 0 44 4 0 Flags H K L 2 Theta Omega Phi Chi X Y Inorm I Sig 1ACHS 16 7 8 30 000 0 271 0 000 0 000 82 85 51 23 626 60 112 02 01 01 0 004 0 26 0 15 2 ACHS 12 6 6 30 000 0 443 0 000 0 000 33 26 99 06 467 95 97 01 00 01 0 022 0 14 0 28 M86 E01008 GADDS Software Reference Manual Peaks Routines 3ACHS 21 11 3 30 000 0 448 0 000 0 000 142 13 309 54 344 28 83 01 00 00 0 012 0 16 0 02 etc M86 E01008 8 63 Peaks Routines GADDS Software Reference Manual 8 19 Peaks gt Refl Array gt Edit View modify the reflection array Menu Command Peaks gt Refl Array gt Edit Accelerator Ctrl E User Level 1 SLAM Syntax REFL_ARRAY EDIT When you select EDIT from the REFL_ARRAY submenu the system displays a scrollable win dow listing all of the reflections currently in the reflection array You can add to delete from or reorganize the list as desired by using the appropriate screen editing functions This is very useful for making minor corrections changes and deletions however some of the other sub comman
177. 0 19636 7 3 11 01 11 99 1 00 0 04587 0 24611 0 02100 8 7 13 00 13 00 0 01 0 05838 0 27656 0 00078 9 2 9 01 7 99 7 02 0 04215 0 17936 0 15221 10 24 8 02 9 02 5 00 0 03361 0 18313 0 10781 11 26 12 99 11 00 5 99 0 06419 0 25246 0 13093 12 14 18 00 14 00 3 02 0 09522 0 33492 0 06701 13 10 10 99 9 99 7 01 0 05529 0 22290 0 15082 14 11 15 00 12 98 4 00 0 07382 0 29497 0 08783 15 4 7 99 9 00 4 01 0 03086 0 18211 0 08697 16 13 16 01 11 00 9 01 0 09371 0 28161 0 19354 17 11 14 00 10 99 7 00 0 07223 0 26154 0 15278 18 6 15 00 9 99 9 00 0 08397 0 25896 0 19665 19 0 5 00 7 01 3 01 0 01564 0 13087 0 06517 20 19 6 00 8 00 2 01 0 01865 0 15188 0 04339 21 10 8 99 9 99 4 01 0 03773 0 20412 0 08625 22 4 9 97 11 00 2 02 0 04029 0 22467 0 04399 M86 E01008 8 43 Peaks Routines GADDS Software Reference Manual 23 12 19 00 14 00 24 19 7 99 9 99 25 16 21 98 13 99 26 5 12 02 10 02 0 10323 0 02880 0 13114 0 05949 0 34409 0 19450 0 37279 0 23122 Example 8 3 Output from indexing of 8 Myoglobin Test Frames after reindexing the Reflection Array Truncated Histograms 00 05 H 26 K 26 L 26 Omega 26 0 00 0 25 xX 20 Y 20 H K AVG 0 001 0 002 0 001 RMS 0 010 0 011 Flags H K L 1ACHS 9 7 8 01 01 02 2ACHS 6 6 6 00 02 02 3 ACHS 10 11 3 01 00 00 ooo o ooo o 0 75 fo 15 20 ooo o 0 0 Omega 0 002 0 017
178. 00 160 272 46 174 89 776 2 00 1 00 0 00 92 865 46 174 89 442 1 00 0 00 0 00 160 272 46 174 90 224 2 00 1 00 0 00 91 906 46 174 89 827 1 00 1 00 0 00 158 674 46 174 90 527 1 00 2 00 0 00 20 0 6 0 Beta 89 827 0 00 90 558 0 00 89 827 0 00 90 736 0 00 90 527 0 00 90 736 0 00 90 745 0 00 90 558 0 00 Gamma 119 323 0 00 1 00 89 971 0 00 1 00 90 661 0 00 1 00 90 689 0 00 1 00 90 029 0 00 1 00 89 311 0 00 1 00 89 339 0 00 1 00 89 971 0 00 1 00 8 50 M86 E01008 GADDS Software Reference Manual Peaks Routines 9 2 45 91 906 1 00 1 00 0 00 10 2 96 160 272 2 00 1 00 0 00 MONOCLINIC P 11 2 55 91 906 1 00 1 00 0 00 TRICLINIC P 12 0 00 46 174 0 00 0 00 1 00 13 2 62 46 174 0 00 0 00 1 00 14 262 46 174 0 00 0 00 1 00 160 341 1 00 91 946 0 00 46 174 0 00 91 906 1 00 91 906 1 00 91 946 0 00 46 174 89 255 1 00 46 174 90 736 1 00 91 946 90 736 0 00 91 946 60 677 1 00 92 865 120 317 1 00 92 865 59 640 1 00 0 00 0 00 1 00 0 00 0 00 0 00 90 173 0 00 90 224 0 00 119 323 0 00 89 264 0 00 90 558 1 00 89 442 1 00 89 339 0 00 1 00 89 311 0 00 1 00 89 827 1 00 0 00 89 827 1 00 0 00 90 173 0 00 0 00 89 264 0 00 0 00 M86 E01008 Peaks Routines GADDS Software Reference Manual
179. 000 counts This procedure accounts for variation in activity of dif ferent Fe sources and the decrease in inten sity of an Fe source as it ages the half life is about 2 5 years Typically it will take about half an hour to accumulate 10M counts In order to set up the acquisition of a new flood field in this manner set the MAX SECONDS argument described below to a large value for example 1 0x10 seconds and set MAX COUNTS to 1 0x10 counts WHEN YOU TAKE A FE 5 FLOOD FIELD IMAGE BE SURE THAT THE DETECTOR BIAS IS SET CORRECTLY FOR FE Also be sure to reset the bias back to the correct level for your x ray generator e g for Cu radiation when finished with flood field and fiducial plate data collection After running FLOOD NEW it is a good idea to take a 120 second frame to verify that you have a good flood field correction The image should look more uniform than a raw image taken with no flood field correction Remember that appearance of any residual lines results only from a bias in the POSITIONING of those events not from any error in the number of counted photons The SPATIAL fiducial plate calibration will reduce or eliminate this residual positional error If lines are present they may have a second order effect on integrated intensi ties due to resulting variation of spot shapes across the detector but they are not a problem unless they are prominent FLOOD NEW computes the flood f
180. 008 13 13 Utility Programs GADDS Software Reference Manual parameters Example DE 0 5 0 5 0 1 0 1 DL Draws a line segment between specified X1 Y1 X2 Y2 fractional coordinates Requires the fractional X1 fractional Y1 fractional X2 and fractional Y2 as parame ters Example DL 0 5 0 5 0 1 0 1 1 IE Erases a rectangular box at specified X Y W H fractional coordinates Requires the fractional X fractional Y fractional W and fractional H as parameters Example 1 E 0 5 0 5 0 1 0 1 See SAXI TEST PLOTSO DAT for an example of a PLOTSO data file The syntax for starting PLOTSO by e NT is PLOTSO X lt n gt Y lt n gt W lt n gt H lt n gt DATA_FILE e IRIX is PLOTSO X lt n gt Y lt n gt W lt n gt H lt n gt DATA_FILE When you start PLOTSO you can also specify the qualifiers W lt n gt and H lt n gt on the com mand line where lt n gt represents a numeric value The value given for W is the desired win dow width in pixels and the one for H is the desired window height if you want the full screen but are not sure of the number of screen pixels use W 9999 H 9999 Under NT or IRIX you can also specify the X and Y pixel numbers desired for the upper left corner of the graphics window with X lt n gt and Y lt n gt If the W and H are not given they default to 704 and 600 respectively providing a screen dump which reasonably covers the full pa
181. 008 3 3 File Routines GADDS Software Reference Manual least squares displaying another frame with this item unchecked or acquiring a new frame clears the override flag but does not reset the check box in this dialog don t leave it inadvertently set effectively restor ing the matrix from the last Peaks gt Refl Array gt LeastSq VIDEO Display Associated Video Image No Specifies whether to automatically display the associated video image on the video program The video program must already be running in a separate window By default it is unchecked OVERLAY 4 Add HKL Overlay No This option when checked directs the pro gram to draw an overlay of predicted spot positions on top of the image automatically every time a frame is displayed The param eters given in the File gt Display gt HKLs dia log are used for these automatic overlays as well By default this option is unchecked The overlay is computed from the current orientation matrix determined in Peaks gt Refl Array gt LeastSq and takes into account any lattice centering determined in Peaks gt Refl Array gt Bravais You can draw overlays on magnified frames by entering the desired magnification and center in the File gt Display panel when the image is dis played the Edit gt Zoom command does not redraw or magnify graphic overlays Three types of marker characters are used to indi cate the difference be
182. 0s ds Is or HKLs 3 Choose where to retrieve the data from LABEL option the frame raw trace or peaks table 4 Choose what marker character to use to highlight the data A crosshairs cursor appears and the selected label appears in the message window 5 Press ENTER to draw the marker at the cur rent cursor position and automatically dis play the TEXT option when you have finished press ESC to return to the POSTER menu without drawing the label 6 Edit position and size the label to be drawn see GRAPH POSTER TEXT 12 16 M86 E01008 GADDS Software Reference Manual SLAM Routines 12 4 6 PEAKS PROFILE PEAKS PROFILE has four subcommands EXIT Close PROFILE submenu and return to PEAKS menu NEW Create a new profile lineshape file ADD Add a profile to existing lineshape file DELETE Delete a profile from an existing lineshape file When you choose PEAKS PROFILE from the PEAKS menu GADDS displays a pop up sub menu containing these subcommands When you start PEAKS PROFILE from the command line you need to specify one of these subcom mands as a qualifier if not the submenu appears and GADDS waits until you have made a selection To select one of the options high light it with the arrows or mouse to highlight the desired selection A help message appears on the bottom status line describing the action taken by the selected item To begin the high lighted action press ENTER When you are fin ish
183. 11111111111111 89 4 59 4 89 4 60 2 Predicted reduced primitive axes are Soln X Y Z Length 4 87 10253 29 05033 1 61254 91 83340 2 68 84866 61 83576 0 53702 92 54236 1 0 90663 0 11663 46 14998 46 15903 Reduced primitive cell is 91 833 92 542 46 159 89 398 89 984 60 372 Difference Vectors Length X1 X2 X3 Freq 40 05527 0 00803 0 00913 0 02180 2 32 87223 0 00410 0 02093 0 02170 2 30 28461 0 01281 0 03043 0 00017 2 25 39675 0 01247 0 03035 0 02177 2 22 04425 0 01167 0 00270 0 04375 2 ARUN 8 42 M86 E01008 GADDS Software Reference Manual Peaks Routines 15 16 18 34492 18 29090 17 00628 16 32388 14 31518 13 87408 12 60927 11 18752 9 18217 9 03692 7 90768 0 01719 0 00113 0 01710 0 00953 0 01803 0 02895 0 02206 0 03342 0 03102 0 01905 0 01505 0 05173 0 00059 2 0 03306 0 04353 2 0 05170 0 02218 2 0 04254 0 04304 2 0 05208 0 04292 2 0 04912 0 04410 2 0 07317 0 02118 2 0 07032 0 04390 2 0 08251 0 06396 2 0 00642 0 10882 2 0 06411 0 10796 2 Least squares cell parameters 92 865 91 946 46 174 89 264 89 442 59 640 340159 50 Full vectors NEAR H K L X1 X2 X3 1 9 8 99 699 7 99 0 04561 0 16710 0 17374 2 20 5 99 6 01 5 98 0 02503 0 12757 0 12977 3 21 9 98 10 99 2 99 0 04181 0 22498 0 06442 4 20 7 01 8 99 1 99 0 02324 0 17308 0 04331 5 15 9 98 9 99 499 0 04328 0 21235 0 10873 6 26 13 00 9 00 9 00 0 07110 0 22841
184. 15 Collect gt Goniometer gt Limits Enter software collision limits 0 5 19 5 15 17 AUMENS eran AREARE EA ae EA DA E E E E ae eases ae AS 2 5 20 5 16 Collect gt Goniometer gt Extlimits e Display extended software collision limits 5 24 SIG ATQUMONIS nite bev a oat ade s one ol bal Peewee bee ie O dae ahd ae 5 24 5 17 Collect gt Goniometer gt Speeds Enter slew drive speeds of axes 0 5 25 SIGL ATQUMOMIS aranin A EREET rE E haa cristo a nice E ERE Bape diese tape ade 5 25 5 18 Collect gt Goniometer gt Zero Drive all angles to home position zero degrees 5 28 SEB ACAKQUMONIS eree AEE Gl A e eats EEE a dtdigien Ed Ea dewanides pte dd 5 28 5 19 Collect gt Goniometer gt Attenuator Insert remove attenuator 000 5 29 S219 ARGUMENTS crau irna a TAREE hare E E ete i ofa alee Ae den ae et ed ae 5 29 M86 E01008 4 04 GADDS Software Reference Manual Table of Contents 5 20 Collect gt Goniometer gt Shutter e Open close x ray shutter 0000 ee eee 5 29 5 2084 Arguments a nd4 debater eas E eso ge oa he NG eet eee ee S 5 30 5 21 Collect gt Goniometer gt Laser Turn on off the laser 000 c eee eee 5 30 5 24 31 Arguments io ates y Oh oe keg ieee all diet bean een eal Oe we a Ea ae wets 5 30 5 22 Collect gt Goniometer gt Generator Control the high voltage generator kv and Ma SCHINGS redai depen KE ee dae del taped H
185. 255 RRRGGGBBB For example the value 255000000 is bright red 000255000 is bright green 255255000 is bright yellow 255255255 is white 050000050 is dark purple 000000000 is black and 080080080 is gray The simplest way to select a color is to enter an asterisk and let the program display a color table map where you can click on any color and have the RGB value calculated When you invoke a command from the menu or the command line without arguments a dialog box appears View or edit its contents or type text Then e Press ENTER or click the OK button to save your entry e Press ESC or click the Cancel button to return to the menu without saving your last entry GADDS displays the angle status in the follow ing color scheme e Non controllable axes in border color e Moving axes in highlight color e Stationary and controllable axes in fore ground color e Axes in collision state in reverse video background on highlight color M86 E01008 Edit Routines GADDS Software Reference Manual 4 6 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses GT eeediechensalen Rew Color Table Filename bb lut Enter name of the color lookup table to be used for frames This entry does not affect the colors used for menus windows screen background etc Color tables are assumed to be located in the directory pointed to by GADDS SYSDA
186. 3 boxcar average filter Menu Command Process gt Smooth gt Average Accelerator none User Level 1 SLAM Syntax SMOOTH AVERAGE Two filters are provided to smooth frame images average will compute the average pixel value while median determines the median pixel value Both filters utilize a 3x3 pixel box and ignore any pixel outside the active pixel map see MASK 6 14 1 Arguments None Command executes immediately 6 15 Process gt Smooth gt Median e Smooth image with 3x3 median filter Menu Command Process gt Smooth gt Median Accelerator none User Level 1 SLAM Syntax SMOOTH MEDIAN Two filters are provided to smooth frame images average will compute the average pixel value while median determines the median pixel value Both filters utilize a 3x3 pixel box and ignore any pixel outside the active pixel map see MASK 6 15 1 Arguments None Command executes immediately M86 E01008 GADDS Software Reference Manual Process Routines 6 16 Process gt Smooth gt Convolve e Smooth image by convolving with average neighborhood Menu Command Process gt Smooth gt Convolve Accelerator none User Level 1 SLAM Syntax SMOOTH CONVOLVE 1 The average neighborhood filter will smooth the frame image using the average pixel value of a user defined pixel box This filter will ignore the active pixel map see MASK 6 16 1 Arguments Each argument is listed below by its SLAM com
187. 62 ArQUMONIS 4 ie ees Gerke a ie ete tees goles DL eee attains 9 7 9 7 Special gt System Suspend program and invoke the Command Prompt processor 9 8 9 7 ACAIQUMENIS saet a aee aes kets bap teenkd muerte bee deeb a ba Rona acne tee 9 8 9 8 Special gt Spawn PROFILEP S e Spawn PROFILEP S or TOPAS P with current spectra 9 9 9 83 ArQuUMENIS e a fae OE Meda eR Paes ee Bae See ar el gaa ve 9 9 9 9 Special gt Redraw Redraw current screen e g if corrupted by window manager 9 9 9 9 1 AFQUMEMS scons tails wae tele eld wii Bene E a Lepeul dade ames fe 9 9 9 10 Special gt Level 1 Special gt Level 2 and Special gt Level 3 e Switch to simple advanced or administrator menu interface 0 0c eee 9 10 QOH AQUMOENIS esis a TEE IREEN T AE T nee a RAT welt One gen aE ees me Ree ee 9 10 10 US r Task ROUNNGS icc iosneiet cewd i a ia betwee wea neat 10 1 10 1 User gt e Execute User task 0000 ects 10 1 11 Help Routines oasis ee aes ek sh ta ene ep ea See Se 11 1 11 1 Help gt Software Reference Display Software Reference online documentation 11 1 WAAL Arguments rean nd oe ee i cil E E AA e 11 1 11 2 Help gt User s guide Display Users Manual online documentation 11 2 TITTAT AUMENS i Sisco een a Eaa dork ans Sk age et eee arias haves aa E 11 2 11 3 Help gt Mapping Display online documentation forGADDSmap 11 2 11 S Arguments crs s
188. 8 GADDS Software Reference Manual Collect Routines 5 19 Collect gt Goniometer gt Attenuator Insert remove attenuator Menu Command Collect gt Goniometer gt Attenuator Accelerator Ctrl Shift N User Level 1 SLAM Syntax GONIOMETER ATTENUATOR When invoked from the menu or run from the command line Collect gt Goniometer gt Attenua tor immediately toggles the status of the hard ware beam attenuator on those systems equipped with an attenuator If the attenuator is currently not inserted the program opens the shutter if not already open and inserts the attenuator If the attenuator is inserted the pro gram removes the attenuator from the beam and must briefly close the shutter to do so The SHUTTER item in the goniometer status area at the lower right of the display is updated to reflect the new attenuator status 5 19 1 Arguments None Command executes immediately 5 20 Collect gt Goniometer gt Shutter Open close x ray shutter Menu Commana Collect gt Goniometer gt Shutter or Collect gt Shutter Accelerator Ctrl Shift S User Level 1 SLAM Syntax GONIOMETER SHUTTER or SHUTTER When invoked from the menu or run from the SLAM command line Collect gt Goniometer gt Shutter toggles the status of the X ray shutter that is if the shutter is currently closed the pro gram opens it and if it is open the program closes it The action is performed immediately with no p
189. 8 GADDS Software Reference Manual Edit Routines 4 10 Edit gt Frame info View a frame header Menu Command Edit gt Frame info Accelerator Ctrl F User Level 1 SLAM Syntax FRAME_INFO 1 Edit gt Frame Info allows you to view the header of the currently displayed frame or that of a specified frame file very useful for detective work for data collection parameters When invoked from the menu or run from the command line without arguments Edit gt Frame Info displays a dialog box where you enter the name of the frame whose header is to be viewed After entering the filename pressing ENTER or clicking the OK button displays the header in a scrollable window pressing ESC or clicking the Cancel button returns you from the dialog to the menu without displaying the header When viewing the header pressing the ENTER key or clicking the OK button terminates the scrollable window and returns you to the menu bar You can click the Write button to write the currently selected header text or the entire header if nothing is selected to an ASCII text file or click the Print button to send the header text to a printer See Appendix A Area Detector Frame Format Headers for more information 4 10 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses AS epee eee eee Frame Filename SFRAME Filename of the frame whose header is to be dis
190. 8 65 36 36 0000 198 8 241 4 0 7 205 64 35 000C 176 6 3088 0 3 65 36 37 0000 95 1 77 1 0 6 175 59 42 000C 176 1 1738 0 7 60 35 3 7 0000 96 6 357 5 0 6 179 60 46 000C 329 7 240 1 0 1 37 27 25 0001 177 8 104 2 0 3 142 53 3 4 000C 2028 377 3 0 5 50 32 32 0000 269 2 1731 0 3 97 44 28 000C Bee abd De eG ES CEES 70000 145 1 403 4 0 7 121 49 36 000C eae Oy ae am a s a ooon eee ee a fe Vee Ses A 106 5 2421 0 4 57 34 5 1 0000 94 6 1496 0 4 81 40 49 000C 225 0 3538 0 8 39 28 31 0001 219 5 4904 30 65 lt 49 3T 2 6 0000 180 7 401 7 0 6 38 28 33 0000 oe oe ee a Se ee meee 215 7 55 4 0 4 33 26 29 0000 192 9 29 7 07 47 31 3 0 000C 199 2 2859 09 39 28 35 0001 SES 9190100 at ee 6B 000C 284 2 352 7 0 6 27 23 27 0000 ae Cee Se 108 7 380 6 0 2 41 29 42 0005 119 6 333 3 0 3 53 33 4 4 000C 142 1 103 7 0 5 38 28 38 0000 141 2 1964 0 3 52 32 43 000C 304 1 240 0 0 6 25 23 26 0000 8 26 M86 E01008 GADDS Software Reference Manual Peaks Routines 294 8 126 9 0 7 23 21 2 6 0000 244 6 2408 0 5 5 10 3 1 0000 321 4 102 0 0 8 20 20 2 4 0005 257 0 218 1 0 2 4 9 3 0 0001 236 8 353 7 0 3 24 22 3 0 0000 213 3 103 9 0 6 5 10 3 1 0000 257 1 285 0 0 2 24 22 2 9 0001 198 6 2188 0 9 5 10 3 5 0001 190 1 354 3 0 5 27 23 3 4 0000 379 1 509 0 3 2 7 2 1 0010 400 8 98 7 0 3 13 16 2 1 0000 337 2 400 8 0 8 3 7 2 3 0010 300 1 503 1 0 5 16 18 2 3 0000 312 7 503 5 0 2 2 7 2 2 0011 211 5 3082 0 4 26 23 3 3 0000 334 0 102 0
191. ALE Log Scale No If checked in the dialog box or given as LOGSCALE the frame image is displayed using a logrithmic scale By default it is unchecked USE_CONFIG Merge Config into Header No If checked in the dialog box or given as USE_CONFIG on the command line this qualifier replaces the following frame header items with the values currently in the Edit gt Config dialog This option always defaults to N unchecked regardless of the previous setting Header Item CONFIGURE EDIT Prompt USER User name DISTANCE Sample detector distance LOWTEMP Low temp device Y N TARGET X ray target material WAVELENGTHS _ X ray source wavelength SOURCEKV Source kilovolts SOURCEMA Source milliamps FILTER Filter monochromator CENTER Direct beam X Direct beam Y LUT Color table filename You can use this option to update frame header values then use SAVE to save the frame with the new values For example if you took a brass plate image at 18 cm but the Edit gt Config dialog contained the wrong distance you could avoid having to retake the image as follows Correct the distance in Edit gt Config gt User settings Read in the brass plate with LOAD USE_CONFIG or with this option checked in the File gt Load input panel Use File gt Save to save the brass plate so that the disk file is also modified Use Process gt Spatial gt Process to com pute the spatial correction with the
192. AM Syntax SCAN ZONE 1 WIDTH lt n gt SCANTIME lt n gt DISPLAY lt n gt Acquire gt Axial acquires an omega rotation pic ture in which the crystal is rotated about the a b orc axis The frame is not automatically written to disk Use Acquire gt Save after collecting the still frame if you want to save the data to disk When invoked from the menu or run from the command line without arguments Acquire gt Axial displays a dialog box where you can view edit the arguments described below before per forming the operation Pressing the ENTER key or clicking the OK button starts the operation Pressing ESC or the Cancel button stops the operation and returns you to the menu You can interrupt the operation by pressing CTRL BREAK 5 39 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses e AEE RIEA Axis 1 Enter 1 to attempt collection of the a axis 2 for b or 3 for c WIDTH lt n gt Frame Width 0 5 Enter the frame width as defined under WIDTH in Section 3 4 SCANTIME lt n gt Seconds Frame 30 0 Enter the seconds per frame as defined under TIME in Section 3 4 DISPLAY lt n gt Max Display Counts 1 See Section 3 7 for an explanation of this argument See Acquire gt Display for more details M86 E01008 GADDS Software Reference Manual Collect Routines 5 40 Collect
193. AT data file ALPHAINC lt n gt Declination Inc 1 0 Step size of alpha declination angle BETAINC lt n gt Azimuthal Inc 1 0 Step size of beta azimuthal angle M86 E01008 Analyze Routines GADDS Software Reference Manual REFLECTION Reflection mode Yes No No Present to produce TEXTURE AT file in reflection mode format 7 26 Analyze gt Pole Figure gt popLA e Create popLA data file from pole figure frame ASCII Menu Command Analyze gt Pole Figure gt PopLA Accelerator None User Level 1 SLAM Syntax POLE_FIG POPLA 1 TITLE lt n gt HKL lt n gt APPEND Besides the storing of bitmapped images the pole figure may be exported in either TEX TURE AT file format or popLA file format for ODF calculations or other processing with those or other software packages See appendices for the format of these data files popLA performs an ODF using vector methods The orientation space is divided up into a num ber of cells within which the ODF is assigned a constant value A simple initial value of each cell is determined from the experimental data The resultant pole figures from such an ODF are compared with the observed pole figures and adjustments are made to improve the match This process is repeated until no further improvement is observed Vector methods are best suited to ODFs that contain a few sharp features M86 E01008 GADDS Software Reference Man
194. ATT Select Project no default Enter the requested project name to remove from the project database You cannot remove the current project No default M86 E01008 Project Management Routines GADDS Software Reference Manual 2 8 Project gt Delete Delete all project files and remove from project database Menu Command Project gt Delete Accelerator None User Level 2 SLAM Syntax PROJECT DELETE 1 Use this command to delete all data files and remove the requested project from the project database Typically you perform a Project gt Backup command before doing a Project gt Delete command A scrollable alphabetized list of all known projects excluding the current project will appear Highlight the project of interest and click OK The message appears Delete all files in data directories and try to remove this directory Click Yes to continue No to abort The pro gram will delete all files in the working directory but not any subdirectories files in subdirecto ries or the calibration files in the calibration directory then it will remove the requested project 2 8 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 E EESE Select Project no default Enter the requested project name to delete working files and remove from the project database You cannot delete the current project No default
195. AX lt n gt BAX lt n gt CAX lt n gt Ul lt n gt U2 lt n gt U3 lt n gt FCELL lt n gt SIGA lt n gt NOREDUCE VERBOSE FGROUP lt n gt HKLTOL lt n gt FFIT lt n gt REFL ARRAY BRAVAIS 1 2 3 4 5 6 7 SIGA lt n gt SIGB lt n gt SIGC lt n gt SIGMA lt n gt SIGBEST lt n gt REFL ARRAY LEASTSO 1 2 3 4 5 6 7 DXC lt n gt DYC lt n gt DISTANCE lt n gt ROLL lt n gt YAW lt n gt Ul lt n gt U2 lt n gt U3 lt n gt HKLTOL lt n gt HALFWIDTH lt n gt MASK lt n gt PARNAME lt n gt REFL ARRAY EDIT REFL ARRAY MODIFY 1 2 FIELD lt n gt VALUE lt s gt REFL ARRAY SORT 1 2 FIELD N DESCENDING REFL ARRAY TRANSFORM 1 2 3 4 5 6 7 8 9 REFL ARRAY MATRIX 1 2 3 4 5 6 7 8 9 REFL ARRAY HCALC 1 2 3 4 5 6 7 8 9 REFL ARRAY CLEAR REFL ARRAY LOAD 1 REFL ARRAY RSPACE REFL ARRAY CDF 1 2 3 4 5 6 7 8 FORMULA lt s gt TYPE lt s gt FILE lt s gt VERBOSE REFL ARRAY SAVE 1 2 3 SAVE 1 TITLE lt s gt XENGEN DISPLAY lt n gt SCAN SINGLERUN 1 2THETA lt n gt THETAl lt n gt OMEGA lt n gt THETA2 lt n gt gt PHI lt n gt CHI lt n gt X lt n Y lt n gt Z lt n gt AUX lt n gt AXIS lt n gt WIDTH lt n gt SCANTIME lt n gt M86 E01008 G 5 SLAM Command Reference GADDS Software Reference Manual TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt n gt NAME lt s gt RUN lt s gt
196. AY lt n gt REALTIME FILE lt s gt XMIN lt n gt YMIN lt n gt MAG lt n gt SHUTTER This selection is used to collect a single frame of data for use in flood field calibration followed by automatic computation and installation of a new flood field correction based on that data The purpose of this calibration is to produce a smooth detector data image from a uniform spherically radiating point source such as the Fe gt source supplied with the system The cor rection works by slightly altering the POSI TIONS of counted photons according to a rubber sheet stretching shrinking in regions along the X and Y detector axes in order to make the Fe image more uniform It does not alter the recorded number of photons FLOOD NEW requires you to enter the approxi mate source to detector distance This distance should be the same as the sample to detector distance since in this case the source is at the sample position Make sure to remove all obstructions to the detector face such as the beam stop Note that the source distance is measured in cm from the flat front of the detec tor where the fiducial plate mounts Usually you should create a new flood field correction prior to data collection on each sample before the brass fiducial plate image is taken M86 E01008 Process Routines GADDS Software Reference Manual The best procedure for acquiring new flood field data is to accumulate 10 000
197. CTRL BREAK to interrupt the scan hard abort or immediate abort To ensure that nothing scrapes the sample sur face between drives GADDS may perform a one mm back drive utilizing three separate drives GADDS drives one mm down the Z axis then drives to the first target position minus one mm down then drives up one mm These extra drives are not performed when omega gt 10 degrees Unlike the MultiRuns command a MultiTargets sequence interrupted by CTRL BREAK or by a power failure can NOT be restarted where it left off with the Collect gt Scan gt Resume command M86 E01008 Collect Routines GADDS Software Reference Manual RESUME works only with MULTIRUN not MULTITARGETS Instead recollect starting at the scan series of the interrupted target position When you interrupt a scan with CTRL BREAK the goniometer returns to the starting scan angle of the current scan This re positioning is performed by backing up to the starting position minus one frame width or 0 5 maximum then driving forward to the starting position The same positioning technique is used when driv ing to the first scan in a new series It makes the positioning extremely repeatable but does require you to allow for an extra scan width at the beginning of the series when you re starting close to the goniometer collision limits SCAN MULTITARTGETS checks for possible collision at the extremes of all scans before beginning the first
198. D When invoked from the master menu or from the command line without arguments SPATIAL PROCESS displays an input panel where you can view edit the items described below prior to computing the spatial correction If you press the ENTER key or left mouse button when in this input panel the computation begins The ESC key or right mouse button returns you from the input panel to SPATIAL submenu When compu tation has started SPATIAL PROCESS dis plays the progress message on the bottom status line BUILDING CORRECTION TABLES Computations should be complete within a few seconds During this process SPATIAL PRO CESS automatically extracts positions of the fiducial spots from the input frame and based on the known positions of the corresponding holes in the fiducial plate computes a new spa tial correction In the course of processing the data it must index the rows and columns curved due to the pincushion distortion of fidu cial spots in order to match each spot with a hole of known position on the fiducial plate When the indexing is complete a graphic map of the fiducial spot positions extracted from the frame is drawn This graph is actually a GRAPH FILE of the plottable ASCII _ix spatial calibra tion file see below Dashed lines are drawn along the rows and columns of the indexed pat tern If a line jumps from one row or column to another the holes have been mis indexed and the spatial calibration will no
199. DDS Software Reference Manual the specified HKL reflection are to be com puted If you ve specified a scan axis of 3 see above any valid value is OK here Default is zero and valid range is 360 to 9999 GONG E Chi 0 00 Enter the chi goniometer angle in degrees at which the scan angle and detector X Y of the specified HKL reflection are to be com puted Default is zero and valid range is 360 to 9999 SO ania crete Frame Size 512 Enter number of linear pixels in a frame 512 or 1024 8 24 2 HCALC Output Example 8 6 below is an output window from REFL_ARRAY HCALC The output window starts with a line containing the input HKL indi ces followed by the two solutions if available The three non scan axes will contain the same values as you specified in the input panel The value of the scan axis that would place the spec ified HKL in the diffracting condition in degrees is also shown The X Y position in pixels in the Bruker convention with 0 0 at the left of a dis played frame is shown both in spatially cor rected coordinates X cor Y cor and in raw coordinates X raw Y raw If the corrected coordinates are too far outside the detector active area for raw coordinates to be computed the X raw Y raw columns contain the text OUTSIDE DETECTOR AREA Example 8 6 REFL_LARRAY HCALC Output Calculated positions for HKL Soln 2Theta Omega 1 30 00 15 45 0 00 2 30 00 162 07 0 00 Dete
200. DS software to be able to change the detector bias the PDC position decoding circuit must be in Detector Bias On Source Select Auto If the bias setting is incorrect when invoking either a Process gt Flood gt New a Process gt Spatial gt New or any Collect gt Scan command GADDS will prompt the user to switch to the cor rect bias setting before collecting the data Fe high bias is used by Flood and Spatial while Cu low bias is used for Scan commands 5 1 1 Arguments None Command executes immediately M86 E01008 Collect Routines GADDS Software Reference Manual 5 2 Collect gt Detector gt Fe Bias e Set PDC to Fe high bias setting Menu Command Collect gt Detector gt Fe bias Accelerator Ctrl Shift F User Level 1 SLAM Syntax DETECTOR FE Use this command to place the PDC and detec tor at the Fe high bias setting The action is performed immediately with no prompt for addi tional input The DETECTOR item in the goni ometer status area at the lower right of the display is updated to reflect the new bias status NOTE For the GADDS software to be able to change the detector bias the PDC position decoding circuit must be in Detector Bias On Source Select Auto If the bias setting is incorrect when invoking either a Process gt Flood gt New a Process gt Spatial gt New or any Collect gt Scan command GADDS will prompt the user to switch to the cor rect bias
201. E Chi override 9999 Enter the chi setting angle in degrees to be assumed for the frame series The default value 9999 specifies that chi is to be extracted from the frames themselves which is the normal mode of operation If M86 E01008 Peaks Routines GADDS Software Reference Manual you re processing old XENGEN format frames acquired with software earlier than FRAMBO Version 2 you ll need to explicitly specify the angle here For frames in XEN GEN or BRUKER format acquired with FRAMBO V2 or higher specify 9999 Pfr EEOC Scan axis override 9999 Enter the scan axis number 2 for omega 3 for phi to be assumed for the frame series The default value 9999 specifies that the scan axis is to be extracted from the frames themselves which is the normal mode of operation If you re processing old XEN GEN format frames acquired with software earlier than FRAMBO Version 2 you ll need to explicitly specify the axis here For frames in XENGEN or BRUKER format acquired with FRAMBO V2 or higher specify 9999 DOr diate Frame width override 9999 Enter the signed frame width in degrees to be assumed for the frame series The default value 9999 specifies that the width is to be extracted from the frames them selves which is the normal mode of opera tion If you re processing old XENGEN format frames acquired with software ear lier than FRAMBO Version 2 you ll need to explicitly specify the width
202. FRAMENO lt s gt DISPLAY lt n gt REALTIME CLEAR OLDXENGEN MODE lt n gt ROTATE VIDEO OSCILLATE lt s gt AMPLITUDE lt n gt SNAME lt s gt SRUN lt n gt SFRAME lt s gt SCAN EDITRUNS interactive command only SCAN MULTIRUN 1 TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt n gt DISPLAY lt n gt REALTIME CLEAR OLDXENGEN STARTRUN lt n gt ENDRUN lt n gt MODE lt n gt ROTATE VIDEO OSCILLATE lt s gt AMPLITUDE lt n gt SNAME lt s gt SCAN RESUMERUNS 1 TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt s gt DISPLAY lt n gt REALTIME CLEAR OLDXENGEN STARTRUN lt n gt ENDRUN lt n gt MODE lt n gt ROTATE VIDEO 2 SNAME lt s gt 2THETA lt n gt THETA1 lt n gt OMEGA lt n gt THETA2 lt n gt PHI lt n gt CHI lt n gt X lt n gt Y lt n gt Z lt n gt AUX lt n gt AXIS lt n gt WIDTH lt n gt SCANTIME lt n gt RUN lt s gt FRAMENO lt s gt 3 SCAN ROTATION 1 TTZERO PHI lt n gt CHI lt n gt DISPLAY lt n gt REALTIME RESET lt n gt SCAN HKL 1 2 3 SCANTIME lt n gt TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt n gt NAME lt s gt RUN lt s gt FRAMENO lt s gt DISPLAY lt n gt REALTIME SCAN PSI 1 2 SCANTIME lt n gt TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt n gt NAME lt s gt RUN lt s gt FRAMENO lt s gt DISPLAY lt n gt REALTIME SCAN COUPLED 1 2 3 WIDTH lt n gt SCANTIME lt n gt TITLE lt s gt SAMPLE
203. GADDS Administrators Manual for e Pre installation installation alignment and calibration instructions e Flood field spatial and beam center instructions e Software installation and release notes e Software customization instructions e Test procedures e General maintenance e Bruker service M86 E01008 General Information GADDS Software Reference Manual 1 1 Program Overview GADDS is part of a suite of programs available from Bruker AXS Inc for using an Area Detec tor for powder diffraction problems In addition to the GADDS software optional packages are DIFFRAC S TOPAS P SAXS ASTRO etc The functions of these programs are briefly summarized as follows GADDS is the essential instrument control and data acquisition program which controls all hardware functions associated with the multi wire based X ray diffractometer sys tems It contains a comprehensive set of online and off line functions and algorithms for instrument calibration specimen screen ing and frame data acquisition GADDS also includes an option to display ICDD PDF2 database patterns and search the NIST database of known unit cell dimen sions These features will be described in detail in this manual ASTRO is a supplementary utility program that may be used in conjunction with the GADDS program to optimize data collection strategies for single crystal type applica tions Use it to minimize data collection time by colle
204. GADDS Software Reference Manual If you get too many matches decrease the DECIMAL FRACTION DEVIATION The output information includes the reduced unknown cell the reduced Crystal Data Cell the chemical name and the literature reference 8 29 Peaks gt Refl Array gt Save Save the reflection array in a p4p file Menu Command Peaks gt Refl Array gt Save Accelerator None User Level 1 SLAM Syntax REFL_ARRAY SAVE Save the current reflection array and other rele vant information in a P4P file for use by other programs such as SHELXTL While Least Squares will automatically create a P4P file after manual editing of the reflection list you may wish to update the P4P file The file name is taken from the current data set name As the command executes you will see the messages OK to create XXXX P4P Yes No Overwrite XXXX P4P Yes No Created Updated XXX P4P 8 29 1 Arguments None Command executes after confirmation M86 E01008 9 Special Routines 9 1 Special gt PDF2 gt View e View PDF2 card on screen Menu Command Special gt PDF2 gt View Accelerator None User Level 1 SLAM Syntax PDF2 VIEW 1 NBS AIDS TYPE lt n gt The PDF2 VIEW command can scroll through selected PDF patterns in either pretty format or in the native NBS AIDS format 9 1 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in paren
205. H lt n gt Frame Width from resume _tm Enter the scan width of each frame to be acquired in degrees This value can be either positive or negative Thus the starting scan angle for the Nth frame in the series where the first frame is N 0 is OMEGA N WIDTH if AXIS above is 2 or PHI N WIDTH if AXIS above is 3 where WIDTH OMEGA and PHI are the values given here on this line of the array M86 E01008 Collect Routines GADDS Software Reference Manual SCANTIME lt n gt Seconds Frame from resume _tm Enter the time in seconds for which each frame is to be acquired You can optionally specify long times in the format HH MM SS SS where HH represents hours MM minutes and SS SS decimal seconds RUN lt S gt eee Run from resume _tm Enter the RUN of the interrupted scan series Make sure it matches the current RUNBASE and RUNCHARS defined in the Edit gt Config dialog FRAMENO lt s gt Frame from resume _tm Enter the Frame Number of first incomplete frame in the interrupted scan series Make sure it matches the current NUMBASE and NUMCHARS defined in the Edit gt Config dialog 8 eit cents Interrupted Run to Resume from resume _tm Enter run line to resume 0 if no run in progress M86 E01008 GADDS Software Reference Manual Collect Routines 5 34 Collect gt Scan gt Rotation Take a phi rotation picture Menu Command Collect gt Scan
206. IELD lt n gt Sort Field 1 Specifies number of the column you want to sort on Column numbers are Field Description Flags for example ACHSX H index K index L index 2 Theta setting swing angle Omega setting angle Phi setting angle Chi setting angle Detector X pixel coordinate 0 Detector Y pixel coordinate ON DOA fF ON Intensity N I sigma DESCENDING Descending Y N No If you enter Y for this item on the input panel or if this qualifier is present on the command line the sort is in descending order otherwise it is in ascending order M86 E01008 Peaks Routines GADDS Software Reference Manual 8 22 Peaks gt Refl Array gt Transform e Transform HKLs in array according to specified 3x3 matrix Menu Command Peaks gt Refl Array gt Transform Accelerator None User Level 1 SLAM Syntax REFL_LARRAY TRANSFORM 1 2 3 4 5 6 7 8 9 REFL_ARRAY TRANSFORM lets you enter the nine elements of a specific HKL transformation matrix and transforms the HKL indices of all indexed reflections i e those whose H flag is set in the Reflection Array by that matrix The input matrix pre multiplies a column HKL vector formed from each input HKL to yield a column vector containing the transformed HKL You would use this function for example if you needed to use a non standard space group set ting e g orthorhombic with the B axis long
207. IXELS PROCESS 1 2 3 4 5 6 7 LOCAL Used by Bruker manufacturing and service engi neers to evaluate detector for aberrations in pixel sensitivity 6 5 1 Evaluation Region Used to determine the area of the frame to eval uate for bad pixels Radius from detector center not beam center should be around 260 for 512 frames or 520 for 1024 frames A circle will be drawn at this radius so you can visual see if you re off Border pixels determine how many rows around the border of the frame should be ignored O ingore only the overflow row 15t and last The algorithm will average the total pixels at each radius from the detector center excluding border pixels up to and including the requested radius then apply a three point smoothing func tion This produces a function of the expected intensity versus distance from detector center Alternately one can use a local average calcu lated using a box 15x15 for 512 frames 31x31 for 1024 frames where the center 3x3 box is excluded from the calculations 6 5 2 Bad Pixel Criteria The user enters the weakness criteria in per centage at the center of the detector and the weakness criteria at the entered radius to evalu ate The program assumes the weakness crite ria function is linear with respect to radius from center Here a pixel at the center must be within 85 of the average intensity to be considered good A pixel near the edge only needs to be within 75 to be co
208. Job Name for frames stored locally can contain a DOS drive and directory name if desired The output filename is except in the special cases discussed below merged with the default frame directory defined in the CONFIGURE EDIT panel prior to creat ing the output frame See CONFIGURE EDIT for a description of how this is done There are two special Job Name cases The first NET is NOT supported under GADDS The second special Job Name is NULL In this case the frames are not out put they are thrown away RUN lt S gt 0006 Run 0 The Run Number of the series This is not actually a number but is rather taken as RUNCHARS characters of ASCII text where RUNCHARS is defined in the CON FIGURE EDIT input panel to be used as the last RUNCHARS characters of the out put base filename i e the last RUN CHARS characters before the extension Make sure that these values and the frame naming parameters in CONFIGURE EDIT are set the way you want before starting to scan as described above 66 M86 E01008 GADDS Software Reference Manual Collect Routines FRAMENUM lt s gt Frame 000 This is the starting frame number for the series defined by this line of the array Make sure it conforms to the frame naming parameters currently set in CONFIGURE EDIT Like the Run Number this is actually taken as text rather than a numeric value The text specified here will be used as the extension
209. K Large CCD CCD PXL ARR Mosaic CCD PXL L6000 CCD PXL KAF1500 UNKNOWN imported OTHER imported 8 8 C 2R Version 8 Added sub mnemonics PIXPERCM and CMTO GRID which are needed for UNKNOWN or OTHER types If these values are missing the defaults are DETTYPE PIXPERCM CMTOGRID MULTIWIRE47 52 0 CCD PXL 2K56 020 8 CCD PXL ARR32 000 4 CCD PXL KAF150051 20 8 CCD PXL L6000N56 020 8 CCD PXL L6000F56 020 8 CCD PXL L6500 32 001 5 CCD PXL KAF281 920 8 CCD PXL KAF 81 920 8 CCD PXL MSPD 81 920 8 CCD PXL 81 920 8 CCD PXL LDI 83 3330 0 CCD MMxXImported frames must ask for settings UNKNOWN Imported frames must ask for settings OTHER Imported frames must ask for settings NEXP 79 7 9 10 7 Int Number of exposures 1 single 2 correlated sum 9 2int followed by fixed bias ADU in Vers 9 10 3Int 9 Adds per exposure bias level in ADU to NEXP line 10 Adds baseline offset normally 32 Adds Orientation value of SAXISINVERTCCD Adds Overscan flag 1 if overscan used CCDPARM 80 7 5R CCD parameters readnoise e ADU e photon bias full scale CHEM 81 7 C Chemical formula in CIFTAB string such as MORPH 82 7 C Crystal morphology in CIFTAB string such as A 8 M86 E01008 GADDS Software Reference Manual Area Detector Frame Format CCOLOR 83 7 Cc Crystal color in CIFTAB string such as CSIZE 84 7 C Crys
210. LA file format for ODF calculations or other processing with those or other software packages See appendices for the format of these data files A 3 x 3 pixel region is averaged before writing to a TEX TURE AT file ODF AT performs an ODF using harmonic methods which represents the ODF as a weighted sum of spherical harmonic functions chosen so as to possess the symmetry of both the specimen and the crystal system Unfortu nately the spherical harmonic expansion can lead to non physical results because the best fit ODF may exhibit regions in which the values are negative which is nonsense for a probability density function Such problems particularly arise in cases where the ODF is sharply peaked thus the harmonic method is more suited to ODFs which are not sharply peaked 7 25 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Slee eae ae Texture AT File Output filename for TEXTURE AT data file Extension defaults to either trw transmis sion or rrw reflection texture TITLE lt n gt Title title Title for data file HKL lt n gt 06 HKL 100 hkl of this pole APPEND Append Y N No Y to add this pole figure to an existing TEX TURE AT file N to deleted any existing file and create a new TEXTURE AT file For ODF calculations two or three poles must be collected in the same TEXTURE
211. LPHA BETA GAMMA values as described above This is NOT recommended for general operation since it bypasses a very important step in determination of the correct unit cell How ever in cases which are difficult to index the additional constraints supplied by the known cell angles used only when NORE DUCE is in effect may help and in cases of 8 36 M86 E01008 GADDS Software Reference Manual Peaks Routines known cells with centered lattices NORE DUCE enables you to index on the centered lattice directly and bypass the extra Bravais lattice transformation step again NOT a good thing to do unless you re very sure that your input cell is the correct one VERBOSE Verbose Output Y N Yes 1 Specifies that long form indexing output is desired If this qualifier is set i e Y in the input panel or present on the command line the first output window contains lists of the difference vectors and full vectors and the second output window contains a reflec tion by reflection listing of observed versus calculated HKL s and scan angles other wise these lists are not written The default in the input panel is Y a ATEAREN Minimum Vectors in Group 2 The small integer value you specify here determines how many difference vectors with nearly identical components must be found before the difference vectors will be included in the autoindexing The vectors in an
212. M86 E01008 GADDS Software Reference Manual SLAM Routines PEAKS POSTER DRAW When you choose PEAKS POSTER DRAW from the menu bar GADDS displays a pop up submenu containing these subcommands EXIT Close the DRAW submenu and return to the POSTER menu ARROW Draw an arrow pointer BOX Draw a rectangular box CIRCLE Draw an ellipse DOT Draw a single dot LINE Draw a straight line STYLE Switch between solid and dashed line styles PEAKS POSTER DRAW ARROW PEAKS POSTER DRAW ARROW is used to draw an arrow When selected a crosshair is visible To draw an arrow 1 Use the mouse to position the crosshairs at the point of the arrow to be drawn and press ENTER The crosshairs are replaced with an arrow that has the point anchored at the selected position and the tail at the cursor position Position the tail of the arrow and press ENTER The arrow is drawn anda crosshairs cursor appears to position the next arrow When you are finished press ESC to return to the DRAW menu PEAKS POSTER DRAW BOX PEAKS POSTER DRAW BOx is used to draw a rectangular box When selected a crosshair cursor is visible To draw a box 1 Use the mouse to position the crosshairs at a corner of the box to be drawn Press ENTER to anchor the corner The crosshairs are replaced with a rectangular box with one corner at the anchored point just selected and the other corner at the cur rent cursor position Position the second box corner
213. MESIZE field Storage requirements per 512 x 512 frames range from 256K bytes 8 bits per pixel to 1 Mbyte 32 bits per pixel GADDS automatically com presses frames this compression results in no data loss and usually results in storage close to 256K bytes or close to 512K bytes if enough diffraction lines are high enough that it cannot be contained in 8 bits pixel 1024 x 1024 frames require four times this amount of storage Acquiring and process ing larger frames is slower but will improve integration results so it is highly recom mended to use 1024 frames for power dif fraction work DISTANCE lt n gt Sample Detector Dis tance current value Enter current nominal sample to detector distance in centimeters The default setting is 12 00 cm It is important that you enter the correct value here whenever you change the detector distance The value is stored in the header of any output frames created in Bruker format and is used by the flood field and spatial corrections the interactive cur sor commands integration commands and all the Reflection Array commands that deal with crystal orientation The distance is also written to output p4p files On systems with a motorized delta axis use the Collect gt Goniometer gt Det Stage com mand to move the detector distance M86 E01008 GADDS Software Reference Manual Edit Routines 4 2 Edit gt Configure gt Admin settings View edit the current
214. MPLE lt s gt NUMSAMPLE lt n gt NAME lt s gt RUN lt s gt FRAMENO lt s gt DISPLAY lt n gt REAL TIME SCAN HKL will collect a frame series for later processing with GRAPH HKL When invoked from the command line SCAN HKL can take the following arguments where lt n gt represents a numeric value and amp indicates continuation on the next line 5 35 1 Arguments Each argument is listed below by its command line name followed by its input panel prompt in parentheses BA ENE Starting HKL 5 1 5 1 5 Enter starting hkl value May be reals PRE Ending HKL 5 2 5 2 5 Enter ending hkl value May be reals GB AREE ATO Frames 101 Number of frames to be acquired in this series Make sure it doesn t exceed the number permitted by FRAME above in conjunction with the frame naming parame ters in the CONFIGURE EDIT panel SCANTIME lt n gt Seconds Frame 1 00 00 Time in seconds for which each frame is to be acquired You can optionally specify long times in the format HH MM SS SS where HH represents hours MM minutes and SS SS decimal seconds TITLE lt S gt Title Scan HKL frame Enter title for output frames 80 characters maximum The default entry is Scan Frame If you invoked this command from the command line you must enclose any title continuing embedded blanks in double quotes M86 E01008 Collect Routines GADDS Software Reference Manual
215. N No Check this option to wait for the generator to reach the desired settings or leave it unchecked to return to the GADDS menu immediately after sending the new settings to the generator current setting or 0 current setting or 0 M86 E01008 Collect Routines GADDS Software Reference Manual 5 23 Collect gt Goniometer gt Det Stage Drive delta axis Menu Command Collect gt Goniometer gt Det Stage Accelerator none User Level 3 SLAM Syntax GONIOMETER DETECTOR 1 Use this command to operate the delta axis detector distance on systems with a motorized delta axis Only Phoenix controllers support a delta axis The minimum and maximum values are taken from the current software collision limit settings see Collect gt Goniometer gt Limits Section 5 15 5 23 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses A E EE Delta current setting Enter the destination delta axis detector distance in cm 5 24 Collect gt Goniometer gt Fixed axes Set reported settings for non controllable axes Menu Command Collect gt Goniometer gt Fixed axes Accelerator none User Level 2 SLAM Syntax GONIOMETER FIXEDAXES 1 2 3 4 5 6 7 8 Use this command to defined the current angles positions of the fixed non controllable axes Collect gt Goniometer gt Fixedaxes dis plays an input panel where y
216. NAME lt s gt FORMAT lt s gt APPEND SCALE lt n gt See Peaks gt Integrate gt Write command 7 14 Analyze gt Percent Crystal gt External e Amorphous region external from Bragg peak Menu Command Analyze gt Percent Crystal gt External Accelerator None User Level 1 SLAM Syntax PER_CRYSTAL EXTERNAL 1 2 3 4 5 6 7 8 COMPTON PER_CRYSTAL provides a quick method to esti mate a percent crystallinity using frame data Frames must have air scatter and sample holder scattering effects subtracted out to obtain meaningful results Calculates percent crystallinity within an user defined region The user must specify both an amorphous only region and a crystalline plus amorphous region These regions should not overlap Pixels are summed in both regions With the separation of amorphous and crystal line contributions the percent crystallinity calcu lation is simply a Te gt Di par C 100 where C percent crystallinity M86 E01008 Analyze Routines GADDS Software Reference Manual intensity in crystalline region intensity in amorphous region 7 14 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 Two Theta Begin for Amorphous Reg 2 Two Theta End for Amorphous Reg 3 Chi Begin for Amorphous Region 0 4 Chi End for Amorphous Region 30 Defines conic region
217. NS DISPLAY FRAME_INFO POLE_FIGURE SPATIAL SMOOTH MASK VIEW obsolete DISPLAY LOAD MASK READ MASK SAVE POLE_FIGURE SCHEME SAVE Purpose To read the currently loaded peak table To read the currently loaded frame image To read the currently loaded active pixel mask Unused avoid using NET in filenames Display the next frame in a frame series Read or save a null file Symbol PREV RUNNEXT RUNPREV SCAN TITLE Where used DISPLAY DISPLAY Display POLE_FIG SCHEME POLE_FIG POPLA POLE_FIG TEXTUREAT SAVE Purpose Display the previous frame in a frame series Displays the next frame in a run series Displays the previous frame in a run series Automatically update the SCAN EDIT pan els for multiple runs When saving a file keep the original title string M86 E01008 2 Project Management Routines Project management is the organization of data files into logical groups Typically you will create a new project to start a new sample run a new batch of samples etc when to start a new project is really a user preference or a defined step in a laboratory procedure for example an ISO 9000 procedure GADDS manages and tracks all projects by using project files prj All users can share the same projects or each user can have their own unique projects When GADDS was installed SETUP created a system wide project file for all u
218. ODE lt n gt ROTATE VIDEO OSCILLATE lt s gt AMPLITUDE lt n gt 2 SNAME lt s gt 2THETA lt n gt THETA1 lt n gt OMEGA lt n gt THETA2 lt n gt PHIl lt n gt CHl lt n gt X lt n gt Y lt n gt Z lt n gt AUX lt n gt AX S lt n gt WIDTH lt n gt SCANTIME lt n gt RUN lt s gt FRAMENO lt s gt 3 This command will restart a scan sequence interrupted manually with CTRL BREAK or ESC or by power failure where it left off The command applies to scans acquired by Collect gt Scan gt MultiRun but not those by Collect gt Scan gt SingleScan GADDS updates the scan parameters in a disk file RESUME _TM at the start of each scan The updating procedure explicitly closes the file to ensure that the information is written to the disk drive GADDS uses this updated parameter information in resume _tm to restart the sequence When invoked from the menu or run from the command line without arguments Collect gt Scan gt Resume displays a dialog box where you can view edit the arguments described below The displayed defaults in this panel are read from the RESUME _TM file and should correspond to the state of the system when scanning was interrupted that is they should correspond to the first incomplete frame You should review edit if necessary these values before restarting data collection Pressing ENTER or clicking the OK button resumes data collection Pressing ESC or the Can
219. OERASE by reissuing the command with the same parameters The CLEAR com mand also provides a way to erase cursors left over from NOERASE options The following output statistics are displayed on screen in real time and are also written to the logfile if applicable Counts Counts at current pixel XY Pixel X and Y coordinate of current pixel range from 0 to framesize 1 with origin X 0 Y 0 being located at lower left of screen 2 Theta 2 Theta value of Debye Scherrer ring at cur rent pixel Angstrms Angstroms of Debye Scherrer ring at cur rent pixel Lambda Wavelength used to calculate statistics Chi Chi value of Debye Scherrer ring at current pixel M86 E01008 GADDS Software Reference Manual Analyze Routines 7 6 Analyze gt Cursors gt Rbox Display statistics of pixels in rotated rectangular region Menu Command Analyze gt Cursors gt Rbox Accelerator F10 User Level 1 SLAM Syntax CURSORS RBOX 1 2 3 4 DELAY lt n gt NOERASE When invoked with the RBOX option from the CURSORS submenu or when run from the com mand line without arguments CURSORS RBOX starts running directly that is there are no items to be filled in on an input panel A rect angular cursor from 2x2 to 128x128 pixels in size appears in the detector frame area and can be moved or re sized under control of the mouse and or keyboard arrow keys Pressing the ENTER key or left mouse butt
220. OIN detecta sigs wv bisenvee eG we T leas E PAE OEE EAE AE E E E MRE a 5 71 5 3751 ArQUMENIS nasere kea age a a a des tale T a a DEE E A 5 71 5 38 Collect gt Scan gt ZonePhoto Acquire a rotational photo along a zone OKL HOL HKO 5 73 5 38 31 ArQuMents rore a T OSE R E E E EE E OO en A E A Ga 5 73 5 39 Collect gt Scan gt Axial Image Acquire a frame showing A B or C axial image 5 74 SILTANEN wines ede aea heta peak etd ade a a ple die e Vallee ad ee 5 74 5 40 Collect gt Scan gt PickTargets Manually drive and select target positions for Muti Target list i sche ties ve Sea ee Pe eee Moni wea ed E DE beet ay ag 5 75 5 40 A ArQUMENTS cog ireen Bei Pt ne eee oe Re anette PG ws Sette ee ped gay OE EARE 5 75 5 41 Collect gt Scan gt GridTargets Set up grid for MultiTarget list 0 5 76 SALTAM witb dt dart coast pai bali entnd atiigt tite teenage ad beas de Bete Ae 5 76 5 42 Collect gt Scan gt LineTargets Set up line for MultiTarget list 0 5 77 524251 AUMENS rop EE eee eae on epee ane aed AOE a aie ne hai enn ee a 5 77 5 43 Collect gt Scan gt EditTargets Edit parameters for MultiTarget scans 5 78 5 43 TALQUMONIS e325 ioe sin anes et alata dees be ate wy ected We ahd ane Pea dea a aur wae dee 5 80 5 44 Collect gt Scan gt MultiTargets Perform same scans on multiple targets on a Single Sample or iera snr Lene A PEREIRAN EEA ie thes eal eee eee
221. OMBIC P Body centered tetragonal Primitive tetragonal Face centered orthorhombic Body centered orthorhombic C centered orthorhombic Primitive orthorhombic MONOCLINIC C C centered monoclinic MONOCLINIC P Primitive monoclinic TRICLINIC P Primitive triclinic If for some reason you need to use a different non standard setting you can use REFL_ARRAY TRANSFOR M to transform the HKL indices in the reflection array prior to run ning the LEASTSQUARES sub command When invoked with the BRAVAIS option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY BRAVAIS displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins refinement of the unit cell and orientation parameters the ESC key or right mouse button returns you to the REFL_ARRAY submenu When refinement starts the program displays the message PERFORMING LATTICE SEARCH on the bottom status line The deter mination should usually be completed within a second or two Upon completion a scrolling out put window is displayed containing the resulting output text If logging is enabled see LOGFILE the contents of this window are also written to the logfile When viewing the output pressing ENTER or the left mouse button displays a pop up menu of options including export of ASCII data for example the contents of the window could be sent
222. OX computa tions to be performed once at a single specified position after which control returns immediately to the command line If logging is turned on see the LOGFILE com mand for more information the quantities com puted for the final position of the cursor prior to exiting the command are written to the output logfile If scripting is enabled again see LOG FILE a non interactive CURSORS command corresponding to the final cursor position is writ ten to the output script file M86 E01008 Analyze Routines GADDS Software Reference Manual The SLAM command arguments are 1 The X coordinate of the center of the box in pixels The range is from 0 to framesize 1 default value is 256 2 The Y coordinate of the center of the box in pixels The range is from 0 to framesize 1 default value is 256 3 The width of the box in pixels The range is from 0 to 128 default value is 32 4 The height of the box in pixels The range is from 0 to 128 default value is 32 DELAY lt n gt Specifies a time interval in seconds to wait before erasing the cursor and returning con trol to the program This is for use in scripts where it is desirable for the cursor to remain on screen long enough for the user to dis cern its position NOERASE Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor
223. PONENT n where the arguments are 1 2THETA Exponent n EXPONENT PEAKS SIMULATE ASYMCAUCHY When started from the command line PEAKS SIMULATE ASYMCAUCHY takes the following arguments PEAKS SIMULATE ASYMCAUCHY 1 LOWEXP n HIGHEXP n where the arguments are 1 2THETA LOWEXP N EXPONENT HIGHEXP N EXPONENT PEAKS SIMULATE PSEUDO When started from the command line PEAKS SIMULATE PSEUDO takes the following argu ments PEAKS SIMULATE PSEUDO 1 FRACTION n where the arguments are 1 2THETA FRACTION n CAUCHY FRACTION 12 22 M86 E01008 GADDS Software Reference Manual SLAM Routines PEAKS SIMULATE PEARSON When started from the command line PEAKS SIMULATE PEARSON takes the following argu ments PEAKS SIMULATE PEARSON 1 EXPONENT n where the arguments are 1 2THETA EXPONENT n EXPONENT PEAKS SIMULATE SPLIT When started from the command line PEAKS SIMULATE SPLIT takes the following argu ments PEAKS SIMULATE SPLIT 1 LOWEXP n HIGHEXP n where the arguments are 1 2THETA LOWEXP n EXPONENT HIGHEXP n EXPONENT PEAKS SIMULATE COSINE When started from the command line PEAKS SIMULATE COSINE takes the following argu ment PEAKS SIMULATE COSINE 1 where the argument is 1 2THETA M86 E01008 12 23 SLAM Routines GADDS Software Reference Manual 12 4 10 PEAKS VIEW VIEW display
224. R input panel If you supply values for the items in this panel pressing the ENTER key or left mouse button begins a RATEMETER operation during which the goniometer remains under control of the manual box This is most useful during instrument alignment with or without the M86 E01008 GADDS Software Reference Manual Collect Routines RESET option to observe changes in the x ray pattern in real time as the goniometer angles are changed If you want to terminate the RATE METER early use the CTRL BREAK key combi nation which returns you to manual mode as will the ESC key or right mouse button pressed while in the RATEMETER input panel While you re controlling the goniometer manu ally the setting angles displayed in the goniome ter status area on the lower right of the screen are not updated in real time However if you press the ENTER on Phoenix controller s or AXIS PRINTOUT button on the GGCS control lers manual control box the values on the screen will be updated to reflect the current angles VIDEO will also be updated with new zoom and XYZ values On the Phoenix control ler you can also press the ACVAL key to display the current angles on the manual control box s LCD The display is also updated automatically when you exit manual mode To operate the manual control box on the Phoe nix controller D8 Discover systems press SHIFT F1 then select the requested axis by pressing 1 for 20 2 for 3 fo
225. R TIFF format for Coreco or JPEG format for The startup command line switch character Maier bRemale optlons arg can be defined as the translation of this 0 TIFF format stored with tif extension name By default SAXISSWCHAR lead Coreco or MIL format stored with mim ing to the default DOS style parsing You extension Walton can set SAXISSWCHAR to change to 1 BMP format stored with bmp extension UNIX style switches The command syn Goreco OF Matrox tax is otherwise the same only the charac 2 TARGA format stored with tga extension ter which precedes the qualifiers is Coreco only changed SAXI SWCHAR affects interpre 3 JPEG format stored with jpg extension tation of only the startup command line not Matrox only the SLAM command line We recommend SAXI 512MAXOVF that you retain the switch character set ting Restricts frame file format to contain a maxi mum overflow table size of 512 bytes for SAXISUSERNAME compatibility with other older software pack The user name given here becomes the ages default name on the GADDS Edit gt Config ure gt User settings command form Under WNT this defaults to the RegisteredOwner name in the Registry M86 E01008 1 9 General Information GADDS Software Reference Manual 1 3 Startup Command Qualifiers The following qualifiers can additionally be given when starting GADDS It is assumed that the qualifier switch character has not been cha
226. REFL_ARRAY PICK where a rectangular cursor like the one in CURSORS BOX is used to select a region within the data frame From this the program calculates the background subtracted intensity for that region in each frame If FRAME HALFWIDTH is greater than zero that is if intensity was obtained from more than a single frame the program also displays the results in a plot of intensity versus scan angle Background sub tracted intensity is determined in the same way as for CURSORS BOX The background is computed as the average of the points on the perimeter of the box excluding those points which are more than 3 standard deviations above the mean You have to be careful to choose the correct box size since in some cases the X Y centroid of the x ray reflection may change as a function of scan angle When invoked with the PICK option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY PICK displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins interactive region of interest selection with a box cursor The ESC key or right mouse button returns you from the input panel to the REFL_ARRAY submenu When you re selecting a region of interest a rectangular cursor from 2x2 to 128x128 pixels in size appears in the detector frame area and can be moved or re sized under control of the mouse and or keyb
227. RESHOLD displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins refinement of the unit cell and orientation parameters the ESC key or right mouse button returns you to the REFL_ARRAY submenu You can interrupt thresholding in progress with the CTRL BREAK key combination When thresholding starts the program displays the name of the last frame thresholded and the number of spots found on the bottom status line Note that if the number of spots per frame is larger than 512 N where N is the number of frames being thresholded your threshold is too low or you re thresholding too many frames Autoindexing and least squares run optimally if they have at least 25 and preferably 50 100 centered spots more is overkill The recom mended procedure prior to indexing but after the detector distance flood field correction spa tial correction and beam center have been determined is to threshold about half the desired number of spots from a few frames say 10 contiguous frames into a blank Reflection Array and then repeat the procedure with another series of 10 frames starting about 90 degrees in scan angle from the first set After all frames have been read in the program requires a few seconds to compute integrated intensities and sort the output Upon comple tion a scrolling output window is displayed con taining the resulting output tex
228. Reference Manual EDIT Like the Run Number this is actually taken as text rather than a numeric value The text specified here will be used as the extension of the first output frame in the series and will be incremented according to the frame naming parameters to form the extensions of subsequent frames DISPLAY lt n gt Max Display Counts 31 0 no display otherwise counts corre sponding to white on the display SAVE will optionally display the data being saved using this value as the upper display limit see DISPLAY NEW for more details The default value is 16 the allowed range is from 0 to 10 counts REAL TIME Real time Display Y N Yes This qualifier when present displays data as it is being collected The display does require additional processing time and will limit the maximum rate at which counts can be accumulated If the MAX DISPLAYED COUNTS qualifier is given a non zero value the frame will be automatically displayed at the end of each scan if real time display is off This latter display method has no effect on observed data rate Unless your data rate is very low it is better NOT to use real time display in the course of a SCAN com mand even though the default here is Y While real time display is active you can change the upper display limit using the plus key to increase or the minus key to decrease the current limit by a factor of two the range is 7 to
229. Routines delete any existing file s and create a new one range raw data file s SCALE o n a Scale Factor 1 0 Enter multiplicative scale factor or 1 0 for none The entire range of the written raw data file will be multiplied by this scale fac 8 12 Peaks gt Integrate gt Clear Clear graph on top of image Menu Command Peaks gt Integrate gt Clear Accelerator None User Level 1 tor SLAM Syntax INTEGRATE CLEAR INTEGRATE CLEAR will remove the results from the previous integration from the screen without erasing the data frame 8 12 1 Arguments None Command executes immediately M86 E01008 8 17 Peaks Routines GADDS Software Reference Manual 8 13 Peaks gt Integrate gt Rectangle VERTICLE Verticle Y N Yes Perform rectangle integration for Check to integrate vertical uncheck to inte detector testing grate horizontal Menu Command Peaks gt Integrate gt Rectangle Accelerator None User Level 1 SLAM Syntax INTEGRATE RECTANGLE 1 2 3 4 VERTICAL Use this command to sum pixel intensities along either the vertical or horizontal directions Useful for diagnostic purposes mainly 8 13 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 whe Geren X start 1 X pixel of rectangle left side 2 cs eee Xend 510 X pixel of rectangle right side 3 cniaei aie Y start 1 Y
230. Runs Run Frame 2 Theta Omega Phi Chi Axis Width Frames Time 0 001 28 00 28 00 0 00 30 00 3 300 1250 10 00 1 001 28 00 43 00 0 00 280 00 2 300 100 10 00 2 001 28 00 43 00 90 00 280 00 2 300 100 10 00 3 001 28 00 43 00 180 00 280 00 2 300 100 10 00 4 001 28 00 43 00 270 00 280 00 2 300 100 10 00 Before performing a scan with the above runs ensure that they agree with the collision limits see Collect gt Goniometer gt Limits for your par ticular system These runs are valid for both Mo and Cu radia tion However Cu data will be complete to a lower resolution For a Platform goniometer a good strategy for collecting higher resolution shells is to swing the detector out farther and interleave the higher resolution scans approxi mately 45 in chi relative to the low resolution scans putting them in the cusps at the outer edges of the low resolution scans You will have to modify this strategy a little for example by trial and error in ASTRO due to potential omega 2theta collisions M86 E01008 GADDS Software Reference Manual Collect Routines 5 33 Collect gt Scan gt ResumeRuns Resume interrupted MultiRun scans Menu Command Collect gt Scan gt ResumeR uns Accelerator None User Level 1 SLAM Syntax SCAN RESUMERUNS 1 TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt s gt DISPLAY lt n gt REAL TIME CLEAR OLDXENGEN STARTRUN lt n gt ENDRUN lt n gt M
231. SQ ignore it These are the X and Y centroids of the reflection on this line in the Bruker pixel coordinate convention THRESHOLD and PICK automatically enter these values into the array If a spatial correction is in effect at the time the entered X Y values are cor rected for spatial distortion and the S flag is set otherwise raw X Y values are entered and the S flag is not set If X and Y are not available for a reflection INDEX and LEASTSQ ignore it INORM This is the normalized intensity for the reflection THRESHOLD and PICK auto matically enter this value into the array The intensity is normalized to 1 deg min scan velocity SIGMA This is the ratio of the reflection intensity to its standard deviation THRESHOLD and PICK automatically enter this value into the array THRESHOLD uses I SIGMA modi fied by a specified sin theta bias as a sort key and reflections entered automatically be THRESHOLD are thus approximately in order of decreasing I SIGMA with cen tered reflections coming before uncen tered reflections M86 E01008 Peaks Routines GADDS Software Reference Manual 8 19 1 Line Editing You can edit text within a line with the same functions used to edit text in an input panel The data you enter on each line is read validated and reformatted according to the flags you sup ply at the beginning of the line For a given com bination of flags the program expects ther
232. Sequence number of this frame in series 0 NFRAMES 36 1 Int Total number of frames in the series ANGLES 37 1 4R Diffractometer angles 2T OM PH CH NOVER64 38 1 Int Number of pixels gt 64K M86 E01008 A 5 Area Detector Frame Format GADDS Software Reference Manual NPIXELB 39 1 Int Number of bytes pixel such as 1 2 or 4 NROWS 40 1 Int Number of rasters in frame such as 512 1024 or 2048 NCOLS 41 1 Int Number of pixels raster such as 512 1024 or 2048 WORDORD 42 1 Int Order of bytes in word O LSB first LONGORD 43 1 Int Order of words in a longword O LSW first TARGET 44 1 Cc X ray target material Cu Mo Ag Fe Cr Co or other SOURCEK 45 1 R X ray source kV SOURCEM 46 1 R X ray source milliamps FILTER 47 1 C Filter monochromator setting Such as Parallel graphite Ni Filter C Filter Zr Filter Cross coupled Goebel Mirrors CELL 48 49 1 6R Unit cell A B C ALPHA BETA GAMMA MATRIX 50 51 1 9R Orientation matrix P3 conventions LOWTEMP 52 1 8 9 1 Int Low temp flag Note Version 8 and 9 headers diverge 8 Int 3R 8 Add sub mnemonic TEMP Adds set point K ramp rate deg min hold time sec 9 3int 9 Adds experimental temperature in hundredths C and CCD sensor temperature in hundredths C ZOOM 53 1 3R Zoom Xc Yc Mag CENTER 54 1 2R X Y of direct beam at 2 theta 0 DISTANC 55 1 R Sample detector distance cm TRAILER 56 1 Int Byte pointer
233. TA and a lut filename extension is assumed if you don t specify one The following color tables are supplied with the program In addition you can sup ply the special value DEFAULT which refers to a table similar to bb lut below which is not disk resident but rather is hard wired into the program code BB LUT The default color table gen erated using a blackbody radiation model Intensities are monotonically increas ing but color provides better discrimination than a straight monochrome scheme CUSTOM LUT Arbitrary multicolor scheme DIFFER LUT Red green color table useful in viewing frames that are built from differences for example a subtraction of one frame from another MONO LUT Monochrome grayscale color table PRINT LUT Reverse monochrome gray scale color table Useful for previewing monochrome hardcopy screen dumps V16 LUT 16 level color table using a scheme similar to the defaults on older PCS sys tems V8 LUT 8 level color table using a scheme similar to the defaults on older PCS sys tems V8SYM LUT Like V8 but with colors sym metrically distributed about the center display memory value VIDEO LUT Another arbitrary multicolor scheme When using the Edit gt Config gt Colors dia log you can select the lookup table name from a list of available filenames by specify ing a wildcard pattern in the COLOR TABLE FILENAME entry or by leaving the entry blank and pressing ENTER or
234. TE options For screen editing options and keys see the section under keyboard con ventions Upon exiting GADDS the current tar get list if any is saved in the file targets txt Upon entering a Collect gt Scan gt EditTargets command GADDS displays a target list with current settings a typical list follows Run Frame x Y Z 0 000 1 0 1 0 2 33 0 001 1 5 1 0 2 33 0 002 1 0 1 5 2 33 0 003 1 5 1 5 2 33 Each line in the array defines one target posi tion The scan series will be acquired in the order they appear in the array When entering the individual target arguments keep in mind the following special considerations e The RUN FRAME and FRAMES must conform to the frame naming parameters See Edit gt Configure gt User settings com mand e All generated filenames must be valid and should not create duplicate names explained later in this section e The number of targets is limited to 2048 e The number of runs or lines must not exceed the maximum number of runs allowed by RUNCHARS and RUNBASE see Edit gt Configure gt User settings com mand The default maximum number of runs is 36 The absolute maximum is 36 36 With these considerations in mind we recom mend that you always configure the frame nam ing conventions as follows e For 36 or fewer runs set the Base of Run in the Edit gt Configure gt User settings dialog to base 36 which will prevent t
235. TEIN 1 2 APPEND POLE FIG NORMALIZE 1 DISPLAY lt n gt NVAL lt n gt 2 POLE FIG CONTOURS 1 INTERVAL lt n gt POLE FIG SURFACE 1 ROTATION lt n gt ELEVATION lt n gt COARSENESS lt n gt LOGSCALE G 4 M86 E01008 GADDS Software Reference Manual SLAM Command Reference POLE FIG FIBERPLOT 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt PRINT 1 FORMAT lt n gt THRESHOLD lt n gt GREYSCALE PROJECT SWITCH 1 PROJECT LOAD 1 not recommended to use in SLAM mode PROJECT NEW CNAME lt s gt 1 TITLE lt s gt WORKDIR lt s gt FORMULA lt s gt MORPH lt s gt CCOL lt s gt DENSITY lt s gt DENSMETH lt s gt PROJECT COPY CNAME lt s gt 1 TITLE lt s gt WORKDIR lt s gt FORMULA lt s gt MORPH lt s gt CCOL lt s gt DENSITY lt s gt DENSMETH lt s gt CLEAR RESET PROJECT EDIT TITLE lt s gt FORMULA lt s gt MORPH lt s gt CCOL lt s gt DENSITY lt s gt DENSMETH lt s gt CLEAR RESET PROJECT BACKUP 1 2 3 NOCALIB NOWORK PROJECT REMOVE 1 PROJECT DELETE 1 P Q ROJECT MAKEDEF UIT RATEMETER 1 RESET lt n gt SHUTTER REFL ARRAY THRESHOLD 1 2 CONTIG lt n gt COUNTS lt n gt SIGMA lt NN gt XEXMIN lt n gt XEXMAX lt n gt RMAX lt n gt DMIN lt n gt DMAX lt n gt DBIAS lt n gt 3 4 5 6 7 8 REFL ARRAY PICK 1 2 3 4 START lt n gt QUADRANT lt n gt FRAME_HALFWIDTH lt n gt REFL ARRAY INDEX 1 A
236. The frame is not automatically written to disk Use File gt Save after collecting the still frame if you want to save the data to disk When invoked from the menu or run from the command line without arguments Add displays a dialog box where you can view edit the argu ments described below before performing the operation function Pressing the ENTER key or clicking the OK button starts the operation Pressing ESC or the Cancel button stops the operation and returns you to the menu You can interrupt the operation by pressing CTRL BREAK 5 47 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GT serach niente Max Seconds 30 0 This is the maximum count time in sec onds The default value is 30 the range is from 1 to 65 535 seconds Times can be entered in decimal seconds or in HH MM SS SS hours minutes and sec onds format Data collection ends when the specified time has elapsed or when the maximum count limit see MAX COUNTS below has been reached ICLEAR eeeee Pre Clear Yes This qualifier when set clears memory before the new data frame is collected If it is not set the new data are added to the image already in the frame accumulation memory for example an image left over from a previous ADD LOAD or SCAN com mand PATTERN Test Pattern Y N No This qualifier when present draws a test g
237. Then there may be either end of file or another set starting with another first line M86 E01008 G SLAM Command Reference The following are the GADDS SLAM Command syntax for all valid commands lt n gt denotes numeric value lt s gt denotes string value any text string filename p1 p2 p3 p4 p5 p6 p7 p8 p9 po ADD BAD CAL CLEAR 1 Q CON CON CON CON CON CON 1 CLEAR PATTERN COUNTS lt n gt DISPLAY lt n gt REALTIME RESET lt n gt SHUTTER PIXELS PROCESS 1 2 3 4 5 6 7 LOCAL IBRATE 1 MININT lt n gt DISTANCE lt n gt 2 ANGLE lt n gt 3 X lt n gt Y lt n gt 4 AUTO NOERASE DELAY lt n gt FIGURE ED KV lt n J j j Tj G G G G UADRANT lt n gt GRAPHICS_SAVE IMAGE_SAVE IT USER lt s gt SITE lt s gt CALIBDIR lt s gt MINCPS lt n gt TIMEOUT lt n gt NAMECHAR lt n gt RUNCHARS lt n gt RUNBASE lt n gt NUMCHARS lt n gt NUMBASE lt n gt LOWTEMP TEMP lt n gt XBEAM lt n gt YBEAM lt n gt FRAMESIZE lt n gt DISTANCE lt n gt FIGURE ADMIN TARGET lt s gt WAVELENGTH lt n gt ALPHAl lt n gt ALPHA2 lt n gt BETA lt n gt UNITS lt s gt gt MA lt n gt STANDBYKV lt n gt STANDBYMA lt n gt MONOCHROMATOR lt s gt OFFSET lt n gt URE READ 1 URE WRITE 1 URE SHOWMODEL URE COI OVERLAY lt n gt MATCH1 lt n gt LORS 1 WINBG lt n gt WINFG lt n gt CURSOR lt n
238. Useful for individual security situations NOPROJECT Prevents GADDS from starting in the last project s working directory Starts in icon s working directory M86 E01008 GADDS Software Reference Manual General Information NORELOAD Prevents GADDS from reading the configu ration file gadds _nc PORT Specifies the goniometer controller com port number Valid options are 1 4 with 1 being the default PROJECT lt projname gt Specifies GADDS to start in the named project s working directory This is the project name as defined in the project data base On failure to load requested project the last projects working directory is used RAXES Instructs GADDS that the goniometer con troller is reporting axes that should be ignored and overridden with the GADDS fixed angles command The default is that all reported angles are used see AXES This is mainly useful for 2 position chi stages with video option where RAXES 8 should be used Axes are specified by using an eight bit bitmask with each bit represent ing the presence ON or absence OFF of each axis Bit Value Axis Bit Value Axis 0 1 2Theta 4 16 x 1 2 Omega 5 32 Y 2 4 Phi 6 64 Z 3 8 Chi 7 128 Zoom TCPORT Specifies the temperature controller com port number Valid options are 1 4 with 2 being the default THETATHETA Modifies behavior to theta theta operation X Y Determines GADDS window po
239. X lt n gt DMIN lt n gt Input Prompt Positive X limit both O none Negative X limit both O none Positive Y limit both O none Negative Y limit both O none Positive Z limit both O none Negative Z limit both O none Positive Aux1 limit both O none Negative Aux1 limit both O none Maximum Delta limit both O none Minimum Delta limit both O none Second numbers are for D8 Discovery systems Phoe nix controllers Defaults 90 00 90 00 90 00 90 00 90 00 90 00 7 00 7 02 1 00 0 98 30 0 6 0 M86 E01008 Collect Routines GADDS Software Reference Manual 5 16 Collect gt Goniometer gt Extlimits e Display extended software collision limits Menu Command Collect gt Goniometer gt Extlimits Accelerator none User Level 2 SLAM Syntax GONIOMETER EXTLIMITS This command is used to graphically draw the extended software collision limits between the omega and chi axes Mainly used for the 1 4 cir cle stage where when chi is at 90 degrees omega is restricted such that the stage will not drive into the collimator GADDS SYSTEM limits_4 P3 systems GADDS SYSTEM limits_r Reflection 1 4 circle GADDSS SYSTEM limits_t Transmission 1 4 circle The extended map limits are read from the vari ous files depending upon which goniometer model is active To change the limits you must manually edit this file Some important consider ations are e The first and last points must
240. Y answer allowing script files to run unattended If you however press a key within the 10s period the wait for timeout is can celled and the program will take the action you ve just specified 8 25 1 Arguments None Command executes immediately M86 E01008 Peaks Routines GADDS Software Reference Manual 8 26 Peaks gt Refl Array gt Load Read in orientation matrix from existing p4p or _pr file Menu Command Peaks gt Refl Array gt Load Accelerator None User Level 1 SLAM Syntax REFL_ARRAY LOAD 1 2 3 When invoked with the LOAD option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY LOAD displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button performs the load command Pressing ESC or the right mouse button returns you to the REFL_ARRAY submenu 8 26 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses liar ee BE Filename lys p4p Enter name of P4P or LS parameter _pr file to load If extension is omitted GADDS will try P4P then _PR GO oes veces cheticeunaceess Overwrite Reflections Check to overwrite reflection array list with list in P4P LS file Ae AE Ee ORT Overwrite Crystal Info Check to overwrite Project gt Edit crystal info items M86 E01008
241. Y UKER BRUKER ADVANCED X RAY SOLUTIONS Ww General ne Detectotl Diffraction System GADD version 4 1 REFERENCE MANUAL M86 E01008 4 04 S UKER BRUKER ADVANCED X RAY SOLUTIONS General Area Detector Diffraction System GADDS Reference Manual Version 4 1 xx M86 E01008 4 04 This manual covers the GADDS software package To order additional copies of this publication request the part number shown at the bottom of the page 2004 1999 Bruker AXS Inc All world rights reserved Printed in the U S A Notice The information in this publication is provided for reference only All information contained in this publi cation is believed to be correct and complete Bruker AXS Inc shall not be liable for errors contained herein nor for incidental or consequential damages in conjunction with the furnishing performance or use of this material All product specifications as well as the information contained in this publication are subject to change without notice This publication may contain or reference information and products protected by copyrights or patents and does not convey any license under the patent rights of Bruker AXS Inc nor the rights of others Bruker AXS Inc does not assume any liabilities arising out of any infringements of patents or other rights of third parties Bruker AXS Inc makes no warranty of any kind with regard to this material including but not limited to the implied
242. YS04 000 LYS04 001 LYS04 002 etc See the description FRAME NAMING CONVENTIONS for more information The default name if none is specified is NEWFRAM The Job Name for frames stored locally can contain a DOS drive and directory name if desired The output filename is except in the special cases discussed below merged with the default frame directory defined in the CONFIGURE EDIT panel prior to creat ing the output frame See CONFIGURE EDIT for a description of how this is done There are two special Job Name cases The first NET is NOT supported under GADDS The second special Job Name is NULL In this case the frames are not out put they are thrown away RUN lt S gt 006 Run 0 The Run Number of the series This is not actually a number but is rather taken as RUNCHARS characters of ASCII text where RUNCHARS is defined in the CON FIGURE EDIT input panel to be used as the last RUNCHARS characters of the out put base filename i e the last RUN CHARS characters before the extension Make sure that these values and the frame naming parameters in CONFIGURE EDIT are set the way you want before starting to scan as described above FRAMENO lt s gt Frame 000 This is the starting frame number for the series defined by this line of the array Make sure it conforms to the frame naming parameters currently set in CONFIGURE M86 E01008 Collect Routines GADDS Software
243. You can optionally form a linear combination of two frames display ing the result File gt Load followed by a File gt Save command can also be used to convert a frame between the XENGEN 1 3 and Bruker for mats or to replace values in a frame header with the current values in the Edit gt Configure panels When invoked from the menu or from the com mand line without arguments File gt Load dis plays a dialog box where you can view edit the items described below If you press ENTER or click the OK button the load operation starts Pressing ESC or the Cancel button returns you to the menu without performing the operation File gt Load is closely related to the File gt Dis play Typically File gt Display is used much more often than File gt Load since it provides a more M86 E01008 GADDS Software Reference Manual File Routines flexible set of display options for example for displaying sequential frames in a series or multi ple frames in quadrants However only File gt Load contains options for combining frames and modifying frame headers 3 7 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses DA street tated Input Filename no default This is the name of the file to be read from disk or of the first file of two to be read when performing a linear combination The special name FRAME can be used here to indica
244. a nben ae det he paul eee ts 5 31 6 22 A AQUMONTS sec peta ie add nada eas Pease Lahde fal eat Gagan dee vate debts ans 5 31 5 23 Collect gt Goniometer gt Det Stage Drive delta axis 0 000 cece eee 5 32 Sea AGUES saraaa ea meee enna eels teas Maat Walaa mroneiate Bkelvea nest we ERA 5 32 5 24 Collect gt Goniometer gt Fixed axes Set reported settings for non controllable axes 5 32 5 24 AVATQUMONTS Pia ested asta tated wi eeatted area ieeal ist REE EO E al date aoe eee dis 5 33 5 25 Collect gt Goniometer gt Home axis e Home goniometer axis 00000e ee ee 5 34 5 25 AGUDOS sxe a dissec th deere Monet al oat elke abut EAE ER pa ee ad 5 35 5 26 Collect gt Goniometer gt Park XYZ Park large XYZ stage OM 0 X far right Z back 5 35 5 26 31 ATQUMONIS ec yar ke iara ng at a Rieti lie ae iavled ia E aa wee a hates 5 36 5 27 Collect gt Goniometer gt XYZ collision e Avoid XYZ stage collision with detector 5 36 5 271 AGUES acid EIEREN ERIRE E aI panel a bloke E gon Richtee eas elses ang 5 36 5 28 Collect gt Goniometer gt Temperature Watlow Series 988 Temperature Controller 5 38 5 28 AUMENS rari oseri a bits aed w A Gm Balada aa Gabe Bi eats O E a a de 5 38 5 29 Collect gt Goniometer gt Encoders Adjust encoder zero offsets 20055 5 39 529A ALQUMONIS ro noite vece kut nT ERE EE ANE hie EA bet aww Wve lag wr ele lag 5 40 5 30 Collect gt Scan gt SingleRun Per
245. ack Menu Command Collect gt Goniometer gt Park XYZ Accelerator none User Level 1 SLAM Syntax GONIOMETER PARK Use this command to park the XYZ stage in an out of the way position When invoked with the PARK option from the GONIOMETER submenu GONIOMETER PARK displays the following prompt on the bottom status line PARK XYZ STAGE ARE YOU SURE Pressing the Y key ENTER key or left mouse button will drive the XYZ stage to the PARK or lock down position First the Z axis is driven back to the current negative Z collision limit see GONIOMETER LIMITS Then both omega and X are driven to 0 0 and far right limit respectively The user can then lock down the large XYZ stage by turning the lock screw Pressing N the ESC key or right mouse button will return you to the GONIOMETER submenu without driving the axes In command line mode the action is the same except that the program does not prompt before driving the axes to park M86 E01008 Collect Routines GADDS Software Reference Manual 5 26 1 Arguments None Command executes immediately after confirmation prompt 5 27 Collect gt Goniometer gt XYZ collision Avoid XYZ stage collision with detector Menu Command Collect gt Goniometer gt XYZ collision Accelerator none User Level 2 SLAM Syntax GONIOMETER XYZ 1 2 3 4 Use this command to define the corners of the detector and XYZ stage to avoid collisions betw
246. adds 12 28 M86 E01008 13 Utility Programs 13 1 FrmFix FRaMe header FIX up utility The program FRMFIX is designed to correct all known problems with Bruker frame file headers Specifically it can e convert frames taken by MICRODIF for DOS to version 8 frame headers These frames can then be read under GADDS for NT but not under MICRODIF for DOS e correct frames taken by GADDS for NT ver sion 3 300 to 3 302 Under these beta NT release the AXES2 and ENDING2 lines were incorrectly located at records 076 and 077 and the FILENAM record contained garbage e correct frames taken with improper fixed angle settings correct frames with negative scan time bug These frames were taken for over 12 hours and overnight under programs for DOS correct frames with 360 degree scan width bug These frames were taken in STEP mode under GADDS for DOS or GADDS for NT prior to v3 310 correct CCD frames taken on large CCD with SMART v4 040 requires the switch BIGCCD correct frames with the first LINEAR frame header parameter having a value that is below 1 0 This is incorrectly stored as the reciprocal of the true value So far this prob lem has only been seen on 2K CCD sys tems when using 512 frame size but theoretically could occur on any area detec tor system M86 E01008 Utility Programs GADDS Software Reference Manual e correct CCD frames for bad OCTMASK fr
247. ader Image data Overflow table Trailer 1 Trailer N A 1 Header The header is 1 typeable ASCII and 2 an even multiple of the 512 byte disk block size Each entry in the header is an 80 byte unterminated ASCII line Thus the header size is always a multiple of 5 disk blocks to hold an integral num ber of lines The first eight characters of each item contain the item name with the remaining 72 characters for ASCII data Thus the organi zation of the header can be represented as HEADER Item_namet 8 char ltem_Data1 72 chars Item_named 8 char ltem_Data2 72 chars Item_nameN 8 char Item_DataN 72 chars This organization has several advantages First fast random access can be performed on the header to pull out or rewrite an individual entry During random access the item names provide a method for checking for corruption of the header block Second frames are actually TYPEable on both PCs and workstations if the screen wraps at 80 columns The padding to a multiple of 5 disk blocks contains ASCII dot characters The last characters of the padding are a CTRL Z anda CTRL D This convention provides a warning indicator on a workstation during which a CTRL S or CTRL C can be issued before the binary pixel values start to appear On a PC an M86 E01008 GADDS Software Reference Manual Area Detector Frame Format MS DOS TYPE command stops when it hits the CTRL Z Presence of the item names make
248. al correction is in use provides spatially corrected Y coordinate otherwise this value will be identical to the raw coordi nate DX Signed pixel X distance from frame center DY Signed pixel Y distance from frame center 2 THETA 2 Theta value at current pixel ANGSTRMS Resolution in Angstroms at current pixel HKL If an orientation matrix is in effect the HKL indices corresponding to the current pixel are also output Pole images are handled slightly differently On these frames the following output statistics are displayed on screen in real time and are also written to the logfile if applicable XY PIXEL X and Y coordinates of current pixel range from 0 to framesize 1 with origin 0 0 being located at lower left of screen COUNTS Counts at current pixel DX Signed pixel X distance from frame center DY Signed pixel Y distance from frame center Alpha Alpha angle at current pixel Beta Beta angle at current pixel Chi Chi angle at current pixel 90 alpha Phi Phi angle at current pixel same as beta M86 E01008 Analyze Routines GADDS Software Reference Manual 7 4 Analyze gt Cursors gt Vector Measure distances on displayed frame Menu Command Analyze gt Cursors gt Vector Accelerator F8 User Level 1 SLAM Syntax CURSORS VECTOR 1 2 3 4 DELAY lt n gt NOERASE When invoked from the menu or when run from the command line without arguments Analyze gt
249. al stress solves p11011 p12012 p22022 p13013 p23023 P33033 In sin 00 sin 6 The final stress report is somewhat different otherwise these three commands are identical Biaxial stress reports Data collection condition Stress report W scan only o11 Chi scan only 622 All other cases 611 0612 622 and Oph Biaxial Shear stress solves Data collection condition Stress report W scan only 011 and 013 Chi scan only 022 and 623 All other cases 011 012 622 613 623 and Oph Triaxial stress solves Data collection condition Stress report All cases must scan 2 axes 011 012 622 613 623 and 033 M86 E01008 GADDS Software Reference Manual Analyze Routines Reprocessing Stress Data Frequently obvious errors can occur and you would like to toss out specific data points from the calculation There are two methods to repro cess data Method 1 Reprocess from lt filename gt txt that must be created using the Write button You must use the base filename with the txt exten sion defaults to edit txt Then use notepad to edit this file and in the last table add an addition column to reject data points Use the letter R or the word rejected case is not important Finally restart the Stress command with the reprocess option checked Method 2 Reprocess from lt filename gt I st that is always created
250. always 304 length of primary range am header in bytes or Unkn for unknown 4 14 number of measured data or fix for fixed 8 R8 theta start in degrees 96 14 2 detector used for this range 16 R8 two theta start in degrees obs detector code for detector 1 24 R8 chi start in degrees use 9999 0 if not 0 none now invalid value 2 present or unknown 1 Scintillation 32 R8 phi start in degrees use 9999 0 if not 2 Proportional present or unknown A z 3 Solid State 40 R8 x start in mm use 9999 0 if not present or unknown 4 Other 48 R8 y start in mm use 9999 0 if not 5 PSD present or unknown 16 X 1000 2 56 R8 z start in mm use 9999 0 if not 17 Hi Star 2 present or unknown 18 CCD 2 Note may use actual values for fixed 19 Large CCD 2 axes 64 R8 div slit start in degrees if divslit_code 20 Mosaic CCD ies fix 9999 unknown 9999 0 if not present 100 R4 2 highvoltage used in V 9999 0 for 72 C8 div slit code ASCIIZ V20 V6 V4 urikiown YO Fix obs highvoltage in V of detector 1 9999 0 for unknown M86 E01008 GADDS Software Reference Manual DIFFRAC S Raw Data File Format 104 R4 2 amplifier gain used in 9999 0 152 R8 start of aux axis 2 up to now 0 0 for unknown i e k of hkl scan obs am
251. am center Answer yes to update the current configuration with the new distance and beam center All future frames collected will have the calibrated values in their frame headers Thus CALI BRATE should be performed before any data frames are collected in order that the proper experimental values are written into the frame header If the detector distance was changed the SPA TIAL UNWARFP file will be wrong You will need to reload the brass image set the correct detec tor distance and reprocess the spatial correc tion tables Secondly the beam center stored in the configuration setup is already unwarped so during any SPATIAL UNWARP command set the NOBEAMCENTER switch to Y 6 17 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses STen eaa Standard filename PDF2 number corundum std The input standard calibration file contains a list of d spacing s and intensities for a given standard GADDS is supplied with files for alumina corundum quartz and silicon Other standards can be added with a text editor By default the directory GADDS SYSDATA or SAXI SYSTEM is used unless otherwise specified If avail able the JCPDS PDF2 CD ROM may be read for any standard simply enter a valid PDF number separated by or MININT lt n gt Minimum relative intensity 5 When reading the standard file
252. ame Number overflows It is automatically incremented however when setting up an EDITRUNS array inside ASTRO RUNCHARS can usually be left at the default value of 1 however if you re per forming more than RUNBASE runs make sure that you set RUNCHARS to 2 to pre vent wrap around of the Run Number other wise earlier scans could be overwritten by later ones For example if RUNCHARS is set to 1 and RUNBASE is 10 instead of the default value of 36 a Run Number of 10 in the EDITRUNS array will result in a Run Number of 0 in the output filename RUNBASE lt n gt Base of Run 36 The numeric base of the Run Number The value must be 10 or 36 If the base is 10 a carry out of each digit is produced when the digit is incremented from a value of 9 and the digit is reset to zero If the base is 36 the digit is incremented from 9 to A then to B etc A carry is produced when the digit reaches Z and the digit is reset to zero RUNBASE should usually be left at the default value of 36 NUMCHARS lt n gt Character in Frame 3 The number of characters to be appended to the filename as an extension represent ing the number of the frame in the current series The number is padded with leading zeros if needed to fill NUMCHARS charac ters This Frame Number is automatically incremented by one after each frame is col lected during an Acquire gt SingleRun Multi Run Hemisphere Quadrant or Matrix command T
253. ame header parameters frame taken by SMART to be used by GADDS e correct for unreasonable scan times when external trigger was used ELAPSDA and CUMULAT values are less than 0 05 sec onds Just use ELAPSDR as the scan time e correct frames collected on systems where the phi axis was configured to rotate in the wrong direction Phi should rotate clock wise The command frmfix runs the program When you run frmfix it starts an interactive dialog Default values are displayed in square brackets after the prompt Pressing the ENTER key is the same as entering this default FRAME FILENAME Enter the name of the input Bruker format frame You must give the full pathname FRMFIX does not merge filenames with the current frame directory However FRMFIX does translate logi cal names under NT or UNIX and wildcard characters that is are allowed AXIS NUMBER TO RESET Enter O none 1 2T 2 Om 3 Ph 4 Ch 5 X 6 Y 7 Z This feature is particularly useful for manually adjustable chi stages where a scan series was collected while the program contained the wrong fixed chi setting VALUE TO SET AXIS Enter new value for scan axis entered above As the program executes Frmfix will display messages stating what was fixed or the mes sage Frame 000 Frame header is OK no fix up was required Alternately all input may be given on the com mand line Brackets signify optional parame te
254. an even ones since the extra thickness is then added symmetrically about the true cursor posi tion By providing arguments on the command line you can direct the CURSORS CONIC computa tions to be performed once at a single specified position after which control returns immediately to the command line If logging is turned on see the LOGFILE com mand for more information the quantities com puted for the final position of the cursor prior to exiting the command are written to the output logfile If scripting is enabled again see LOG FILE a non interactive CURSORS command corresponding to the final cursor position is writ ten to the output script file The SLAM command arguments are 1 X coordinate in pixels of the crosshair cen ter The range is from 0 to framesize 1 default value is 256 2 Y coordinate in pixels of the crosshair cen ter The range is from 0 to framesize 1 default value is 256 DELAY lt n gt Specifies a time interval to wait before eras ing the cursor and returning control to the program This is for use in scripts where it is desirable for the cursor to remain on screen long enough for the user to discern its position M86 E01008 Analyze Routines GADDS Software Reference Manual NOERASE Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor left from a N
255. anchor the segment and press ENTER The crosshairs are replaced with a line segment between the anchored point and the current cursor position 2 Position the line segment end point and press ENTER The line segment is drawn and a crosshairs cursor appears to position the next line 3 When you are finished press ESC to return to the POSTER menu PEAKS POSTER DRAW STYLE PEAKS POSTER DRAW STYLE is used to tog gle between drawing objects with a solid line and drawing objects with a dashed line style The current style is displayed in the submenu title bar PEAKS POSTER EDIT All poster annotations are stored in a PLOTSO file format These commands can be edited with a simple screen editor After exiting EDIT the graphics plane is erased and the poster annota 12 14 M86 E01008 GADDS Software Reference Manual SLAM Routines tions are redrawn This erases all graphs dis played before starting PEAKS POSTER PEAKS POSTER CLEAR PEAKS POSTER CLEAR is used to clear a rectangular region When selected a crosshair cursor appears To clear a region 1 Position the crosshairs at a corner of the box to be erased 2 Press ENTER to anchor the corner The crosshairs are replaced with a rectangular box that has one corner anchored at the point just selected and the other corner at the current cursor position 3 Position the second box corner and press ENTER The box is erased and a crosshairs cursor appears to
256. and continues collecting data 5 45 Collect gt Scan gt Master e Place frame buffer into single detector or dual master mode Menu Command Collect gt Scan gt Master Accelerator None User Level 3 SLAM Syntax SCAN MASTER 1 SEND_CONFIG SCAN MASTER is used to select single or dual detector operation mode and to optionally update the SLAVE configuration menu NOTE Invoking SCAN MASTER on a frame buffer connected to a GGCS not a SLAVE frame buffer may place the GGCS in an inoper able mode The most recent release of the GGCS software fixes this problem The MASTER frame buffer can function in two modes The default single detector mode mim ics the standard single detector system the SLAVE detector becomes dead weight on the goniometer Flood fields and fudicial plate images are collected in single detector mode Alternately the MASTER frame buffer may be placed in dual detector mode Here the MAS TER may send the SLAVE specific instructions begin collecting data stop collecting save image etc as well as control the GGCS how M86 E01008 GADDS Software Reference Manual Collect Routines ever the user will only notice a few changes to the Scan menus For single run data collections on dual detec tors three new options appear in the input panel for Scan Singlerun They are SNAME oaae Slave Job name NEWFRA2 Enter base name for frames SRUN ciiirt Slave Run 0 Enter data
257. and sample holder scattering effects subtracted out to obtain meaningful results Calculates the percent crystallinity by extracting an amorphous background frame With the sep aration of amorphous and crystalline contribu tions the percent crystallinity calculation is simply Die I C 100 ST where C percent crystallinity Ig observed intensity IR intensity background frame In the case of polymers where part of the struc ture is unstructured and part of it is crystalline in nature there are two contributors to the diffrac tion pattern a lower level broadly distributed intensity which is the result of amorphous scat tering and the stronger peeks which are the result of structure element of the polymer A method for background estimation that has proven effective in other domains is based on morphological processing Morphological image processing is based on two operations dilation and erosion The parameters of the operations are defined by a matrix of kernel values called the operator s structure element SE The dilation of an image F by a structuring element S denoted as F S is defined as d x y max f x i y j st J where de D fe F and s e S Conversely the erosion of an image F by a structuring element S denoted as E F _ S is defined as e x y min f x i y j sli j where f and s are as before and e e E The background of a diffraction pattern can be estimated wi
258. ant NOCLEAR No Clear Y N No This parameter is specified to suppress clearing any previously displayed graph It is useful in script mode to add labels to graphs before printing M86 E01008 7 24 Analyze Routines GADDS Software Reference Manual 7 8 Analyze gt Graph gt Vector e Plot profile along vector in displayed frame Menu Command Analyze gt Graph gt Vector Accelerator Ctrl V User Level 1 SLAM Syntax GRAPH VECTOR 1 2 3 4 QUADRANT lt n gt DELAY lt n gt NOERASE When you want to plot an arbitrary one pixel slice through the data use the GRAPH VEC TOR sub command This routine is similar to CURSOR VECTOR in that you use the cursor to identify the beginning and ending points of a rubber band vector When you ve specified the path of interest in this manner GRAPH VEC TOR then plots the intensities of all pixels located along that path as an X Y graph of inten sity counts versus position along the line in pixels When invoked with the VECTOR option from the GRAPH submenu or when run from the com mand line without arguments GRAPH VEC TOR displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins interactive path of interest selection with a vector cursor The ESC key or right mouse button returns you from the input panel to the GRAPH submenu When you re selecting a p
259. aphic axis being perpendicular to the z axis A condition of no orientation is the origin White Spruiell orientation indices are useful on polymer films where orientations occur with some degree of biaxial character White Spruiell orientation indices are usually displayed on an isosceles triangle The three apexes of the trian gle correspond to perfect orientation along a particular direction whereas the center of the triangle corresponds to isotropic orientation S MD x 2 lt cos a gt MD x lt cos a gt TD x 1 S TD x 2 lt cos a gt TD x lt cos a gt MD x 1 7 27 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses E S Pole Figure File FRAME Enter pole figure file name or FRAME for current frame DISPLAY 00 Max Display Counts 15 Enter counts corresponding to white VEET Increment 1 0 Enter delta angle in degrees for summa tions JAPPEND Append Y N No Enter Y to append results to previous trian gle plot IFILM ooe Film Y N No Enter Y for 2D structures such as films N for 1D structures such as fibers JHKL lt S gt vseeeeseeees HKL 001 Enter hkl of pole figure used for labelling purposes If unknown enter hkl M86 E01008 Analyze Routines GADDS Software Reference Manual 7 28 Analyze gt Pole Figure gt Stein Plot Stein trian
260. are 360 to 360 but are typically reduced by the current software collision limits as defined in Collect gt Goniometer gt limits command Entering will be auto matically replaced with current angle set ting AXIS The number of the axis to be scanned as follows 2 for omega scans 3 for phi scans 4 for chi 5 for X 6 for Y 7 for Z or 1 for coupled Note that while SAINT can reduce phi scans taken at any chi angle some data reduction programs XENGEN may not be able to reduce phi scan data unless it was taken at CHI 0 When using a restrictive data reduction package you must perform M86 E01008 Collect Routines GADDS Software Reference Manual omega scans on both the Platform goniom eter and the older Aztalan black 3 axis WIDTH The scan width in degrees either positive or negative of each frame to be acquired Thus the starting scan angle for the Nth frame in the series where the first frame is N 0 is OMEGA N WIDTH if the axis above is 2 or PHI N WIDTH if the axis above is 3 where WIDTH OMEGA and PHI are the values given on the same line of the array The intensity within a frame is uniformly distributed with respect to scan angle over the range WIDTH specified here unless 3 circle frames are taken by oscilla tion in which case the ends of the range have slightly higher weight and there may be some overlap or underlap of successive frames oscillation can however compen
261. are a subset of current range Range start end 1 10 0 40 0 2 05 0 90 0 lt Fails 13 6 PDFnoind PDF2 index generator PDFnoind builds a hard disk resident index to an ICDD PDF2 CD ROM It is required for ICDD PDF2 set 47 and higher For set 46 and earlier PDFnoind also works but the index file is also distributed on the PDF2 CDROM GADDS uses this index to reduce the time required to perform a PDF2 search Normally this index file will reside in PDF2 IND pdfno ind You must use PDFNOIND to create this file before GADDS will perform a PDF2 search To run PDFNOIND the following environment variables should be defined and the ICDD PDF2 CD ROM must also be placed in the CD ROM drive PDF2 PDF This variable defines the drive and directory for the ICDD PDF2 Database File PDF2 DAT This is usually a CDROM disk and directory of lt drive gt PDFa2 PDF2 IND This variable defines the drive and directory for the ICDD PDF2 Index File PDFNO IND created by this utility This must be a hard disk usually C PC PDF When you run PDFNOIND it starts immediately and will then run for several minutes periodi cally printing the number of entries processed as a progress indicator 13 10 M86 E01008 GADDS Software Reference Manual Utility Programs 13 7 Plotso PLOTSO is a separate program for displaying X Y graphs of data stored in simple ASCII text files PLOTSO can be started by entering the name o
262. areas wed 5 81 SAA TAGUES ise ti ieecte kep hd Mae Pada dL Hee ee da ROR ae Oke be ek od Se ee oe be 5 83 5 45 Collect gt Scan gt Master Place frame buffer into single detector or dual master mode 5 84 SAST Arguments inter nom eb hee ee Bebe a E A EENS k 5 85 5 46 Collect gt Scan gt Slave e Place frame buffer into slave mode for dual detector system 5 86 546s ATQUMENTS wie tse eee pede hatha wee bia tt a bel se ed oe eb ed ee ee 5 87 5 47 Collect gt Add Accumulate an area detector frame Still frame 00 5 87 5 47 1 Argument ged EE ae ithe Abe eee eae pee ew E beet ead 5 88 5 48 Collect gt Shutter e Open close X ray beam shutter 0 0000 cee eee 5 90 6 Process Routines fui oiee dete di ee hee Rete tee ha ea owe mre eee ores 6 1 6 1 Process gt Flood gt New Acquire data to generate new flood field correction 6 1 Ol AGUEMI rran Rein Biante tated A E R E tne adie E E a unite Ge Brel 6 4 vi M86 E01008 4 04 GADDS Software Reference Manual Table of Contents 6 2 Process gt Flood gt Load Install a disk resident flood field correction table 6 6 6 221 ArQUMOEMNIS gt 4 06 Wr Woda ete hs ae bead eu lee whe i tava shake 6 6 6 3 Process gt Flood gt Reprocess Generate a new table from previous projection data ONGISK sco k 2 eee Eee E le eile ed Be Mark a at ellie te baer dan R 6 7 GITAN G en Reese huh arene E w Sa Rea Ral LAE ca aie tale nee
263. argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Siera me arn X Origin 256 The X coordinate of the lower left of the box defining the region of interest in pixels The range is from 0 to framesize 1 default value is 256 G2 ok telecine As Y Origin 256 The Y coordinate of the lower left of the box defining the region of interest in pixels The range is from 0 to framesize 1 default value is 256 3 inet cas Width 16 The width of the box defining the region of interest in pixels The range is from 0 to 128 default value is 16 ER Ea Height 16 The height of the box defining the region of interest in pixels The range is from 0 to 128 default value is 16 QUADRANT lt n gt Quadrant 0 This parameter specifies whether you want the graph to appear covering the entire data frame enter O or just one of the four M86 E01008 GADDS Software Reference Manual Analyze Routines quadrants enter 1 through 4 as appropri ate The default value is O full frame win dow Quadrants are 0 full window 1 lower left 2 lower right 3 upper left and 4 upper right FRAME_HALFWIDTH lt n gt Frame Half width 5 Enter the number of frames ON EACH SIDE of the currently displayed frame to be included in the rocking curve Make sure that you don t exceed the number of frames actually available for processing in ei
264. ases are han dled t thickness of plate a incident beam angle to normal b diffracted beam angle to normal u absorption coefficient 1 1 cosa cosb x Reflection absorption formula is given by l e ens x cosa Transmission absorption formula is given by pp HIDE cosh aig ih Neos A uxcosa M86 E01008 GADDS Software Reference Manual Process Routines 6 13 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses PTni Input File FRAME Enter filename for first input frame in series to process G2 AENEA Frames to Process 1 Enter consecutive frames to process PIi nans Output File NULL Enter filename for first output corrected frame 4 aion Sample vector X 1 VEEN wnciiienwss Sample vector Y 0 ZENS A a Sample vector Z 0 Input the coordinates in the goniometer head coordinate system of the vector which is normal to the face of the sample and points away from the incident beam side of the sample If the x ray beam is along the normal to the sample face the vector coordi nates are equal to 1 0 0 MU lt N gt on eee Sample mucm 1 8 0 Enter sample mu in cm 1 THICKNESS lt n gt Thickness cm 0 03 Enter sample thickness in cm M86 E01008 Process Routines GADDS Software Reference Manual 6 14 Process gt Smooth gt Average Smooth image with 3x
265. ated If the MAX DISPLAYED COUNTS qualifier is given a non zero value the frame will be automatically displayed at the end of each scan if real time display is off This latter display method has no effect on observed data rate Unless your data rate is very low it is better NOT to use real 46 M86 E01008 GADDS Software Reference Manual Collect Routines time display in the course of a SCAN com MODE lt s gt Mode Step Scan Oscillate mand even though the default here is Y Scan Note Real time is not permitted whenever display _ 0 While real time display is active you can change the upper display limit using the plus key to increase or the minus key to decrease the current limit by a factor of two Range is 7 to 524287 Modify the contrast using the left and right arrow keys Modify the brightness using the up and down keys Holding the control key down in combination with any arrow key results in a greater change of contrast or brightness CLEAR 00005 Pre Clear Yes This parameter specifies whether or not the memory will be cleared before the new data frame is collected If clearing is not per formed each successive frame in the series will be added to the counts accumulated before is collection is begun effectively pro ducing a rotation picture Enter Y to clear the memory N otherwise The default value is Y clear OLDXENGEN Xengen Output Format
266. ath of interest a rub ber band like vector cursor appears in the detec tor frame area and can be moved or re sized under control of the mouse and or keyboard arrow keys Pressing the ENTER key or left mouse button plots the graph of pixel value ver sus distance along the vector then exits return ing you to the GRAPH submenu Pressing the ESC key or right mouse button toggles between position change mode and size change mode where the vector origin remains anchored while the vector endpoint moves under mouse control If you want to exit without computing and draw ing the graph use CTRL BREAK The lineweight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cursors Odd values are better than even ones since the extra thickness is then added symmetrically about the true cursor posi tion By providing arguments on the command line you can direct the GRAPH VECTOR computa tions and graphing to be performed once at a single specified position after which control returns immediately to the command line If logging is turned on see the LOGFILE com mand for more information the quantities com puted for the final position of the cursor prior to exiting the command are written to the output M86 E01008 GADDS Software Reference Manual Analyze
267. ating so The frame is not automatically written to disk Use Acquire gt Save after collecting the still frame if you want to save the data to disk When invoked from the menu or run from the command line without arguments Acquire gt Zone displays a dialog box where you can view edit the arguments described below before per forming the operation Pressing the ENTER key or clicking the OK button starts the operation Pressing ESC or the Cancel button stops the operation and returns you to the menu You can interrupt the operation by pressing CTRL BREAK 5 38 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Bde seszcnevesictiaeis et Zone 1 Enter 1 to attempt collection of the OKL zone 2 for HOL or 3 for HKO WIDTH lt np gt Frame Width 5 0 Enter the frame width as defined under WIDTH in Section 3 4 SCANTIME lt n gt Seconds Frame 30 0 Enter the seconds per frame as defined under TIME in Section 3 4 DISPLAY lt n gt Max Display Counts 1 See Section 3 7 for an explanation of this argument See Acquire gt Display for more details M86 E01008 Collect Routines GADDS Software Reference Manual 5 39 Collect gt Scan gt Axial Image Acquire a frame showing A B or C axial image Menu Command Collect gt Scan gt Axial Accelerator Ctrl Shft F8 User Level 1 SL
268. atisfactory in most cases that is if two difference vector end points are identical within about 1 3 of the M86 E01008 Peaks Routines GADDS Software Reference Manual shortest possible difference vector they are included in the same group HKLTOL lt n gt Fractional HKL Devia tion 0 1 Difference vector groups whose calculated HKL indices are integers within this speci fied tolerance are considered to be fit by the current axial vector solution For each difference vector group the difference between H K or L index calculated from the trial axis vector solution and the nearest integer to that index is computed If the absolute value of the difference is within the HKLTOL value the solution fits that differ ence vector group In order for an axis vec tor solution to be accepted it must fit at least FFIT N difference vector groups where FFIT is described below and N is the total number of difference vector groups included in the indexing The default value of 0 1 should be suitable in most cases although if you have large unit cell axis lengths say gt 250 A you may want to increase it for example to 0 2 Valid input range is 0 1 although it is not a good idea to increase this parameter to much above 0 25 IFFITS T Fraction which must be fit 0 8 A trial axis vector is accepted only if the number of difference groups it fits is at least FFIT N where FFIT is the value spe
269. aws it on the screen Pressing the ESC key or right mouse button toggles between position change mode and size change mode where the lower left corner of the box remains anchored while the upper left corner moves under mouse control If you want to exit without computing and drawing the graph use CTRL BREAK Depending on the number of frames specified with the FRAME HALFWIDTH argu ment see below the rocking curve can take several seconds to compute The lineweight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cursors Odd values are better than even ones since the extra thickness is then added symmetrically about the true cursor posi tion By providing arguments on the command line you can direct the GRAPH ROCKING computa tions and graphing to be performed once at a single specified position after which control returns immediately to the command line If logging is turned on see the LOGFILE com mand for more information the quantities com puted for the final position of the cursor prior to exiting the command are written to the output logfile If scripting is enabled again see LOG FILE a non interactive GRAPH ROCKING command corresponding to the final cursor posi tion is written to the output script file 7 9 1 Arguments Each
270. aximum display memory value for example corresponding to white on the dis play The special value 1 directs the pro gram to pick a reasonable value by scanning through the pixels in the frame prior to display the special value 2 directs the program to use whatever setting is cur rently in effect The default value is 2 the allowed range is from 2 to 10 counts Smaller values make the displayed image look brighter larger values make look darker WIDTH lt n gt Width 2 Half width of interpolation box in pixels 2 scien Outputfile NULL Output filename to store interpolated pole figure image or null M86 E01008 GADDS Software Reference Manual Analyze Routines 7 21 Analyze gt Pole Figure gt Tilt Tilt the maximum display memory value for _ pole figure about a new polar origin example corresponding to white on the dis play The special value 1 directs the pro Menu Command Analyze gt Pole Figure gt Tilt gram to pick a reasonable value by scanning through the pixels in the frame prior to display the special value 2 directs Accelerator None User Level 1 the program to use whatever setting is cur SLAM Syntax POLE_FIG TILT 1 rently in effect The default value is 2 the DISPLAY lt n gt X lt n gt Y lt n gt 2 allowed range is from 2 to 10 counts Smaller values make the displayed image look brighter larger values make look darker Frequently the d
271. ayed raw data pattern After entering or modifying peaks parameters with MANUAL PEAKS REFINE performs a least squares fit of all variable parameters Very accurate results can be obtained from user specified peaks MANUAL can be used in interactive mode only When you choose PEAKS MANUAL from the menu bar a vertical cursor appears Within the statistics window is the wavelength 20 d spac ing and intensity for the current cursor position If the cursor resides within a peak region the region start end and backgrounds area also dis plays in the statistics window The peak parame ters 2T d FWHM of the nearest peak within the peak region are also displayed MANUAL has four options Press ENTER or the left mouse button to display the submenu or press the first letter of the subcommand to directly enter that option Choices are ADD Add a new peak All peak parameters are defaulted using values obtained at the current cursor position and a pop up entry menu appears Upon exiting the peak is saved and a peak profile is drawn DELETE Delete the peak nearest the current cursor position No further arguments are required The peak profile is also deleted MODIFY Modify a peak s current parameters A menu appears with the current peak parameters Upon exiting the peak profile is erased and redrawn with the new parameters REGION Add or modify a region s current parameters A menu appears with the current or defaulted reg
272. be identical to form a closed loop e Omega ranges of 180 to 180 degrees are special case gt no limit e Valid drive range is INSIDE the graphed region e These extended limits are used in addition to normal limits Any system without a controllable chi circle is unaffected by the extended limits command It is important that the environment variable SAXISADMODEL is defined correctly for your goniometer type since the default limits are dif ferent between 4 circle and 1 4 circle systems See Edit gt Configure gt ShowModel Section 4 5 for more information 5 16 1 Arguments None Command executes immediately M86 E01008 GADDS Software Reference Manual Collect Routines 5 17 Collect gt Goniometer gt Speeds Enter slew drive speeds of axes Menu Command Collect gt Goniometer gt Speeds Accelerator none User Level 2 SLAM Syntax GONIOMETER SPEEDS 1 2 3 4 5 6 7 8 9 or GONIOMETER SPEEDS 1 2 3 or GONIOMETER SPEEDS 1 2 This command is used to set the maximum drive speeds for the goniometer axes These speeds are also used as the fast drive speeds in man ual mode see Collect gt Goniometer gt Manual Section 5 11 When invoked from the menu or run from the command line without arguments Collect gt Goniometer gt Speeds displays a dialog box where you can view edit the arguments described below Pressing the ENTER key or clicking the OK button upda
273. breviated form which contains only those commands needed for routine diffraction prob lems and those needed for expert diffraction ists Additionally the detector administrator account will see a third level for the full set of commands needed for calibration and manage ment of the system in addition to data collection The abbreviated form is the Special gt Level 1 menu bar the full form is the Special gt Level 2 menu bar and the administration form is the Special gt Level3 menu bar You can use these commands to switch between the two or three menu bars You can also use the startup qualifi ers LEVEL2 LEVEL3 and LOCK to start GADDS at a specific user level and or disable the Level menu commands locking GADDS at the startup user level See Startup Qualifiers Section 1 3 for more information 9 10 1 Arguments None Command executes immediately M86 E01008 10 User Task Routines 10 1 User gt Execute user task Menu Command User gt user defined Accelerator Ctrl F1 through Ctrl F12 User Level 1 SLAM Syntax None Up to sixteen user defined commands called User Tasks may be added to the User menu on the menu bar by modifying GADDS SYS DATA usertask ini When GADDS is started it reads this file to modify the menu bar to add all the defined user tasks When a user task is selected GADDS reads this file again to retrieve the parameter prompts parameter help line and
274. ce Manual Peaks Routines the ESC key had been pressed Similarly the prompt RE INDEX REFLECTION ARRAY described above will in that case time out after 10 s as if the ENTER key had been pressed 8 16 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses IAAX lt ND gt nnana Expected A Axis Length A trial A axis vector is accepted only if its length is in the range AAX MAX 1 FCELL 0 01 to AAX 1 FCELL The allowed input range is 1 2500 Angstroms and the default value is 80 A If you know the axis length enter it here and make FCELL small otherwise make the best guess you can You can use the CURSORS VECTOR and CURSORS CIRCLE com mands to derive approximate unit cell axis lengths IBAX lt N gt onnan Expected B Axis Length A trial B axis vector is accepted only if its length is in the range BAX MAX 1 FCELL 0 01 to BAX 1 FCELL The allowed input range is 1 2500 Angstroms and the default value is 80 A If you know the axis length enter it here and make FCELL small otherwise make the best guess you can You can use the CURSORS VECTOR and CURSORS CIRCLE com mands to derive approximate unit cell axis lengths ICAX lt N gt eee Expected C Axis Length 80 00 A trial C axis vector is accepted only if its length is in the range CAX MAX 1 FCELL 0 01 to CAX 1 FCELL The allowed input range is 1 2500 Angs
275. cel button exits the dialog and returns you to the menu When invoked from the command line SCAN RESUMERUNS can take the arguments shown in the SLAM syntax description above where lt n gt represents a numeric value and lt s gt repre sents a string value The first 13 arguments correspond to those that were specified in the Acquire gt MultiRun Hemisphere or Quadrant input dialog The next 15 represent the values obtained from the run list for the interrupted scan M86 E01008 Collect Routines GADDS Software Reference Manual 5 33 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Pl EEEn A Job Name from resume _tm TITLE lt S gt cce Title from resume _tm SAMPLE lt s gt Sample Name from resume _tm NUMSAMPLE lt s gt Sample Number from resume _tm DISPLAY lt n gt Max Display Counts from resume _tm REAL TIME Real time Display from resume _tm CLEAR pinna Pre Clear from resume _tm OLDXENGEN Xengen Output Format from resume _tm STARTRUN lt n gt Sequence of Starting Run from resume _tm ENDRUN lt n gt Sequence of Ending Run from resume _tm MODE lt n gt Mode Scan Oscillate Step from resume _tm ROTATE 0 0ee Rotate Sample from resume _tm NIDEO oasis Capture Video Image from resume
276. cheme can be determined using the SCHEME command After inputting the goniom eter settings the scan angle step and number of frames along with the 2 theta of the desired pole the SCHEME option will display where the simulated data will map on the pole figure pro jection Complete coverage of the pole sphere can be assured along with the reduction of duplicate data for shorter data collection times For complete coverage omega must be half of the frame 2 theta angle Otherwise a hole will be in the center of the pole image In script mode always use 2THETA1 lt gt through 2THETA4 lt gt where runs not used should have blank values 7 18 2 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 EA E Pole 2T 10 2 theta of desired hkl pole While the pole 2T can be different than the detector 2T it must intersect the detector face DISTANCE lt n gt Distance 7 0 Detector distance in cm NUM lt n gt Frames 36 Number of frames to collect at these set tings 2THETA lt n gt 2Theta 0 0 THETA1 lt n gt Theta 1 0 0 Initial 2 theta goniometer setting On 0 0 systems this is the 61 tube axis OMEGA lt n gt Omega 0 0 THETA2 lt n gt Theta 2 0 0 Initial omega goniometer setting On 0 6 systems this is the 02 detector axis PHl lt n gt 00 Phi 0
277. cified here and N is the total number of difference vector groups included in the indexing The default value of 0 8 should be suitable in most cases If the program cannot find a solution and you ve checked the spatial cor rection beam center etc as described above you might try decreasing this number e g to 0 7 Valid input range is 0 1 but if you have to reduce this number to 0 5 or lower to find a solution something is wrong 8 16 2 Autoindexing Output Two examples of the output from REFL_ARRAY INDEX is shown below Both have the VER BOSE qualifier set Example 1 is the first output window from indexing of the eight myoglobin test frames If you re familiar with Bruker s scin tillation counter software this output is similar The indexing was performed with 26 centered reflections extracted with a THRESHOLD sub command as performed by the FVERIFY SLM test sequence supplied with the program how ever the indexing here was performed specify ing AAX 90 BAX 90 CAX 45 FCELL 0 1 The output and indexing time in this case are significantly shorter than those obtained in the test sequence which specifies AAX 80 BAX 80 CAX 80 FCELL 0 75 The first output line contains the axis length lim its in Angstroms used to filter trial axis vector solutions in the order minimum maximum A minimum maximum B minimum maximum C followed by the maximum HKL difference vector M86 E01008 GADDS Software Refere
278. com mand line name followed by its dialog box prompt in parentheses PEEN TEA Filename brass _ix Name of the spatial correction to read This filename is merged with the current frame directory specified in the CONFIGURE EDIT panel before the program attempts to access the file See CONFIGURE EDIT for a description of how this is done If you leave this field blank or specify a wildcard filename pattern in the SPATIAL LOAD input panel the program will display a list of filenames from which you can select the desired correction see DISPLAY NEW for a more complete description of filename selection The default filespec for filename selection is Frame_root _IX where Frame_root is the frame directory specified in the CONFIGURE EDIT panel The special filename of 6DEFAULT is replaced with the standard naming conven tion of SIZE_DDD _IX where SIZE is replaced by 0512 or 1024 and DDD is replaced by the detector distance in cm 18 M86 E01008 GADDS Software Reference Manual Process Routines 6 8 Process gt Spatial gt Linear Revert to linear table i e no correction Menu Command Process gt Spatial gt Linear Accelerator none User Level 2 SLAM Syntax SPATIAL LINEAR Selecting SPATIAL LINEAR with the LINEAR option from the SPATIAL submenu or from the command line specifies that no spatial correc tion will be used in subsequent data acquisition lin
279. cribed below The normal method deter mines the reduced primitive unit cell whose axis lengths must fall within the ranges specified in the input if you don t know the axis lengths specify large ranges Following this method of autoindexing you should run REFL_ARRAY BRAVAIS to determine the correct Bravais lat tice based on the metric symmetry of the reduced primitive cell for example if you have a centered lattice BRAVAIS will determine the parameters of the centered cell and will trans form the reflection indices to the centered cell indices Following the Bravais lattice determina tion you would then run REFL_ARRAY LEASTSQ to refine the unit cell parameters crystal orientation and detector positional cor rections The second indexing method used when NOREDUCE is set suppresses the conversion to the reduced primitive cell In this case the program looks for a solution which fits both the input axis length ranges AND the input cell angle ranges The method can be useful for example for indexing a known centered unit cell directly on the centered lattice Following index ing by this NOREDUCE method you will typi cally bypass the Bravais lattice step and run REFL_ARRRAY LEASTSQ to refine the cell orientation etc However if you do use the Bra vais lattice option after indexing by the NORE DUCE method be sure to specify the correct lattice type in the BRAVAIS input panel For example if you index on a k
280. cting only a unique portion of the reflection data or to design custom data col lection strategies This program is described in detail in the ASTRO Technical Reference Manual TOPAS P is a profile fitting program for fun damental parameter and general lineshape fitting of diffraction spectra This program is described in detail in the PROFILE S Man ual DIFFRAC S for GADDS is a complete set of integrated programs for evaluation search match etc on 1D spectra Pro grams included in the DIFFRAC S package include EVA Graphical evaluation package Diffrac File Exchange Similar to Raw2Raw utility but more limited except with UXD file formats PDF Database Maintenance Utility to view and manipulate PDF database XRD Evaluation Program Graphical evalu ation package with optional search match algorithm XRD Quantification Program Graphical quantification package These programs are described in detail in the DIFFRAC S Manual M86 E01008 GADDS Software Reference Manual General Information GADDS may be executed in either online or off line mode The online version of GADDS sup ports a variety of goniometer stages and other instrument configurations including the following hardware options e _HISTAR detector and dual HISTAR detec tors e D8 Discovery Platform Aztalan or P4 goni ometers e Phoenix D8 or GGCS all others goniom eter controllers e Numerous different gonio
281. ction tables limits etc 2 header errors user tasks 3 echo controller commands general messages etc 4 echo controller responses detector messages raw files etc 5 echo flushed serial characters sent ASCII codes 6 timeouts 7 extended debug output callbacks etc 8 COM port characters received SAXISNOBOXLIM This optional variable if defined will increase the maximum Cursor gt Box and Cursor gt RBox size limit from 64 to 256 for diagnostic purposes SAXISOLDNAMES When set to any value this instructs the pro gram to use the old frame naming conven tions when creating new frame files SAXISON If non zero we continue command file pro cessing regardless of error code If zero or undefined command files stop on error code SAXI PKZIP If defined it is set to the full pathname of PKZIP for console version 2 50 which is used in the Project gt Backup command SAXI PRINTER This optional variable points to the default GADDS print queue A useful trick is to setup a GADDS print queue with typical set tings for GADDS printing such as landscape orientation SAXIS SITE The site name given here is stored in the header of frames written in Bruker format M86 E01008 GADDS Software Reference Manual General Information Under WNT this defaults to the Regis SAXI VIDEOFORMAT teredOrganization name in the Registry Overrides the saving of video images in SAXISSWCHA
282. cumulation memory for example an image left over from a previous ADD LOAD or SCAN com manq PATTERN 0 Test Pattern N This qualifier when present draws a test grid into the frame accumulation memory prior to collecting data The test grid is used for factory alignment and consists of grid lines on a 64 pixel spacing two circles one with a 270 pixel radius and one with a 280 pixel radius and two crosses rotated to 45 degrees one linear cross and one passed through the current flood field correction COUNTS lt n gt Max Counts 10 000 000 This qualifier sets an upper limit on how many counts may occur before data collec tion is terminated When the specified num ber is reached the system ends the data collection saving the data frame The default value is 10 000 000 counts with a range from 0 to 10 counts Data collection will also be terminated if MAX SECONDS is reached before MAX COUNTS DISPLAY lt n gt Max Displayed Counts 7 0 no display otherwise counts corre sponding to white on the display The initial default is 7 the allowed range is from 0 to 10 REALTIME Real time Display Y This qualifier when present displays data as it is being collected The display does require additional processing time and will limit the maximum rate at which counts can be accumulated If the MAX DISPLAYED COUNTS qualifier is given a non zero value t
283. current program settings from a specified disk file These config uration files which have file extensions of _nc contain the current flood file correction spatial correction and current values of nearly all input panel items for nearly all the GADDS com mands a few exceptions 4 3 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses A eee oer Configuration Filename gadds _nc Enter the filename where the configuration is to be saved or read The default file is gadds _nc If you omit the file extension __nc is assumed M86 E01008 GADDS Software Reference Manual Edit Routines 4 4 Edit gt Configure gt Write Save the current configuration to a disk file Menu Command Edit gt Configure gt Write Accelerator None User Level 2 SLAM Syntax CONFIGURE WRITE 1 Use this command to save current program set tings to a specified disk file for later read in using the Edit gt Configure gt Read command Typically you would use these commands to save a good configuration play around with the program and if something fails restore the good configuration These configuration files which have file exten sions of _nc contain the current flood file cor rection spatial correction and current values of the input panel items for nearly all the GADDS commands a few exceptions On startup GADDS normally reads its confi
284. d line name followed by its dialog box prompt in parentheses 1 to 8 See Collect gt Goniometer gt Manual Sec tion 5 11 NOTE This command is designed to work only on stages with a goniometer head 5 13 Collect gt Goniometer gt Flatsam ple Perform check flat sample plane on XYZ stage Menu Command Collect gt Goniometer gt Flat sample Accelerator Ctrl Shift W User Level 1 SLAM Syntax GONIOMETER FLATSAMPLE X1 lt n gt V1 lt n gt Z1 lt n gt X2 lt n gt Y2 lt n gt Z2 lt n gt X3 lt n gt Y3 lt n gt Z3 lt n gt On systems equipped with an XYZ stage it is possible to collect scans at multiple target loca tions On flat samples such as wafers one fre quently wishes to take scans on target positions laid out on a rectangular grid Instead of manu ally determining the Z axis position of each tar get on the grid one can pre determine the flat sample plane then lay out the target locations using Collect gt Scan gt GridTargets see Section 5 41 which will automatically calculate the cor rect Z axis value from the flat sample plane FLATSAMPLE works on the simple principle that 3 points determine a flat plane Initially these points are defaulted to form a small trian gle about the current goniometer position in XYZ For greater accuracy the user should enlarge this triangle of points M86 E01008 Collect Routines GADDS Software Reference Manual Next th
285. d the endpoint is on a reflection taken at omega 0 chi is the angle to which you would drive the goniometer to place the reflection in the equatorial plane on the pos itive 2 theta side M86 E01008 GADDS Software Reference Manual Analyze Routines 7 9 Analyze gt Graph gt Rocking Plot rocking curve profile through frames Menu Command Analyze gt Graph gt Rocking Accelerator Ctrl R User Level 1 SLAM Syntax GRAPH ROCKING 1 2 3 4 QUADRANT lt n gt FRAME_HALFWIDTH lt n gt DELAY lt n gt NOERASE GRAPH ROCKING draws a graph in the frame window or a specified quadrant called a rock ing curve This graph shows integrated intensity in a specified rectangular area as a function of scan angle and requires that you have a contig uous series of frames available for input Before running GRAPH ROCKING a set of data frames must be collected with fixed step size in any angle Use the DISPLAY or LOAD command to display the central frame about which you want the rocking curve to be com puted Then invoke GRAPH ROCKING where a rectangular cursor like the one in CURSORS BOX is used to select a region within the data frame From this the program calculates the background subtracted intensity for that region in each frame and displays the results in a plot of intensity versus scan angle Background sub tracted intensity is determined in the same way as for CURSORS BOX The background i
286. d then using either white below that value or print ing a 25 level grayscale in landscape format Color scale plots ignore the threshold value and print the screen in 16 colors When invoked from the menu or from the com mand line without arguments File gt Print dis plays a dialog box where you can view edit the following items before performing the print oper ation If you press ENTER or click the OK but ton printing begins Pressing ESC or the Cancel button returns you to the menu Use CTRL BREAK to interrupt printing in progress You can also print the current display screen from just about anywhere in the program by pressing CTRL P allowing you to plot screens containing menus input panels etc Don t use CTRL P during real time data collection Timing of real time operations could be compromised The parameters on the PRINT input panel affect CTRL P screen dumps the same way as PRINT command screen dumps Note Under NT the CTRL P option does not work when GADDS is in either a menu panel or a message box 3 11 1 Arguments Each option is listed below by its SLAM com mand line name followed by its dialog panel prompt in parentheses Srii Output Device or Filename default Enter either the filename or device which is to receive the printout The default device is SAXI PRINTER which you can define as a logical name to point to a file or device if desired For example the DOS command SET SAXI PRINTER PRN w
287. d leave part of the image area blank the image is translated only far enough to place the edge of the frame at the edge of the image area No arguments are prompted for when ZOOM is invoked from the menu ZOOM displays a full screen crosshair the zoom center is selected with the crosshair which can be dragged with the mouse or cursor keys Once the zoom cen ter is selected press ENTER or release the left mouse button to display the following pop up menu from which you can choose the desired magnification factor Exit 1X 2X 4X 8X 16X Select the EXIT option to exit and return to the menu Cursor commands that return pixel values and positions can be used on zoomed images Posi tions are reported relative to the original image for example if the magnification factor is 16 you would need to press the left arrow key 16 times in Analyze gt Cursor to change from one X pixel coordinate to another assuming you start at the edge of an unmagnified pixel When invoked from the command line inter preter mode the ZOOM command accepts three arguments i Ree a aera X 255 Enter X pixel to try to center on screen The range is from 0 to framesize 1 SD xe traces Y 255 Enter Y pixel to try to center on screen The range is from 0 to framesize 1 GS a tic ek hs Magnification 1 Enter the magnification zoom to examine a specific area in greater detail The allowed range is from 1 to 16 M86 E0100
288. d orphaned project from database D frames 20002 Oct MyProject0 gadds _nc Then you are automatically sent to the Project gt New command see Section 2 3 Project gt New Enter appropriate values and click OK Inform your GADDS administrator if you get the mes sage Can t open gaddsdef _nc Using default settings You must use Project gt Overwrite defaults command When GADDS is started you are automatically sent to the last project most recently accessed You can override this default behavior by modify ing the GADDS shortcut with command line qualifiers noproject Forces GADDS to always create a new project when it starts project lt projname gt Forces GADDS to always open into the same project lt projname gt GADDS prevents offline instances from over writing the defaults for online operation When operating in offline mode GADDS always appends _offline to the configuration filename before saving When reading the configuration offline GADDS tries to read this offline version but if missing GADDS reads the online version This allows you to operate online GADDS ina directory while simultaneously running offline GADDS for processing the newly collected frames in the same directory could be from a different computer using mapped network drives M86 E01008 GADDS Software Reference Manual Project Management Routines 2 1 Project gt Switch Change toa different existi
289. degrees to be added to subsequent omega values reported by the controller Or theta2 axis detector Sette onl Phi 0 00 Enter the phi encoder zero offset in degrees to be added to subsequent phi values reported by the controller ra e erasia teats Chi 0 00 Enter the chi encoder zero offset in degrees to be added to subsequent chi values reported by the controller PEETA X 0 00 Enter the X encoder zero offset in mm to be added to subsequent X values reported by the controller PESEE Y 0 00 Enter the Y encoder zero offset in mm to be added to subsequent Y values reported by the controller PEE Z 0 00 Enter the Z encoder zero offset in mm to be added to subsequent Z values reported by the controller antsagllesevensteysbreens Aux1 0 00 Enter the Aux1 encoder zero offset in units to be added to subsequent Aux values reported by the controller M86 E01008 GADDS Software Reference Manual Collect Routines GO es fel aragua Delta 0 00 Enter the Delta encoder zero offset in cm to be added to subsequent Delta values reported by the controller 5 30 Collect gt Scan gt SingleRun e Perform a single scan series Resume an interrupted SingleRun Menu Command Collect gt Scan gt SingleRun Accelerator Ctrl Shft F 1 User Level 1 SLAM Syntax SCAN SINGLERUN 1 2THETA lt n gt THETA1 lt n gt OMEGA lt ns gt THETA2 lt n gt gt PHl lt n gt CHl lt
290. do not contain command information are prefixed with the comment character Lines that contain command output are prefixed with I gt Note that the cursor was at X Y 435 190 when the command started but the user moved the cursor to a final position of 139 311 before exiting the command With scripting enabled the same command pro duced the following output script file containing just one line CURSORS PIXEL 139 311 DELAY 0 0 M86 E01008 File Routines GADDS Software Reference Manual 3 9 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its input panel prompt in parentheses E E Log Filename frame _lg Filename of the log file to which output is directed By convention log files have the extension _lg If you don t supply a filename extension the program will add the _lg extension If you leave this item blank or specify a wildcard filename pattern press ing ENTER or clicking the OK button will dis play a list of the current filenames matching the pattern You can choose one from the displayed list by moving to it with the arrow page keys or mouse and pressing ENTER or clicking the OK button You will be returned to the File gt LogFile dialog with the selected filename filled in If you leave this item blank it is the same as entering a _Ig wildcard pattern APPEND 4 Append Yes If you check this option output w
291. ds such as SORT and MODIFY can operate globally on the entire array and provide a faster method for making more extensive changes REFL_ARRAY EDIT is an interactive command only You can invoke it from the command line but it will not proceed without intervention There is no built in 10s timeout on REFL_ARRAY EDIT like there is on other scrolling output win dows The command line syntax is REFL_ARRAY EDIT Some of the other sub commands such as MODIFY automatically invoke EDIT on com pletion but only when they have been invoked from the REFL_ARRAY submenu so you can review the results Operation in such a case is the same as described here Like other scrollable windows the REFL_ARRAY EDIT window displays the ASCII icon IAVI at the left of the title bar You can move through the text in the array with the page keys arrow keys or mouse motion If you press the ESC key or right mouse button the program will return to the REFL_ARRAY submenu If you press the ENTER key or left mouse button when in the scrolling edit window the program dis plays a pop up menu of editing functions You can then use the cursor keys or mouse to select a specific function to implement Press ENTER or the left mouse button again to execute it or ESC right button to return to the editing window The functions in the pop up menu are as fol lows Exit Return to REFL_ARRAY submenu saving changes to array The ESC key or right
292. ds _nc which will be read the next time you start GADDS Then a box appears with OK and Cancel but tons and the message EXIT Are you sure The purpose is to provide a safety net in case EXIT was selected by mistake Click the OK but ton or press the ENTER key to exit the pro gram If you do not wish to exit at this time click the Cancel button or press Esc and you ll be returned to the GADDS menu In command mode EXIT terminates GADDS after saving the current configuration without displaying any prompts 2 10 1 Arguments None Command executes immediately after confirmation message M86 E01008 3 File Routines 3 1 File gt Display gt Open Display a detector frame on the screen Menu Command File gt Display gt Open Accelerator Ctrl D User Level 1 SLAM Syntax DISPLAY NEW 1 QUADRANT lt n gt LO lt n gt Hl lt n gt X lt n gt Y lt n gt MAG lt n gt AUTOINCREMENT GRAPHICS_SAVE ORIENTATION VIDEO OVERLAY Use this command to display a specified data file from disk or to display or redisplay the cur rent contents of the frame accumulation mem ory Up to four different data files can be displayed at the same time using File gt Display to place them into separate quadrants You can also display a region within a frame magnified in a quadrant or in the full image window by setting the input arguments appropriately While multiple images can be displayed in differ
293. e Draw 2D surface plot of pole figure 7 64 1 31 ATGUMENS bee eripe Role he bee hae ek bebe eat ae Poe et bo pe eee 7 64 7 32 Analyze gt Pole Figure gt Fiber Take a cut through pole figure and display versus Utange n Seca Ue pel ba ee oe E oa E E kcatbedele Yee gees 2 7 65 C325 AUMENS rriad Ke EAEE Bele ahora Se ASEE EA Bad Seeds eee ae 7 65 7 33 Analyze gt Stress gt Conventional Process frame images into data file for STRESSPS package ein heehee uice eE 7 66 7 33 1 Hardware Requirement for Stress Measurements 0000 cee eeu 7 66 7 33 2 Data Collection with GADDS 0 0 00 ae 7 66 7 33 3 Data Processing with GADDS 0 0 c eae 7 67 7 394 Suess Calculation s ca girse end bee tea ewe eed ots alesis od dan a dx 7 67 33 5 Arguments ccs eke cans Seed eee een eee ade tye Yale ed Gas 7 67 7 34 Analyze gt Stress gt Scheme 2D itisto Era a a TANE eet ene n eens 7 69 TAT APQUMENTSS 125 Ace nd en eid eee PE ove ea en Polos feb he vetted es 7 69 7 35 Analyze gt Stress gt Biaxial 2D e Biaxial stress measurements from frame images Analyze gt Stress gt BiaxialShear2D Analyze gt Stress gt Triaxial2D 04 7 70 7 80 ALAQUMOENIS aosa a EE meee tai eae deni eal heed w eel hew Weis Be 7 71 7 36 Analyze gt Stress gt View 2D View biaxial stress and original frame images 7 74 03631 AUMENS aria aa EEEE EEEE em EN AEN ee etd adeno edge ee 7 74 7 37 Analy
294. e O single range 40 39 x xR4 Data in raw counts not counts second 16384 chi range 16384 8192 phi range where x number of steps in range M86 E01008 DIFFRAC AT Raw Data File Format GADDS Software Reference Manual Additional ranges use this same format and are appended to the end of the first range NOTE Early Diffrac AT raw data files did not repeat the RAW on additional ranges Profile PRO File Format identical to Diffrac AT V1 with these changes Record Format Field description 1 A4 PRO instead of RAW 29 R4 Two theta of Imax in profile 30 R4 FWHM of profile 31 R4 Offset of peak angle position from the Imax position in profile Diffrac AT V2 V3 raw data files are stored in a direct access binary file without any record deliminators The structure starts with a 256 byte file header block followed by a range header and data block which are repeated for each range in the file Offset Format Field description 0 A4 RAW File identification text 4 12 Number of ranges in this file 6 2 Unused 8 A32 Sample base name 40 A128 Sample extended name comments 168 A20 Date time measured 07 Jun 1995 18 20 00 188 A2 Chemical symbol for tube anode 190 3R4 Lambda1 Lambda2 Intensity ratio 202 12 Diffractomete
295. e series from resume _tm ICHI lt N gt nonna Chi from resume _tm Enter the goniometer chi setting angle in degrees at which the remaining frames in the current scan series are to be collected A Platform goniometer is fixed at CHI 54 74 An older Aztalan black 3 cir cle goniometer is fixed at CHI 45 IXEKN gt eai e X Enter the goniometer chi setting angle in degrees at which the remaining frames in the current scan series are to be collected NEN voccecccsssecenees Y Enter the goniometer chi setting angle in degrees at which the remaining frames in the current scan series are to be collected from resume _tm from resume _tm IZSEN gt aaa Z from resume _tm Enter the goniometer chi setting angle in degrees at which the remaining frames in the current scan series are to be collected AUX lt N gt nnnnnnn Aux from resume _tm Enter the goniometer chi setting angle in degrees at which the remaining frames in the current scan series are to be collected AXIS lt N gt nnnnnnn Scan Axis from resume _tm Enter the number of the axis to be scanned either 2 for omega scans or 3 for phi scans Remember that some data reduc tion programs cannot reduce phi scan data unless it was taken at CHI 0 A Platform goniometer is fixed at CHI 54 74 An older Aztalan black 3 circle goniometer is fixed at CHI 45 SAINT can reduce phi scans taken at nonzero chi WIDT
296. e DIFFRAC 5000 V1 VAX VMS e NACS VAX VMS e NACS PDP 11 TSXIRT 11 e DIFFRAC 11 PDP 11 RSX e DIFFRAC 5 PDP 11 RSX e Philips UDF format may read only a subset of UDF files 13 18 M86 E01008 GADDS Software Reference Manual Utility Programs RAW2RAW only requires the names of certain files as user input The user has the option of entering ALL filenames on the command line or to leave the command line blank and have the program prompt the user for all filenames Wild cards are permitted in filename inputs Syntax for command line RAW2RAW B FORMAT filename raw OUT filename out Additional switches for UXD output C l N Sc W 2 B Batch mode suppresses final Hit lt Return gt to continue message filename raw Required The name of the RAW data file containing ranges The input file format is automatically determined filename out Optional Defaults to lt filename gt out 4 PLOTSO 5 DBW 6 DBWS 7 GSAS 8 UDX C CPS mode Outputs data points in CPS default is intensity 1 Item number Outputs data points N Noheader mode Suppress output of header information Sc Separator comma semi colon s space t tab n none W Width Width of each item in characters for default separator Optional Defaults to DIFFRAC PLUS Pos 2 SONA USRA 2theta mode Include 2T angle on each li
297. e been loaded Verify that the appropriate calibration files have been loaded and that the goniometer angles and the values of the distance and X and Y beam centers are correct Update if necessary Select the appropriate level for the experi ment e g Level 1 beginner or Level 2 experienced Mount the specimen and proceed with the experiment Individual steps will be described this manual To exit from the program drive all angles to zero and click on the File gt Exit option Do not exit from the program by clicking the Windows NT close button this will cause abnormal termination and loss of configura tion data M86 E01008 GADDS Software Reference Manual General Information 1 2 Environment Variables Logical Names Under WNT logical names are stored as envi ronment variables Entering environment vari ables are done through Control Panel s System Applet You may enter environment variables as either system available to all users or as user available only to the current user Logical names which point to directories should end with a colon and the translation should end with the directory separator V Example Defining the GADDS FRAMES direc tory set GADDS FRAMES C FRAMES To display a frame say cor1 001 from the GADDS FRAMES directory the name to enter in the DISPLAY NEW panel would then be GADDS FRAMES cor1 001 If the default working directory in the GADDS
298. e driving the goniometer manually to look for or maximize the intensity of a reflec tion it helps to clear the screen frequently for example every 1 second by setting the reset interval to 1 SHUTTER Open amp Close Shutter No If present on the command line or checked Y in the dialog box this qualifier causes the shutter to open at the start of Collect gt Add and to close at the end Otherwise the shutter stays in its current state for the dura tion of the exposure M86 E01008 Collect Routines GADDS Software Reference Manual ATTENUATOR Insert Attenuator No If present on the command line or checked Y in the dialog box this qualifier causes the shutter to open with the attenuator inserted at the start of Collect gt Add and to close at the end Otherwise the shutter stays in its current state for the duration of the exposure 5 48 Collect gt Shutter Open close X ray beam shutter Menu Command Collect gt Goniometer gt Shutter or Collect gt Shutter Accelerator Ctrl Shift S User Level 1 SLAM Syntax GONIOMETER SHUTTER or SHUTTER See Section 5 20 Collect gt Goniometer gt Shut ter M86 E01008 6 Process Routines 6 1 Process gt Flood gt New e Acquire data to generate new flood field correction Menu Command Process gt Flood gt New Accelerator none User Level 3 SLAM Syntax FLOOD NEW 1 COUNTS lt n gt DISPL
299. e is 0 the range is from 0 to 16365 YMIN lt n gt 006 Lower Y of Corrected Frame 0 Enter the Y detector bin number to use as bottom of corrected frame The default value is 0 the range is from 0 to 16365 IMAG lt n gt 0006 Magnification of Corrected Frame 1 Enter the magnification factor of the correc tion table The default value is 1 the range is from 1 to 32 SHUTTER Open amp Close Shutter Y N N This qualifier if present on the command line or given as Y in the input panel causes the shutter to open at the start of each exposure and to close at the end Oth erwise the shutter stays in its current state for the duration of the command It is used for the Fe foil method of generating a point source Keep the shutter closed for Fe sources M86 E01008 Process Routines GADDS Software Reference Manual 6 2 Process gt Flood gt Load Install a disk resident flood field correction table Menu Command Process gt Flood gt Load Accelerator none User Level 2 SLAM Syntax FLOOD LOAD 1 This command is used to read and install a flood field calibration file that was previously created with FLOOD NEW or FLOOD REPROCESS These commands compute a flood field table from an X projection and Y projection of an Fe gt image By convention each flood field correc tion is stored in a plottable ASCII file ending ina _FL extension in the curre
300. e number of frames actually available for processing in either direction If FRAME_HALFWIDTH is zero intensity will be taken from only the frame which is currently displayed The scan angle centroid will not be precisely determined in this case and the C flag will not be set for the new record inserted into the reflection array In this case a rocking curve is not dis played and response is therefore much faster M86 E01008 GADDS Software Reference Manual Peaks Routines 8 16 Peaks gt Refl Array gt Index Autoindex to compute HKL s of angles only reflections Menu Command Peaks gt Refl Array gt Index Accelerator Ctrl I User Level 1 SLAM Syntax REFL_ARRAY INDEX 1 AAX lt n gt BAX lt n gt CAX lt n gt U1 lt n gt U2 lt n gt U3 lt n gt FCELL lt n gt SIGA lt n gt NOREDUCE VERBOSE FGROUP lt n gt HKLTOL lt n gt FFIT lt n gt REFL_ARRAY INDEX is used following REFL_ARRAY THRESHOLD and or PICK to determine HKL indices for those reflections in the array which have at least the A and C flags set that is those reflections which contain set ting angles X Y and span more than one frame are centered Autoindexing determines in addition to HKL indices for each reflection a rough crystal orientation and unless specified otherwise the reduced primitive unit cell There are two ways to perform indexing depend ing on the setting of the NOREDUCE qualifier des
301. e swing 2 theta setting angle in degrees to be assumed for the frame series The default value 9999 specifies that the swing angle is to be extracted from the frames themselves which is the normal mode of operation If you re processing old XENGEN format frames acquired with soft ware earlier than FRAMBO Version 2 you ll need to explicitly specify the angle here For frames in XENGEN or BRUKER format acquired with FRAMBO V2 or higher spec ify 9999 T A Omega override 9999 Enter the starting omega setting angle in degrees to be assumed for the frame series The default value 9999 specifies that omega is to be extracted from the frames themselves which is the normal mode of operation If you re processing old XEN GEN format frames acquired with software earlier than FRAMBO Version 2 you ll need to explicitly specify the angle here For frames in XENGEN or BRUKER format acquired with FRAMBO V2 or higher spec ify 9999 E ecbevhkt Phi override 9999 Enter the starting phi setting angle in degrees to be assumed for the frame series The default value 9999 specifies that phi is to be extracted from the frames themselves which is the normal mode of operation If you re processing old XENGEN format frames acquired with software earlier than FRAMBO Version 2 you ll need to explicitly specify the angle here For frames in XEN GEN or BRUKER format acquired with FRAMBO V2 or higher specify 9999 ci AA T E EA
302. e the default range s settings filein raw First input filename Must be entered but extension will default to raw The input file format is automatically determined Additional input filename s and their ranges to merge may be specified up to a maximum of 10 filenames merge out Output merged data file Defaults to merge out NOTE Brackets are not type They are used to bracket optional or defaulted values NOTE All command line switches may be abbreviated and the separator character may be P or that is F 1 F 1 and FOR MAT 1 are equivalent NOTE The command line arguments are order specific Current limitations ignored fields in file for mats e RAW PLUS supplemental range header records osc psd com e RAW PLUS reading RAW1 00 measuring electronics may be incorrect e RAW V2 diffractometer configuration word e RAW V2 oscillating drive amplitude speed e RAW V2 supplemental range header record for comment 4 M86 E01008 Utility Programs GADDS Software Reference Manual Other limitations e Cannot merge an additional range in between two other ranges One must reor der the ranges such that the additional range is being added to the head or tail of the previously merged ranges Range start end 1 10 0 40 0 2 60 0 90 0 3 35 0 65 0 lt Fails e Cannot merge a range when previous ranges
303. e the discussion above Valid range is 0 1 to 9999 SHUTTER Open amp Close Shutter Y N No This qualifier if present on the command line or given as Y in the input panel causes the shutter to open at the start of each exposure and to close at the end Oth erwise the shutter stays in its current state for the duration of the command It is used for the Fe foil method of generating a point source Keep the shutter closed for Fe sources 16 M86 E01008 GADDS Software Reference Manual Process Routines 6 7 Process gt Spatial gt Load Install a disk resident spatial correction Menu Command Process gt Spatial gt Load Accelerator none User Level 2 SLAM Syntax SPATIAL LOAD 1 This command is used to read and install a spa tial correction that was previously created with SPATIAL NEW or SPATIAL PROCESS These commands compute a spatial correction from an Fe image taken with the brass fiducial plate fastened to the front of the area detector By convention each spatial correction is stored ina plottable ASCII file ending in a _IX extension in the current frame directory specified in the CONFIGURE EDIT panel Although you can thus keep several different spatial corrections available at any time re using old spatial correc tions is really not very useful since your results will be better if you run SPATIAL NEW prior to data collection on each new sample Howe
304. e to follow a certain number of numeric values in free separated by spaces If the number of items or their type doesn t agree with the flag settings the program issues and error message and asks you to re enter the line Modifying the A and H flags from with REFL_ARRAY EDIT as opposed to MODIFY can be a tricky process and is therefore not recommended M86 E01008 GADDS Software Reference Manual Peaks Routines 8 20 Peaks gt Refl Array gt Modify e Alter specified item for a range of reflections in the array Menu Command Peaks gt Refl Array gt Modify Accelerator None User Level 1 SLAM Syntax REFL_ARRAY MODIFY 1 2 FIELD lt n gt VALUE lt s gt This option lets you make global changes to all or part of a specified column in the Reflection Array It is possible to add and subtract flags from a range of lines set a particular column to a constant value negate the values in a column or transfer the values from one column into another column When invoked with the MODIFY option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY MODIFY displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button performs the specified modifications then displays the resulting array in an editing window for review identical to the REFL_ARRAY EDIT window see REFL_ARRAY EDIT Pressing ESC
305. e user will be given the option to drive to each point on the triangle The program will pre drive to the selected point then allow the user to manually drive X Y and Z Remember that Z is aligned only when the laser is positioned within the video cross hairs When all three points have been positioned the flat sample plane is fully defined 5 13 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses X neiii X VALUE FOR POINT 1 Nioatuanaa Y VALUE FOR POINT 1 IZM eset aA Z VALUE FOR POINT 1 Enter the X Y Z coordinates for the top ver tex of imaginary triangle on the sample KO sits EE EET X VALUE FOR POINT 2 IN Discos ccieesisteieins Y VALUE FOR POINT 2 Z2 alee Z VALUE FOR POINT 2 Enter the X Y Z coordinates for the second vertex of imaginary triangle on the sample XS eccctieche pene X VALUE FOR POINT 3 Nocna eana Y VALUE FOR POINT 3 IDB ete E Z VALUE FOR POINT 3 Enter the X Y Z coordinates for the third vertex of imaginary triangle on the sample M86 E01008 GADDS Software Reference Manual Collect Routines 5 14 Collect gt Goniometer gt Update Enter observed goniometer angles Menu Command Collect gt Goniometer gt Update Accelerator none User Level 2 SLAM Syntax GONIOMETER UPDATE 1 2 3 4 5 6 7 8 9 or GONIOMETER UPDATE 1 2 3 4 This command is used to reset the goniometer co
306. ear scaling of frame X Y coordinates The name of the current spatial correction is shown on the display in the current status area at the bottom right of the screen SPATIAL LINEAR updates this name to LINEAR Since you will in general not be able to determine HKL indices and crystal orientation if no spatial correction is in effect the REFL_ARRAY INDEX and LEASTSQ will issue a warning if you run them with a linear spatial correction SPATIAL LINEAR runs immediately without prompting for additional input 6 8 1 Arguments None Command executes immediately M86 E01008 Process Routines GADDS Software Reference Manual 6 9 Process gt Spatial gt Process e Compute correction from current LOADed brass plate frame Menu Command Process gt Spatial gt PROCESS Accelerator none User Level 3 SLAM Syntax SPATIAL PROCESS 1 THRESHOLD lt n gt SPATIAL PROCESS can be used to compute and install a spatial correction given a fiducial plate image collected with a previous SPATIAL NEW or ADD command The fiducial plate image must reside in the 32 bit frame accumula tion memory prior to running this command It must therefore be left from an earlier SPATIAL NEW ADD or SCAN with no intervening com mands which overwrite accumulation memory having been issued see the SAVE command description for a list of these commands or must be read in with a LOAD command not DISPLAY and not SPATIAL LOA
307. easurement coda Offset Format Field description 1 texture less standard 0 8A8 hkl parameters in ASCII for up to 8 with background pole figures Blank unused 2 texture less standard 64 8R4 2theta values for up to 8 pole fig without background ures 1E31 unused 3 unknown sample without 96 8R4 low background 2theta for up to 8 background pole figures 1E31 unused 4 unknown sample back 128 8R4 high background 2theta for up to 8 ground measured for first chi pole figures 1E31 unused only 160 R4 alpha start for reflection 5 unknown sample back 1E6 unused ground measured at phi 0 for 164 R4 alpha end for reflection all chi s 1E6 unused 6 unknown sample with full 168 R4 alpha step background measurements 4172 R4 beta start 138 14X Pii for future use Must be 4176 R4 beta end 180 R4 beta step size 152 14 Number of data ranges after this a one 184 R4 measuring time per step for reflec tion 0 0 unused 188 R4 alpha start for transmission 1E6 unused 192 R4 alph end for transmission 1E6 unused E 2 M86 E01008 GADDS Software Reference Manual TEXTURE AT Raw Data File Format file ignore R and T repeats 196 R4 measuring time per circle for back 591 12 max number of alpha scans ground s 1 unused 1 90 alpha_step 200 4X unused reserved bytes 593 12 max numb
308. ecords 232 14 display plane number needed for 3D if there are no extra defined records display this value is 0 236 C4 4 bytes of padding for alignment 260 R4 2 smoothing width in degrees 0 0 not smoothed 240 R8 actually selected wavelength in A 264 14 2 flagword for simulated meas 248 14 currently 0 but reserved for varying condition during a single scan in a non standard fashion bit 0 gt simulate a different slit option two_theta gt bit 0 bit 1 gt variable slits are simulated Thus the valid settings are theta gt bit 1 00 no data manipulation M86 E01008 GADDS Software Reference Manual DIFFRAC S Raw Data File Format 01 converted to fixed slits from var 10 no data manipulation 11 converted to var slits from fixed 268 C4 2 4 bytes of padding for alignment 272 R4 2 step size increment of 3rd scan axis 0 0 280 C24 reserved for expansion RAW SUPPLEMENTARY RANGE HEADERS Each supplementary range header record is composed of a variable number of bytes The total number of supplementary range header bytes is store in offset 256 of the range header A value of 0 indicates that there are no supple mentary range headers The currently defined supplementary range header records are listed below Offset Code Description for Oscillat
309. ection 13 7 for more details 7 7 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA osrves tives dsiueeass Plot Data Filename plotso dat This parameter specifies the ASCII data file to graph This filename is merged with the current data directory specified in the Project gt New Edit Copy dialog before the program attempts to access the file If you leave this field blank or enter a wildcard file name pattern in the Analyze gt Graph gt File dialog the program will display a list of file names from which you can select the desired data file QUADRANT lt n gt Quadrant 0 This argument specifies whether you want the graph to appear covering the entire frame display area enter O or just one of the four quadrants enter 1 through 4 as appropriate The default value is O full frame window Quadrants are 0 full win dow 1 lower left 2 lower right 3 upper left and 4 upper right PRECLEAR Pre Clear Y N No This argument specifies whether or not the screen area full or quadrant depending on the value of QUADRANT above will be cleared before the plot is drawn In menu M86 E01008 GADDS Software Reference Manual Analyze Routines mode check this item to clear the memory or leave it unchecked if you want to superim pose the graph on the data frame currently displayed in that quadr
310. ed select EXIT or press ESC to return to the menu bar Representative profile lineshapes can be either collected data or simulated data using mathe matical functions SIMULATE allows you to use a Cauchy Lorentian Gaussian modified Cauchy asymmetrical Cauchy Pseudo Voight Pearson VII or a split Pearson VII function to model the profile shape PROFILE creates the profile lineshape file by allowing you to select one or more representa tive lineshapes at various 20 positions Each lineshape should be an isolated peak and the profile fitting algorithm works best with line shapes taken at low medium and high 20 angles The a contribution must be either con sistently present or consistently absent from all peak profiles Profile lineshape is selected by specifying a 20 background range on both sides of a peak The average intensity within the low and high back ground regions is used to subtract a linear back ground from beneath the Bragg peak The resulting peak function is rescaled and stored with the FWHM and 2T position in a profile parameter file which is a special format of a DIFFRAC AT v1 raw data file Individual profile functions can be displayed with PEAKS LOAD PEAKS PROFILE NEW When started from the command line PEAKS PROFILE NEW takes the following arguments PEAKS PROFILE NEW 1 2 3 4 5 M86 E01008 12 17 SLAM Routines GADDS Software Reference Manual where the arguments are 1
311. ed SYSTEM without having to save or reload the configuration file display or other parameters Under NT use the syntax CMD K lt com mand gt to execute the lt command gt in a Com mand Prompt window DOS emulator CMD or CMD K to execute a session or lt pro gram gt to execute a specific program To return to GADDS type exit at the prompt GADDS will confirm your request with the message Suspend GADDS while spawning another task Continue and GADDS closes the logfile and autoscript file then minimizes the GADDS win dow while the spawn tasks runs When the spawned task finishes and exits the GADDS window is restored and the logfile and auto script file s are restored reactivated 9 7 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA secant ceeds Command lt program gt to spawn a single program CMD K lt command gt to spawn a single command for example dir or CMD K to spawn a command prompt session M86 E01008 GADDS Software Reference Manual Special Routines 9 8 Special gt Spawn PROFILEP S Spawn PROFILEP S or TOPAS P with current spectra Menu Command Special gt Spawn PROFILE plus Accelerator None User Level 1 SLAM Syntax SPAWN Use this command to spawn start as separate task the profile fitting package with the current integra
312. ed exclusively That is if the bitmask is define the octagon mask is ignored and visa versa 8 1 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GAC NRE PE E Threshold 1 Threshold in counts All Pixels whose value is below this threshold are flagged as inac tive FILTER voeeseesseeeee Filter No Entering Y will filter out isolated inactive pixels and restore them to active status BORDER lt n gt Border 1 Number of pixels to extend the inactive pix els regions to eliminate partially blocked pix els from the active pixel bitmask M86 E01008 Peaks Routines GADDS Software Reference Manual 8 2 Peaks gt Mask gt Edit Edit the active pixel mask Menu Command Peaks gt Mask gt Edit Accelerator None User Level 1 SLAM Syntax MASK EDIT interactive only Use this command to manually edit the active pixel mask pixel by pixel You can turn off or on masked pixels with a click of the mouse Hint Zoom in on the image for better visualizing of individual pixels 8 3 Peaks gt Mask gt Save Save active pixel mask to disk file Menu Command Peaks gt Mask gt Create Accelerator None User Level 1 SLAM Syntax MASK SAVE 1 MASK SAVE will store the current active bit mask to a disk file Active bitmasks must be explicitly saved because only the filename is stored in the frame head
313. ed to set your new collision limits for and y under Col lect gt Goniometer gt Limits see Section 5 15 Otherwise you might break your expensive glassware M86 E01008 GADDS Software Reference Manual Edit Routines 4 1 3 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses USER lt S gt 04 User Name SAXIS USERNAME Enter the user name default is UNKNOWN If you define the environment variable SAXISUSERNAME its translation will be taken as the default value The name you supply will be stored in the header of any output frames created in Bruker the normal format and in output p4p files ISITE lt S gt eee Site SAXI SITE Enter the site name default is UNKNOWN If you define the environment variable SAXI SITE its translation will be taken as the default value The name you supply will be stored in the header of any output frames created in Bruker the normal format and in output p4p files CALIBDIR lt s gt Calibration Data Direc tory GADDS CALIB The directory where calibration data are to be stored such as flood field and spatial correction files The default is GADDS CALIB which is an environment variable that usually translates to D FRAMES CALIB The special symbol means the current directory MINCPS lt n gt Minimum Counts per Second 25 Enter the minimum counts
314. eels bea he Pee d baed ed 8 24 8 15 Peaks gt Refl Array gt Pick Select spots from currently displayed frame to put in array 8 28 BTS AGUES wing a wine lee dale ere dene Geek e andes wee a anda Reet ede ate a eee ee 8 30 8 16 Peaks gt Refl Array gt Index Autoindex to compute HKL s of angles only reflections 8 31 8 1 6 1 Arguments rera me etna ete B aati oth etek EEA EE a baa E dake dee ERD 8 35 8 16 2 Autoindexing Output 0 2 20 tae 8 38 8 17 Peaks gt Refl Array gt Bravais e Determine Bravais lattice and perform AKL transtormations 2 ores reni rnad cages ga dak ope T aeeh ade be bhp pelweedau eee os 8 45 Boal AUNES aiarar Barbie nad wad a E Pamela oe Rega nad Ge een at glade eset d 8 47 8 17 2 Bravais Lattice Output 0 2 cae 8 49 8 18 Peaks gt Refl Array gt LeastSq Determine orientation and refined cell parameters 8 52 M86 E01008 4 04 xi Table of Contents GADDS Software Reference Manual 8181 ArgQuments seen dirk eet eatin ele ah moe ew kee Ade ae AA AE 8 53 8 18 2 Least Squares Output 1 2 0 0 tee 8 59 8 19 Peaks gt Refl Array gt Edit e View modify the reflection array 00000 eee 8 64 8 19 1 Line EIG eps 4 ature eke eke eee Eyer eee bt Chae aes 8 68 8 20 Peaks gt Refl Array gt Modify Alter specified item for a range of reflections in the array 8 69 8 20 1 Arguments o droee ea thw steer a has ex eal ea Apel ged es 8 69 8 21 Peaks gt Refl Array gt Sort
315. een the two units when attempting a drive operation When invoked with the XYZ option from the GONIOMETER submenu or when run from the command line without arguments GONIOME TER XYZ displays an input panel where you can view modify the desired settings 5 27 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses 1 Anite Detector Distance current distance in mm The detector distance in mm is measured from the center of the goniometer to the physical face of the detector It is the same detector distance which is entered in CON 5 36 M86 E01008 GADDS Software Reference Manual Collect Routines FIGURE EDIT menu except in mm not cm This value defaults to the current detec tor distance P2 a eet Detector Half Width 115 mm The detector half width in mm is mea sured from the center of the 2 theta arm to the edge of the detector housing PIi aa XYZ Stage Sample Half Width 76 mm The sample half width is measured from center of the XYZ stage to the edge of the sample which can approach the detector face This value is always entered as posi tive 4 E A XYZ Stage Depth Reference 0mm The sample depth reference is the Z offset which when added to the current Z axes set ting will give zero when the plane of the sample face touches the center of the goni ometer This value is SIGNED M86 E01008 Collect
316. effect The default value is 2 the allowed range is from 2 to 10 counts Smaller values make the displayed image look brighter larger values make look darker Ga encanta ont Output File NULL Output filename to store symmetrized pole figure image or null LAUE lt S gt 004 Laue Symmetry 2 m Enter Laue symmetry as i 2 m mmm Alm 4 mmm Currently other Laue sym metries are not supported but some may be approximated by using a lower inherent symmetry For instance hexagonals 6 m inherently possess 2 m symmetry and 6 mmm possess mmm symmetry while cubics m3 or m3m possess mmm sym metry M86 E01008 Analyze Routines GADDS Software Reference Manual 7 24 Analyze gt Pole Figure gt Invert Invert pole figure about x axis Menu Command Analyze gt Pole Figure gt Invert Accelerator None User Level 1 SLAM Syntax POLE_FIG INVERT 1 DISPLAY lt n gt 2 Frequently the diffractionist would like to visual ize the pole sphere from a different viewing angle or orientation or perhaps the pole figure needs to be positioned with particular sample directions For these reasons the TILT and ROTATE options have been provided The TILT option allows a new position on the sphere to be positioned at the origin of the projection while the ROTATE option performs rotation of the image about the origin INVERT flips the
317. el Following the overall statistics is a reflection by reflection summary of the agreement for each reflection in the reflection array Each record consists of two lines the first containing the reflection as it s entered in the reflection array i e the observed values and the second containing the differences for HKL scan angle always converted into omega rotation and detector X Y with the sense OBSERVED CAL CULATED This output shows both those reflec tions included in the least squares and those not included for example reflections without the C flag set It also shows computed HKL indices for reflections which do not have the H flag set It does not include reflections which do not have the A flag set since there are many possible combinations of setting angles and detector X Y which could correspond to given HKL indices M86 E01008 Peaks Routines GADDS Software Reference Manual The two example outputs follow neither case assumes a known unit cell Example 8 2 Output from indexing of 8 Myoglobin Test Frames prior to re indexing the Reflection Array Axis limits max index 81 000 99 000 81 000 99 000 40 500 49 500 13 Length FOM H1H 2H 3 Reflections fit Angles between solutions 1 46 159 0 01 1 1 O 1111111111111111 2 92 542 0 01 O 1 1 1111111111111111 89 4 3 92 318 0 02 2 2 O 1111111111111111 0 0 89 4 4 91 833 0 01 1 1 2 1111111111111111 90 0 119 6 90 0 5 92 707 0 03 1 2 3 11
318. el at vector endpoint X ORIGIN X coordinate of origin in pixels Y ORIGIN Y coordinate of origin in pixels X ENDPT X coordinate of endpoint in pixels Y ENDPT Y coordinate of endpoint in pixels A Origin Alpha angle at origin in degrees A Endpt Alpha angle at end point in degrees B Origin Beta angle at origin in degrees B Endpt Beta angle at end point in degrees Angle Angle between two poles in degrees M86 E01008 GADDS Software Reference Manual Analyze Routines 7 5 Analyze gt Cursors gt Conic Display constant two theta conic lines Menu Command Analyze gt Cursors gt Conic Accelerator F9 User Level 1 SLAM Syntax CURSORS CONIC 1 2 DELAY lt n gt NOERASE When invoked with the CONIC option from the CURSORS submenu or when run from the com mand line without arguments CURSORS CONIC starts running directly that is there are no items to be filled in on an input panel A full window conic cursor appears in the detector frame area and can be moved under control of the mouse and or keyboard arrow keys Press ing the ENTER key or left mouse button exits returning you to the CURSORS submenu The lineweight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cursors Odd values are better th
319. elow as defined in Edit gt Configure gt User settings Frame Naming Parameters see Section 4 1 1 Because one typically starts a scan and walks away from the instrument GADDS will pre check that the available disk space is sufficient for storing the requested number of frames in 8 bit mode However if the frames are stored in 16 bit mode you may still run out of disk space during the requested scan operation M86 E01008 GADDS Software Reference Manual Collect Routines The CPU intensive VIDEO program is always set to frozen mode at the start of all scan com mands 5 30 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses EE EEE AE rames 1 The number of frames to be acquired in this series Ensure that the generated filename of the last frame in the series is a valid file name with regard to the frame naming parameters in the Edit gt Configure gt User settings dialog 2THETA lt n gt 2 Theta 0 00 THETA1 lt n gt Theta1 0 00 The detector swing angle goniometer 2 theta setting angle in degrees at which GADDS positions the goniometer at the start of the frame series Valid values are 180 to 180 but are typically reduced by the current software collision limits as defined in Collect gt Goniometer gt limits command Entering will be automati cally replaced with current angle
320. ems GADDS confirms the current angle settings 12 M86 E01008 GADDS Software Reference Manual General Information 1 5 Dialog Box and Keyboard Conventions 1 5 1 Dialog Boxes GADDS has been designed with standard Win dows dialog boxes so you can use standard methods when responding The action buttons vary depending on the function of the dialog box The following types of dialogs are used classified according to type of action button Message Boxes These display informational and error mes sages and have only an OK button The ENTER key is equivalent to OK Yes No Dialog Boxes These display a message and request a Yes or No response Pressing the Y key is equiv alent to clicking Yes The N key is equivalent to No Pressing ENTER executes whichever button is highlighted The TAB key moves the highlight between the two buttons OK Cancel Dialog Boxes These display a message that requires an OK or Cancel response or they may contain a series of Windows or Motif controls for entering data Pressing ENTER is equiva lent to clicking the currently highlighted action button which is initially the OK but ton Pressing ESC is equivalent to clicking the Cancel button The TAB and SHIFT TAB keys move to the next or preceding control in the dialog box respectively If the dialog box contains edit fields you can copy cut and paste text within these fields with CTRL C CTRL X and CTRL V These operatio
321. en and subsequent frames positioned further into the screen 3 5 File gt Display gt Next Run and File gt Display gt Prev Run Menu Command File gt Display gt Next Run File gt Display gt Prev Run Accelerator Ctrl Shift RightArror next Ctrl Shift LeftArrow previous User Level 1 SLAM Syntax DISPLAY RNEXT DISPLAY RPREV These commands are identical to the File gt Dis play gt Next Prev commands except that it steps through the run number instead of the frame number M86 E01008 File Routines GADDS Software Reference Manual 3 6 File gt Display gt Movie Run and File gt Display gt Movie Run Menu Command File gt Display gt Movie Run File gt Display gt Movie Run Accelerator Ctrl Shift UpArror moview Ctrl ShifttDownArrow movie User Level 1 SLAM Syntax DISPLAY RMOVIE DISPLAY RMOVIEW These commands are identical to the File gt Dis play gt Movie commands except that it steps through the run number instead of the frame number 3 7 File gt Load e Read a frame from disk into frame accumulation memory Menu Command File gt Load Accelerator Ctrl O User Level 1 SLAM Syntax LOAD 1 2 DISPLAY lt n gt SCALE lt n gt OFFSET lt n gt LOGSCALE USE_CONFIG The File gt Load command copies a data frame from a disk into the 32 bit frame accumulation memory for display and evaluation The image is also displayed on the screen
322. engths 6 64 Unit cell angles For example if you specify a value of 96 32 64 the program would refine the M86 E01008 Peaks Routines GADDS Software Reference Manual crystal orientation and detector parameters leaving the unit cell parameters axis lengths and angles fixed Note that if you wanted them to remain fixed at the values specified in the input panel rather than at the initial guesses computed by the linear least squares you would have to specify a negative value for the constraint type see 1 above PARNAME lt n gt Output Parameter File name newfram0 p4p Specifies the filename to which the orienta tion matrix and refined parameters are writ ten This file can be read by ASTRO It is an ASCII file which can be typed edited and transferred to other computer types as long as the transfer software handles any differ ing end of line conventions correctly By convention these filenames end with a _pr extension The base name of the file defaults to the base name of the last set of frames processed with REFL_ARRAY THRESHOLD if any otherwise to NEWFRAMO An example of a _pr file is NAME swmyot WAVE 1 541840 ORT1 0 008553 0 012507 0 000284 ORT2 0 009394 0 002745 0 000005 ORT3 0 000143 0 000237 0 021975 DIST 12 000000 DETP 4 5299 0 5312 0 2006 0 0000 0 1999 0 0029 XCYC 255 000000 242 000000 Each line contains a 5 character item name followed by data i
323. ent Each line of a run list contains the following items RUN This is the Run Number of the series This is not actually a number but is rather taken as RUNCHARS characters of ASCII text Also all characters must be valid characters to be used with filenames because the Run Num ber becomes part of the generated output filename Basically the Run Number is for matted and appended to the output base filename before the file extension See Frame Naming Conventions Edit gt Config ure gt User settings command and Collect gt Scan gt MultiRun command for more details FRAME This is the starting frame number for the series Like the Run Number this is actually taken as text of length NUMCHARS rather than as a numeric value The text specified here will be used as the extension of the first output frame in the series and will be incre mented according to the frame naming parameters to form the extensions of subse quent frames See Frame Naming Conven tions Edit gt Configure gt User settings command and Collect gt Scan gt MultiRun command for more details 50 M86 E01008 GADDS Software Reference Manual Collect Routines 2 THETA Swing THETA1 Tube The detector swing angle goniometer 2 theta setting angle in degrees at which GADDS positions the goniometer for the frame series scans Valid values are 180 to 180 but are typically reduced by the current software colli sion limi
324. ent quadrants at one time only the image in the current quadrant is actually in memory Thus for example the Ana lyze gt Cursor functions work only on the image in the current quadrant GADDS will read and automatically configure internal parameters for imported Bruker CCD formats based on the DETTYPE frame header item and version 9 header items But whenever the DETTYPE is unknown or other then GADDS tries to read the sub items PIX PERCM and CMTOGRID On failure GADDS must ask for the Pixels per cm and Cm to grid parameters When invoked from the menu or run from the command line without arguments File gt Display displays a dialog box where you can view edit M86 E01008 File Routines GADDS Software Reference Manual the arguments described below Pressing the ENTER key or clicking the OK button starts the display Pressing ESC or the Cancel button returns you to the menu Both filenames and filename patterns entered in the input panel are merged with the working directory specified in the Project gt New dialog box before GADDS attempts to open the file 3 1 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA EEEE Input Filename FRAME Filename of the frame to be displayed Input filename defaults to gfrm file extension if missing The special name FRAME the default refers to the curre
325. entry updated to the refined value on exit See comments for 2 above ETT C Axis Length 10 0 Initial guess for the C axis length in Ang stroms on entry updated to the refined value on exit See comments for 2 above TETEE EEN Alpha Cell Angle 90 0 Initial guess for the alpha unit cell angle in degrees on entry updated to the refined M86 E01008 GADDS Software Reference Manual Peaks Routines value on exit Valid range is 1 179 degrees See comments for 2 above DO EEEE Beta Cell Angle 90 0 Initial guess for the beta unit cell angle in degrees on entry updated to the refined value on exit Valid range is 1 179 degrees See comments for 2 above TARENTE ATT Gamma Cell Angle 90 0 Initial guess for the gamma unit cell angle in degrees on entry updated to the refined value on exit Valid range is 1 179 degrees See comments for 2 above IDXCHK lt N gt onnan X Beam Center Correc tion 0 0 Initial guess for the CORRECTION to the detector beam center X coordinate in pixels Zero is usually a good value Note that if the constraint type 1 is 1 9 the value you start with here doesn t matter since the pro gram will set the initial guesses for the detector positional corrections to zero when it performs the linear least squares This entry is updated with its refined value on exit Valid range is 256 to 256 IDYCHKN gt ceeeeeeee Y Beam Center Correc tion 0 0
326. enu Command Analyze gt Pole Figure gt Pro cess Accelerator None User Level 1 SLAM Syntax POLE_FIG PROCESS 1 2 3 4 5 POLE lt n gt MAPPING lt s gt BACKGROUND 6 7 8 9 FIBERGEOM ABSORPTION lt s gt X lt n gt Y lt n gt Z lt n gt MU lt n gt RADIUS lt n gt NSTEPS lt n gt REFLECTION Pole figure frames are stereographic projections of the pole density sphere where each pixel of the pole figure frame represents the pole density of crystallites possessing a particular orienta tion Pole maps of this kind are the preferred method for describing a material s texture The radius of the pole figure is called alpha and the azimuthal angle is called beta These angles are related to the sample orientation by alpha angle between reflecting plane and normal to the reference plane in the sample beta angle between the reference direc tion and the normal to the diffractometer direction Consider a polycrystalline textured specimen at a fixed orientation within an x ray beam The dif fracted rays from a particular hkl plane form a cone where the azimuthal intensity variation is related to the orientation of the sample about the incident x ray beam The intersection of this diffraction cone and an area detector form a cir cle of intensity data that maps to a great circle on the pole sphere By varying the sample ori entation to the incident beam this circle of data can map to other regions
327. er One may also need to re save the frame image if the frame header was modified to include a new bitmask The user should be aware the bitmask or the octagon mask is used exclusively That is if the bitmask is define the octagon mask is ignored and visa versa 8 3 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA orice eich esheets Bitmask Filename active msk Filename of active pixel bitmask NULL will cancel M86 E01008 GADDS Software Reference Manual Peaks Routines 8 4 Peaks gt Mask gt Read Read active pixel mask from disk file Menu Command Peaks gt Mask gt Create Accelerator None User Level 1 SLAM Syntax MASK READ 1 MASK READ will read an active bitmask file from disk and load it as the current bitmask The special NULL can be used to define a bit mask with all active pixels The user should be aware the bitmask or the octagon mask are used exclusively That is if the bitmask is define the octagon mask is ignored and visa versa 8 4 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Sa A at Bitmask Filename active msk Filename of active pixel map NULL to load an all active bitmask 8 5 Peaks gt Mask gt View View active pixel mask on screen Menu Command Peaks gt Mask gt Crea
328. er Level 1 SLAM Syntax INTEGRATE 2THETA 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt INTEGRATE 2THETA will integrate a region along the 2 theta direction and plot the results as intensity versus chi Such chi plots are useful for examining texture effects within the data The resulting trace may be written to a file using INTEGRATE WRITE command or inputted into the PEAKS LOAD command The area to integrate is defined by specifying the 2 theta and chi range for the Debye Scher rer cone Chi zero is defined at 6 o clock and goes CCW Interactively the user may redefine any of the integration region s limits by selecting the limit s line number 1 to 4 and then using the cursor keys The current integration region limits are continuously updated and displayed on the screen While interactively modifying an integration limit the lt ESC gt key or right button will restore the limit to its original value while the lt ENTER gt or left button will accepts the new value for this limit It is also feasible to move the entire integration window by pressing the M key using the cursors to position a new center of the integration window then pressing the lt ENTER gt key Once the integration window is defined press ing lt ENTER gt will start the integration calcula tions and display the message Wait Integrate ESC Other buttons Quit Normally one waits for the calculations to finish and to plot the resul
329. er PLOTSO file Usage run saxii_read_plotso saxii_read_plotso xarray yarray filename where xarray dimension 500 10 returns the 2theta values of up to ten ranges yarray dimension 500 10 returns the intensity counts of up to ten ranges filename PLOTSO filename If missing the procedure will ask for it 13 16 M86 E01008 GADDS Software Reference Manual Utility Programs 13 9 4 SAXII_SAVE_D5000 VAX only P V wave procedure to save an array as a Bruker d5000 file Usage run saxii_save_d5000 saxii_save_d5000 xarray yarray file name where xarray dimension 500 10 2theta values of up to ten ranges yarray dimension 500 10 intensity counts of up to ten ranges filename DIFFRAC 5000 RAW filename If missing the procedure will ask for the file name 13 9 5 SAXII_SAVE_FRAME PV Wave function to save a Bruker area detec tor frame Header is modified from the original frame header This version handles 8 16 or 32 bit frames WITHOUT an overflow table Usage run saxii_save_frame saxii_save_frame image filename header where image dimension 512 512 byte word dword image data filename Frame data filename If missing the procedure will ask for it header dimension 80 header informa tion 13 9 6 SAXII_SAVE_PLOTSO P V wave procedure to save an array as a Bruker PLOTSO file Usage run saxii_save_plotso saxii_save_plotso
330. er of beta steps 204 R4 x oscillation amplitude in mm 360 beta_step 208 R4 x oscillation speed in mm sec 595 R4 actual alpha start in the file 212 R4 measuring time per step for trans 599 R4 alpha start 2 in radians mission 0 0 unused 595 PI 360 216 16R4 contour levels 15 values maxi TROS n4 beta siar in radians mum 1 unused 16 must be 1 172 P1 180 280 1612 display colors for contours 607 R4 delta alpha 2 in radians 168 P1 360 312 1612 lotter pen colors for contours p 611 R4 delta beta in radians 344 R4 CRT aspect ratio unused 180 P1 180 348 R4 x scale factor of printer unused 615 12 actual number of pole figures in 352 R4 y scale factor of printer unused the file 356 R4 linear absorption of sample 617 12 number of pole figures currently T360 Xo sndceu selected for display 362 AeA axis label 619 12 current display mode 42 A64 ite label 1 color 3D 2 BW 3D 3 con 426 6 site tebe tours 4 maxima 5 phi cut 490 ASS erea tale comments i e 621 12 pole figure rotation degrees as vee integer normally 0 994 ee nd of date me i ee 623 12 inclination for 3D view degrees as sample i e correction file integer 986 L1 a COnnnUOUS step scan 625 312 3 values of chi for 3 phi cuts as mode integers 587 L1 hala inverted transmission 631 2X unused 588 L1 true no reference sample avail t93 een hkl of pole Adler sae ae le able used 697 12 maxima search option 589 12 actual
331. erator None User Level 1 SLAM Syntax MAPPING 1 FRAME lt s gt RUN lt s gt 2 SLAM lt s gt Use this command to process a run series where each run is identically processed to obtain a mapping parameter value per each run A run could be frames collected on a sam ple position in X and Y or Y and Z or a sample position in a sample library see Collect gt Scan gt Grid Targets Each resultant value across the runs is sent to and mapped in the GADDSMAP utility program The mapping pat tern will show sample variations with position or variations in samples in a sample library Such information is frequently used for quality control When selected a dialog box appears to enter the mapping parameters You must select what parameter you want to map across all the runs You must enter the first frame in the run series and the last run number After clicking OK the frame headers of these runs will be read to determine the XY or YZ mapping grid Frames must be collected on a grid but some missing frames are allowed Next GADDS brings up the dialog box for input ting processing parameters needed to calculate the requested parameter to map Which dialog box appears depends on which parameter is being mapped For more information see the appropriate command for this dialog box 7 37 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses
332. erface card For normal configurations the SETUP pro gram will properly install and configure this driver SAXAD driver will allocate 4 25 Mbytes of NON PAGED memory This will greatly affect perfor mance on low memory NT systems A system with at least 20 Mbytes of memory is recom mend Increase virtual memory to at least 35 Mbytes the WNT default of 21 Mbytes is insuffi cient For users who do not collect large frames set MaxFrameSize 512 in the registry as this will free 3 Mbytes of unused non paged mem ory During data collection and flood fields the SAXAD driver executes at the level LOW_REALTIME_PRIORITY Only when the driver checks for an event and no event is in the queue does the driver permit any time alloca tion to other processes For real time display during data collection or flood field the NT system must be equipped with a super fast video card such as a PCI local video card An ISA bus video card will be excru ciatingly slow Possible error messages during loading of driver Not enough memory was available to allocate internal storage needed STATUS_INSUFFICIENT_ RESOURCES if out of system memory Reboot might work else add memory Or set MaxFrameSize 512 The hardware locations for saxadO could not be translated to something STATUS_NONE_MAPPED if NT cannot map port Hopefully this error never occurs The hardware addresses for saxadO are already in use by a
333. es for reflections which do not have the H flag set It does not include reflections which do not have the A flag set since there are many possible combinations of setting angles and detector X Y which could correspond to given HKL indices Use the HCALC sub command if you need to determine angles corresponding to specific HKLs An example output truncated after the first few reflections for least squares on reflections from the series of eight contiguous test frames pro duced with a hexagonal myoglobin crystal is shown below The refinement was uncon strained The cell parameters in this example are not very good and their standard deviations are correspondingly large They would be better if we thresholded an additional set of frames starting at a scan angle 90 degrees or so away from the first eight prior to indexing and least squares M86 E01008 Peaks Routines GADDS Software Reference Manual Example 8 5 Least Squares Output from the Eight Test Frames Orientation Matrix 0 00855331 0 01250697 0 00028393 0 00939403 0 00274520 0 00000470 0 00014339 0 00023734 0 02197455 Lattice parameters amp Standard deviations 90 8317 90 1132 45 5042 90 314 89 964 119 944 322733 90 0 9975 1 8806 0 4779 0 348 0 091 0 238 13974 49 Histograms 00 05 10 15 20 25 30 35 40 45 inf H 26 0 0 0 0 0 o 0 0 O K 26 0 0 0 0 0 o 0 0 0 L 2 00 0 0 0 o 0 0 0 Omega 26 0 0 0 0 0 0 0 0 0 0 00 0 25 0 50 0 75 1 00 1 25 1 5
334. esponds to the upper left corner of the display the 512th to the upper right and the last pixel to the lower right This data ordering con vention is the one used by most display devices and by the X Windows library Frames display as if viewed from the source toward the detector A 3 Overflow Table The overflow table is stored as ASCII values Each overflow entry is 16 characters compris ing a 9 character intensity and a 7 character pixel offset The table is padded to a multiple of 512 bytes In an 8 bit frame any pixel with a value of 255 in the image needs to be looked up in the overflow table to determine its true value even if the true value is 255 to allow overflow table validity checks which could not otherwise be made In a similar manner any pixel in a 16 bit frame with a value of 65535 must be looked up in the overflow table to determine its true value To look up a pixel value compute its pixel displacement for example in a 512x512 frame 512 j k where j is the zero based row number and k is the zero based column number and compare the displacement with that of each overflow table entry until a match is found While the overflow table is normally sorted on dis placement it is not guaranteed to be sorted so we recommend that you search the whole table until you find a match A 10 M86 E01008 GADDS Software Reference Manual Area Detector Frame Format A 4 Trailers The header contains a byte
335. est to transform the indices to correspond to the desired setting prior to performing least squares When invoked with the TRANSFORM option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY TRANSFORM displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button performs the specified transformation the ESC key or right mouse button returns you directly to the REFL_ARRAY submenu without updating the matrix Following a successful transformation the program displays the resulting Reflection Array in an editing window for review identical to the REFL_ARRAY EDIT window see REFL_ARRAY EDIT Pressing ESC or the right mouse button in the editing window returns you to the REFL_ARRAY submenu 8 22 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Note that the element order on the input panel corresponds to the standard mathematical con vention e g 1 3 is 3 column on 1st row It has nothing to do with FORTRAN storage con ventions As entered the matrix will pre multiply a column HKL vector to give a transformed col umn HKL vector STel u Matrix 1 1 1 0 Value for row 1 column 1 of orientation matrix e RAE A A Matrix 1 2 0 0 Value for row 1 column 2 of orientation matrix M86 E01008 GADDS Softwa
336. est RGB print able color see your PaintJet manual For this reason some greytones are printed in either brown olive green or pink colors For PostScript printers specifies to print using 16 greyscales FORMAT 2 or 256 colors FORMAT 4 If absent on the com mand line or specified as N in the input panel prints in black white FORMAT 2 or 16 colors FORMAT 4 TIFF files behave similar to monochrome PostScript printers A Y specifies 16 grey scales while N signifies black and white TIFF file NOTE To preview a print file without actually printing the file load the color lookup table with PRINT LUT in the Edit gt Config gt Colors panel which displays the frame in reverse black white greyscale M86 E01008 File Routines GADDS Software Reference Manual 3 24 M86 E01008 4 Edit Routines 4 1 Edit gt Configure gt User settings e Edit the current user configuration settings Menu Command Edit gt Configure gt User set tings Accelerator Ctrl C User Level 1 view edit 3 full edit SLAM Syntax CONFIGURE EDIT USER lt s gt SITE lt s gt CALIBDIR lt s gt MINCPS lt n gt TIMEOUT lt n gt NAMECHAR lt n gt RUNCHARS lt n gt RUNBASE lt n gt NUMCHARS lt n gt NUMBASE lt n gt LOWTEMP TEMP lt n gt KBEAM lt n gt YBEAM lt n gt FRAMESIZE lt n gt DISTANCE lt n gt Edit gt Configure gt User settings displays a dia log box where yo
337. f NAME part used for run SAXI RUNBASE Numeric base of run 10 or 36 SAXISNUMCHARS characters in extension used as frame SAXISNUMBASE Numeric base of frame 10 or 36 These names translate to numeric values which establish the initial frame naming parameters which can be viewed and modi fied on the Edit gt Configure gt User settings form If the configuration has been saved from a previous run of GADDS the values in the configuration file override these values when GADDS is restarted Thus these names are used by GADDS only if there is no existing GADDS _GC file SAXI BIGFONT When set to a non zero value gadds dis plays the screen using a larger character font SAXISCURSWEIGHT This name can be defined with an integer value from 2 to 7 to specify the line thick ness of the cursors in pixels This is prima rily for use on IRIS systems where single M86 E01008 General Information GADDS Software Reference Manual weight lines can look very thin If SAXI CURSWEIGHT is undefined or assigned the value 1 the cursors appear as in earlier versions The cursors drawn in the ZOOM and GRAPH commands are also affected in the same manner SAXISDBGLEVEL This variable translates to the program debug level that is used to determine which debug statements are sent to the file std out txt This is only used to debug the pro gram 0 off 1 serial communications setup mes sages corre
338. f SAXISOLDNAMES is set the Run is appended directly to the Job Name then the Frame is added as the filename extension it is concatenated after pre pending a dot Prior to concatenation the Run and Frame are expanded with leading zeros if required to the number of characters specified by the Runchars and Numchars parameters For your conve nience GADDS generates and displays an example filename using the current settings 4 1 2 Sample to Detector Distance and Beam Center Measurement Your GADDS Administrator should follow the 269 0223xx Detector Distance and Beam Cen ter Calibration for GADDS procedure see GADDS Administrator s Manual to define the true detector distance and beam center parame ters In general the beam center is stable over long periods of time However if you replace or realign the X ray tube or realign the goniometer your GADDS Administrator should repeat this procedure NOTE To process frames collected before these settings were properly set see the Use_config argument in Section 3 7 When you change the detector distance in menu mode you will be prompted with Reset to default collision limits for new distance Enter Y and GADDS will read the default collision limits for 26 and w 26 from the file GADD SYS TEM limits d see Collect gt Goniometer gt Limits Section 5 15 for more details When you change the low temp flag in menu mode on P4 systems you are inform
339. f the ASCII file to be plotted on the DOS command line as in the following example PLOTSO SAXI TEST PLOTSO DAT If the filename is not given PLOTSO will prompt for it You can print the plot to any supported printer that is HP compatible printer by press ing CTRL P after the graph has been drawn A PRINT SCREEN panel appears with default set tings for both the printer device and printer type The default print filename is SAXISPRINTER You can either define this name as a logical name or environment variable or input a differ ent filename on the panel use PRN to write directly to a printer on the PC or SYS PRINT to write directly to the VAX print queue The default printer type is PCL4 HP LaserJet or compatible printer PLOTSO can also create TIFF files which can be imported into word processors TIFF files produced on the PC will include the PLOTSO window border and title while on other computer platforms only the plot is sent to the TIFF file PLOTSO data files are simple ASCII text files which contain X Y pairs in FORTRAN compati ble free format one pair per line This results in a simple X Y plot with automatic scaling of the axes to accommodate the data The data file may optionally contain directives which are lines starting with the special 3 character sequence that allow you greater control over the appearance of the plot and also allow multiple plots to be defined in the same file The directive prefix
340. f you re driving the goniometer manually to look for or maximize the intensity of a reflec tion it helps to clear the screen frequently for example every 1 second by setting the reset interval to 1 M86 E01008 5 5 Collect Routines GADDS Software Reference Manual 5 6 Collect gt Detector gt Reset Reset to x position vs y position Cu bias Menu Command Collect gt Detector gt Reset Accelerator Ctrl Shift R User Level 1 SLAM Syntax DETECTOR DETRESET Use this command to place the PDC and detec tor at the Cu low bias setting and into normal X Y position display The action is performed immediately with no prompt for additional input The DETECTOR item in the goniometer status area at the lower right of the display is updated to reflect the new bias status NOTE For the GADDS software to be able to change the detector bias the PDC position decoding circuit must be in Detector Bias On Source Select Auto If the bias setting is incorrect when invoking either a Process gt Flood gt New a Process gt Spatial gt New or any Collect gt Scan command GADDS will prompt the user to switch to the cor rect bias setting before collecting the data Fe high bias is used by Flood and Spatial while Cu low bias is used for Scan commands 5 6 1 Arguments None Command executes immediately 5 7 Collect gt Detector gt X E vs X Set PDC for X preamp calibration Menu Command Collec
341. fect from the amorphous result The Compton scattering must be previously calculated using PER_CRYSTAL COMPTON M86 E01008 GADDS Software Reference Manual Analyze Routines 7 16 Analyze gt Percent Crystal gt Compton Define the incoherent scattering due to the Compton effect Menu Command Analyze gt Percent Crystal gt Compton Accelerator None User Level 1 SLAM Syntax PER_CRYSTAL COMPTON 1 SCALE lt n gt KSCALE lt n gt Calculates and displays the Compton scattering curve Uses table in file GADDS SYSDATA compton tbl 7 16 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 Empirical Formula Al 3 2 O 2 3 Enter empirical formula with valence states of ions SCALE lt n gt Scale 1 0 Enter scaling factor multiplier XSCALE lt np gt X Scale 0 Enter X scale 0 sin theta lambda 1 theta 2 2theta M86 E01008 39 Analyze Routines GADDS Software Reference Manual 7 17 Analyze gt Percent Crystal gt Full e Calculate and use an amorphous background frame Menu Command Analyze gt Percent Crystal gt Full Accelerator None User Level 1 SLAM Syntax PER_CRYSTAL FULL 1 DISPLAY lt n gt 2 RADIUS lt n gt HEIGHT lt n gt PER_CRYSTAL provides a quick method to esti mate a percent crystallinity using frame data Frames must have air scatter
342. ference Manual 11 2 Help gt User s guide Display User s Manual online documentation Menu Command Help gt User s Guide Accelerator None User Level Ctrl M SLAM Syntax HELP USERGUIDE Spawns or displays the GADDS User s Manual This is either a PDF document a windows help file or ASCII _TP files located in the GADDS SYSTEM directory The Acrobat reader must be installed to display PDF files 11 2 1 Arguments None Command executes immediately 11 3 Help gt Mapping Display online documentation for GADDSmap Menu Command Help gt Mapping program Accelerator None User Level None SLAM Syntax HELP MAP Spawns or displays the GADDSmap online doc umentation This is either a PDF document or a windows help file The Acrobat reader must be installed to display PDF files 11 3 1 Arguments None Command executes immediately M86 E01008 GADDS Software Reference Manual Help Routines 11 4 Help gt About Display program trademark copyright and license information Menu Command Help gt About Accelerator None User Level 1 SLAM Syntax ABOUT Displays the program s version number copy right notice trademarks license information and developer names For information about the goniometer see Edit gt Configure gt ShowModel Section 4 5 11 4 1 Arguments None Command executes immediately 11 5 Help gt Errata Display changes to printed documen
343. file Analyze gt Cursor writes a copy of any 17 x 17 pixel dumps Process gt Stress gt Biaxial2D writes a copy of the contents of its scrollable output window etc Commands and output are added to the log file until the File gt LogFile gt Enabled option is turned off or the user switches projects which will automatically close any open log file The File gt LogFile gt Enabled command does not actually close the log file it just tells the pro gram to temporarily stop writing output to the file If you need to access the current log file in another process while GADDS is still running for example to edit it from another window you should close the file first You can close the log file by running File gt LogFile with another file name The program will close the current file before starting a new one M86 E01008 GADDS Software Reference Manual File Routines An example of a log file output for a CURSORS PIXEL command is CURSORS 1 435 2 190 DUMP N DELAY 0 0 NOERASE N l gt gt PIXEL Statistics SAXISTEST swmyol 005 11 22 91 15 49 36 l gt Xraw Yraw Counts 139 311 596 gt X Y Unwarped 142 68 309 13 gt X Y XENGEN 372 200 l gt DX DY 113 00 66 52 gt 2 Theta Angstroms 21 333 4 165 gt HKL 20 97 10 98 2 597 Different types of output lines are prefixed with character sequences that make the types easier to separate with editors text filters etc Lines that
344. filename before the file extension See Frame Naming Conventions Edit gt Config ure gt User settings command and Collect gt Scan gt MultiRun command for more details FRAMENO lt s gt Frame 000 This is the starting frame number for the series Like the Run Number this is actually taken as text of length NUMCHARS rather than as a numeric value The text specified here will be used as the extension of the first output frame in the series and will be incre mented according to the frame naming parameters to form the extensions of subse quent frames See Frame Naming Conven tions Edit gt Configure gt User settings command and Collect gt Scan gt MultiRun command for more details DISPLAY lt n gt Max Display Counts 31 Enter the number of counts to be mapped to the highest display memory value that is to set the display for acquiring frames This value is usually white on the screen The valid value range is 2 to 1 000 000 How ever Three special values are defined as follows O suppresses display of frames as they are acquired 1directs the program to pick a reasonable value and 2 directs the program to use the current level The default value is 31 REAL TIME Real time Display Yes This qualifier when present displays data as it is being collected The display does require additional processing time and will limit the maximum rate at which counts can be accumul
345. flections are outside the tolerance where lt n gt is the number of reflections removed lt n gt REFLECTION S REMOVED FROM LS OUTSIDE HKL TOL PRESS ENTER TO CONTINUE ESC TO QUIT Pressing ENTER or the left mouse button continues with the refinement pressing ESC or the right mouse button returns you to the REFL_ARRAY submenu however the H flags of the out of tolerance reflec tions remain cleared you can restore them with a MODIFY command If the command was started from a script or from the com mand line this prompt will time out in 10s if it receives no response before then assum ing an ENTER response to allow scripts to run without intervention 56 M86 E01008 GADDS Software Reference Manual Peaks Routines The default of 0 25 should be satisfactory in most cases Valid range is 0 1 to 999 this quantity is dimensionless HALFWIDTH lt n gt Frame Halfwidth 0 125 Specifies half the scan width per frame in degrees on average of the frames from which the records in the reflection array were extracted This value is used to deter mine the weighting of observed X Y posi tions versus that of observed scan angle in the least squares That is the non linear least squares minimizes the residual sum Wxy Xobs Xcalc Wxy Yobs Ycalc Wz Zobs Zcalc 7 where Xobs and Xcalc are the observed and calculated detector X Yobs and Ycalc are the observed and calculated detector
346. for manual control box Default is 14 This parameter has no effect on Phoenix control lers D8 Discovery systems which has a fixed slow speed 5 12 Collect gt Goniometer gt Optical Perform check optical centering of sample Menu Command Collect gt Goniometer gt Optical Accelerator Ctrl Shift O User Level 1 SLAM Syntax GONIOMETER OPTICAL 1 2 3 4 5 6 7 8 or GONIOMETER OPTICAL 1 2 3 4 5 Use this command to drive the goniometer between a few useful pre defined positions to minimize the effort required to center the sample crystal mounted on a goniometer head as viewed through the sample microscope or video microscope mounted on the goniometer base These pre defined positions are relative to a specified starting position whose setting angles are referred to as the base angles The pro gram contains suitable default values for the base angles for D8 3 circle Platform 3 circle older Aztalan black 3 circle and 4 circle goni ometers however these base angles can also be modified from the input panel here if neces sary The base angles should place the phi axis normal to the microscope axis and one set of M86 E01008 Collect Routines GADDS Software Reference Manual goniometer head adjustments normal to the microscope axis It is important that the environment variable SAXISADMODEL be defined correctly for your goniometer type since the alignment philosophy is differe
347. form a single scan series Resume an interrupted Single RUN ai adware d eee eet bea a hee E A a wala a Sea al ad eect mei ais ane 5 41 5 30 1 Arguments cas yan FOEREN DIENE LN eek ver aaa ye yous eae aes 5 43 5 31 Collect gt Scan gt EditRuns Edit parameters for MultiRun scans 5 49 SSI Arguments poteram Pedawet s to dlpe delve he we dode Gh eating Melek aa ease eh 5 53 5 32 Collect gt Scan gt MultiRun Perform several series as setup in the EditRuns form 5 54 9 92 51 Arguments soho we et pak oh Be Bot ee Be wee red et ee eh ome oe aad Wats 5 55 5 33 Collect gt Scan gt ResumeRuns Resume interrupted MultiRun scans 5 59 SBSH AMQUMOENTS msira hound Pee ae ee be eel tee be Pee eat ad pes 5 60 5 34 Collect gt Scan gt Rotation Take a phi rotation picture 000 a eee 5 63 5 34 21 Arguments orke y oa DO te hee he ee tate eel vale Gein RRS 5 63 5 35 Collect gt Scan gt HKL Reciprocal space scan from starting HKL to ending HKL 5 65 M86 E01008 4 04 v Table of Contents GADDS Software Reference Manual 5 36 1 Arguments caya iaa weak wiles ale ile dee eked bi ie eRe pedo at eae a 5 65 5 36 Collect gt Scan gt Psi e Take a Psi scan of 360 around reciprocal vector 5 68 5 361 ArQUMOIS ssc eee wo lated dh noe see E E etek ed eg d Reged ed 5 68 5 37 Collect gt Scan gt CoupledScan Conventional 20 0 coupled scan Uses AD as a D
348. forms e DIFFRAC is the file format used by the Bruker DIFFRAC S software This file for mat is binary and is difficult to read on non INTEL platforms INTEGRATE WRITE is capable of output any one of the supported file formats All four file for mats are also capable of supporting multiple ranges To write the data to a new scan range of an existing file set the append flag 8 11 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses a EEE Title Title of plot In SLAM mode enclose the title in quotes FILENAME lt n gt File Name Name of the RAW data file to create or append FORMAT lt n gt Format auto default auto default DIFFRACplus Enter file format as either DIFFRACP4S DIFFRAC AT OLD DIFFRAC AT or PLOTSO DIFFRAC is the latest file for mat and thus the preferred option PLOTSO files have standard ASCII format Non Bruker programs should be able to read PLOTSO files i e LOTUS 123 and MS EXCEL File extensions are defaulted to RAW for most formats and to PLT for PLOTSO format APPEND 4 Append as Additional Range Yes Enter Y to write this new data range as the next range in any existing file If the file doesn t exists it will be created with this data as the first and only range Enter N to M86 E01008 GADDS Software Reference Manual Peaks
349. frame image is equivalent to a perfect flat detector Pixels are perfect squares across this flat detector There is no spatial dis tortion or pin cushioning effects There is no variation of intensity sensitivity between pixels A perfectly radiating point source will not pro duce a flat intensity image but rather a slight decay of intensity from the detector center to the edges Geometric effects cause pixels at the edges to represent a smaller solid angular region than the pixels at the detector center Software processing will handle these geometric variations of frame pixels during integration into raw spectrum NOTE The isotope source is not a true point source but rather a Lambert radiator where the intensity will drop as the cosine of the incidence angle M86 E01008 Process Routines GADDS Software Reference Manual 6 10 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA tort everest Mates Input Frame Filename frame1 000 Name of first file to be unwarped Default is frame1 000 If you leave this item blank or specify a wildcard filename pattern press ing the ENTER key or the left mouse button will display a list of the current filenames matching the pattern You can choose one from the displayed list by moving to it with the arrow page keys or mouse and pressing ENTER or the left mouse button You will be returned to t
350. frame will be automatically displayed at the end of the frame collection if realtime display is off This latter display method has no effect on observed data rate Since the data rate in Fe source frames is not very high use of REALTIME with SPATIAL NEW will rarely cause any loss in counting efficiency and you can keep this set to Y FILE lt S gt 0006 Output Filename brass Enter the base filename for the output frame and correction data By default all four out put files _br _ix _if and _it as described above in the frame directory specified in the CONFIGURE EDIT input panel More specifically the filename you enter here is merged with the default filespec Frame_root _br _ix etc where Frame_root refers to the directory in the CONFIGURE EDIT panel See CONFIG URE EDIT for details on how filenames are merged The default name is brass In menumode the filename is defaulted to the standard naming convention of SIZE_DDD _BR where SIZE is replaced by 0512 or 1024 and DDD is replaced by the detector distance in cm If you supply a filename extension here it is overridden with the extensions _br _ix _it and _if as appropriate M86 E01008 Process Routines GADDS Software Reference Manual If you leave this item blank or specify a wildcard filename pattern pressing the ENTER key or the left mouse button will dis play a li
351. from the reduced primitive cell when you run INDEX Default is 90 Valid input range is 0 to 179 TREPET Current Gamma Cell Angle 90 0 Specifies the GAMMA unit cell angle in degrees of the input unit cell to be tested for correspondence with other lattices This item is automatically filled in with the value from the reduced primitive cell when you run INDEX Default is 90 Valid input range is 0 to 179 SIGA lt N gt Standard Deviation of A 0 03 Specifies the A axis standard deviation in Angstroms of the input unit cell to be tested for correspondence with other lattices This item is automatically filled in with the value from the reduced primitive cell when you run INDEX Default is 0 03 Valid input range is 0 to 999 M86 E01008 GADDS Software Reference Manual Peaks Routines SIGB lt n gt 06 Standard Deviation of B 0 03 Specifies the B axis standard deviation in Angstroms of the input unit cell to be tested for correspondence with other lattices This item is automatically filled in with the value from the reduced primitive cell when you run INDEX Default is 0 03 Valid input range is 0 to 999 SIGC lt n gt Standard Deviation of C 0 03 Specifies the C axis standard deviation in Angstroms of the input unit cell to be tested for correspondence with other lattices This item is automatically filled in with the value from the reduced primitive cell when you r
352. ft half of the available area you could issue the directive 1 V0 0 5 1 1 X This directive specifies the X axis label Fol low the directive with the text to be drawn along the X axis By default the text is X AXIS For example if you re plotting a func tion versus time you might issue the direc tive XTime seconds 1 Y This directive specifies the Y axis label Fol low the directive with the text to be drawn along the Y axis By default the text is Y AXIS For example if you re plotting pixel values as a function of position you might issue the directive YPixel Value Nor mally Y axis text is written vertically but not rotated since some graphic environments most notably X Windows don t support rotated text however if the text contains hyphens or parentheses it writes the text horizontally In this latter case you need to keep the axis label very short DB Draws a rectangular box at specified X Y W H fractional coordinates Requires the fractional X fractional Y fractional W and fractional H as parameters Example DB 0 5 0 5 0 1 0 1 DD Draws a dot at specified X Y fractional coor dinates Requires the fractional X and frac tional Y as parameters Example DD 0 5 0 5 DE Draws an ellipse at specified X Y W H frac tional coordinates Requires the fractional X fractional Y fractional W and fractional H as M86 E01
353. g displayed on the screen Enter a file name for this file VERBOSE Verbose Output N Controls the amount of information sent to the output file Choose Y to put the entire CDF record s out to the output file 8 28 2 CDF Search Algorithm The current version of the NIST Crystal Data File contains unit cell parameters for over 144 000 crystals whose lattice parameters have been published This file is not included with GADDS It can be obtained in CD ROM format from NIST Need address here An index file containing reduced cell axial lengths and cell volumes was prepared to enable the search algorithm to search the CD ROM very efficiently INDXTL a program that builds this index is included in the GADDS dis tribution From the input lattice parameters and lattice type the reduced unit cell parameters are calcu lated The index file is searched for all possible matches that have a b c and volume within the DECIMAL FRACTION DEVIATION For each match the corresponding NIST Crystal Data File record is read If the cell angles are within the prescribed limits all information for that record is written to a match file The matches are then sorted by a goodness of fit parameter the best matches will be first and written to the output file The search algorithm takes only a few seconds to complete If you get too few matches increase the DECIMAL FRACTION DEVIATION M86 E01008 Peaks Routines
354. ge width of both the LaserJet at 100 dpi and the PaintJet at 90 dpi The window width affects the print screen option The program requests a dot per inch resolution from the printer that is equal to or higher than the screen width in pixels divided by 7 75 inches The following screen widths fill the printed page reasonably well W 704 default LaserJet 100 dpi Paintuet 90 dpi W 520 LaserJet 75 dpi PaintUet 90 dpi IW 1024 LaserJet 150 dpi PaintJet 180 dpi NOTE The smaller widths result in faster screen dumps especially when the printer is on a serial port 13 14 M86 E01008 GADDS Software Reference Manual Utility Programs 13 8 Prbatch e Profile fitting in batch mode utility Used internally by GADDS to perform profile fit ting on raw spectra For more information see PROFILE 4S manual 13 9 PVWave Precision Visual s Wave procedures Bruker provides procedures for importing and exporting data in Bruker file formats from within Precision Visual s Wave software version 3 0 Directory C SAXI PVWAVE SAXII_READ_ PV wave procedure to read a D5000 PRO Bruker D5000 file SAXII_READ_ PV wave procedure to read a FRAME PRO Bruker frame file SAXII_READ_ PV wave procedure to read a PLOTSO PRO Bruker PlotSO file SAXII_SAVE_ PV wave procedure to save a D5000 PRO Bruker D5000 file SAXII_SAVE_ PV wave procedure to save a FRAME PRO Bruker frame file SAXII_SAVE_ PV wave procedure to sa
355. gle using calculated Hermans indices Menu Command Analyze gt Pole Figure gt Stein Accelerator None User Level 1 SLAM Syntax POLE_FIG STEIN 1 2 APPEND Typically Herman s indices are plotted on a Stein triangle The three apexes of the triangle correspond to the crystallographic axis a b c being parallel to the z axis of the sample The edges of the triangle represent the orientation of a crystallographic axis being perpendicular to the z axis A condition of no orientation is the origin In certain cases the reflection from the hkl plane will be too week in intensity to give useful data In such cases one must interpolate the desired second moment from second moments of two or more other hkl poles for which data is obtain able For our orthogonal case the expression of second moments for orthogonal relationships 2 lt COS a Z gt lt cos b z gt lt cos C z gt 1 eq 1 From which it follows Fa z Fb z Fe z 0 eq 2 Second moment for an hkO pole can be interpo lated using 2 2 lt cos hk0 z gt e lt cos a z gt f lt cos b z gt eq 3 where e and f are the direction cosines between the a and b axes with the hkO plane Stein triangles are plotted using Fa z and Fc z Herman s indices These are directly calculated from hOO and OOl poles Alternately one can obtain these two values from h00 and OkO poles or OkO and OO poles and applying equation 2 Otherwise it gets more co
356. gs to standby mode whenever the program has been idle for 10 minutes and the time is not between 8a m and 5 p m on a weekday This feature fails after 16 Jan 2038 STANDBYMA lt n gt Standby settings Current 5 Enter the standby X ray generator milliamps setting default is 5 ma See above STANDBYKV STANDBYIDLETIME lt n gt Standby settings Idle time 30 min Enter the standby idle time after which the generator is set to standby values STANDBYNOEXCLUDE Standby settings Don t exclude weekdays 8AM to 5 PM No Check Y to allow standby to occur during normal working hours MONOCHROMATOR lt s gt Filter Monochro mator parallel graphite Enter a short description of filter or mono chromator default is parallel graphite Currently this value has no effect on the operation of the program but it is stored in the header of output Bruker format frames OFFSET lt n gt 2 Theta Offset 0 0 This only affects dual detector systems On Master frame buffer enter 0 0 On Slave M86 E01008 Edit Routines GADDS Software Reference Manual frame buffer enter the slave s detector 20 offset in degrees from the goniometer s 20 setting 4 3 Edit gt Configure gt Read Read a new configuration from a disk file Menu Command Edit gt Configure gt Read Accelerator None User Level 2 SLAM Syntax CONFIGURE READ 1 Use this command to restore
357. gu ration from a file called gadds _nc in the current project s working directory You can override this startup behavior with a startup command line qualifier See Section 1 3 for details On exit ing GADDS normally saves its configuration file into a file called gadds _nc in the current project s working directory N CAUTION These commands are active and do not prompt before performing an operation i e overwriting an existing file 4 4 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses Plea Configuration Filename gadds _nc Enter the filename where the configuration is to be saved or read The default file is gadds _nc If you omit the file extension _nc is assumed M86 E01008 Edit Routines GADDS Software Reference Manual 4 5 Edit gt Configure gt Show model Display the current goniometer and controller type Menu Command Edit gt Configure gt Show model Accelerator None User Level 1 SLAM Syntax CONFIGURE SHOWMODEL Use this command to display the current goni ometer model type maximum frame size cur rent frame size current flood correction current spatial correction project working directory and calibration directory Normally the goniometer type is defined when the software is installed but occasionally when one changes the goniometer stage you must also change the goniometer type as fo
358. haracter is plotted at each subsequent X Y point The marker character must immediately follow the direc tive that is it must be the fifth character on the line Examples are M to plot a at each input X Y position or M to dis able plotting of a character at each X Y posi tion L 0 0 0 0 0 0 0 0 Sets plot axis limits overriding the auto scaling normally performed Requires four parameters Xmin Ymin Xmax Ymax cor responding to the lower X lower Y upper X and upper Y axis limits respectively If both the lower and upper limit for an axis are specified as zero autoscaling is restored for that axis The default limits are 0 0 0 0 meaning that auto scaling is performed on each axis When an axis is auto scaled a nice interval for tic marks is determined This interval is always 1 2 or 5 times some power of 10 Limits are then chosen which are integer multiples of this interval and which contain the range of values input for the axis being auto scaled An example of this directive is L0 0 100 0 This example specifies that the X axis will range from 0 to 100 and the Y will be auto scaled based on the range of the input Y values XDegrees This directive specifies the X axis label Follow the directive with the text to be drawn along the X axis By default the text is X AXIS For example if you re plotting a func tion versus time you might issue the direc ti
359. he menu bar select EXIT or press ESC PEAKS uses profile analysis to produce very accurate peak positional intensity and FWHM data Also standard deviations of peak parame ters can be obtained At least once after installa tion and prior to executing either PEAKS AUTO or PEAKS REFINE you must generate the required peak profile s by running PEAKS PROFILE These profile lineshapes are used in the least squares refinement of all peak parame ters During the least squares refinement any peak parameter may be fixed or variable refined Representative profile lineshapes can be either collected data or simulated data using mathe matical functions PEAKS SIMULATE allows you to use a Cauchy Lorentian Gaussian modified Cauchy asymmetrical Cauchy Pseudo Voigt Pearson VII or split Pearson VII function to model the profile shape PEAKS PROFILE creates the profile lineshape file by allowing you to select one or more repre sentative lineshapes at various 26 positions Each lineshape should be an isolated peak and the profile fitting algorithm works best with line shapes taken at low medium and high 20 angles The a contribution must be either con sistently present or consistently absent from all peak profiles All profiles are stored in a special format of DIFFRAC AT raw data structure and the individual profile shapes can be displayed with PEAKS LOAD PEAKS AUTO analyzes a diffraction pattern by searching for peaks re
360. he frame will be automatically displayed at the end of the ADD if real time display is off This latter display method has no effect on observed data rate If you re not sure whether real time display will affect the observed data rate signifi M86 E01008 GADDS Software Reference Manual Collect Routines cantly at your current incident count rate check the late counts in the frame header of a representative frame with the FRAME_INFO command If the late counts are more than a few percent of the total counts your data collection will be more effi cient if real time display is turned off In gen eral you should be able to use real time display for set up and sample evaluation but you should disable it during collection of frame series which will be used as input to data reduction see the similar SCAN com mand display options SHUTTER Open amp Close Shutter N This qualifier if present causes the shutter to open at the start of the ADD and to close at the end Otherwise the shutter stays in its current state for the duration of the ADD RESET lt n gt Bar Graph Hold Time 0 0 This qualifier specifies the number of sec onds before repetitive auto clear of frame memory 0 do not clear The default value is 0 the range is from 1 to 65 535 seconds This parameter is useful in conjunction with real time display if you re looking for a change in intensity over time For instance i
361. he input panel with the selected filename filled in If you leave this item blank it is the same as entering a wild card pattern Both filenames and patterns entered here are merged with the CONFIG URE EDIT frame directory as described above n ss Seda dies sees ET of Frames to Process 1 Number of frames in the series to unwarp 3 EART ETET Output Frame Filename frame1u 000 Name of unwarped frame file that will be created The default is frame1 unw If no output extension is specified a unw exten sion is used If you leave this item blank or specify a wildcard filename pattern press ing the ENTER key or the left mouse button will display a list of the current filenames matching the pattern You can choose one from the displayed list by moving to it with the arrow page keys or mouse and pressing ENTER or the left mouse button You will be returned to the input panel with the selected filename filled in If you leave this item blank it is the same as entering a wild card pattern Both filenames and patterns entered here are merged with the CONFIG URE EDIT frame directory as described above NONORMALIZATION Suppress Normaliza tion Y N no In command line mode enter nonormaliza tion if you want the system to bypass inten sity normalization described above In the input panel specify Y at the prompt to bypass intensity normalization the default N causes the sy
362. he run M86 E01008 GADDS Software Reference Manual Collect Routines number from wrapping from 9 to 0 The Characters in Run should be 1 These are the default settings e For greater than 36 runs you must set the Characters in Run in the Edit gt Config ure gt User settings dialog to 2 characters The Base of Run can be base 10 if you find it more convenient and you are collect ing 100 or fewer targets X Each line of the EDITTARGETS array contains the following items RUN This is the Run Number of the series This is not actually a number but is rather taken as RUNCHARS characters of ASCII text Also all characters must be valid characters to be used with filenames because the Run Num ber becomes part of the generated output filename Basically the Run Number is for matted and appended to the output base filename before the file extension See Frame Naming Conventions Edit gt Config ure gt User settings command and Collect gt Scan gt MultiTargets command for more details here will be used as the extension of the first output frame in the series and will be incre mented according to the frame naming parameters to form the extensions of subse quent frames See Frame Naming Conven tions Edit gt Configure gt User settings command and Collect gt Scan gt MultiTar gets command for more details This is the sample X position in mm at which the goniometer wil
363. heath ee Be eae BO a ge a Be ee ore 11 2 11 4 Help gt About Display program trademark copyright and license information 11 3 11 427 Argument 2e 2 ceed dicta ea eb a ee eee et ke i Be ae ee a ee er ee ee 11 3 11 5 Help gt Errata Display changes to printed documentation 0 00 0 eee 11 3 11 25 41 Argument 22st See Sen a hen Bae do ea oe Be eee 11 3 11 6 Help gt Release notes Display release notes 0 eee eee 11 4 M86 E01008 4 04 xiii Table of Contents GADDS Software Reference Manual 116 1 AUMENS iiss og d sated eine Bes TAE aay eee waa aie ae Mac eed ee 11 4 12 SLAM Routines ics ted wi erbaa ra hoe ni wild eed aed leh wae 12 1 IZLE neiareas EE aes Aaa aie et tye Sed Se et ER Dak feted 2 12 1 12 2 MENUMOUG argon or Get on ena eatin eee a oe bahia ee Eo ete ae PN ey Ade eG ae 12 3 12 3 Quit oo oy Gus baie aE a e Mewar bad G wwe THe A ole dae gata ed at dean wile ey 12 3 12 4 ROAKS EEE A PE EE do EOE vet A eee anna pe Ode ee ed Baas eee 12 4 12 4 1 PEAKS AUT Ord perce tin haan Gd dn De eee ee a nde ia aes Se ogide aaah led Ha 12 7 12 4 2 PEAKS GLEAR asia rare began E AE N E Mawar aia E a A i 12 9 124 3 PEAKS LOAD e es re Libba ged whet E Ara A A eke hie E aed oe Boles 12 10 12 4 4 PEAKS MANUAL idi oud nad a a teens 12 11 12 4 5 PEAKS POSTER mre ri ba Pele tees wie tae a E A ne eid as 12 12 2 4 6 PEAKS PROFILE ier nasu eden See ee Seg ho ae ew nn wr eee es 12 17 12 47 PEAKS REFINE 2
364. her and is analogous to a brightness control or to selecting the length of exposure of a film When you re using the arrow keys to modify contrast you can press CTRL simultaneously with an arrow key to jump in intervals ten times larger than the arrow key alone To exit and save your changes to the color map ping press ENTER or the left mouse button To exit and reset the mapping to default wide open levels press ESC or the right button When invoked from the command line with both the arguments shown below the mapping is changed to the specified lower and upper limits and control returns immediately to the command line SLAM arguments follow The number of counts to be mapped to the lowest display color The default value is 0 The valid range is 255 to 65535 a ES 255 The number of counts to be mapped to the highest display color The default value is 255 The valid range is 255 to 65535 M86 E01008 Edit Routines GADDS Software Reference Manual 4 9 Edit gt Zoom Magnify a specified square area on the display Menu Command Edit gt Zoom Accelerator Ctrl Z User Level 1 SLAM Syntax ZOOM 1 2 3 Analyze gt Zoom displays the pixels surrounding a specified center point as a magnified image Magnification is performed by pixel replication with the replication factor a power of 2 from 1 to 16 where 1 corresponds to the normal unmag nified display If the specified X or Y center woul
365. her the frame raw trace or peaks table And choose what marker char 7 30 M86 E01008 GADDS Software Reference Manual Analyze Routines Menu Command Analyze gt Annotate gt Box SLAM Syntax GRAPH POSTER DRAW BOX acter to use to highlight the data A crosshairs cursor will appear and the selected label will appear within the mes sage window Pressing ENTER or the left mouse button will draw the marker at the current cursor position and automatically send the user into the TEXT option to edit position and size the label to be drawn see Analyze gt Annotate gt Text Pressing ESC or the right mouse button will return you to the menu without drawing the label This command will draw a rectangular box When selected a crosshair cursor is visible Position the crosshairs at a corner of the box to be drawn Anchor the corner by pressing ENTER or the left mouse button The crosshairs will disappear and be replaced with a rectangular box with one corner being the anchored point just selected and the other corner at the current Menu Command Analyze gt Annotate gt Arrow A ad cursor position Position the second box cor SLAM Syntax GRAPH POSTER DRAW ner press ENTER or the left mouse button ARROW The box is drawn and a crosshair cursor appears for positioning the next box Press ing ESC or the right mouse button will return you to the menu This command will draw an arrow When selected a cross ha
366. here For frames in XENGEN or BRUKER format acquired with FRAMBO V2 or higher specify 9999 8 14 2 Threshold Output An example of the output from REFL_ARRAY THRESHOLD is shown below resulting from thresholding of the eight myoglobin test frames supplied with the software It begins with an overall statistical summary of the number of reflections found and their disposition This sum mary contains FOUND Total number of reflections above the threshold found ON FIRST OR LAST FRAME Reflections which have intensity on the first or last frame are rejected because their scan angle cannot be accurately deter mined IN X EXCLUSION RANGE This is the number of reflections rejected because their X centroid was between the limits specified as KEXMIN and KEXMAX OUTSIDE RADIUS LIMIT This is the number of reflections rejected because the distance of their X Y centroid from the detector center was larger than the limit given as RMAX M86 E01008 GADDS Software Reference Manual Peaks Routines OUTSIDE RES LIMITS This is the number of reflections rejected because their X Y centroid was outside of the resolution limits specified as DMIN and DMAX lt I SIGMA THRESHOLD This is the number of reflections rejected because their I SIGMA EXP DBIAS S was below of the threshold specified as SIGMA ORPHAN PIXELS This is the number of reflections rejected because there was only a single
367. his command to backup all files in the project s working directory and or the current calibration files into a single compressed archive file which you may wish to transfer to tape or CD R media for archiving purposes A scrollable alphabetized list of all known projects will appear Highlight the project of interest and click OK Next a dialog of options appears You must enter a filename for the archive file and enter the directory to place the archive file Optionally you may choose to exclude the calibration files or the current work ing files from the archive however typically you backup all your working files but not the calibra tion files Requesting archive file already exists Update existing archive file Click Yes to update No to abort Updating adds new or updates existing data files in the archive but does not remove any old data files If you wish to overwrite an existing archive file then you must pre delete the archive use Win dows NT Explorer No PKZIP file is defined SAXI PKZIP Your GADDS administrator must configure the console version of PKZIP for use with GADDS Simply extract the PKZIP files to a directory and define the System Variable SAXISPKZIP to point to the full file specification GADDS was tested with PKZIP for Console version 2 50 2 6 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses
368. his value should be left at its default setting of 3 if you re collecting to a FAT 16 formatted disk partition A special case occurs when NUMBASE see below is set to 10 the default the most significant digit only is treated as base 36 Thus the frame number following 999 will be a00 This special case allows up to 3600 frames in a series when NUM BASE 10 while maintaining the DOS 8 3 filename convention NUMBASE lt n gt Base of Frame 10 This value represents the numeric base to be used for the frame number like RUN BASE NUMBASE must be 10 or 36 When NUMBASE is 10 the most significant digit in the Frame Number is still treated as base 36 as described above under NUMCHARS M86 E01008 GADDS Software Reference Manual Edit Routines Base 10 is easier to interpret but limits the number of frames in a run to 3600 under DOS which allows at most 3 characters in the extension Base 36 allows a larger num ber 36s of frames per run under DOS This parameter should usually be left at its default of 10 unless you re performing scans which require single sweeps of more than 3600 frames LOWTEMP Low Temp Device Y N No Check this box if the LT 2 low temperature device is installed Specify N here or omit the qualifier in command line mode if no low temperature device is installed This value is stored in the header of output Bruker format frames If you enter Y
369. ied square area on the display 000 5 4 18 4 10 Edit gt Frame info View a frame header 0 eee 4 19 45101 Arguments cox toc i Lattwew teeth Lalande pee bos pela ae aai gia 4 19 5 Collect Routines ocsecw toe fy Pew saniata tern fe anaes cee ad be 5 1 5 1 Collect gt Detector gt Cu bias Set PDC to Cu low bias setting 004 5 1 B A ARQUMENTS ead ete Sate ea Reo ep Bak athe E E E an Baie haan ate ae 5 1 5 2 Collect gt Detector gt Fe Bias Set PDC to Fe high bias setting 5 2 672 1 Arguments arenae Sere ene A ea area BE epee eee BAe oe 5 2 5 3 Collect gt Detector gt Y vs X e Set PDC for normal positional display 5 2 M86 E01008 4 04 iii Table of Contents GADDS Software Reference Manual 5 31 AMQUMONTS neice dig tween Abe Sebi ERRA CER aiid 2 ae E E ANAA TA 5 2 5 4 Collect gt Detector gt E vs E e Set PDC for energy versus energy for bias calibration 5 3 5 41 ArQUMOMS aia pae aa EA RAA ate EA EA E EN didee Gee an nade oe es ae de 5 3 5 5 Collect gt Detector gt Add Accumulate a frame with temporary linear flood field 5 3 525 F APQUMOMISY sera ua al OEN eGue ns area k Gran She Acid yee ia te ete eae E DE ane Get ee Be 5 4 5 6 Collect gt Detector gt Reset Reset to x position vs y position Cu bias 5 6 5 6 1 ArQUMOMS 25s ee nadine ab tive iets ar ateeeaceata pat dete cuban S a ls wend dbs
370. ield table from an X projection and Y projection of the Fe image These projection arrays are by con vention stored in a plottable ASCII file ending in a _pj extension in the current frame directory specified in the CONFIGURE EDIT panel The flood field correction itself is stored similarly except with a _fl extension The name of the current flood field correction is shown on the display in the current status area at the bottom right of the screen FLOOD NEW updates this name when a new correction is acquired When you exit FLOOD NEW after successful comple tion the new correction automatically goes into effect The XMIN lt n gt YMIN lt n gt and MAG lt n gt arguments described below allow you to create a flood field table that results in 512x512 or 1024x1024 output data frames that correspond to a specific area of the detector rather than to its entire area For this calculation the full detec tor is considered to be an array of 16376 x 16376 bins Its origin is by default coincident with the output frame origin and its bins are by default summed in 32 x 32 blocks to form a nor mal 512 x 512 output frame These arguments allow you to choose the detector bin at which the output frame origin is placed and to use a re binning factor less than 32 to effectively mag nify a smaller detector region to cover the whole 512 x 512 output frame For example MAG 2 M86 E01008 GADDS Software Reference Manual Pr
371. ies the number of counts mapped into the maximum display memory value for example corresponding to white on the dis play The special value 1 directs the pro gram to pick a reasonable value by scanning through the pixels in the frame prior to display the special value 2 directs the program to use whatever setting is cur rently in effect The default value is 1 the allowed range is from 2 to 10 counts Smaller values make the displayed image M86 E01008 File Routines GADDS Software Reference Manual SCALE lt n gt Scale Factor look brighter larger values make look darker n If you supply a second filename for the 2 argument described above the two files are combined pixel by pixel according to the equation PO P1 P2 A B where PO is the pixel value in the resulting frame P1 and P2 are the pixel values in the first and second input frames A is the scale factor supplied here and B is the offset described below Any resulting PO values less than zero are clipped to zero A positive scale factor results in a weighted addition of the two frames while a negative scale factor results in a weighted subtraction of frame 2 from frame 1 If instead of supplying a numeric value for the scale factor you sup ply the special characters n or n the program weights the addition or subtraction according to the acquisition time ratio between the two frames That is a value of
372. iffractionist would like to visual ize the pole sphere from a different viewing angle or orientation Or perhaps the pole figure needs to be positioned with particular sample XEN ia X Origin 0 directions For these reasons the TILT and ROTATE options have been provided The TILT option allows a new position on the sphere to be N AS s Y Origin 0 positioned at the origin of the projection while the ROTATE option performs rotation of the image about the origin INVERT flips the image AEAT Output File NULL from top to bottom x offset of new origin y offset of new origin Output filename to store tilted pole figure 7 21 1 Arguments image or null Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses F esaik Input File FRAME Input filename for pole figure or frame DISPLAY lt n gt Max Display Counts 2 Enter 0 for no display otherwise this item specifies the number of counts mapped into M86 E01008 7 51 Analyze Routines GADDS Software Reference Manual 7 22 Analyze gt Pole Figure gt Rotate Rotate pole figure about beta azimuthal angle Menu Command Analyze gt Pole Figure gt Rotate Accelerator None User Level 1 SLAM Syntax POLE_FIG ROTATE 1 DISPLAY lt n gt 2 Frequently the diffractionist would like to visual ize the pole sphere from a different viewing angle or orientation or perhaps the pole f
373. igure needs to be positioned with particular sample directions For these reasons the TILT and ROTATE options have been provided The TILT option allows a new position on the sphere to be positioned at the origin of the projection while the ROTATE option performs rotation of the image about the origin INVERT flips the image from top to bottom 7 22 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses an eee on Input File FRAME Input filename for pole figure or frame DISPLAY lt n gt Max Display Counts 2 Enter 0 for no display otherwise this item specifies the number of counts mapped into the maximum display memory value for example corresponding to white on the dis play The special value 1 directs the pro gram to pick a reasonable value by scanning through the pixels in the frame prior to display the special value 2 directs the program to use whatever setting is cur rently in effect The default value is 2 the allowed range is from 2 to 10 counts Smaller values make the displayed image look brighter larger values make look darker ANGLE lt n gt CCW Angle 0 0 Angle of rotation about the origin center 2 sotsiaa Output File NULL Output filename to store rotated pole figure image or null M86 E01008 GADDS Software Reference Manual Analyze Routines 7 23 Analyze gt Pole Figu
374. ill be appended to the log file if the file already exists If the option is unchecked that is missing from the command line or unchecked in the dialog box the output file is overwritten if it already exists 18 M86 E01008 GADDS Software Reference Manual File Routines 3 10 File gt Scriptfile e Create a new script file and start recording Menu Command File gt Scriptfile File gt Scriptfile gt Enabled Accelerator None User Level 2 SLAM Syntax LOGFILE SCRNEW 1 APPEND LOGFILE SCRON SCROFF File gt ScriptFile lets you create record a script containing a list of one or more GADDS com mands in SLAM format that execute sequentially as a group as you interactively invoke the com mands of your choice SLAM stands for Script ing Lexical Analyzer and Monitor and is the command language used by most Bruker pro grams See more details below under Com mand and Script File Conventions and Command The File gt ScriptFile gt Enabled command tog gles the current state of recording to the script file If scripting is enabled the command dis ables it If scripting is disabled the command re enables it A check mark displays in the menu next to the File gt ScriptFile gt Enabled command if scripting is currently enabled From the SLAM command line LOGFILE SCRON and LOG FILE SCROFF enable and disable scripting respectively The File gt ScriptFile command ca
375. image to either the average intensity of a random sample or psuedo normal ize to the average intensity of the collect pole image In the normalized pole image an inten sity of 100 represents the random intensity 7 29 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses EEE EAT Input File frame Input filename for pole figure or frame INVAL lt N gt nanaa Norm Value 0 Normalization value or 0 pseudo normalize using the average intensity value of the dis played pole image DISPLAY lt n gt Max Display Counts 255 Intensity to map as white 7 62 M86 E01008 GADDS Software Reference Manual Analyze Routines 7 30 Analyze gt Pole Figure gt Contours Draw contour plot of pole figure Menu Command Analyze gt Pole Figure gt Contours Accelerator None User Level 1 SLAM Syntax POLE_FIG CONTOURS 1 INTERVAL lt n gt Pole figures can be displayed in three methods 1 As frame images were each pixel is dis played by a color indicating it s intensity 2 Asacontour plot were lines of equal inten sity are drawn at given intervals 3 As a 3D surface plot where intensity is rep resented by height 7 30 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses nee Input File FRAME Enter the input pole figure filename or
376. imal seconds or in HH MM SS SS hours minutes and sec onds format Data collection ends when the specified time has elapsed or when the maximum count limit see MAX COUNTS below has been reached M86 E01008 GADDS Software Reference Manual Process Routines Usually a fiducial plate frame with a time cutoff of about 30 min or a count cutoff of about 100 000 counts is adequate a rule of thumb which works well is to use the same collection time as for the flood field data plus 5 minutes but no less than 15 minutes COUNT lt n gt Max Counts 150 000 This qualifier sets an upper limit on how many counts may occur before data collec tion is terminated When the specified num ber is reached the system ends the data collection saving the data frame The default value is 150 000 counts with a range from 0 to 10 counts Data collection will also be terminated if MAX SECONDS is reached before MAX COUNTS DISPLAY lt n gt Max Displayed Counts 100 0 no display otherwise counts corre sponding to white on the display The initial default is 100 the allowed range is from 1 to 10 REALTIME Realtime Yes This qualifier when present displays data as it is being collected The display does require additional processing time and will limit the maximum rate at which counts can be accumulated If the MAX DISPLAYED COUNTS qualifier is given a non zero value the
377. in the specified column and range of lines are to be set REFL_ARRAY MODIFY also sup ports the following special values f f where f is one of the flag characters A C H or S This sets or clears the speci fied flag leaving the state of the other flags unaffected for each reflection The field must be 1 if you use this option Negates all the numeric values in the specified range The field number must be 2 8 i e only applies to HKL indices and setting angles N where N is the number of a field in the same group This copies the values from column N into the column being modified This works within two differ ent groups of columns the HKL group 2 4 and the setting angle group 5 8 Thus if the value you specified for FIELD is 7 only 5 6 7 or 8 is a valid copy operation 2 would not work in this case Examples 1 Set the C flags of all reflections in the array leaving all the other flags intact REFL_ARRAY MODIFY 1 512 FIELD 1 VALUE C 2 Change the scan angle extracted from a frame series from omega to phi effectively reversing the sense of the scans assuming all the existing phi values in the array are the same REFL_ARRAY MODIFY 1 512 FIELD 7 VALUE 6 REFL_ARRAY MODIFY 1 512 FIELD 6 VALUE 0 0 M86 E01008 GADDS Software Reference Manual Peaks Routines 3 Change the swing angle for reflections 107 200 to 30 degrees REFL_ARRAY MODIFY 107 200
378. increment in mm for the grid in the Y direction The Y begin and end values may be equal Also Y end may be less than Y begin TRANSMISSION Transmission mode X Y Y Z No Check for samples mount in transmission mode where you wish to grid in Y amp Z axes APPEND Append to existing target list No Check for append new grid list to end of existing list of targets Unchecked will pre clear the target list M86 E01008 GADDS Software Reference Manual Collect Routines 5 42 Collect gt Scan gt LineTargets Set up line for MultiTarget list Menu Command Collect gt Scan gt LineTargets Accelerator None User Level 1 SLAM Syntax SCAN LINETARGETS XBEG lt n gt XEND lt n gt YBEG lt n gt YEND lt n gt INC lt n gt TRANSMISSION APPEND On systems equipped with an XYZ stage it is possible to collect scans at multiple target loca tions On flat samples such as wafers usually scans are taken on target positions laid out along a line Instead of manually determining the Z axis position of each target on the grid one can predetermine the flat sample plane then lay out the target locations using SCAN LINETARGETS which will automatically calcu late the correct Z axis value from the flat sample plane See GONIOMETER FLATSAMPLE 5 42 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses XBEG lt n g
379. ines 12 2 Menumode Menu Command None Accelerator None User Level Command SLAM Syntax MENUMODE MENUMODE is available in command line mode at the GADDS gt prompt Use this com mand to exit command mode and to return to menu mode MENUMODE takes no arguments 12 3 Quit Menu Command App menu Close Close box Accelerator Alt F4 NT only User Level Command All SLAM Syntax QUIT QUIT is available in command line mode at the GADDS gt prompt or from the application menu or close box on the title bar Whereas File gt Exit GADDS updates the configuration file before returning to the operating system QUIT does not save the configuration but instead throws away any changes you ve made since starting the program QUIT takes no arguments M86 E01008 SLAM Routines GADDS Software Reference Manual 12 4 Peaks While the TOPAS software package sports superior profile fitting algorithms GADDS still has some primitive profile fitting features If your profile fitting needs are minimal the GADDS PEAKS command may be sufficient for your needs To access PEAKS 1 Goto Special gt Command Mode 2 Select Peaks A pop up menu of all the PEAKS commands will appear 3 Type MENUMODE or MENU to exit com mand mode and return to menubar control If you constantly use these old PEAKS com mands add them to your usertasks The pro vided file usertask pks is a good start Replace your use
380. ing the current frame soft abort e press CTRL BREAK to interrupt the scan hard abort or immediate abort During actual frame data collection a small summary file is written and updated after each frame is collected This file contains the current status of data collection including the current run and frame number current angle settings and elapsed data collection time This file is M86 E01008 GADDS Software Reference Manual Collect Routines used to resume a data set that has been inter rupted To resume acquiring data where the scan opera tion was interrupted even by power failure use the Collect gt Scan gt ResumeRuns command See Section 5 33 for more details When you interrupt a scan with CTRL BREAK the goniometer returns to the starting scan angle of the current scan This repositioning is performed by backing up to the starting position minus one frame width or 0 5 maximum then driving forward to the starting position The same positioning technique is used when driv ing to the first scan in a new series which makes the positioning extremely repeatable but does require you to allow for an extra scan width at the beginning of the series when you re start ing close to the goniometer collision limits The current configuration is saved in the current default configuration file usually gadds _nc before starting the first scan which makes recovery easier in the event of a power fail
381. input panel The first and last generated filena mes in each frame series must be valid Also the generated filenames between frame series should not overlap Always check the bottom status line when you first start a new Collect gt Scan gt MultiRun to ensure that filena mes are being synthesized the way you want to avoid duplication of filenames during data col lection which will overwrite the previous file M86 E01008 GADDS Software Reference Manual Collect Routines The EditRuns command is an interactive com mand meaning that you can invoke it from the command line but it will not proceed without user intervention And it has no built in com mand mode time out as with other scrolling out put windows Additionally the Collect gt Scan gt MultiRun does not work well from script files as you cannot define the run list in command mode Thus we recommend using the equiva lent SCAN SINGLERUN script commands instead 5 31 1 Arguments None Command executes immediate for inter active editing M86 E01008 Collect Routines GADDS Software Reference Manual 5 32 Collect gt Scan gt MultiRun e Perform several series as setup in the EditRuns form Menu Command Collect gt Scan gt MultiRun Accelerator Ctrl Shft F3 User Level 1 SLAM Syntax SCAN MULTIRUN 1 TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt n gt DISPLAY lt n gt REAL TIME CLEAR OLDXENGEN STARTRUN lt n gt
382. installed preferably prior to thresholding frames to populate the Reflection Array 4 When using frames written in XENGEN for mat by earlier versions of the software the setting angles contained in the frame may not be correct In particular frames taken with phi scans on a 4 circle goniometer may be incorrectly interpreted as omega scans The setting angles in the reflection array may thus show the scan angle in the OMEGA position instead of the PHI posi tion with the result that the sense of the scan angle will be reversed from its true direction OMEGA is a right handed rotation and PHI is left handed Autoindexing does not work correctly unless the sense of the scan angle is correct If this problem occurs use the MODIFY sub command to negate the scan angle values or to move the omega values into the phi field then zero the omega values see REFL_ARRAY MOD IFY Frames written in XENGEN format by earlier versions of the software can contain zero for the swing angle Again you can use MODIFY to insert the correct values in the Reflection Array 5 Make sure you haven t used too low a threshold in the REFL_LARRAY THRESH OLD command The Reflection Array should contain the positions of strong spots not those of high background points When invoked with the INDEX option from the REFL_ARRAY submenu or when run from the command line without arguments M86 E01008 Peaks Routines GADDS Software Reference Manua
383. ion record record type 100 oscillation parame ters record length 40 bytes oscillation drive 6 y 7 z 12 C4 4 bytes of padding for alignment 16 R8 oscillation amplitude in degrees or mm 24 R4 oscillation speed in degrees or mm per sec 28 C12 reserved for expansion Offset Code Description for PSD record 0 14 record type 110 PSD parameters 4 14 record length 40 bytes 8 R8 actual two theta of goniometer in deg 16 14 first channel used 20 C20 reserved for expansion Offset Code Description for Optimized Quantitative Measurement record 14 record type 120 OQM parameters 14 record length 72 bytes undefined at this time tube 1 sample 2 detector 3 chi 4 phi 5 x M86 E01008 DIFFRACP S Raw Data File Format GADDS Software Reference Manual Offset Code Description for Quantitative Offset Code Description for Offset Assigned Compound Indicator record by EVA record 0 14 record type 130 QCI parameters 0 14 record type 190 offset assigned by obsolete EVA 4 14 record length variable number of 4 14 record length 32 bytes bytes 8 R4 2 theta offset in degrees 8 14 variable type 0 peak 1 low back 12 R4 intensi ers ensity offset in of ma ground 2 high backg
384. ion parameters Upon exiting all peaks within the region are erased and redrawn with the new region parameters M86 E01008 12 11 SLAM Routines GADDS Software Reference Manual If you try to add a peak before you specify a peak region both REGION and ADD are exe cuted When started from the command line PEAKS MANUAL takes no arguments and can only be run in interactive mode Command line syntax is PEAKS MANUAL 12 4 5 PEAKS POSTER With this command you can interactively anno tate plots or frame images PEAKS POSTER has seven subcommands EXIT Close the POSTER submenu and return to GADDS menu DRAW Draw various objects on screen EDIT Edit current annotations CLEAR Clear annotations within rectangular region LABEL Label spots peaks using d I HKL TH 2T etc SAVE Save annotations to PLOTSO file TEXT Position text on screen When you choose PEAKS POSTER from the menu bar GADDS displays a pop up submenu containing these subcommands When you start PEAKS POSTER from the command line no qualifiers are allowed The submenu appears and GADDS waits until you have made a selec tion PEAKS POSTER runs in interactive mode only To select one of the options highlight it with the arrows or mouse A help message appears on the bottom status line describing the action taken by the selected item Press ENTER to run the selected item To exit or return to the menu bar select EXIT or press ESC 12 12
385. ipt directory Whenever a script file is specified without a M86 E01008 General Information GADDS Software Reference Manual directory the program will search for the script file in three places current project directory system data directory and com mon script directory GADDS SYSTEM This variable must translate to the name of the directory where the area detector pro grams utility programs new project defaults and help files reside e g C SAXI GADDSnew GADDS SYSDATA This variable must translate to the name of the directory where the area detector data files e g color lookup tables calibration files usertask ini reside C SAXI GADDSnew GADDSS TEST This variable must translate to the name of the directory where the test frames and test command files reside e g C SAXI GADDSnew TEST GADDS CDCODE This variable translates to the directory which contains the NIST journal file CODENS DAT If missing it defaults to GADDS CDROM waxind e g D crys tal vaxind GADDSS CDF This variable translates to the directory which contains the NIST index file CRY IDX BIN e g C saxi GADDS CDROM This variable translates to the directory which contains the NIST database file CRYSTAL DAT e g E crystal PROF SYSTEM This optional variable translates to the name of the directory where the profile fitting package resides e g C TopasP See Special
386. ir cursor is visible Posi tion the crosshairs at the point of the arrow to be drawn press ENTER or the left mouse Menu Command Analyze gt Annotate gt Circle buton The crosshairs will giSappearand be SLAM Syntax GRAPH POSTER DRAW CIR replaced with an arrow with the point CLE anchored at the selected position and the tail at the current cursor position Position the tail of the arrow press ENTER or the left mouse button The arrow is drawn and a crosshair cursor appears for positioning the next arrow Pressing ESC or the right mouse button will return you to the menu This command will draw an ellipse When selected a crosshair cursor is visible Posi tion the crosshairs at the center of the ellipse and press ENTER or the left mouse button to anchor this spot The crosshairs will disappear and be replaced with an ellipse drawn with the center anchored and the width and height selected from the cur sor Move the mouse until the width and height are correct press ENTER or the left mouse button The ellipse is drawn and a M86 E01008 Analyze Routines GADDS Software Reference Manual crosshair cursor appears for positioning the Menu Command Analyze gt Annotate gt Style ellipse center Pressing ESC or the right SLAM Syntax GRAPH POSTER DRAW mouse button will return you to the menu STYLE Monu Command Analyze aANT e This command will toggle between drawing SLAM Syntax GRAPH POSTER DRAW DOT objects with
387. ires no parameters If you use this directive you ll want to make sure to specify separate V viewport directives for each plot so they don t overlap within the graph ing window IP Specifies that the X Y points encountered so far are to be drawn and that subsequent points will be drawn as a separate curve If you re drawing multiple plots issue a P after the X Y pairs of the first plot to draw it followed by a N to begin the second If you re drawing multiple curves in the same plot issue P after the X Y pairs in each curve 13 12 M86 E01008 GADDS Software Reference Manual Utility Programs S Specifies a line style for a connecting line to be drawn between X Y pairs Supply one of the characters 0 N S or D as a parameter Line styles are SO or SN for no connecting line for example for scatter plots SS for a solid connecting line and SD for a dotted connecting line 1 V Specifies the viewport to be used for the subsequent plot in fractional coordinates representing the fraction of the entire area available for graphs Requires the four parameters Xmin Ymin Xmax and Ymax which represent the lower X lower Y upper X and upper Y viewport limits respectively By default these limits are 0 0 1 1 meaning that the viewport occupies the entire graph ing area For example if you wanted to con fine the graph to the le
388. is usually better for this purpose The default is unconstrained refinement When invoked with the LEASTSQ option from the REFL_ARRAY submenu or when run from the command line without arguments REFL_ARRAY LEASTQ displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins refinement of the unit cell and orientation parameters the ESC key or right mouse button returns you to the REFL_ARRAY submenu You can interrupt a refinement in progress with the CTRL BREAK key combination however the current orientation matrix e g for use by the CURSORS commands for computing HKL indi ces at that point is undefined When refinement starts the program displays the message REFINING on the bottom sta tus line Refinement should usually be com pleted within 10 or 15s Upon completion a scrolling output window is displayed containing the resulting output text If logging is enabled see LOGFILE the contents of this window are also written to the logfile When viewing the out put pressing ENTER or the left mouse button displays a pop up menu of options including export of ASCII data for example the contents of the window could be sent to a file or printer with this function You can also move through the window contents with the page keys arrow keys or with mouse motion Pressing ESC or the right mouse button exits the output window retur
389. ission 564 R4 goniometer radius in mm 4 Open cradle 9999 0 unknown 0 0 unknown 5 Closed cradle 2 6 Phi 568 R4 diverg slit fix incidence in degrees 9999 0 unknown T ehi 572 R4 sample slit fix incidence in degrees 8 XYZ 9999 0 unknown 9 Low temp 576 14 primary soller slit 10 High temp 0 not present 11 External temp 1 present 12 Other 1 2 deg 2 1 16 Phi stage at fixed chi 2 2 4 deg 2 1 B 2 M86 E01008 GADDS Software Reference Manual DIFFRAC S Raw Data File Format 3 other 2 1 1 0 4 deg 2 1 9999 unknown 2 0 15 deg 2 1 580 14 primary monochromator 3 0 08 deg 2 1 0 None 9999 unknown 1 Transmission 600 14 beta filter Yes 1 No 0 9999 2 Reflection unknown 3 Ge220 2 bounce 604 14 secondary monochromator 4 Ge220 4 bounce 0 None 5 Ge440 4 bounce 1 graphite 6 Flat graphite 2 1 2 LiF 7 Single Goebel mirror 2 1 3 Ge220 channel cut 8 Crossed Goebel mirror 2 1 4 Goebel mirror 9 Flat Germanium 111 2 1 9999 unknown 10 Flat Silicon 111 2 1 608 C4 ASCIIZ 2 Anode material e g Cu 9999 unknown 612 C4 4 bytes of padding for alignment 584 R4 anti slit diffracted side in degrees 6 16 R8 average wavelength in A Obs or nm 9999 0 unknown i
390. it the arguments described below Pressing the ENTER key or clicking the OK button starts the operation Pressing ESC or the Cancel button returns you to the menu 4 7 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses Sais eae Seve atest eee Screen Data or All ALL Selects either the screen the frame buffer accumulation memory data or both are to be cleared SCREEN erase display DATA erase accumulation memory ALL erase both The default value is ALL QUADRANT lt n gt Screen Quadrant 0 Specifies the targeted display quadrant s to be cleared The selection criteria are 0 all the entire image area 1 first quadrant lower left 2 second quadrant lower right 3 third quadrant upper left and 4 fourth quadrant upper right The default value is O clears everything GRAPHICS_SAVE Preserve Graphics Y N No Specifies whether or not to preserve the graphics if you clear the screen Enter Y to erase just the displayed image and retain any overlaid graphics N otherwise The default value is N IMAGE_SAVE Preserve Image Y N No Specifies whether or not to preserve the image if you clear the screen Enter Y to erase only the overlaid graphics and retain the underlying image N otherwise The default value is N M86 E01008
391. ithout intervention If you do not press a key or mouse button within 10 s after the output window is displayed the program will continue as if the ESC key had been pressed When invoked from the command line REFL THRESHOLD can take the following arguments where lt n gt represents a numeric value amp indi cates continuation on the next line Optional command line parameters are shown in square brackets If you don t supply these parameters on the command line the command still runs without intervention with the default value 9999 get value from frame header assumed 8 14 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses hh Reece eee eee cere First Input File Name FRAME 000 Enter the file name for the first frame in the series to process For example if you have 15 data frames to be thresholded beginning with SAMPL 001 and ending with SAMPL 015 then you would enter SAMPL 001 as the first frame in the series When in the input panel if you leave this entry blank or specify a wildcard filename pattern pressing the ENTER key or the left mouse button will display a list of the current filenames matching the pattern You can choose one from the displayed list by mov ing to it with the arrow page keys or mouse and pressing ENTER or the left mouse but ton You will be returned to the input panel with the selected filename filled
392. k Older PCS computers used a XENGEN format for data frames These files can be converted to the newer SAXII format using TOSAXII The user will be prompted for any missing header information Example session follows gt TOSAXII Under DOS UNIX or VMS the command tosaxii runs the program which prompts you for the following additional information Default val ues are displayed in square brackets after the prompt Pressing the lt ENTER gt key lt Return gt key on VAX is the same as entering this default INPUT FILENAME M86 E01008 13 23 Utility Programs GADDS Software Reference Manual Enter the name of the input XENGEN format frame You must give the full pathname TOSAXII does not merge filenames with GADDS s or VGADDS s current frame directory however TOSAXII does translate logical names under DOS VMS or UNIX INPUT UPR FILENAME BLANK IF NONE If you want to insert orientation information determined by XENGEN s REFINE program into the output frame header supply the full path name of the XENGEN parameter file See the discussion above for more information Other wise press the lt ENTER gt key without supplying a filename lt Return gt key on VAX GADDS users will simply press lt ENTER gt INPUT UCA FILENAME BLANK IF NONE If you have a uca spline spatial calibration file from XENGEN TOSAXII will obtain the beam center coordinates from it Supply the full pathname
393. l REFL_ARRAY INDEX displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins refinement of the unit cell and orientation parameters the ESC key or right mouse button returns you to the REFL_ARRAY submenu You can interrupt autoindexing progress with the CTRL BREAK key combination When autoindexing starts the program displays the message AUTOINDEXING on the bot tom status line Indexing should usually be com pleted within 10 to 30s Upon completion a scrolling output window is displayed containing the resulting output text If logging is enabled see LOGFILE the contents of this window are also written to the logfile When viewing the out put pressing ENTER or the left mouse button displays a pop up menu of options including export of ASCII data for example the contents of the window could be sent to a file or printer with this function You can also move through the window contents with the page keys arrow keys or with mouse motion Pressing ESC or the right mouse button exits the output window con tinuing with the REFL_ARRAY INDEX com mand This first output window contains the results of the indexing and reduced primitive unit cell determination and is presented for review PRIOR to re indexing the Reflection Array It is described in more detail below When you ve reviewed the output and exited the window fol lowi
394. l Routines GADDS Software Reference Manual 9 5 Special gt PDF2 gt Clear Clear PDF2 overlay graph Menu Command Special gt PDF2 gt Clear Accelerator None User Level 1 SLAM Syntax PDF2 CLEAR PDF2 CLEAR command will clear the graphics overlay plane while preserving the displayed frame image Thus any pattern displayed with PDF2 DISPLAY command can be quickly cleared 9 5 1 Arguments None Command executes immediately M86 E01008 GADDS Software Reference Manual Special Routines 9 6 Special gt Commandmode Switch between command line and menu mode Menu Command Special gt Commandmode Accelerator Ctrl K User Level 1 SLAM Syntax MENUMODE The MENUMODE command requires no argu ments It toggles back and forth between menu mode and command line command file mode When operating the system in menu mode the software is programmed to automatically prompt you for input of options and arguments via dia log boxes when a menu item is selected This is particularly useful when first learning the sys tem or when you do not wish to either memo rize the parameters for all commands or continually refer to this manual On the other hand the command mode allows you to execute command scripts which can be used for exam ple to automate repetitive tasks Special gt Command Line makes both these operating modes available To go from menu mode to command line mode click the Special
395. l be positioned for this frame series Entering will be automati cally replaced with current angle setting This is the sample Y position in mm at which the goniometer will be positioned for this frame series Entering will be automati cally replaced with current angle setting This is the sample Z position in mm at which the goniometer will be positioned for this frame series Entering will be automati cally replaced with current angle setting When you select this command gt EditTargets FRAME GADDS displays a scrollable editing window This is the starting frame number for the series Like the Run Number this is actually taken as text of length NUMCHARS rather than as a numeric value The text specified listing all of the targets currently in the target array You can add to delete from or reorganize the list as desired by using the appropriate screen editing functions M86 E01008 Collect Routines GADDS Software Reference Manual When you invoke the MultiTarget scan com 5 43 1 Arguments mand Collect gt Scan gt MultiTargets each series will be acquired in the order they appear in the corresponding array GADDS generates output filenames for each frame from the Job Name in the Collect gt Scan gt MultiTargets dia log box GADDS also generates the Run Num ber given for the series in the array the starting Frame given for the series in the array the Frame being c
396. l values for the upper limit 1 for auto matic limit setting etc we ignore these special cases in the following discussion The first step is the mapping of pixel values into display memory Display hardware components differ in the number of color levels available for each pixel With GADDS we always assume that the hardware can support at least 64 differ ent values 0 63 The LO and HI qualifiers in File gt Display let you specify any linear transfor mation between the pixel values and the values written into the display hardware with the mapped values clipped to the range 0 to 63 so that values outside this range don t show up in the wrong colors Thus if you need fine dis crimination within a narrow range of pixel val ues you could specify LO and HI to cover that range On the other hand if wide latitude is more important you would specify LO and HI to cover the whole range of pixel values in the frame After the pixel values have been converted and stored into display memory the display memory values are mapped into colors with a second lin ear transformation according to the current lim its set in the Edit gt Contrast command Display memory values less than or equal to the lower Edit gt Contrast limit are shown in the color at the bottom of the color table for example black And values at or above the upper Edit gt Con trast limit are shown in the color at the top of the color table for exam
397. lect Routines GADDS Software Reference Manual 5 15 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt and default values in degrees Note that a positive limit is a limit on drives which proceed in the positive direction A negative limit limits drives in the negative direction If both the positive and negative limit for any angle or axis are zero the program considers its motion unlimited Table 5 1 D8 DISCOVER Goniometers Defaults Parameter Input Prompt D8 6 6 D8 1 Positive 2 Theta limit 90 00 Positive Theta limit 80 00 2 Negative 2 Theta limit 90 00 Negative Theta1 limit 10 00 3 Positive Omega limit 180 00 Positive Theta2 limit 80 00 4 Negative Omega limit 180 00 Negative Theta2 limit 10 00 5 Positive Omega 2 Theta limit 60 00 Positive Theta1 Theta2 limit 0 00 6 Negative Omega 2 Theta limit 240 00 Negative Theta1 Theta2 limit 0 00 7 Positive Phi limit both O none 0 00 0 00 8 Negative Phi limit both O none 0 00 0 00 9 Positive Chi limit both O none 0 00 0 00 0 Negative Chi limit both O none 0 00 0 00 5 20 M86 E01008 GADDS Software Reference Manual Collect Routines Table 5 2 PLATFORM Goniometers Defaults Parameter Input Prompt Platform Circle 1 Positive 2 Theta limit 90 00 90 00 2 Negative 2 Theta limit 90 00 90 00 3 Positive Omega limit 180 00 180 00 4 Negative Omega limit 180 00 180 00 5 Positive O
398. lections found by THRESHOLD If a valid spatial correction is in effect highly recommended the X Y values entered into the array will represent the spatially corrected X Y position and the S flag for that reflection will be set otherwise the raw X Y will be entered and the S flag will be clear In the special case where you re thresholding reflections from a single frame 2 1 see below the program automatically sets the C flags This makes indexing from a single frame or better from two nearly orthogonal oscillation pictures more convenient When attempting to index from one or two oscillation pictures it is best to use fairly wide frames e g 0 5 1 5 degrees to insure that changes in all three HKL indices are represented in each picture Normally the setting angles for each frame are extracted directly from the frame itself however XENGEN format frames taken with data collec tion software earlier than FRAMBO Version 2 do not contain the required information You can still threshold frames acquired with earlier ver sions with use of the setting angle override options described below Make sure that these override options are all set at their default values of 9999 unless you re processing old frames When invoked with the THRESHOLD option from the REFL_ARRAY submenu or when run from the command line without arguments M86 E01008 Peaks Routines GADDS Software Reference Manual REFL_ARRAY TH
399. les in degrees IAXIS lt N gt ee Scan axis 2 omega Goniometer axis for scanning 2 omega 3 phi 4 chi WIDTH lt n gt Frame width 5 0 deg Step size of scan axis between frames CLEAR oaa Pre clear Y Check Y to clear both the screen display and the output file or Scan gt MultiRun list Uncheck N to append to screen and output file or run list M86 E01008 Analyze Routines GADDS Software Reference Manual 7 35 Analyze gt Stress gt Biaxial 2D e Biaxial stress measurements from frame images Analyze gt Stress gt BiaxialShear2D Analyze gt Stress gt Triaxial2D Menu Command Analyze gt Stress gt Biaxial 2D Analyze gt Stress gt BiaxialShear2D Analyze gt Stress gt Triaxial2D Accelerator None User Level 1 SLAM Syntax STRESS BIAXIAL2D SHEAR2D TRIAXIAL2D 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt NUMBER lt n gt 2THETA lt n gt 5 FILENAME lt s gt HKL lt s gt YOUNG lt n gt POISSON lt n gt ARX lt n gt LINESHAPE lt n gt CUTOFF lt n gt REPROCESS BKGFIT lt s gt KALPHA2 PHl lt n gt PSl lt n gt UNITS lt s gt Preferred stress calculation algorithm See the User Manual for details Biaxial stress solves P11911 P12012 P22022 1 2v E Oph In sin Q sin 0 Biaxial Shear stress solves p11011 p12012 p22022 p13013 p23023 1 2v E oph In sin 60 sin 0 Triaxi
400. lip board with CTRL X and paste with CTRL V However ensure that any text you paste into such a dialog is correctly format ted since format is not checked before a paste The Write and Print buttons allow you to send selected text or all the text if no selection was made to a disk file ora printer respectively The Read button allows you to insert text from a disk file at the cur rent position As with the paste operation ensure that text in the file is correctly format ted since format is not checked before file text is inserted 1 5 2 Keyboard Conventions Following are definitions used by Bruker for common keyboard keys and key combinations Note that the keys used in interactive com mands may also be used as menu accelerators For example when the GADDS menu has the focus CTRL LEFT ARROW displays the next image in a sequence But when a cursor com mand has the focus the same key moves the cursor left in 10 pixel increments CTRL BREAK and CTRL C NT only CTRL C SGI only Interrupts an operation in progress Under some workstation environments CTRL C is polled so that to may need to hold the key combination down long enough for the pro gram to detect it ESC Works like the Cancel button in dialogs with a Cancel button Also works as a soft abort stop after current frame is finished in the Acquire gt SingleRun MultiRun Hemi sphere Quadrant and Matrix commands ENTER Works like the OK butt
401. ll frame of data at a fixed goniometer position using a lin ear flood field Data is continuously acquired until either a specified amount of time has elapsed or a specified number of counts is reached whichever occurs first You can optionally display the accumulated frame after it has been acquired or update the display immediately as each count is recorded referred to as real time display If you elect one of the display options ADD also updates the current frame status information displayed at the upper right of the screen The frame remains in the frame buffer s accu mulation memory it is not written directly to disk Use the SAVE command to save the data to disk M86 E01008 Collect Routines GADDS Software Reference Manual 5 5 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses A ee ee ere Max Seconds 30 This is the maximum count time in sec onds The default value is 30 the range is from 1 to 65 535 seconds Times can be entered in decimal seconds or in HH MM SS SS hours minutes and sec onds format Data collection ends when the specified time has elapsed or when the maximum count limit see MAX COUNTS below has been reached CLEAR naaa Pre Clear Y This qualifier when set clears memory before the new data frame is collected If it is not set the new data are added to the image already in the frame ac
402. llows 4 5 1 Arguments None Command executes immediately X100 Obsolete setting X200 Obsolete setting P3X1000 Obsolete setting P3X2000 HI STAR on P4 goniometer X1000 Obsolete setting X2000 HI STAR on Aztalan goniometer PLATFORM HI STAR on PLATFORM goniometer Y CIRCLE Obsolete setting use T 4 CIRCLE T CIRCLE PLATFORM 1 circle in transmission mounting R 4 CIRCLE PLATFORM circle in reflection mounting D8 HI STAR on D8 DISCOVER goniometer 4 12 M86 E01008 GADDS Software Reference Manual Edit Routines 4 6 Edit gt Configure gt Colors Edit the current color configuration settings Menu Command Edit gt Configure gt Colors Accelerator None User Level 1 SLAM Syntax CONFIGURE COLORS 1 WINBG lt n gt WINFG lt n gt CURSOR lt n gt HIGHLIGHT lt n gt BORDER lt n gt GRAPH lt n gt OVERLAY lt n gt MATCH1 lt n gt This command displays a dialog box where you can view or edit the colors used for the windows displayed by the program and the color scheme called a color table or color lookup table used to display detector frame pixel values Each window color WINBG WINFG CURSOR HIGHLIGHT and BORDER is specified as a 9 digit decimal integer The first three digits corre spond to the red level the second three to the green level the last three to the blue level The range for each color is 0 255 Thus the number itself has a range from 000000000 to 255255
403. loops only NOERASE No Prevents erasing the calibration lines when exiting routine M86 E01008 7 Analyze Routines 7 1 Analyze gt Cursors gt Box Display statistics of pixels in rectangular region Menu Command Analyze gt Cursors gt Box Accelerator F5 User Level 1 SLAM Syntax CURSORS BOX 1 2 3 4 DELAY lt n gt NOERASE When invoked from the menu or when run from the command line without arguments Analyze gt Cursor gt Box starts running directly that is there are no dialog items to be filled in A rect angular cursor from 2x2 to 1024x1024 pixels in size appears in the detector frame area and can be dragged or resized by the mouse or key board arrow keys Several quantities described below related to the currently displayed frame at the cursor position are displayed in real time at the right of the image Pressing ENTER or releasing the left mouse button exits returning you to the menu Pressing ESC or clicking the right mouse button while dragging with the left button pressed toggles between position change mode and size change mode The cen ter of the box remains fixed while the size changes as the mouse is dragged When moving or sizing the box with the arrow keys you can press CTRL along with an arrow key to move in increments ten times larger than for the unmodified arrow key Analyze gt Cursor gt Box can also be used to clear or fill the area inside
404. lowed by SAVE with the XENGEN format option set to convert a frame from Bruker to XENGEN format This option is rarely used When invoked from the menu or run from the command line without arguments File gt Save displays a dialog box where you can view edit the arguments described below Pressing the ENTER key or clicking the OK button starts the operation Pressing ESC or the Cancel button returns you to the menu Upon saving the pro gram displays the message SAVING on the bottom status line Saving should be completed within a few seconds If the output filename starts with the five characters NULL case independent the output is sent to the null han dler and discarded If the output file already exists you are prompted as to whether or not you want to over write the file M86 E01008 GADDS Software Reference Manual File Routines 3 8 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses DT EO EA Output Filename no default Enter filename for output frame the default extension is gfrm unless the old frame naming conventions are being used The output filename is merged with the frame data directory in the Project gt New dialog box If the output filename starts with the five characters NULL case independent the output is sent to the null handler i e is thrown away Note The special NET is no longer
405. lt line gt represents the number of the line starting at 1 in the run list which produced the message You can continue with the scans or quit to re edit the run list and try again The current program configuration is saved in the current default configuration file usually gadds _nc before starting the first scan which makes recovery easier in the event of a power failure etc For single crystal type applications you can use Collect gt Scan gt MultiRun collect multiple scan series which covers a little more than half the entire Ewald sphere This strategy allows you to obtain the full amount of coverage needed to solve the structure regardless of unit cell size or Laue class without any need for preplanning with ASTRO M86 E01008 GADDS Software Reference Manual Collect Routines The default hemisphere runs require about 7 5 hours for full data collection with 10 seconds per frame scan time and comprise 3 runs total ing about 1250 frames They are set up assum ing a sample to detector distance of about 6 cm which provides full coverage out to better than 0 93 A 45 with Mo radiation These default hemisphere runs provides the best redundancy which improves the quality of the data and absorption corrections For high symmetry Laue groups it s possible to collect a full data set in less time typically about 4 hours 750 frames However the default hemisphere runs will prob ably produce a highe
406. lue High Initializes and refines high right background low back ground is fixed at initial value Neither Init Both amp Fixed Initializes and fixes both back grounds Zero amp Fixed Initializes at zero and fixes both backgrounds M86 E01008 GADDS Software Reference Manual Analyze Routines Init Low amp Fixed Initializes at low and fixes both backgrounds Init High amp Fixed Initializes at high and fixes both backgrounds Init Avg amp Fixed Initializes at average of low and high and fixes both back grounds KALPHA2 see Fit Kalpha2 N Check Y to fit Kalpha2 wavelength in pro file fitting routine PHI lt Nn gt eesseeeseees Phi 0 0 PSI lt N gt veeceesceessees Psi 90 0 Enter the sample angles for the arbitrary stress in the stress report UNITS lt S gt Stress units MPa Select MPa Ksi or Psi 1 0 MPa 0 145 Ksi 145 0 Psi M86 E01008 Analyze Routines GADDS Software Reference Manual 7 36 Analyze gt Stress gt View 2D View biaxial stress and original frame images Menu Command Analyze gt Stress gt View 2D Accelerator None User Level 1 SLAM Syntax STRESS VIEW2D 1 DISPLAY lt n gt DATA LINE DELAY lt n gt DIRECTION lt s gt Use this command to display the fitted observed data and or the calculated stress line to the orig inal frame files for quick visual confirmation of correctness Ca
407. ly created frame headers Interrupting with lt Ctrl Break gt will not store the new temperature settings 5 28 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses a RENTE A EET Set Point 22 0 Enter the requested temperature in degrees C RAMP lt n gt Ramp Rate 100 0 Enter requested ramping rate in degrees C per minute HOLD lt n gt Hold Time 0 0 Enter hold time for stabilizing in seconds Whenever this value is non zero the pro gram will pause until the temperature has been held at the requested set point for the required amount of time M86 E01008 GADDS Software Reference Manual Collect Routines NAIT beam teases Wait Y Y to wait for ramping up to requested tem perature setting If the hold time is non zero waiting for ramping up to temperature set point is automatically performed 5 29 Collect gt Goniometer gt Encoders Adjust encoder zero offsets Menu Command Collect gt Goniometer gt Encoders Accelerator none User Level 3 SLAM Syntax GONIOMETER ENCODERS 1 2 3 4 or GONIOMETER ENCODERS 1 2 3 4 5 6 7 8 9 This command allows you to access the Phoe nix AV or GGCS EZ command without leaving GADDS Because this command changes the zero positions of the goniometer angles it is rec ommended that only the person in charge of your system for example
408. m DEFAULT OF CODENS FILE NAME lt default name gt CHOOSE DEFAULT OR INPUT NEW NAME Enter the pathname of the CODENS DAT file Typically this will be on the CD ROM in lt cd rom drive gt CRYSTAL VAX IND CODENS DAT where lt cd rom drive gt represents the drive letter of the CD ROM on your system M86 E01008 Utility Programs GADDS Software Reference Manual 13 5 Merge RAW file range merging utility This utility program combines the specified ranges from up to ten RAW data files into a sin gle range RAW data file Mostly Merge is used to combine the integrated 2T spectra from sev eral area detector frames of differing swing angle into a single continuous range which is more suitable for most DIFFRAC S routines such as phase characterization and identifica tion The user has the option of entering ALL filena mes on the command line or to leave the com mand line blank and have the program prompt the user for all filenames ranges and options The resultant merged raw file is always written in DIFFRAC format however the inputted raw files may be of several and even different file formats e DIFFRAC PLUS raw or sim file format e DIFFRAC AT V2 a k a V3 raw or sim file format e DIFFRAC AT V1 raw or sim file format e PLOTSO file format ASCII Merge checks the file and range header records to ensure the mergibility of the ranges Several checks produce fatal errors e Collected
409. me is 100 000 total counts see the discussion brass above Valid range is 0 1 to 9999 If you supply a filename extension here it is overridden with the extensions _ix _it and __if as appropriate If you leave this item blank or specify a wildcard filename pattern pressing the ENTER key or the left mouse button will dis play a list of the current filenames matching the pattern You can choose one from the displayed list by moving to it with the arrow page keys or mouse and pressing ENTER or the left mouse button You will be returned to the input panel with the selected filename filled in If you leave this item blank it is the same as entering a _ix wild card pattern Both filenames and patterns entered here are merged with the CONFIG URE EDIT frame directory as described above THRESHOLD lt n gt Sigmas Spot Thresh old 8 0 When extracting fiducial spots from the brass plate image the I sigma l i e inten sity divided by its standard deviation of each spot is computed based on counting statistics Spots with an I sigma l less than the value specified here are considered to be background fluctuations and are ignored The default value of 8 should be satisfactory for brass plate images with 80 000 to 6 22 M86 E01008 GADDS Software Reference Manual Process Routines 6 10 Process gt Spatial gt Unwarp Apply spatial correction and write unwarped output frame s Menu Co
410. mega 2 Theta limit 60 00 40 00 6 Negative Omega 2 Theta limit 240 00 40 00 7 Positive Phi limit both O none 0 00 0 00 8 Negative Phi limit both O none 0 00 0 00 9 Positive Chi limit both O none 0 00 0 12 90 12 0 Negative Chi limit both O none 0 00 90 12 0 12 First number is for transmission mounting second is for reflection mounting of 4 circle stage M86 E01008 5 21 Collect Routines GADDS Software Reference Manual Table 5 3 Other Older Goniometers Parameter 1 2 3 4 5 6 7 8 9 0 Input Prompt Positive 2 Theta limit Negative 2 Theta limit Positive Omega limit Negative Omega limit Positive Omega 2 Theta limit Negative Omega 2 Theta limit Positive Phi limit both O none Negative Phi limit both O none Positive Chi limit both O none Negative Chi limit both O none Second numbers are for LT attachment in co axial mode Third for LT in 30 offset mode Defaults 4 Circle 110 00 110 00 58 00 45 00 58 00 55 00 58 00 58 00 0 00 0 00 0 00 40 00 93 00 0 00 90 00 93 00 3 Circle 30 00 85 00 180 00 180 00 60 00 240 00 0 00 0 00 0 00 0 00 M86 E01008 GADDS Software Reference Manual Collect Routines Table 5 4 All Goniometers with X Y Z or Aux axes Parameter XMAX lt n gt XMIN lt n gt YMAX lt n gt YMIN lt n gt ZMAX lt n gt ZMIN lt n gt AMAX lt n gt AMIN lt n gt DMA
411. mega axis is driven to within 3 of the home position and a 6 degree search for the home mark is initiated Phi and chi axes have a home mark every degree During the drive the following message dis plays DRIVING PRESS ANY KEY TO STOP You can halt the drive by pressing a keyboard key for example ENTER or the space bar Pressing ESC or clicking Cancel in the input dia log returns you to the menu without performing the homing operation On completion of homing the program updates the current goniometer angles displayed in the goniometer status area at the lower right of the screen A CAUTION Aborting homing in the middle of a drive may result in loss of the current angle position Should you abort homing you MUST update the current angle and re home the axis M86 E01008 GADDS Software Reference Manual Collect Routines 5 25 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA EE EE EE Axis Number 1 This is the number of the axis to be homed either 1 for 2 theta theta1 2 for omega theta2 3 for phi 4 for chi axis 5 for X 6 for Y 7 for Z 8 for zoom 9 for delta detector distance P2 aei Velocity 250 Velocity to drive during home search in steps degree Range 1 to 1024 On D8 sys tems this parameter is ignored 5 26 Collect gt Goniometer gt Park XYZ Park large XYZ stage OM 0 X far right Z b
412. ments i s5i ee Pela Baieanace ee Sega ott al waulid e N lao AE vale 6 33 6 17 Process gt Calibrate Calibrate detector distance angle and center using a known Standard synde mane gesting at EA ald EEE ann ed eae anda ER ne lcelele Bes Gow eee a4 6 34 EIT ArQUMOeNTS wee eh neti deemed petewe baa eda ye yaad oh nbt a 6 35 7 Analyze Routines iiceiatanwcs seit cee atiineeewdeee Raw eee caw 7 1 7 1 Analyze gt Cursors gt Box Display statistics of pixels in rectangular region 7 1 7 2 Analyze gt Cursors gt Circle Display position and size of circular cursor 7 5 7 3 Analyze gt Cursors gt Pixel e Show pixel positions and values in displayed frame 7 9 7 4 Analyze gt Cursors gt Vector e Measure distances on displayed frame 7 12 7 5 Analyze gt Cursors gt Conic Display constant two theta conic lines 7 15 7 6 Analyze gt Cursors gt Rbox Display statistics of pixels in rotated rectangular region 7 17 7 7 Analyze gt Graph gt File Plot points from ASCII disk file 0 0000 e eae 7 20 TTACAIQUMEIMNS gt 2 8 04s eee a Od tie E eee ee ee eg i E Pa oh E 7 20 7 8 Analyze gt Graph gt Vector Plot profile along vector in displayed frame 7 22 28 1 AQUMOMS etae eek cee ela Peewee tee A wb bade bos Gea AM patna dee oe 7 23 7 9 Analyze gt Graph gt Rocking Plot rocking curve profile through frames
413. mes sages May overflow queue PortlOAddress 340 hex Port IO Address of SAXAD Inter face Card MaxFrameSize 1024 Valid values are 512 or 1024 Orientation 0 Defines the mounting orientation of the HISTAR detector 0 x y The default 1 x y Useless 2 X Y Useless 3 X y Rotated 180 CW 4 y x Useless 5 y X Rotated 270 CW 6 y X Rotated 90 CW 7 Y X Useless 13 22 M86 E01008 GADDS Software Reference Manual Utility Programs 13 13 SaxHelp Bruker help topic display utility NOTE This program is now obsolete Bruker now supplies help files in either Windows help file format or Acrobat PDF file format SaxHelp is used to display the Bruker help topic files _ tp 13 14 ToSAXIl e Convert PCS XENGEN format frames to new SAXII format The new SAXII format for data frames addresses the issues of data portability speed of image I O and display and storage of all the data acquisition conditions required to reduce the data Header and overflow information are stored in portable ASCII rather than binary critical data such as setting angles can thus be stored portably as floating point values The pixel values themselves are necessarily binary but are assured to start on a 512 byte boundary and are stored a a byte stream without delimit ers of any kind This format is completely trans portable between a VAX and X 1000 frame buffer over the networ
414. meter stages e Watlow temperature controller e Sealed tube or rotating anode generators e SMART rotary shutter e Optical microscope or CCD video camera with zoom control and laser alignment The online version of GADDS is a powerful and flexible instrument control sample analysis data collection package The program couples the precise control of the goniometer angles and X ray shutters through the GGCS controller with the operation of two dimensional multi wire X ray detectors to yield highly accurate and repro ducible two dimensional images frames of X ray diffraction patterns GADDS includes a wide range of instrument functions e g open close shutter drive angles etc calibration routines sample screening options e g add rotation etc automatic routines e g scripts and auto mated frame data collection Frame data may be collected in a variety of modes optimized for individual instrument configurations or sample properties Examples of typical applications of the GADDS system are e Routine data collection on transmission of reflection samples e Phase ID problems e Micro diffraction problems e Texture analysis e Stress analysis e Crystallite size e Percent crystallinity e SAXS M86 E01008 General Information GADDS Software Reference Manual 1 1 1 Basic GADDS Operation 1 Click on the GADDS icon to execute the online version of GADDS Verify that the correct project hav
415. meters you want to find matching entries for Normally they will be those for the mounted crystal but you may enter parameters for any unit cell The values in the input panel are auto matically updated with the results of the REFL BRAVAIS or REFL LEASTSQ when ever these commands are run TENET Decimal Fraction Devia tion 0 01 The program searches for any unit cell with axis lengths in the range of 1 d input axis length to 1 d input axis length The variable d is the DECIMAL FRACTION DEVIATION A value of 0 01 is a good value for the first search M86 E01008 GADDS Software Reference Manual Peaks Routines 8 rainira Lattice Centering Type Enter the lattice type P A B C I F or R where P Primitive A B or C Edge cen tered Body centered F Face centered or R Rhombohedral The input panel value is automatically updated with the results of the REFL BRAVAIS or REFL LEASTSQ whenever these commands are run FORMULA lt s gt Chemical Formula This item is currently unused in a later ver sion the program may allow selection by chemical formula ITYPE lt S gt o Search Type BOTH The NIST Crystal Data File is divided into Organic and Inorganic structures Choose Organic Inorganic or Both FILE lt S gt oo Output File Name hits out The information from the NIST Crystal Data File for each match that is found is written to an output file in addition to bein
416. mmand Process gt Spatial gt Unwarp Accelerator Ctrl U User Level 1 SLAM Syntax SPATIAL UNWARP 1 2 3 DISPLAY lt n gt NOBEAMCENTER SPATIAL UWWARP writes an output data frame generated by spatially remapping the specified input frame to correct the inherent geometrical pincushion distortion based on the currently active spatial correction Unwarping is important for frames which are to be processed by GADDS or other programs which need spa tially corrected input The data reduction pro grams for crystallographic data perform the spatial correction internally and do not require unwarped frames Users of FRAMBO and SADIE would use SPATIAL UNWARP only in special cases Each pixel of the corrected output frame is gen erated by splitting the counts of each raw pixel into its corresponding unwarped pixel bins First the exact unwarped pixel location real value is computed from the raw pixel location integer value Next the weighting fractions real values are computed for the four surrounding unwarped pixel locations integer values Using these weighting fractions the raw pixel s counts are divided into the four surrounding unwarped pixel bins so the sum of bins equals the original raw pixel counts Therefore each count is preserved during the unwarping process although some counts are spatially corrected off the frame image dimensions so the total counts in the frame will decrease slightly An unwarped
417. mmon script directory see GADDS SCRIPT Follow the filename with the optional replaceable parameters Replaceable parameters are space deliminated Any replace able parameter with embedded spaces must be enclosed within double quotes A script file is simply an ASCII file containing a list of SLAM commands in which each line is an individual SLAM command that is executed in sequential order It is very powerful and pro vides a convenient means for automating the more mundane sequence of commands from within the GADDS environment For more infor mation on script files creating editing nesting replaceable parameters and running scripts see the GADDS User s Manual Scripts section When the script is invoked each of the lines executes in sequence as if it had been typed at the command line using the parameters and arguments included within the script That is GADDS simply starts at the beginning of the script file and proceeds one line at a time until it reaches the end at which point it stops To interrupt a script while in use press CTRL BREAK This will stop the script execu tion and exit from the script returning the user to the program s command line prompt To return to menus enter menu mode Several example scripts are provided in your system The scripts are stored in the GADDSS TEST directory and are used as part of the demo loop To execute this demo on the frame buffer enter GADDS gt GADDS TEST g
418. mon convention used in FRAMBO P3 XSCANS ASTRO GADDS etc A sel eae candice Matrix 1 1 1 0 Value for row 1 column 1 of orientation matrix M86 E01008 GADDS Software Reference Manual Peaks Routines VARIE TE Matrix 1 2 0 0 Value for row 1 column 2 of orientation matrix E Matrix 1 3 0 0 Value for row 1 column 3 of orientation matrix EE EEEE Matrix 2 1 0 0 Value for row 2 column 1 of orientation matrix PENTE E EEE Matrix 2 2 1 0 Value for row 2 column 2 of orientation matrix PETE AOTEA Matrix 2 3 0 0 Value for row 2 column 3 of orientation matrix A EEE Matrix 3 1 0 0 Value for row 3 column 1 of orientation matrix EEE RENE Matrix 3 2 0 0 Value for row 3 column 2 of orientation matrix AAEE EE Matrix 3 3 1 0 Value for row 3 column 3 of orientation matrix M86 E01008 Peaks Routines GADDS Software Reference Manual 8 24 Peaks gt Refl Array gt Hcalc Compute X Y and scan angle for specified HKL Menu Command Peaks gt Refl Array gt Hcalc Accelerator None User Level 1 SLAM Syntax REFL_ARRAY HCALC 1 2 3 4 5 6 7 8 9 Given an orientation matrix specified HKL indi ces ascan axis and setting angles for the other axes REFL_ARRAY HCALC computes the detector X and Y in pixels and the scan angle at which the reflection will be observed You must already have computed a valid orientation matrix
419. mplicated One needs the crystal lattice and at least three poles such as 110 210 and 001 By applying equation 3 one can derive the Herman s indices For more details and for other non orthogonal crystal systems the reader is referred to Wilchinsky Z W Recent Developments in the Measurement of Orientation in Polymers by X ray Diffraction Advances in X ray Analysis 6 231 241 1962 Alexander L E X ray Diffraction Methods in Polymer Science Wiley Interscience 1969 sec tion 4 4 M86 E01008 GADDS Software Reference Manual Analyze Routines 7 28 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses OF Xe setter a dete F a z 0 0 Enter fa z typically F MD h00 from ORIENTATE command GD Pei a ak F c z 0 0 Enter fc z typically F MD OOl from ORIENTATE command APPEND 0 Append Y N No Enter Y to append results to previous trian gle plot M86 E01008 Analyze Routines GADDS Software Reference Manual 7 29 Analyze gt Pole Figure gt E S APE Output File null Normalize Normalize pole image so Output filename to store interpolated pole random 100 counts figure image or null Menu Command Analyze gt Pole Figure gt Normalize Accelerator None User Level 1 SLAM Syntax POLE_FIG NORMALIZE 1 DISPLAY lt n gt NVAL lt n gt 2 Normalize the pole
420. n be used in movie or single frame mode 7 36 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses DA ised ae coed 2 tata First frame stress 000 Enter first frame of series to display DISPLAY lt n gt Display limit 1 Enter 0 for no display otherwise this item specifies the number of counts mapped into the maximum display memory value for example corresponding to white on the dis play The special value 1 directs the pro gram to pick a reasonable value by scanning through the pixels in the frame prior to display the special value 2 directs the program to use whatever setting is cur rently in effect The default value is 1 the allowed range is from 2 to 10 counts Smaller values make the displayed image look brighter larger values make look darker IDATA Tectia Overlay data points Yes Check Y to display the 2T CH data points as X JEINE iiien Overlay stress line Yes Check Y to display the calculated stress as a line DELAY lt n gt Movie delay time 1 0 Enter time in seconds between frames or 1 0 for no movie DIRECTION lt s gt Movie direction CIRE co Enter either or through frames for the direction M86 E01008 GADDS Software Reference Manual Analyze Routines 7 37 Analyze gt Mapping Menu Command Analyze gt Mapping Accel
421. n be used to build script files automatically To do so toggle the script feature on and operate the system using the exact sequence of commands that you want to appear in the script To end the script toggle the scripting feature off To execute a script file issue the command lt filename gt from the GADDS command line where lt file name gt represents the name you gave the script file If you attempt to play back a script just recorded before exiting and restarting GADDS you must invoke File gt ScriptFile with another filename to close the script file before starting playback File gt ScriptFile gt Enabled does not close the script file It only disables recording For the same reason in order to access a script file from another process you should close the script file 3 10 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses DA EE NET Script Filename script slm Filename of the script file to which output is directed By convention script files have the extension slm If you don t supply a file name extension the program will add the sim extension If you leave this item blank or specify a wildcard filename pattern M86 E01008 File Routines GADDS Software Reference Manual pressing ENTER or clicking the OK button will display a list of the current filenames matching the pattern You can choose one from the dis
422. n free format The items are NAME The data set name usually the base name of the frames processed in the last REFL_ARRAY THRESHOLD command WAVE X ray wavelength in Angstroms ORT1 2 3 Rows of the orientation matrix The storage convention is that as written here you could use the matrix to pre multi ply a column HKL vector in the standard mathematical notation to give a column reciprocal lattice vector DIST Nominal detector distance CM DETP The six positional corrections In order they are Detector X positional correction pixels Detector Y positional correction pixels Detector distance correction CM Detector pitch deg Detector roll deg Detector yaw deg XCYC Raw X Y pixel coordinates of the direct beam at swing angle of zero The matrix determined by FRAMBO is a true orientation matrix that is it is indepen dent of the starting goniometer angles of the scan series used to determine it While it cannot be used directly by XENGEN in many cases it is possible to use the Eulerian M86 E01008 GADDS Software Reference Manual Peaks Routines angles output by FRAMBO s least squares to derive initial pseudo goniostat angles for the XENGEN REFINE program The follow ing relationships apply ONLY IN THE CASE WHERE THE STARTING GONIOMETER OMEGA PHI AND CHI FOR THE FRAME SERIES INPUT TO THE SPOTS PRO GRAM ARE ALL ZERO Note that a 3 circle goniometer is always at chi 45 degrees Belo
423. n matrix in the same convention as described above for the _pr file and the refined unit cell parameters The unit cell parameters are listed horizontally in the order A B C ALPHA BETA GAMMA VOLUME with lengths in Angstroms angles in degrees and the vol ume in cubic Angstroms Below each cell parameter is its estimated standard deviation Next are several tabular histograms showing the distribution of the unsigned differences between observed and calculated values of H K L scan angle always labeled OMEGA M86 E01008 Peaks Routines GADDS Software Reference Manual even if the scan angle was actually PHI and detector X Y position In all cases the more closely bunched toward the left side of the histo gram the differences are the better the refine ment Scan angle differences are in degrees and X Y differences are in pixels Following the histograms are the overall average and rms dif ferences for these same quantities H K L scan angle X and Y The myoglobin example shown below is a very good one Often the numbers are two or three times higher The AVG values indicate any systematic bias in the results if these values are a substantial fraction of the corresponding RMS values you might suspect mis indexing or mis alignment of the system In such a case make sure you have a good spatial correction and correct estimates for the detector distance and beam center entered in the CON FIGURE EDIT panel
424. n negative 2T space the 1D spec trum is stored as positive 2T space The omega axis is always driven at half the rate of the 2 theta axis When invoked from the command line SCAN COUPLED can take the following arguments where lt n gt represents a numeric value and amp indicates continuation on the next line 5 37 1 Arguments Each argument is listed below by its command line name followed by its input panel prompt in parentheses Sle ea cee ox 2 Theta start 5 0 Enter the starting 2 Theta in degrees current setting G2 treatin sted Soe 2 Theta end 90 0 Enter the ending 2 Theta in degrees current setting GS AAN Omega start 2 5 Enter the starting omega in degrees current setting WIDTH lt n gt Step width 0 1 Enter degrees per step as a positive num ber M86 E01008 Collect Routines GADDS Software Reference Manual SCANTIME lt n gt Step time 10 0 Enter counting time in seconds for this frame TITLE lt S gt 00 Title Coupled scan Enter title for output frames 80 characters max SAMPLE lt s gt Sample name Corundum n y i Enter sample name to be stored in frame header NUMSAMPLE lt s gt Sample number 0 n y i Enter sample number to be stored in frame header NAME lt s gt Job name CORUND Enter base name for frames IRUN lt S gt eee Run 0 Ente
425. n of Bresenham s algorithm see Figure 8 2 used by Bruker improves inte gration through summing the individual intensity values multiplied by a weighting factor x1 x2 either arc length or solid angle While solid angle is technically more correct in practice this weighting scheme gives nearly identical results as arc length but is slower This modified inte gration method must consider the previously chosen pixel and so four cases arise for each slope region The weighting given to each inten sity value varies by as much as forty percent which improves the relative integrated intensi ties between vertical or horizontal regions and moderately sloped regions along a Debye ring With highly textured samples the resultant 20 profiles exhibit true relative intensities between peaks of varying x positions y t true conic line true conic line Ne dy i O O dx x X2 X2 region 2 O i O O O x1 lt discrete A 2 conic O region 1 line discrete conic line last x true conic line Figure 8 2 Modified version of Bresenham s algorithm true conic line O discrete conic line M86 E01008 Peaks Routines GADDS Software Reference Manual When executed interactively the INTEGRATE WRITE is executed upon successful termina tion For more information see the description of the INTEGRATE WRITE sub command 8 7 1 Arguments Each argument is listed below by its SLAM com mand line name
426. n of interest in pixels The range is from 0 to framesize 1 default value is 256 G2 Boos trees ue bieene Y Origin 256 The Y coordinate of the lower left of the box defining the region of interest in pixels The range is from 0 to framesize 1 default value is 256 S hindi Width 16 The width of the box defining the region of interest in pixels The range is from 0 to 128 default value is 16 ye eae Height 16 The height of the box defining the region of interest in pixels The range is from 0 to 128 default value is 16 START lt n gt Reflection 0 This specifies the position in the Reflection Array into which the new reflection is to be stored The first line in the Reflection Array is numbered 1 If you specify a value of zero here the default the new reflection will be placed in the first available empty line of the array QUADRANT lt n gt Quadrant 0 This parameter specifies whether you want the graph to appear covering the entire data frame enter O or just one of the four quadrants enter 1 through 4 as appropri ate The default value is O full frame win dow Quadrants are 0 full window 1 lower left 2 lower right 3 upper left and 4 upper right FRAME_HALFWIDTH lt n gt Frame Halfwidth 5 Enter the number of frames ON EACH SIDE of the currently displayed frame to be included in the rocking curve Make sure that you don t exceed th
427. na tented 8 84 8 28 1 Arguments ciau e ebsites cea eae eee tie deme areata NAE fue ya i 8 84 8 28 2 CDF Search Algorithm 0 0 00 ccc eee ee 8 85 8 29 Peaks gt Refl Array gt Save Save the reflection array ina p4p file 8 86 8 29 1 Arguments mira evn e eaten ena mtg eth Mh Meio ene ya ae od 8 86 9 Sp cial Routines icis crcoci t siryen nspa toa rete heehee ws dae aes 9 1 9 1 Special gt PDF2 gt View View PDF2 card on screen 0 cee ee 9 1 OS A AIQUMONTS 24 A5ei nds A oor OENE ae nak T OS vole he edie ede dedi a ated dee 9 1 9 2 Special gt PDF2 gt Print Print PDF2 card to printer or file 00000 e eee eee 9 2 O 2 TAGUNE teers Akaan Gites grein A TE AEE hea Pe melas tas bute BRT 9 2 xii M86 E01008 4 04 GADDS Software Reference Manual Table of Contents 9 3 Special gt PDF2 gt Display Graph PDF2 card above frame image as Debye Scherrer rings 9 4 OSA AIQUMEMS went etiwanda EEPE AA EA und aed em halena Pah ew eee ae 9 4 9 4 Special gt PDF2 gt Search Search PDF2 by mineral inorganic or organic name 9 5 SAT Arguments a wacecud Maen eal Sathana tale as Ad tanta ie ae EE a beeen 9 5 9 5 Special gt PDF2 gt Clear Clear PDF2 overlay graph 0 00 0c eee eee 9 6 IG AIQUMENISS ico 4 ake ta wea tale Pee ade ce wee Gate Aw Lana lt ante E Be 9 6 9 6 Special gt Commandmode Switch between command line and menu mode 9 7 9
428. nce OMEGA lt n gt THETA2 lt n gt PHI lt n gt CHI lt n gt AXIS lt n gt WIDTH lt n gt CLEAR STRESS BIAXIAL2D 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt NUMBER lt n gt 2THETA lt n gt 5 FILENAME lt s gt HKL lt s gt YOUNG lt n gt POISSON lt n gt ARX lt n gt LINESHAPE lt n gt CUTOFF lt n gt BKGFIT lt s gt KALPHA2 PHI lt n gt PSI lt n gt REPROCESS STRESS SHEAR2D same as biaxial2d STRESS TRIAXIAL same as biaxial2d STRESS VIEW2D 1 DISPLAY lt n gt DATA LINE DELAY lt n gt DIRECTION lt s gt SYSTEM 1 VIDEO LIVE VIDEO FREEZE WAIT 1 ZOOM 1 2 3 M86 E01008 G 7 SLAM Command Reference GADDS Software Reference Manual G 8 M86 E01008 H Remote Operations SMARTservice Online GADDS now supports remote operation from another program when GADDS is in com mand mode and another package called SMARTservice is loaded and started SMART service operates as an NT Service which is always running as part of the operating system From any networked computer you can connect to SMARTservice using winsockets You can either use TELNET or write your own winsocket program to communicate with SMARTservice Remotely you can send to GADDS e Any SLAM command e Hard abort CTRL C or CTRL BREAk e Soft abort ESC e Pause CTRL S e Resume CTRL Q Remotely you can receive from GADDS e Log file as it s generated e Informational messages
429. nce Manual Peaks Routines index used to compute test solutions These val ues are computed from the input AAX BAX CAX and FCELL Next is a list of the trial axis vector solutions Each record consists of two or more lines The first line contains the solution number the axis length in angstroms a figure of merit actually a residual lower values are better indicating the rms deviation from integer HKL indices calcu lated from the solution combined with a mea sure of the vector length three integers which define the direction of the axis this is the integer triple described by Sparks in Computational Crystallography D Sayre ed Oxford 1982 pp 1 18 and a bit mask containing a 1 for each difference vector group which is fit by the solu tion and a 0 for each group that is not fit The first line holds mask elements for up to 50 groups if the number of groups is larger the mask is continued on the second line immedi ately below the first 50 elements Starting at the second line of each record the third if the bit mask requires a second line is a list of angles between the solutions The num bers are in degrees with the first number in the list representing the angle from the current solu tion to solution 1 the second to solution 2 and so on Angles near 90 degrees are high lighted with a trailing angles near 60 or 120 degrees with a Following the list of axis vectors is the chosen
430. nce Manual Table of Contents TAPO 3 inte tee ee Be eee ee eg anaes eta dled eel tas Suen aged erat Bie ees 13 11 13 8 Prbatch Profile fitting in batch mode utility 0 0 ee eee 13 15 13 9 PVWave Precision Visual s Wave procedures 000 c eee eee ees 13 15 13 9 1 SAXII_READ_D5000 VAX only 0000 c eee tee 13 15 13 9 2 SAXIIL READ FRAME 63 sek anaa eh Pare a e garb a betes 13 16 13 9 3 SAXII READ PEOTSO oe esama hard Gas Hee Peete bine be nel ae She bean 13 16 13 9 4 SAXII_SAVE_D5000 VAX only anaana eee 13 17 13 9 5 SAXII SAVE FRAME syd prett eaa martha Yee eet eee eda ee ae ed Hecate hat 13 17 13 9 6 SAXII SAVEPLOTSO waa mi eala ile tiptoe ohana Baie den eet aero ele ed 13 17 13 10 Raw12Fix Fixes file headers of DIFFRAC 5000 files ported from PC to VAX 13 18 13 11 Raw2Raw e RAW to RAW file format conversion utility 0 00 0a 13 18 13 12 SAXAD SYS Bruker HISTAR NT Driver 0000 0c cece eee 13 21 13 12 1 Registry Keys Optional 2 00 00 cect 13 22 13 13 SaxHelp Bruker help topic display utility 00 0000 c eee eee 13 23 13 14 ToSAXII e Convert PCS XENGEN format frames to new SAXII format 13 23 Appendix A Area Detector Frame Format 000e eee eee eeeeee A 1 AN Had ef oaair ea Gini Gadi E ee ee Pt aie eae eg ies Gea a od A 2 A 2 IMage Data resore doarn ok AN etree Big betise IMA E eee a ae ey at A 10 A S
431. nd The goniometer is said to be in manual mode when in this state During manual mode the fol lowing message appears on the bottom status line MANUAL MODE ESC EXIT S SHUTTER T ATTENUATOR A ADD C COUNT L LASER Pressing ESC or CTRL G exits manual mode closing the shutter if open and returns you to the main menu Pressing the S key toggles the state of the X ray shutter open closed Its status is updated in the goniometer status area at the lower right of the screen Pressing the T key per forms the same function for the incident beam attenuator on systems equipped with an attenu ator Similarly pressing the L key will toggle the state of the laser on systems equipped with a laser Pressing the A key displays the Collect gt Add input dialog After you edit the items in this dia log pressing ENTER or clicking the OK button begins a Collect gt Add operation during which the goniometer remains under control of the manual box This feature is most useful in con junction with Collect gt Add s REALTIME real time display option with or without the RESET periodic redisplay option to observe changes in the X ray pattern as the goniometer angles are changed If you want to terminate the acquisition early use CTRL BREAK which returns you to manual mode as will the ESC key or Cancel button pressed while in the ADD input panel See Collect gt Add Section 5 47 Pressing the C key displays the RATEMETE
432. nd intensity as well as the back grounds GADDS then reiterates identifying and removing the largest peak from the remaining data until either 15 peaks are found or the larg est residual intensity is below PEAKSIG times standard deviation The standard deviations generated by AUTO are measures of the precision of the refined param eters Systematic errors such as 26 zero error sample positional error and absorption must be taken into account During the least squares the refined parameters are background peak 20 peak intensities and the FWHM The FWHM are grouped variable but all peaks within a region possess the same FWHM however dur ing the final refinement the FWHM are set to variable If the least squares fails to converge the FWHM are fixed and a final refinement is performed PEAKS MANUAL is used to interactively choose peaks and their parameters The most frequent use of PEAKS MANUAL is to correct any short comings of PEAKS AUTO which is known to have difficulties whenever the scan range begins or ends within a peak and with extremely complicated patterns with more than 15 overlap ping peaks PEAKS MANUAL lets you enter all peak and background data as well as variables which you wish to refine See Applied Crystal lography by J Taupin 1973 volume 6 page 266 M86 E01008 SLAM Routines GADDS Software Reference Manual When started from the command line PEAKS AUTO takes the following arguments
433. ne 1 DIFFRAC AT V1 of data points 2 DIFFRAC AT V2 V3 3 DIFFRAC PLUS M86 E01008 13 19 Utility Programs GADDS Software Reference Manual NOTE are not typed They are used to bracket optional or defaulted values NOTE All command line switches may be abbreviated and the separator character may be EA a or Mote i e IF 21 F 1 FORMAT 1 are equivalent NOTE The command line arguments may be in any order Current limitations ignored fields in file for mats e RAW PLUS supplemental range header records osc psd com e RAW PLUS reading RAW1 00 measuring electronics may be incorrect e RAW V2 diffractometer configuration word e RAW V2 oscillating drive amplitude speed e RAW V2 supplemental range header record for comment 4 e DIFFRAC 5000 V2 scintillation detector parameters conversions of slit settings mm to degrees temperature parameters other angle settings chi phi x y DIFFRAC 5000 V1 many fields are not con verted NACS VMS temperature hold time NACS TSX RT 11 not yet implemented DIFFRAC 11 variable slit settings fixed theta angle delay time DIFFRAC 5 totally untested UXD Only minimal information is in header 13 20 M86 E01008 GADDS Software Reference Manual Utility Programs 13 12 SAXAD SYS Bruker HISTAR NT Driver SAXAD SYS is the NT Driver to support and access the Bruker s Area Detector Fast Int
434. ng project Menu Command Project gt Switch Accelerator None User Level 1 SLAM Syntax PROJECT SWITCH 1 Use this command to switch to an existing project A scrollable alphabetized list of all known projects will appear Highlight the project of interest and click OK Before the program switches to the requested project the message appears Save the current configuration before changing projects Typically you click Yes as this is the safest option The program will switch to the requested project by loading that project s settings clearing the frame buffer clearing the displayed frame and displaying the current project settings However if the requested project is no longer valid the program will display a message restore the original project settings and remove the cor rupted project from the project database 2 1 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses BA EO AT Select Project first in list Enter the existing project name In menu mode a scrollable alphabetized list of all valid projects appears and you may simply click the requested project The default is the first project in the list M86 E01008 Project Management Routines GADDS Software Reference Manual 2 2 Project gt Load Load a configu ration file and create a new project Menu Command Project gt Load Accelerator None
435. ng prompt is displayed RE INDEX REFLECTION ARRAY ARE YOU SURE Y OR ENTER YES N OR ESC NO Press the Y key the ENTER key or the left mouse button to write HKL indices into the reflections in the array and set the H flag of each reflection otherwise press the N key ESC key or right mouse button to quit autoindexing and return to the REFL_ARRAY submenu without changing the Reflection Array If you ve chosen to continue the program updates the Reflection Array HKL indices and flags then displays a second scrolling output window containing least squares statistics related to the differences between observed and calculated HKL indices and scan angle includ ing histograms of the distributions of these dif ferences This is very similar to the output from REFL_ARRAY LEASTSQ but is derived from a relatively crude linear least squares and will show substantially larger deviations It is described in more detail below When you exit this second output window with the ESC key or right mouse button the program returns to the REFL_ARRAY submenu to the BRAVAIS sub command since it s usually invoked next If REFL INDEX was invoked from the command line each output window is displayed subject to a 10 s timeout to allow command scripts to run without intervention If you do not press a key or mouse button within 10 s after the output win dow is displayed the program will continue as if M86 E01008 GADDS Software Referen
436. nged from its standard value of If it has substitute the appropriate switch character e g AXES Starts GADDS with support for specified axes By default GADDS is started with support for 2theta omega phi and chi of which chi may be fixed at 54 74 degrees Axes are specified by using an eight bit bit mask with each bit representing the pres ence ON or absence OFF of each axis Bit Value Axis Bit Value Axis 0 1 2Theta 4 16 x 1 2 Omega 5 32 Y 2 4 Phi 6 64 Z 3 8 Chi 7 128 Zoom COMMAND Starts GADDS in command line mode instead of menu mode COMMAND lt filename gt lt parm1 gt lt parm2 gt Starts GADDS and automatically invokes SLAM script file with optional parameters of parm1 parm2 etc CONFIGURATION lt filename gt Causes GADDS to read the initial configura tion from lt filename gt rather than from GADDS _GC DEFAULT lt filename gt Causes GADDS to read the initial configura tion from lt filename gt if the configuration file is either not found or creates a read error or the NORELOAD switch is used DEFAULT lt filename gt Causes GADDS to read the initial configura tion from lt filename gt if the configuration file is either not found or creates a read error or the NORELOAD switch is used DUAL Allow dual detector operations LEVEL1 LEVEL2 LEVEL3 Starts GADDS in requested menu level Default is 1 LOCK Disables the menu level commands
437. nic region in degrees Valid range is 180 to 360 M86 E01008 13 Peaks Routines GADDS Software Reference Manual 8 10 Peaks gt Integrate gt Slice Perform chi integration in rectangular region gt F 2t Menu Command Peaks gt Integrate gt Slice Accelerator None User Level 1 SLAM Syntax INTEGRATE SLICE 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt INTEGRATE SLICE will integrate a rectangular region along the chi direction and plot the results as intensity versus 2 theta The resulting trace may be written to a file using INTEGRATE WRITE command or inputted into the PEAKS LOAD command The area to integrate is defined by specifying the 2 theta range chi and height of rectangular box Chi zero is defined at 6 o clock and goes CCW Interactively the user may redefine any of the integration region s limits by selecting the limit s line number 1 to 4 and then using the cursor keys The current integration region limits are continuously updated and displayed on the screen While interactively modifying an integra tion limit the lt ESC gt key or right button will restore the limit to its original value while the lt ENTER gt or left button will accepts the new value for this limit Once the integration window is defined press ing lt ENTER gt will start the integration calcula tions and display the message Wait Integrate ESC Other buttons Quit Normally one waits for the calc
438. ning you to the REFL_ARRAY submenu The output is described in more detail below If REFL LEASTSQ was invoked from the com mand line the output window is displayed sub ject to a 10 s timeout to allow command scripts to run without intervention If you do not press a key or mouse button within 10 s after the output window is displayed the program will continue as if the ESC key had been pressed Upon completion the program updates the val ues in the input panel to their refined values which you ll see if you re run REFL LEASTSQ for example to apply a different set of con straints 8 18 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses ERTE ieee LSQRS Constraint Type 0 9 1 Specifies the type of crystal system con straints to be applied Types are 0 Perform only the linear least squares don t proceed with non linear refinement M86 E01008 Peaks Routines GADDS Software Reference Manual 1 Linear least squares followed by uncon strained non linear refinement 2 Linear least squares followed by non lin ear refinement with monoclinic C con straints alpha beta 90 3 Linear least squares followed by non lin ear refinement with monoclinic B con straints alpha gamma 90 4 Linear least squares followed by non lin ear refinement with monoclinic A con straints beta gamma 90 5 Linear least squares foll
439. nly FRM2FRM B Z FORMAT filename tif OUT filename out PIXPERCM CMTOGRID filename ext1 Required The name of the frame image file The input file format is automatically deter mined filename ext2 Optional Defaults to lt filename gt out Optional Defaults to Bruker Possible values are 1 Bruker frame file 2 small Bruker frame file half size that is 1K gt 512 3 Bruker ASCII file 4 TIFF file 5 JPEG courtesy of Larry Finger 6 imageNCIF n y i M86 E01008 Utility Programs GADDS Software Reference Manual B Batch mode suppresses final Hit lt Return gt to continue message z Allow frame dimensions in multiples of 512 instead of 512 2 512 1024 2048 4096 SAINT currently does NOT support these odd frame dimensions of 1536 3072 and 6144 Force output frame file to be 1 2 or 4 bytes per pixel file is saved without an overflow table P PIXPERCM for imported frames Default is 0 0 ignore C CMTOGRID for imported frames Default is 0 0 ignore NOTE Brackets are not type They are used to bracket optional or defaulted values NOTE All command line switches may be abbreviated and the separator character may be P or that is F 1 F 1 and FOR MAT 1 are equivalent NOTE The command line arguments may be in any
440. nother device STATUS_DEVICE_ CONFIGURATION_ERROR if IO port is already in use Change IO port address on FAD interface card and in registry Unable to detect Bruker s FAD interface board STATUS_NO_SUCH_DEVICE if Bruker FAD interface fails to respond Possibly bad board or jumper settings Or PDC was off when computer was booted Unable to create the symbolic link for saxad0 STATUS _NO_SYMBOLICLINK_ CRE ATED NT cannot create a link to driver Hopefully this error never occurs M86 E01008 13 21 Utility Programs GADDS Software Reference Manual Unable to create the device map entry for saxad0 STATUS_NO_DEVICEMAP_CREATED Driver could not update registry Hopefully this error never occurs Possible error messages during execution of driver Application program passed a buffer too small to device saxad0 STATUS_BUFFER_TOO_SMALL Bug in GADDS EXE report it Application program passed an invalid parame ter to device saxad0 STATUS_INVALID_PARAMETER Bug in GADDS EXE report it 13 12 1 Registry Keys Optional DebugLevel 0 Determines which additional debug mes sages are sent to the Event Log Range is 0 to 5 0 Normal warning and error messages only 1 Above plus driver load and unload mes sages 2 Above plus device I O messages 3 Above plus data collection messages 4 Above plus dispatch control messages 5 Above plus data collection polling
441. nown C centered lattice but specify a P primitive input lattice in the BRAVAIS panel the Bravais lattice output will probably not be what you intended This NOREDUCE indexing method should be used ONLY when you re sure you already know the M86 E01008 Peaks Routines GADDS Software Reference Manual correct unit cell since it bypasses a very impor tant step in the unit cell determination Remem ber that errors in an initial determination of unit cell from a few precession pictures are fairly common the normal indexing method followed by the Bravais lattice determination should always be used in early stages of a problem to check the initial choice of unit cell The Reflection Array can hold a maximum of 512 reflections however autoindexing and determination of orientation requires only a small fraction of this number Usually 25 reflec tions is the bare minimum you ll need with 50 100 reflections about optimal While determina tion of orientation from just a few contiguous frames is possible for example the FRAMBO and SADIE verification tests determine the ori entation of a myoglobin crystal from eight con tiguous frames you ll get much more precise cell parameters if you threshold a few frames taken 90 degrees or so in scan angle from the first set adding them to the Reflection Array prior to indexing If you can t obtain enough reflections with the C flag set you can set this flag with the MODIFY
442. ns use the clipboard so you can also use these keys to transfer text informa tion among different dialogs or between pro grams Output Dialog Boxes These display a scrolling multi line text con trol a scroll bar and OK Write and Print buttons The arrow and page keys allow you to scroll the output text as does the scroll bar ENTER is equivalent to click ing the highlighted button initially OK You can highlight text in the text control with the mouse or shifted arrow keys and copy it to the clipboard with CTRL C However you cannot alter the text in this type of dialog The Write and Print buttons allow you to send selected text or all the text if no selection was made to a disk file or a printer respectively Edit Dialog Boxes These display a scrolling multi line edit con trol a scroll bar and OK Cancel Write Print and Read buttons The text in the edit control can be edited according to the normal system conventions The arrow and page keys allow you to scroll the text as M86 E01008 General Information GADDS Software Reference Manual does the scroll bar ENTER is equivalent to clicking the highlighted button initially OK and the TAB and SHIFT TAB keys cycle the highlight focus over the edit control and buttons ESC is equivalent to Cancel You can highlight text in the text control with the mouse or shifted arrow keys and copy it to the clipboard with CTRL C cut to the c
443. nsidered good At a radius of 130 the criterion is 80 Hot pixels are treated similarly with the tightest restriction being for the center and the least restrictive requirement at the edge 6 5 3 Rejection Criteria After all bad pixels are determined the program displays the evaluation radius the border and all bad pixels as an overlay on top of the flood field image Next a table is displayed consisting of the bad pixels with comments and clusters identified Comments include e gt Weaker lt 5 weaker than criteria e gt Hotter lt 5 hotter than criteria e gt gt gt DEAD lt lt lt Below 10 of expected e gt gt gt BURNT lt lt lt Above 900 of expected M86 E01008 GADDS Software Reference Manual Process Routines Currently we add up the total adjacent bad pix els around each bad pixel number of bad neigh bor pixels If this number is greater than or equal to the entered cluster size then the pixel is identified as Cluster This will not identify long single pixel lines of bad pixels 6 5 4 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses A E EE Radius 260 520 1040 Radius in pixels from center pixel not beam center which defines evaluation region A T E ER Border 0 Border in pixels to exclude from evaluation region 0 means to exclude only the over flow rows first and last rows columns
444. nsity at those pixels are never used in the spectra Even with a good step width the intensity at some pixels will be used for consecutive integration steps and an occasional pixel or two could be completely skipped M86 E01008 Peaks Routines GADDS Software Reference Manual gt region 2 region 1 last x Figure 8 1 Bresenham s algorithm true conic line D C O ey true conic M line A B Xiyp Xiyi The two cases for gently sloping regions adapts easily to computer graphics displays tor Essentially Bresenham bisected the problem line drawing into two cases depending upon the slope of the The area detector image is stored as intensity line For steep slopes the next pixel along the values on a square pixel grid For integrating line always increases by one pixel in the vertical along either 20 or x lines Bresenham s algo direction Y while the horizontal direction X rithm is used to determine the pixels along the may or may not increase by one pixel Similarly line and the intensities at each pixel are the converse exists for gentle slopes the next summed method 0 or averaged method 1 pixel always increments in W with or without an These methods equally weight the intensities of increment in Y Negative slopes are handled by all pixels negating the X axis Bresenham s algorithm M86 E01008 GADDS Software Reference Manual Peaks Routines The modified versio
445. nt each pixel may be weighted by a normalization factor Available normaliza tions are O none sums all active pixels 1 average pixel Sum of pixels number of pixels 2 arc length sum of pixels arc length sum of arc lengths 3 solid angle sum of pixels solid angle sum of solid angle See Peaks gt Integrate gt Chi for a full description of this normalization method STEPSIZE lt n gt Step size 0 1 The angle step width in degrees The default of 0 1 works well for frames taken at 7 cm Frames taken at 10 cm may need a smaller stepsize M86 E01008 Peaks Routines GADDS Software Reference Manual 8 11 Peaks gt Integrate gt Write Write integration results to disk file Menu Command Peaks gt Integrate gt Write Accelerator None User Level 1 SLAM Syntax INTEGRATE WRITE 1 FILENAME lt n gt FORMAT lt n gt APPEND INTEGRATE WRITE will output the results from either integration to a disk file format which is compatible with conventional powder diffraction data processing software Four file formats are supported e PLOTSO is simple ASCII file format which is very portable to any computer platform e OLD_DIFFRAC AT is the file format used by ancient PC based software This file format is binary and is difficult to read on non PC platforms e DIFFRAC AT is the file format used by older PC based software This file format is binary and is difficult to read on non PC plat
446. nt between D8 3 circle Platform 3 cir cle 4 circle and old 3 circle systems You also need to make sure that any configuration files you read in correspond to the correct goniome ter type since the values in the configuration file will be transferred to GADDS and the goniome ter controller on program startup See Edit gt Configuration gt Show Model Section 4 5 for more information 4 circle systems use settings at the base chi and base chi 180 for estimating sample height 3 circle systems use the base omega and base omega 180 When in the panel pressing the ESC key or clicking Cancel button returns you to the main menu menu Pressing the ENTER key or click ing OK button initiates the optical command The goniometer is said to be in manual mode when in this state During manual mode the message appears on the bottom status line MANUAL MODE ESC EXIT S SHUTTER T ATTENUATOR A ADD C COUNT L LASER The Optical command enables the manual con trol box for interactive control of the goniometer but unlike the Collect gt Goniometer gt Manual command it assigns a different functions to the ENTER button on the Phoenix s manual control box and to the AXIS PRINTOUT button on the GGCS s manual control box On the Phoenix s manual control box press SHIFT F2 then 1 for 26 then press ENTER to drive the goniometer to the base angles Addi tional presses of ENTER will drive phi by 180 If you select
447. nt data in frame accumulation memory Thus FRAME can be used to display the contents of accumu lation memory if you ve acquired a frame suppressing display or can be used to redisplay a newly acquired with different lower and upper limits If you leave this item blank or specify a wildcard filename pat tern pressing ENTER or clicking the OK button will allow you to choose from a list of the current filenames matching the pattern after which you will be returned to the input dialog with the selected filename filled in If you leave this item blank it is the same as entering a wildcard pattern Remember that both filenames and patterns entered here are merged with the Project gt New working directory as described above QUADRANT lt n gt Screen Quadrant 0 full Select the quadrant in which the frame is to be displayed In the dialog box you can select the quadrant from a drop down list While multiple images can be displayed in different quadrants at one time only the image in the current quadrant is actually in memory thus for example the cursor func tions work only on the image in the current quadrant Quadrants are 0 full window 1 lower left 2 lower right 3 upper left and 4 upper right Default is 0 ILOHKND nonna Lower Limit 0 The number of counts to be mapped to zero in display memory Pixel values lower than this are truncated to zero on display although the cursor commands will
448. nt frame directory specified in the CONFIGURE EDIT panel Although you can thus keep several different flood field corrections available at any time re using old flood field corrections is not really very useful since your results will be better if you run FLOOD NEW prior to data collection on each new sample The name of the current flood field correction is shown on the display in the current status area at the bottom right of the screen FLOOD LOAD updates this name when the correction is changed When invoked with the LOAD option from the FLOOD submenu or when run from the com mand line without arguments FLOOD LOAD displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins reading in the specified correction the ESC key or right mouse button returns you to the FLOOD submenu 6 2 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Pi oha r Filename normal _fl Name of the flood field correction to read This filename is merged with the current frame directory specified in the CONFIG URE EDIT panel before the program attempts to access the file See CONFIG URE EDIT for a description of how this is done If you leave this field blank or specify a wildcard filename pattern in the FLOOD LOAD input panel the program will display a list of filename
449. nter the destination y angle in degrees Default is current setting 5 ial a teat tes X Enter the destination X position in mm Default is current setting E S Y Enter the destination Y position in mm Default is current setting current setting current setting current setting current setting current setting current setting current setting current setting current setting Enter the destination Z position in mm Default is current setting TEE Aux1 Enter the destination aux position in aux units Default is current setting Typically this axis is used for the video zoom option thus its units are magnification factor in the range 1 0 to 7 0 current setting M86 E01008 Collect Routines GADDS Software Reference Manual 5 11 Collect gt Goniometer gt Manual Control goniometer from manual box Menu Command Collect gt Goniometer gt Man ual Accelerator Ctrl Shift M User Level 1 SLAM Syntax GONIOMETER MANUAL 1 2 3 4 5 6 7 8 or GONIOMETER MANUAL 1 2 3 4 5 also RATEMETER 1 RESET lt n gt SHUTTER Use this command to operate the goniometer motors using the manual control box While the manual control is activated the program control is suspended When in the panel pressing the ESC key or clicking Cancel button returns you to the main menu menu Pressing the ENTER key or click ing OK button initiates the manual comma
450. ntinuously updated and displayed on the screen While interactively modifying an integration limit the lt ESC gt key or right button will restore the limit to its original value while the lt ENTER gt or left button will accepts the new value for this limit It is also feasible to move the entire integration window by pressing the M key using the cursors to position a new center of the integration window then pressing the lt ENTER gt key Once the integration window is defined press ing lt ENTER gt will start the integration calcula tions and display the message Wait Integrate ESC Other buttons Quit Normally one waits for the calculations to finish and to plot the resulting data trace however should you wish to abort the procedure press lt ESC gt If too few data points were calculated the command will terminate immediately Other wise the message below appears Warning aborted early Press ENTER to continue ESC to abort Pressing lt ESC gt will terminate the INTEGRATE CHI command immediately while lt ENTER gt will accept the truncated data trace from the par tially integrated window the upper chi limit was lowered and display the trace While GADDS provides several methods of con verting frame images into raw spectra you should be familiar with the differences between each method Methods 0 and 4 are summations while methods 1 2 3 and 5 are normalized to a ten pixel region 1
451. ntroller s Phoenix s or GGCS s memory to the correct goniometer position That is if the readings on the goniometer s angular scales are different from those reported by the program use this command to enter the readings from the angular scales to the nearest 0 5 The pro gram then sends these readings to the goniom eter controller which very accurately maintains the current positions modulo 1 degree but must rely occasionally on this type of user input for the coarse absolute position On 4 circle P3 style goniometers all angles are entered to the nearest 0 5 degree The pro gram then sends these readings to the goniom eter controller which very accurately maintains the current positions modulo 1 degree but must rely occasionally on this type of user input for the coarse absolute position On all other goniometers for example D8 Plat form or Aztalan all angles and positions are entered with full fractional values Rarely if ever does one know the exact axis setting so typi cally one performs a Collect gt Goniometer gt Home see Section 5 25 command after updat ing an axis to accurately position the axis When invoked from the menu or run from the command line without arguments Collect gt Goniometer gt Update displays a dialog box where you can view edit the arguments described below Pressing the ENTER key or clicking the OK button updates the angles Pressing ESC or clicking the Cancel button
452. nvironment variable GADDS PROJECT to point to a project database in this directory 1 18 M86 E01008 GADDS Software Reference Manual General Information 1 7 Frame Indexes Frame indexes have been implemented When a frame name is given in the format INDEXNAME N or INDEXNAME H the program looks for a frame index file INDEX NAME with the extension defaulting to fin for Frame INdex N is a decimal number represent ing the line number in the index file which con tains the filename of the frame H represents the same only in base 36 Lines are numbered starting from 0 GADDS will remember the name of the last index specified so that you can omit IN_DEXNAME in subsequent references thus N and H become valid frame names The frame index is an ASCII file in the Harvard format where each line contains a number which is ignored by GADDS followed by the frame name The default directory for frame index files is the frame directory as specified in the CONFIGURE EDIT panel In the DISPLAY commands NEXT PREVIOUS MOVIE and MOVIE the auto increment or decrement will be performed on the index line number not the frame name M86 E01008 General Information GADDS Software Reference Manual 1 8 Special Symbols Throughout the various input panels special symbols are reserved for special purposes Symbol DATA FRAME MASK NET NEXT NULL Where used PEAKS LOAD CORRECTIO
453. ny arrow key results in a greater change of contrast or brightness M86 E01008 Collect Routines GADDS Software Reference Manual 5 36 Collect gt Scan gt Psi Take a Psi scan of 360 around reciprocal vector Menu Command Collect gt Scan gt Psi Accelerator Ctrl Shft F6 User Level 1 SLAM Syntax SCAN PSI 1 2 SCANTIME lt n gt TITLE lt s gt SAMPLE lt s gt NUMSAMPLE lt n gt NAME lt s gt RUN lt s gt FRAMENO lt s gt DISPLAY lt n gt REAL TIME SCAN PSI will collect a frame series for later processing with GRAPH PSI When invoked from the command line SCAN PSI can take the following arguments where lt n gt represents a numeric value and amp indicates continuation on the next line 5 36 1 Arguments Each argument is listed below by its command line name followed by its input panel prompt in parentheses 1 EESE HKL 022 Enter the hkl position for psi scan n EAA EEE Frames 180 Enter the number of frames to collect deter mines the step size SCANTIME lt n gt Seconds Frame 1 00 00 Time in seconds for which each frame is to be acquired You can optionally specify long times in the format HH MM SS SS where HH represents hours MM minutes and SS SS decimal seconds TITLE lt S gt o n Title Scan psi frame Enter title for output frames 80 characters maximum The default entry is Scan Frame If you invoked SCAN SINGLERUN f
454. oard arrow keys The arrow M86 E01008 GADDS Software Reference Manual Peaks Routines keys are very useful for precise 1 pixel adjust ments Pressing the ENTER key or left mouse button computes the intensity versus scan angle curve and draws it on the screen Pressing the ESC key or the right mouse button toggles between position change mode and size change mode where the lower left corner of the box remains anchored while the upper left cor ner moves under mouse control If you want to exit without computing drawing the graph and entering the reflection into the array use CTRL BREAK Depending on the number of frames specified with the FRAME HALFWIDTH argu ment see below the rocking curve can take several seconds to compute The lineweight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cursors Odd values are better than even ones since the extra thickness is then added symmetrically about the true cursor posi tion On completion the setting angles the X Y and scan angle centroids the intensity and I sigma are entered into the Reflection Array in the spec ified record number or in the next available record number if specified as zero The A flag is set in the new Reflection Array entry If the scan angle centroid was computed f
455. ocess Routines results in re binning by 16 1 instead of 32 1 In general this feature is useful only for special e g non crystallographic applications and these settings should be left at their defaults In the case of a foil illumination by the electrical x ray source causes fluorescence creating a secondary point source where the incident beam strikes the foil 1 mil Fe foil is a good choice for a Cu source Because the foil not only fluoresces but also scatters and diffracts the incident beam you need to swing the detector far enough in 2 theta to 1 avoid any beam stop shadow or scatter and 2 eliminate any diffrac tion rings strong enough to affect the calibration For Fe Cu calibrations 50 to 60 degrees appears to work well at a 15 cm distance with the 9 cm diameter detector When illuminating the foil use a collimator barrel from which all pinholes have been removed This not only increases the intensity but also substantially smooths any diffraction rings which you can t otherwise avoid In order to evenly illuminate the detector it is very important that the plane of the foil be parallel to the detector face If your image does not appear uniform it is probably because either the foil is not centered at the instrument center the foil plane must contain the 2 theta rotation axis or the plane of the foil is not paral lel to the detector face Prior to performing the calibration take an exposure with ADD to make
456. of aux axis 1 up to now 0 0 13 hkl scan 2 i e h of hkl scan 14 reciprocal space scan 2 1 M86 E01008 DIFFRACP S Raw Data File Format GADDS Software Reference Manual multiple scan parameters 129 PSD fixed scan 2 chi gt bit 2 130 PSD fast scan 2 phi gt bit3 257 pixel s can SAXS v4 X 2 x gt bit 4 200 R4 delay time before a measurement was y gt bit 5 started in seconds gt bite obs 9999 0 unknown 2 1 0 auxi SUF unknown z 7 aux2 gt bit8 204 R4 the time the range was started relative to the time when the aux3 gt bit 9 sample was started in sec obs time gt bit 10 9999 0 unknown temp gt bit11 2 1 0 unknown e g chi and phi 2 2 2 3 12 208 R4 rotation speed in rps 0 0 no rota 252 14 length of each data record in bytes tion currently 4 float 212 R4 temperature in K 1 0 for room but if the varying parameters are not 216 R4 heating cooling rate of the TC in K s 0 the data record length 220 R4 delay in sec before measurement if is 4 8 number of bits set in above TC 1 0 for unknown 2 varying parameter flag 224 14 generator voltage kV or e g chi and phi vary gt data record 9999 unknown length 8 8 4 20 228 14 generator current mA or 256 14 total size of all supplementary range 9999 unknown header r
457. ollected and the frame naming parameters defined in the Edit gt Configure gt User settings input panel The first and last generated filenames in each frame series must be valid Also the generated filena mes between frame series should not overlap Always check the bottom status line when you first start a new Collect gt Scan gt MultiTargets to ensure that filenames are being synthesized the way you want to avoid duplication of filenames during data collection which will overwrite the previous file None Command executes immediately This is an interactive command only The EditTargets command is an interactive com mand meaning that you can invoke it from the command line but it will not proceed without user intervention And it has no built in com mand mode time out as with other scrolling out put windows Additionally the Collect gt Scan gt MultiTargets does not work well from script files as you cannot define the run list in command mode Thus we recommend using the equiva lent SCAN SINGLERUN script commands instead 5 80 M86 E01008 GADDS Software Reference Manual Collect Routines 5 44 Collect gt Scan gt MultiTargets Perform same scans on multiple tar gets on a single sample Menu Command Collect gt Scan gt MultiTargets Accelerator Ctrl Shft F12 User Level 1 SLAM Syntax SCAN MULTITARGETS 1 2THETA lt n gt THETA1 lt n gt OMEGA lt n gt THETA2 lt n
458. om mand line name followed by its dialog box prompt in parentheses CNAME lt s gt Sample Name Unknown Enter the name of the sample project name sample name number Default is Unknown D1 S e EEATT Sample Number 0 Enter the number of the sample negative to ignore Default is 0 TITLE lt 8 gt 0 202 Title 2 Enter a descriptive title for this project sam ple Default is WORKDIR lt s gt Working Directory SPROJECT Enter the Drive Directory to make current or the working directory The program will place all data files in this directory Or enter PROJECT and the program will generate a project working directory name from the project name and using GADDS FRAMES as the root Default is PROJECT FORMULA lt s gt Chemical Formula Enter the chemical formula for this sample or enter Default is MORPH lt s gt Sample Morphology Enter a description of the physical sample or enter Default is CCOL lt S gt Sample Color Enter a description of the sample color or enter Default is DENSITY lt s gt Measured Density Enter the measured sample density includ ing units or enter Default is M86 E01008 GADDS Software Reference Manual Project Management Routines DENSMETH lt s gt Density Method 7 Enter a
459. omputed for the final position of the cursor prior to exiting the command are written to the output logfile If scripting is enabled see File gt Script File a non interactive CURSOR command cor M86 E01008 Analyze Routines GADDS Software Reference Manual responding to the final cursor position is written to the output script file The SLAM command arguments are 1 X coordinate of the circle center in pixels The range is from 0 to framesize 1 default value is 256 2 Y coordinate of the circle center in pixels The range is from 0 to framesize 1 default value is 256 3 Radius of the circle in pixels The range is from 0 to framesize 2 1 the default value is 64 DELAY lt n gt Specifies a time interval in seconds to wait before erasing the cursor and returning con trol to the program This is for use in scripts where it is desirable for the cursor to remain on screen long enough for the user to dis cern its position NOERASE Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor left from a NOERASE by reissuing the command with the same parameters The Analyze gt Clear command is another way to erase cursors left over from NOERASE options The following output statistics are displayed on screen in real time and written to the logfile if applicable for non pole figure frames
460. on exits returning you to the CURSORS submenu Pressing the ESC key or the right mouse button toggles between position change mode and size change mode where the lower left corner of the box remains anchored while the upper left corner moves under mouse control Analyze gt Cursor gt RBox can also be used to clear or fill the area inside a box to a specified value allowing you to edit the image with basic functions When you press BACKSPACE or DELETE on the extended middle keypad GADDS displays a dialog box where you can enter a value to set all pixels inside the box cur sor The default value is equal to the current background estimate based on pixel values around the box perimeter Pressing ESC or clicking the Cancel button exits without chang ing pixel values After editing the image you can use the SAVE command to write the image in edited form This function can be performed only interactively that is there is no way to clear the area in a box with command line commands The lineweight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cursors Odd values are better than even ones since the extra thickness is then added symmetrically about the true cursor posi tion By providing arguments on the command line you can direct the CURSORS RB
461. on in OK Cancel dia logs or executes the currently highlighted button in most other dialogs TAB Moves to the next field in a dialog box M86 E01008 GADDS Software Reference Manual General Information SHIFT TAB Moves to the preceding field in a dialog box UP ARROW and DOWN ARROW keys Move through items in a menu or multi line edit control In most interactive commands they can also be used to position the cursor as an alternative to the mouse By default they move the cursor by 1 pixel in graphic cursor commands see PLUS key descrip tion below LEFT ARROW and RIGHT ARROW keys Move non destructively one character left or right when editing text in a dialog as with up down arrows they can position the cur sor in interactive cursor commands plus key Increases by a factor of 2 the number of pix els that a cursor is moved whenever a cur sor key is pressed Values of 1 2 and 4 are possible in conjunction with arrow keys or 10 20 and 40 in conjunction with CTRL arrow keys minus key Decreases by a factor of 2 the number of pixels that a cursor is moved whenever a cursor key is pressed opposite of the key described above CTRL ARROW keys Move the cursor 10x faster in interactive cur sor commands like Analyze gt Cursor Ana lyze gt Cursor gt Box etc PAGEUP Move up a page in scrolling text dialogs PAGEDOWN Move down a page in scrolling text dialogs INS Toggle
462. on to remotely control the frame buffer see PCAny where license agreement Use PCAnywhere32 when you wish to run the GADDS program but are sitting in front of a different computer Use SMARTservice when you wish to control the GADDS program from another program such as EPICS LABVIEW SPECS or TELNET M86 E01008 I Electronic Tracking of Instrument Configuration Changes Bruker Log Service GADDS now supports electronic tracking of instrument configuration changes GADDS only logs the Bruker Instrument Administrator changes such as e Calibrate New detector parameters e Collect gt Goniometer gt Encoders New encoder offset s e Edit gt Configure gt User Admin New cali bration direction New detector parameters and New wavelength parameters e Flood gt New New flood correction e Project gt Overwrite defaults New system defaults e Spatial gt New New spatial correction NOTE Currently goniometer controller configu ration changes other than encoder offsets are not logged such as direct editing of device ini when changing stages These changes are converted to a two line ASCII string containing information for program and version date time user and log string For example GADDS 4 1 02 Date Thu 12 Oct 2000 Time 14 54 17 User SmitKL Log Configure gt Edit New wavelen parms Cu 1 54184 1 54056 1 54439 139222 M86 E01008 Electronic Tracking of Instrument Config
463. one of the other axis buttons instead of 20 certain fixed angles are added to the base position as listed in the table below As with the 1 20 Additional presses of the ENTER button when in one of these other positions will drive phi by 180 On the GGCS s manual control box depress the 2 THETA axis button on the manual box all three others should be up then press AXIS PRINTOUT to drive the goniometer to the base angles Additional presses of AXIS PRINTOUT will drive phi 180 If you depress one of the three other axis buttons instead of 2 THETA certain fixed angles are added to the base posi tion as listed in the following table Axis Position Position Button 4 Circle 3 Circle 2 THETA Base Position Base Position OMEGA 90 in phi 90 in phi PHI 180 in chi 180 in omega CHI 180 in chi 180 in omega 90 in phi 90 in phi As with the 2 THETA button additional presses of the AXIS PRINTOUT button when in one of these other positions drive phi 180 M86 E01008 GADDS Software Reference Manual Collect Routines While the Collect gt Goniometer gt Optical dialog box allows you to modify the fast slow speed ratio used by Collect gt Goniometer gt Manual it is not used here The slow speed is instead fixed at 30 degrees minute See Collect gt Goniome ter gt Manual Section 5 11 for more information about the speed ratio 5 12 1 Arguments Each argument is listed below by its comman
464. oniometer gt Home axis e Home goniometer axis Menu Command Collect gt Goniometer gt Home axis Accelerator none User Level 2 SLAM Syntax GONIOMETER HOME 1 2 When a goniometer controller is first powered up or power cycled the setting angle positions may be different from those reported by the con troller While the Collect gt Goniometer gt Update command allows you to make sure the reported angles agree with those you read from the angu lar scales on the goniometer it s difficult to tell if the reported position is off by a small amount Collect gt Goniometer gt Home Axis allows a specified axis to be driven to an internal fiducial mark and its position to be updated so that the reported position is exactly consistent from power up to power up In the case of a Platform goniometer absolute fiducial marks are avail able typically at 30 00 in 2 theta and 30 00 in omega and the axis will seek the fiducial mark when homed Some systems such as micro diffraction systems have a modified 2 theta fiducial position In the case of a P4 the axis seeks the degree mark nearest its current location When invoked from the menu or run from the command line without arguments Collect gt Goniometer gt Home Axis displays a dialog box where you can view edit the input arguments Pressing the ENTER key or clicking the OK but ton initiates the homing of the requested axis The goniometer 2 theta or o
465. ons Subsequent annotation com mands are appended to the annotation list which can then be saved with the Analyze gt Annotate gt Save subcommand A saved annotation list can later be redisplayed with the Analyze gt Graph gt File command Menu Command Analyze gt Annotate gt Edit SLAM Syntax GRAPH POSTER EDIT All poster annotations are stored ina PLOTSO file format These commands can be edited with a simple screen editor After M86 E01008 Analyze Routines GADDS Software Reference Manual NOTE This will erase all graphs displayed prior to invoking the Analyze gt Annotate command exiting the EDIT command the graphics plane is erased and the poster annotations are redrawn Menu Command Analyze gt Annotate gt Clear SLAM Syntax GRAPH POSTER CLEAR This command will clear a rectangular region When selected a cross hair cursor is visible Position the crosshairs at a corner of the box to be erased Anchor the corner by pressing ENTER or the left mouse but ton The cross hairs will disappear and be replaced with a rectangular box with one corner being the anchored point just selected and the other corner at the current cursor position Press ENTER or the left mouse button to position the second box corner The box is erased and a crosshair cursor appears for positioning the next box Pressing ESC or the right mouse button will return you to the menu Menu Command Analyze gt Annotate g
466. ons above the mean M86 E01008 Analyze Routines GADDS Software Reference Manual Sigma I Standard deviation of integrated intensity in the central frame This value is not dis played if an orientation matrix is available Instead the HKL s area displayed I Sigmal Integrated intensity divided by its standard deviation in the central frame This value is not displayed if an orientation matrix is avail able Instead the HKL s area displayed 3D 3D integrated intensity for the spot This is the sum of the 2D background subtracted intensity on each of the component frames I3D Sig The 3D integrated intensity divided by its standard deviation XCntroid The X centroid in pixels of the 3D inte grated intensity YCntroid The Y centroid in pixels of the 3D inte grated intensity ZCntroid The Z centroid of the 3D integrated inten sity This is the centroid in the direction through the frames and is expressed in degrees or in frame number if the scan angle wasn t available in the component frame headers That is the units are the same as those indicated for the X axis on the resulting graph HKL If an orientation matrix is in effect the HKL indices corresponding to the 3D intensity centroid are also output M86 E01008 GADDS Software Reference Manual Analyze Routines 7 10 Analyze gt Graph gt Poster Interactively annotate displayed graph or frame Menu
467. or clicking the right mouse button while dragging with the left button pressed toggles between position change mode and size change mode where the center of the circle remains fixed while the size changes as the mouse is dragged When moving or sizing the circle with the arrow keys you can press CTRL along with an arrow key to move in increments ten times larger than for the unmodified arrow key When used in this interactive manner the com mand also provides the option to drive the spin dle axis phi to a position where the zero layer diffraction circle represented by the circular cur sor would be at its closest approach to the direct beam center Pressing the D key drives the phi axis to the new position as indicated in the prompt on the bottom status line By providing arguments on the command line you can direct the cursor computations to be performed once at a single specified position after which control returns immediately to the command line The line weight of the cursor can be increased from the default thickness of 1 pixel by defining the environment variable SAXISCURSWEIGHT with an integer value from 2 to 7 In general SAXISCURSWEIGHTS 3 is a good value to use if you want thick cursors Odd values are better than even ones since the extra thickness is then added symmetrically about the true cursor posi tion If logging is turned on see the File gt LogFile command for more information the quantities c
468. or Y energy his eee eee Bias 0 Enter 0 for Cu low BIAS 1 for Fe high bias M86 E01008 Collect Routines GADDS Software Reference Manual 5 10 Collect gt Goniometer gt Drive Move goniometer angles to specified positions Menu Command Collect gt Goniometer gt Drive Accelerator Ctrl Shift D User Level 1 SLAM Syntax GONIOMETER DRIVE 1 2 3 4 5 6 7 8 or GONIOMETER DRIVE 1 2 3 4 Use this command to drive the goniometer angles and axes to a specified position The default settings are the current angles positions so you only change the axes that you wish to drive The minimum and maximum allowed val ues are taken from the current software collision limit settings see Collect gt Goniometer gt Limits settings Section 5 15 but on a 14 circle sys tem the extended limits see Collect gt Goniom eter gt ExtLimits Section 5 16 can restrict goniometer motion and detector XYZ limits see Collect gt Goniometer gt XYZ stage Section 5 27 can further restrict goniometer motion When in the panel pressing the ESC key or clicking Cancel button returns you to the main menu menu Pressing the ENTER key or click ing OK button initiates the drive command GADDS checks the specified angles against the current collision limits and extended limits and displays an error message if the requested angles positions are not allowed Otherwise GADDS begins moving the goniometer to the
469. order Current limitations ignored fields in file header of various frame formats e Bruker Defaults to version 8 frame headers with 4096 byte overflow e Bruker ASCII Cannot read this format only writes this format e TIFF Reading TIFF files has many limita tions TIFF must be a single full size mono chrome and uncompressed image File headers are defaulted to best guess values CHESS private tags are not translated Numerous frame header items are defaulted to best guesses MMX MarCCD handles only omega or phi scan series e Assume angles are already in Bruker conventions except for chi CHImar 90 0 CHibruker This works for frame series collected at 2t 0 Om 0 phi Ch 0 which convert to 0 0 phi 90 in Bruker angle conventions e Frame number and Number of frames in series are not converted M86 E01008 GADDS Software Reference Manual Utility Programs e CCD temp is not converted e Detector roll pitch and yaw are not con verted e NEXP and CCDparms are not converted e imageNCIF n y i e APS Read only FRM2FRM cannot write this frame file format Angles in frame header are not converted to Bruker conventions NOTE For compatibility with software requiring 512 byte overflow table use the environment variable SET SAXI 512MAXOVF 1 M86 E01008 13 5 Utility Programs GADDS Software Reference Manual 13 3 GADDSMAP GADDS MAPping program This u
470. orm goniometer is fixed at CHI 54 74 An older Aztalan black 3 circle goniometer is fixed at CHI 45 Valid values are 360 to 360 but are typically reduced by the current software collision limits as defined in Collect gt Goniometer gt limits command Entering will be auto matically replaced with current angle set ting a X 0 00 The X axis position in mm at which GADDS positions the goniometer at the start of the frame series Entering will be automatically replaced with current axis position setting NSEM gt secscsssesscetesse Y 0 00 The Y axis position in mm at which GADDS positions the goniometer at the start of the frame series Entering will be automatically replaced with current axis position setting IZ PEND ensiscecnees Z 0 00 The Z axis position in mm at which GADDS positions the goniometer at the start of the frame series Entering will be automatically replaced with current axis position setting WIDTH lt n gt Frame Width IAUX lt N gt 0cee Aux 1 00 The Aux1 axis position in units at which GADDS positions the goniometer at the start of the frame series Entering will be automatically replaced with current set ting Typically this axis is used for the video zoom lens and is entered as a magnification factor in the range 1 0 to 7 0 AXIS lt N gt 660 Scan Axis 2 The number of the axis to be
471. ou can view modify the desired destination angles The values in the input panel default to the current goniometer position When in the panel pressing the ENTER key or left mouse button the program updates the current goniometer angles dis played in the goniometer status area at the lower right of the screen NOTE To change the settings of controllable axes see the Collect gt Goniometer gt Update command Section 5 14 M86 E01008 GADDS Software Reference Manual Collect Routines 5 24 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses a OEE EEE 2 Theta current setting a EAEE E THETA1 current setting The destination 2 Theta swing angle in degrees Or theta1 tube axis E AEA Omega current setting e T THETA2 current setting The destination Omega angle in degrees Or theta2 detector axis GS ET Phi current setting The destination Phi angle in degrees GAs EEEE TET Chi current setting The destination Chi angle in degrees 5 tecdstetaievanctiieiies X current setting The destination X position in mm 6 selects cist Y current setting The destination Y position in mm Trnem airs Z current setting The destination Z position in mm G8 EA Aux1 current setting The destination AUX position in aux units M86 E01008 Collect Routines GADDS Software Reference Manual 5 25 Collect gt G
472. ould direct output to a parallel printer Alternatively you can just enter the output name directly in the input panel for example PRN If you spec ify a filename the system prints to disk M86 E01008 File Routines GADDS Software Reference Manual FORMAT lt n gt Format creating a file with that filename on the sys tem hard disk which may later be output directly to a printer without having to run GADDS Under DOS a command like COPY B lt filename gt PRN would copy your output file to a parallel LaserJet printer NOTE You cannot print to a disk file if you use the Native format option Under NT the GADDS printer device is often different than the default print device Thus it is a good idea to create an unique GADDS print queue with your favorite printer settings and set the environment variable SAXISPRINTER equal to the Printer name Printing to SAXISPRINTER will proceed without user intervention Print ing to DEFAULT will default to the NT default printer but will always display the Print Setup dialog box 1 native Enter the desired output format of the print data Interactively under NT valid formats are native BMP TIFF color TIFF grey PostScript color and PostScript grey Native refers to the native operating system drivers for printers In addition to the native NT support the pro gram supports embedded drivers for ce
473. ow by its command line name followed by its input panel prompt in parentheses 1 PEAKS FILE Filename to create or append another peak table APPEND APPEND Y N Check the box to append the new peak table at the end of any existing file Leave it blank to overwrite any existing peak file 12 20 M86 E01008 GADDS Software Reference Manual SLAM Routines 12 4 9 PEAKS SIMULATE SIMULATE has nine subcommands When you choose it from the menu bar GADDS displays a submenu containing the subcommands When you start PEAKS SIMULATE from the command line you need to specify one of the subcom mands as a qualifier if not the submenu appears and GADDS waits until you have made a selection The subcommands are EXIT Close REFINE submenu and return to PEAKS menu CAUCHY Symmetric Cauchy function Lorentzian GAUSSIAN Symmetric Gaussian function MODCAUCHY Modified Cauchy function ASYMCAUCHY Asymmetric Cauchy function PSEUDO Pseudo Voigt function PEARSON Pearson VII function SPLIT Split Pearson VII function COSINE Cosine function for c scans To select one of the options highlight it with the arrows or mouse A help message appears on the bottom status line describing the action taken by the selected item To begin the high lighted action press ENTER When you are fin ished select EXIT or press ESC to return to the menu bar Profile lineshapes are used in the least squares refinement of all peak parameters Re
474. owed by non lin ear refinement with orthorhombic con straints alpha beta gamma 90 6 Linear least squares followed by non lin ear refinement with tetragonal constraints A B alpha beta gamma 90 7 Linear least squares followed by non lin ear refinement with trigonal hexagonal con straints A B alpha beta 90 gamma 120 8 Linear least squares followed by non lin ear refinement with rhombohedral con straints A B C alpha beta gamma 9 Linear least squares followed by non lin ear refinement with cubic constraints A B C alpha beta gamma 90 If you negate constraint type 1 9 the pre ceding linear least squares is suppressed and initial guesses are obtained directly from the values in the input panel This might save a few seconds if you re re run ning the previous least squares which updated the input panel parameters to their refined values on previous exit with a differ ent constraint type The default 1 should be satisfactory for most purposes aidasta eii A Axis Length 10 0 Initial guess for the A axis length in Ang stroms on entry updated to the refined value on exit Note that if the constraint type 1 is 1 9 the value you start with here doesn t matter since the program will per form a linear least squares to compute initial guesses for refinement Valid range is 1 9999 Angstroms E wetaghetede B Axis Length 10 0 Initial guess for the B axis length in Ang stroms on
475. parameters Verbose output lists regions refinements with standard deviations as well as the final peak parameter table GRAPH PROFILE Y N Check the box to draw the resulting fitted peak profiles NO OF WAVELENGTHS Default 1 Flag 1 or 2 Determines the number of wavelengths present NOTE If the profile shapes contain a1 and a2 lines FLAG must be set to 1 ALPHA1 ALPHA2 SPLIT Default 0 0 a1 to a2 split at true zero May be non zero for incident beam monochromator systems ALPHA2 ALPHA1 RATIO Default 0 5 a1 a2 intensity ratio 2THETA START Starting 26 for peak fitting 2THETA END Ending 20 for peak fitting M86 E01008 12 19 SLAM Routines GADDS Software Reference Manual 12 4 8 PEAKS SAVE SAVE copies the peak parameter table from memory to a specified disk file for retention The peak file is ASCII and can easily be printed on any printer or read by any screen editor The ASCII peak parameter files consist of three sec tions e General header with file date title wave lengths and range e Peak data table with ds 2Ts Is Irel and FWHMs e Background data table with 2T start and end of each region and background The peak parameter table is created with either AUTO or MANUAL It is modified with MANUAL and REFINE and can be destroyed with CLEAR When started from the command line PEAKS SAVE takes the following arguments PEAKS SAVE 1 APPEND Each argument is listed bel
476. peak region Peame saninin Output file pole_fig dat Output file name for pole figure which is stored as a psuedo frame image POLE lt n gt Projection direction 1 The processed pole figure may have it s nor mal direction along 1 X beam 2 Y or 3 Z up The correct value depends on the ori entation of the sample MAPPING lt s gt Mapping STEREO Enter STEREO or POLAR Usually STE REO BACKGROUND Remove background Y N Yes Present to perform background correction Background is calculated for each frame 6 ccs na Low bkg begin 24 0 SF aaan Low bkg end 24 2 Two theta start and end of low background region G83 unnai High bkg begin 26 8 GO REE TAE High bkg end 27 0 Two theta start and end of high background region FIBERGEOM One fiber frame Y N No Enter Y to extract a pole figure from a sin gle frame using fiber geometry Basically the phi direction is indeterminate for fibers thus the single frame will be used at various phi positions every two degrees ABSORPTION lt s gt Absorption model None Enter absorption model as None Fiber or Plate M86 E01008 GADDS Software Reference Manual Analyze Routines IXEKN gt veccccccssecerees Sample vector X 0 N N Sample vector Y 0 ZENS eelne os Sample vector Z 1 Enter sample vector in X Y Z direction on goniometer head IMU lt ND gt
477. pixel over the threshold BIFURCATED This is the number of spots where the 2D intensity on one frame merges with the 2D intensity of more than one spot on an adja cent frame These reflections are rejected TOTAL USEABLE Number of non rejected reflections found CENTERED FORLS The number of reflections with the C flag set These are reflections whose intensity spanned more than one frame and are especially suitable for autoindexing or least squares LS TOTAL UNUSED Number of rejected reflections Following the overall statistics is a reflection by reflection summary For each reflection a line contains in order the X Y and scan angle cen troids X and Y are in pixels and scan angle is in degrees the integrated intensity normalized to 1 deg min the intensity divided by its standard deviation the resolution of the reflection in Ang stroms and a hexadecimal code where each set bit indicates a status condition Conditions 4 and 8 code 000C hex when combined are desir able the others cause the reflection to be rejected Bit assignments in the status code are Bit Value Hex Meaning 0 1 Reflection rejected if set 1 2 Reflection is bifurcated 2 4 Found a close 2D spot on adjacent frame 3 8 Reflection spans frames 4 10 Orphan pixel 5 20 Excluded by X limits 6 40 Excluded by resolution limits 7 80 Excluded by radius limit 8 100 Excluded by I sigma limit M86 E01008 Peaks Routines GADDS
478. played The special name FRAME the default refers to the currently displayed frame If you leave this item blank on the input panel or specify a wildcard filename pattern pressing ENTER or clicking the OK button will display a list of the current filena mes matching the pattern You can choose one from the displayed list by moving to it with the arrow page keys or scroll bars and mouse then pressing ENTER or clicking OK You will be returned to the input panel with the selected filename filled in If you leave this item blank it is the same as enter ing a wildcard pattern Remember that both filenames and patterns entered here are merged with the Crystal gt New Project data directory see Crystal gt New Project for details See the Appendix A Bruker Area Detector Frame Data Format for details on the frame header M86 E01008 Edit Routines GADDS Software Reference Manual 4 20 M86 E01008 5 Collect Routines 5 1 Collect gt Detector gt Cu bias Set PDC to Cu low bias setting Menu Command Collect gt Detector gt Cu bias Accelerator Ctrl Shift C User Level 1 SLAM Syntax DETECTOR CU Use this command to place the PDC and detec tor at the Cu low bias setting The action is per formed immediately with no prompt for additional input The DETECTOR item in the goniometer status area at the lower right of the display is updated to reflect the new bias status NOTE For the GAD
479. played list by moving to it with the arrow page keys or mouse and pressing ENTER or clicking the OK button You will be returned to the File gt ScrFile dialog with the selected filename filled in If you leave this item blank it is the same as entering a slm wildcard pattern APPEND 4 Append Yes If this option is checked output will be appended to the script file if the file already exists If the option is unchecked that is missing from the command line or unchecked in the dialog box the output file is overwritten if it already exists 3 20 M86 E01008 GADDS Software Reference Manual File Routines 3 11 File gt Print e Dump screen to printer device or file Menu Command File gt Print Accelerator Ctrl P User Level 1 SLAM Syntax PRINT 1 FORMAT lt n gt THRESHOLD lt n gt GREYSCALE This command prints a copy of the data cur rently loaded into memory or on the display on a designated printer or to a disk file for later transfer to a printer or into a word processor pro gram Under NT a special native format is available to specify using the native operation system s printer drivers Text and border lines are printed in black while the frame image is printed in either colors or gray tones depending on the selected printer device During printing the black white or grayscale of the image is approximated by the printer by assigning a minimum threshold for black an
480. ple white The values in between are linearly mapped into the colors in the color table Although you enter the contrast limits in terms of pixel value unless you re using Edit gt Contrast interactively in which case you re changing the limits in real time without specifying explicit values Edit gt Contrast works internally strictly with the values in display mem ory In general you don t have to worry much about display limits since the program takes care of all the pixel value display memory conversion details For normal data collection you should usually leave the lower File gt Display limit set at zero and the upper limit at 511 or use the auto matic setting 1 described above Anyway pow ers of two make some internal calculations more precise so 7 15 31 63 127 etc are good general upper limit settings If your frames look too dark you can make them brighter by using a smaller File gt Display upper limit If they look too bright use a larger File gt Display upper limit Since the Edit gt Contrast command gives you a lot of extra latitude and is much faster use the display limits just for getting your images into the ballpark then use Edit gt Contrast for interactive adjustments M86 E01008 File Routines GADDS Software Reference Manual 3 2 File gt Display gt Next and File gt Display gt Previous Display next pre vious frame in this series Menu Command File gt
481. plifier gain in of detector 160 R8 start of aux axis 3 up to now 0 0 1 9999 0 for unknown i e of hkl scan 108 R4 2 lower level used in V 9999 0 for i e psi of psi scans unknown 168 14 scan mode step SS 0 or continu obs lower level in V of detector 1 ous SC 1 SSeS OOP UN DOWN 172 C4 4 bytes of padding for alignment ve B4 ad upper level used in V 9999 0 for 176 R8 step size increment of 1st scan axis in SEN drive units obs pen ie in V of detector 1 184 R8 step size increment of 2nd scan axis 92993 0 10r unknown in drive units 0 0 iG 4 2 measuring channel 1 or 2 192 R4 step time in seconds 1 0 if unknown obs detector code for detector 2 2 120 R4 2 unused field 196 14 scan type obs highvoltage in V of detector 2 0 locked coupled 9999 0 for unknown 1 unlocked coupled 124 R4 2 unused field 2 2theta scan detector scan obs amplifier gain in of detector 3 omega scan rocking curve 2 9999 0 for unknown 4 chi scan 128 R4 2 alternate LLD as fraction of channel full scale 5 phi scan obs Lower level in V of det 2 6 x scan 9999 0 for unknown 7 y scan 132 R4 2 alternate ULD as fraction of 8 z scan channel full scale 9 aux1 scan 2 obs Upper level in V of det 2 9999 0 for unknown 10 aux2 scan 2 136 C8 ASCIIZ IN or OUT no if not 11 aux3 scan 2 present Unkn for unknown 12 psi scan 2 144 R8 start
482. pointer item name TRAILER set to zero if none to the location in the file of any trailer data that has been tacked onto the image This provision won t be used immediately but provides later expansion capa bility For example if a frame is derived from processing some other parent frame the header of the parent could be tacked onto the processed frame as a trailer to provide process ing history The format of a trailer is TRAILER Trailer size in 512 byte blocks 1 byte 3 byte pad Trailer data M86 E01008 A 11 Area Detector Frame Format GADDS Software Reference Manual A 12 M86 E01008 B DIFFRAC S Raw Data File Format The general format of a RAW file is a general file header of 712 bytes followed by a variable length range header which in turn is followed by the range s data records Range header and data records are repeated for all defined ranges RAW_HEADER 712 bytes of information that starts every RAW file This is identical to DIF_HEADER structure except for the initial ID code 3 aborted 4 interrupted 10 simulated data 2 Offset Code Description 0 c8 ASCIIZ RAW1 01 for the 2 release 2 RAW1 00 for the 1 release Note RAW2 and RAW are DIFFRAC AT current file status 12 14 total number of measured ranges 16 C10 ASCIIZ 2 in mm dd yy format e g 12 31 95
483. position NOERASE Suppresses erasure of the cursor on exit Since the cursors are drawn by toggling the sense of the screen pixels you can erase a cursor left from a NOERASE by reissuing the command with the same parameters The Analyze gt Clear command is another way to erase cursors left over from NOERASE options The following output statistics are displayed on screen in real time and are also written to the log file if applicable XY PIXEL X and Y center of box in pixels range from 0 to framesize 1 with the origin X 0 Y 0 at the lower left of the screen WIDTH HT Width and height of the box in pixels TOTALCTS Sum of the pixel values in rectangular box MAXIMUM Largest pixel value in the box MEAN The average of the pixels values contained in the box Integrated intensity minus background The background is computed as the aver age of the points on the perimeter of the box excluding all points which are more than 3 standard deviations above the mean SIGMA I Standard deviation of integrated intensity I SIGMA I Integrated intensity divided by its standard deviation BACKGND Average of points on perimeter of box excluding those points which are more than 3 standard deviations above the mean XCNTROID Raw X coordinate of centroid of intensity in pixels YCNTROID Raw Y coordinate of centroid of intensity in pixels HKL If an orientation matrix is
484. position of the reflection rela tive to detector origin in the standard Bruker pixel coordinate convention This flag is automatically set by REFL_ARRAY THRESHOLD and PICK when they enter a new reflec tion into the array If this flag is not set the INDEX and LEASTSQ sub com mands ignore the reflection This reflection record includes the HKL indices Autoindexing automatically sets this flag when it computes the HKL indices If this flag is not set REFL_ARRAY LEASTSQ ignores the reflection This reflection is centered in scan angle that is there was sufficient information to determine the centroid in scan angle to better than 1 frame width REFL_LARRAY THRESHOLD and PICK automatically set this flag if the spot intensity e g for those pixels above the threshold spanned more than one frame If the reflection appeared on only one data frame it the C flag is not set In a case where there are too few spots spanning frames you can use the MODIFY sub command to add the C flag to all reflections in the set In general it doesn t affect the autoindexing capa bility of the program to do this how ever the RMS deviation in the scan angle as output by the LEASTSQ sub commanq is typically much larger when these spots are included and the orientation and cell parameters may not be as precise Indicates that the values of the X Y spot positions in this reflection record have been corrected with a valid spa
485. position the next box 4 When you are finished press ESC to return to the DRAW menu PEAKS POSTER SAVE PEAKS POSTER SAVE saves all poster anno tations in a PLOTSO file on disk It can later be retrieved with PEAKS FILE Enter the PLOTSO filename and choose whether to APPEND PEAKS POSTER TEXT Text can be positioned and sized interactively with PEAKS POSTER TEXT To use TEXT 1 Select TEXT from the PEAKS POSTER submenu and press ENTER You are prompted to enter the text string to be dis played 2 Enter the text string to be displayed and press ENTER All trailing spaces are removed from the text string but leading spaces are retained A box cursor appears that reflects the size of the text string Press ESC to return to the DRAW menu Move the cursor left or right to increase or decrease the size of the text string in the x direction Move the cursor up and down to change the height of the text Press ENTER to anchor the text size Use the mouse to position the box cursor and press ENTER The box disappears and the text is drawn You are then prompted to enter the next text string to draw PEAKS POSTER LABEL Spots or peaks can be labeled interactively with PEAKS POSTER LABEL To use LABEL 1 Select LABEL from the PEAKS POSTER submenu A pop up menu appears M86 E01008 12 15 SLAM Routines GADDS Software Reference Manual 2 Choose what type of data to retrieve Data type Os 2
486. pply Lorentz polarization air and faceplate absorption corrections then apply the reverse corrections for Lorentz and polar ization to obtain intensities equivalent to a con ventional powder diffractometer with a monochromator and scintillation counter 6 11 1 Lorentz For a completely random sample the forward and reverse Lorentz corrections are identical and effectively cancel each other out 6 11 2 Polarization The forward polarization correction 1 cos 2a where 2a two theta of monochromator 20 two theta of Bragg reflection 2B angle of reflection vector from horizon tal plane 6 11 3 Air and Faceplate Absorption Be absorption calculations account for path length differences due to geometry Photons at the center of the detector travel through a shorter Be path than a photon at the edge of the detector Nominal AIRMU is 0 00021 per pixel about 01 per cm assuming 8 0KV Cu K alpha 80 20 N2 02 20 C 760mm Hg 47 5 pixels cm At detector distance of 12 cm difference in correc tion across face is lt 1 so AIRMU need not be very precise For speed considerations we will only calculate the LPA correction every 16 or 32 for 1K frames pixels along the detector Intermediate pixel corrections may be determined using linear extrapolation corr I The reverse polarization correction corr T 1 cos 2a cos 26 2 cos 28 sin 28 cos 2a sin 2B cos 28 cos 2a cos 20 M86
487. presenta tive profile lineshapes can be either collected data or simulated data using mathematical functions SIMULATE lets you use a Cauchy Lorentzian Gaussian modified Cauchy asym metrical Cauchy Pseudo Voigt Pearson VII ora split Pearson VII function to model the profile shape Profile lineshape functions used by SIMULATE are given below Gaussian A exp x k 2 Cauchy Lorentzian A 1 k2 x2 1 Modified Cauchy A 1 k2 x2 N Asymmetric Cauchy above with different N for each side of peak PSEUDO Voigt A w x 1 w G x Pearson VII A 1 4 2 M 1 x k 2 M SPLIT Pearson VII above with different M for each side of peak Cosine 1 cos x You must supply the 26 value of the peak and any required exponents or weight fractions PEAKS SIMULATE VIEW then calculates and displays the lineshape function M86 E01008 12 21 SLAM Routines GADDS Software Reference Manual PEAKS SIMULATE CAUCHY When started from the command line PEAKS SIMULATE CAUCHY takes the following argu ment PEAKS SIMULATE CAUCHY 1 where the argument is 1 2THETA PEAKS SIMULATE GAUSSIAN When started from the command line PEAKS SIMULATE GAUSSIAN takes the following argu ment PEAKS SIMULATE GAUSSIAN 1 where the argument is 1 2THETA PEAKS SIMULATE MODCAUCHY When started from the command line PEAKS SIMULATE MODCAUCHY takes the following arguments PEAKS SIMULATE MODCAUCHY 1 EX
488. pts to run without intervention If you do not press a key or mouse button within 10 s after the output window is displayed the program will continue as if the ESC key had been pressed In com mand line mode the best solution is always selected no second input window is displayed for selecting a solution number 8 17 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses BT EE Lattice Type P Usually the unit cell parameters you supply in this input panel correspond to the reduced primitive cell determined by REFL_ARRAY INDEX which are automati cally transferred from INDEX to the BRA VAIS input panel While you ll normally use the default input panel values set up be the INDEX sub command you can also per form Bravais lattice determination by directly entering unit cell parameters on the input panel If you know that the parameters you enter here correspond to a non primitive lat tice enter the known lattice type here Valid types are P Primitive A A centered B B centered C C centered Body centered F Face centered R Rhombohedral If you change this entry it is a good idea to reset it to P when you exit The INDEX sub command does NOT automatically update this item when it exits The default is P P2 tet iche tects Current A Axis Length 10 0 Specifies the A axis length in Angstroms of the input unit cell
489. r 4 for x 5 for X 6 for Y 7 for Z 8 for Aux1 Select drive speed by pressing for fast or for slow To drive the axis press and hold the down arrow for reverse or up arrow for forward Release the arrow to stop the drive NOTE The D8 controller will drive for 120 and stop this is normal To display axes angles and positions press the ACVAL actual values but ton NOTE If angles are dashes you need to initial ize the drive with a home command To operate the manual control box on the GGCS controller Platform and earlier systems select the requested axis by pressing the button If a non controllable axis is selected then the mes sage appears Bad button combination The buttons are labeled A B C and D also labeled o x 20 and Multiple button presses are required to control the additional axes A B for X A C for Y A D for Z and C D for Aux1 To drive the selected axis press and hold the fast forward slow forward fast reverse or slow reverse button To stop the drive release the drive button NOTE On R 1 4 circle platform goniometers the chi axis will drive in the opposite direction that is the forward buttons will drive chi in the reverse direction M86 E01008 Collect Routines GADDS Software Reference Manual While the Collect gt Goniometer gt Manual dialog allows you to modify the base goniometer angles used for optical alignment they are not actually used in
490. r code 0 2th th 1 th th 204 12 Diffractometer configuration word 206 R4 Lambda 3 or K beta wavelength 210 R4 Total sample run time in seconds 214 R8 Date time measured in Lotus123 for mat 222 34 Unused Offset Format Field description 0 12 Total number of bytes in range header 12 Step count for this range 12 Stepping drive ID 1 6 drive 1 to 6 8 PSD fixed position 9 PSD fast scan 10 drives 1 and 2 6 12 Step mode bit 0 step scan mode 1 continuous bit 1 calibration indicator 8 R4 Step time time per step in sec onds 12 R4 Step size for range 16 6R4 Starting axes position for range 40 12 Slit position 32767 FA1 32766 FA2 42 12 Slit II position 32767 FA1 32766 FA2 44 12 Detector slit 0 fine 1 coarse 46 12 Temperature in Kelvin 1 room M86 E01008 GADDS Software Reference Manual DIFFRAC AT Raw Data File Format 48 12 Oscillating drive 0 none 1 6 drives 1 to 6 7 spinner 10 11 1 and 2 coupled 50 R4 Oscillation amplitude 999 mechan ically fixed 54 R4 Oscillation speed 58 12 Rotation code 0 none 1 4 15 120 rpm 5 sync 6 SC 60 Variable supplementary information records 60 x nR4 Raw data counts 4 bytes per step M86 E01008 C 3 DIFFRAC AT Raw Data File Format GADDS Software Reference Manual C 4 M86 E01008 D PLOTSO Raw Data File Format The PLOTSO Raw Data File Format is a subset of
491. r data set base 10 or 36 see CON FIGURE form ROTATE 0 005 Rotate sample Y N N n y i Y to perform sample rotation in phi N otherwise IXEKN gt i anaa Active width 2 0 Enter active detector width about center in mm NENS iiai Active height 2 0 Enter active detector height about center in mm REAL TIME Real time Display Yes Enter Y for real time display N otherwise 5 72 M86 E01008 GADDS Software Reference Manual Collect Routines 5 38 Collect gt Scan gt ZonePhoto e Acquire a rotational photo along a zone OKL HOL HKO Menu Command Collect gt Scan gt Zone Accelerator Ctrl Shft F8 User Level 1 SLAM Syntax SCAN ZONE 1 WIDTH lt n gt SCANTIME lt n gt DISPLAY lt n gt Acquire gt Zone acquires an omega rotation pic ture centered on a crystallographic HOL OKL or HKO zone according to the current orientation matrix With a 3 circle goniometer GADDS does not guarantee that all three zones will be acces sible Typically you will have two possible omega settings at which to observe a zone If more than one solution is accessible GADDS will record the one which places omega farthest from the detector at swing angle zero NOTE Ensure that your collision limits are set correctly before using this command GADDS uses them to determine if a solution is accessi ble If the requested zone is not accessible GADDS displays a message indic
492. r output filename for RAW data HKL lt S gt onnan hkl 211 Enter hkl of line YOUNG lt n gt Young s modulus 210 000 Enter Young s modulus for material POISSON lt n gt Poisson s ratio 0 28 Enter Poisson s ratio for material IARX lt NP onanan Arx 1 0 Enter anisotropicity factor 1 0 isotropic LINESHAPE lt n gt Lineshape 4 Enter 1 Gaussian 2 Lorentzian or 4 Pseudo Voigt2 CUTOFF lt n gt Cutoff 0 Enter peak cutoff in percent of max ignore peaks below cutoff LINESHAPE Lineshape 4 Psuedo Voigt 2 stress raw Enter 0 centroid Note for centroid method you cannot refine the backgrounds fit Kalpha2 or use the peak cutoff value but you can subtract out a fixed background REPROCESG Reprocess only N Check Y to skip integration of all input frames Program will try to read the stress report file lt basename gt txt must be created with verbose output to get data table If that fails it will read profile fitting output lt base name gt Ist Reprocessing is useful to throw out bad data points or recalculate stress from new input parameters BKGFIT lt s gt Background fit Both This command can handle the backgrounds during profile fitting in eight ways Both Initializes and refines both back grounds Low Initializes and refines low left background high background is fixed at initial va
493. r plate shipped with the detector is good for this purpose with a sealed tube or with a rotat ing anode run at low power setting 5 KW or less with 0 3 x 3mm filament and 0 3 mm collimator less if your beam is larger The ADD command is useful for accumulating a direct beam image M86 E01008 GADDS Software Reference Manual Peaks Routines Always take another image WITH THE ALU MINUM COVER PLATE IN PLACE after replacing repositioning the beam stop to make sure it is properly re located If you need to make positional adjustments use the ADD command with realtime display enabled and a RESET interval of 1 to a few seconds for coarse positioning You may than want to take some longer frames to perform fine adjustments based on the background recorded immediately around the beam stop after removing the cover plate Remember if your specified beam center coordinates are in error by more than half the smallest center to center spot spacing the chances for mis indexing increase sub stantially 2 You must use the same flood field correction for taking the data frames from which spots are extracted as for taking the fiducial plate image used as input to the spatial correc tion Take the brass plate image AFTER the flood field 3 A good recently determined spatial correc tion computed from a fiducial plate frame taken at the SAME distance as the frames from which the Reflection Array spots were obtained must be
494. r quality data set In addition ASTRO is available for preplanning a data collection strategy that minimizes data collection time for a single asymmetric unit or asymmetric unit plus Bijvoet pairs With this approach you can often collect enough data for structure solution in 2 or 3 hours on crystals with orthorhombic or higher symmetry again sacri ficing redundancy Before invoking Collect gt Scan gt MultiRun you can view edit the runs to be performed as needed with Collect gt Scan gt EditRuns although the default runs supplied should be satisfactory in most cases unless you are using more restrictive collision limits GADDS retrieves the defaults for multirun scans from the gadds _nc file located in the project directory The defaults for new projects are taken either from the current settings or the gaddsdef _nc file located in the GADDS system directory Should you need to change between 3 circle and 4 circle runs here are the currently used defaults for you to enter Table 5 10 Default 3 circle Hemisphere Runs Run Frame 2 Theta Omega Phi Chi Axis Width Frames Time 0 001 28 00 28 00 0 00 54 70 2 0 300 606 10 00 1 001 28 00 28 00 90 00 54 70 2 0 300 435 10 00 2 001 28 00 28 00 180 00 54 70 2 0 300 230 10 00 3 001 28 00 28 00 0 00 54 70 2 0 300 50 10 00 M86 E01008 57 Collect Routines GADDS Software Reference Manual Table 5 11 Default 4 circle Hemisphere
495. re gt Symmetrize Symmetrize pole figure using various Laue symmetries Menu Command Analyze gt Pole Figure gt Symmetrize Accelerator None User Level 1 SLAM Syntax POLE_FIG SYMMETRIZE 1 DISPLAY lt n gt 2 LAUE lt s gt All pole spheres possess Laue symmetry e g orthorhombic materials exhibit mmm symme try therefore one needs to collect only an octant or quadrant of the pole sphere to gener ate the entire sphere Conversely one can use the symmetry feature as a smoothing function SYMMETRIZE supports Laue symmetries for triclinics i monoclinics 2 m orthorhombics mmm and tetragonals 4 m 4 mmm Laue symmetries for trigonals hexagonals and cubics are not supported at this time however one can use 2 m or mmm for hexagonals and mmm for cubics 7 23 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GT erecta saute Input File FRAME Input filename for pole figure or frame DISPLAY lt n gt Max Display Counts 2 Enter 0 for no display otherwise this item specifies the number of counts mapped into the maximum display memory value for example corresponding to white on the dis play The special value 1 directs the pro gram to pick a reasonable value by scanning through the pixels in the frame prior to display the special value 2 directs the program to use whatever setting is cur rently in
496. re Reference Manual Peaks Routines E Matrix 1 3 0 0 Value for row 1 column 3 of orientation matrix E E Matrix 2 1 0 0 Value for row 2 column 1 of orientation matrix PEENE E Matrix 2 2 1 0 Value for row 2 column 2 of orientation matrix ite E EE Matrix 2 3 0 0 Value for row 2 column 3 of orientation matrix ere Matrix 3 1 0 0 Value for row 3 column 1 of orientation matrix E EE Matrix 3 2 0 0 Value for row 3 column 2 of orientation matrix EEE EEEREN Matrix 3 3 1 0 Value for row 3 column 3 of orientation matrix M86 E01008 Peaks Routines GADDS Software Reference Manual 8 23 Peaks gt Refl Array gt Matrix Enter an orientation matrix e g from external program Menu Command Peaks gt Refl Array gt Matrix Accelerator None User Level 1 SLAM Syntax REFL_ARRAY MATRIX 1 2 3 4 5 6 7 8 9 REFL_ARRAY MATRIX lets you enter the nine elements of a specific orientation matrix The resulting matrix is treated as if it had been deter mined by REFL_ARRAY LEASTSQUARES In general this is not as accurate as running REFL_ARRAY LEASTSQUARES since the lat ter simultaneously refines both the matrix ele ments and the detector positional corrections here we re only entering a matrix Nevertheless if you have an existing matrix for example from P3 or XSCANS REFL_ARRAY MATRIX could allow you to immediately index a few spots on
497. re Reference Manual Area Detector Frame Format SITE 4 1 Cc Site name from Edit gt Configure gt User settings MODEL 5 1 Cc Diffractometer model from SAXISADMODEL USER 6 1 C Username from Edit gt Configure gt User settings SAMPLE 7 1 C Sample ID from Project gt New Edit SETNAME 8 1 C Basic data set name RUN 9 1 Int Run number within the data set SAMPNUM 10 1 Int Specimen number within the data set TITLE 11 18 1 C User comments 8 lines NCOUNTS 19 1 9 Int Total frame counts followed by reference counts in Ver 9 9 Adds direct beam monitor counts to NCOUNTS line NOVERFL 20 1 Int Number of overflows MINIMUM 21 1 Int Minimum counts in a pixel MAXIMUM 22 1 Int Maximum counts in a pixel NONTIME 23 1 Int Number of on time events NLATE 24 1 Int Number of late events FILENAM 25 1 C Original frame filename CREATED 26 1 C Date and time of creation CUMULAT 27 1 R Accumulated exposure time in seconds ELAPSDR 28 1 R Requested time for last exposure in seconds ELAPSDA 29 1 R Actual time for last exposure in seconds OSCILLA 30 1 Int Nonzero if acquired by oscillation NSTEPS 31 1 Int steps or oscillations in this frame RANGE 32 1 R Scan range in decimal degrees unsigned START 33 1 R Starting scan angle value decimal degrees INCREME 34 1 R Scan angle increment between frames signed NUMBER 35 1 Int
498. required for future software updates On PCs and workstations the same logical names are used to point to the programs and data Following is the normal directory layout shown schematically for GADDS M86 E01008 General Information GADDS Software Reference Manual C Root directory containing parent of SAXI_ROOT system startup files on PC Bruker program directories C SAXI Bruker supplied application programs in the subdirectories C SAX GADDSnew GADDS programs utilities and help files The environment variables GADDS SYSTEM and GADDS SYSDATA by default point to this directory C SAXIVGADDSnew SRCS Example source files for reading Bruker format data files C SAXIVGADDSnew TEST Test data for verification of proper installation and setup The environment variable GADDS TEST normally points to this directory C SAXI PVWAVE Command procedures to import Bruker data files into Precision Visual s Wave program C SAXI WVIDEO32 VIDEO executable and help files D FRAMES Root of frame data storage It is recommended that you use a subdirectory under this root as the project working directory for each sample D FRAMES CALIB Directory where GADDS stores all calibration files for the detector The environment variable GADDS CALIB by default points to this directory D FRAMES PROJECTS Directory where GADDS project databases are maintained Each user should define the e
499. rid into the frame accumulation memory prior to collecting data The test grid is used for factory alignment and consists of grid lines on a 64 pixel spacing two circles one with a 270 pixel radius and one with a 280 pixel radius and two crosses rotated to 45 degrees one linear cross and one passed through the current flood field correction ICOUNTS 06 Max Counts 10 000 000 This qualifier sets an upper limit on how many counts may occur before data collec tion is terminated When the specified num ber is reached the system ends the data collection saving the data frame The default value is 10 000 000 counts with a range from 0 to 2 147 483 647 i e 23 1 counts Data collection will also be termi nated if MAX SECONDS is reached before MAX COUNTS DISPLAY lt n gt Max Displayed Counts 7 0 no display otherwise counts corre sponding to white on the display The initial M86 E01008 GADDS Software Reference Manual Collect Routines default is 7 the allowed range is from 1 to 10 REAL TIME Real time Display Yes This qualifier when present displays data as it is being collected The display does require additional processing time and will limit the maximum rate at which counts can be accumulated If the MAX DISPLAYED COUNTS qualifier is given a non zero value the frame will be automatically displayed at the end of the ADD if real time display is off
500. ring the specified Y in the quadrant would leave part of the quadrant blank the image is translated only far enough to place the edge of the frame at the edge of the IMAG lt nN gt 006 Magnification 1 The magnification zoom factor to examine a specific area in greater detail The allowed range is from 1 to 16 the default value is 1 AUTOINCREMENT Autolncrement No This allows successive frames to be dis played in different quadrants for example when the MOVIE option is used Check this option to increment quadrant 1 4 after display By default it is unchecked GRAPHICS_SAVE Preserve Graphics No Specifies whether or not to preserve any overlaid graphics if you clear the screen Check this option to preserve graphics if clearing screen By default it is unchecked ORIENTATION Use Orientation in Header No Normally you ll want the cursor commands to read out HKL s based on the orientation matrix computed in the last Peaks gt Refl Array gt LeastSq command This is the default setting unchecked However if you display a frame that was stored with its own orientation matrix in Bruker format you can override GADDS s internal orientation matrix with the one in the frame header and quadrant read HKL s on that frame without having to recompute its orientation matrix In that case check this option Note that this option does not overwrite the matrix from the last M86 E01
501. rmine desired solution 16 00 7 00 8 00 Chi X cor Y cor X raw Y raw 0 00 632 24 548 21 outside detector area 0 00 175 03 427 07 173 71 425 44 1 or 2 Press ESC to continue 8 80 M86 E01008 GADDS Software Reference Manual Peaks Routines 8 25 Peaks gt Refl Array gt Clear Erase the reflection array and current orientation matrix Menu Command Peaks gt Refl Array gt Clear Accelerator None User Level 1 SLAM Syntax REFL_ARRAY CLEAR Use this command to erase the reflection array that is currently in use and to delete the orienta tion matrix associated with it This is useful if you re starting analysis of a new sample have for example used too low a threshold in speci fying spots for the array and wish to start over or if you suspect twinning and would like to cal culate the orientation matrices for different sets of reflections to test the crystal quality When you invoke CLEAR from the REFL_ARRAY submenu or specify REFL_ARRAY CLEAR on the command line the program issues the warning on the bottom status line ERASE REFLECTION ARRAY ARE YOU SURE Y or ENTER YES N or ESC NO Press the Y key Enter key or left mouse button to erase the array and return control to the pro gram or the N key ESC key or right mouse but ton to return without erasing the array If you ve invoked REFL_ARRAY CLEAR from the com mand line this prompt will time out in 10s assuming a
502. rmining a thresh old is to display a frame with the minimum display counts set to zero and the maximum display counts set to a power of 2 for exam ple 64 or 128 then use the CONTRAST command to threshold the image Move the mouse all the way to the left for maximum contrast i e a sharp black to white transi tion then move the mouse up and down until a reasonable number of spots for example 100 divided by the number of frames you re going to threshold is visible You can then estimate the threshold from the point where the black to white transition occurs in the color bar at the right of the screen SIGMA lt n gt l Sigma Threshold 20 Retain only those reflections with I sigma that is its intensity divided by its standard deviation at or above this value times the thermal falloff compensation derived from the value given for DBIAS below I SIGMA computed for each reflection is multiplied by EXP DBIAS S where S is sin theta lambda If the result is lower than the value specified here the reflection is rejected XEXMIN lt n gt Minimum Excluded X 0 Exclude spots with an X centroid between the value specified here and that specified as XEXMAX below This is useful for excluding the area near the beam stop The value is in pixels in the Bruker coordinate convention with X Y 0 0 at the lower left of a displayed frame XEXMAX lt n gt Maximum Excluded X 30 Exclude
503. rom 0 to framesize 1 with origin 0 0 being located at lower left of screen R Pixels Radius in pixels TotalCts Sum of counts on inside circular box Maximum Maximum pixel intensity in circular box Mean Average counts in circular box Integrated intensity minus background The background is computed as the aver age of the points on the perimeter of the box excluding all points which are more than three standard deviations above the mean sigma l Standard deviation of integrated intensity I Simgal Integrated intensity divided by its standard deviation Backgna Average of points on perimeter of box excluding those points which are more than three standard deviations above the mean XCntroid Raw X coordinate of centroid of intensity M86 E01008 Analyze Routines GADDS Software Reference Manual YCntroid Raw Y coordinate of centroid of intensity ACnitroid Alpha angle of centroid of intensity BCntroid Beta angle of centroid of intensity 7 8 M86 E01008 GADDS Software Reference Manual Analyze Routines 7 3 Analyze gt Cursors gt Pixel Show pixel positions and values in displayed frame Menu Command Analyze gt Cursors gt Pixel Accelerator F7 User Level 1 SLAM Syntax CURSORS PIXEL 1 2 DELAY lt n gt NOERASE DUMP When invoked from the menu or run from the command line without arguments Analyze gt Cursor gt Pixel starts directly
504. rom intensity on more than one frame the C flag is set If a valid spatial correction is in effect the corrected X Y are placed in the Reflection Array and the S flag is set otherwise the raw X Y are stored and the S flag is clear If a valid orientation matrix is in effect the nearest integer HKL indices are also entered into the array and the H flag is set The output statistics written to the status area in the middle right of the screen and to the output logfile if logging is enabled are detailed in the description of the GRAPH ROCKING com mand By providing arguments on the command line you can direct the REFL_ARRAY PICK compu tations and graphing to be performed once at a single specified position after which control returns immediately to the command line If logging is turned on see the LOGFILE com mand for more information the quantities com puted for the final position of the cursor prior to exiting the command are written to the output logfile If scripting is enabled again see LOG FILE a non interactive REFL_ARRAY PICK command corresponding to the final cursor posi tion is written to the output script file M86 E01008 Peaks Routines GADDS Software Reference Manual 8 15 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses GA E X Origin 256 The X coordinate of the lower left of the box defining the regio
505. rom the command line you must enclose any title continuing embedded blanks in double quotes FILE lt filename gt will read up to eight 72 character title lines from an ASCII file and place these title strings into the eight TITLE lines in the frame header The for mat of the ASCII file is R lt single line of title information gt where R is the run M86 E01008 GADDS Software Reference Manual Collect Routines number taken from the filename Repeat up to eight times for each run SAMPLE lt s gt Sample Name YLID Enter sample name to be stored in frame header If no name is specified the default name of Lysozyme will be entered NUMSAMPLE lt s gt Sample Number 0 Enter sample number to be stored in frame header The permitted range is from 0 to 32 767 with a default setting at 1 JNAME lt Ss gt 0 2 00 Job Name PSIFRAM Enter the base filename for the output frames The filenames for each series of output frames are generated by adding the series RUN see below window and an extension built from the series starting FRAME see below to the end of this base name For example if the Job Name is LYS the Run Number is 04 and the starting Frame Number is 000 assuming that the number of characters in a Run Number is set to 2 and number characters in a Frame Number is set to 3 in the CONFIGURE EDIT panel the data files are named in sequence as L
506. rompt for additional input The SHUT TER item in the goniometer status area at the lower right of the display is updated to reflect the new shutter status GADDS supports an optional high precision rotary shutter This shutter is intended for use with rotating anodes and synchrotron sources The normal Bruker shutter on sealed tube sys tems is perfectly adequate for acquiring high quality data as is However in the case where the high precision shutter is added to a sealed tube system with existing shutter GADDS con M86 E01008 Collect Routines GADDS Software Reference Manual trols both shutters When shutter open close commands are issued from GADDS both shut ters are operated except in the cases of Collect gt Add Collect gt Scan gt commands SingleRun MultiRun Rotation etc Process gt Flood gt New Process gt Spatial gt New In these cases the safety old shutter is pre opened at the start of the command and is closed when the com mand has been completed Operations per formed between these two events for example collection of a frame series open and close only the high precision shutter 5 20 1 Arguments None Command executes immediately 5 21 Collect gt Goniometer gt Laser Turn on off the laser Menu Command Collect gt Goniometer gt Laser Accelerator Ctrl Shift L User Level 1 SLAM Syntax GONIOMETER LASER When invoked with the LASER option from the master menu
507. rompt in parentheses TARGET lt s gt X ray Target Material Cu Enter the standard 2 letter chemical symbol for the source target material Cu Mo etc if applicable Otherwise enter a short description of the radiation source The default target selection is Cu If you enter one of the recognized target types Cu Mo Ag Fe Cr or Co the X ray wavelengths in the following fields will be updated automati cally The value is stored in the header of output Bruker format frames and in output p4p files M86 E01008 Edit Routines GADDS Software Reference Manual WAVELENGTH lt n gt X ray Source Wave length 1 541838 ALPHA2 lt n gt Alpha 2 1 54439 Enter the Ka2 X ray wavelength in Ang Enter the weighted average X ray wave length in Angstroms The default value is based on the default target Cu and is set at 1 541838 A This value is automatically updated when the target is re entered if the target is one of the known types Cu Mo Ag Fe Cr or Co It is important that you update this entry whenever the source wavelength is changed The value is stored in the header of any output frames created in Bruker format and in output p4p files It is also used by the interactive cursor com mands all the Reflection Array commands that deal with crystal orientation Peaks commands and Stress commands ALPHA1 lt n gt Alpha 1 1 54056 Enter the Ka1 X ray wavelength in Ang
508. round ais i 16 C16 reserved for expansion 12 C ASCII compound name ui rEaNSI 16 C12 reserved for expansion Offset Code Description for Area Detector Parameters record 2 Offset Code ee for Comment 5 a record ype 200 area deiedior SRO parameters K record type 140 comment 4 14 record length 72 bytes 14 record length variable number of 3 C8 reserved bytes 16 R4 integration range 2T start 8 C __ ASCII comment stored without nul gi heal termination 20 R4 integration range 2T end 24 R4 integration range chi start or chi angle 28 R4 integration range chi end or height Offset Code Description for Removed Data 1000 0 record 32 14 normalization method 1 avg 2 arc 0 14 record type 150 removed data for length Sol angle tabin search 36 C20 program name i e GADDS NT ver 4 14 record length 32 bytes 9 901 8 R4 excluded 2 theta start in degrees 38 R4 actual athera of goniometer 12 R4 excluded 2 theta end in degrees ee R4 actual omega of goniometer 16 14 obs number of points in this part ot R4 actual phig goniometer 20 C12 reserved for expansion 68 as actual chi goniometer M86 E01008 GADDS Software Reference Manual DIFFRAC S Raw Data File Format RAW_DATA The data records immediately fol low the range header and supplementary range headers if any The data is stored as counts in R4 format Should non standard varying param eters be used then each data record is com prised
509. rs and are not typed lt n gt signifies that a number is required FRMFIX filename AXIS lt n gt NALUE lt n gt BIGCCD BIGCCD Updates frame header of CCD frames col lected under SMART v4 040 to specify large CCD detector instead of small CCD M86 E01008 GADDS Software Reference Manual Utility Programs 13 2 Frm2Frm FRaMe to FRaMe file format conversion utility Frm2Frm is useful to import of export frame data files to other programs Frm2Frm converts to and or from e Bruker frame format ASCII header BINARY counts ASCII overflow table e Bruker ASCII frame format ASCII header ASCII counts e TIFF CHESS format BINARY header BINARY counts It can also convert to but cannot read these file formats e Small Bruker frame format half size that is 1K gt 512 e JPEG courtesy of Larry Finger And finally it can also convert from but cannot write these file formats e Bruker new frame format ASCII header BINART counts Overflow tables e APS frame format ASCII header BINARY counts e TIFF MMX MarCCD frame format BINARY header BINARY counts FRM2FRM only requires the names of certain files as user input The user has the option of entering all filenames on the command line or leaving the command line blank and having the program prompt the user for all filenames Wild cards are permitted in filename inputs Syntax for command line console version o
510. rsors Odd values are better than even ones since the extra thickness is then added symmetrically about the true cursor posi tion Analyze gt Cursor gt Pixel can display HKL indi ces corresponding to the cursor position based on the current orientation matrix that is the one refined in the last Crystal gt LS command These values will be correct for frames acquired with GADDS and for Bruker format frames in general They will probably NOT be correct for XENGEN 1 3 format multi wire detector frames acquired data collection software earlier than FRAMBO V2 since those frames do not contain the required setting angle information If logging is turned on see the File gt LogFile command for more information the quantities M86 E01008 Analyze Routines GADDS Software Reference Manual computed for the final position of the cursor prior to exiting the command are written to the output logfile as are the values in each 17x17 numeric pixel dump If scripting is enabled see File gt ScriptFile a non interactive CURSOR com mand corresponding to the final cursor position is written to the output script file The SLAM command arguments are 1 X coordinate in pixels of the crosshair cen ter The range is from 0 to framesize 1 default value is 256 2 Y coordinate in pixels of the crosshair cen ter The range is from 0 to framesize 1 default value is 256 DELAY lt n gt Specifies a time interval to
511. rtain printers and file formats Format Description 1 Native NT driver default value 0 PCL4 printers such as the HP LaserJets 1 Monochrome TIFF files 2 Monochrome PostScript files and printers 3 PCL4 color printers that is HP PaintJets 4 Color PostScript Level 2 files and printers that is Tektronix Phaser II and HP1200C PS 5 Color TIFF files 6 BMP files 7 Codonics printer TIFF and BMP files are printed in portrait orientation while all other output formats use landscape orientation to make maxi mum use of the page THRESHOLD lt n gt Threshold 16 GREYSCALE Highest Resolution Specifies the minimum number of counts to be plotted as black Higher thresholds cause the printout to look less black lower thresh olds cause it to look more black Threshold is ignored for color plots Yes For PCL5 printers specifies that any counts at or above the threshold are black Counts between zero and the threshold are printed in a 25 greytone If absent on the com 22 M86 E01008 GADDS Software Reference Manual File Routines mand line or specified as N in the input panel all counts below the threshold are printed as white For color PCL4 printers specifies to print using 16 colors If absent on the command line or specified as N in the input panel prints in black white with all counts below the threshold printed as white Colors are approximated with the near
512. rtask ini with this file rename to user task ini Then you will see these old Peaks commands under the User heading NOTE If you cancel or get an error message the message is displayed below and the pro gram stays in command mode you must type menu While it is possible to write script files with error handling so MENUMODE is always executed then you don t see an error message PEAKS has twelve subcommands EXIT AUTO CLEAR LOAD MANUAL POSTER PROFILE REFINE SAVE SIMULATE VIEW ZOOM Close the PEAKS submenu and return to the GADDS menu Automatically locate and refine peaks Clear pattern graphs in selected quadrant s Load PKS file Manually select peak positions and parameters Annotate screen before printing Define peak profile shapes Refine peak parameters after manual editing Save peak table to disk file Simulate peak profile shapes View the current peak parameter table Select new plotting limits M86 E01008 GADDS Software Reference Manual SLAM Routines When you start PEAKS from the command line you need to specify one of these subcommands as a qualifier if not the submenu appears and GADDS waits until you have made a selection To select one of these options highlight it with the arrows or mouse A help message appears on the bottom status line describing the action taken by the selected item To start the selected option press ENTER To exit and return to t
513. s 1 Asthinwiievienecs PDF Number 33 1161 The PDF number is defined by a set number and a pattern number These numbers can be separated by a space a comma ora dash i e 33 1161 83 1161 or 33 1161 are all valid PDF numbers LEER er eeeeee ee Print Device SAXISPRINTER Enter either the filename or device which is to receive the printout The default device is SAXISPRINTER which you can define as a logical name to point to a file or device if desired For example the DOS command M86 E01008 GADDS Software Reference Manual Special Routines SET SAXISPRINTER PRN would direct output to a parallel printer Alternatively you can just enter the output name directly in the input panel for example PRN If you specify a filename the system prints to disk creat ing a file with that filename on the system hard disk which may later be output directly to a printer without having to run GADDS Under DOS a command like COPY B lt file name gt PRN would copy your output file to a parallel LaserJet printer NBS AIDS Format No Information about each diffraction pattern is stored in NBS AIDS format on the CD ROM see the ICDD JCPDS NBS AIDS83 man ual for more details Users can choose to view the complete NBS AIDS image format or view the pretty format which is much easier to read The output is in 80 columns ITYPE lt n gt 06 Data type 3 The D
514. s available All pixels selected within the amor phous only region are used to solve for a 2nd order polynomial using a least squares tech nique bkg a a4 X a2 y a3 Xx a4 X y as y With the separation of amorphous and crystal line contributions the percent crystallinity calcu lation is simply LT I C 100 _ Io A C where C percent crystallinity lo 0bserved intensity Ic calculated background C over crystalline region A C over amorphous and crystalline region 7 15 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 Two Theta Begin for Amorphous Reg 2 Two Theta End for Amorphous Reg 3 Chi Begin for Amorphous Region 0 M86 E01008 Analyze Routines GADDS Software Reference Manual 4 Chi End for Amorphous Region 360 Defines conic region for amorphous region 5 Two Theta Begin for Crystalline Region 6 Two Theta End for Crystalline Region 7 Chi Begin for Crystalline Region 5 8 Chi End for Crystalline Region 355 Defines conic region for crystalline region LINEAR ooien Linear Algorithm Y N Yes Use to specify either a linear amorphous func tion underneath the crystalline peak or a poly nomial function COMPTON Compton Scattering Y N No Enter Y to subtract the Compton scattering ef
515. s computed as the average of the points on the perimeter of the box excluding those points which are more than 3 standard deviations above the mean You have to be careful to choose the correct box size since in some cases the X Y centroid of the x ray reflection may change as a function of scan angle While the program attempts to graph the inten sity as a function of scan angle if the scan angle is not available in the frame headers or if the frame headers all contain the same value for the scan angle the intensity is graphed as a func tion of frame number When invoked with the ROCKING option from the GRAPH submenu or when run from the command line without arguments GRAPH ROCKING displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins interactive region of interest selection with a box cursor The ESC key or right mouse button returns you from the input panel to the GRAPH submenu When you re selecting a region of interest a rectangular cursor from 2x2 to 128x128 pixels in size appears in the detector frame area and can be moved or re sized under control of the mouse and or keyboard arrow keys The arrow keys are very useful for precise 1 pixel adjust ments Pressing the ENTER key or left mouse M86 E01008 Analyze Routines GADDS Software Reference Manual button computes the intensity versus scan angle curve and dr
516. s from 1 to 65 535 seconds Times can be entered in decimal seconds or in HH MM SS SS hours minutes and sec onds format Data collection ends when the specified time has elapsed or when the maximum count limit see MAX COUNTS below has been reached COUNTS lt n gt Max Counts 10 000 000 This qualifier sets an upper limit on how many counts may occur before data collec tion is terminated When the specified num ber is reached the system ends the data collection saving the data frame The default value is 10 000 000 counts with a range from 0 to 10 counts Data collection will also be terminated if MAX SECONDS is reached before MAX COUNTS DISPLAY lt n gt Max Displayed Counts 100 0 no display otherwise counts corre sponding to white on the display The initial default is 100 the allowed range is from 1 to 108 REALTIME Realtime Display Y N This qualifier when present displays data as it is being collected The display does require additional processing time and will limit the maximum rate at which counts can be accumulated If the MAX DISPLAYED COUNTS qualifier is given a non zero value the frame will be automatically displayed at the end of the frame collection if realtime display is off This latter display method has no effect on observed data rate Since the data rate in Fe source frames is not very high use of REALTIME with FLOOD NEW will rarely cau
517. s the output easily interpretable Third the format is highly portable because dif ferent byte and word ordering conventions don t enter into the interpretation of ASCII data Items currently contained in the header are listed below in positional order The format is expand able New information to be added to the header will always be added at the end A version num ber is present at the start of the header so pro grams can deal with new header information M86 E01008 Area Detector Frame Format GADDS Software Reference Manual The header items are Mnemonic Offset Version Type Description FORMAT 0 1 Int Frame format Always 86 for Bruker format frames or 100 for New Bruker format frames VERSION 1 1 Int Header version such as 1 2 3 4 5 7 8 9 10 or 11 HDRBLKS 2 1 Int Header size in 512 byte blocks such as 10 or 15 TYPE 3 1 Cc String indicating king of data in the frame Valid primary types are DEFAULT Add frame Rotation frame SCAN FRAME UNWARPED UNWARPED LINEAR FIDUCIAL PLATE FLOOD FRAMES FLOOD TABLE BACKGROUND lt A gt amp lt B gt COMBINATION POLE FIGURE POLAR STEREO WULFF STRESS SCHEME Sometimes the primary type is appended with CALIBRATED FIBER LPA MULT_FF PLATE SMOOTHED Pole figure type may be appended with INTERPOLATED INVERTED NORMED ROTATED SCHEME SYMMETRIZED TILTED A 4 M86 E01008 GADDS Softwa
518. s between character insert and over strike modes when editing a line in a dialog box DEL Deletes forward one character when editing a line in a dialog box The character under the cursor is deleted Backspace Deletes backward one character when edit ing a line in a dialog box The character to the left of the cursor is deleted HOME Moves to beginning of line when editing a line in an input panel END Moves to end of line M86 E01008 General Information GADDS Software Reference Manual F2 F3 F4 In interactive commands these are equiva lent to left center right mouse buttons respectively CTRL C In a dialog box edit control copies high lighted text to the clipboard CTRL X In a dialog box edit control cuts highlighted text to the clipboard CTRL V In a dialog box edit control pastes from the clipboard CTRL P Prints main GADDS screen to currently selected printer Under NT this function does not work when the user is in a dialog box or message box however PRTSC will send a copy of the entire screen including GADDS window or ALT PRTSC for just active window to the clipboard M86 E01008 GADDS Software Reference Manual General Information 1 6 GADDS Directory Organization GADDS s directory organization as shipped from the factory is shown below We recom mend that you maintain this directory convention for Bruker supplied files to minimize the effort
519. s from which you can select the desired correction see DISPLAY NEW for a more complete description of filename selection The default filespec for filename selection is Frame_root _FL where Frame_root is the frame directory specified in the CONFIGURE EDIT panel The special filename of 6DEFAULT is replaced with the standard naming conven tion of SIZE_DDD _FL where SIZE is M86 E01008 GADDS Software Reference Manual Process Routines replaced by 0512 or 1024 and DDD is replaced by the detector distance in cm 6 3 Process gt Flood gt Reprocess Generate a new table from previous projection data on disk Menu Command Process gt Flood gt Reprocess Accelerator none User Level 3 SLAM Syntax FLOOD REPROCESS 1 2 XMIN lt n gt YMIN lt n gt MAG lt n gt This command is used to reprocess an existing flood field file projection file to use it with differ ent X Y or magnification settings The XMIN lt n gt YMIN lt n gt and MAG lt n gt arguments described below allow you to create a flood field table that results in 512x512 or 1024x1024 output data frames that correspond to a specific area of the detector rather than to its entire area For this calculation the full detec tor is considered to be an array of 16376 x 16376 bins Its origin is by default coincident with the output frame origin and its bins are by default summed in 32 x 32 blocks
520. s the current peak parameter table The peak parameter table is created with either AUTO or MANUAL It is modified with MANUAL and REFINE and may be destroyed with CLEAR When started from the command line VIEW takes no arguments PEAKS VIEW 12 4 11 PEAKS ZOOM ZOOM lets you rescale the currently displayed raw data pattern with new axes Both the upper left corner and lower right corner of the graph must be specified Enter the new values or select them with the mouse Interactively press R to restore the graph to full axes When started from the command line PEAKS ZOOM takes the following arguments PEAKS ZOOM 1 2 3 4 RESTORE Each argument is listed below by its command line name followed by its input panel prompt in parentheses 1 ZOOM 2T LEFT 2 ZOOM 2T RIGHT 3 ZOOM I MIN 4 ZOOM I MAX RESTORE RESTORE Y N overrides 1 4 and restores to original axes 12 24 M86 E01008 GADDS Software Reference Manual SLAM Routines 12 5 Ratemeter Menu Command None Accelerator None User Level Command SLAM Syntax RATEMETER 1 RESET lt n gt SHUTTER The ratemeter option of Collect gt Goniometer gt Manual command is available in command mode See Collect gt Goniometer gt Manual Section 5 11 for more details Each argument is listed below by its command line name GA escrito max seconds 9999 Enter maximum number of seconds for exposure RESET lt n gt Re
521. s the resulting reduced primitive unit cell with parameters in the order A B C Angstroms ALPHA BETA GAMMA degrees If verbose output has been specified a list of the difference vector groups follows A line for each group contains the group number its length in Angstroms its reciprocal lattice components and the number of difference vectors in the group A linear least squares is then performed to refine the parameters of the reduced primitive cell with the refined parameters displayed in the same order followed by the unit cell volume in cubic Angstroms These values and their stan dard deviations are automatically transferred to the BRAVAIS sub command input panel for subsequent determination of the BRAVAIS lat tice based on the metric symmetry of the reduced primitive cell If verbose output was specified the least squares result is followed by a list of the input full vectors with their calculated HKL indices A line for each vector contains the vector number the number of the vector closest to it i e the one which yielded the smallest difference vec tor the calculated HKL indices expressed as real numbers if these values are not close to being integers something is wrong most should be within 0 1 of an integer value and the corre sponding reciprocal lattice vector components Example 2 below is sample output from the same indexing run displayed in the second out put window following re indexing
522. se any loss in counting effi ciency and you can keep this set to Y While real time display is active change the upper display limit using the plus key to increase or the minus key to decrease the current limit by a factor of two The range is 7 to 524287 Modify the contrast using the left and right arrow keys Modify the bright ness using the up and down keys Hold down the control key and an arrow key to increase the change of contrast or bright ness M86 E01008 GADDS Software Reference Manual Process Routines FILES anas Output Filename normal _fl Enter the filename for the output correction data By default output files are created with a _fl extension in the frame directory specified in the CONFIGURE EDIT input panel More specifically the filename you enter here is merged with the default filespec Frame_root _fl where Frame_root refers to the directory in the CONFIGURE EDIT panel See CONFIGURE EDIT for details on how filenames are merged The intermediate X and Y projection arrays are stored similarly but with a _pj extension In menumode the filename is defaulted to the standard naming convention of SIZE_DDD _FL where SIZE is replaced by 0512 or 1024 and DDD is replaced by the detector distance in cm IXMIN lt n gt 006 Lower X of Corrected Frame 0 Enter the X detector bin number to use as left side of corrected frame The default valu
523. sers and a GADDS administrator project file for only the account that installed the GADDS software GADDS locates the project file by translating the environment variable GADDS PROJECT which contains the com plete file specification of the project file for example D frames projects gadds prj SETUP creates this environment variable in the System Variables space to create the system wide project file You may override the system wide setting by creating a user specific project file as follows 1 Start gt Settings gt Control Panel gt System applet Click on the Environment tab Click on a line in the User Variable for lt User gt section 4 Inthe Variable edit box enter GADDS PROJECT 5 Inthe Value edit box enter the full file spec ification The drive and directory path must already exist Bruker recommends using our naming convention of D frames projects GADDS_ lt user name gt prj you replace lt username gt with your actual user account name 6 Click on Apply M86 E01008 Project Management Routines GADDS Software Reference Manual 7 Click on OK Because initially there is no project file the first time GADDS is started you will see several messages Unable to open project database file for reading GADDS PROJECT Unable to use last project Each time GADDS is started the current project database is checked for orphaned projects NOTE Remove
524. ses 0 or for 4 circle sys tems 30 4 EEEE Base Chi Enter the home chi value in degrees for optical alignment Default is current setting Typically one uses the fixed chi value of 54 74 45 on Aztalan or for T 1 4 circle systems 54 74 for R 1 4 circle systems 54 74 or for 4 circle sys tems 330 AT 2T OM PH CH Fast Slow Ratio 14 Enter the slew speed to slow speed ratio for manual control box Default is 14 The man ual control box allows driving at two speeds The fast speed for each axis corresponds to the speed set in Collect gt Goniometer gt Speeds The slow speed will be that of the fast speed divided by this number The ratio used is the same for each axis This param eter has no effect on Phoenix controllers D8 Discovery systems which has a fixed slow speed varies varies M86 E01008 GADDS Software Reference Manual Collect Routines PO iia X Y Fast Slow Speed Ratio Enter the slew speed to slow speed ratio for manual control box Default is 14 This parameter has no effect on Phoenix control lers D8 Discovery systems which has a fixed slow speed G7 anana Z Fast Slow Speed Ratio Enter the slew speed to slow speed ratio for manual control box Default is 14 This parameter has no effect on Phoenix control lers D8 Discovery systems which has a fixed slow speed G8 PERETE TET Aux Fast Slow Speed Ratio Enter the slew speed to slow speed ratio
525. set base 10 or 36 see CON FIGURE form SFRAMENO Slave Frame 000 Enter starting frame base 10 or 36 see CONFIGURE form For multirun data collections on dual detectors only the job name is additional SNAME 0 005 Slave Job name NEWFRA2 Enter base name for frames Should be dif ferent from the Master s job name Before starting data collection the Master will update the Slave with new values for title sam ple sample number display counts real time pre clear xengen output oscillate and name Before each frame series the Master will update the Slave with new values for of frames time set and frame no Finally while collecting indi vidual frames the Master communicates to the Slave when to prepare for next frame queue the drive request collect frame and save frame or retry collecting the same frame The user must ensure that the frame naming conventions for both the Master and Slave will produce unique filenames This becomes crucial whenever both the Master and Slave collect frames directly to the same host computer direc tory Also while the Master will prompt to over write the first frame the Slave will always overwrite any existing frame files NOTE This command is not available on theta theta systems 5 45 1 Arguments Each argument is listed below by its command line name followed by its input panel prompt in parentheses GA rich eed lees Num
526. set Interval 0 5 Enter number of seconds between read outs SHUTTER Open amp Close Shutter No Check to open shutter before and close after this command 12 6 Spawn Menu Command None Accelerator None User Level Command SLAM Syntax SPAWN SPAWN is available in command mode at the GADDS gt prompt Use this command to spawn another program but unlike the SYSTEM com mand GADDS is not suspended until the spawned command terminates Each argument is listed below by its command line name GV ect N Command See system command M86 E01008 12 25 SLAM Routines GADDS Software Reference Manual 12 7 Video Live Menu Command None Accelerator None User Level Command SLAM Syntax VIDEO LIVE Use this command to place the VIDEO program into live video mode This command executes immediately without any arguments 12 8 Video Freeze Menu Command None Accelerator None User Level Command SLAM Syntax VIDEO FREEZE Use this command to place the VIDEO program into frozen video mode This command exe cutes immediately without any arguments 12 26 M86 E01008 GADDS Software Reference Manual SLAM Routines 12 9 Wait Menu Command None Accelerator None User Level Command SLAM Syntax WAIT 1 WAIT is available only in command line mode at the GADDS gt prompt WAIT suspends execution of the program for a specified time If you press ENTER
527. setting On 0 0 systems this is the 61 angle tube OMEGA lt n gt Omega 0 00 THETA2 lt n gt Theta2 0 00 The omega angle in degrees at which GADDS positions the goniometer at the start of the frame series scans If you spec ify a scan axis see AXIS lt n gt below of 2 omega will be scanned as each frame is taken Otherwise omega remains fixed throughout the frame series Valid values are 360 to 360 but are typically reduced by the current software collision limits as defined in Collect gt Goniometer gt limits command Entering will be automati cally replaced with current angle setting On 0 0 systems this is the 62 angle detector PHI lt N gt veeeseeeseeee Phi 0 00 The phi angle in degrees at which GADDS positions the goniometer at the start of the frame series scans If you specify a scan axis see AXIS lt n gt below of 3 phi will be scanned as each frame is taken Otherwise phi remains fixed throughout the frame series Valid values are 360 to 360 but are typically reduced by the current software collision limits as defined in Collect gt Goni ometer gt limits command Entering will be automatically replaced with current angle setting M86 E01008 Collect Routines GADDS Software Reference Manual CH ee Chi 0 00 The chi angle in degrees at which GADDS positions the goniometer at the start of the frame series A Platf
528. si tilt of GADDS data is saved as the chi value for DIFFRAC SSTRESS As such DIFFRAC SSTRESS will process GADDS data as if it were collected in side inclination mode although the GADDS data was collected in iso inclination mode This will not change the stress result as long as the absorption and polarization corrections are not performed in DIFFRACP SSTRESS These corrections can be made in GADDS before data processing with DIFFRAC SSTRESS Verify that those correc tion functions are disabled when analyzing GADDS data with DIFFRAC SSTRESS 7 33 5 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Geeta ketene 2 theta start 0 0 Enter lower 2T of conic region in degrees GO saute seus zach 2 theta end 30 0 Enter upper 2T of conic region in degrees GB TAEAE Chi start 0 0 Enter lower chi of conic region in degrees M86 E01008 Analyze Routines GADDS Software Reference Manual 4 sedate Chi end 860 0 Enter upper chi of conic region in degrees NORMAL lt n gt Normalize intensity 3 Normalize intensities 0 none 1 avg 2 arc length 3 solid angle 4 bin method STEPSIZE lt n gt Step size 0 1 Enter step size in degrees 2THETA lt n gt Peak 2T 156 0 Enter peak 2T for calculations Poean a Title TITLE Enter title string or TITLE to leave unchanged FILENAME lt
529. sidual inten sity is below PEAKSIG times standard deviation The standard deviations generated by AUTO are measures of the precision of the refined param eters Systematic errors such as 20 zero error sample positional error and absorption must be taken into account PEAKS MANUAL is used to interactively choose peaks and their parameters The most frequent use of MANUAL is to correct any shortcomings of PEAKS AUTO which is known to have diffi culties whenever the scan range begins or ends within a peak and with extremely complicated patterns with more than 15 overlapping peaks MANUAL lets you enter all peak and back ground data as well as variables you want to refine After entering or modifying peaks param eters with MANUAL PEAKS REFINE performs a least squares fit of all variable parameters Very accurate results can be obtained from user specified peaks The final peak parameter table can be saved to an ASCII file with PEAKS SAVE Also PEAKS VIEW re lists the current peak parameter table on the screen The ASCII peak parameter files consist of three sections General header with file date title wave lengths and range e Peak data table with ds 2Ts Is Irel and FWHMs Background data table with 2T start and end of each region and backgrounds Full visual screen control is accomplished with PEAKS CLEAR Screen text windows can be cleared or the raw data trace peak profiles or both can be cleared from an
530. sition offset from upper left corner in screen pixels A value of 1 default will center GADDS in the screen display M86 E01008 General Information GADDS Software Reference Manual 1 4 GADDS Startup Behavior When GADDS is started the program goes through many checks to determine the operating state of the program 1 Command line qualifiers and environment variables are used to override or set the default behavior All environment variables must be defined prior to starting GADDS The working directory is defined By default GADDS uses the last project s working directory unless the command line qualifi ers noproject or project projname are present If the last project does not exist not defined an error occurred or noproject was used then GADDS will prompt the user to define a new project which includes defining the working directory The program default settings are defaulted or read By default the configuration is read from the project s working directory gadds _nc If error or noreload is present from the GADDS system directory GADDS SYSTEM gaddsdef _nc On complete failure the hard coded defaults are used The names of the normal configu ration file and the default configuration file can be changed using configuration lt file name gt and default lt filename gt command line qualifiers Diffractometer communications with the goniometer controller is initiated On P4 sys t
531. sively That is if the bitmask is define the octagon mask is ignored and visa versa 8 6 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 512 mode_ 1024 mode Defaults Defaults 1 MIN X 0 0 2 MIN X Y 60 120 3 MIN Y 0 0 4 MAX X Y 451 902 5 MAX X 511 1023 6 MAX X Y 962 1924 7 MAX Y 511 1023 8 MAX Y X 451 902 Enter requested values in frame pixels M86 E01008 GADDS Software Reference Manual Peaks Routines 8 7 Peaks gt Integrate gt Chi Perform chi integration in conic region gt F 2T Menu Command Peaks gt Integrate gt Chi Accelerator None User Level 1 SLAM Syntax INTEGRATE CHI 1 2 3 4 NORMAL lt n gt STEPSIZE lt n gt INTEGRATE CHI will integrate a region along the chi direction and plot the results as intensity versus 2 theta The resulting trace may be writ ten to a file using INTEGRATE WRITE com mand or inputted into the PEAKS LOAD command The area to integrate is defined by specifying the 2 theta and chi range for the Debye Scher rer cone Chi zero is defined at 6 o clock and goes CCW Interactively the user may redefine any of the integration region s limits by selecting the limit s line number 1 to 4 and then using the cursor keys The current integration region limits are co
532. solving overlapping peaks and refining the position intensity and FWHM of all peaks If the selected profile line shapes have a removed AUTO can refine both the a and a lines simultaneously providing the resolution of the overlapped amp line with an unrelated line as in the five fingers of quartz region AUTO first dissects the scan range into multiple regions which include data points of at least BKGDSIG standard deviations above background Each region must start in background and end in background or the peak s are not found in this case you must use PEAKS MANUAL to locate peaks Each region has a maximum number of steps cur rently 1024 and a maximum number of allowed peaks 15 You may have to manually manipu late regions with numerous overlapping peaks For each region the background is assumed to be a linear function in 20 Least squares esti mates of the left and right backgrounds are per M86 E01008 SLAM Routines GADDS Software Reference Manual formed With the removal of background the largest remaining sample point is compared to PEAKSIG times the standard deviation of that point Values greater than this quantity result in a peak being added Least squares estimates are performed on peak position FWHM and intensity as well as the backgrounds GADDS then reiterates identifying and removing the largest peak from the remaining data until either 15 peaks are found or the largest re
533. spots with an X centroid between the value specified as KEXMIN above and the value specified here This is useful for excluding the area near the beam stop The value is in pixels in the Bruker coordinate convention with X Y 0 0 at the lower left of a displayed frame RMAX lt n gt Radius Cutoff 265 Enter the maximum allowed distance of a reflection centroid from the detector center in pixels Reflections which exceed this value are rejected Valid range is from 0 to 300 DMIN lt n gt Minimum Angstroms 1 5 Enter the minimum allowed interplanar spacing in Angstroms corresponding to a reflection centroid Reflections at higher M86 E01008 GADDS Software Reference Manual Peaks Routines better resolution than the value specified here are rejected DMAX lt n gt Maximum Angstroms 100 DBIAS lt n gt Temperature Factor Enter the maximum allowed interplanar spacing in Angstroms corresponding to a reflection centroid Reflections at lower worse resolution than the value specified here are rejected 10 Enter the B factor in Angstroms used to bias the I sigma threshold test as a function of resolution I SIGMA computed for each reflection is multiplied by EXP DBIAS S where S is sin theta lambda If the result is lower than the value specified as SIGMA see above the reflection is rejected AE 2 Theta override 9999 Enter th
534. st of the current filenames matching the pattern You can choose one from the displayed list by moving to it with the arrow page keys or mouse and pressing ENTER or the left mouse button You will be returned to the input panel with the selected filename filled in If you leave this item blank it is the same as entering a _ix wild card pattern Both filenames and patterns entered here are merged with the CONFIG URE EDIT frame directory as described above XENGEN 4 Xengen Output Format Y N No In the input panel enter Y to write the out put _br frame in XENGEN format more correctly in the old PCS computer format N otherwise The default selection is N Bruker format While the Bruker format will be used increasingly in later releases you need to be sure that your data reduction package will support it before using it If you re not sure whether your data reduction package will read Bruker format it is proba bly safer to specify Y here THRESHOLD lt n gt Threshold 8 0 When extracting fiducial spots from the brass plate image the I sigma l i e inten sity divided by its standard deviation of each spot is computed based on counting statistics Spots with an I sigma l less than the value specified here are considered to be background fluctuations and are ignored The default value of 8 should be satisfactory for brass plate images with 80 000 to 100 000 total counts se
535. stem to normalize intensi ties DISPLAY lt n gt Max Display Counts 16 Enter 0 if you do not want the correction frame displayed any other number selects display and is used to set the white level of the display M86 E01008 GADDS Software Reference Manual Process Routines XENGEN 0006 Xengen output format Y N no In the input panel enter Y to write the out put frame in XENGEN format more cor rectly in the old PCS computer format N otherwise The default selection is N Bruker format If you re going to use these frames as input to GADDS use N here NOBEAMCENTER Suppress Unwarping Beam Ctr Y N yes Normally SPATIAL UNWARP overwrites the X Y beam center coordinates stored in the output frame header with the spatially corrected values NOBEAMCENTER sup presses the update of the beam center in the output header In GADDS where the beam center may already be unwarped NOBEAMCENTER is usually required while in FRAMBO where the beam center is always stored in warped coordinates this option is left off The default in the input panel is Y M86 E01008 Process Routines GADDS Software Reference Manual 6 11 Process gt Corrections gt LPA Menu Command Process gt Corrections gt LPA Accelerator none User Level 2 SLAM Syntax CORRECTIONS LPA 1 2 3 MONOCHROMATOR lt n gt AIRMU lt n gt NOREVERSE Calculate and a
536. sub command however the precision of the resulting cell parameters and orientation will not be as good as if centered reflections were used Autoindexing is performed with the algorithm developed by Sparks operating on difference vectors derived from the input reflections Differ ence vectors are classified into groups based on a specified input tolerance Any group formed from fewer than 1 difference vectors where 1 is specified on input as defined below is ignored Up to 100 such groups are used by the program This is a very reliable indexing tech nique If indexing on difference vectors fails the program tries indexing on the full vectors how ever the difference vector approach is more reli able and if it fails the full vector approach will seldom succeed If for some reason the pro gram cannot find a solution check for one of the following 1 Prior to taking data on a new sample including new flood field and spatial correc tions make sure you have entered the cor rect sample detector distance and correct X Y beam center in the CONFIGURE EDIT panel REFL_ARRAY INDEX displays the current X Y beam center coordinates in its input panel title bar for your review Don t guess at the beam center measure it from an image taken with after removing or repo sitioning the beam stop make sure the direct beam is suitably attenuated before trying to record it or you could damage the detector The 0 060 aluminum cove
537. sulting reduced primitive unit cell parameters and their standard deviations in the BRAVAIS input panel and you can usually invoke BRA VAIS without changing any of the input panel values The goodness of fit is a measure of how well a trial Bravais lattice fits the input unit cell parame ters Lower values are better The scale is arbi trary this is NOT a true least squares goodness of fit don t expect values near 1 but in general good solutions will have values less than 10 The input panel allows you to set two different thresholds on the goodness of fit The first is the threshold below which a solution is listed in the output The second is the threshold below which a solution can be flagged as the best solution The highest symmetry solution whose goodness of fit is below this second threshold is marked as the best solution The default values are 20 and 6 respectively for these thresholds and they should work well in most cases M86 E01008 Peaks Routines GADDS Software Reference Manual The possible Bravais lattices determined by the program are Program Output Description CUBIC F Face centered cubic CUBIC Body centered cubic CUBIC P Primitive cubic RHOMBOHEDRAL OBV HEXAGONAL R Rhombohedral on hexago SETTING nal axes TRIGONAL P NO C AXIS SYMMETRY HEXAGONAL P C AXIS Trigonal nexagonal SYMMETRY TETRAGONAL TETRAGONAL P ORTHORHOMBIC F ORTHORHOMBIC ORTHORHOMBIC C ORTHORH
538. supported by GADDS TITLE lt S gt 0 0 Title TITLE Enter title for output frame 72 characters maximum If you re invoking File gt Save from the command line you must enclose titles containing imbedded blanks in double quotes The special TITLE will default the title to the current title string The default is TITLE FILE lt filename gt will read up to eight 72 character title lines from an ASCII file and place these title strings into the eight TITLE lines in the frame header The for mat of the ASCII file is R lt single line of title information gt where R is the run number taken from the filename Repeat up to eight times for each run XENGEN aaaea Xengen Format Y N No Check this option to write frame in XENGEN 1 3 more correctly in the old PCS computer format The default is unchecked Bruker format This option is rarely used By default it is unchecked DISPLAY lt n gt Max Displayed Counts 0 Enter 0 for no display otherwise this item specifies the number of counts mapped into the maximum display memory value for example corresponding to white on the dis play The special value 1 directs the pro gram to pick a reasonable value by scanning through the pixels in the frame prior to display the special value 2 directs the program to use whatever setting is cur rently in effect The default value is 0 the allowed range is from
539. sure that you re getting uniform illumination The predominant low frequency feature in the image should be a reasonably symmetric radial falloff When the setup looks good make sure the detector distance and beam center are correctly set in the CONFIGURE EDIT input panel then take a good 10 000 000 count flood field image with the shutter control option set to Y When invoked with the NEW option from the FLOOD submenu or when run from the com mand line without arguments FLOOD NEW displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins collection of flood field data with subsequent automatic computation and installation of a new flood field correction the ESC key or right mouse button returns you to the FLOOD submenu You can interrupt a flood field data collection in progress with the CTRL BREAK key combination however the current flood field correction at that point is undefined either re collect new data or restore the correction to a known state with the FLOOD LOAD or FLOOD LINEAR command M86 E01008 Process Routines GADDS Software Reference Manual 6 1 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses DA E VEES EAA PE TA Max Seconds 15 00 This is the maximum count time in sec onds The default value is 900 the range i
540. system manager or Bruker service personnel use this command This command subtracts the specified amount to the encoder zero of the specified axis For example entering a value of 0 05 for omega will add 0 05 to all subsequent observed omega val ues The refined values for the omega and chi encoder zeros provide a general indication when encoder zeros need to be adjusted BUT BE VERY CAREFUL Because of the large number of parameters refined in the unit cell M86 E01008 Collect Routines GADDS Software Reference Manual least squares and the potential for coupling among parameters DON T CHANGE ENCODER ZEROS BASED ON THE RESULT OF A SINGLE LEAST SQUARES Over time you ll get a general feeling whether your data sets for example all tend to indicate that the omega zero is high make adjustments based on average results accumulated over time The least squares zero adjustments are values that should be added to the angle zero so negate the value determined from least squares before entering it here 5 29 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses Gl AEAEE EEA 2 Theta 0 00 SEEE E AE Theta1 0 00 Enter the 2 theta encoder zero offset in degrees to be added to subsequent 2 theta values reported by the controller Or theta1 axis tube n eA cede eer Omega 0 00 A pel ATOT Theta2 0 00 Enter the omega encoder zero offset in
541. t X Begin 5 0 YBEG lt n gt Y Begin 5 0 Enter the starting point in mm for the line XEND lt n gt X End 5 0 YEND lt n gt Y End 5 0 Enter the ending point in mm for the line NNC lt N gt n nnnnnnn Y Incremen 1 0 Enter the increment in mm along the line TRANSMISSION Transmission mode X Y Y Z No Check for samples mount in transmission mode where you wish to grid in Y and Z axes APPEND Append to existing target list No Check for append new grid list to end of existing list of targets Unchecked will pre clear the target list M86 E01008 Collect Routines GADDS Software Reference Manual 5 43 Collect gt Scan gt EditTargets Edit parameters for MultiTarget scans Menu Command Collect gt Scan gt EditTargets Accelerator Ctrl Shft F 11 User Level 1 SLAM Syntax SCAN EDITTARGETS Use this command to create edit or review a target list of sample positions that you wish to acquire in a single run fashion where one series of contiguous frames are collected at each sample target position without interven tion Because target positions are unique to particu lar samples and to a particular mounting of that sample GADDS will not automatically load any previous target list However the user can easily save and load target lists from within Collect gt Scan gt EditTargets using the READ and WRI
542. t Clear command also provides a way to erase cur sors left over from NOERASE options The following output statistics are displayed on screen in real time and are also written to the logfile if applicable for non pole figure frames ORIGCNTS Counts of pixel at vector origin ENDPCNTS Counts of pixel at vector endpoint X ORIGIN X coordinate of origin in pixels Y ORIGIN Y coordinate of origin in pixels X ENDPT X coordinate of endpoint in pixels Y ENDPT Y coordinate of endpoint in pixels X MIDPT X coordinate of midpoint in pixels Y MIDPT Y coordinate of midpoint in pixels D PIXEL Length of vector in pixels D DEG Length of vector in degrees 2 theta M86 E01008 Analyze Routines GADDS Software Reference Manual D ANGST Length of vector in Angstroms CHI Angle of the vector in degrees clockwise from x This chi convention is the same as that used on a 4 circle diffractometer that is if the vector origin is at the beam center and the endpoint is on a reflection taken at omega 0 chi is the angle to which you would drive the goniometer to place the reflection in the equatorial plane on the pos itive 2 theta side Pole image frames are handled slightly differ ently On these frames the following output sta tistics are displayed on screen in real time and are also written to the logfile if applicable ORIGCNTS Counts of pixel at vector origin ENDPCNTS Counts of pix
543. t If logging is enabled see LOGFILE the contents of this win dow are also written to the logfile When viewing the output pressing ENTER or the left mouse button displays a pop up menu of options including export of ASCII data for example the contents of the window could be sent to a file or printer with this function You can also move through the window contents with the page keys arrow keys or with mouse motion Press ing ESC or the right mouse button exits the out put window The program then displays the prompt lt n gt SPOTS WILL BE INSERTED IN ARRAY AT lt M gt PRESS ENTER TO CONTINUE ESC TO QUIT where lt n gt represents the number of reflections found and lt M gt represents the line number of the first empty record in the Reflection Array If you press the ENTER key or left mouse button the program stores the thresholded reflections in the array then displays the Reflection Array in an editing window for review see REFL_ARRAY EDIT for description and operation of the edit ing window Pressing the ESC key or right mouse button at the above prompt or from within this editing window returns you to the REFL_ARRAY submenu The output window contents are described in more detail below If REFL THRESHOLD was invoked from the command line the output window is displayed subject to a 10 s timeout to allow command M86 E01008 GADDS Software Reference Manual Peaks Routines scripts to run w
544. t Save SLAM Syntax GRAPH POSTER SAVE This command will save all poster annota tions ina PLOTSO file on disk It can later be loaded with the Analyze gt Graph gt File command Menu Command Analyze gt Annotate gt Text SLAM Syntax GRAPH POSTER TEXT Text can be positioned and sized interac tively using GRAPH POSTER TEXT When selected the user must first enter the text string to be displayed All trailing spaces are removed from the text string but leading spaces are retained A box cursor will appear reflecting the size of the text string Position the box cursor then press ENTER or the left mouse button The box will disap pear the text will be drawn and the user will be prompted to enter the next text string to drawn Pressing ESC or the right mouse button will return you to the draw menu Pressing lt F1 gt or the center mouse button will toggle the size mode Moving the cursor left or right will increase or decrease the size of the text string in the x direction Up and down cursor movement will change the height of the text Press ENTER or the left mouse button to anchor the text size Menu Command Analyze gt Annotate gt Label SLAM Syntax GRAPH POSTER LABEL Spots or peaks can be labeled interactively with this command When selected a dialog box will appear Choose what type of data to retrieve either theta s 2 theta s d s I s or hkl s and choose where to retrieve that data from eit
545. t gt Detector gt X E vs X Accelerator none User Level 2 SLAM Syntax DETECTOR XEVSX Use this command to place the PDC and detec tor for X preamp calibration The action is per formed immediately with no prompt for additional input 5 7 1 Arguments None Command executes immediately M86 E01008 GADDS Software Reference Manual Collect Routines 5 8 Collect gt Detector gt Y E vs X e Set PDC for Y preamp calibration Menu Command Collect gt Detector gt Y E vs X Accelerator none User Level 2 SLAM Syntax DETECTOR YEVSX Use this command to place the PDC and detec tor for Y preamp calibration The action is per formed immediately with no prompt for additional input 5 8 1 Arguments None Command executes immediately 5 9 Collect gt Detector gt Custom e Enter values to be loaded into PDC setup registers Menu Command Collect gt Detector gt Custom Accelerator none User Level 3 SLAM Syntax DETECTOR PDCCUSTOM 1 2 3 Use this command to place the PDC and detec tor into a custom configuration Useful for testing purposes only 5 9 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses OTs cadet ne X ADC Source 0 Enter 0 for X position 1 for X energy 2 for Y position or 3 for Y energy DO ete hee ors Y ADC Source 2 Enter 0 for X position 1 for X energy 2 for Y position or 3 f
546. t Ctrl G gt and lt Ctrl Break gt The SLAVE frame processor accepts goniometer commands from the MASTER frame buffer and passes these through to the GGCS When GGCS status reports are received these are passed through to the MASTER frame buffer Thus in the default SLAVE mode the SLAVE frame buffer is simply a pass through device the MASTER frame buffer doesn t know or care if it s there This enables the MASTER frame buffer to collect flood fields and fudicial plate images or to operate in single detector mode Alternately the MASTER frame buffer may be placed in dual detector mode Here the MAS TER may send the SLAVE specific instructions begin collecting data stop collecting save image etc as well as control the GGCS how ever the user will only notice a few changes to the Scan menus see Scan Master command Only minimal information will be displayed on the Slave such as the drive shutter and attenu ator status the frame being collected and any repeat frame attempts By default the message Frame Buffer in SLAVE mode is displayed Errors during data acquisition or frame saves will terminate the Slave process and typically create a controller timeout error on the Master frame buffer M86 E01008 GADDS Software Reference Manual Collect Routines Before exiting slave mode terminate Gadds on the master frame buffer then on the slave frame buffer exit slave mode by typing lt Ctrl Break gt
547. t Management Routines 2 3 Project gt New Create a new project from scratch Menu Command Project gt New Accelerator None User Level 1 SLAM Syntax PROJECT NEW CNAME lt s gt 1 TITLE lt s gt WORKDIR lt s gt FORMULA lt s gt MORPH lt s gt CCOL lt s gt DENSITY lt s gt DENSMETH lt s gt Use this command to create a new project from scratch Typically whenever you mount a new sample or a new batch of samples you want to define a new directory for all your data files You must enter information in all the project information parameters The sample name and sample number are combined to form the project name If the generated project name is invalid the message appears Sample name and number are too long or contain non alphanumeric characters Name will be shortened modified as needed if you continue Click Yes to continue or No to return to dialog input box You must enter information in the directory infor mation parameters You may enter an existing directory but typically you enter a new directory and the program will create it You may enter the special value PROJECT which instructs the program to use the directory GADDS FRAMES YEAR MON lt projname gt which is typically defined as D frames 2003 Mar lt projname gt The advan tage of using PROJECT is that it automatically generates a directory name that should be unique If you try to re use a project directory
548. t be valid If this happens use the CONTRAST command to check the quality of the fiducial plate frame If the frame looks OK you can try re processing it with SPATIAL PROCESS with a different I sigma level for thresholding spots from the image Another possibility is to acquire a fidu cial plate image for a longer period of time Usu M86 E01008 GADDS Software Reference Manual Process Routines ally mis indexing occurs because the I sigma threshold is set too low causing the program to interpret background as a spot The default threshold of 4 works well on brass plate images which contain 80 000 to 100 000 total counts If your image contains more counts you will prob ably have to raise the threshold accordingly for example if the image contains 1 000 000 counts i e about 10 times the nominal number increase the threshold by a factor of about sqrt 10 12 would be a good value in this case The name of the spatial correction is updated in the current status area at the lower right of the screen This correction is used by the CURSOR commands when they output HKL values and unwarped X Y coordinates and by all the REFL_ARRAY commands which extract spots from a series of frames index the diffraction pat tern and compute a least squares crystal orien tation matrix SPATIAL PROCESS writes three output files All three files are ASCII files in PLOTSO format which can be displayed with the GRAPH FILE
549. t files and remove from project database 2 12 2 8 AGUEN oriee n paced ake Mae E ah oleic Meson pe wea dh Baa tee de 2 12 2 9 Project gt Overwrite defaults e Overwrite the default configuration with the current settings 2 13 2 9 1 AFQUIMEGMIS rario dea a wins EV pueda Seeded EE A aren eh are laterite ged hans aie ee eg 2 13 2 10 Project gt Exit e Leave program and return to operating system 0000 2 14 ZTO TARUM deei edie A eats eaves eR ene aad oe ele a eas ae ae 2 14 3 PIQIROUINGS 23unedaei ees Ohta hein a senna ea eae 3 1 3 1 File gt Display gt Open Display a detector frame on the screen 2 000 eevee 3 1 Sali VACQUMOMS s oaa e aE EE eae m ah aiid embed E atta ty chet nett 6 dvbaea dee Bete dds 3 2 3 1 2 Display LIMIS ec veces yates eros EE RREN EDE EE Wenn hte ene want ieee a 3 4 3 2 File gt Display gt Next and File gt Display gt Previous Display next previous frame in TIS SOMGS E E atid Site AE A Lei bats weeded te ee eid ees hoe As wate daleba ces 3 6 S21 APQUMOENS bic ne nr de E AEEA meds Aba ee ode ae bees Bee dale hte 3 6 3 3 File gt Display gt Movie and File gt Display gt Movie e Repeatedly display next previous frame until key is pressed 1 0 0 0 0c cee tees 3 7 3 33 APQUMONIS ee eve a Rea ees ca ede aiglna a aa eee dae bene edhe oe 3 7 3 4 File gt Display gt HKLs Overlay predicted HKL pattern on the display 3 8 3 4 1 Arguments
550. t from the series starting FRAME to the end of this base name For example if the Job Name is LYS the Run Number is 04 and the starting Frame Number is 000 assuming that the number of characters in a Run Number is set to 2 and the number of characters ina Frame Number is set to 3 in the Edit gt Con fig dialog the data files would be named in sequence LYS04 000 LYS04 001 LYS04 002 and so forth For more informa tion see Section 4 1 1 Edit gt Configure gt User settings Frame Naming Conventions M86 E01008 Collect Routines GADDS Software Reference Manual The default name if none is specified is NEWFRAM The Job Name can contain an NT drive and directory name if desired but you should use the project data directory instead The output filename is merged with the project s working directory defined in the Project gt New CopylEdit dialog prior to creating the output frame If you specify NULL as the Job Name the frames are sent to the null handler and discarded Note NET is NOT supported under GADDS please do not use IRUN lt S gt 0 0 Run 0 This is the Run Number of the series This is not actually a number but is rather taken as RUNCHARS characters of ASCII text Also all characters must be valid characters to be used with filenames because the Run Num ber becomes part of the generated output filename Basically the Run Number is for matted and appended to the output base
551. t list Menu Command Collect gt Scan gt GridTargets Accelerator Ctrl Shft F10 User Level 1 SLAM Syntax SCAN GRIDTARGETS XBEG lt n gt XEND lt n gt XINC lt n gt YBEG lt n gt YEND lt n gt YINC lt n gt TRANSMISSION APPEND On systems equipped with an XYZ stage it is possible to collect scans at multiple target loca tions On flat samples such as wafers one fre quently wishes to take scans on target positions laid out on a rectangular grid Instead of manu ally determining the Z axis position of each tar get on the grid one can pre determine the flat sample plane then lay out the target locations using SCAN GRIDTARGETS which will auto matically calculated the correct Z axis value from the flat sample plane See GONIOMETER FLATSAMPLE NOTE The list of targets is now optimized sorted for minimized drive between targets 5 41 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses XBEG lt n gt X Begin 5 0 XEND lt n gt X End 5 0 IXINC lt nNn gt nonan X Increment 1 0 Enter the starting ending and increment in mm for the grid in the X direction The X begin and end values may be equal Also X end may be less than X begin YBEG lt n gt Y Begin 5 0 YEND lt n gt Y End 5 0 IYINC lt n gt oonan Y Incremen 1 0 Enter the starting ending and
552. ta reduction pro grams such as XENGEN be sure it is written in the correct format _Ix Contains the indexed fiducial spot positions It can be used to restore a previously computed spatial correction when it is read in with the SPATIAL LOAD command _if Shows the spatial correction table used to transform pixel X Y coordi nates FROM raw to corrected values _it Shows the table which transforms cor rected coordinates TO raw coordi nates Both the _if and _it plot files are strictly infor mationalthe program doesn t require them since the information in them is automatically re generated from the _ix file by FRAMBO when SPATIAL LOAD is used and you can delete them if desired When invoked with the NEW option from the SPATIAL submenu or when run from the com mand line without arguments SPATIAL NEW displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins collecting the fiducial plate image the ESC key or right mouse button returns you to the SPATIAL submenu You can interrupt acquisition in progress by pressing the CTRL BREAK keyboard combination however at that point the current spatial correction is undefined Before taking data SPATIAL NEW displays the current CONFIGURE EDIT distance and direct beam center on the bottom status line and asks you to confirm that they are correct before pro ceeding If these
553. tal dimensions 3 ea in CIFTAB string such as DNSMET 85 7 C Density measurement method in CIFTAB string such as DARK 86 7 C Name of dark current correction AUTORNG 87 7 5R Auto ranging gain high speed time scale offset full scale ZEROADJ 88 7 4R Goniometer zero corrections refined in least squares XTRANS 89 7 3R Crystal XYZ translations refined in least squares HKL amp XY 90 8 5R HKL and pixel XY for reciprocal space scan AXES2 91 8 4R Diffractometer setting linear axes 4 ea X Y Z Aux ENDING2 92 8 4R Actual goniometer linear axes end of frame X Y Z Aux 93 94 95 NOTE Items in version 6 headers are obsolete MICRODIF Use FRMFIX to convert these frame headers to version 8 NOTE Version 5 and 8 items are mainly for GADDS NOTE Version 7 and 9 items are mainly for SMART NOTE Version 9 and 10 items do not add addi tional lines to the header but instead append additional values to a previously existing line M86 E01008 Area Detector Frame Format GADDS Software Reference Manual A 2 Image Data The image data is a simple byte stream no record delimiters with one two or four bytes per pixel as defined in the header If the data are two bytes per pixel the least significant byte is first The order of the pixels in the file corresponds to the display of pixels on a screen like the raster scan order of a CRT display The first pixel in the file corr
554. tation Menu Command Help gt Errata Accelerator None User Level 1 SLAM Syntax HELP ERRATA Displays the online errata for the printed GADDS manuals 11 5 1 Arguments None Command executes immediately M86 E01008 Help Routines GADDS Software Reference Manual 11 6 Help gt Releases notes Display release notes Menu Command Help gt Release notes Accelerator None User Level 1 SLAM Syntax HELP RELNOTES Displays the program s online release notes 11 6 1 Arguments None Command executes immediately M86 E01008 12 SLAM Routines Most SLAM commands have been discussed in earlier sections with headings corresponding to the menu bar where menu commands equiva lent to the SLAM commands can be found Some SLAM commands are unique to com mand mode and are fully discussed in this sec tion All SLAM commands are listed in Appendix G for reference 12 1 Echo Menu Command None Accelerator None User Level Command SLAM Syntax ECHO OUT lt s gt APPEND IWAIT lt n gt 1 2 3 8 9 0 ECHO is available only on the SLAM command line that is at the GADDS gt prompt and is used for writing command scripts For example it can be used to write a specific set of PLOTSO direc tives into a file for subsequent screen display with the GRAPH FILE command all from within the SLAM command script Each argument is listed below by its command line name 1 2 9
555. te Accelerator None User Level 1 SLAM Syntax MASK VIEW 1 MASK VIEW allows viewing the active pixels mask on top of a frame image All inactive pixels are masked out with a dot Active pixels are left alone The special bitmask NULL can be used to clear the mask image while 6MASK refers to the current bitmask NOTE MASK VIEW does not change the cur rent active bitmask or octagon mask 8 5 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses A EEEE ES ee Bitmask Filename MASK Filename of active pixel map NULL to clear window MASK to view current active pixel map M86 E01008 Peaks Routines GADDS Software Reference Manual 8 6 Peaks gt Mask gt Octagon e Alternate active pixel mask using octagon region Menu Command Peaks gt Mask gt Create Accelerator None User Level 1 SLAM Syntax MASK OCTAGON 1 2 3 4 5 6 7 8 MASK OCTAGON defines an octagon shaped mask which excludes pixels located on or out side the octagon from all INTEGRATE SMOOTH and PER_CRYSTAL commands MASK OCTAGON is frequently used on off axis frames where the beam stop does not occlude a portion of the image and on short time dura tion frames where the counting statistics are inadequate to properly define a bitmask of active pixels The user should be aware the bitmask or the octagon mask is used exclu
556. te that the first data set in a linear combination is to be the data currently residing in frame accumulation memory for example from the last Collect gt Add com mand If you leave this item blank or specify a wildcard filename pattern pressing ENTER or clicking the OK button will display a list of the current filenames matching the pattern You can choose one from the dis played list by moving to it with the arrow page keys or mouse and pressing ENTER or clicking OK You will be returned to the File gt Load dialog with the selected file name filled in If you leave this item blank it is the same as entering a wildcard pat tern Remember that both filenames and patterns entered here are merged with the project s working directory G2 tes ate TT Background Filename SNULL This is the name of a second frame file to be read from disk and linearly combined with the first according to the scale and offset described below If you leave this field blank or supply the special name NULL only the first file above is read in and no linear com bination is performed In order to run File gt Load without intervention from a command script you must supply this second file name and must therefore specify NULL if you want to load single frame from the com mand line without intervention Default is NULL DISPLAY lt n gt Maximum Display Counts 1 Enter 0 for no display otherwise this item specif
557. ted floating point values The pixel values them selves are binary but they are assured to start on a 512 byte boundary for quick easy access using Byte IO routines and they are stored as a byte stream without delimiters of any kind This format is completely transportable between all computers and networks including PCs NT workstations and SGI systems The only coding difference on these systems is that big endian systems such as SGI must byte swap the pixel values in the relatively rare case where it encounters a 16 bit frame Up to 32 bits pixel are supported although frames are stored where possible as 8 or 16 bits per pixel with an overflow table like that on ear lier systems but this overflow table is ASCII as described below BYTE ORDER OF PIXEL VALUES IN FRAMES WHICH ARE STORED IN THIS FORMAT ON DISK TAPE ETC IS ALWAYS LITTLE ENDIAN LSB first even though the header contains a flag indicating the pixel byte ordering Bruker does not support big endian frames that otherwise look like this format The 16 bit format is fully implemented If more than 4096 overflows occur on attempted compression to 8 bits the frame buffer will com press to 16 bits with an overflow table the GADDS HI STAR and SMART CCD frame buff ers accumulate 32 bits pixel internally M86 E01008 Area Detector Frame Format GADDS Software Reference Manual At the top level a frame in Bruker format can be represented as He
558. ted spectra Either TOPAS2 TOPAS P or PROFILE S can be spawned By default the program is found in either e GADDS SYSTEM directory e PROF SYSTEM directory e lt Drive gt Topas2P directory e lt Drive gt TopasP directory e lt Drive gt Profile directory e lt Drive gt DiffPlus directory So if the program cannot file the executable define the environment variable PROF SYS TEM to point to the directory specification 9 8 1 Arguments None Command executes immediately 9 9 Special gt Redraw e Redraw current screen e g if corrupted by window manager Menu Command Special gt Redraw Accelerator None User Level 1 SLAM Syntax REDRAW Use this command to force GADDS to redraw the screen Useful whenever the screen becomes corrupted Only the current frame image display header and goniometer status windows are redrawn when you choose this command Any information displayed in the pre vious quadrants and the statistics window are lost as is any overlay graphics 9 9 1 Arguments None Command executes immediately M86 E01008 Special Routines GADDS Software Reference Manual 9 10 Special gt Level 1 Special gt Level 2 and Special gt Level 3 Switch to simple advanced or admin istrator menu interface Menu Command Special gt Level 1 Level 2 or Level 3 Accelerator None User Level 1 SLAM Syntax LEVEL1 LEVEL2 LEVEL3 GADDS s menu bar can be switched between an ab
559. tedly display next previous frame until key is pressed Menu Command File gt Display gt Movie File gt Display gt Movie Accelerator Alt UpArrow movie Ctrl tDownArrow movie User Level 1 SLAM Syntax DISPLAY MOVIE DISPLAY MOVIE These commands are used to step through a series of sequentially numbered data frames displaying them in sequence Successive frames continue to be displayed until the end of the series that is a nonexistent frame is encountered or until a key or mouse button is pressed The MOVIE option displays the frames in an ascending frame number sequence and the MOVIE option displays them in descending order The display arguments in the File gt Display dia log are in effect for the duration of the File gt Dis play gt Movie or File gt Display gt Movie subcommand including the display quadrant and autoincrement qualifiers If the specified quadrant is 1 4 and autoincrement is set suc cessive frames will be displayed cyclically in the different quadrants When invoked from the menu or when run from the command line these commands start imme diately without prompting for additional input The next or previous sequential name in a series of frames is computed according to the frame naming parameters set in the Edit gt Con figure gt User settings dialog box see Section 4 1 There is a 0 1 second delay between frame displays 3 3 1 Arguments None Command
560. tern lines are drawn using a solid or dashed conic lines on top of the frame image M86 E01008 GADDS Software Reference Manual Special Routines 9 4 Special gt PDF2 gt Search e Search PDF2 by mineral inorganic or organic name Menu Command Special gt PDF2 gt Search Accelerator None User Level 1 SLAM Syntax PDF2 SEARCH 1 MINERAL INORGANIC ORGANIC Perform an ASCII search on various indexes on the PDF2 CDROM The search is case insensi tive Wildcard characters are not permitted The inputted search text must match the first letters of the index keys to be considered a hit Thus Quartz will match all keys starting with Quartz 05 0490 D QUARTZ 33 1161 QUARTZ end Return to main menu You can display any hit by selecting that line and OK To exit select the last line end Return to main menu and OK 9 4 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses BA E Search string Quartz Enter search string up to 40 characters may truncate MINERAL Mineral index Yes Y to search mineral name index file PDF2 KEY pdf2 s04 INORGANIC Inorganic index No Y to search inorganic name index file PDF2 KEY pdf2 s03 ORGANIC Organic index No Y to search organic name index file PDF2 KEY pdf2 s09 M86 E01008 Specia
561. tes the drive speeds Pressing ESC or clicking the Cancel button exits without changing the speeds Ensure that the environment variable SAXIS ADMODEL is defined correctly for your goniometer type since the speed conventions are different among Platform 4 circle and older Aztalan black 3 circle systems Also ensure that any configuration files you read in corre spond to the correct goniometer type since the values in the file will be transferred to GADDS and the goniometer controller program See Edit gt Configure gt Show model Section 4 5 for more details 5 17 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses The conventions are different for Platform 3 circle 4 circle and older Aztalan 3 circle systems and are listed separately with all values in degrees minute or mm minute except for delta that is in cm min M86 E01008 Collect Routines GADDS Software Reference Manual Table 5 5 D8 DISCOVER Multi Axes Systems Parameter 1 or 1 2 or 2 3 4 5 6 7 8 9 NOTE On PHOENIX controllers the maximum Dialog Box Prompt 2 THETA SPEED THETA SPEED OMEGA SPEED THETA2 SPEED PHI SPEED CHI SPEED X SPEED Y SPEED Z SPEED AUX SPEED DELTA SPEED Default 600 00 600 00 600 00 600 00 3600 00 600 0 150 0 150 0 150 0 50 0 100 0 Maximum Allowable 100
562. th a composite morphological oper ation called opening The morphological opening operation denoted as M F o S is defined as m x y FOS S M86 E01008 GADDS Software Reference Manual Analyze Routines where m e M and the same SE is used in both the erosion and the dilation Opening can be interpreted physically as taking an object whose top surface is described by the SE pressing it up against the underside of the intensity surface of the image and moving it about as shown in Figure 7 1 The result of the opening is found by tracing the highest point reached by the object at each pixel in the image If the object is a sphere then the algorithm has been called the rolling ball algorithm As long as the ball is large enough it can not enter the positive excursions that correspond to the peaks however it can track a slowly varying background very well Figure 7 1 A metaphor for the rolling ball algorithm Unfortunately the background estimate pro duced by the rolling ball filter is not robust in the presence of noise As shown in Figure 7 2 noise spike gouges jutting sharply into the background will force the ball sharply down ward producing erroneous background estima tion i e the ball will follow the noise spike not the true background By applying a noise reduction technique to remove these negative excursions before the rolling ball operation the background estimation
563. the center of the pixel lies within the specified chi integration region then the entire pixel is used If the pixel center is outside region then the entire pixel is unused So narrow chi integration regions less than a pixel width should not be used for chi integration For 2 theta integration if the center of the pixel lies within the specified 2 theta inte gration region then the entire pixel is used If the pixel center is outside the region but any pixel corner is inside the 2 theta region then 1 4 of the pixel is used So narrow or zero width 2 theta integration regions can be used for 2 theta integration needed for pole figure processing The normalized bin method varies from the above only by normalizing each bin by the total M86 E01008 GADDS Software Reference Manual Peaks Routines fractional area of all pixels for that bin eq 3 We scale the result by a factor of ten N N i 10 Lian l Lani ea 3 n 1 n 1 The quick and dirty methods utilizes Bresen ham s Algorithm which draws the conic lines with discrete pixels on a grid See Figure 8 1 Its main advantage over the bin method is speed Its disadvantages are accuracy with broader FWHM and noisier spectra With Bresenham s algorithm you must select an appropriate inte gration step width Too small and you integrate all the same pixels as in the previous integration step Too large and you skip pixels between inte gration steps the inte
564. the course of this command See Collect gt Goniometer gt Optical Section 5 12 for more information about the base angles 5 11 1 Arguments Each argument is listed below by its command line name followed by its dialog box prompt in parentheses SD a e PEE E cesta Base 2 Theta GA PE Base Theta1 Enter the home 29 or 01 value in degrees for optical alignment On most goniometers this is the swing angle to which the goniom eter is driven to begin optical alignment On 8 0 systems this is the generator tube axis Default is current setting Typically this value is 0 or 60 which will drive the detector to an out of the way position 2 inaen Base Omega 2 cave EEE Base Theta2 Enter the home omega or 02 value in degrees for optical alignment Default is cur rent setting On most goniometers the microscope is mounted to the goniometer base at a fixed angle from the collimator On D8 Discover system this angle is user set table On Platform systems this was 30 varies varies varies varies use 330 On Aztalan systems this was 90 use 270 On 4 circle goniometers the microscope is mounted to the circle and one uses 0 or 330 for these systems but if the LT device is attached 345 is recommended to avoid glassware breakage EEEE AET Base Phi Enter the home phi value in degrees for optical alignment Default is current setting Typically one u
565. the general PLOTSO data file format see PLOTSO Section 13 7 The general format is an ASCII header followed by an ASCII table of data Range and data records are repeated for all defined ranges GADDS PLOTSO FILE Chi R C 2th Rect Pixel integration type Identified file as PLOTSO RAW file Title string Sample title Comment string General comment such as original frame file name Wavelengths Kavg Kal Ka2 Beta Wavelengths Integration range 2Theta X to X Gamma X to X Integration range 2Theta X to X Gamma X Width X Area detector integration region Integration method pixel summation aver age pixel normalized by arc length normalized by solid angle bin summation bin normalized interpolated unknown How data was converted from frame to spectra I IN Specifies that subsequent X Y points should be drawn as a new plot rather than added to the existing set of axes M86 E01008 PLOTSO Raw Data File Format GADDS Software Reference Manual SS Specifies a line style for a connecting line to be drawn between X Y pairs Supply one of the characters 0 N S or D as a parameter Line styles are S0 or SN for no connecting line for example for scatter plots SS for a solid connecting line and SD for a dotted connecting line IM Specifies the character to be used as a Marker The Marker C
566. the left mouse button The default filespec used to M86 E01008 GADDS Software Reference Manual Edit Routines search for available lookup tables is GADDS SYSDATA lut WINBG lt np gt Window Background Color 000000050 Specifies the window background color as a 9 digit number in RRRGGGBBB format see above This is the color of the background outside of the image area when the program is started By default it is dark blue 000000050 WINFG lt n gt Window Foreground Color 255255255 Specifies the window foreground color as a 9 digit number in RRRGGGBBB format see above This is the color of the screen text you see in the status areas menus and panels By default it is white 255255255 CURSOR lt n gt Cursor Color 000255255 Specifies the color of the cursors that appear in the interactive cursor commands as a 9 digit number in RRRGGGBBB format see above This same color is used to draw graphic overlays for example X Y plots By default it is cyan 000255255 HIGHLIGHT lt n gt Highlight Color 210000000 Specifies the background color of high lighted text as a 9 digit number in RRRGGGBBB format see above Text which is highlighted includes window title bars and prompts warnings and error mes sages displayed on the bottom status line By default it is read 210000000 BORDER lt n gt Border Color 064192200 Specifies
567. ther direction DELAY lt n gt mand mode only 0 0 available in com Specifies a time interval in seconds to wait before erasing the cursor and returning con trol to the program This is for use in scripts where it is desirable for the cursor to remain on screen long enough for the user to dis cern its position NOERASE mand mode only No available in com Suppresses erasure of the cursor on exit Note that the cursors are drawn by tog gling the sense of the screen pixels thus you can erase a cursor left from a NOERASE by reissuing the command with the same parameters The CLEAR com mand also provides a way to erase cursors left over from NOERASE options The following output statistics are displayed on screen and are also written to the logfile if appli cable X Center X center of box in pixels range from 0 to framesize 1 with origin X 0 being located at lower left of screen Y Center Y center of box in pixels range from 0 to framesize 1 with origin Y 0 being located at lower left of screen Width Width of box in pixels Height Height of box in pixels TotalCts Sum of counts in rectangular box in the cen tral frame Integrated intensity minus background in the central frame The background is com puted as the average of the points on the perimeter of the box excluding all points which are more than three standard devia ti
568. theses E ET PDF Number 33 1161 The PDF number is defined by a set number and a pattern number These numbers can be separated by a space a comma or a dash i e 33 1161 33 1161 or 33 1161 are all valid PDF numbers NBS AIDS Format No Information about each diffraction pattern is stored in NBS AIDS format on the CD ROM see the ICDD JCPDS NBS AIDS83 man ual for more details Users can choose to view the complete NBS AIDS image format or view the pretty format which is much easier to read The output is in 80 columns TYPE lt n gt 0 Data Type 3 The D I table can be outputted as either 0 author s reported method original data as reported in literature 1 theta values in degrees 2 2 theta values in degrees M86 E01008 Special Routines GADDS Software Reference Manual 3 d spacings in Angstroms 4 sin theta 5 Q values 9 2 Special gt PDF2 gt Print Print PDF2 card to printer or file Menu Command Special gt PDF2 gt Print Accelerator None User Level 1 SLAM Syntax PDF2 PRINT 1 2 NBS AIDS TYPE lt n gt CARD PDF2 PRINT command can print any selected PDF patterns in either pretty format the native NBS AIDS format or the standard JCPDS card image in 128 column format 9 2 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parenthese
569. tility program is automatically started when the Analyze gt Mapping command starts to process the run series As each map parameter e g integrated area is calculated the X Y and map parameter value is sent to GADDS MAP The result is a map of a parameter versus XY sample position or different samples if a sample library was used The mapping can be displayed by either a value scale or by a pass fail criteria Ratio between two map files can be displayed and saved The gmap file format is documented in online help For more information see online documentation for GADDSMAP 13 4 Indxtl NIST index generator INDXTL builds a hard disk resident index to a NIST CDF CD ROM GADDS uses this index to reduce the time required to perform a CDF search Normally this index file will reside in GADDS SYSTEM cryidx bin You must use INDXTL to create this file before GADDS will perform a CDF search The NIST Crystal Data CD is available in two major forms 1 NIST 1999 and later The inorganic and organic databases reside in separate files which are CR LF terminated 2 ICDD 1997 and earlier One file contains the inorganic followed by the organic which is not CR LF terminated To run INDXTL the following environment vari ables should be defined and the NIST CDF CD ROM must also be placed in the CD ROM drive SAXI CDF This variable defines the directory in which to write the Crystal Data Information File binar
570. ting data trace however should you wish to abort the procedure press lt ESC gt If too few data points were calculated the command will terminate immediately Other wise the message below appears Warning aborted early Press ENTER to continue ESC to abort Pressing lt ESC gt will terminate the INTEGRATE 2THETA command immediately while lt ENTER gt will accept the truncated data trace from the partially integrated window the upper chi limit was lowered and display the trace When executed interactively the INTEGRATE WRITE is executed upon successful termina tion For more information see the description of the INTEGRATE WRITE sub command M86 E01008 Peaks Routines GADDS Software Reference Manual 8 8 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses Cy ee ae eee ER 2 Theta Start 0 00 Enter lower 2 theta of conic region in degrees Valid range is 0 to 179 2 io n 2 Theta End 30 00 Enter upper 2 theta of conic region in degrees Valid range is 1 to 180 3 E EA Chi Start 0 00 Enter lower chi of conic region in degrees Valid range is 360 to 180 OENE NEA Chi End 360 00 Enter upper chi of conic region in degrees Valid range is 180 to 360 NORMAL lt n gt Normalize intensity 3 When integrating pixels along a conic line segment each pixel may be weighted by a normalization
571. to the nearest 0 5 mm current value current value The current Z positional reading from the goniometer to the nearest 0 5 mm T Aux1 The current AUX angular positional reading from the goniometer to the nearest 0 5 degree mm EEEE Aux1 The current delta position reading from the goniometer This is only available on sys tems with a motorized delta axis current value current value M86 E01008 GADDS Software Reference Manual Collect Routines 5 15 Collect gt Goniometer gt Limits Enter software collision limits Menu Command Collect gt Goniometer gt Limits Accelerator none User Level 2 SLAM Syntax GONIOMETER LIMITS 1 2 3 4 5 6 7 8 9 0 or GONIOMETER LIMITS 1 2 3 4 5 6 7 8 9 0 KMAX lt n gt XMIN lt n gt YMAX lt n gt YMIN lt n gt ZMAX lt n gt ZMIN lt n gt AMAX lt n gt AMIN lt n gt DMIN lt n gt DMAX lt n gt This command is used to specify the software collision limits for the goniometer axes They are particularly useful if special devices for exam ple a He beam path are being used or the detector distance has been changed from the factory default and you do not wish to use the preprogrammed defaults When invoked from the menu or run from the command line without arguments this com mand displays a dialog box where you can view edit the arguments described below Pressing the ENTER key or clicking the OK button s
572. tored in ASCII format Valid extensions are e epf experimental pole figure e npf normalized pole figure e rpf rotated pole figure e tpf tilted pole figure line 1 specimen date and title A8 specimen name filename no central spaces allowed trailing OK A72 popLA suggests that date is first part of title line 2 parameter line A5 hkl or other identification for pole image F5 1 alpha step usually 5 0 currently only 5 0 is sup ported F5 1 alpha max range 5 0 80 0 GADDS always writes 80 0 F5 1 beta step usually 5 0 currently only 5 0 is sup ported F5 1 beta max usually 360 0 or 90 0 GADDS always uses 360 0 12 alpha offset start 0 0 0 1 2 5 GADDS always uses 1 12 beta offset start 0 0 0 1 2 5 GADDS always uses 1 312 choice of axes labels GADDS always assumes 1 2 3 I5 scaling factor times 100 0 Default is 100 scal ing factor of 1 I5 scaled background counts usually 0 GADDS always writes 0 A extra bytes are unknown and unnecessary M86 E01008 POPLA Data File Format GADDS Software Reference Manual line 3 data lines 1X 1814 data in integers scaled by factor in line 2 Scal ing factor is only used when Imax exceeds 9999 otherwise one uses 1 0 scale factor Data is outputted one beta scan at a time start ing at alpha 0 0 to alpha max The start of each beta scan begins a new line line last line must be blank to identify the end of a set
573. tores the limits you ve entered Pressing ESC or click ing the Cancel button exits without modifying the limits Ensure that the environment variable SAXIS ADMODEL is defined correctly for your goniometer type since the default limits are dif ferent between 4 and 3 circle systems Also ensure that any configuration files you read in correspond to the correct goniometer type since the limits in the file will be transferred to both the GADDS program and the goniometer controller program On three axis systems you might see the mes sage Warning Possible omega cable wrap issue when both omega and omega 2theta lim its are not used Recommend using omega 2theta limits of 269 to 89 Also you cannot enter a limit range equal to or exceeding 360 degrees Obviously if you have 360 degrees of unrestricted movement then you have unlimited movement and you should enter 0 0 0 0 for both limits Finally whenever the detector distance setting is changed see Edit gt Configure gt User settings Section 4 1 the program will asked Reset to default collision limits for new dis tance yes No Answer yes and GADDS will read the ASCII file GADDS SYSTEM limits d for new collision lim its based on the goniometer type stage video option and detector distance for the 28 and w 20 or 01 62 and 61 62 limits Your GADDS administrator may wish to edit this file for your particular system M86 E01008 Col
574. troms and the default value is 80 A If you know the axis length enter it here and make FCELL small otherwise make the best guess you can You can use the CURSORS VECTOR and CURSORS CIRCLE com mands to derive approximate unit cell axis lengths 110 4 nonna Expected Alpha Cell Angle Specifies the alpha unit cell angle in degrees when a known unit cell is assumed This value is used ONLY when assuming a known unit cell if ASSUME KNOWN UNIT CELL is specified as N on the input panel or NOREDUCE is absent in command line mode this value is ignored U2 lt N gt nonna Expected Beta Cell Angle 90 00 Specifies the beta unit cell angle in degrees when a known unit cell is assumed This M86 E01008 Peaks Routines GADDS Software Reference Manual value is used ONLY when assuming a known unit cell if ASSUME KNOWN UNIT CELL is specified as N on the input panel or NOREDUCE is absent in command line mode this value is ignored UB lt N gt oececeeeeeees Expected Gamma Cell Angle 90 00 Specifies the gamma unit cell angle in degrees when a known unit cell is assumed This value is used ONLY when assuming a known unit cell if ASSUME KNOWN UNIT CELL is specified as N on the input panel or NOREDUCE is absent in command line mode this value is ignored FCELL lt n gt Axis Length Deviation 0 75 Specifies the fractional range of axis lengths which will be accepted for
575. ts as defined in Collect gt Goniometer gt limits command Entering will be automati cally replaced with current angle setting On 0 0 systems this is 01 tube OMEGA THETA2 detector The omega angle in degrees at which GADDS positions the goniometer at the start of the frame series scans If you spec ify a scan axis below of 2 omega will be scanned as each frame is taken Otherwise omega remains fixed throughout the frame series Valid values are 360 to 360 but are typically reduced by the current software collision limits as defined in Collect gt Goni ometer gt limits command Entering will be automatically replaced with current angle setting On 0 0 systems this is 02 detec tor PHI The phi angle in degrees at which GADDS positions the goniometer at the start of the frame series scans If you specify a scan axis below of 3 phi will be scanned as each frame is taken Otherwise phi remains fixed throughout the frame series Valid val ues are 360 to 360 but are typically reduced by the current software collision limits as defined in Collect gt Goniometer gt limits command Entering will be auto matically replaced with current angle set ting The chi angle in degrees at which GADDS positions the goniometer for this frame series A Platform goniometer is fixed at CHI 54 74 An older Aztalan black 3 cir cle goniometer is fixed at CHI 45 Valid values
576. ttempts to access the file See CONFIG URE EDIT for details on how this merging is performed If you leave this item blank or specify a wildcard filename pattern press ing the ENTER key or the left mouse button will display a list of the current filenames matching the pattern You can choose one from the displayed list by moving to it with the arrow page keys or mouse and pressing ENTER or the left mouse button You will be returned to the input panel with the selected filename filled in If you leave this item blank it is the same as entering a wild card pattern which is then merged as described above nN EEES Output Correction File name zoom _fi Enter the filename for the output correction data The default file is ZOOM _FL conven tion these files reside in the frame directory specified in the CONFIGURE EDIT input panel The filename you specify here is merged with the default specification Frame_root _ fl before the program attempts to access the file See CONFIG URE EDIT for details on how this merging is performed XMIN lt n gt 0 Lower X of Corrected Frame 1024 Enter the X detector bin number to use as left side of corrected frame The default value is 0 the range is from 0 to 4095 YMIN lt n gt Lower Y of Corrected Frame 1024 Enter the Y detector bin number to use as bottom of corrected frame The default value is 0 the range is from 0 to 4095 M86
577. tween the scan angle corresponding to the centroid of the dis played frame and the predicted scan angle of a reflection Predicted Scan Angle Marker Within scan range of the current frame Box Within scan range of a preceding frame Circle Within scan range of a subsequent frame Cross X The circle and cross can be thought of as the tip and tail of an arrow which points from the current frame to the predicted position assuming a stack of frames with earlier frames positioned in front of the screen and subsequent frames positioned further into the screen 3 1 2 Display Limits The translation of pixel values to colors involves two separate translation steps These steps allow you to view the images with nearly photo graphic quality and to refine the color mapping in real time however this refining makes the mapping process more complicated The mapping process is discussed in detail below specifically with reference to the File gt Display command This command allows you to set both lower and upper display limits which represents the most general case Most of the frame acquisition commands also allow you to display the result according to a specified upper display limit exactly equivalent to the upper limit M86 E01008 GADDS Software Reference Manual File Routines discussed below However these commands fix the lower limit at zero which works well most of the time While most commands recognize a few specia
578. u can view edit certain general setup variables including the current sample to detector distance beam center coordinates default calibration data directory and frame naming conventions Unless you are the GADDS Administrator some fields are only viewable calibration directory beam center and detector distance To change a view only field see your GADDS Administrator 4 1 1 Frame Naming Parameters Several qualifiers NAMECHARS RUNCHARS RUNBASE NUMCHARS NUMBASE comprise the convention GADDS uses for generating a series of sequential frame names These nam ing parameters are used by the Collect gt Scan gt SingleRun MultiRun etc commands which collect one or more series of frames and by File gt Display which can display a frame series in sequence Thus to display a series of frames the naming parameters must be set M86 E01008 Edit Routines GADDS Software Reference Manual appropriately to match those in effect when the frames were written New conventions The filename is created with the jobname an underscore the run number an underscore and then the frame number Prior to concatenation the Run and Frame are expanded with lead ing zeros if required to the number of charac ters specified by the Runchars and Numchars parameters The file extension is gfrm For your convenience GADDS generates and displays an example filename using the current settings Old conventions I
579. ual Analyze Routines 7 26 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses DT EE EA Popla File popla epf Enter output popLA file name epf MITLE lt N gt Title TITLE Enter pole figure title or TITLE for frame title HKL lt n gt 0ee HKL 100 Enter hkl indices i e 111 or hkl if unknown APPEND 4 Append Y N No Append to existing output file no gt over writes M86 E01008 Analyze Routines GADDS Software Reference Manual 7 27 Analyze gt Pole Figure gt Orientate e Calculate Hermans and White Spruiell orientation indices Menu Command Analyze gt Pole Figure gt Orientate Accelerator None User Level 1 SLAM Syntax POLE_FIG ORIENT 1 DISPLAY lt n gt 2 APPEND FILM HKL lt s gt A widely used analytical representation of unit cells in a specimen is based on the second order moment of a specific unit cell direction hkl with respect to a specific direction in the specimen M These second moment functions are used to define an orientation index for a one dimensional structure fiber and an index for a two dimensional structure film These indices are directly related to certain physical properties such as birefringence Calculation of orientation indices requires evalu ation of the angle between a specific crystallo graphic direction
580. ulations to finish and to plot the resulting data trace however should you wish to abort the procedure press lt ESC gt If too few data points were calculated the command will terminate immediately Other wise the message below appears Warning aborted early Press ENTER to continue ESC to abort Pressing lt ESC gt will terminate the INTEGRATE SLICE command immediately while lt ENTER gt will accept the truncated data trace from the par tially integrated window the upper chi limit was lowered and display the trace When executed interactively the INTEGRATE WRITE is executed upon successful termina tion For more information see the description of the INTEGRATE WRITE sub command 8 10 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses 1 ok ee 2 Theta Start 0 00 Enter lower 2 theta of conic region in degrees Valid range is 0 to 179 2 leiar s 2 Theta End 30 00 Enter upper 2 theta of conic region in degrees Valid range is 1 to 180 M86 E01008 GADDS Software Reference Manual Peaks Routines ic ae aE Chi Angle 90 00 Enter chi of rectangular region in degrees Valid range is 360 to 360 GA A Height in Pixels 10 Enter height in pixels of rectangular region Valid range is 0 to framesize 1 NORMAL lt n gt Normalize intensity 3 When integrating pixels along a conic line segme
581. un INDEX Default is 0 03 Valid input range is 0 to 999 SIGMA lt n gt Max Sigmas for any SOLN 20 Solutions with goodness of fit below this value are listed in the output window Those with goodness of fit above the value are rejected The default of 20 should be satis factory for most purposes Valid input range is 0 to 999 SIGBEST lt n gt Max Sigmas for best SOLN 6 Solutions with goodness of fit below this value are candidates for the best solution indicated in the output window with the char acters gt gt gt The highest symmetry solu tion with goodness of fit below this value is flagged as the best solution The default of 6 should be satisfactory for most purposes Valid input range is O to 999 8 17 2 Bravais Lattice Output An example of the BRAVAIS output window contents is shown below in EXAMPLE 1 It con tains a summary of the values on the input panel followed by the number of solutions found with goodness of fit within the SIGMA threshold Next is a list of the solutions Solutions are grouped according to lattice type with each group preceded by a line containing one of the Bravais lattice types listed above Higher sym metry Bravais lattices are listed before those with lower symmetry Each solution is displayed on two lines The first line contains the solution number its goodness of fit labeled SIG its unit cell parameters in the order A B C Ang
582. uration Changes Bruker Log Service GADDS Software Reference Manual This informational string is sent to two places e BrukerlnstrumentLog txt e Bruker_FDA_GLP_LogService The BrukerlnstrumentLog txt is typically located in the directory C saxi You can use notepad to view this file The Bruker_FDA_GLP_LogService is a Win dows 2000 NT Service that can be written to accept these electronic signatures and send it anywhere on your network Essentially Bruker provides a hook for easy customization so you can provide electronic tracking of the Bruker instrument in a means compatible with your spe cial laboratory requirements regulations and company policy Bruker does not write this Bruker_FDA_GLP_LogService Interested par ties should contact Bruker to obtain the docu ment Integrating Bruker Instruments into an FDA 21 CFR part 11 compliant laboratory NOTE VIDEO 1 3 02 also supports electronic tracking of instrument configuration changes M86 E01008
583. ure etc The filename of the first frame is generated from the Job Name Run and Starting Frame from the appropriate line in the run list as defined in Edit gt Configure gt User Settings Frame Naming Parameters see Section 4 1 1 Because one typically starts a scan and walks away from the instrument GADDS will pre check that the available disk space is sufficient for storing the requested number of frames in 8 bit mode However if the frames are stored in 16 bit mode you may still run out of disk space during the requested scan operation s 5 32 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses These arguments are the same as the similar singlerun type scans and are thus explained in Section 5 30 See that section for explanations SETAREA Job Name NEWFRAM See NAME lt s gt in Section 5 30 TITLE lt S gt Title Scan Frame SAMPLE lt s gt Sample Name Corundum NUMSAMPLE lt n gt Sample Number 0 DISPLAY lt n gt Max Display Counts 31 REAL TIME Real time Display Y CLEAR 0 e008 Pre Clear Y OLDXENGEN Xengen Output Format N See Section 5 30 STARTRUN lt n gt Sequence of Starting Run 1 You can collect just a specified range of the scan series set up in the run list using STARTRUN and ENDRUN With STAR M86 E01008 Collect Ro
584. utines GADDS Software Reference Manual TRUN you enter the first line number not the RUN in the run list for which data col lection is to be performed The lines are numbered 1 50 The default is 1 and the valid range is 1 50 ENDRUN lt n gt Sequence of Ending Run 9999 You can collect just a specified range of the scan series set up in the run list using STARTRUN and ENDRUN With ENDRUN you enter the line number not the RUN in the run list after which data collection is to be terminated The lines are numbered 1 50 The default is 9999 which works the same as 50 and the valid input range is 1 32767 MODE lt S gt Mode Scan Oscillate Step Scan ROTATE 0 0 Rotate Sample No NIDEO eee Capture Video Image No OSCILLATE lt s gt Sample Osc None AMPLITUDE lt n gt Amplitude 0 0 See Section 5 30 Only on dual detector systems are addi tional parameters for control of the Slave frame buffer SNAME 06 Slave Job Name NEWFRA2 See Section 5 30 Collect gt Scan gt MultiRun checks for possible collision at the extremes of all scans before beginning the first run If the first or last frame in a run is outside the set limits the program dis plays a box with the message PROBABLE COLLISION IN 1ST SCAN OF EDITRUNS LINE lt line gt or PROBABLE COLLISION IN LAST SCAN OF EDITRUNS LINE lt line gt Here
585. utput is described in more detail below In GADDS the program will prompt you on the bot tom status line as to whether you want to drive to one of the solutions for example DRIVE TO SOLN 1 AT 30 00 150 62 0 00 0 00 Y OR ENTER YES N OR ESC NO If you answer one of these prompts with the Y key ENTER key or left mouse button GADDS attempts to drive the goniometer to that position If you answer with the N key ESC key or right mouse button the goniometer remains where it is The operation in SADIE is the same except that the drive prompts are not issued In some cases no rotation about the specified scan axis exists which will place the specified M86 E01008 GADDS Software Reference Manual Peaks Routines HKL in the diffracting condition If this occurs the program displays the message REFLECTION NOT OBSERVABLE PRESS ENTER OR MOUSE TO RETURN Pressing the ENTER key or left mouse button returns you to the input panel or to the com mand line if the command was invoked from there 8 24 1 Arguments Each argument is listed below by its SLAM com mand line name followed by its dialog box prompt in parentheses ERS PEE H 0 Enter the H index of the reflection whose position is to be computed Default is 0 and valid range is 9999 to 9999 Real values may be used they are not rounded to inte ger values prior to computing the position E AA K 0 Enter the K index of the reflection whose
586. ve XTime seconds YCounts This directive specifies the Y axis label Fol low the directive with the text to be drawn along the Y axis By default the text is Y AXIS For example if you re plotting pixel values as a function of position you might issue the directive YPixel Value Nor mally Y axis text is written vertically but not rotated since some graphic environments most notably X Windows don t support rotated text however if the text contains hyphens or parentheses it writes the text horizontally In this latter case you need to keep the axis label very short M86 E01008 GADDS Software Reference Manual PLOTSO Raw Data File Format 2theta Intensity data pairs or 2theta Intensity Q stderr table The actual data spectra M86 E01008 PLOTSO Raw Data File Format GADDS Software Reference Manual D 4 M86 E01008 E TEXTURE AT Raw Data File Format Texture AT raw data files are stored in a byte stream binary file without any record delimina tors File extensions are rrw for reflection or trw for transmission Table E 1 Range Header Block Offset Format Field description 16384 8192 phi range meaningful bits are 1024 theta fixed 0 A4 RAW File identification text 4 14 Number of steps for this range 1 32767 8 R4 Measurement time per step 1 999 0 12 R4 Step size for this range in degrees
587. ve a PLOTSO PRO Bruker PlotSO file 13 9 1 SAXII_READ_D5000 VAX only PV Wave procedure to read a Bruker DIFFRAC 5000 raw data file Up to ten ranges will be read and displayed Usage run saxii_read_d5000 saxii_read_d5000 xarray yarray filename where M86 E01008 13 15 Utility Programs GADDS Software Reference Manual xarray dimension 500 10 returns the 2theta values of up to ten ranges yarray dimension 500 10 returns the intensity counts of up to ten ranges filename DIFFRAC 5000 RAW filename If missing the procedure will ask for the file name 13 9 2 SAXII_READ_FRAME P V Wave procedure to read a Bruker area detector frame Header is type to screen and the image is displayed and the color table is stretch to fit This version handles 8 16 or 32 bit frames WITHOUT an overflow table PV Wave s image color table works only on byte images Values above 256 are clipped upon being displayed Thus the user may wish to use the HIST_EQUAL function to rescale 16 or 31 bit frames into byte images image hist_equal image tv image Usage run saxii_read_frame saxii_read_frame image filename header where image dimension 512 512 returns the byte word dword image data filename Frame data filename If missing the procedure will ask for it header dimension 80 returns the header information 13 9 3 SAXII_READ_PLOTSO PV wave procedure to read a Bruk
588. ver if you re analyzing frames on a different computer from that on which the spatial correction was determined you can transfer the spatial correc tion by moving the _IX file over the network if necessary and loading it with SPATIAL LOAD Don t confuse SPATIAL LOAD with the LOAD command on the master menu which reads a detector frame instead of an ASCII spatial cor rection file The name of the current spatial correction is shown on the display in the current status area at the bottom right of the screen SPATIAL LOAD updates this name when the correction is changed When invoked with the LOAD option from the SPATIAL submenu or when run from the com mand line without arguments SPATIAL LOAD displays an input panel where you can view modify the arguments described below When in the panel pressing the ENTER key or left mouse button begins reading in the specified correction the ESC key or right mouse button returns you to the SPATIAL submenu During the loading process SPATIAL LOAD dis plays the progress messages Reading table Building correction tables Some computation is necessary since the _IX file contains just the fiducial spot positions not the correction tables themselves Loading and computation of the correction tables should be completed in a few seconds M86 E01008 Process Routines GADDS Software Reference Manual 6 7 1 Arguments Each argument is listed below by its SLAM
589. vew da a onal da sts achat and 8 10 8 8 Peaks gt Integrate gt 2Theta Perform 2 theta integration in conic region gt F chi 8 11 8 8 ATQUMENIS Jre aiar ea ERAN A O E E EOS EE AT E eet EE EE RA and 8 12 8 9 Peaks gt Integrate gt Area Perform area integration in conic region gt integer 8 13 89 4 ArQUMONIS crearea tr aAA Red wi fais se oe E AE bY wea ee REE A DS 8 13 8 10 Peaks gt Integrate gt Slice Perform chi integration in rectangular region gt F 2t 8 14 SIO TAGUES vrea rone Nis a doit Gee ea Sea aNd oS csi laeactiew aah Pelco on Shee aed 8 14 8 11 Peaks gt Integrate gt Write Write integration results to disk file 8 16 BILIAU MS gaeran ien a dvd 4 Gaseats Gaeta ai ued dvb bial eg EEEE E ans 8 16 8 12 Peaks gt Integrate gt Clear Clear graph on top of image 0 0c eee eee 8 17 S24 AGUES cho ms ica eet nS wheel Ve whee EEA E Weg lena ay Rete AR eee ahs 8 17 8 13 Peaks gt Integrate gt Rectangle Perform rectangle integration for detector testing 8 18 Su1 LAUNE MS 25 Sn oteat a aside kets balay m eine asta A ed ot eats AA wala ace dans 8 18 8 14 Peaks gt Refl Array gt Threshold Place spots threshold in a series of frames into TNOVANAY deenen ted get Marina E a anette Bitpedia E E weet wae oh Sareea 8 19 S44 VAQUMONTS ice dead dae te Se A ee ee pee eee ed ht peed oe gee 8 21 8 14 2 Threshold Output jcc2 0 de whee bee poe aa E A de
590. w OMEGA X PHI X and CHI X rep resent the XENGEN pseudo goniostat omega phi and chi respectively The U1 Eulerian angle in FRAMBO is equivalent to PHI X The U2 Eulerian angle in FRAMBO is equivalent to 180 CHI X The U3 Eulerian angle in FRAMBO is equivalent to OMEGA X If your starting frame angles were different from zero you can use the XENGEN NEWRUN program to compute the pseudo goniostat angles in the following steps e Use REFINE to create a upr file containing zero setting angle pseudo goniostat angles according to the relationships above e Run NEWRUN Enter 0 0 0 for the old set ting angles and the omega chi phi starting angles of your frame series for the new set ting angles e NEWRUN will print the values of the pseudo goniostat angles at your starting setting angles Since the parameters used in the least squares refinement are different in FRAMBO from those in XENGEN there is no guarantee that pseudo goniostat angles derived from FRAMBO s Eulerian angles will be close enough to permit REFINE to run We are not recommending that you try to use FRAMBO s indexing and least squares instead of the autoindexing in REFINE on a regular basis the relation ships between the angles are described above because they may occasionally be useful under special circumstances 8 18 2 Least Squares Output An example of the output frame REFL_ARRAY LEASTSQ is shown below It begins with the orientatio
591. warranties of merchantibility and fitness for a particular purpose No part of this publication may be stored in a retrieval system transmitted or reproduced in any way including but not limited to photocopy photography magnetic or other record without prior written per mission of Bruker AXS Inc Address comments to Publications Department Bruker AXS Inc 5465 East Cheryl Parkway Madison Wisconsin 53711 5373 USA All trademarks and registered trademarks are the sole property of their respective owners Revision Date Changes 0 12 99 Original release 1 4 04 Updated all sections ii M86 E01008 4 04 Table of Contents NOTICE Nc on Suh a arepa nated Eb ea sae t Pe we die dete Gaede glee aes Yate Oatmeal feted ii 1 General Information lt 2 6 ees dcws ered dae weenie eae eas aad aes 1 1 1 1 Program Overview 0 0 0 1 2 1 1 1 Basic GADDS Operation 0 0 00 ee aaa tee 1 4 1 2 Environment Variables Logical Names 0 0000 eee 1 5 1 3 Startup Command Qualifiers 0 0 0 0 0c ae 1 10 1 4 GADDS Startup Behavior eniris a nenia ETE EENE tte ae 1 12 1 5 Dialog Box and Keyboard Conventions 0 00 cee 1 13 ToT Dialog BOOS pic eaeslanwad pap yd mela hee aed Go aay a el EET D 1 13 1 5 2 Keyboard Conventions 0000 anean 1 14 1 6 GADDS Directory Organization 000 cece 1 17 LA Frame INd xe S irete ieee eee hee owed adeeb seed ts eben wae ean aah oe 1 19 1 8 Special SyMbols
592. xarray yarray filename where xarray dimension 500 10 2theta values of up to ten ranges yarray dimension 500 10 intensity counts of up to ten ranges filename PLOTSO filename If missing the procedure will ask for it M86 E01008 13 17 Utility Programs GADDS Software Reference Manual 13 10 Raw12Fix Fixes file headers of DIFFRAC 5000 files ported from PC to VAX After copying a Diffrac 5000 file from PC to a VAX over the network the RECL in the file header on the VAX file may be incorrectly set at 512 bytes This is the default for the Community DOS NETCOPY V command and other net work packages RAW12F IX will change the RECL in the file header Syntax RAW12FIX filename raw or run saxi system RAW12FIX Enter filename ra raw filename NOTE RAW12FIX VMS must be copied to VMS computer and renamed to RAW12FIX EXE 13 11 Raw2Raw RAW to RAW file format conversion utility Use RAW2RAW to export or import RAW spec tra in various data file formats Converts to and or from e DIFFRAC PLUS raw or sim file format e DIFFRAC AT V2 aka V3 raw or sim file for mat e DIFFRAC AT V1 raw or sim file format e PLOTSO file format ASCII Can also convert to but cannot read these file formats e DBW and DBWS file formats ASCII e GSAS file format ASCII e UXD file format ASCII Can also convert from but cannot write these file formats e DIFFRAC 5000 V2 VAX VMS
593. y cluster which does not contain at least this number of difference vectors are ignored The default of 2 should be satisfac tory in most cases If you supply a value of 1 every difference vector will be included in the calculations As you specify higher val ues you increase the confidence level that an observed group corresponds to a true reciprocal lattice difference vector however you at the same time reduce the number of groups available for autoindexing Valid range is 1 999 however you ll want to stay at the lower end of this range FGROUP lt n gt Length Fraction for Group 0 3 Specifies how closely the components of difference vectors must agree before they will be placed in the same group Difference vectors which belong to the same group are averaged together and the autoindexing is actually performed on the groups not on the individual difference vectors The value given here divided by the largest allowed unit cell axis length computed from AAX BAX CAX and FCELL below represents the maximum allowed distance between the endpoints of two difference vectors assum ing they re at a common origin If the dis tance between a difference vector endpoint and that of the current group average is larger than this value it is not included in the group and in fact starts a new group If the distance is within this limit the difference vector is averaged into the group The default of 0 3 should be s
594. y index files CRYIDXINO BIN and CRYIDXORG BIN new or CRYIDX BIN old SAXI CDROM This variable defines the drive and directory for the Crystal Data Information Files M86 E01008 GADDS Software Reference Manual Utility Programs CRYSTI DAT and CRYSTO DAT new or CRYSTAL DAT old This is usually a CDROM disk and directory of lt drive gt ORIGFMT new or drive gt CRYS TAL old SAXI CDCODE This variable defines the drive and directory for the Crystal Data CODENS Files CODENINO TXT and CODENORG TXT new or CODENS DAT old This is usually a CDROM disk and directory of lt drive gt new or lt drive gt CRYSTAL VAXIND old When you run INDXTL it starts an interactive dialog Default values are displayed on the line before the prompt Pressing a forward slash fol lowed by the ENTER key is the same as enter ing this default The program requests the following information and will then run for sev eral minutes periodically printing the number of entries processed as a progress indicator OPTIONS 9 Exit 1 Create indexes for new format 1999 or later 0 Create index for old format DEFAULT OF CRYSTAL DATA FILE NAME lt default name gt CHOOSE DEFAULT OR INPUT NEW NAME Enter the pathname of the CRYSTAL DAT file Typically this will be on the CD ROM in lt cd rom drive gt CRYSTAL CRYSTAL DAT where lt cd rom drive gt represents the drive letter of the CD ROM on your syste
595. y quadrant Addi tional options permit the destruction of the raw or peak data from internal memory M86 E01008 GADDS Software Reference Manual SLAM Routines 12 4 1 PEAKS AUTO AUTO analyzes a diffraction pattern searching for peaks resolving overlapping peaks and refining the position intensity and FWHM of all peaks If the selected profile lineshapes have a removed AUTO can refine both the a and ap lines simultaneously providing resolution of the overlapped a line with an unrelated o line as in the five fingers of quartz region AUTO first dissects the scan range into multiple regions which include data points of at least BKGDSIG standard deviations above background Each region must start in background and end in background or the peak s are not found in this case you must use PEAKS MANUAL to locate peaks Each region has a maximum number of steps currently 1024 and a maximum number of allowed peaks 15 You may have to manu ally manipulate regions with numerous overlap ping peaks For each region the background is assumed to be a linear function in 26 Least squares esti mates of the left and right backgrounds are per formed With the removal of background the largest remaining sample point is compared to PEAKSIG multiplied by the standard deviation of that point Values greater than this quantity result in a peak being added Least squares estimates are performed on peak position FWHM a
596. ze gt Mapping y 02 soe aeaa nee ee eee bende Rete lee yey ode yes 7 75 SEA APQUMENIS sere cides oe a8 Bed EA TERE SA eae E a Pad wi ER e E ae a ac 7 75 8 Peaks HOUUNGS ace vient ns trae ede belie Ce ew ee ae EE bee 8 1 8 1 Peaks gt Mask gt Create Create a new active pixel mask for this frame 8 1 8b ACATQUMONTS reesen e AEAEE eG A ate AEA O my Bite a Ow Shee soot a ee 8 1 8 2 Peaks gt Mask gt Edit Edit the active pixel mask 0 0 00 c eee eee 8 2 8 3 Peaks gt Mask gt Save Save active pixel mask to disk file 0 000000 ee 8 2 8 3 1 Arguments oie eho etwas REE AE TE ETE steel etyay ie reas at 8 2 8 4 Peaks gt Mask gt Read Read active pixel mask from disk file 00 005 8 3 Xx M86 E01008 4 04 GADDS Software Reference Manual Table of Contents BAT ATQUMOINS Hadi eae Saget a aol tein wee aes a teeta bud heen Ae aL Bee ee ete 8 3 8 5 Peaks gt Mask gt View View active pixel mask on screen 000 e eee eee 8 3 SS LAGUNEN 2 2 4 sweats deed alec dam aces eld dene al Bae ae oe dees 8 3 8 6 Peaks gt Mask gt Octagon Alternate active pixel mask using octagon region 8 4 SETAGEN 2 ab each batt aie oe fw mena e ad SHS cas eel a aa owe ena ed oto Rollei ay SS 8 4 8 7 Peaks gt Integrate gt Chi e Perform chi integration in conic region gt F 2T 8 5 82721 ANQUMENIS ven gin prea Pee heaves wee a nel ace ni i

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