Manual for the Single software
Contents
1. installation guide They should not normally be changed The difprof dat file also contains default parameters for centering scans and for data collections These parameters are only used when a new mat file is created at startup of the Single software Difprof dat must reside in the same directory as the single executable 2 single log The instrument log file Resides in the same directory as the single executable Created by Single Holds any warning or error messages generated by the program Do not edit as it provides a permanent record of instrument errors 3 mat file Contains all of the information related to the individual experiment on one crystal including the experiment title the UB matrix wavelength and scan parameters the indices setting angles and intensities of reflections used in centering data collection parameters The file name extension must always be mat The file can reside anywhere but best not with the single executable Note If an old matfile is opened at start up or later all of the scan parameters etc are loaded from the file If a new matfile is created when starting the Single program the parameters are loaded immediately from the values in difprof dat If a new matfile is created with the set matfile command then all of the current parameters are written to the new file not the ones in difprof dat The matfile is immediately re written with the current parameters whenever the parameters or peak list i2. the displacement of the crystal from the centre of the goniometer Thus to correct for a reported negative offset along the y axis the crystal must be moved away from the X ray source The circle zero errors reported by zref are the apparent values of the angles when the motor controller has set the angle to zero Therefore to correct a circle zero errors e use mot to drive to the reported zero error e use Idmt to redefine this position as zero SINGLE04 USER MANUAL 8 RJ ANGEL MARCH 2006 Reflection List Manipulation and Crystallographic Operations Crystallographic operations are performed upon the reflection list and upon the UB matrix which also contains cell parameter information The reflection list consists of up to 60 reflections Each reflection entry consists of a list number hkl setting angles the numbered of centred positions a use flag and the intensity The list number is only the position of the reflection data in the list some operations such as DEL or SORT lead to reallocation of list numbers to reflection data The use flags are set with the USE command and unset with the OMIT command Data entry into the reflection list may be made either by some of the commands INH INA or IND or as the result of centering reflections on the diffractometer CENT or CNTR Reflection indices may be input as command arguments as integers or reals They are stored and manipulated by the program as reals except when then are r
3. 1 An alternative algorithm to AUTO SINGLE04 USER MANUAL 9 RJ ANGEL MARCH 2006 indl 3 sub options Clear all list indices to zero Input indices for individual reflections Index all reflections with the current UB matrix indx Index a set of setting angles input by the user according to the current UB matrix inh Insert reflections into the list by inputting indices hkl Setting angles in the list are calculated from the current UB matrix list Outputs the reflection list to the terminal Isq Perform unconstrained least squares determination of the UB matrix by using the indices and setting angles of all reflections in the list with their use flags set to 1 Outputs unit cell parameters unconstrained by symmetry om input UB matrix with three values per line omit unset the use flags of reflections in the list The user inputs the list numbers Sets of consecutive reflections may be selected by the end of the set being input as a negative number see use command prom lists the UB matrix on the terminal sort Reorders the list into ascending 2theta order List numbers of specific reflections are changed tlsq Perform symmetry constrained refinement of the unit cell parameters to only the 2theta angles of all reflections in the list with their use flags set to 1 This code written by Bob Downs tran transform the unit cell parameters according to a 3x3 matrix input by the user The UB matrix and the indices o
4. 31 steps width parameter 0 20 Final omega scan 51 steps width 0 40 0 35 tan th Final omega scan will be fit by PROFILE Value of eta is fixed at 0 00 Current 2 wavelengths are 0 709316 and 0 713606 Intensity ratio 0 530 Current Device is NONE Bisecting Mode 30 MAR 04 08 32 SINGLE gt The program is now ready for your commands see section below If the previous user did not exit the Single software with the exit command then the physical positions of the diffractometer will not be those of the park position and an error message will have appeared If this happens check that the positions shown on the display match the physical positions of the diffractometer circles and slits If not correct with Idmt The Single GUI You can type commands in to the terminal window by clicking anywhere in the window with the left mouse button and then typing commands Output from the Single software also appears in this window just like an old fashioned terminal There is no type ahead buffer You have to wait for the program to be ready to read your commands before typing them in Be patient When the diffractometer is busy the terminal area will be grey and no commands can be entered On the upper part of the display there are two sections On the right side is information about the current diffractometer activity the current action SINGLE04 USER MANUAL 5 RJ ANGEL MARCH 2006 shutter status
5. SINGLE 04 TFM R J ANGEL Crystallography Laboratory Dept Geological Sciences Virginia Tech Blacksburg VA24060 USA http www crystal vt edu crystal INTRODUCTION SINGLE04 is a program written by RJ Angel Virginia Tech Crystallography Lab to carry out the calculations necessary for controlling a four circle Eulerian cradle diffractometer It is developed from earlier versions of SINGLE written LW Finger Geophysical Laboratory CIW and RJ Angel Much of the code is derived from software written earlier by L W Finger and some of the interface code for the AMS motor controllers was provided by Bob Downs The software is currently supplied on a non commercial basis The author would therefore appreciate acknowledgement of the use of the code being made in all publications that make use of data collected or processed using SINGLE Relevant literature is The SINGLE code itself and many of the algorithms used Angel RJ Downs RT Finger LW 2001 High Temperature High Pressure Diffractometry In Hazen R M Downs R T Eds High pressure high temperature crystal chemistry Reviews in Mineralogy and Geochemistry 41 559 596 The peak centering algorithms are described in Angel et al J Appl Cryst 30 461 466 1997 The method of diffracted beam centering otherwise known as 8 position centering used in the ZREF utility was originally developed by Hamilton The practical implementation was first described by K
6. a relative to bisecting d When you have loaded all six motor positions with Idmt drive each circle to zero with the mot command Watch the diffractometer carefully because if you made an error in step b or c you will have a collision Check the odometer If the motor is not at physical zero reset the position with Idmtr Continue until the motor is at physical zero and the position displayed by both the SMC 9000 and Single is zero Do the axes in this order phi then chi then 2theta then omega e When all circles are zeroed check the motion of the slits by driving them to other non zero values Do not drive the slits to zero f If all appears ok try calc and driv to a known reflection position The counts display on the GUI normally shows the maximum from the last scan that was performed unless the coun command is used in which case the measured count rate is displayed SINGLE04 USER MANUAL 16 RJ ANGEL MARCH 2006 SPECIAL VTX HUBER OPERATION NOTES 1 Motors are 1 2theta 2 omega 3 chi 4 phi 5 vertical aperture 6 horizontal aperture 2 Motor drives are in degrees slits in mm For centering the usual slit sizes are motorS 1mm motor6 9mm 3 The program works with omega values as the deviation from bisecting The motor controller uses absolute omega om abs om bi theta 4 WARNING Take care redefining omega with Idmt The safe method is to drive both 2theta and omega to physical zero and then use Idmt to set 1 0 a
7. appears answer YES to the question about running a real diffractometer The main window will appear In the scrolling region of the window the following messages will appear in order a OPENING COMMUNICATIONS ON COM please wait b Opened COM1 If this does not appear you have a windows system problem c Checking motor positions please wait d For each motor you should see either OK or a message to say that the stored position in the controller does not match the park position PIE E3 LW FINGER RJ ANGEL RT DOWNS BASE VERSION OF FEB 2004 ERSION FOR BGI HUBER ON SMC3000 CONTROLLER Opened COM1 Checking motor positions please wait MOTOR1 OK MOTOR 2 MOTOR 3 MOTOR 4 MOTOR 5 MOTOR 6 4 Then the diffractometer positions and shutter state will be updated on the display and a file browser will appear 5 Use the browser to select the data directory where you want to store your mat file 6 Type in the name for the experiment mat file or select an existing file Do not use an extension SINGLE04 USER MANUAL 4 RJ ANGEL MARCH 2006 7 The program will now load some parameters and the window should look something like Cell 4 76036 4 76040 12 99467 89 999 90 000 119 999 255 0267 Peak Centering Parameters Minimum Count Rate 30 cps an Ratio 2 0 Max Time Step 10 secs Required counts on maximum 250 cp Initial Omega Scan width 0 60 0 5 tanith Final Chiscan
8. dates the setting angles in the list for each successfully centred reflection For failures the angles in the list are left unchanged and the use flag set to 0 view positions the diffractometer so that the sample can be viewed See local instructions for exact action zero drives all of the diffractometer circles to zero zref performs 8 position centering on reflections in the list whose use flags are set to 1 Centering parameters can be reset with the SET CENT command The slit settings on the detector are also defined by the parameters entered in SET CENT The user specifies whether the starting position for the centering process for each reflection is taken as the angles from the list or is calculated from the indices in the lost and the current UB matrix For the purposes of instrument alignment it is possible to request zref to continue with a set of 8 equivalents after centering failures This option should not be used for routine measurements The true angles of each refelction are determined from the eight equivalents by the method of King and Finger J Appl Cryst 12 374 378 1979 and are put in to the reflection list The reflection list intensity is the mean value of the intensity at each of the eight positions For failures the angles in the list are left unchanged and the use flag set to 0 The crystal offsets reported by zref are defined on the Busing Levy phi axis system see above The value of these offsets is
9. diffractometer angles and slit positions The hkl values displayed here are calculated from the displayed angles with the current UB matrix On the bottom right are listed the names of the current mat and data files The behaviour of the counter display depends on the installation On the left side is a display of the last completed scan with the angles and hkl at which it was performed This is only updated at the end of the scan RUNNING THE PROGRAM WITHOUT THE DIFFRACTOMETER Single can also be used to perform diffractometer calculations without being connected to a diffractometer To start in this DMSINGLE or dummy mode answer NO to the question about running a real diffractometer at the start of the program After selecting the mat file the window should look something like this Eismacs aT Simulation of BG HUBER ON SMC9000 CONTROLLER Cell 10 00000 10 00000 10 00000 90 000 90 000 90 000 999 9999 Peak Centering Parameters Minimum Count Rate 30 cps Max Min Ratio 2 0 Max Time Step 10 secs Required counts on maximum 250 cps Initial Omega Scan width 1 00 0 35 tan th Final Chi scan 31 steps width parameter 0 20 Final omega scan 51 steps width 0 40 0 35 tan th Final omega scan will be fit by PROFILE Value of eta is fixed at 0 00 Current 2 wavelengths are 0 709316 and 0 713606 Intensity ratio 0 530 Current Device is NONE Bisecting Mode 29 MAR 04 05 18 DMSINGLE gt This vers
10. er none DCOM direct control of the interface For experts only none DEL delete reflections from the list as selected by list number list numbers Sets of consecutive reflections may be selected by the end of the set being input as a negative number List numbers of specific reflections left in the list are changed DEMO drives the diffractometer around a preset list of positions none DRIV drive the diffractometer to the last set of angles produced by none CALC if they were valid angles DVLS drive the diffractometer to the setting angles of a reflection in list number the list if they are valid angles EXIT parks the diffractometer and exits from the program none FILT set the filter wheel if present filter number GOTO drive to requested angles 20 X gt HALF set the half slits if present T top B bottom L left R right O open HALT stops the diffractometer drives none HELP Provides a list of commands none INA Input a set of setting angles into the list Indices in the list are none calculated from the current UB matrix IND Input a set of indices and setting angles into the list none INDC perform an automatic indexing with all reflections in the list none SINGLE04 USER MANUAL 12 RJ ANGEL MARCH 2006 with their use flags set to 1 INDL 3 sub options none Clear all list indices to zero Inpu
11. f all list reflections may also be transformed use set the use flags of reflections in the list The user inputs the list numbers Sets of consecutive reflections may be selected by the end of the set being input as a negative number Thus 4 7 would indicate reflections 4 5 6 and 7 Reflections with numbers not input have their use flags unchanged upon exit Data Collection Data collection parameters such as scan type width step size 2theta limits etc are chosen with set data This information is displayed on the terminal when any of these commands is input and before the data collection starts Data is stored as step scans in an ASCII file selected with the set datfile utility inta initiate a data collection scan over a set of reflections Indices are generated by the program SINGLE04 USER MANUAL 10 RJ ANGEL MARCH 2006 subject to the limits provided by the user in SETU ints initiate a data collection scan over single reflections The user is prompted for the hkl of each reflection in turn intl initiate a data collection scan over a list of reflections The list may be either an ASCII file with one set of hkl per line or the reflections in the reflection list whose use flags are set to 1 psi perform a psi scan of a single reflection General Utilities The utility commands include note to make notes into the log file log to provide extra logging facilities especially for debugging set to set many parame
12. g options none SET MATFILE Select mat file none SET TITLE Input a title none SET WAVE Input wavelengths SHOW List parameters for centering reflections none CENTER SHOW DATA List data collection parameters none SHOW Print name of the file for storing scans from data collection none DATFILE SHOW Show the selected diffraction geometry and restrictions none DEVICE SHOW List all available device types none DEVTYPES SHOW LOG Show logging options none SHOW Print the name of the mat file none MATFILE SHOW TITLE Print the title none SHOW UB Print the UB matrix none SORT Reorders the list into ascending 2theta order List numbers none of specific reflections are changed TLSQ Perform symmetry constrained refinement of the unit cell crystal system number parameters to only the 2theta angles of all reflections in the 1 6 list with their use flags set to 1 TRAN transform the unit cell parameters according to a 3x3 matrix none input by the user The UB matrix and the indices of all list reflections may also be transformed USE set the use flags of reflections in the list The user inputs the list numbers list numbers Sets of consecutive reflections may be selected by the end of the set being input as a negative number Thus 4 7 would indicate reflections 4 5 6 and 7 Reflections with numbers not input have their use flags unchanged upon exit VIEW drives diffractometer so that the sample can be viewed with none t
13. he telescope ZERO Drives the diffractometer circles to zero none ZREF Performs 8 position centering on reflections in the list whose none use flags are set to 1 Updates the setting angles in the list for each successfully centred reflection For failures the angles in the list are left unchanged and the use flag set to 0 The following commands available in earlier versions have been discontinued SINGLE04 USER MANUAL 14 RJ ANGEL MARCH 2006 Command Description AUTO Perform an automatic indexing with all reflections in the list with their use flags set to 1 The resulting unit cell is normally reduced The reflections are indexed BRAV Cell reduction routine CALP calculates the 2theta and chi angles of a reflection from the coordinates of spots on a rotation photograph CONE Perform a cone search FACE Orientation of crystal faces with respect to the telescope GRID performs static intensity measurements at points of a grid defined in reciprocal space PHOT Perform rotation photo scan starting from preset photo position PRNT Turn printer on and off SCAN Perform a linear scan in reciprocal space SRCH Search for reflections ERRORS Errors in the program or the diffractometer are of two levels WARNING Non fatal error which the software will either ignore or attempt recovery Examples are individual failures in communications failure to open shutter failure
14. heta WARNING Take care redefining omega with Idmt The safe method is to drive both 2theta and omega to physical zero and then use Idmt to set 1 0 and 2 0 in this order To stop the Single program during a measurement Open the radiation enclosure Wait The next time the program issues a command to open the shutter it will display an error message When you select OK the program will return to the Single prompt Then you should enter the cpos command to ensure that the program has the correct angles loaded from the interface If a motor limit switch is activated by the diffractometer the single program will detect the limit switch and halt with an error message When you select OK the program will return to the Single prompt It is critical that you now complete the following instructions a Clear the error flag from the SMC 9000 controller by pushing the RESET button If the limit switch message reappears on the SMC 9000 then the limit switch is still active and you will have to move the diffractometer manually to clear the switch and then RESET again b Read the physical positions of the diffractometer circles and the slits from the odometers c The RESET clears the motor positions from the SMC 9000 controller Use the Idmt command to reload the correct physical positions of the circles and slits into the SMC 9000 Remember to allow for the fact that the SMC 9000 displays omega as absolute whereas Single uses omeg
15. ing and Finger J Appl Cryst 12 374 378 1979 SINGLE04 USER MANUAL 1 RJ ANGEL MARCH 2006 The method of constrained vector least squares to obtain cell parameters in the CLSQ utility was developed by Ralph and Finger J Appl Cryst 15 537 539 1982 While the authors are pleased to receive reports of bugs in the code and suggestions for changes and improvements the authors take no responsibility for any incorrect operation of the code The authors accept no liability for damage caused through use of this code to control equipment GENERAL PRINCIPLES The program is written to be mainly diffractometer independent It can also be run without a diffractometer attached This option can be selected by the user upon starting the program and is indicated by the command line prompt of the program including the string DMSINGLE The circle conventions and parities and axial systems of Busing and Levy 1967 are used for all calculations When all circles are at their zero positions e the 20 arm lies in the position of the undiffracted direct beam 20 0 e the plane of the y circle is perpendicular to the direct beam 0 e the axis is perpendicular to the diffraction plane y 0 e the choice of 0 is arbitrary These conventions also define the normal beam equatorial geometry of Arndt and Willis 1966 subsequently generalised by Dera and Katrusiak 1998 In these zero positions the Cartesian basis of the d axis c
16. ion of the program will accept all commands except those that drive the diffractometer Even if you are using the code in dummy mode the single executable must be accompanied by a difprof dat file for the machine for which you wish to do calculations SINGLE04 USER MANUAL 6 RJ ANGEL MARCH 2006 COMMANDS Diffractometer Control Commands that control the diffractometer are only accessible if the computer is connected to a diffractometer In DMSINGLE they are disabled cent Perform 1 position centering of the reflection currently in the detector window If centering is successful the user is asked whether the resulting setting angles should be added to the reflection list clsh close the shutter centr Perform 2 position centering at 2theta and 2theta of the reflection currently in the detector window If centering is successful the user is asked whether the resulting setting angles should be added to the reflection list coun Perform a static count for 5 seconds at the current position cpos reports current positions of the goniometer circles demo drives the diffractometer around a preset list of positions driv drive the diffractometer to the last set of angles produced by CALC if they were valid angles dvls drive the diffractometer to the setting angles of a reflection in the list if they are valid angles User input number of a reflection in the list filt set the filter wheel if present goto input f
17. le without being interpreted as commands Exit from the utility by typing EXIT on a line on its own OM input UB matrix with three values per line none OMIT Unset the use flags of reflections in the list The user inputs list numbers the list numbers Sets of consecutive reflections may be selected by the end of the set being input as a negative number Thus 4 7 would indicate reflections 4 5 6 and 7 Reflections with numbers not input have their use flags unchanged upon exit OPSH open the shutter none PARK drive the diffractometer to the preset park positions none PROF performs step scan of any diffractometer circle about the none current position and outputs measured profile to the screen PROM prints the current UB none PSI perform a psi scan of up to 30 reflections none REF performs 2 position centering on reflections in the list whose none use flags are set to 1 Updates the setting angles in the list for each successfully centred reflection For failures the angles in the list are left unchanged and the use flag set to SINGLE04 USER MANUAL 13 RJ ANGEL MARCH 2006 0 SET CENTER Input parameters for centering reflections none SET DATA Input data collection parameters none SET DATFILE Open a file for storing scans from data collection none SET DEVICE Select diffraction geometry and restrictions due to devices none eg DAC SET LOG Set loggin
18. nd 2 0 in this order 5 If a motor limit switch is activated by the diffractometer the single program will detect the limit switch and halt with an error message When you select OK the program will return to the Single prompt Then a Read the physical positions of the diffractometer circles and the slits from the odometers and compare them to the values displayed on the Single GUI b If necessary reinitialise the motor controllers with Idmt Drive the motors to zero and recheck the odometer values d When all circles are zeroed check the motion of the slits by driving them to other non zero values Do not drive the slits to zero e If all appears ok try calc and driv to a known reflection position SINGLE04 USER MANUAL 17 RJ ANGEL MARCH 2006
19. nformation is changed e g upon centering 4 User log file Created by Single and given the same name as the mat file but with the extension og Resides in the same directory as the mat file All of the information on the terminal screen input and output is copied to this file as a permanent record of the expeirment Can be examined while the program is running or afterwards by a text editor such as Wordpad 5 Centering scans file Created by Single and given the same name as the mat file with _cntr rfl added Resides in the same directory as the mat file A standard format reflection file containing the step scan data of the final omega scans from centering with the zref command Also other omega scans if log is activated Can be used by WinIntegrStp to examine and refit the profiles after the experiment 6 Data collection file Created by user with the set datfile command Can reside anywhere A standard format reflection file containing the step scan data collected during a data collection 7 Reflection list file Created by user with a text editor Can reside anywhere Contains a list of reflection indices one reflection per line to be collected with the intl command SINGLE04 USER MANUAL 3 RJ ANGEL MARCH 2006 RUNNING THE PROGRAM WITH THE DIFFRACTOMETER 1 Double click on the Single shortcut on the desk top SINGLE Single04 ico 2 Start the Single program from the shortcut on the desktop 3 A small dialogue box
20. oordinate system Busing and Levy 1967 has its axes defined as follows e the origin is at the centre of the diffractometer e the positive y axis extends from the crystal towards the detector i e along the undiffracted direct beam e the positive z axis is parallel to the axis perpendicular to the diffraction plane and away from the axis carrier e the positive x axis makes a right handed set and corresponds to an imaginary diffraction vector at 20 0 The sense of positive rotations of the four diffractometer circles under the Busing and Levy 1967 convention are left handed for all axes except for the y axis To be explicit when viewed from the z direction looking down on the diffractometer from above positive movement of the 20 and p axes away from their zero positions is clockwise When viewed from the y direction looking towards the crystal from the detector arm positive movement of the y axis is anti clockwise These senses of rotations are defined as having positive parities SINGLE04 USER MANUAL 2 RJ ANGEL MARCH 2006 FILES The SINGLE software uses several files They are all Ascii files that can be read by any text editor such as Notepad or Wordpad They can become corrupted if opened with a utility such as Word The files are 1 difprof dat Holds two types of information First diffractometer dependent parameters such as motor drive information Further details of these parameters are given in the
21. ounded to the nearest integer for calculations with COM LSQ and CLSQ angl calculate from the setting angles the angles between all reflections in the list with their use flags set to 1 calc calculates the setting angles of a reflection hkl input by user cell input of cell parameters by the user Blank angle fields are set to 90 clsq Perform symmetry constrained refinement of the unit cell parameters by the method of vector least squares by using the indices and setting angles of all reflections in the list with their use flags set to 1 The method used is that of Ralph and Finger J Appl Cryst 15 537 539 1982 com calculate UB matrix from the unit cell parameters and two reflections in the list selected by the user in terms of the list numbers Before using this utility the user should have indexed the reflections with INDL Note that COM rounds off the indices of reflections to the nearest integer del delete reflections from the list as selected by list number Sets of consecutive reflections may be selected by the end of the set being input as a negative number see USE List numbers of specific reflections left in the list are changed ina Input a set of setting angles into the list Indices in the list are calculated from the current UB matrix ind Input a set of indices and setting angles into the list indc perform an automatic indexing with all reflections in the list with their use flags set to
22. our angles and drive to that position halt stops the diffractometer drives See local instructions for exact action half set half slits on detector arm if present Idmt redefines the current physical position of a motor to the value input by the user User input motor number angle value WARNING Take care not to enter an incorrect value as this may later cause physical collisions of the diffractometer Take care redefining omega on diffractometers using absolute omega values the safe method is to drive both 2theta and omega to values which you wish to define as zero mot direct drive of individual motors User input motor number target angle The motors are numbered as follows 1 2theta 2 omega 3 chi 4 phi If diffracted beam motorised slits are installed those defining the opening in the omega 2theta plane are motor 6 the SINGLE04 USER MANUAL 7 RJ ANGEL MARCH 2006 perpendicular set are motor 5 opsh open the shutter Consult local instructions as to action when the shutter is prevented from opening for example by safety circuits park drive the diffractometer circles to the park position prof performs step scan of any diffractometer circle about the current position and outputs measured profile to the screen The user is prompted for the motor number step size number of steps and count time per step ref performs 2 position centering on reflections in the list whose use flags are set to 1 Up
23. t indices for individual reflections Index all reflections with the current UB matrix INDX Index a set of setting angles input by the user according to setting angles the current UB matrix INH Insert reflections into the list by inputting indices hkl Setting none angles in the list are calculated from the current UB matrix INTA initiate a data collection scan over a set of reflections none Indices are generated by the program subject to the limits provided by the user in set data INTL initiate a data collection scan over a list of reflections The none list may be either an ASCII file with one set of hkl per line or the reflections in the reflection list whose use flags are set to 1 INTS initiate a data collection scan over single reflections The none user is prompted for the hkl of each reflection in turn LDMT redefines the current physical position of a motor to the motor number angle value input by the user LIST Outputs the reflection list to the terminal none LOG initiate logging of profile and centering information either to none the terminal or to a file LSQ Perform unconstrained least squares determination of the none UB matrix by using the indices and setting angles of all reflections in the list with their use flags set to 1 Outputs unit cell parameters unconstrained by symmetry MOT direct drive of individual motors motor number angle NOTE Allows text to be typed on the terminal to be echoed to the none user logfi
24. ters including centering data scan parameters etc show to display parameters SINGLE04 USER MANUAL 11 RJ ANGEL MARCH 2006 COMMAND LIST SUMMARY In this list the arguments column details the arguments that can be entered on the same line as the command itself If no argument is given the program will provide a prompt for the required input Many commands will also issue questions for the user to answer Command Description Arguments ANGL calculate from the setting angles the angles between all none reflections in the list with their use flags set to 1 CALC calculates the setting angles of a reflection h k CELL input of cell parameters by the user Blank angle fields are a b c a B y set to 90 CENT Perform 1 position centering of the reflection currently inthe none detector window CLSH close the shutter none CLSQ Perform symmetry constrained refinement of the unit cell crystal system number parameters by the method of vector least squares 1 6 by using the indices and setting angles of all reflections in the list with their use flags set to 1 CNTR Perform 2 position centering at 2theta and 2theta of the none reflection currently in the detector window COM calculate UB matrix from the unit cell parameters and two two list numbers reflections in the list COUN Perform a static count for 5 seconds at the current position none CPOS Reads motor positions from motor controll
25. to open files software failures unusual results failure of least squares failure of user to specify necessary information problems reading the mat file The program will log the warning to the user log the terminal and the instrument log If communication or instrument problems continue a fatal error will be logged If they are cleared then the program will issue a message noting the recovery that again will be logged to the user log the terminal and the instrument log FATAL ERROR Examples are failures in reading the difprof dat file diffractometer limit switches active shutter failure after 5 attempts persistent error in communications These force the program to stop request acknowledgement from the operator and return the program to the main prompt to allow appropriate action to be taken by the operator Fatal errors are logged to the user log the terminal and the instrument log Persistent fatal errors should be investigated before they lead to damage to the diffractometer SINGLE04 USER MANUAL 15 RJ ANGEL MARCH 2006 SPECIAL BAYREUTH HUBER OPERATION NOTES k 7 Motors are 1 2theta 2 omega 3 chi 4 phi 5 vertical aperture 6 horizontal aperture Motor drives are in degrees slits in mm For centering the usual slit sizes are motor5 1mm motor6 9mm The program works with omega values as the deviation from bisecting The omega values displayed by the SMC 9000 are absolute omega om abs om bi t
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