Bruker Microdiffractometer User Manual (Version: 2012.12.06)
Contents
1. Goniometer Manual 3 7 7 axis v NG position screw x axis yo pa position screw 4 uga position screw Height extender set screw and hit the OK button Turn the alignment laser ON Hit the L keyboard key notice the commands at the bottom of the GADDS software Display the Video software If the camera is not displaying an updated image make sure to press the green triangle button the Record button in the software Move the sample into the proper position by adjusting the z axis position screw on the goniometer head The sample will be properly aligned if the laser is centered in the crosshairs and the sample is in focus a If you can t see the laser zoom the microscope out buttons 20 and w pressed simultaneously on the manual box adjust the sample in the z direction Zoom in and fine tune the z adjustment If you cannot get the laser to align with the crosshairs you may have to manually adjust the goniometer head s starting height Loosen the height extender set screws to lengthen or shorten the goniometer head s starting height See the goniometer head picture above to change the starting height Fine adjustment of the z height should be done at the maximum zoom Aux 6 8 Once the laser is close to the center move the goniometer head x and y positioning b screws to the area to be analyzed and readjust the z position 1f necessary Camera display Reflection mode alignme2. Job name This is the filename and is saved to the folder set up in project file Title Title of your run Sample name Copy the Title here for it to display in JADE Sample number Another sample identifier any number will work Maximum display counts Sets the initial max scale value for the 2D image This setting can be adjusted during the range Realtime display Check YES to see the data collected in real time Pre clear Check YES Sequence of starting run Run number to start scans with usually set to 1 Sequence of ending run Run number to end scans with Leaving value to 50 will run all scans in the listing Mode Step 1s usually used here the Frame Width 1s discretely moved after each frame Rotate sample check YES if sample is to be rotated in which helps to randomize sample orientation Capture Video Image Gives you a snapshot of your sample while scanning Do not check this for the multi scan option 7 When done click OK go to the Video software and say OK to any error messages The run will then begin Options for Collect Scan MultiRun E3 Job name Filename 2 0000 00000 ES Title Title Sample name Sample Name 7 0000 Sample number i Max display counts at Realtime display Pre clear sequence of starting run 1 sequence of ending run 50 Mode STEP Rotate sample Sample Osc None Amplitude 0 0 Capture Yideo Image ce Data Analysis NOTE This section describe
3. 3 Detector Base of Frame 10 Direct beam X unw 512 50 pixels boooooooooooooooooooooooox 12_000 gfr Direct beam Y 505 00 pixels Check these Framesize 1024 values Sample to detector face 5 000 cm 7 Check to make sure that the correct software drive limits are configured The limit values should automatically load when creating the job file Step 5 but due to a bug in the software they are not always loaded THIS IS EXTERMELY IMPORTANT TO CHECK a Go to the Collect tab Goniometer Limits and check to make sure the limit values registered in the popup windows match EXACTLY what is shown below Options for Collect Goniometer Limits Theta limit Omega limit Omega 2 Theta limit Phi limit both U none Chi limit both O none X limit both O none Y limit both none Z limit both O none Aux limit both O none ce b If the values loaded do not match the above image you have two options to correct the problem i Method 1 Delete your gadds nc job file that was just created in Step 5 and then create a new one The new job file will typically have the correctly loaded limits Method 2 Manually input the values shown above into the Limits popup window and then hit OK 8 Check to see if the correct collimator is installed For most applications the 0 8 mm collimator should be used but smaller collimators can be installed Please see XRD staff for help if you are uncomfortabl
4. one axis movement 1 Go to the Collect tab Scan Single Run sya C Em o evon5pgc V Frames Number of scans Seconds frame Data collection time per frame in seconds 20 Center 20 angle in frame Incident beam angle typically set to 12 of 20 for general analysis 9 In plane rotation angle entering will put o exactly where you aligned it X Tilt angle 90 or 0 for transmission or reflection mode respectively Aux Camera zoom typically set to 6 8 Scan Axis What angle changes between each frame 1 20 2 5 3 4 none coupled Frame Width Step size of Scan Axis angle if more than 1 frame 1s used Mode Step 1s usually used here the Frame Width 1s discretely moved after each frame Rotate sample check YES if sample is to be rotated in which helps to randomize sample orientation Title Title of sample scans sample identifier information Sample name Copy the Title here for it to display in JADE Sample number Another sample identifier any number will work Job name This 1s the filename and 1s saved to the folder set up in project file Run This will be added to the filename Frame This 1s added to the filename and generally is iterated with 001 002 Maximum display counts Sets the initial max scale value for the 2D image This setting can be adjusted during the range Realtime display Check YES to see t
5. the current status concerns of the diffractometer Calibrating the goniometer after a power outage After a power outage the goniometer will restart not knowing the current position Follow these steps to recalibrate the goniometer 1 2 3 4 5 6 Open up the GADDS software package Once the software has established a connection to the goniometer locate the goniometer controller box near the bottom of the diffractometer The front panel will have a power button a restart button and the manual control box will be connected to it Turn the power off to the goniometer control box Wait 30 seconds and then turn the power on Wait about 2 minutes for the system to reboot There is a floppy drive in the controller and it needs to load the firmware into memory before the goniometer can be used You need to now tell the software the angle positions the goniometer is at Go to Collect tab Goniometer Update Refer to the Goniometer Calibration section for more details a Update the 20 and w values by reading them off of the goniometer stage and then entering these values in the Update pop up window b When the power goes out the y stage typically relaxes to 75 so it is best to enter this value for a first guess Home the axis first by going to the Collect tab Goniometer Home Axis Select 4 y and wait till the axis is calibrated a If a few minutes pass and the goniometer has not stopp
6. 1024 015 mA 40 0 1024x1024 Cu Bias Cancel 1 2 3 4 Select edge ENTER L button Integrate ESC O buttons Quit 5 Go to the Special tab Level 2 6 Go to the Collect tab Goniometer Home axis For most applications calibrate the goniometer in the order 1 20 angle 4 y angle and 2 w angle IT IS IMPORTANT TO FOLLOW THIS ORDER This will drive 20 to 28 925 y to 42 124 and to 329 408 If you are aligning a single crystal to a particular alignment follow the order 1 20 angle 4 y angle 8 Aux 2 angle and 3 o angle If you feel that the goniometer is moving too far during a Home axis step press any keyboard key except Enter to abort the process Goniometer after M Home Axes procedure nm Axis number Velocity steps sec Sample Setup This section contains generalized sample mounting procedures for the Microdiffractometer For mounting of odd sample shapes or difficult alignment configurations it is best to consulate the XRD support staff first Reflection Mode 1 Make sure the beam stop is on the collimator if measuring at a low 20 2 Drive the goniometer to the reflection alignment position Go to the Collect tab Goniometer Drive Set 20 50 55 y 90 3 Mount the sample on the sample holder and attach it to the 1 4 circle Eulerian cradle 4 5 6 7 8 9 Put the goniometer into Manual mode Go to the Collect tab
7. University of Minnesota College of Science and Engineering Characterization Facility Bruker Microdiffractometer User Manual Version 2012 12 06 14 circle Eulerian cradle reference 20 two theta Detector angle GADDS angle 1 omega Sample incident beam angle GADDS angle 2 phi Sample rotation angle GADDS angle 3 X chi Sample tilt angle GADDS angle 4 Aux Video microscope GADDS angle 8 Translation 4 stage W Sample e goniometer uu mM Aligning camera Note 20 detector rotation axis same as W Initial Setup 1 Obtain a TLD ring from the ring bin found on the counter in room 22 Enter your name ring number user number sign in time and machine in the log book 2 Log on to the Microdiffractometer computer using your University x500 user name and password Domain AD a If you are associated with the University of Minnesota log on to the Characterization Facility s online reservation system Make sure to enter your TLD ring number the x ray generator counter time and the correct budget number 3 Open the video microscope program Video The software will automatically begin to display an image a Make sure that the video microscope is centered properly In Video select Tools Options and check that the origin x and y are correct These values are typically found in the Microdiffractometer maintenance binder If these values are not what they sho
8. ar user where year is the year of the measurement and user is either your name or user number NOTE A location must be entered here in order to create a project file GADDS does not accept periods in the folder or file name iv You may get a dialogue box saying D frames year user directory does not exist Create it Click Yes and the directory will be created PROJECT Options Project Information Sample Name 32 chars Sample Name Sample Number up to 4 digits 1 Directory Information Working Directory C frames 201 1 user Sample Information Clear Crystal info Y Reset to defaults Y 6 Make sure GADDS has loaded the correct calibration files Go to the Edit tab Configure User Settings and check the fields Direct beam X Direct beam Y and Sample to detector face The values can be found in the Microdiffractometer maintenance binder Again if these values are not what they should be first try restarting the GADDS software If the values are still incorrect contact the XRD staff Options for Edit Configure User Settings General User name Characterization Facility Site University Of Minnesota TC O Calibration data directory CADDSSCALIDS 7 Minimum 25 cps Timeout 10 sec Filename generation Temperature Controller Characters in base frame name 28 Low temp device Characters in Run 2 Current temperature Ho K Base of Run 36 Characters in Frame
9. e in changing the collimator tube c The top thumb screw must first be loosened to remove the installed collimator Once loosened the collimator tube can be remove Be careful that you do not bump the support structure or monochromator during this process d To install a new collimator tube the small hole on the collimator s cylinder face must be aligned with the alignment pin on the collimator support structure If properly attached the collimator size label should be facing upwards The thumb screw must be tightened such that the collimator is secured so it cannot shift or rotate 4 down perspective Say label Collimator support facing up thumb screw _ IN stad v pe N u moan e A Monochromator i EN labyrinth Goniometer Calibration Done at the beginning of each session 1 To prepare for goniometer calibration remove both the sample holder and the beam stop 2 The last user may have left the goniometer in an odd configuration so it is best to manually move the goniometer to a safe position Go to the Collect tab Goniometer Manual mode A window will pop up ignore these settings and press OK In Manual mode the goniometer angles can be manually driven with the control box Select the desired angle button and press the forward or back buttons choose fast or slow speed to drive the goniometer angles Manually drive 20 c and to roughly 50 50 and 90 respectively Both 20 and an
10. e previous file that was integrated Scale factor Multiplies integrated counts by factor Usually set to 1 When ready hit Ok button The file is now a raw file which may be read into JADE 2 GADDS General Area Detector Diffraction System V4 1 36 Copyr 1997 2009 Bruker tz mix Chi LaBF6 coupled 5_5_2011 LaBF6 coupled 5 5 2011 01 002 gfrm 102 59 deg 05 05 11 17 34 18 C t 77 60 deg reate 05 05 11 Normalize intensity 5 Bin normalized Sum pixels Avg pixel Normalized by arc length Normalized by solid angle Bin summation Step size INTEGRATE Options Title SamplID Sample Name File name 1 begi 103 77 2000 2Th 50 000 Format DIFFRACplus Append Y N Cancel 3 260 Scale factor 15 FloodFld 1024 015 KV 45 Spati 1024 015 mA 40 0 1024x1024 Cu Bias 1 2 3 4 Select edge M Move ENTER L button Integrate ESC O buttons Quit 5 Open the file in JADE as a Bruker Diffract plus file 6 There may be a question File appears in cts sec reload with total counts Select No and select No to subsequent questions until the file opens 7 If you measured more than one detector frame you can use JADE to combine the frames Open all of the frames at once using the green folder open icon at the top of the screen and use ctrl left click to select the desired frames 8 To align all the frames use the Dra
11. ed calibrating hit Ctrl C to abort the home step b Put the goniometer back to Manual mode and drive y to near 0 Then update y position to 0 following the procedure in step 6 c Put the goniometer back to Manual mode and drive y back to near 90 Then update position to 90 following the procedure in step 6 Re calibrate all the other axes following the procedure in the Initial Setup section Be extra mindful of where the goniometer drives to If you feel the goniometer 1s driving too far and may hit anything hit any keyboard key EXECPT Enter to abort the Home process 7 Record the event in the Microdiffractometer maintenance binder and contact the XRD support staff Laser does not turn on 1 Restart the computer 2 Follow the procedure described in the calibrating the goniometer after a power outage 3 Record the event in the Microdiffractometer maintenance binder Adding PDF library to your version of JADE 8 0 In Jade 8 0 s drop down menu select PDF then setup A warning message will appear select Ok Click on the top hand icon browse and select C PDF22004 pdf2 dat Click on the bottom hand 1con browse and select C Program Files MDI Jade 8 pdf jade pdf idx Click Close You should now be able to access the PDF library you may get an error message but if you enter Ok you will be able to access the library
12. et 20 0 0 and y 0 3 4 5 6 7 9 Capillary with Height extender 7 axis set screw position screw x axis v lt TT ee axis position screw 22 y position screw Mount the sample in the sample holder and attach it to the 1 4 circle Eulerian cradle Put the goniometer into Manual mode Go to the Collect tab Goniometer Manual and hit the OK button Rotate so either the x or y positioning screw points towards the camera see figure below Using the manual control box change the zoom on the microscope buttons 20 and o pressed simultaneously on the manual box to see the capillary To center the sample adjust the other positioning screw x or y that does not point towards camera and move the center of the capillary into the cross hairs of the alignment camera Rotate p by 90 so that the other positioning screw is now pointing towards the camera Again adjust the positioning screw that does not point towards the camera so that the middle of the capillary 1s centered in the camera cross hairs Continue to rotate g by 90 and adjust until the capillary does not significantly move out the center of the crosshairs and remains focused The edges of the capillary should be in focus Camera display Sample alignment x axis adjustment MA E m K y axis normal to camera 1 Sen pro E x axis adjustment E Transmission m
13. g scan overlays option to line them up 9 To merge the overlays together go to the Edit tab Merge Overlays Take the maximum 10 To save the merged file go to the File tab Save as dif or txt for an ascii file 11 The preferred method of data transfer is using either email or Netfiles It 1s best to zip all your files first so you don t have to email each item individually Shutting Down 1 To exit GADDS go to Project tab Exit The software will prompt to power the x rays down to standby levels Press the OK button 2 Close the Video alignment software 3 Remember to sign off the instrument with Charfac s online reservation system and entering the final meter reading 4 Return your TLD ring to the visitor drawer 5 Please keep the work area tidy by cleaning the sample area and sample holder Remember CharFac is a user facility and we all need to do our part to keep the work area clean Appendix Troubleshooting How to restart the x ray generator 1 2 3 4 Press the center black button located on the left side of the front panel of the x ray instrument with a circle in 1t The green light on the right black button On should light up Press the On black button and the x rays should come on Power up the x rays by opening the GADDS software Record the event in the Microdiffractometer maintenance binder with your name and date Please email the XRD staff about the incidence and
14. gles can be monitored by looking at the position post below the collimator see figure below and y 90 when the sample holder normal vector is parallel to the goniometer top 20 amp W position indicator Goniometer controller 3 When driven to these positions press the Esc key to exit Manual mode 4 It is important to check to see that 20 c and y are reasonably close to 50 50 and 90 respectively These values do not need to be exact but should be within 5 If this is not true the goniometer needs to have the axes values updated Go to the Collect tab Goniometer Update Enter 20 50 50 and y 90 in the window and press Ok NOTE It is important to only do this if the values reported by software are significantly different from actual positions Contact the XRD support staff 1f you feel uncomfortable in performing this step 2 GADDS General Area Detector Diffraction System V4 1 36 Copyr 1997 2009 Bruker X LaBF6 coupled 5 5 2011 LaBF6 coupled 5 5 2011 01 002 gfrm 05 05 11 17 34 18 05 05 11 a 0 Options for Collect Goniometer Update 2 Theta 40 0000 0 00000 6755027 1 299 991 Distance 15 0000 Size 1024 2th begi 23 6000 2th en 56 7000 chi begi 103 500 chi ed 77 2000 Phi 90 l Check these BEP Ome 50 000 Phi 306 267 Chi 90 000 Aux 3 260 values Shutter CLOSED Distance 15 0000 FloodFld 1024 015 KV 45 Spatial
15. he data collected in real time Pre clear Check YES Capture Video Image Gives you a snapshot of your sample while scanning Auto Z align Option is not available on this system 2 When everything is configured check to see if the doors are closed and the reset button 1s pushed To start click OK Options for Collect Scan SingleRun Frames Seconds frame B o 2 Theta 50 000 deg Omega 50 000 deg Phi 306 267 deg Chi 90 000 deg X 0 000 Y 0 000 Z 0 000 Aux 3 260 mm Scan Axis Coupled Frame width Mode STEP Rotate sample Sample Osc None Amplitude 0 Frame header information Title Title Sample name Sample Name Sample number 1 Filename generation Job name Filename Run 1 Frame 001 First filename Max display counts 30 M iv Realtime display iv Pre clear Capture video image Auto Z Align cm For a series of scans which require moving more than one axis 1 Go to the Collect tab Scan Edit Run 2 Enter or edit a set of collections 3 Remember the line number s counting from the top line 4 WRITE this set up to your folder 5 Select OK SCAN MultiRun List 51 lines Run Frame Theta Omega Chi Asis Width Frames Time 01 01 001 223 613 106 020 0 000 45 000 4 15 000 4 6000 00 005 223 613 106 020 180 000 45 000 4 15 000 4 6000 00 Cancel Print Write Read 6 Go to the Collect tab Scan Multi Run ono He ga bn l
16. nt BISA A C T adjustment Reflection mode for optically transparent films and substrates Advanced users 1 Optically transparent films on transparent substrates can be problematic as the alignment laser can penetrate through the substrate and reflect back towards the camera This effect can produce multiple laser spots at different z height positions Alignment of the z axis to one of these incorrect laser spots will produce shifts in the measured diffraction pattern There are a couple methods to align to an optically transparent film amp substrate system 2 Method 1 Align the laser to the top laser spot shown in the video software NOTE This method should only be used when the user is comfortable with the alignment process and sometimes the top most laser spot may not be visible 3 Method 2 Using the reflection mode method described in the last section align to a piece of dust fingerprint scratch or a marked structure a Sharpie pen spot at the corner of the sample works great After alignment adjust the x or y position screws to move towards a region of interest to measure 4 Method 3 Drive the goniometer to the perpendicular alignment position a Goto Manual mode Go to the Collect tab Goniometer Manual and hit the OK button Manually drive to 20 0 330 and y 90 NOTE o will need to be rotated with decreasing angle passing thru 0 in order to reach 330 b Drive slowly until
17. ode for films 1 Make sure the beam stop is on and rotated back 2 Drive the goniometer to the alignment position Go to the Collect tab Goniometer 3 4 5 6 T 8 Height extender set screw axis ang position screw Drive Set 20 0 0 and y 0 Type L to turn the laser on Sample alignment Sample normal to y axis position screw 7 axis position screw position screw to camera Mount the sample in the sample holder and attach it to the 1 4 circle Eulerian cradle It 1s important to have the film s surface normal to point parallel with either the x or y positioning screw Rotate o so the film surface normal points towards the camera see figure above This should also make one of the position screws to point towards the camera as well Using the manual control box change the zoom on the microscope buttons 20 and o pressed simultaneously on the manual box to see the sample and laser To center the sample adjust the positioning screw that points towards the camera so that the laser 1s centered in the camera cross hairs and the image is focused Use both the z axis and the other x or y which was not used to focus positioning screw to position the desired sample location to the cross hairs When aligned rotate o manually to align the film s surface normal to point perpendicular with the collimator Simple scan data collection single run or scans with only
18. rew position screw SS E LI X axis position screw AA y axis position screw 4 Rotate so either the x or y positioning screws is parallel with the goniometer base horizontal and the other position screw is pointing towards the ceiling vertical see figure below 5 Using the manual control box change the zoom on the microscope buttons 20 and pressed simultaneously on the manual box to see the capillary 6 To center the sample adjust the vertical positioning screw x or y which raises or lowers the capillary vertically such that the center of the capillary is in the cross hairs of the alignment camera The positioning screw to adjust is perpendicular to the goniometer base 7 Rotate p by 90 so that the other positioning screw is now horizontal x or y center the sample Again adjust the vertical positioning screw so that the middle of the capillary is centered in the camera cross hairs 8 Continue to rotate by 90 intervals and adjust until the capillary does not significantly move out the center of the crosshairs and remains focused Camera display sample alignment pnm x or y axis adjustment oe Capillary E to camera NE x or y axis Transmission mode for capillaries Method 2 1 Make sure the beam stop 1s on and rotated back 2 Drive the goniometer to the alignment position Go to the Collect tab Goniometer Drive S
19. s how to convert a two dimensional diffraction pattern to an one dimensional intensity versus 20 data set For more advanced data processing 1 texture analysis crystallite size percent crystallinity etc please consult the XRD staff 1 3 4 Options for Peaks Integrate Chi 2theta Start End Display the first file collected Go to the File tab Display Open If you want to save the 2D image go to the File tab Print Enter a filename and path using the button and select the desired image format bmp or tiff recommended Integrate the 2D data Go to the Peaks tab Integrate Chi a b d Normalize Intensity Method of integration and averaging over 2D dataset Usually set to 5 Bin normalized for wide angle XRD measurements Step Size 0 04 at 15 0 cm sample to detector distance 0 02 at 30 0 cm sample to detector distance or 0 08 at 6 0 cm sample to detector distance Click OK and manually move the edges of the integration box by pressing 1 2 3 and 4 on the keyboard see bottom of screen for info Left mouse click or hit Enter to integrate the data A window will appear for saving the data set a b C d ng 36 40 deg Start 48 90 deg End Title SampleID Sample name goes here Filename Location and filename for saved data Format DIFFRAC Plus for post JADE processing or PLOTSO ascii file Append Check Yes 1f you are adding the integrated to th
20. the substrate s surface appears to be parallel with the vertical crosshair of the alignment camera It is best to slowly rock back and forth to observe when the surface becomes normal with respect to the camera c Adjust the z positioning screw to align the substrate s surface on top of the vertical cross hair of the alignment camera d Once aligned manually drive back to 55 5 NOTE Aligning optically transparent film substrate systems can be challenging and requires significant practice for proper alignment Be aware that there may be alignment errors in measured diffraction patterns if the sample is not properly aligned Camera display Substrate ERE 8 surface zaxis BE adjustmentp Transmission mode for capillaries Method 1 Transparent sample alignment 7 axis V adjustment Lowy p Sample normal _L to camera direction 1 Make sure the beam stop is on and rotated back 2 Go to Manual mode Go to the Collect tab Goniometer Manual and hit the OK button Manually drive to 20 20 w 330 and y 90 NOTE will need to be rotated with decreasing angle passing thru 0 in order to reach 330 3 Mount the capillary sample on the sample holder and attach it to the 1 4 circle Eulerian cradle See the image below for a picture of the capillary holder mounting Capillary with Height extender pi z axis set sc
21. uld be contact the XRD laboratory staff Options Scaling C j f ance Pixels zoom 1 Reticle Color Microns Select Color from T able R 0 G 0 255 Reticle zoom 1 Tilt 0 000 degrees x Pixels Major 100 0 Y Pixel e Minor 20 0 microns Magnification Zoom Current 11 371 Check these values Camera Zero Offset Angle 0 000 degrees True Mag 7x A 4 Open the diffractometer software GADDS There should be a desktop shortcut labeled GADDS 3 or 4 Circle A window will appear asking to power the generator to operating condition 45 kV amp 40 mA Click the Yes button a NOTE Do not open the program GADDS offline to control the goniometer This program is useful for data analysis but cannot control the goniometer 5 Create a new project file typically referred to as a gadds nc file This will allow you use the most recent calibration values a Goto the Special tab select Level 2 b Goto the Project tab select New c Enter all relevant information in the corresponding fields values can also be left blank for now except for the Working Directory field i Sample Name Enter sample name This 1s associated to the filename and cannot contain spaces or period Title Enter the title for your first sample i Working Directory Enter the folder directory where you would like to save your data Typical location is D frames ye
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