Bruker D8 Discover User Manual (Version: 2012.08.08)
Contents
1. 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 library2. integrated e Scale factor Multiplies integrated counts by factor Usually set to 1 f When ready hit Ok button The file is now a raw file which may be read into JADE Options for Peaks Integrate Chi X GADDS General Area Detector Diffraction System 4 1 36 Copyr 1997 2009 Bruker f fei 2theta Chi LaBF6 coupled 5_5_2011 Start 36 40 deg Start 102 50 deg os os in 1734718 O 007 9frm E n 28 90 dea End 77 60 dee i Created 05 05 11 ae i 00000 l wes ounts Normalize intensity 5 Bin normalized ime s 99 991 G 15 nce gt i aan Siz 02 Step size Sum pixels ize 44 Avg pixel i 1 begi 23 6000 gt Normalized by arc length h en 56 7000 Normalized by solid angle H chi begi 103 500 chi en 77 2000 Bin summation INTEGRATE Options Title SampID Sample Name File name C A framestyearjuserifilename B i S 2Th 50 000 i r e 00 Format DIFFRACplus Append Y N Scale factor 1 Spatial 1024_015 mA 40 0 Cancel 1024x1024 Cu Bias 1 2 3 4 Select edge M Move ENTER L button Integrate ESC O buttons Quit 3 260 Distanc A FloodFld 1024_015 KV 45 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
3. all scans in the listing l Mode Step is usually used here the Frame Width is discretely moved after each frame m Rotate sample Does not work in this goniometer n 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 om SCAN MultiRun List 51 lines Run Frame 2 Theta Onega Chi Axis Width Frames Time 01 001 20 000 10 000 0 000 0 000 1 0 250 360 120 00 Options for Collect Scan MultiRun Job name Job name e Title Tite Sample name Sample name see Sample number a Max display counts 31 l v Realtime display v Pre clear Sequence of starting run 1 Sequence of ending run 50 Mode SCAN l Rotate sample Sample Osc None Amplitude 0 0 mm Capture Video Image Multi sample target setup 1 To scan multiple samples it is best to either mount multiple samples on a single sample holder or mount multiple holders in a vertical fashion across the goniometer stage as seen in the image below 2 Using Manual Mode drive 20 and to the sample alignment position Set 26 50 55 Be extra mindful of sample collisions 3 Go to the Collect tab Scan PickTargets 4 5 6 7 8 9 A window will appear displaying Pre clear existing target list select Yes to clear out the existing target location list I
4. 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 camera software NOTE This method should only be used when the user is comfortable with the alignment process as sometimes the top most laser spot may not be visible 3 Method 2 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 to move towards a region of interest to measure Simple scan data collection single run or scans with only one axis movement 1 Go to the Collect tab Scan Single Run ono oR e de Qi o Frames Number of scans Seconds frame Data collection time per frame in seconds 20 Center 20 angle in frame w Incident beam angle typically set to 1 2 of 20 for general analysis x Horizontal position of sample stage in mm entering will put x exactly where you aligned it y Vertical position of sample stage in mm x Height position of sample stage in mm Aux Camera zoom typically set to 6 8 Scan Axis What angle changes between each frame 1 20 2 5 gt x 6 y 7 z none coupled Frame Width Step size of Scan Axis angle if more than 1 frame is used k Mode Step is usually used here the Frame Width
5. is discretely moved after each pi ry nop Ong a2 s 6 frame Sample Osc Option to oscillate sample in x y z x amp y or y amp z to increase number of crystallites being analyzed Useful for large crystallite samples Amplitude Magnitude of oscillation in mm 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 is the filename and is saved to the folder set up in project file Run This will be added to the filename Frame This is 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 the data collected in real time Pre clear Check YES Capture Video Image Gives you a snapshot of your sample while scanning x Auto Z align Auto height alignment NOT RECOMMENDED 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 1 Seconds frame 12000 2 Theta 37 440 deg Omega 13 530 deg Phi0 000 Chi 90 000 x 24 221 mm Y 30 910 mm Z 6 531 mm Aux 7 000 mm Scan Axis Coupled Frame width 300 amp 8 Mode STEP vl Rotate sample Sample Osc tc Amplitude 02 mm Frame header inform
6. press the Esc key to exit Manual mode 4 It is important to check to see that 20 is reasonably close to 50 and is reasonably close to 10 before continuing 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 and 10 in the window and then 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 if you feel uncomfortable in performing this step C3 GADDS General Area Detector Diffraction System 4 1 36 Copyr 1997 2009 Bruker EB x LaBF6 coupled 5_5_2011 LaBF6 coupled 5_5_2011_01_002 gfrm OS OS 11 17 34 18 Created 05 05 11 Mag Quad 1 0 2 Theta 40 0000 width 0 00000 Counts 6755027 Time s 299 991 Distance 15 0000 Size 1024 2th begi 23 6000 2th en 56 7000 chi begi 103 500 chi e 77 2000 Options for Collect Goniometer Update 2 Theta Omega Phi i an Check these Senak Ome 50 000 Phi 306 267 Chi 90 000 Aux 3 260 values Shutter CLOSED Distance 15 0000 FloodFld 1024_015 KV 45 Spatial 1024_015 mA 40 1024x1024 Cu Bias Cancel 1 2 3 4 Select edge M Move 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 goniomete
7. 0 mictons Y Pixel iig Minor 20 0 microns Check these values Magnification Camera Zero Offset Zoom Curent 1 371 x Angle 0 000 degrees True Mag 7x x 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 Go to the Special tab select Level 2 b Go to 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 1 Sample Name Enter sample name This is associated to the filename and cannot contain spaces or period ii Title Enter the title for your first sample ti Working Directory Enter the folder directory where you would like to save your data Typical location is C frames year 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 asking i
8. 8 9 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 to the proper position by pressing the x or y drive buttons Button 5 or Button 6 respectively in either fast or slow speed mode to the desired location Then adjust the sample height with the z drive button Button 7 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 Button 8 on the goniometer controller adjust the sample in the z direction Zoom in and fine tune the z adjustment Fine adjustment of the z height should be done at the maximum zoom Once the laser is close to the center move the goniometer head x and y positioning screws to the specific area to be analyzed and readjust the z position if necessary Camera display R ae z axis 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
9. 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 9999 will run all scans in the listing q Mode Step is usually used here the Frame Width is discretely moved after each frame r Rotate sample Does not work in this goniometer s Capture Video Image Gives you a snapshot of your sample while scanning Do not check this for the multi scan option t Pre clear Check YES ono oe gq rh Shee eS oO SS 10 When done press OK and check for any pre run error messages SCAN MultiTargets List 2048 lines Runt Frames Two samples X Y Z 01 001 02 001 Options for Collect Scan MultiTargets Omega fi 2 5 Phi 0 000 Chi 90 000 Frame width 25 Secondsfframe 300 21 500 18 193 6 718 26 24 1 30 910 6 531 vertically mounted d Sample name Sample name Sample number 1 Max display counts 31 W Realtime display W Pre clear Sequence of starting run 1 v Sequence of ending run 3999 xj Mode STEP l Rotate sample Sample Osc None Amplitude 0 mm M Capture Video I
10. University of Minnesota College of Science and Engineering Characterization Facility Bruker D8 Discover User Manual Version 2012 08 08 Auto x y z Stage Reference 20 two theta Detector angle GADDS angle 1 w omega Sample incident beam angle GADDS angle 2 x Horizontal position of sample stage GADDS angle 5 y Vertical position of stage GADDS angle 6 z Height position of stage GADDS angle 7 Aux Video microscope GADDS angle 8 Collimating tube a Translation J jenna stage Pami ME a me Aligning TA laser a WwW y are gt FA we eee 3 GAE Detector Rex 42 A GIAA i Goniometer Controller Reference Button legend Button 1 26 drive button Button 2 drive button Button 3 Not used Button 4 Not used Button 5 x axis drive button Button 6 y axis drive button Button 7 z axis drive button Button 8 Aux zoom drive button Button Faster drive velocity Button Slower drive velocity Button 1 Drive angle axis to a higher value Button Drive angle axis to a lower value To drive an angle axis Enter Manual mode in the GADDS software see the Goniometer calibration section of the manual for details Press the Shift and then the DRVC button to toggle between different drive modes Most users prefer to select the drive m
11. 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 Drag 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 Nettfiles It is 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 6 Remember CharFac is a user facility and we all need to do our part to keep the work are clean Appendix Troubleshooting Adding PDF library to your version of JADE 8 0 1 2 3 4 5 6 In Jade 8 0 s drop down menu select PDF then setup A warning message will appear select Ok Click on the top hand or icon browse and select C PDF22004 pdf2 dat Click on the bottom hand icon browse and select
12. ation Title Tithe O OO a aaaaa Sample name Sample name Sample number 1 Filename generation Job name Job Name Run 1 Frame 003 First filename 9 Max display counts 1 5 Vv Realtime display iv Pre clear Capture video image Auto Z Align cmt For a series of scans which require moving more than one axis Multi run 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 6 Go to the Collect tab Scan Multi Run 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 Sample Osc Option to oscillate sample in x y z x amp y or y amp z to increase number of crystallites being analyzed Useful for large crystallite samples g Amplitude Magnitude of oscillation in mm h Realtime display Check YES to see the data collected 1n real time i Pre clear Check YES ono oe mh 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 9999 will run
13. f you should save the previous user settings Click NO v You may get a dialogue box saying C frames year user directory does not exist Create it Click Yes and the directory will be created PROJECT Options Project Information Sample Name 32 X chars Sample_Name Sample Number up to 4 digits i Theme Directory Information Working Directory C frames 2011 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 D8 Discover 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 OfMinnesota 1 SCS Calibration data directory 8000990800 Minimum 25 cps Timeout 10 sec Filename generation Temperature Controller Characters in base frame name 28 I Low temp device Y N Characters in Run Current temperature 1 K Base of Run Characters in Frame Detector Base of Frame Direct beam X unw Direct beam Y unw Check these Framesize values Sample to detector face cn 7 Check to make sure that the correct software drive limits are conf
14. igured 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 Gomiometer Limits 2 Theta limit 10 000 To Omega limit 5 000 gt To Omega 2 Theta limit 180 000 To Phi limit both O none 0 000 To Chi limit both O none 0 000 To X limit both 0 none 50 000 To Y limit both O none 50 000 To Z limit both O none 50 000 To Aux limit both O none 1 000 To cnet b If the values loaded do not match the above image you have two options to correct the problem 1 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 ii 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 uncomfortable in changing the collimator a The top thumb screw must first be loosened to remove the installed collimator Once loosened the collimator tube can be removed Be careful that y
15. mage M Auto Z alignment aj Data Analysis NOTE This section describes how to convert a two dimensional diffraction pattern to an one dimensional intensity versus 20 data set For more advanced data processing i e texture analysis crystallite size percent crystallinity etc please consult the XRD staff 1 Display the first file collected Go to the File tab Display Open 2 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 3 Integrate the 2D data Go to the Peaks tab Integrate Chi a Normalize Intensity Method of integration and averaging over 2D dataset Usually set to 5 Bin normalized for wide angle XRD measurements b 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 c 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 d Left mouse click or hit Enter to integrate the data 4 A window will appear for saving the data set a Title SampleID Sample name goes here b Filename Location and filename for saved data c Format DIFFRAC Plus for post JADE processing or PLOTSO ascii file d Append Check Yes if you are adding the integrated to the previous file that was
16. n this mode the software places GADDS in Manual Mode Align the goniometer to the first desired target as one would do for a Single Run scan Once aligned in x y and z press Esc on the keyboard A popup window will display Do you want to enter this position in the targets list press Yes Another popup window will appear displaying Do you want to enter more positions in the target list press Yes if there are more samples to align press No if this is the last sample to align If Yes is pressed GADDS will be placed back into Manual mode for alignment of the next sample Repeat Steps 6 amp 7 until all samples have been aligned The sample list can be checked by going to the Collect tab Scan EditTarget An example of the EditTarget window 1s shown below Go to the Collect tab Scan MultiTaregets Frames Number of scans Seconds frame Data collection time per frame in seconds 20 Center 26 angle in frame w Incident beam angle typically set to 1 2 of 20 for general analysis Scan Axis What angle changes between each frame 1 20 2 5 gt x 6 y 7 z none coupled Frame Width Step size of Scan Axis angle if more than 1 frame is used Sample Osc Option to oscillate sample in x y z x amp y or y amp z to increase number of crystallites being analyzed Useful for large crystallite samples Amplitude Magnitude of oscillation in mm Title Title of your run Sample name
17. ode that configures the controller screen to display an image similar to what is shown above Next press the button corresponding to the desired angle axis to be driven The press either the or button to change the velocity speed and hold the t or button to drive the angle axis to the desired position The screen will update during the driving procedure 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 D8 Discover computer using your x500 username 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 D8 Discover maintenance binder If these values are not what they should be contact the XRD laboratory staff Options Scaling c f ance j Pixels zoom 1 Reticle Color Microns Select Color from T able F fo G fo B 1255 Reticle zoom 1 Tilt 0 000 degrees x Pixels Major 100
18. ou do not bump the support structure or monochromator during this process b To install a new collimator tube the small hole on the collimator 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 Top down perspective me M Collimator support thumb screw Keii i y n e N ug gt r a Monochromator Collimator label N labyrinth facing up E amp i 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 drive speed and then press the forward or back arrow buttons to drive the goniometer angles Manually drive 20 to roughly 50 and to roughly 10 Both 20 and angles can be monitored by looking at the position post below the collimator see figure below 20 amp w position indicator ee nh M 3 When driven to these positions
19. r in the order 1 26 angle and 2 angle IT IS IMPORTANT TO FOLLOW THIS ORDER This will drive 20 to 22 742 and to 7 659 The software may ask to Pre drive x amp z axes to zero are you sure before performing the Home command click the Yes button a Ifa multi sample measurement is desired follow the order 1 20 angle 8 Aux 2 angle 5 x translation 6 y translation 7 z translation 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 Home Axes procedure Options for Collect Goniometer Home axis Axis number 1 2Theta 1 2Theta cn 2 Omega X 6 Y Z 8 Aux 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 3 Put the goniometer into Manual mode Go to the Collect tab Goniometer Manual and hit the OK button 4 Mount the sample on the sample holder and attach it to a stage screw hole The x axis may need to be driven to allow for the holder to be mounted 5 6 7
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