Collecting Powder Data on a Mo SMART1000 CCD
Contents
1. Default option Makes a scale factor based on the overlap of range A and range B Thus range A may vary from 100 to 0 and the reverse for range B i e x A 1 x B The background of range B is not compensated to match the background of A Scale option Same as the default option but the background of range B is compensated to match the background of A by the addition of a constant so that the B background is either raised or lowered to match A Average option Range A and range B are averaged such that A B 2 Both the Average and Scale Options may be checked to obtain an Average with background compensation as in A B s 2 We will use the Scale option only here 1 Complete the data in the window Project directory E Geology Sam Input filenames provide each filename in name raw refers to Diffracplus files for MDI JADE or DiffracPlus This is the most likely format you would want to use name plt refers to Plotso file name uxd refers to ascii file type Set range to 1 all in first box Output file set to name_T to create name_T out file for raw file output set to name_TP to create name_TP out file for Plotso file output 2 Transfer the file to the Powder Diffractometer computer for further processing with the MDI JADE or Bruker DIFFRAC program For reasons of your own you may want to continue to PLOTSO h Enter Plotso program Bruker AXS Plotso Input filename dat Use the o2. The Merge program places all three frames on to one scale Default option Makes a scale factor based on the overlap of range A and range B Thus range A may vary from 100 to 0 and the reverse for range B i e x A 1 x B The background of range B is not compensated to match the background of A Scale option Same as the default option but the background of range B is compensated to match the background of A by the addition of a constant so that the B background is either raised or lowered to match A Average option Range A and range B are averaged such that A B 2 example list Both the Average and Scale Options may be checked to obtain an Average with background compensation as in A B s 2 Use the Scale option only here 1 Complete the data in the window Project directory E Geology Sam Input filenames provide each filename in name raw refers to Diffracplus files for MDI JADE or DiffracPlus This is the most likely format you would want to use Set range to 1 all in first box Output file set to name_T to create name_T out file for raw file output 2 Transfer the file to the Powder Diffractometer computer for further processing with the MDI JADE or Bruker DIFFRAC program At UIC and for GADDS the best calibration values of a detector position at a resolution of 1024 and for 12 cm the best values are 11 906 distance 514 50 x and 516 93 y h Enter the DIFFRAC or
3. The values here are given as examples they will change depending on the latest calibration Change resolution frame size setting from 512 to 1024 Change sample to detector setting from 5 972 cm to 11 891 cm Change x distance from 257 884 to 517 488 Change y distance from 255 864 to 512 428 When exiting the Configuration file the system will ask if it should modify the collision limit settings Answer yes to do this WHEN FINISHED WITH YOUR EXPERIMENTS BE CERTAIN TO RESET THE DETECTOR TO 60 mm ON THE DETECTOR ARM CHANGE BACK TO THE 0 5 MM COLLIMATOR AND RETURN TO THE REGULAR BEAM STOP c Place the 0 2 mm capillary containing the powder on the goniometer and optically align in the Bruker APEX System as you would a single crystal See Data Collection section p 4 7 to 4 11 stopping at item 14 of the User s Manual for the SMART APEX Now establish the appropriate dark current Go to Detector Dark Current Set seconds per exposure to 1200 of exposures to average 2 Output file 3125H 120 _DK Label the new dark current as 3125H120 _DK where 3120 is the serial number of the UIC APEX Use your serial number instead of course H high resolution of 1024 x 1024 and 120 1200 sec The dark current needs to be collected just once prior to data collection The APEX detector does not require a spatial correction The flood field correction will not differ for the APEX running at different frame collection times in con
4. JADE program Compare the scan to the JCPDS PDF file use the same one that GADDS uses as given above in the frist page of the Appendix 1 Check to determine that the scan does NOT appear as Figure 2 or with a consistently smaller or larger two theta for all peaks in the pattern when compared to the standard indicating an error in x and possibly y If so you will need to start the calibration process over paying special attention to errors in the x or d parameter Once the patterns appear correct make a least squares refinement of the cell parameters Compare to the JCPDS and determine the best possible cell parameters you can achieve end of calibration Appendix 3 Listing of slm files used for data collection in SMART Powd1200 sIm file listing GONIOMETER ZERO SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLA Y 1 SAVE POWD_0 rot TITLE Powder generic data collection file amp DISPLAY 1 GONIOMETER DRIVE 20 00 0 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE POWD_20 rot TITLE Powder generic data collection file amp DISPLAY 1 GONIOMETER DRIVE 35 000 0 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLA Y 1 SAVE POWD_35 rot TITLE Powder generic data collection file amp DISPLAY 1 Gan_1200 sIm file listing GONIOMETER DRIVE 35 000 20 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GAN35m20 rot TITLE Gan
5. scale factor based on the overlap of range A and range B Thus range A may vary from 100 to 0 and the reverse for range B i e x A 1 x B The background of range B is not compensated to match the background of A Scale option Same as the default option but the background of range B is compensated to match the background of A by the addition of a constant so that the B background is either raised or lowered to match A Average option Range A and range B are averaged such that A B 2 Note Both the Average and Scale Options may be checked to obtain an Average with background compensation as in A B s 2 1 Complete the data in the window Project directory E Geology Sam example Input filenames provide each filename in list First take all the files of one two theta value and merge by the Average option name raw refers to Diffracplus files for MDI JADE or DiffracPlus This is the most likely foramt you would want to use name plt refers to Plotso file name uxd refers to ascii file type Set range to 1 all in first box Output file setto name_T to create name_T out file for raw file output 2 You should now have three output files containing the merged via average data for each of the two theta ranges Now take the output files and make them input for the next merge this time via the Scale Option Complete the data in the window Project directory E Geology Sam example Inp
6. Tech note 2008 04 09 Joseph H Reibenspies Department of Chemistry Texas A amp M University Copyright 2008 Collecting Powder Data on a Mo SMART1000 CCD APEX and APEXII Move the beam stop as close to the sample as possible without blocking the very low angle diffraction peaks Move the detector to about 6 cm and set size to 1024 Use the calibration single crystal to obtain crystal to detector distance x distance and y distance values Mount your sample on a loop or pin by first wetting the sample with a minimum of mineral oil and rolling the sample into a sphere If possible produce a sample that is larger than the X ray beam this will reduce air scatter but will increase non Bragg scattering from the oil and the mount Place your sample on the diffractometer and cool to at least 60C Center the sample as you would for a single crystal SMART APEX I Drive the goniometer to 30 deg two theta 0 0 deg theta and 0 0 deg phi chi fixed Take a rotation photo be sure to uncheck the DRIVE to ZERO box For the Smart 1000 unwarp the frame not necessary for the APEXI and save the file APEXII Start the APEX2server program Center your sample and then choose simple scans Drive the goniometer to 30 deg two theta 0 0 deg theta and 0 0 deg phi Select the 360 deg phi scan Use the frmutility in Bruker AXS folder to convert the frames to the older SMART frame FIT2D Use FIT2D http www esrf eu computing scientific FIT2D to gen
7. YLID should be done with the resolution in the config file set at 1024 Using YLID at UIC determined values at d 11 891 x distance 517 488 y distance 512 428 were determined You will use the same technique as is done for the 60 mm calibration b Double click on the SMART icon to open Then go to Edit Config User Settings Change resolution Frame size setting from 512 to 1024 Change crystal to detector setting from 5 972 cm to 11 891 cm Change Direct beam x distance from 257 884 to 517 488 Change Direct beam y distance from 255 185 to 512 428 Your values for the crystal to detector distance x distance and y distance may be slightly different depending on the results from the last tube optimization or realignment When exiting the Configuration file the system will ask if it should modify the collision limit settings Answer yes to do this WHEN FINISHED WITH YOUR EXPERIMENTS BE CERTAIN TO RESET THE DETECTOR TO 60 mm ON THE DETECTOR ARM c Place the capillary on the goniometer and optically align in the Bruker APEX System as you would a single crystal See Data Collection section p 4 7 to 4 11 stopping at item 14 of the User s Manual for the SMART APEX Now establish the appropriate dark current Go to Detector Dark Current Set seconds per exposure to 1200 of exposures to average 2 Output file 3125H 120 _DK Label the new dark current as 3125H120 _DK where 3120 is the serial number of the UIC APEX H h
8. ak integration Two theta and chi start and end points will be set graphically so leave values as is In future releases of GADDS the chi integration angle is renamed to gamma At omega of zero chi equals gamma but at any other omega value chi is not equal to gamma Bin Normalize intensity 5 Future releases of GADDS will drop other intensity algorithms step size 0 02 always keep the same for all rotation frames usually 0 02 A white outline will be superimposed over the frame Sequentially type 1 2 3 and 4 to see how each can be adjusted 1 adjusts center point 2 adjusts 2theta region 3 adjusts the lower chi region 4 adjusts the upper chi region Adjust to the extremes of the frame but not beyond where there are no data Keep adjustments to within 180 and maintain for all frames After each adjustment 1 2 3 or 4 click the left mouse button to accept adjustment After the 4 adjustment is entered click the left mouse button to see integrate options display Formats Use DiffracPlus format for Siemens DiffracPlus software and for MDI JADE software name raw Append Choose Y check to set the output up to allow the merging of several sets of data 1 e at 0 20 35 rotation frames Repeat chi integration sequence for each rotation frame i e at 0 20 and 35 3 Minimize the GADDS window g Enter Merge program click on Bruker AXS Programs Merge
9. and calculated rings in the detector center Then use the distance parameter to get full coincidence To adjust the settings toggle between center mode which changes x and y and calibrate mode which changes the crystal to detector distance by pressing keyboard c and nudging the rings with the arrow keys or with the mouse Record the settings for x y and distance Repeat the procedure above for the remaining frame e g 35 Then review the recorded settings and determine the optimum parameters that best fit the 20 and 35 frames if your phases involve mostly low angle reflections then it may be advisable to consider the 0 and 20 frames NOTE Now treat the frames of the calibration sample e g 0 20 35 as an unknown and determine an Intensity vs Two theta plot a scan You should compare the scan to the JCPDS pattern in DIFFRAC or JADE and then determine the cell parameters Because the same frames were used to derive the scan that was also used in calibration the observed unit cell parameters should be in close agreement with those given in JCPDF f First generate a scan 1 File Display Open Bring in the first Frame Set High Counts to a large number e g 4095 If Mag is left as 1 0 recommended then Region X Y can be left at the default setting and they have no effect on the data 2 Integrate the Debye rings to one linear integrated value Peaks integrate chi to set conic pe
10. dolfi pattern DISPLA Y 1 GONIOMETER DRIVE 35 000 0 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GAN350 rot TITLE Gandolfi pattern DISPLAY 1 GONIOMETER DRIVE 35 000 20 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GAN3520 rot TITLE Gandolfi pattern DISPLAY 1 GONIOMETER DRIVE 20 000 20 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GAN20m20 rot TITLE Gandolfi pattern DISPLA Y 1 GONIOMETER DRIVE 20 000 0 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GAN200 rot TITLE Gandolfi pattern DISPLAY 1 GONIOMETER DRIVE 20 000 20 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GAN2020 rot TITLE Gandolfi pattern DISPLAY 1 GONIOMETER DRIVE 0 000 20 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GANOm20 rot TITLE Gandolfi pattern DISPLAY 1 GONIOMETER DRIVE 0 000 0 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GANO00 rot TITLE Gandolfi pattern DISPLAY 1 GONIOMETER DRIVE 0 000 10 000 0 000 54 736 SCAN ROTATION 1200 00 PHI 0 00 CHI 54 74 DISPLAY 1 SAVE GANO10 rot TITLE Gandolfi pattern DISPLAY 1 GONIOMETER ZERO
11. entered click the left button to see integrate options display Formats Use DiffracPlus format for Siemens DiffracPlus software and for MDI JADE software name raw Use Plotso to get format that graph the Intensity vs Theta name pH Not usually done Append Choose Y check to set the output up to allow the merging of several sets of data 1 e at 0 20 rotation frames Note After making a diffraction profile check to make certain that the profile produced makes sense for the frame undergoing the conic peak integration chi or gamma Occasionally a hot pixel will be present in the frame that causes a high peak in the diffraction profile that should not exist If you notice an apparently anomalous peak File gt Display gt Open set High Counts to 50 000 A white pixel should be evident at the two theta position where there is an anomalous peak It is possible to work around the hot pixel but it is not necessary at this point In JADE for example it is very easy to remove a peak that formed from an exited pixel Peaks formed from hot pixels appear as spikes and they have a different shape from peaks obtained from the sample Repeat chi integration sequence for each rotation frame i e at 0 20 and 35 4 Minimize the GADDS window g Enter Merge program click on Bruker AXS Programs Merge The Merge program places all three frames on to one scale example list
12. erated the 1D trace Save in the chi format Use ConVX to convert the file to a Bruker EVA RAW file Use PowderX to read the file and locate peaks Appendix 1 A Beginner s Guide to SMART Gadds Brief procedures for powder diffraction data collection on the APEX SMART System S Guggenheim 3 May 2004 The first two parts of this guide Appendix 1 provides recipes for obtaining Debye Scherrer type and Gandolfi type data respectively It is assumed that the user has minimal experience with SMART and no experience with GADDS Appendix 2 shows how to calibrate the instrument a necessary requirement before data collection This needs to be done once after a tube installation and perhaps every 6 months thereafter Appendix 3 lists the slm files for batch data collection for part 1 and part 2 It is required that the user has a program for peak locate JCPDF PDF searches etc such as either DIFFRAC or DIFFRAC the Bruker software for processing a pattern or MDI JADE 1 Data Collection for Debye Scherrer type Patterns Using the APEX SMART System a Change the detector to crystal distance to 12 cm on the goniometer It is best to use an extended beam stop and the 0 2 mm Monocap if you have these available otherwise use the normal beam stop and the standard collimator The Administrator should mount the beam stop and collimator for you b Double click on the SMART icon to open Then go to Edit Config User Settings
13. frame of first rotation frame collected at 0 two theta i e cor_0 rot In high counts use a fairly high value i e 4095 because the frame was collected at 1200 seconds This will give nice contrast in color in red yellow white NOTE ON THE CALIBRATION PROCESS There are three parameters in GADDS that require calibration namely d x and y Parameters x and y locate the center of the frame and ideally but rarely are x 512 y 512 fora 1024 frame Variation in the x parameter will cause a Debye ring to be offset along the x horizontal axis variations in the y parameter with affect the position of a Debye ring along the y vertical axis and variations in d will cause expansion or contraction from the center of the frame Thus the effect on the diffraction pattern for an error in the x parameter will cause observed peaks to be either all at lower than the ideal two theta or greater than the ideal two theta To illustrate the effect on the diffraction pattern for an error in the d parameter note the shift in peak positions in Figure 2 The y parameter would be expected to locate the horizontal line that intersects the Debye ring at its widest part however peak positions in an x ray pattern appear relatively insensitive to this error Figure 2 7 The effect of an incorrect d parameter in the diffraction pattern of corundum The line positions of the standard are given as superimposed vertical lines in green the position
14. he left button to see integrate options display Formats Use DiffracPlus format for Siemens DiffracPlus software and for MDI JADE software name raw Use Plotso to get format that graph the Intensity vs Theta name pH Append Choose Y check to set the output up to allow the merging of several sets of data 1 e at 0 20 rotation frames Note After making a diffraction profile check to make certain that the profile produced makes sense for the frame undergoing the conic peak integration chi or gamma Occasionally a hot pixel will be present in the frame that causes a high peak in the diffraction profile that should not exist If you notice an apparently anomalous peak File gt Display gt Open set High Counts to 50 000 A white pixel should be evident at the two theta position where there is an anomalous peak Corrections to eliminate the effects of the hot pixel are most easily made in for example JADE Repeat chi integration sequence for each rotation frame 4 Minimize the GADDS window g Enter Merge program click on Bruker AXS Programs Merge The Merge program places all nine or more frames on to one scale To do this those frames of equal two theta are merged by average overlap not scaling Then the three two theta output files are merged without averaging but by scaling that is a function of the overlap percentage along with the background adjusted Default option Makes a
15. idence of the X ray on the Be window and the optical fiber twist as viewed by the CCD chip The spatial correction file builds a correction table based on observed vs actual hole and spot position The APEX CCD chip is 4K x 4K and does not use a magnifying glass fiber lens system so no spatial correction is needed Unwarp In GADDS this is the term used for applying the spatial flood field and dark current to the raw image of the frame This creates a new image without distortion i e unwarping the distortion Because data from the APEX is already corrected for the dark current and the flood field in the SMART software and the spatial correction is unnecessary do not apply an unwarp in GADDS Goal of taking frames for powder data d The aim is to take a series of rotation frames i e photographs so that there is about 20 overlap of each frame with its neighbor in 22 For Mo radiation detector to crystal distance of about 12 cm take three rotation frames at 22 0 20 and 35 maximum Omega and phi should both be 0 Read through the directions before you do this because the frames may be taken in batch mode which is explained at the end of this discussion thereby making data collection automatic 1 Goniom Drive set the angles for first rotation 2 Acquire Rotation Exposure time 1200 seconds Do not click zero 2 theta omega box After each frame is taken you must save the frame to your directo
16. igh resolution of 1024 x 1024 and 120 1200 sec The APEX detector does not require a spatial correction The floodfield correction will not differ for the APEX running at different frame collection times in contrast with dark current times Use at UIC D Frames ccd_1K 3125H150 _FL The file name is based on the APEX serial number at UIC 3125 and high resolution of 1024 H Go to Detector flood field D Frames ccd_1K 3125H150 _FL OK Go to Detector Dk Flood enabled Yes check d The aim is to take a series of rotation frames i e photographs so that there is about 20 overlap of each frame with its neighbor in 22 For Mo radiation and for the detector to crystal distance of 12 cm take three rotation frames at 22 0 20 and 35 maximum Omega and phi should both be 0 Note A batch program is available to collect this data see Appendix 3 for the file listing and instructions in Appendix 2 page 2 1 Goniom Drive set the angles for first rotation 2 Acquire Rotation Exposure time 1200 seconds Do not click zero 2 theta omega box After each frame is taken you must save the frame to your directory Thus you should have three frames after completing the series as cor_O rot cor_20 rot and cor_35 rot or a similar name for each e Close the SMART software Open the GADDS off line software by 1 Bruker AXS Programs GADDS off line File Display Open Use file
17. llision limit settings Answer yes to do this c Place the single crystal on the goniometer and optically align in the Bruker APEX System as you would any other single crystal See Data Collection section p 4 7 to 4 11 stopping at item 14 of the User s Manual for the SMART APEX Now establish the appropriate dark current Go to Detector Dark Current Set seconds per exposure to 1200 of exposures to average 2 Output file 3125H 120 _DK Label the new dark current as 3125H120 _DK where 3120 is the serial number of the UIC APEX and you should use the appropriate serial number for your lab H high resolution of 1024 x 1024 and 120 1200 sec The dark current needs to be collected just once before the data collection For a discussion of the different types of corrections for the APEX detector see the section previous to this one Debye Scherrer The APEX detector does not require a spatial correction The flood field correction will not differ for the APEX running at different frame collection times in contrast with dark current times Thus use the high resolution flood field Use at UIC D Frames ccd_1K 3125H150 _FL The file name is based on the APEX serial number at UIC 3125 and high resolution of 1024 H Go to Detector flood field D Frames ccd_1K 3125H150 _FL OK Go to Detector Dk Flood enabled Yes check d Read through the directions before you do the following because the frames
18. may be taken in batch mode with special directions given at the end of this section The aim is to take a series of rotation frames 1 e photographs so that there is about 20 overlap of each frame with its neighbor in 22 For Mo radiation detector to crystal distance of about 12 cm take three rotation frames at 22 0 20 and 35 maximum Phi should be kept at 0 Omega needs to be systematically varied for each two theta value which must be done at allowable values So at two theta of 35 degrees omega is first set to 20 a rotation is taken then at 0 degrees followed by another rotation and then at 20 degrees followed by another rotation Each rotation must be saved Lower symmetry crystals triclinic and monoclinic may require two or more mountings The procedure is followed for each two theta Two theta Omega 35 20 35 0 35 20 20 20 20 0 20 20 0 20 0 0 0 10 20 is not allowed 1 Goniom Drive set the angles for first rotation 2 Acquire Rotation Exposure time 1200 seconds Do not click zero 2 theta omega box After each frame is taken you must save the frame to your directory file save Thus you should have at least nine frames after completing the series as samp_010 rot samp_00 rot samp_0m20 rot etc for 0 two theta 10 omega etc where samp is the sample user name NOTE A routine has been developed to collect this data automatically To use this r
19. mended then Region X Y can be left at the default setting and they have no effect on the data 2 The Lp Lorentz polarization correction may be applied to the powder data but this correction is rarely used and depends on how you plan to use the data If you choose to apply these corrections Process Corrections Choose LPA only Set Mono 2T 12 0 degrees 3 Integrate the Debye rings to one linear integrated value Peaks integrate chi to set conic peak integration Two theta and chi start and end points will be set graphically so leave values as is In future releases of GADDS the chi integration angle is renamed to gamma At omega of zero chi equals gamma but at any other omega value chi is not equal to gamma Bin Normalize intensity 5 Future releases of GADDS will drop other intensity algorithms step size 0 02 always keep the same for all rotation frames usually 0 02 A white outline will be superimposed over the frame mouse mouse will 35 Sequentially type 1 2 3 and 4 to see how each can be adjusted 1 adjusts center point 2 adjusts 2theta region 3 adjusts the lower chi region 4 adjusts the upper chi region Adjust to the extremes of the frame but not beyond where there are no data Keep adjustments to within 180 and maintain for all frames After each adjustment 1 2 3 or 4 click the left button to accept adjustment After the 4 adjustment is
20. of the peaks in the observed pattern are in brown and the pattern is in blue Errors in peak position are symmetrical about a central point or peak with that peak near 17 degrees Note that at lower two theta the peak positions brown are at lower two theta positions than the standard green and at higher two theta above 17 the peak positions brown are at higher two theta positions than the standard green We will make a calibration in GADDS from different portions of an x ray pattern obtained in SMART It is easiest to make a y parameter calibration at a low two theta frame e g 0 and x and d parameter calibration from a frame taken at a medium two theta e g 20 These calibrations will be considered coarse adjustments because it is difficult to see the effect of small changes in values Final and precise calibration is obtained only after comparison to the diffraction patterns generated from all three frames at 0 20 and 35 3 Process Calibrate Set Calibration file to corundum std which is a resident file with JCPDF PDF data in the GADDS software minimum relative intensity 5 sample to detector distance should be set to approximately what the APEX was set at near 12 0 or 11 895 detector angle set to 22 value 0 and later 20 or 35 delta distance 0 005 this is the amount of movement sensitivity in d delta angle must be set to 0 000 for factory calibration Detector x center of near 512 a
21. outine 1 Level Command line 2 at the SMART cursor type E Geology Gand Gan_1200 slm without the quotes followed with an enter Gan_1200 slm is the file containing the directions see Appendix 3 for a listing 3 After data collection is complete and to leave the command line dialogue type menu without quotes followed by an enter Note For samples with low symmetry and if precise intensity data are required it may be necessary to remount the crystal in a different orientation and to collect additional frames instrument e Exit SMART File exit WHEN FINISHED WITH YOUR EXPERIMENTS BE CERTAIN TO RESET THE DETECTOR TO 60 mm ON THE DETECTOR ARM CHANGE BACK TO THE 0 5 mm COLLIMATOR AND RETURN TO THE REGULAR SIZE BEAM STOP f Enter GADDS click on GADDS off line icon First determine that the settings are correct go to Edit Config User Settings should be at a resolution frame size setting 1024 The crystal to detector setting is at 11 906 cm The Direct beam x distance is 514 50 The Direct beam y distance is 516 93 The actual values depend on the calibration of the 1 File Display Open Bring in the first photograph Frame filename Set High Counts to a large number e g 4095 If Mag is left as 1 0 recommended then Region X Y is left at the default setting and it has no effect on the data 2 The Lp Lorentz polarization correction may be applied to the powder data but this correc
22. ry file save Thus you should have three frames after completing the series as samp_0 rot samp_20 rot and samp_35 rot where samp is the sample user name NOTE A batch routine has been developed to collect this data automatically To use this routine 1 Go to Level Command line 2 at the SMART cursor type E Geology Powd Powd1200 slm without the quotes followed with an enter 3 After data collection is complete and to leave the command line dialogue type menu without quotes followed by an enter e Exit SMART File exit WHEN FINISHED WITH YOUR EXPERIMENTS BE CERTAIN TO RESET THE DETECTOR TO 60 mm ON THE DETECTOR ARM CHANGE BACK TO THE 0 5 mm COLLIMATOR AND RETURN TO THE REGULAR SIZE BEAM STOP f Enter GADDS click on GADDS off line icon First determine that the correct calibration values in GADDS by Edit Config User Settings and change resolution Frame size setting 1024 Change crystal to detector setting to 11 906 cm At UIC the present GADDS software does not allow changes from 11 99 but this has been changed in future releases The values are usually pre set in the calibration section and in most cases they do not require changing Change Direct beam x distance to 514 50 Change Direct beam y distance to 516 93 1 File Display Open Bring in the first photograph Frame filename Set High Counts to a large number e g 4095 If Mag is left as 1 0 recom
23. ssuming that you are using a frame resolution of 1024 Detector y center of near 512 assuming that you are using a frame resolution of 1024 Delta xy movement 0 2 movement sensitivity in x y Values for sample to detector distance detector x and detector y values will change based on the calibration Blue rings will be overlaid on the Debye rings The rings indicate the calculated positions of the resident corundum file You need to adjust the d parameter detector x and detector y to have the resident pattern superpose over the rings of your experimental pattern NOTE For a low angle i e 0 two theta frame there will be at least one Debye ring forming a full circle This will allow an initial determination a very rough estimate when compared to other frames for the y parameter Figure 2 2 shows the effect of an error in the y parameter Figure 2 2 The Debye ring shows an offset in the vertical caused by an error in the y parameter A complete Debye ring occurs at low two theta values thereby allowing the effect to be readily observed However because most data i e Debye rings or partial rings and the more accurate data will occur at medium and high two theta it is best to calibrate using the 20 and 35 frames For a medium angle frame the values for the d parameter and x parameter in addition to the y parameter can be more easily determined Use the x parameter to locally adjust the ring sections of measured
24. tion is rarely used and depends on how you plan to use the data If you choose to apply these corrections Process Corrections Choose LPA only Set Mono 2T 12 0 degrees 3 Integrate the Debye rings to one linear integrated value This is done by treating each of the nine or more files Peaks integrate chi to set conic peak integration Two theta and chi start and end points will be set graphically so leave values as is In future releases of GADDS the chi integration angle is renamed to gamma At omega of zero chi equals gamma but at any other omega value chi is not equal to gamma Bin Normalize intensity 5 Future releases of GADDS will drop other intensity algorithms step size 0 02 always keep the same for all rotation frames usually 0 02 A white outline will be superimposed over the frame Sequentially type 1 2 3 and 4 to see how each can be adjusted integrate only areas of intensity 1 adjusts center point 2 adjusts 2theta region 3 adjusts the lower chi region 4 adjusts the upper chi region Adjust to the extremes of the frame but do not go beyond where there are no data Do not adjust beyond 180 and keep each region the same for a set of 2 theta mouse mouse will 35 After each adjustment 1 2 3 or 4 click the left button to accept adjustment At UIC always keep the same settings for each set of 2theta frames After the 4 adjustment is entered click t
25. trast with dark current times Use at UIC D Frames ccd_1K 3125H150 _FL The file name is based on the APEX serial number at UIC 3125 and high resolution of 1024 H Go to Detector flood field D Frames ccd_1K 3125H150 _ FL OK Go to Detector Dk Flood enabled Yes check The following corrections and related items are of interest Description of Corrections Dark Current This correction is a function of accumulation time and thermal noise related to the CCD detector Thus the dark current and bias depends on collection time and temperature and because there are no useful data in the dark current relating to the crystal under study dark current is subtracted from the frames during data processing Note Never leave the light for orientation on in the hutch either during dark current collection or during data collection because the light will produce thermal noise Flood field This correction relates to the response across the detector face depending on the orientation of the Be window the phosphor and fiber bonding agent uniting the CCD to the optical fibers The flood field file never needs updating unless there has been a mechanical change to the Be phosphor or binding agent of the fibers Spatial The APEX detector does not require this correction although the GADDS software often is used with detectors that do This correction involves a change to the spot imaging or distortion that is a function of the angle of inc
26. ut filenames provide each filename in list This time take the files containing the three two theta ranges and merge by the Scale option name raw refers to Diffracplus files for MDI JADE or DiffracPlus This is the most likely foramt you would want to use name plt refers to Plotso file name uxd refers to ascii file type Set range to 1 all in first box Output file set to name_TT to create name_TT out file for raw file output 3 Transfer the file to the Powder Diffractometer computer for further processing with the MDI JADE program Appendix 2 Calibration of the GADDS software 1 Calibration This section may be skipped if the system has already been calibrated Only the Laboratory Administrator calibrates the instrument Calibration is for detector distance and x y coordinates for detector center and symmetry of shape of powder rings A more detailed description of the parameters are given below GADDS supports the following standards Corundum PDF 10 0173 Aluminum PDF 04 0787 Silicon PDF 27 1402 and Quartz PDF 33 1161 We use Corundum NBS NIST 674a in 0 2 mm capillary STEP 1 Calibration of SMART using the YLID crystal for 120 mm a Change the detector to crystal distance to 12 cm on the goniometer Use the calibration single crystal YLID to obtain crystal to detector distance x distance and y distance values if this has not been done previously for this detector position These values using
27. utput file from Merge name_TP out This produces a plot I vs Theta of file i Other utility programs by Bruker 1 To convert an image file use Frm2Frm Program to Tiff JPeg Bruker ASCII or Bruker Frame File For example a rotation frame photograph is already in the Bruker Frame File format but it can be converted to a Tiff file for another program e g to display in PhotoShop 2 To convert one raw file to another use Raw2Raw Output file examples include Diffracplus Plotso DBW GSAS UXD Bruker Ascii 3 GADDSmap is for sample mapping and cannot be used in our lab 2 Data Collection for Gandolfi type Patterns Using SMART Software a Change the detector to sample distance to 12 cm on the goniometer If available use the extended beam stop and the 0 2 mm Monocap have the administrator change these for you do this for you If not available use the standard beam stop and 0 3 collimator instead b Double click on the SMART icon to open Then go to Edit Config User Settings The following values will be different for your instrument depending on its current calibration Change resolution frame size setting from 512 to 1024 Change sample to detector setting from 5 972 cm to 11 891 cm Change Direct beam x distance from 257 884 to 517 488 Change Direct beam y distance from 255 864 to 512 428 When exiting the Configuration file the system will ask if it should modify the co
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