source: trunk/help/Fit Peaks.htm @ 585

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585<body lang=EN-US style='tab-interval:.5in'>
586
587<div class=WordSection1>
588
589<div style='mso-element:para-border-div;border:none;border-bottom:solid #4F81BD 1.0pt;
590mso-border-bottom-themecolor:accent1;padding:0in 0in 4.0pt 0in'>
591
592<p class=MsoTitle><span style='mso-spacerun:yes'> </span>Fit Peaks/<span
593class=SpellE>Autoindexing</span> in GSAS-II <o:p></o:p></p>
594
595</div>
596
597<p class=MsoNormal>In this exercise you will use the GSAS-II program to search
598for a unit cell that matches a set of diffraction peaks -- a process known as
599auto-indexing. First peaks must be located and optimized and then indexing can
600be done.<o:p></o:p></p>
601
602<p class=MsoNormal>Step 1: read in data<o:p></o:p></p>
603
604<p class=MsoNormal>Download the sample data file and matching instrument
605parameter file from these links:<o:p></o:p></p>
606
607<p class=MsoNormal><span style='mso-spacerun:yes'>   
608</span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.fxye?format=raw<o:p></o:p></p>
609
610<p class=MsoNormal><span style='mso-spacerun:yes'>   
611</span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.prm?format=raw<o:p></o:p></p>
612
613<p class=MsoNormal><o:p>&nbsp;</o:p></p>
614
615<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>(One can also use
616this links<span style='mso-spacerun:yes'>    </span><o:p></o:p></p>
617
618<p class=MsoNormal><span style='mso-spacerun:yes'>   
619</span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.fxye
620and <o:p></o:p></p>
621
622<p class=MsoNormal><span style='mso-spacerun:yes'>   
623</span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.prm<o:p></o:p></p>
624
625<p class=MsoNormal><span style='mso-spacerun:yes'>    </span><span class=GramE>to</span>
626obtain the file, but this is more complex).<o:p></o:p></p>
627
628<p class=MsoNormal><o:p>&nbsp;</o:p></p>
629
630<p class=MsoNormal>=== Step 2: Start GSAS-II ===<o:p></o:p></p>
631
632<p class=MsoNormal><o:p>&nbsp;</o:p></p>
633
634<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This is done in
635different ways, depending on your OS and how GSAS-II is installed.<o:p></o:p></p>
636
637<p class=MsoNormal><o:p>&nbsp;</o:p></p>
638
639<p class=MsoNormal>=== Step 3: read in the data file ===<o:p></o:p></p>
640
641<p class=MsoNormal><o:p>&nbsp;</o:p></p>
642
643<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the '''Data/Read
644powder data''' menu item to read the data file into the current GSAS-II
645project. <o:p></o:p></p>
646
647<p class=MsoNormal><span style='mso-spacerun:yes'> </span><o:p></o:p></p>
648
649<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
650{{{11bmb_3844.fxye}}} data file in the first dialog and press Open.<o:p></o:p></p>
651
652<p class=MsoNormal><o:p>&nbsp;</o:p></p>
653
654<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
655{{{11bmb_3844.prm}}} instrument parameter file in the second dialog and press
656Open.<o:p></o:p></p>
657
658<p class=MsoNormal><o:p>&nbsp;</o:p></p>
659
660<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>At this point the
661data tree window will have several entries <o:p></o:p></p>
662
663<p class=MsoNormal><span style='mso-spacerun:yes'>   
664</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w2.png
665view]);<o:p></o:p></p>
666
667<p class=MsoNormal><span style='mso-spacerun:yes'>    </span><span class=GramE>and</span>
668the plot window will show the powder pattern<o:p></o:p></p>
669
670<p class=MsoNormal><span style='mso-spacerun:yes'>    </span><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w1.png
671view]).</span><o:p></o:p></p>
672
673<p class=MsoNormal><o:p>&nbsp;</o:p></p>
674
675<p class=MsoNormal>=== Step 4: Select Data Range ===<o:p></o:p></p>
676
677<p class=MsoNormal><o:p>&nbsp;</o:p></p>
678
679<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
680more data than we need, so it is helpful to cut down the range. Click on the
681Limits item in the data tree. A new window is created. Use the
682&quot;changed&quot; row of entry boxes to set <span class=SpellE>Tmin</span>
683and <span class=SpellE>Tmax</span> to 4 and 30. You may also drag the limits lines
684to the desired location or place them by a left mouse click on a data point for
685the lower limit or a right click on a data point for the upper limit.<o:p></o:p></p>
686
687<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w3.png
688view]).</span> <o:p></o:p></p>
689
690<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note the green and
691red vertical lines in the plot window move. <o:p></o:p></p>
692
693<p class=MsoNormal><o:p>&nbsp;</o:p></p>
694
695<p class=MsoNormal><o:p>&nbsp;</o:p></p>
696
697<p class=MsoNormal>=== Step 5: Determine Peak Positions ===<o:p></o:p></p>
698
699<p class=MsoNormal><o:p>&nbsp;</o:p></p>
700
701<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the Peak
702List item in the data tree. This creates an empty window of peak positions. At
703this point it is wise to <o:p></o:p></p>
704
705<p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>zoom</span>
706in on the data that will be used for indexing. This can be done by clicking on
707this button:<o:p></o:p></p>
708
709<p class=MsoNormal><o:p>&nbsp;</o:p></p>
710
711<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the
712magnification button: [[Image(d3z1.png)]], then press the left mouse in one
713corner of the region to be used; holding the mouse button down, drag over the
714region to the opposite corner. <o:p></o:p></p>
715
716<p class=MsoNormal><o:p>&nbsp;</o:p></p>
717
718<p class=MsoNormal><span style='mso-spacerun:yes'> </span>'''Important:'''
719Click on the magnification [[<span class=GramE>Image(</span>d3z1.png)]] button
720again to turn off the zoom mode. <o:p></o:p></p>
721
722<p class=MsoNormal><o:p>&nbsp;</o:p></p>
723
724<p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>Using
725the left mouse button click on a data point near the top of each peak to be
726added to the peak list.</span> As this is done, a line is <o:p></o:p></p>
727
728<p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>drawn</span>
729in the plot window<o:p></o:p></p>
730
731<p class=MsoNormal><span style='mso-spacerun:yes'> 
732</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w4.png
733view]) and<o:p></o:p></p>
734
735<p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>peaks</span>
736are added to the Peak List window<o:p></o:p></p>
737
738<p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w5.png
739view]).</span> Note that if peaks are <o:p></o:p></p>
740
741<p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>not</span>
742being added, you probably have not exited zoom mode.<o:p></o:p></p>
743
744<p class=MsoNormal><o:p>&nbsp;</o:p></p>
745
746<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Once peaks in that
747region have been added, move to a new region of the pattern. This can be done
748by clicking on the shift button: [[<span class=GramE>Image(</span>d3z2.png)]].
749Dragging with the left mouse will shift the data to follow the mouse. <span
750class=GramE>Clicking with the right button (on the Mac, control + mouse) and
751moving up increases the vertical scale and to the right increases the
752horizontal scale.</span><span style='mso-spacerun:yes'> 
753</span>'''Important:''' Click on the shift [[<span class=GramE>Image(</span>d3z2.png)]]
754button again to turn off this mode. <o:p></o:p></p>
755
756<p class=MsoNormal><o:p>&nbsp;</o:p></p>
757
758<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Again, using the
759left mouse button, click on the tops of more peaks to be added to the peak
760list. Note that if peaks are <o:p></o:p></p>
761
762<p class=MsoNormal><span style='mso-spacerun:yes'>  </span><span class=GramE>not</span>
763being added, you probably have not exited shift mode.<o:p></o:p></p>
764
765<p class=MsoNormal><o:p>&nbsp;</o:p></p>
766
767<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Add approximately 24
768peaks total to the peak list. Be sure to add the lowest angle peaks that are
769visible in the plot. You may drag a peak position as needed; be sure the
770zoom/shift buttons are off. A position may be deleted with a right click with
771the mouse on the blue line.<o:p></o:p></p>
772
773<p class=MsoNormal><o:p>&nbsp;</o:p></p>
774
775<p class=MsoNormal>=== Step 6: Refine Peak Positions ===<o:p></o:p></p>
776
777<p class=MsoNormal><o:p>&nbsp;</o:p></p>
778
779<p class=MsoNormal>First, refine the peak intensities and the background. These
780parameters have their refinement flag turned on by default. Use the menu item
781'''Peak Fitting/<span class=GramE>LSQ !<span class=SpellE>PeakFit</span>'''</span>.
782A window will show the progress of the refinement and will close when the least
783<span class=GramE>squares is</span> complete. A summary of the refinement is
784shown on the console window as well.<o:p></o:p></p>
785
786<p class=MsoNormal><o:p>&nbsp;</o:p></p>
787
788<p class=MsoNormal>Second, add refinement of the peak positions. This can be
789done by clicking on all the refinement flags for the individual peaks or it is
790possible to set them all at the same time using this recipe: <o:p></o:p></p>
791
792<p class=MsoNormal><span style='mso-spacerun:yes'> </span>* <span class=GramE>single-click</span>
793on any value in the table to select it, for example the first peak position. A
794black box appears around the value. If the field if opened for editing (the box
795turns to blue), select a different item in the table.<o:p></o:p></p>
796
797<p class=MsoNormal><span style='mso-spacerun:yes'> </span>* double-click on the
798refine label above the peak position check-boxes. The entire column of
799checkboxes is highlighted in blue. Press the y key to turn on all refinement
800flags (n would turn them off).<o:p></o:p></p>
801
802<p class=MsoNormal><span style='mso-spacerun:yes'> </span><o:p></o:p></p>
803
804<p class=MsoNormal>Third, repeat the refinement using the '''Peak Fitting/<span
805class=GramE>LSQ !<span class=SpellE>PeakFit</span>'''</span> menu item.<o:p></o:p></p>
806
807<p class=MsoNormal><span style='mso-spacerun:yes'> </span><o:p></o:p></p>
808
809<p class=MsoNormal>Fourth, select peak widths for refinement. This can be done
810by refining sigma (Gaussian width) and/or gamma (Lorentzian width) for
811individual peaks, but here we constrain the peaks to follow an instrumental
812broadening equation. Select the Instrumental Parameters item in the data tree. <o:p></o:p></p>
813
814<p class=MsoNormal>This opens a window for peak profile terms<o:p></o:p></p>
815
816<p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w6.png
817view]).</span> <o:p></o:p></p>
818
819<p class=MsoNormal>Select the refine flag checkbox for Gaussian U, V, W,
820Lorentzian X, Y and the asymmetry parameter SH/L. <o:p></o:p></p>
821
822<p class=MsoNormal><o:p>&nbsp;</o:p></p>
823
824<p class=MsoNormal>Fifth, repeat the refinement. First click on the Peak List
825item in the data tree and then refine using the '''Peak Fitting/<span
826class=GramE>LSQ !<span class=SpellE>PeakFit</span>'''</span> menu item. At this
827point a good fit should be seen by zooming in on individual peaks. (For example
828see <o:p></o:p></p>
829
830<p class=MsoNormal><span class=GramE>[https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w7.png
831this]).</span> The <span class=SpellE>Rwp</span> is ~6% as shown on the console
832window.<o:p></o:p></p>
833
834<p class=MsoNormal><o:p>&nbsp;</o:p></p>
835
836<p class=MsoNormal>=== Prepare Indexing Peak List ===<o:p></o:p></p>
837
838<p class=MsoNormal><o:p>&nbsp;</o:p></p>
839
840<p class=MsoNormal>A separate list of peaks is kept for use in <span
841class=SpellE>autoindexing</span>. This list is manipulated by clicking on the
842Index Peak List item in the data tree. In the initially empty window created by
843this action, use menu item '''Index Peaks Operations/Load''' to copy over the
844fitted peaks from the Peak List tree entry<o:p></o:p></p>
845
846<p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w1.png
847view]).</span> <o:p></o:p></p>
848
849<p class=MsoNormal>Note that by default all peaks are selected to be used. <o:p></o:p></p>
850
851<p class=MsoNormal><o:p>&nbsp;</o:p></p>
852
853<p class=MsoNormal>=== Run <span class=SpellE>Autoindexing</span> ===<o:p></o:p></p>
854
855<p class=MsoNormal><o:p>&nbsp;</o:p></p>
856
857<p class=MsoNormal>Select the Unit Cells List data item. This brings up a
858window for indexing and cell refinement options<o:p></o:p></p>
859
860<p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w2.png
861view]).</span> For the most rapid search (since we know the right answer),
862select Cubic-P and launch the search using menu item '''Cell Index/Index
863Cell'''. The search then runs and he console shows a running list of possible
864cells as they are found; the sorted by M20 list of possible matching cells is
865shown in the window<o:p></o:p></p>
866
867<p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w3.png
868view]).</span> <o:p></o:p></p>
869
870<p class=MsoNormal><o:p>&nbsp;</o:p></p>
871
872<p class=MsoNormal>=== Review Cell Choices === <o:p></o:p></p>
873
874<p class=MsoNormal><o:p>&nbsp;</o:p></p>
875
876<p class=MsoNormal>Review the list of cells associated with the Unit Cells List
877data item. Note that as one selects a unit cell, the generated reflections for
878that cell are shown in the plot with dashed red lines. Sliding the cursor over
879these lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
880for them. Note how the 8.312 <span class=GramE>A</span> cell generates very
881many lines with no corresponding peaks <o:p></o:p></p>
882
883<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w4.png
884view])<o:p></o:p></p>
885
886<p class=MsoNormal><span class=GramE>while</span> the 2.939 A cell generates
887not enough lines to match all the peaks<o:p></o:p></p>
888
889<p class=MsoNormal><span class=GramE>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w5.png
890view]).</span> <o:p></o:p></p>
891
892<p class=MsoNormal><o:p>&nbsp;</o:p></p>
893
894<p class=MsoNormal>=== Select/Refine Cell === <o:p></o:p></p>
895
896<p class=MsoNormal><o:p>&nbsp;</o:p></p>
897
898<p class=MsoNormal>Select the top option, a 4.1568 <span class=GramE>A</span>
899cell with M20 figure of merit of 2700. This indexes all peaks, though peak
900positions are not exactly perfect if one zooms in enough. Import the cell
901information using the '''Cell Index/Copy Cell''' menu option. Then optimize the
902cell by refining the lattice parameters and the two-theta zero: click on the
903refine checkbox next to the Zero offset value and then the '''Cell Index/Refine
904Cell''' menu option. <span class=GramE>The a</span> cell parameter value shifts
905from 4.15679 to 4.15684 when zero is refined. <o:p></o:p></p>
906
907<p class=MsoNormal><o:p>&nbsp;</o:p></p>
908
909<p class=MsoNormal>(Optional) Finally, use of the '''Cell Index/New phase'''
910menu option allows one to assign a phase with these lattice parameters to the
911data set (histogram). A name for the new phase is then requested. This adds a
912Phases entry to the data tree, as well as an entry for the new phase. This new
913phase can be used in future code.</p>
914
915</div>
916
917</body>
918
919</html>
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