source: trunk/help/Fit Peaks.htm @ 586

Last change on this file since 586 was 586, checked in by vondreele, 10 years ago

tutorial stuff

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685
686<body lang=EN-US style='tab-interval:.5in'>
687
688<div class=WordSection1>
689
690<h1><span style='mso-spacerun:yes'> </span>Fit Peaks/<span class=SpellE>Autoindexing</span>
691in GSAS-II </h1>
692
693<p class=MsoNormal>In this exercise you will use the GSAS-II program to search
694for a unit cell that matches a set of diffraction peaks -- a process known as
695auto-indexing. First peaks must be located and optimized and then indexing can be
696done.</p>
697
698<h2>Step 1: read in data</h2>
699
700<p class=MsoNormal>Download the sample data file and matching instrument
701parameter file from these links:</p>
702
703<p class=MsoNormal><span style='mso-spacerun:yes'>   
704</span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.fxye?format=raw</p>
705
706<p class=MsoNormal><span style='mso-spacerun:yes'>   
707</span>https://subversion.xor.aps.anl.gov/trac/pyGSAS/browser/Examples/powder%20data/11bmb_3844.prm?format=raw</p>
708
709<p class=MsoNormal><o:p>&nbsp;</o:p></p>
710
711<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>(One can also use
712this links<span style='mso-spacerun:yes'>    </span></p>
713
714<p class=MsoNormal><span style='mso-spacerun:yes'>   
715</span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.fxye
716and </p>
717
718<p class=MsoNormal><span style='mso-spacerun:yes'>   
719</span>https://subversion.xor.aps.anl.gov/pyGSAS/Examples/powder%20data/11bmb_3844.prm</p>
720
721<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>to obtain the
722file, but this is more complex).</p>
723
724<p class=MsoNormal><o:p>&nbsp;</o:p></p>
725
726<h2>Step 2: Start GSAS-II </h2>
727
728<p class=MsoNormal><o:p>&nbsp;</o:p></p>
729
730<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This is done in
731different ways, depending on your OS and how GSAS-II is installed.</p>
732
733<p class=MsoNormal><o:p>&nbsp;</o:p></p>
734
735<p class=MsoNormal>=== Step 3: read in the data file ===</p>
736
737<p class=MsoNormal><o:p>&nbsp;</o:p></p>
738
739<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Use the '''Data/Read
740powder data''' menu item to read the data file into the current GSAS-II
741project. </p>
742
743<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
744
745<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
746{{{11bmb_3844.fxye}}} data file in the first dialog and press Open.</p>
747
748<p class=MsoNormal><o:p>&nbsp;</o:p></p>
749
750<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Select the
751{{{11bmb_3844.prm}}} instrument parameter file in the second dialog and press
752Open.</p>
753
754<p class=MsoNormal><o:p>&nbsp;</o:p></p>
755
756<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>At this point the
757data tree window will have several entries </p>
758
759<p class=MsoNormal><span style='mso-spacerun:yes'>   
760</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w2.png
761view]);</p>
762
763<p class=MsoNormal><span style='mso-spacerun:yes'>    </span>and the plot
764window will show the powder pattern</p>
765
766<p class=MsoNormal><span style='mso-spacerun:yes'>   
767</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w1.png
768view]).</p>
769
770<p class=MsoNormal><o:p>&nbsp;</o:p></p>
771
772<p class=MsoNormal>=== Step 4: Select Data Range ===</p>
773
774<p class=MsoNormal><o:p>&nbsp;</o:p></p>
775
776<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
777more data than we need, so it is helpful to cut down the range. Click on the Limits
778item in the data tree. A new window is created. Use the &quot;changed&quot; row
779of entry boxes to set <span class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span>
780to 4 and 30. You may also drag the limits lines to the desired location or
781place them by a left mouse click on a data point for the lower limit or a right
782click on a data point for the upper limit.</p>
783
784<p class=MsoNormal><span
785style='mso-spacerun:yes'> </span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w3.png
786view]). </p>
787
788<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Note the green and
789red vertical lines in the plot window move. </p>
790
791<p class=MsoNormal><o:p>&nbsp;</o:p></p>
792
793<p class=MsoNormal><o:p>&nbsp;</o:p></p>
794
795<p class=MsoNormal>=== Step 5: Determine Peak Positions ===</p>
796
797<p class=MsoNormal><o:p>&nbsp;</o:p></p>
798
799<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the Peak
800List item in the data tree. This creates an empty window of peak positions. At
801this point it is wise to </p>
802
803<p class=MsoNormal><span style='mso-spacerun:yes'> </span>zoom in on the data
804that will be used for indexing. This can be done by clicking on this button:</p>
805
806<p class=MsoNormal><o:p>&nbsp;</o:p></p>
807
808<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Click on the
809magnification button: [[Image(d3z1.png)]], then press the left mouse in one
810corner of the region to be used; holding the mouse button down, drag over the
811region to the opposite corner. </p>
812
813<p class=MsoNormal><o:p>&nbsp;</o:p></p>
814
815<p class=MsoNormal><span style='mso-spacerun:yes'> </span>'''Important:'''
816Click on the magnification [[Image(d3z1.png)]] button again to turn off the
817zoom mode. </p>
818
819<p class=MsoNormal><o:p>&nbsp;</o:p></p>
820
821<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Using the left mouse
822button click on a data point near the top of each peak to be added to the peak
823list. As this is done, a line is </p>
824
825<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>drawn in the plot
826window</p>
827
828<p class=MsoNormal><span style='mso-spacerun:yes'> 
829</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w4.png
830view]) and</p>
831
832<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>peaks are added to
833the Peak List window</p>
834
835<p class=MsoNormal><span style='mso-spacerun:yes'> 
836</span>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w5.png
837view]). Note that if peaks are </p>
838
839<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>not being added, you
840probably have not exited zoom mode.</p>
841
842<p class=MsoNormal><o:p>&nbsp;</o:p></p>
843
844<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Once peaks in that
845region have been added, move to a new region of the pattern. This can be done
846by clicking on the shift button: [[Image(d3z2.png)]]. Dragging with the left
847mouse will shift the data to follow the mouse. Clicking with the right button (on
848the Mac, control + mouse) and moving up increases the vertical scale and to the
849right increases the horizontal scale.<span style='mso-spacerun:yes'> 
850</span>'''Important:''' Click on the shift [[Image(d3z2.png)]] button again to
851turn off this mode. </p>
852
853<p class=MsoNormal><o:p>&nbsp;</o:p></p>
854
855<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Again, using the
856left mouse button, click on the tops of more peaks to be added to the peak
857list. Note that if peaks are </p>
858
859<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>not being added, you
860probably have not exited shift mode.</p>
861
862<p class=MsoNormal><o:p>&nbsp;</o:p></p>
863
864<p class=MsoNormal><span style='mso-spacerun:yes'>  </span>Add approximately 24
865peaks total to the peak list. Be sure to add the lowest angle peaks that are
866visible in the plot. You may drag a peak position as needed; be sure the
867zoom/shift buttons are off. A position may be deleted with a right click with
868the mouse on the blue line.</p>
869
870<p class=MsoNormal><o:p>&nbsp;</o:p></p>
871
872<p class=MsoNormal>=== Step 6: Refine Peak Positions ===</p>
873
874<p class=MsoNormal><o:p>&nbsp;</o:p></p>
875
876<p class=MsoNormal>First, refine the peak intensities and the background. These
877parameters have their refinement flag turned on by default. Use the menu item
878'''Peak Fitting/LSQ !<span class=SpellE>PeakFit</span>'''. A window will show
879the progress of the refinement and will close when the least squares is
880complete. A summary of the refinement is shown on the console window as well.</p>
881
882<p class=MsoNormal><o:p>&nbsp;</o:p></p>
883
884<p class=MsoNormal>Second, add refinement of the peak positions. This can be
885done by clicking on all the refinement flags for the individual peaks or it is
886possible to set them all at the same time using this recipe: </p>
887
888<p class=MsoNormal><span style='mso-spacerun:yes'> </span>* single-click on any
889value in the table to select it, for example the first peak position. A black
890box appears around the value. If the field if opened for editing (the box turns
891to blue), select a different item in the table.</p>
892
893<p class=MsoNormal><span style='mso-spacerun:yes'> </span>* double-click on the
894refine label above the peak position check-boxes. The entire column of
895checkboxes is highlighted in blue. Press the y key to turn on all refinement
896flags (n would turn them off).</p>
897
898<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
899
900<p class=MsoNormal>Third, repeat the refinement using the '''Peak Fitting/LSQ !<span
901class=SpellE>PeakFit</span>''' menu item.</p>
902
903<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
904
905<p class=MsoNormal>Fourth, select peak widths for refinement. This can be done
906by refining sigma (Gaussian width) and/or gamma (Lorentzian width) for
907individual peaks, but here we constrain the peaks to follow an instrumental
908broadening equation. Select the Instrumental Parameters item in the data tree. </p>
909
910<p class=MsoNormal>This opens a window for peak profile terms</p>
911
912<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w6.png
913view]). </p>
914
915<p class=MsoNormal>Select the refine flag checkbox for Gaussian U, V, W,
916Lorentzian X, Y and the asymmetry parameter SH/L. </p>
917
918<p class=MsoNormal><o:p>&nbsp;</o:p></p>
919
920<p class=MsoNormal>Fifth, repeat the refinement. First click on the Peak List
921item in the data tree and then refine using the '''Peak Fitting/LSQ !<span
922class=SpellE>PeakFit</span>''' menu item. At this point a good fit should be
923seen by zooming in on individual peaks. (For example see </p>
924
925<p class=MsoNormal>[https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d3w7.png
926this]). The <span class=SpellE>Rwp</span> is ~6% as shown on the console
927window.</p>
928
929<p class=MsoNormal><o:p>&nbsp;</o:p></p>
930
931<p class=MsoNormal>=== Prepare Indexing Peak List ===</p>
932
933<p class=MsoNormal><o:p>&nbsp;</o:p></p>
934
935<p class=MsoNormal>A separate list of peaks is kept for use in <span
936class=SpellE>autoindexing</span>. This list is manipulated by clicking on the
937Index Peak List item in the data tree. In the initially empty window created by
938this action, use menu item '''Index Peaks Operations/Load''' to copy over the
939fitted peaks from the Peak List tree entry</p>
940
941<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w1.png
942view]). </p>
943
944<p class=MsoNormal>Note that by default all peaks are selected to be used. </p>
945
946<p class=MsoNormal><o:p>&nbsp;</o:p></p>
947
948<p class=MsoNormal>=== Run <span class=SpellE>Autoindexing</span> ===</p>
949
950<p class=MsoNormal><o:p>&nbsp;</o:p></p>
951
952<p class=MsoNormal>Select the Unit Cells List data item. This brings up a
953window for indexing and cell refinement options</p>
954
955<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w2.png
956view]). For the most rapid search (since we know the right answer), select
957Cubic-P and launch the search using menu item '''Cell Index/Index Cell'''. The
958search then runs and he console shows a running list of possible cells as they
959are found; the sorted by M20 list of possible matching cells is shown in the
960window</p>
961
962<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w3.png
963view]). </p>
964
965<p class=MsoNormal><o:p>&nbsp;</o:p></p>
966
967<p class=MsoNormal>=== Review Cell Choices === </p>
968
969<p class=MsoNormal><o:p>&nbsp;</o:p></p>
970
971<p class=MsoNormal>Review the list of cells associated with the Unit Cells List
972data item. Note that as one selects a unit cell, the generated reflections for that
973cell are shown in the plot with dashed red lines. Sliding the cursor over these
974lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
975for them. Note how the 8.312 A cell generates very many lines with no
976corresponding peaks </p>
977
978<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w4.png
979view])</p>
980
981<p class=MsoNormal>while the 2.939 A cell generates not enough lines to match
982all the peaks</p>
983
984<p class=MsoNormal>([https://subversion.xor.aps.anl.gov/trac/pyGSAS/attachment/wiki/DemoAutoIndex/d4w5.png
985view]). </p>
986
987<p class=MsoNormal><o:p>&nbsp;</o:p></p>
988
989<p class=MsoNormal>=== Select/Refine Cell === </p>
990
991<p class=MsoNormal><o:p>&nbsp;</o:p></p>
992
993<p class=MsoNormal>Select the top option, a 4.1568 A cell with M20 figure of
994merit of 2700. This indexes all peaks, though peak positions are not exactly
995perfect if one zooms in enough. Import the cell information using the '''Cell
996Index/Copy Cell''' menu option. Then optimize the cell by refining the lattice
997parameters and the two-theta zero: click on the refine checkbox next to the
998Zero offset value and then the '''Cell Index/Refine Cell''' menu option. The a
999cell parameter value shifts from 4.15679 to 4.15684 when zero is refined. </p>
1000
1001<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1002
1003<p class=MsoNormal>(Optional) Finally, use of the '''Cell Index/New phase'''
1004menu option allows one to assign a phase with these lattice parameters to the
1005data set (histogram). A name for the new phase is then requested. This adds a
1006Phases entry to the data tree, as well as an entry for the new phase. This new
1007phase can be used in future code.</p>
1008
1009</div>
1010
1011</body>
1012
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