source: Tutorials/CWInstDemo/FindProfParamCW.htm @ 3342

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add fit profile terms tutorial

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691
692<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
693
694<div class=WordSection1>
695
696<h1>Determining Profile Parameters from a Standard</h1>
697
698<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
699
700<p class=MsoNormal><span style='font-size:14.0pt'>The goal of this exercise is
701to determine approximate instrument profile parameters by a quick peak fit to a
702sample with a lab diffractometer. Ideally, one should use a material or mixture
703of materials that has peaks over the entire range where you collect data and
704use a material(s) that have negligible sample broadening (from crystallite size
705or <span class=SpellE>microstrain</span>). The NIST LaB<sub>6</sub> standards
706(SRM 660, 660a and 660b) are good choices for this, as it has very little
707sample broadening and a relatively small number of peaks over a wide angular
708range, although it would be good to have peaks starting somewhat lower in
7092theta. <o:p></o:p></span></p>
710
711<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
712
713<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
714style='font-size:14.0pt'>Note</span></b><span style='font-size:14.0pt'> that it
715is highly recommended to collect reference data to a much higher 2theta angle
716than here. What is done here serves as an example, and is sufficient only if
717one will never collect and use data above 70 degrees (unlikely!). <o:p></o:p></span></p>
718
719<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
720
721<p class=MsoNormal><span style='font-size:14.0pt'>To get started, create a new
722project in GSAS-II, either by starting the program fresh or using <b
723style='mso-bidi-font-weight:normal'>File/New Project</b>. <o:p></o:p></span></p>
724
725<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
726
727<p class=MsoNormal><span class=Heading3Char><span style='font-size:14.0pt'>Step
7281: Read in the Diffraction Data</span></span><span style='font-size:14.0pt'><o:p></o:p></span></p>
729
730<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
731
732<p class=MsoNormal style='mso-pagination:none;tab-stops:28.0pt 56.0pt 84.0pt 112.0pt 140.0pt 168.0pt 196.0pt 224.0pt 3.5in 280.0pt 308.0pt 336.0pt;
733mso-layout-grid-align:none;text-autospace:none'><span style='font-size:14.0pt'>Use
734<b style='mso-bidi-font-weight:normal'>Import/Powder Data/from <span
735class=SpellE>Brucker</span> RAW file</b> to read </span><span style='font-size:
73614.0pt;font-family:Courier'>file </span><span style='font-size:14.0pt;
737font-family:Courier;mso-bidi-font-family:"Menlo Regular";color:black;
738mso-fareast-language:EN-US'>LaB6_Jan2018.raw</span><span style='font-size:14.0pt;
739font-family:"Menlo Regular";color:black;mso-fareast-language:EN-US'> </span><span
740style='font-size:14.0pt'>from the Tutorials <span class=SpellE>CWInstDemo</span>/data
741directory (download from <a
742href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWInstDemo/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWInstDemo/data/</a>).
743After selecting this file, answer yes to ÒIs this the file you want?Ó<o:p></o:p></span></p>
744
745<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
746
747<h3><span style='font-size:14.0pt'>Step 2: Select Default Instrument Parameters<o:p></o:p></span></h3>
748
749<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
750
751<p class=MsoNormal><span style='font-size:14.0pt'>The next dialog to appear is
752titled, ÒChoose inst. <span class=SpellE>Param</span> file for LaB6_Jan2018.raw
753Scan 1 (or Cancel for default)Ó since we do not have a set of parameters to
754read, we must use a default set. <b style='mso-bidi-font-weight:normal'>Press
755Cancel</b>.<o:p></o:p></span></p>
756
757<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
758
759<p class=MsoNormal><span style='font-size:14.0pt'>This raises the default <span
760class=SpellE>inst</span> <span class=SpellE>parms</span> dialog, as below<o:p></o:p></span></p>
761
762<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
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788style='font-size:14.0pt'><o:p></o:p></span></p>
789
790<p class=MsoNormal><span style='font-size:14.0pt'>Here, <b style='mso-bidi-font-weight:
791normal'>choose the first option</b> for <span class=SpellE>CuKa</span> lab data
792(which is for a standard instrument with Kalpha1 and Kalpha2 radiation) and <b
793style='mso-bidi-font-weight:normal'>press OK</b>. A plot of the data will
794appear as below.<o:p></o:p></span></p>
795
796<p class=MsoNormal><span style='font-size:14.0pt'><span
797style="mso-spacerun:yes">&nbsp;</span></span><span style='font-size:14.0pt;
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804style='font-size:14.0pt'><o:p></o:p></span></p>
805
806<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
807
808<p class=MsoNormal><span class=Heading3Char><span style='font-size:14.0pt'>Step
8093: Change Data Range</span></span><span style='font-size:14.0pt'>. <o:p></o:p></span></p>
810
811<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
812
813<p class=MsoNormal><span style='font-size:14.0pt'>Note that the data begins at
81410 degrees, but the first peak is above 21 degrees, we can simplify the
815background fitting by changing the data limits. <b style='mso-bidi-font-weight:
816normal'>Click on the Limits</b> data tree item, and either change the <span
817class=SpellE>Tmin</span> value from 10 to 20 or in the plot <b
818style='mso-bidi-font-weight:normal'>ÒdragÓ the green line to the right</b> to approximately
81920 degrees. <o:p></o:p></span></p>
820
821<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
822mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_3" o:spid="_x0000_i1027"
823 type="#_x0000_t75" style='width:310pt;height:222pt;visibility:visible'>
824 <v:imagedata src="FindProfParamCW_files/image005.png" o:title=""/>
825</v:shape><![endif]--><![if !vml]><img border=0 width=312 height=224
826src="FindProfParamCW_files/image006.png" v:shapes="Picture_x0020_3"><![endif]></span><span
827style='font-size:14.0pt'><o:p></o:p></span></p>
828
829<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
830
831<h3><span style='font-size:14.0pt'>Step 4: Add Peaks to Fit<o:p></o:p></span></h3>
832
833<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
834
835<p class=MsoNormal><span style='font-size:14.0pt'>To define peaks, <b
836style='mso-bidi-font-weight:normal'>click on the ÒPeak List</b>Ó data tree item.
837Note that as below, the peak list is initially empty. <o:p></o:p></span></p>
838
839<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
840mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4" o:spid="_x0000_i1028"
841 type="#_x0000_t75" style='width:370pt;height:238pt;visibility:visible'>
842 <v:imagedata src="FindProfParamCW_files/image007.png" o:title=""/>
843</v:shape><![endif]--><![if !vml]><img border=0 width=372 height=240
844src="FindProfParamCW_files/image008.png" v:shapes="Picture_x0020_4"><![endif]></span><span
845style='font-size:14.0pt'><o:p></o:p></span></p>
846
847<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
848
849<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
850style='font-size:14.0pt'>Move</span></b><span style='font-size:14.0pt'> the
851mouse to any of the data points close to the <b style='mso-bidi-font-weight:
852normal'>top of the first peak and click </b>the left mouse button. A line will
853be drawn through the peak and the position will be added to the peak table and
854a line marking this is added to the plot, as below. <o:p></o:p></span></p>
855
856<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
857mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5" o:spid="_x0000_i1029"
858 type="#_x0000_t75" style='width:319pt;height:267pt;visibility:visible'>
859 <v:imagedata src="FindProfParamCW_files/image009.png" o:title=""/>
860</v:shape><![endif]--><![if !vml]><img border=0 width=321 height=269
861src="FindProfParamCW_files/image010.png" v:shapes="Picture_x0020_5"><![endif]></span><span
862style='font-size:14.0pt'><o:p></o:p></span></p>
863
864<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
865
866<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
867style='font-size:14.0pt'>Repeat this for all 8 peaks</span></b><span
868style='font-size:14.0pt'> in the pattern. Note that if a peak is entered in the
869wrong place <span class=GramE>it can be moved by ÒdraggingÓ it with the mouse</span>,
870or use a right-click to delete it. Be careful to make sure two peaks are not entered
871in the same place by accident<span class=GramE>,.</span><o:p></o:p></span></p>
872
873<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
874mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6" o:spid="_x0000_i1030"
875 type="#_x0000_t75" style='width:333pt;height:251pt;visibility:visible'>
876 <v:imagedata src="FindProfParamCW_files/image011.png" o:title=""/>
877</v:shape><![endif]--><![if !vml]><img border=0 width=335 height=253
878src="FindProfParamCW_files/image012.png" v:shapes="Picture_x0020_6"><![endif]><o:p></o:p></span></p>
879
880<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
881mso-no-proof:yes'>The peak table appears as:</span><span style='font-size:14.0pt'><o:p></o:p></span></p>
882
883<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
884mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7" o:spid="_x0000_i1031"
885 type="#_x0000_t75" style='width:523pt;height:218pt;visibility:visible'>
886 <v:imagedata src="FindProfParamCW_files/image013.png" o:title=""/>
887</v:shape><![endif]--><![if !vml]><img border=0 width=525 height=220
888src="FindProfParamCW_files/image014.png" v:shapes="Picture_x0020_7"><![endif]></span><span
889style='font-size:14.0pt'><o:p></o:p></span></p>
890
891<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
892
893<h3><span style='font-size:14.0pt'>Step 5: Refine Peak Areas<o:p></o:p></span></h3>
894
895<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
896
897<p class=MsoNormal><span style='font-size:14.0pt'>By default, the peak
898intensities <span class=GramE>are flagged as to be varied</span>, but not any
899of the other parameters. It is wise to refine them all, but we want to make
900sure the parameters have a chance to converge one step at a time and we should
901start with only the intensities.<span style="mso-spacerun:yes">&nbsp;
902</span>Use the <b style='mso-bidi-font-weight:normal'>Peak Fitting/<span
903class=SpellE>Peakfit</span></b> menu item to perform a peak refinement. You
904will be asked for a name to save the project (enter a name such as <span
905class=SpellE>peakfit.gpx</span> and press Save). The peaks are then fit, here
906optimizing only the intensity values. The console window shows the details of
907the refinement:<o:p></o:p></span></p>
908
909<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
910
911<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
912mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_8" o:spid="_x0000_i1032"
913 type="#_x0000_t75" style='width:475pt;height:178pt;visibility:visible'>
914 <v:imagedata src="FindProfParamCW_files/image015.png" o:title=""/>
915</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=180
916src="FindProfParamCW_files/image016.png" v:shapes="Picture_x0020_8"><![endif]></span><span
917style='font-size:14.0pt'><o:p></o:p></span></p>
918
919<p class=MsoNormal><span style='font-size:14.0pt'>The warning at the end is
920because the default peak parameters describe a peak shape that is significantly
921sharper than what is actually present for these data; the step size is actually
922fine. This warning will later go away, but if it did not this would indicate
923that it would be better to recollect the data with a step size decreased by a
924factor of 3-4. <o:p></o:p></span></p>
925
926<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
927
928<h3><span style='font-size:14.0pt'>Step 6: Refine peak areas and heights<o:p></o:p></span></h3>
929
930<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
931
932<p class=MsoNormal><span style='font-size:14.0pt'>In the peak list window, <b
933style='mso-bidi-font-weight:normal'>double click in the refine heading for the
934peak position</b> <span class=GramE>flags,</span> this will bring up a dialog
935that allows all peak positions to be varied. <o:p></o:p></span></p>
936
937<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
938mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9" o:spid="_x0000_i1033"
939 type="#_x0000_t75" style='width:158pt;height:123pt;visibility:visible'>
940 <v:imagedata src="FindProfParamCW_files/image017.png" o:title=""/>
941</v:shape><![endif]--><![if !vml]><img border=0 width=160 height=125
942src="FindProfParamCW_files/image018.png" v:shapes="Picture_x0020_9"><![endif]></span><span
943style='font-size:14.0pt'><span style="mso-spacerun:yes">&nbsp;</span><o:p></o:p></span></p>
944
945<p class=MsoNormal><span style='font-size:14.0pt'>Select Òvary allÓ and press
946OK. Now all peak positions and areas will be refined.<o:p></o:p></span></p>
947
948<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
949mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_10" o:spid="_x0000_i1034"
950 type="#_x0000_t75" style='width:514pt;height:217pt;visibility:visible'>
951 <v:imagedata src="FindProfParamCW_files/image019.png" o:title=""/>
952</v:shape><![endif]--><![if !vml]><img border=0 width=516 height=219
953src="FindProfParamCW_files/image020.png" v:shapes="Picture_x0020_10"><![endif]></span><span
954style='font-size:14.0pt'><o:p></o:p></span></p>
955
956<p class=MsoNormal><span style='font-size:14.0pt'>Use the <b style='mso-bidi-font-weight:
957normal'>Peak Fitting/<span class=SpellE>Peakfit</span></b> menu item to start
958peak refinement.<o:p></o:p></span></p>
959
960<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
961
962<p class=MsoNormal><span style='font-size:14.0pt'>The fit improves
963significantly, as below, but further improvements are needed. <o:p></o:p></span></p>
964
965<p class=MsoNormal><span style='font-size:14.0pt;mso-fareast-language:EN-US;
966mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11" o:spid="_x0000_i1035"
967 type="#_x0000_t75" style='width:258pt;height:187pt;visibility:visible'>
968 <v:imagedata src="FindProfParamCW_files/image021.png" o:title=""/>
969</v:shape><![endif]--><![if !vml]><img border=0 width=260 height=189
970src="FindProfParamCW_files/image022.png" v:shapes="Picture_x0020_11"><![endif]></span><span
971style='font-size:14.0pt'><o:p></o:p></span></p>
972
973<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
974
975<h3><span style='font-size:14.0pt'>Step 7: Refine peak areas, heights and
976widths (optional)<o:p></o:p></span></h3>
977
978<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
979
980<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
981style='font-size:14.0pt'>Double-Click</span></b><span style='font-size:14.0pt'>
982on the refine headings for the <b style='mso-bidi-font-weight:normal'>sigma</b>
983(Gaussian width) and <b style='mso-bidi-font-weight:normal'>gamma</b>
984(Lorentzian width) parameters so that all parameters can be refined. Use the <b
985style='mso-bidi-font-weight:normal'>Peak Fitting/<span class=SpellE>Peakfit</span></b>
986menu item to start peak refinement. The results in the console window are as
987below. <span style="mso-spacerun:yes">&nbsp;</span>This is being done here just
988to see how the individual peaks vary before we fit them with a parametric
989equation. This step is not necessary, but provides a useful graphical reference
990to look for any anomalous peaks that one might not want to use. <span
991style="mso-spacerun:yes">&nbsp;</span><o:p></o:p></span></p>
992
993<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
994
995<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
996 id="_x0000_i1036" type="#_x0000_t75" style='width:6in;height:2in'>
997 <v:imagedata src="FindProfParamCW_files/image023.png" o:title=""/>
998</v:shape><![endif]--><![if !vml]><img border=0 width=434 height=146
999src="FindProfParamCW_files/image024.png" v:shapes="_x0000_i1036"><![endif]><o:p></o:p></span></p>
1000
1001<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1002
1003<h3><span style='font-size:14.0pt'>Step 8: Add more Background terms<o:p></o:p></span></h3>
1004
1005<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1006
1007<p class=MsoNormal><span style='font-size:14.0pt'>Use the zoom feature
1008(magnifying glass) to draw a box around the low intensity data<o:p></o:p></span></p>
1009
1010<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1011
1012<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1013 id="_x0000_i1037" type="#_x0000_t75" style='width:441pt;height:180pt'>
1014 <v:imagedata src="FindProfParamCW_files/image025.png" o:title="fig"/>
1015</v:shape><![endif]--><![if !vml]><img border=0 width=443 height=182
1016src="FindProfParamCW_files/image026.png" v:shapes="_x0000_i1037"><![endif]><o:p></o:p></span></p>
1017
1018<p class=MsoNormal><span style='font-size:14.0pt'>Looking at the plot (see
1019below<span class=GramE>),</span> makes it clear that the background is not well
1020fit. Adding more background terms will fix this. <o:p></o:p></span></p>
1021
1022<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1023 id="_x0000_i1038" type="#_x0000_t75" style='width:431pt;height:324pt'>
1024 <v:imagedata src="FindProfParamCW_files/image027.png" o:title=""/>
1025</v:shape><![endif]--><![if !vml]><img border=0 width=433 height=326
1026src="FindProfParamCW_files/image028.png" v:shapes="_x0000_i1038"><![endif]><o:p></o:p></span></p>
1027
1028<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1029
1030<p class=MsoNormal><span style='font-size:14.0pt'>Select the <b
1031style='mso-bidi-font-weight:normal'>Background</b> tree item and change the <b
1032style='mso-bidi-font-weight:normal'>number of coefficients to 6</b>, as shown
1033below. <o:p></o:p></span></p>
1034
1035<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1036 id="_x0000_i1039" type="#_x0000_t75" style='width:553pt;height:231pt'>
1037 <v:imagedata src="FindProfParamCW_files/image029.png" o:title=""/>
1038</v:shape><![endif]--><![if !vml]><img border=0 width=555 height=233
1039src="FindProfParamCW_files/image030.png" v:shapes="_x0000_i1039"><![endif]><o:p></o:p></span></p>
1040
1041<p class=MsoNormal><span style='font-size:14.0pt'>Then return to the <b
1042style='mso-bidi-font-weight:normal'>Peak List</b> data tree item and use the <b
1043style='mso-bidi-font-weight:normal'>Peak Fitting/<span class=SpellE>Peakfit</span></b>
1044menu item to perform a peak refinement. At this point it is instructive to
1045click on the <b style='mso-bidi-font-weight:normal'>Instrument Parameters</b>
1046data tree item to see a plot of peak widths:<o:p></o:p></span></p>
1047
1048<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1049 id="_x0000_i1040" type="#_x0000_t75" style='width:457pt;height:374pt'>
1050 <v:imagedata src="FindProfParamCW_files/image031.png" o:title=""/>
1051</v:shape><![endif]--><![if !vml]><img border=0 width=459 height=376
1052src="FindProfParamCW_files/image032.png" v:shapes="_x0000_i1040"><![endif]><o:p></o:p></span></p>
1053
1054<p class=MsoNormal><span style='font-size:14.0pt'>Note that the solid curves
1055here are plots of the profile coefficients from the default instrument
1056parameters (which are unimportant here), but the fits for the individual peaks
1057are shown (in units of Q/delta-Q <span class=SpellE>vs</span> Q), with
1058Lorentzian widths (gamma) in green, Gaussian widths (sigma) in red and their
1059convolution (total broadening) in blue. <o:p></o:p></span></p>
1060
1061<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1062
1063<h3><span style='font-size:14.0pt'>Step 9: Refine Profile Parameters<o:p></o:p></span></h3>
1064
1065<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1066
1067<p class=MsoNormal><span style='font-size:14.0pt'>Now, select the profile terms
1068to be <b style='mso-bidi-font-weight:normal'>refine</b>d. Use <b
1069style='mso-bidi-font-weight:normal'>Gaussian U, V, &amp; W and Lorentzian X
1070&amp; Y</b> (note that Z, which provides constant broadening, independent of Q,
1071is provided as an option, but is rarely if ever needed.)<o:p></o:p></span></p>
1072
1073<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1074 id="_x0000_i1041" type="#_x0000_t75" style='width:505pt;height:263pt'>
1075 <v:imagedata src="FindProfParamCW_files/image033.png" o:title=""/>
1076</v:shape><![endif]--><![if !vml]><img border=0 width=507 height=265
1077src="FindProfParamCW_files/image034.png" v:shapes="_x0000_i1041"><![endif]><o:p></o:p></span></p>
1078
1079<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1080
1081<p class=MsoNormal><span style='font-size:14.0pt'>Note that these U, V &amp; W
1082values will be used to set the Gaussian peak widths for those peaks where sigma
1083is not being refined and likewise X, Y &amp; Z will be used to determine the
1084Lorentzian widths where gamma is not refined for that peak. If we had any peaks
1085that were not consistent with the width of the others, we might choose to
1086continue to refine their sigma &amp; gamma values so they would not affect U, <span
1087class=GramE>V,É,</span> but here we will refine U, V, W, X &amp; Y against all
1088peaks. Select the <b style='mso-bidi-font-weight:normal'>Peak List data</b>
1089tree item and <b style='mso-bidi-font-weight:normal'>remove refinement of sigma
1090&amp; gamma</b> for all peaks by double-clicking on the refine column headers
1091for each and select ÒN &#8211; vary noneÓ so that the table appears as below:<o:p></o:p></span></p>
1092
1093<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1094 id="_x0000_i1042" type="#_x0000_t75" style='width:533pt;height:207pt'>
1095 <v:imagedata src="FindProfParamCW_files/image035.png" o:title=""/>
1096</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=209
1097src="FindProfParamCW_files/image036.png" v:shapes="_x0000_i1042"><![endif]><o:p></o:p></span></p>
1098
1099<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1100
1101<p class=MsoNormal><span style='font-size:14.0pt'>Use the <b style='mso-bidi-font-weight:
1102normal'>Peak Fitting/<span class=SpellE>Peakfit</span></b> menu item to perform
1103a peak refinement optimizing U, V, W, <span class=GramE>X</span> &amp; Y:<o:p></o:p></span></p>
1104
1105<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1106
1107<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1108 id="_x0000_i1043" type="#_x0000_t75" style='width:510pt;height:198pt'>
1109 <v:imagedata src="FindProfParamCW_files/image037.png" o:title=""/>
1110</v:shape><![endif]--><![if !vml]><img border=0 width=512 height=200
1111src="FindProfParamCW_files/image038.png" v:shapes="_x0000_i1043"><![endif]><o:p></o:p></span></p>
1112
1113<p class=MsoNormal><span style='font-size:14.0pt'>Note that the sigma and gamma
1114values are now computed from U, V, &amp; W and X &amp; Y, respectively. The
1115difference curve shows very small deviations.<o:p></o:p></span></p>
1116
1117<p class=MsoNormal><span style='font-size:14.0pt'><span
1118style="mso-spacerun:yes">&nbsp;</span><!--[if gte vml 1]><v:shape id="_x0000_i1044"
1119 type="#_x0000_t75" style='width:460pt;height:323pt'>
1120 <v:imagedata src="FindProfParamCW_files/image039.png" o:title=""/>
1121</v:shape><![endif]--><![if !vml]><img border=0 width=462 height=325
1122src="FindProfParamCW_files/image040.png" v:shapes="_x0000_i1044"><![endif]><o:p></o:p></span></p>
1123
1124<p class=MsoNormal><span style='font-size:14.0pt'>Note that the background is
1125also quite well fit now. <o:p></o:p></span></p>
1126
1127<h3><span style='font-size:14.0pt'>Step 10: Save the Profile Parameters<o:p></o:p></span></h3>
1128
1129<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1130
1131<p class=MsoNormal><span style='font-size:14.0pt'>So that we can use these
1132profile terms as the starting point for a future refinement, <b
1133style='mso-bidi-font-weight:normal'>save the profile terms</b> to a file by
1134clicking on the <b style='mso-bidi-font-weight:normal'>Instrumental Parameters</b>
1135data tree item and use the <b style='mso-bidi-font-weight:normal'>Operations/Save
1136Profile</b> menu command. Give the file a name that will be helpful for future
1137use (&lt;<span class=SpellE><i style='mso-bidi-font-style:normal'>MyInstrument</i></span><i
1138style='mso-bidi-font-style:normal'>&gt;</i>20-70deg.instparm might be good) and
1139put this file in the directory(s) where you will keep your data files. <o:p></o:p></span></p>
1140
1141<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1142
1143<p class=MsoNormal><span style='font-size:14.0pt'>Clicking on the Instrument
1144Parameters data tree item will show the peak widths from U, V, W, X &amp; Y,
1145and also the individual peak widths generated from those values (not very
1146useful). For a more useful plot we refining the individual peak widths
1147independently again, as shown in the next section. <o:p></o:p></span></p>
1148
1149<h3><span style='font-size:14.0pt'>Step 11: Plot Profile Parameters with
1150Individual Peak Widths (optional)<o:p></o:p></span></h3>
1151
1152<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1153
1154<p class=MsoNormal><span style='font-size:14.0pt'>First we <b style='mso-bidi-font-weight:
1155normal'>stop refining U, V, W, <span class=GramE>X</span> &amp; Y</b> by
1156clicking on <b style='mso-bidi-font-weight:normal'>Instrumental Parameters</b>
1157data tree item and turning the refinement flags off. <o:p></o:p></span></p>
1158
1159<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1160 id="_x0000_i1046" type="#_x0000_t75" style='width:393pt;height:254pt'>
1161 <v:imagedata src="FindProfParamCW_files/image041.png" o:title=""/>
1162</v:shape><![endif]--><![if !vml]><img border=0 width=395 height=256
1163src="FindProfParamCW_files/image042.png" v:shapes="_x0000_i1046"><![endif]><o:p></o:p></span></p>
1164
1165<p class=MsoNormal><span style='font-size:14.0pt'>In the <b style='mso-bidi-font-weight:
1166normal'>Peak List</b> data tree item, turn on<b style='mso-bidi-font-weight:
1167normal'> refine</b>ment of<b style='mso-bidi-font-weight:normal'> all
1168individual peak widths</b> (as we did in Step 7)<o:p></o:p></span></p>
1169
1170<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1171 id="_x0000_i1047" type="#_x0000_t75" style='width:545pt;height:195pt'>
1172 <v:imagedata src="FindProfParamCW_files/image043.png" o:title=""/>
1173</v:shape><![endif]--><![if !vml]><img border=0 width=547 height=197
1174src="FindProfParamCW_files/image044.png" v:shapes="_x0000_i1047"><![endif]><o:p></o:p></span></p>
1175
1176<p class=MsoNormal><span class=GramE><span style='font-size:14.0pt'>and</span></span><span
1177style='font-size:14.0pt'> use the <b style='mso-bidi-font-weight:normal'>Peak
1178Fitting/<span class=SpellE>Peakfit</span></b> menu item to perform a peak
1179refinement optimizing individual peak widths, as before. Returning to the <b
1180style='mso-bidi-font-weight:normal'>Instrumental Parameters</b> data tree item
1181provides this plot:<o:p></o:p></span></p>
1182
1183<p class=MsoNormal><span style='font-size:14.0pt'><o:p>&nbsp;</o:p></span></p>
1184
1185<p class=MsoNormal><span style='font-size:14.0pt'><!--[if gte vml 1]><v:shape
1186 id="_x0000_i1048" type="#_x0000_t75" style='width:537pt;height:426pt'>
1187 <v:imagedata src="FindProfParamCW_files/image045.png" o:title=""/>
1188</v:shape><![endif]--><![if !vml]><img border=0 width=539 height=428
1189src="FindProfParamCW_files/image046.png" v:shapes="_x0000_i1048"><![endif]><o:p></o:p></span></p>
1190
1191<p class=MsoNormal><span style='font-size:14.0pt'>The displayed lines and
1192points are as follows, where Lorentzian widths are shown in green, Gaussian
1193widths are in red and their convolution (total broadening) is shown in blue: <o:p></o:p></span></p>
1194
1195<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
1196style='font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
1197mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>á<span
1198style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1199style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>Solid curves</span></b><span
1200style='font-size:14.0pt'>: profile terms from original instrument parameter
1201file (here the <span class=SpellE>CuKa</span> lab data defaults). Note since X,
1202Y &amp; Z are zero, there is only Gaussian broadening and the total broadening
1203is exactly the same as the Gaussian so the blue curve hides the red one. <o:p></o:p></span></p>
1204
1205<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
1206style='font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
1207mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>á<span
1208style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1209style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>Dashed
1210curves:</span></b><span style='font-size:14.0pt'> <span class=GramE>these
1211values are generated by U, V &amp; W and X, Y &amp; Z. Note that the broadening
1212from this instrument is significantly greater than the default</span> values. <o:p></o:p></span></p>
1213
1214<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
1215style='font-size:14.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
1216mso-bidi-font-family:Symbol'><span style='mso-list:Ignore'>á<span
1217style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1218style='mso-bidi-font-weight:normal'><span style='font-size:14.0pt'>Plus signs
1219(points):</span></b><span style='font-size:14.0pt'> these are the widths for
1220the individual reflections unconstrained. Note that they agree well with the
1221fitted curves (dashed lines).<span style="mso-spacerun:yes">&nbsp; </span><o:p></o:p></span></p>
1222
1223</div>
1224
1225</body>
1226
1227</html>
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