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531 | |
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532 | <h1><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
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533 | "Times New Roman"'>Simulating Powder Diffraction with GSAS-II<o:p></o:p></span></h1> |
---|
534 | |
---|
535 | <P><B>A video version of this tutorial is available at |
---|
536 | <A href="https://anl.box.com/v/SimTutorial" target="_blank"> |
---|
537 | https://anl.box.com/v/SimTutorial</A></B></P> |
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538 | |
---|
539 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
540 | mso-bidi-font-family:"Times New Roman"'>While GSAS-II provides an environment |
---|
541 | for fitting of diffraction data, it can also be used to simulate diffraction |
---|
542 | experiments, where results are quantitative models for what can be expected, |
---|
543 | provided that an accurate instrument description is used. Here we demonstrate |
---|
544 | how a simulation is done for a two-phase mixture with multiple instrument |
---|
545 | types. <o:p></o:p></span></p> |
---|
546 | |
---|
547 | <h2><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
548 | "Times New Roman"'>Step 1: Read in Phases<o:p></o:p></span></h2> |
---|
549 | |
---|
550 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
551 | mso-bidi-font-family:"Times New Roman"'>First we will read in two phases, CuCr<sub>2</sub>O<sub>4</sub> |
---|
552 | and <span class=SpellE>CuO</span> from files CuCr2O4.cif and <span |
---|
553 | class=SpellE>CuO.cif</span>, which can be downloaded from <a |
---|
554 | href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data/">directory |
---|
555 | https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data/</a>. <o:p></o:p></span></p> |
---|
556 | |
---|
557 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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558 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
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559 | |
---|
560 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
561 | mso-bidi-font-family:"Times New Roman"'>Create a new project by starting GSAS-II |
---|
562 | or by using the File/New Project menu item. Then use the Import/Phase/“from CIF |
---|
563 | file” and select the CuCr2O4.cif for the “Choose Phase input file” dialog window. |
---|
564 | Click “Ok” and “Yes” in the “Is this <span class=SpellE>the</span> file you |
---|
565 | want?” confirmation window. <span style="mso-spacerun:yes"> </span>The default |
---|
566 | Phase name, CuCr2O4 is fine.<o:p></o:p></span></p> |
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567 | |
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604 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
605 | "Times New Roman"'>Repeat this to read in the second phase: use the |
---|
606 | Import/Phase/“from CIF file” and select the <span class=SpellE>CuO.cif</span> |
---|
607 | for the “Choose Phase input file” dialog window. Click “Ok” and “Yes” in the “Is |
---|
608 | this the file you want?” confirmation window. <span |
---|
609 | style="mso-spacerun:yes"> </span>The default Phase name, <span class=SpellE>CuO</span> |
---|
610 | is also fine.<o:p></o:p></span></p> |
---|
611 | |
---|
612 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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613 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
---|
614 | |
---|
615 | <h2><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
616 | "Times New Roman"'>Step 2: Create Simulation Histograms<o:p></o:p></span></h2> |
---|
617 | |
---|
618 | <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span |
---|
619 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
620 | "Times New Roman"'>Part A</span></b><span style='font-size:12.0pt;mso-fareast-font-family: |
---|
621 | "Times New Roman";mso-bidi-font-family:"Times New Roman"'>: Use the |
---|
622 | Import/Powder Data/“Simulate a dataset” menu item (at bottom of menu list) to |
---|
623 | create a simulation (dummy) histogram. The program then requests an instrument |
---|
624 | parameter file name. Click Cancel and a list of default instrument parameters |
---|
625 | are then displayed, as shown to the right. Select the APS 11-BM instrument |
---|
626 | listing and press OK.</span> <span style='font-size:12.0pt;mso-fareast-font-family: |
---|
627 | "Times New Roman";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> |
---|
628 | |
---|
629 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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630 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
---|
631 | |
---|
632 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
633 | mso-bidi-font-family:"Times New Roman"'>A dialog window is then displayed that with |
---|
634 | the name for the histogram, the range of data and the step size. Below, note |
---|
635 | that the name and start angle have been changed from the defaults. Then press |
---|
636 | OK and the “Add to phase(s)” dialog is displayed. <o:p></o:p></span></p> |
---|
637 | |
---|
638 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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641 | height:203pt;visibility:visible;mso-wrap-style:square'> |
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642 | <v:imagedata src="SimTutorial_files/image003.png" o:title=""/> |
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643 | </v:shape><![endif]--><![if !vml]><img border=0 width=224 height=205 |
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644 | src="SimTutorial_files/image004.png" v:shapes="Picture_x0020_8"><![endif]></span><span |
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645 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
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646 | "Times New Roman"'><o:p></o:p></span></p> |
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647 | |
---|
648 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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649 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
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650 | |
---|
651 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
652 | mso-bidi-font-family:"Times New Roman"'>Finally, in this dialog, we need to |
---|
653 | indicate which phases are linked with this histogram. We want to include both |
---|
654 | in the simulation, so use the “Set All” button (or select each phase) and press |
---|
655 | OK.<o:p></o:p></span></p> |
---|
656 | |
---|
657 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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663 | src="SimTutorial_files/image006.png" v:shapes="Picture_x0020_9"><![endif]></span><span |
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664 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
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665 | "Times New Roman"'><o:p></o:p></span></p> |
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666 | |
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667 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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668 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
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669 | |
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670 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
671 | mso-bidi-font-family:"Times New Roman"'>Note that a new histogram is now added |
---|
672 | to the data tree, as below. (Note the "Edit range" button which can be |
---|
673 | used to change the values entered on the previous dialog). |
---|
674 | <o:p></o:p></span></p> |
---|
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679 | height:244pt;visibility:visible;mso-wrap-style:square'> |
---|
680 | <v:imagedata src="SimTutorial_files/image007.png" o:title=""/> |
---|
681 | </v:shape><![endif]--><![if !vml]><img border=0 width=383 height=246 |
---|
682 | src="SimTutorial_files/image008.png" v:shapes="Picture_x0020_10"><![endif]></span><span |
---|
683 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
684 | "Times New Roman"'><o:p></o:p></span></p> |
---|
685 | |
---|
686 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
687 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
---|
688 | |
---|
689 | <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span |
---|
690 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
691 | "Times New Roman"'>Part B</span></b><span style='font-size:12.0pt;mso-fareast-font-family: |
---|
692 | "Times New Roman";mso-bidi-font-family:"Times New Roman"'>: Again use the |
---|
693 | Import/Powder Data/“Simulate a dataset” menu item (at bottom of menu list) to |
---|
694 | create a simulation (dummy) histogram. This time when the program then requests |
---|
695 | an instrument parameter file name, supply file BT1.prm, which can also be |
---|
696 | downloaded from <a |
---|
697 | href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data/">directory |
---|
698 | https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data/</a>. <o:p></o:p></span></p> |
---|
699 | |
---|
700 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
701 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
---|
702 | |
---|
703 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
704 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
705 | id="Picture_x0020_13" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:405pt; |
---|
706 | height:197pt;visibility:visible;mso-wrap-style:square'> |
---|
707 | <v:imagedata src="SimTutorial_files/image009.png" o:title=""/> |
---|
708 | </v:shape><![endif]--><![if !vml]><img border=0 width=407 height=199 |
---|
709 | src="SimTutorial_files/image010.png" v:shapes="Picture_x0020_13"><![endif]></span><span |
---|
710 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
711 | "Times New Roman"'><o:p></o:p></span></p> |
---|
712 | |
---|
713 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
714 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
---|
715 | |
---|
716 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
717 | mso-bidi-font-family:"Times New Roman"'>Click Open and a dialog opens for the |
---|
718 | dataset name and range for this histogram. Change the range to 1 to 120 degrees |
---|
719 | with 0<span class=GramE>.025 degree</span> steps and optionally change the |
---|
720 | name, as below. <o:p></o:p></span></p> |
---|
721 | |
---|
722 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
723 | mso-bidi-font-family:"Times New Roman"'><span style="mso-spacerun:yes"> </span></span><span |
---|
724 | style="mso-spacerun:yes"> </span><span style='font-size:12.0pt;mso-fareast-font-family: |
---|
725 | "Times New Roman";mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
726 | id="Picture_x0020_16" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:211pt; |
---|
727 | height:195pt;visibility:visible;mso-wrap-style:square'> |
---|
728 | <v:imagedata src="SimTutorial_files/image011.png" o:title=""/> |
---|
729 | </v:shape><![endif]--><![if !vml]><img border=0 width=213 height=197 |
---|
730 | src="SimTutorial_files/image012.png" v:shapes="Picture_x0020_16"><![endif]></span><span |
---|
731 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
732 | "Times New Roman"'><o:p></o:p></span></p> |
---|
733 | |
---|
734 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
735 | mso-bidi-font-family:"Times New Roman"'>Press OK and then <span class=GramE>the |
---|
736 | <span class=SpellE>the</span></span> “Add to phase(s)” dialog is displayed. As |
---|
737 | before, add link both phases to this histogram. <span |
---|
738 | style="mso-spacerun:yes"> </span>At this point a second histogram is shown in |
---|
739 | the data tree:<o:p></o:p></span></p> |
---|
740 | |
---|
741 | <p class=MsoNormal><span style="mso-spacerun:yes"> </span><span |
---|
742 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
743 | "Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_17" |
---|
744 | o:spid="_x0000_i1033" type="#_x0000_t75" style='width:364pt;height:228pt; |
---|
745 | visibility:visible;mso-wrap-style:square'> |
---|
746 | <v:imagedata src="SimTutorial_files/image013.png" o:title=""/> |
---|
747 | </v:shape><![endif]--><![if !vml]><img border=0 width=366 height=230 |
---|
748 | src="SimTutorial_files/image014.png" v:shapes="Picture_x0020_17"><![endif]></span><span |
---|
749 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
750 | "Times New Roman"'><o:p></o:p></span></p> |
---|
751 | |
---|
752 | <h2><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
753 | "Times New Roman"'>Step 3: Set Phase Fractions<o:p></o:p></span></h2> |
---|
754 | |
---|
755 | <p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_1" o:spid="_x0000_s1026" |
---|
756 | type="#_x0000_t75" alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f1.png" |
---|
757 | style='position:absolute;margin-left:300.4pt;margin-top:70.5pt;width:351.6pt; |
---|
758 | height:188.1pt;z-index:251658240;visibility:visible;mso-wrap-style:square; |
---|
759 | mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt; |
---|
760 | mso-wrap-distance-top:0;mso-wrap-distance-right:9pt; |
---|
761 | mso-wrap-distance-bottom:0;mso-position-horizontal:right; |
---|
762 | mso-position-horizontal-relative:text;mso-position-vertical:absolute; |
---|
763 | mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0; |
---|
764 | mso-width-relative:page;mso-height-relative:page'> |
---|
765 | <v:imagedata src="SimTutorial_files/image015.png" o:title="f1.png"/> |
---|
766 | <w:wrap type="tight"/> |
---|
767 | </v:shape><![endif]--><![if !vml]><img width=354 height=190 |
---|
768 | src="SimTutorial_files/image016.png" align=right hspace=9 |
---|
769 | alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f1.png" v:shapes="Picture_x0020_1"><![endif]><span |
---|
770 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
771 | "Times New Roman"'>It is important to understand how the scale factor (found |
---|
772 | each histogram's Sample Parameters tree entry) and phase fractions (found in |
---|
773 | each phase's data tab) are used in GSAS-II. The scattering contribution for |
---|
774 | each phase is set from the product of the histogram scale factor multiplied by |
---|
775 | the phase fraction for each phase in that histogram which multiplies the |
---|
776 | scattering power of each atom in the unit cell. This means that the phase |
---|
777 | fraction effectively represents the relative number of unit cells present for |
---|
778 | each phase. Note that after reading in the two phases in the previous step, |
---|
779 | their phase fractions default to 1 for each. The contents of each phase are |
---|
780 | shown on the General tab. Note that the unit cell contents for each phase are |
---|
781 | Cu<sub>8</sub>Cr<sub>16</sub>O<sub>32</sub> (1852.3 g/<span class=SpellE>mol</span>) |
---|
782 | and Cu<sub>4</sub>O<sub>4</sub> (318.2 g/<span class=SpellE>mol</span>), with |
---|
783 | equal numbers of unit cells, the mass (or equivalently weight) fractions will |
---|
784 | be 1852.3/(318.2+1852.3)=85.3% and 318.2/(318.2+1852.3)=14.7%. This can be |
---|
785 | confirmed on the Data for each phase, as below.<o:p></o:p></span></p> |
---|
786 | |
---|
787 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
788 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
789 | id="Picture_x0020_3" o:spid="_x0000_i1032" type="#_x0000_t75" alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f2.png" |
---|
790 | style='width:453pt;height:170pt;visibility:visible;mso-wrap-style:square'> |
---|
791 | <v:imagedata src="SimTutorial_files/image017.png" o:title="f2.png"/> |
---|
792 | </v:shape><![endif]--><![if !vml]><img border=0 width=455 height=172 |
---|
793 | src="SimTutorial_files/image018.png" |
---|
794 | alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f2.png" v:shapes="Picture_x0020_3"><![endif]></span><span |
---|
795 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
796 | "Times New Roman"'><o:p></o:p></span></p> |
---|
797 | |
---|
798 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
799 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
---|
800 | |
---|
801 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
802 | mso-bidi-font-family:"Times New Roman"'>For this tutorial, we will choose to |
---|
803 | set the mass fractions to give 90% CuCr<sub>2</sub>O<sub>4</sub> and 10% <span |
---|
804 | class=SpellE>CuO</span>, so 90/1852.3=</span><span style='font-size:12.0pt; |
---|
805 | font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman"; |
---|
806 | color:black'>0.04859 and 10/</span><span style='font-size:12.0pt;mso-fareast-font-family: |
---|
807 | "Times New Roman";mso-bidi-font-family:"Times New Roman"'>318.2=0.03143. Equivalently, |
---|
808 | we can normalize the phase fractions sum to 1 or so that either phase fraction is |
---|
809 | 1. We will use 1 for CuCr<sub>2</sub>O<sub>4</sub>, and </span><span |
---|
810 | style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family: |
---|
811 | "Times New Roman";color:black'>10*</span><span style='font-size:12.0pt; |
---|
812 | mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'>1852.3</span><span |
---|
813 | style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family: |
---|
814 | "Times New Roman";color:black'>/(</span><span style='font-size:12.0pt; |
---|
815 | mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'>318.2*90)=0.6468 |
---|
816 | for <span class=SpellE>CuO</span>. Enter 0.6468 for the <span class=SpellE>CuO</span> |
---|
817 | Phase fraction. <span style="mso-spacerun:yes"> </span>When the mouse is moved |
---|
818 | out of the box, the mass fraction to be recomputed and appears as 10%, as |
---|
819 | expected:<o:p></o:p></span></p> |
---|
820 | |
---|
821 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
822 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
823 | id="Picture_x0020_18" o:spid="_x0000_i1031" type="#_x0000_t75" alt="Description: BHT14 HD:Users:toby:Library:Mobile Documents:com~apple~Preview:Documents:Untitled.png" |
---|
824 | style='width:451pt;height:238pt;visibility:visible;mso-wrap-style:square'> |
---|
825 | <v:imagedata src="SimTutorial_files/image019.png" o:title="Untitled.png"/> |
---|
826 | </v:shape><![endif]--><![if !vml]><img border=0 width=453 height=240 |
---|
827 | src="SimTutorial_files/image020.png" |
---|
828 | alt="Description: BHT14 HD:Users:toby:Library:Mobile Documents:com~apple~Preview:Documents:Untitled.png" |
---|
829 | v:shapes="Picture_x0020_18"><![endif]></span><span style='font-size:12.0pt; |
---|
830 | mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> |
---|
831 | |
---|
832 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
833 | mso-bidi-font-family:"Times New Roman"'>This must be set for both histograms. |
---|
834 | Clicking on the second histogram allows that phase fraction to be edited. Even easier |
---|
835 | is to use the “Edit Phase”/“Copy data” menu item to copy all <span |
---|
836 | class=SpellE>CuO</span> data settings from histogram 1 to histogram 2. Note |
---|
837 | that if the CuCr<sub>2</sub>O<sub>4 </sub>Data tab is selected for either phase, |
---|
838 | the mass fraction is now shown as 90%. <o:p></o:p></span></p> |
---|
839 | |
---|
840 | <h2><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
841 | "Times New Roman"'>Step 4: Turn off Optimization<o:p></o:p></span></h2> |
---|
842 | |
---|
843 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
844 | mso-bidi-font-family:"Times New Roman"'>A refinement computation is needed to |
---|
845 | cause the pattern to be simulated. When a pattern is first simulated, the |
---|
846 | observed pattern is set to the computed pattern (this can be reset by |
---|
847 | using the "Edit range" button when the histogram data tree item is |
---|
848 | selected. This means that it is actually |
---|
849 | possible to optimize any parameters that are selected to be refined, |
---|
850 | which can be used to test the sensitivity of different models refined |
---|
851 | against a |
---|
852 | simulated dataset. In this case we only need to compute the simulated |
---|
853 | pattern, so we will turn off optimization by setting the |
---|
854 | number of cycles to zero. Do this by clicking on the Controls data tree entry and set the Max |
---|
855 | cycles value to 0 using the pull-down menu:<o:p></o:p></span></p> |
---|
856 | |
---|
857 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
858 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
859 | id="Picture_x0020_5" o:spid="_x0000_i1030" type="#_x0000_t75" alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f4.png" |
---|
860 | style='width:442pt;height:114pt;visibility:visible;mso-wrap-style:square'> |
---|
861 | <v:imagedata src="SimTutorial_files/image021.png" o:title="f4.png"/> |
---|
862 | </v:shape><![endif]--><![if !vml]><img border=0 width=444 height=116 |
---|
863 | src="SimTutorial_files/image022.png" |
---|
864 | alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f4.png" v:shapes="Picture_x0020_5"><![endif]></span><span |
---|
865 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
866 | "Times New Roman"'><o:p></o:p></span></p> |
---|
867 | |
---|
868 | <h2>Step 5: Change Histogram Scale Factor</h2> |
---|
869 | |
---|
870 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
871 | mso-bidi-font-family:"Times New Roman"'>As discussed earlier, the range of |
---|
872 | intensities is determined by the histogram scale factor. For x-rays, a |
---|
873 | histogram scale factor with the default value of 1 produces a reasonable |
---|
874 | intensity range, but with CW neutrons, a much larger scale factor value is |
---|
875 | needed to produce a pattern with non-negligible intensity values. Note that |
---|
876 | GSAS-II adds simulated noise to patterns, so if the scale factor is too small, |
---|
877 | only random counts are seen. Select the Sample Parameters tree item for the |
---|
878 | second histogram and change the scale factor to 1000, as below. </span></p> |
---|
879 | |
---|
880 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
881 | id="Picture_x0020_20" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:370pt; |
---|
882 | height:232pt;visibility:visible;mso-wrap-style:square'> |
---|
883 | <v:imagedata src="SimTutorial_files/image023.png" o:title=""/> |
---|
884 | </v:shape><![endif]--><![if !vml]><img border=0 width=372 height=234 |
---|
885 | src="SimTutorial_files/image024.png" v:shapes="Picture_x0020_20"><![endif]></span></p> |
---|
886 | |
---|
887 | <h2>Step 6: Simulate the Pattern</h2> |
---|
888 | |
---|
889 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
890 | mso-bidi-font-family:"Times New Roman"'>Use the Calculate/Refine menu item to |
---|
891 | compute the simulated pattern. Clicking on the histogram entry in the data tree |
---|
892 | causes the pattern to be displayed as below. This has the reflection <span |
---|
893 | class=SpellE>tickmarks</span> and the difference curve located at zero. While |
---|
894 | both can be dragged to new positions, this is hard to do when they are obscured |
---|
895 | by the “observed” and computed patterns. (The observed pattern has been set to |
---|
896 | the computed pattern with the addition of simulated noise, which is why the |
---|
897 | difference curve is non-zero.)<o:p></o:p></span></p> |
---|
898 | |
---|
899 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
900 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
901 | id="Picture_x0020_11" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:285pt; |
---|
902 | height:243pt;visibility:visible;mso-wrap-style:square'> |
---|
903 | <v:imagedata src="SimTutorial_files/image025.png" o:title=""/> |
---|
904 | </v:shape><![endif]--><![if !vml]><img border=0 width=287 height=245 |
---|
905 | src="SimTutorial_files/image026.png" v:shapes="Picture_x0020_11"><![endif]></span><span |
---|
906 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
907 | "Times New Roman"'><o:p></o:p></span></p> |
---|
908 | |
---|
909 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
910 | mso-bidi-font-family:"Times New Roman"'>A nice trick for resetting the <span |
---|
911 | class=SpellE>tickmarks</span> to their usual default positions is to press “s” |
---|
912 | to scale to <span class=SpellE><span class=GramE>sqrt</span></span><span |
---|
913 | class=GramE>(</span>I) and press it again to return to normal scaling, as shown |
---|
914 | below. These changes in scaling can also be done via the “K” (keyboard) button |
---|
915 | on the bottom toolbar. <o:p></o:p></span></p> |
---|
916 | |
---|
917 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
918 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
919 | id="Picture_x0020_12" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:285pt; |
---|
920 | height:220pt;visibility:visible;mso-wrap-style:square'> |
---|
921 | <v:imagedata src="SimTutorial_files/image027.png" o:title=""/> |
---|
922 | </v:shape><![endif]--><![if !vml]><img border=0 width=287 height=222 |
---|
923 | src="SimTutorial_files/image028.png" v:shapes="Picture_x0020_12"><![endif]></span><span |
---|
924 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
---|
925 | "Times New Roman"'><o:p></o:p></span></p> |
---|
926 | |
---|
927 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
928 | mso-bidi-font-family:"Times New Roman"'>Note that the Commands menu offers menu |
---|
929 | items for moving the difference curve and <span class=SpellE>tickmarks</span>, |
---|
930 | as well as using drag and drop. Use of this, as well as using the rescaling graphics |
---|
931 | toolbar item (the home button indicated by small house on the lower left) |
---|
932 | allows more fine arrangement of locations. Exporting the plot (using the “floppy |
---|
933 | disk” button allows the plots below to be created. Note the very big |
---|
934 | differences in intensities, data range and resolution between the two |
---|
935 | simulations. <o:p></o:p></span></p> |
---|
936 | |
---|
937 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
---|
938 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
---|
939 | id="Picture_x0020_22" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:335pt; |
---|
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951 | |
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956 | |
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958 | |
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