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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 | |
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| 535 | <P><BL> |
|---|
| 536 | <LI><B>A video version of this tutorial is available at |
|---|
| 537 | <A href="https://anl.box.com/v/SimTutorial-" target="_blank"> |
|---|
| 538 | https://anl.box.com/v/SimTutorial-</A></B> |
|---|
| 539 | <LI>Exercise files are found <A href="./data/" target="_blank">here</a> |
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| 540 | </BL></P><P></P> |
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| 541 | |
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| 542 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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| 543 | mso-bidi-font-family:"Times New Roman"'>While GSAS-II provides an environment |
|---|
| 544 | for fitting of diffraction data, it can also be used to simulate diffraction |
|---|
| 545 | experiments, where results are quantitative models for what can be expected, |
|---|
| 546 | provided that an accurate instrument description is used. Here we demonstrate |
|---|
| 547 | how a simulation is done for a two-phase mixture with multiple instrument |
|---|
| 548 | types. <o:p></o:p></span></p> |
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| 549 | |
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| 550 | <h2><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 551 | "Times New Roman"'>Step 1: Read in Phases<o:p></o:p></span></h2> |
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| 552 | |
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| 553 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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| 554 | mso-bidi-font-family:"Times New Roman"'>First we will read in two phases, CuCr<sub>2</sub>O<sub>4</sub> |
|---|
| 555 | and <span class=SpellE>CuO</span> from files CuCr2O4.cif and <span |
|---|
| 556 | class=SpellE>CuO.cif</span>, which can be downloaded from <a |
|---|
| 557 | href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data/">directory |
|---|
| 558 | https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data/</a>. <o:p></o:p></span></p> |
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| 559 | |
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| 560 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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| 561 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
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| 562 | |
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| 563 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 564 | mso-bidi-font-family:"Times New Roman"'>Create a new project by starting GSAS-II |
|---|
| 565 | or by using the File/New Project menu item. Then use the Import/Phase/“from CIF |
|---|
| 566 | file” and select the CuCr2O4.cif for the “Choose Phase input file” dialog window. |
|---|
| 567 | Click “Ok” and “Yes” in the “Is this <span class=SpellE>the</span> file you |
|---|
| 568 | want?” confirmation window. <span style="mso-spacerun:yes"> </span>The default |
|---|
| 569 | Phase name, CuCr2O4 is fine.<o:p></o:p></span></p> |
|---|
| 570 | |
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| 607 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
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| 608 | "Times New Roman"'>Repeat this to read in the second phase: use the |
|---|
| 609 | Import/Phase/“from CIF file” and select the <span class=SpellE>CuO.cif</span> |
|---|
| 610 | for the “Choose Phase input file” dialog window. Click “Ok” and “Yes” in the “Is |
|---|
| 611 | this the file you want?” confirmation window. <span |
|---|
| 612 | style="mso-spacerun:yes"> </span>The default Phase name, <span class=SpellE>CuO</span> |
|---|
| 613 | is also fine.<o:p></o:p></span></p> |
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| 614 | |
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| 615 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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| 616 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
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| 617 | |
|---|
| 618 | <h2><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 619 | "Times New Roman"'>Step 2: Create Simulation Histograms<o:p></o:p></span></h2> |
|---|
| 620 | |
|---|
| 621 | <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span |
|---|
| 622 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 623 | "Times New Roman"'>Part A</span></b><span style='font-size:12.0pt;mso-fareast-font-family: |
|---|
| 624 | "Times New Roman";mso-bidi-font-family:"Times New Roman"'>: Use the |
|---|
| 625 | Import/Powder Data/“Simulate a dataset” menu item (at bottom of menu list) to |
|---|
| 626 | create a simulation (dummy) histogram. The program then requests an instrument |
|---|
| 627 | parameter file name. Click Cancel and a list of default instrument parameters |
|---|
| 628 | are then displayed, as shown to the right. Select the APS 11-BM instrument |
|---|
| 629 | listing and press OK.</span> <span style='font-size:12.0pt;mso-fareast-font-family: |
|---|
| 630 | "Times New Roman";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> |
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| 631 | |
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| 632 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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| 633 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
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| 634 | |
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| 635 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
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| 636 | mso-bidi-font-family:"Times New Roman"'>A dialog window is then displayed that with |
|---|
| 637 | the name for the histogram, the range of data and the step size. Below, note |
|---|
| 638 | that the name and start angle have been changed from the defaults. Then press |
|---|
| 639 | OK and the “Add to phase(s)” dialog is displayed. <o:p></o:p></span></p> |
|---|
| 640 | |
|---|
| 641 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 642 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 643 | id="Picture_x0020_8" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:222pt; |
|---|
| 644 | height:203pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 645 | <v:imagedata src="SimTutorial_files/image003.png" o:title=""/> |
|---|
| 646 | </v:shape><![endif]--><![if !vml]><img border=0 width=224 height=205 |
|---|
| 647 | src="SimTutorial_files/image004.png" v:shapes="Picture_x0020_8"><![endif]></span><span |
|---|
| 648 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 649 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 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"'><o:p> </o:p></span></p> |
|---|
| 653 | |
|---|
| 654 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 655 | mso-bidi-font-family:"Times New Roman"'>Finally, in this dialog, we need to |
|---|
| 656 | indicate which phases are linked with this histogram. We want to include both |
|---|
| 657 | in the simulation, so use the “Set All” button (or select each phase) and press |
|---|
| 658 | OK.<o:p></o:p></span></p> |
|---|
| 659 | |
|---|
| 660 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 661 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 662 | id="Picture_x0020_9" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:224pt; |
|---|
| 663 | height:177pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 664 | <v:imagedata src="SimTutorial_files/image005.png" o:title=""/> |
|---|
| 665 | </v:shape><![endif]--><![if !vml]><img border=0 width=226 height=179 |
|---|
| 666 | src="SimTutorial_files/image006.png" v:shapes="Picture_x0020_9"><![endif]></span><span |
|---|
| 667 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 668 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 669 | |
|---|
| 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"'><o:p> </o:p></span></p> |
|---|
| 672 | |
|---|
| 673 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 674 | mso-bidi-font-family:"Times New Roman"'>Note that a new histogram is now added |
|---|
| 675 | to the data tree, as below. (Note the "Edit range" button which can be |
|---|
| 676 | used to change the values entered on the previous dialog). |
|---|
| 677 | <o:p></o:p></span></p> |
|---|
| 678 | |
|---|
| 679 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 680 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 681 | id="Picture_x0020_10" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:381pt; |
|---|
| 682 | height:244pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 683 | <v:imagedata src="SimTutorial_files/image007.png" o:title=""/> |
|---|
| 684 | </v:shape><![endif]--><![if !vml]><img border=0 width=383 height=246 |
|---|
| 685 | src="SimTutorial_files/image008.png" v:shapes="Picture_x0020_10"><![endif]></span><span |
|---|
| 686 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 687 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 688 | |
|---|
| 689 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 690 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
|---|
| 691 | |
|---|
| 692 | <p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span |
|---|
| 693 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 694 | "Times New Roman"'>Part B</span></b><span style='font-size:12.0pt;mso-fareast-font-family: |
|---|
| 695 | "Times New Roman";mso-bidi-font-family:"Times New Roman"'>: Again use the |
|---|
| 696 | Import/Powder Data/“Simulate a dataset” menu item (at bottom of menu list) to |
|---|
| 697 | create a simulation (dummy) histogram. This time when the program then requests |
|---|
| 698 | an instrument parameter file name, supply file BT1.prm, which can also be |
|---|
| 699 | downloaded from <a |
|---|
| 700 | href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data/">directory |
|---|
| 701 | https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data/</a>. <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"'><o:p> </o:p></span></p> |
|---|
| 705 | |
|---|
| 706 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 707 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 708 | id="Picture_x0020_13" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:405pt; |
|---|
| 709 | height:197pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 710 | <v:imagedata src="SimTutorial_files/image009.png" o:title=""/> |
|---|
| 711 | </v:shape><![endif]--><![if !vml]><img border=0 width=407 height=199 |
|---|
| 712 | src="SimTutorial_files/image010.png" v:shapes="Picture_x0020_13"><![endif]></span><span |
|---|
| 713 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 714 | "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"'><o:p> </o:p></span></p> |
|---|
| 718 | |
|---|
| 719 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 720 | mso-bidi-font-family:"Times New Roman"'>Click Open and a dialog opens for the |
|---|
| 721 | dataset name and range for this histogram. Change the range to 1 to 120 degrees |
|---|
| 722 | with 0<span class=GramE>.025 degree</span> steps and optionally change the |
|---|
| 723 | name, as below. <o:p></o:p></span></p> |
|---|
| 724 | |
|---|
| 725 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 726 | mso-bidi-font-family:"Times New Roman"'><span style="mso-spacerun:yes"> </span></span><span |
|---|
| 727 | style="mso-spacerun:yes"> </span><span style='font-size:12.0pt;mso-fareast-font-family: |
|---|
| 728 | "Times New Roman";mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 729 | id="Picture_x0020_16" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:211pt; |
|---|
| 730 | height:195pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 731 | <v:imagedata src="SimTutorial_files/image011.png" o:title=""/> |
|---|
| 732 | </v:shape><![endif]--><![if !vml]><img border=0 width=213 height=197 |
|---|
| 733 | src="SimTutorial_files/image012.png" v:shapes="Picture_x0020_16"><![endif]></span><span |
|---|
| 734 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 735 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 736 | |
|---|
| 737 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 738 | mso-bidi-font-family:"Times New Roman"'>Press OK and then the |
|---|
| 739 | “Add to phase(s)” dialog is displayed. As |
|---|
| 740 | before, add link both phases to this histogram. <span |
|---|
| 741 | style="mso-spacerun:yes"> </span>At this point a second histogram is shown in |
|---|
| 742 | the data tree:<o:p></o:p></span></p> |
|---|
| 743 | |
|---|
| 744 | <p class=MsoNormal><span style="mso-spacerun:yes"> </span><span |
|---|
| 745 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 746 | "Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_17" |
|---|
| 747 | o:spid="_x0000_i1033" type="#_x0000_t75" style='width:364pt;height:228pt; |
|---|
| 748 | visibility:visible;mso-wrap-style:square'> |
|---|
| 749 | <v:imagedata src="SimTutorial_files/image013.png" o:title=""/> |
|---|
| 750 | </v:shape><![endif]--><![if !vml]><img border=0 width=366 height=230 |
|---|
| 751 | src="SimTutorial_files/image014.png" v:shapes="Picture_x0020_17"><![endif]></span><span |
|---|
| 752 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 753 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 754 | |
|---|
| 755 | <h2><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 756 | "Times New Roman"'>Step 3: Set Phase Fractions<o:p></o:p></span></h2> |
|---|
| 757 | |
|---|
| 758 | <p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_1" o:spid="_x0000_s1026" |
|---|
| 759 | type="#_x0000_t75" alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f1.png" |
|---|
| 760 | style='position:absolute;margin-left:300.4pt;margin-top:70.5pt;width:351.6pt; |
|---|
| 761 | height:188.1pt;z-index:251658240;visibility:visible;mso-wrap-style:square; |
|---|
| 762 | mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt; |
|---|
| 763 | mso-wrap-distance-top:0;mso-wrap-distance-right:9pt; |
|---|
| 764 | mso-wrap-distance-bottom:0;mso-position-horizontal:right; |
|---|
| 765 | mso-position-horizontal-relative:text;mso-position-vertical:absolute; |
|---|
| 766 | mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0; |
|---|
| 767 | mso-width-relative:page;mso-height-relative:page'> |
|---|
| 768 | <v:imagedata src="SimTutorial_files/image015.png" o:title="f1.png"/> |
|---|
| 769 | <w:wrap type="tight"/> |
|---|
| 770 | </v:shape><![endif]--><![if !vml]><img width=354 height=190 |
|---|
| 771 | src="SimTutorial_files/image016.png" align=right hspace=9 |
|---|
| 772 | alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f1.png" v:shapes="Picture_x0020_1"><![endif]><span |
|---|
| 773 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 774 | "Times New Roman"'>It is important to understand how the scale factor (found |
|---|
| 775 | each histogram's Sample Parameters tree entry) and phase fractions (found in |
|---|
| 776 | each phase's data tab) are used in GSAS-II. The scattering contribution for |
|---|
| 777 | each phase is set from the product of the histogram scale factor multiplied by |
|---|
| 778 | the phase fraction for each phase in that histogram which multiplies the |
|---|
| 779 | scattering power of each atom in the unit cell. This means that the phase |
|---|
| 780 | fraction effectively represents the relative number of unit cells present for |
|---|
| 781 | each phase. Note that after reading in the two phases in the previous step, |
|---|
| 782 | their phase fractions default to 1 for each. The contents of each phase are |
|---|
| 783 | shown on the General tab. Note that the unit cell contents for each phase are |
|---|
| 784 | Cu<sub>8</sub>Cr<sub>16</sub>O<sub>32</sub> (1852.3 g/<span class=SpellE>mol</span>) |
|---|
| 785 | and Cu<sub>4</sub>O<sub>4</sub> (318.2 g/<span class=SpellE>mol</span>), with |
|---|
| 786 | equal numbers of unit cells, the mass (or equivalently weight) fractions will |
|---|
| 787 | be 1852.3/(318.2+1852.3)=85.3% and 318.2/(318.2+1852.3)=14.7%. This can be |
|---|
| 788 | confirmed on the Data for each phase, as below.<o:p></o:p></span></p> |
|---|
| 789 | |
|---|
| 790 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 791 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 792 | id="Picture_x0020_3" o:spid="_x0000_i1032" type="#_x0000_t75" alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f2.png" |
|---|
| 793 | style='width:453pt;height:170pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 794 | <v:imagedata src="SimTutorial_files/image017.png" o:title="f2.png"/> |
|---|
| 795 | </v:shape><![endif]--><![if !vml]><img border=0 width=455 height=172 |
|---|
| 796 | src="SimTutorial_files/image018.png" |
|---|
| 797 | alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f2.png" v:shapes="Picture_x0020_3"><![endif]></span><span |
|---|
| 798 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 799 | "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"'><o:p> </o:p></span></p> |
|---|
| 803 | |
|---|
| 804 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 805 | mso-bidi-font-family:"Times New Roman"'>For this tutorial, we will choose to |
|---|
| 806 | set the mass fractions to give 90% CuCr<sub>2</sub>O<sub>4</sub> and 10% <span |
|---|
| 807 | class=SpellE>CuO</span>, so 90/1852.3=</span><span style='font-size:12.0pt; |
|---|
| 808 | font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman"; |
|---|
| 809 | color:black'>0.04859 and 10/</span><span style='font-size:12.0pt;mso-fareast-font-family: |
|---|
| 810 | "Times New Roman";mso-bidi-font-family:"Times New Roman"'>318.2=0.03143. Equivalently, |
|---|
| 811 | we can normalize the phase fractions sum to 1 or so that either phase fraction is |
|---|
| 812 | 1. We will use 1 for CuCr<sub>2</sub>O<sub>4</sub>, and </span><span |
|---|
| 813 | style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family: |
|---|
| 814 | "Times New Roman";color:black'>10*</span><span style='font-size:12.0pt; |
|---|
| 815 | mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'>1852.3</span><span |
|---|
| 816 | style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family: |
|---|
| 817 | "Times New Roman";color:black'>/(</span><span style='font-size:12.0pt; |
|---|
| 818 | mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'>318.2*90)=0.6468 |
|---|
| 819 | for <span class=SpellE>CuO</span>. Enter 0.6468 for the <span class=SpellE>CuO</span> |
|---|
| 820 | Phase fraction. <span style="mso-spacerun:yes"> </span>When the mouse is moved |
|---|
| 821 | out of the box, the mass fraction to be recomputed and appears as 10%, as |
|---|
| 822 | expected:<o:p></o:p></span></p> |
|---|
| 823 | |
|---|
| 824 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 825 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 826 | 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" |
|---|
| 827 | style='width:451pt;height:238pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 828 | <v:imagedata src="SimTutorial_files/image019.png" o:title="Untitled.png"/> |
|---|
| 829 | </v:shape><![endif]--><![if !vml]><img border=0 width=453 height=240 |
|---|
| 830 | src="SimTutorial_files/image020.png" |
|---|
| 831 | alt="Description: BHT14 HD:Users:toby:Library:Mobile Documents:com~apple~Preview:Documents:Untitled.png" |
|---|
| 832 | v:shapes="Picture_x0020_18"><![endif]></span><span style='font-size:12.0pt; |
|---|
| 833 | mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><o:p></o:p></span></p> |
|---|
| 834 | |
|---|
| 835 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 836 | mso-bidi-font-family:"Times New Roman"'>This must be set for both histograms. |
|---|
| 837 | Clicking on the second histogram allows that phase fraction to be edited. Even easier |
|---|
| 838 | is to use the “Edit Phase”/“Copy data” menu item to copy all <span |
|---|
| 839 | class=SpellE>CuO</span> data settings from histogram 1 to histogram 2. Note |
|---|
| 840 | that if the CuCr<sub>2</sub>O<sub>4 </sub>Data tab is selected for either phase, |
|---|
| 841 | the mass fraction is now shown as 90%. <o:p></o:p></span></p> |
|---|
| 842 | |
|---|
| 843 | <h2><span style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 844 | "Times New Roman"'>Step 4: Turn off Optimization<o:p></o:p></span></h2> |
|---|
| 845 | |
|---|
| 846 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 847 | mso-bidi-font-family:"Times New Roman"'>A refinement computation is needed to |
|---|
| 848 | cause the pattern to be simulated. When a pattern is first simulated, the |
|---|
| 849 | observed pattern is set to the computed pattern (this can be reset by |
|---|
| 850 | using the "Edit range" button when the histogram data tree item is |
|---|
| 851 | selected. This means that it is actually |
|---|
| 852 | possible to optimize any parameters that are selected to be refined, |
|---|
| 853 | which can be used to test the sensitivity of different models refined |
|---|
| 854 | against a |
|---|
| 855 | simulated dataset. In this case we only need to compute the simulated |
|---|
| 856 | pattern, so we will turn off optimization by setting the |
|---|
| 857 | number of cycles to zero. Do this by clicking on the Controls data tree entry and set the Max |
|---|
| 858 | cycles value to 0 using the pull-down menu:<o:p></o:p></span></p> |
|---|
| 859 | |
|---|
| 860 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 861 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 862 | id="Picture_x0020_5" o:spid="_x0000_i1030" type="#_x0000_t75" alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f4.png" |
|---|
| 863 | style='width:442pt;height:114pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 864 | <v:imagedata src="SimTutorial_files/image021.png" o:title="f4.png"/> |
|---|
| 865 | </v:shape><![endif]--><![if !vml]><img border=0 width=444 height=116 |
|---|
| 866 | src="SimTutorial_files/image022.png" |
|---|
| 867 | alt="Description: BHT14 HD:Users:toby:Scratch:SimTutorial:f4.png" v:shapes="Picture_x0020_5"><![endif]></span><span |
|---|
| 868 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 869 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 870 | |
|---|
| 871 | <h2>Step 5: Change Histogram Scale Factor</h2> |
|---|
| 872 | |
|---|
| 873 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 874 | mso-bidi-font-family:"Times New Roman"'>As discussed earlier, the range of |
|---|
| 875 | intensities is determined by the histogram scale factor. For x-rays, a |
|---|
| 876 | histogram scale factor with the default value of 1 produces a reasonable |
|---|
| 877 | intensity range, but with CW neutrons, a much larger scale factor value is |
|---|
| 878 | needed to produce a pattern with non-negligible intensity values. Note that |
|---|
| 879 | GSAS-II adds simulated noise to patterns, so if the scale factor is too small, |
|---|
| 880 | only random counts are seen. Select the Sample Parameters tree item for the |
|---|
| 881 | second histogram and change the scale factor to 1000, as below. </span></p> |
|---|
| 882 | |
|---|
| 883 | <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 884 | id="Picture_x0020_20" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:370pt; |
|---|
| 885 | height:232pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 886 | <v:imagedata src="SimTutorial_files/image023.png" o:title=""/> |
|---|
| 887 | </v:shape><![endif]--><![if !vml]><img border=0 width=372 height=234 |
|---|
| 888 | src="SimTutorial_files/image024.png" v:shapes="Picture_x0020_20"><![endif]></span></p> |
|---|
| 889 | |
|---|
| 890 | <h2>Step 6: Simulate the Pattern</h2> |
|---|
| 891 | |
|---|
| 892 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 893 | mso-bidi-font-family:"Times New Roman"'>Use the Calculate/Refine menu item to |
|---|
| 894 | compute the simulated pattern. Clicking on the histogram entry in the data tree |
|---|
| 895 | causes the pattern to be displayed as below. This has the reflection <span |
|---|
| 896 | class=SpellE>tickmarks</span> and the difference curve located at zero. While |
|---|
| 897 | both can be dragged to new positions, this is hard to do when they are obscured |
|---|
| 898 | by the “observed” and computed patterns. (The observed pattern has been set to |
|---|
| 899 | the computed pattern with the addition of simulated noise, which is why the |
|---|
| 900 | difference curve is non-zero.)<o:p></o:p></span></p> |
|---|
| 901 | |
|---|
| 902 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 903 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 904 | id="Picture_x0020_11" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:285pt; |
|---|
| 905 | height:243pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 906 | <v:imagedata src="SimTutorial_files/image025.png" o:title=""/> |
|---|
| 907 | </v:shape><![endif]--><![if !vml]><img border=0 width=287 height=245 |
|---|
| 908 | src="SimTutorial_files/image026.png" v:shapes="Picture_x0020_11"><![endif]></span><span |
|---|
| 909 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 910 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 911 | |
|---|
| 912 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 913 | mso-bidi-font-family:"Times New Roman"'>A nice trick for resetting the <span |
|---|
| 914 | class=SpellE>tickmarks</span> to their usual default positions is to press “s” |
|---|
| 915 | to scale to <span class=SpellE><span class=GramE>sqrt</span></span><span |
|---|
| 916 | class=GramE>(</span>I) and press it again to return to normal scaling, as shown |
|---|
| 917 | below. These changes in scaling can also be done via the “K” (keyboard) button |
|---|
| 918 | on the bottom toolbar. <o:p></o:p></span></p> |
|---|
| 919 | |
|---|
| 920 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 921 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 922 | id="Picture_x0020_12" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:285pt; |
|---|
| 923 | height:220pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 924 | <v:imagedata src="SimTutorial_files/image027.png" o:title=""/> |
|---|
| 925 | </v:shape><![endif]--><![if !vml]><img border=0 width=287 height=222 |
|---|
| 926 | src="SimTutorial_files/image028.png" v:shapes="Picture_x0020_12"><![endif]></span><span |
|---|
| 927 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 928 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 929 | |
|---|
| 930 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 931 | mso-bidi-font-family:"Times New Roman"'>Note that the Commands menu offers menu |
|---|
| 932 | items for moving the difference curve and <span class=SpellE>tickmarks</span>, |
|---|
| 933 | as well as using drag and drop. Use of this, as well as using the rescaling graphics |
|---|
| 934 | toolbar item (the home button indicated by small house on the lower left) |
|---|
| 935 | allows more fine arrangement of locations. Exporting the plot (using the “floppy |
|---|
| 936 | disk” button allows the plots below to be created. Note the very big |
|---|
| 937 | differences in intensities, data range and resolution between the two |
|---|
| 938 | simulations. <o:p></o:p></span></p> |
|---|
| 939 | |
|---|
| 940 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 941 | mso-bidi-font-family:"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape |
|---|
| 942 | id="Picture_x0020_22" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:335pt; |
|---|
| 943 | height:214pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 944 | <v:imagedata src="SimTutorial_files/image029.png" o:title=""/> |
|---|
| 945 | </v:shape><![endif]--><![if !vml]><img border=0 width=337 height=216 |
|---|
| 946 | src="SimTutorial_files/image030.png" v:shapes="Picture_x0020_22"><![endif]><!--[if gte vml 1]><v:shape |
|---|
| 947 | id="Picture_x0020_21" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:335pt; |
|---|
| 948 | height:214pt;visibility:visible;mso-wrap-style:square'> |
|---|
| 949 | <v:imagedata src="SimTutorial_files/image031.png" o:title=""/> |
|---|
| 950 | </v:shape><![endif]--><![if !vml]><img border=0 width=337 height=216 |
|---|
| 951 | src="SimTutorial_files/image032.png" v:shapes="Picture_x0020_21"><![endif]></span><span |
|---|
| 952 | style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: |
|---|
| 953 | "Times New Roman"'><o:p></o:p></span></p> |
|---|
| 954 | |
|---|
| 955 | <p class=MsoNormal><span style='font-size:12.0pt;mso-fareast-font-family:"Times New Roman"; |
|---|
| 956 | mso-bidi-font-family:"Times New Roman"'><o:p> </o:p></span></p> |
|---|
| 957 | |
|---|
| 958 | </div> |
|---|
| 959 | |
|---|
| 960 | </body> |
|---|
| 961 | |
|---|
| 962 | </html> |
|---|
