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- Sep 9, 2017 8:20:15 AM (6 years ago)
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- Tutorials/MerohedralTwins
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Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm
r2394 r3059 24 24 <o:DocumentProperties> 25 25 <o:Author>Von Dreele</o:Author> 26 <o:LastAuthor> Von Dreele</o:LastAuthor>27 <o:Revision> 4</o:Revision>28 <o:TotalTime> 3</o:TotalTime>26 <o:LastAuthor>vondreele</o:LastAuthor> 27 <o:Revision>7</o:Revision> 28 <o:TotalTime>1108</o:TotalTime> 29 29 <o:Created>2016-05-26T15:52:00Z</o:Created> 30 <o:LastSaved>201 6-07-28T19:27:00Z</o:LastSaved>31 <o:Pages> 1</o:Pages>32 <o:Words> 3302</o:Words>33 <o:Characters>1 8828</o:Characters>34 <o:Lines>1 56</o:Lines>35 <o:Paragraphs> 44</o:Paragraphs>36 <o:CharactersWithSpaces> 22086</o:CharactersWithSpaces>30 <o:LastSaved>2017-09-09T13:13:00Z</o:LastSaved> 31 <o:Pages>22</o:Pages> 32 <o:Words>2841</o:Words> 33 <o:Characters>16194</o:Characters> 34 <o:Lines>134</o:Lines> 35 <o:Paragraphs>37</o:Paragraphs> 36 <o:CharactersWithSpaces>18998</o:CharactersWithSpaces> 37 37 <o:Version>16.00</o:Version> 38 38 </o:DocumentProperties> … … 44 44 <!--[if gte mso 9]><xml> 45 45 <w:WordDocument> 46 <w:View>Print</w:View> 47 <w:Zoom>124</w:Zoom> 46 48 <w:SpellingState>Clean</w:SpellingState> 47 49 <w:GrammarState>Clean</w:GrammarState> … … 659 661 mso-generic-font-family:swiss; 660 662 mso-font-pitch:variable; 661 mso-font-signature:-5368 70145 1073786111 1 0 4150;}663 mso-font-signature:-536859905 -1073732485 9 0 511 0;} 662 664 /* Style Definitions */ 663 665 p.MsoNormal, li.MsoNormal, div.MsoNormal … … 811 813 812 814 <p class=MsoNormal>In these exercises you will use GSAS-II to refine the 813 structure of a few single crystal structures where there is merohedral twinning. 814 There is a general discussion of twinning in International Tables for 815 Crystallography (2006), Vol. C, Chapter 1.3, pp 10-14. Merohedral twinning 816 occurs when the twin operation (2, m or <span style='position:relative; 817 top:3pt'><span style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1057" 818 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image015.png"></span>) 819 belongs to the point group of the vector lattice but not of the crystal 820 structure. Of the 230 space groups only 159 of them may have merohedral 821 twining. </p> 822 823 <p class=MsoNormal><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600" 824 o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f" 825 stroked="f"> 815 structure of a few single crystal structures where there is merohedral 816 twinning. There is a general discussion of twinning in International Tables for 817 Crystallography (2006), Vol. C, Chapter 1.3, pp 10-14. <span class=SpellE>Merohedral</span> 818 twinning occurs when the twin operation (2, m <span class=GramE>or </span><span 819 style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:bar><m:barPr><m:pos 820 m:val="top"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family: 821 "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic; 822 mso-bidi-font-style:normal'><m:ctrlPr></m:ctrlPr></span></m:barPr><m:e><i 823 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>1</m:r></span></i></m:e></m:bar></m:oMath><![endif]--><![if !msEquation]><span 824 style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family: 825 "Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative; 826 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 827 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shapetype id="_x0000_t75" 828 coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" 829 filled="f" stroked="f"> 826 830 <v:stroke joinstyle="miter"/> 827 831 <v:formulas> … … 841 845 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/> 842 846 <o:lock v:ext="edit" aspectratio="t"/> 843 </v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1026" type="#_x0000_t75" 844 style='position:absolute;margin-left:0;margin-top:0;width:278.25pt;height:461.25pt; 845 z-index:251658240;visibility:visible;mso-wrap-style:square; 846 mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt; 847 mso-wrap-distance-top:0;mso-wrap-distance-right:9pt; 847 </v:shapetype><v:shape id="_x0000_i1025" type="#_x0000_t75" style='width:6.75pt; 848 height:15.75pt'> 849 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.png" 850 o:title="" chromakey="white"/> 851 </v:shape><![endif]--><![if !vml]><img width=9 height=21 852 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image001.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>) 853 belongs to the point group of the vector lattice but not of the crystal 854 structure. Of the 230 space groups only 159 of them may have merohedral 855 twining. </p> 856 857 <p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_2" o:spid="_x0000_s1026" 858 type="#_x0000_t75" style='position:absolute;margin-left:0;margin-top:0; 859 width:278.25pt;height:461.25pt;z-index:251658240;visibility:visible; 860 mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0; 861 mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt; 848 862 mso-wrap-distance-bottom:0;mso-position-horizontal:left; 849 863 mso-position-horizontal-relative:text;mso-position-vertical:absolute; … … 864 878 the Laue class of the crystal (only for space groups marked with * in above 865 879 table) and multiple twin components may be found. For Type 1 the twin lattice 866 exactly <span class=GramE>superimpose</span> so that if Friedels law is obeyed 867 the twin components have the same value of |F|<sup>2</sup> (the twinning is 868 undetectable!). However, in the presence of resonant scattering the |F|<sup>2</sup> 869 components differ and if the twin components have unequal volumes then the 870 Bragg intensities will differ from that obtained from the <span class=SpellE>untwinned</span> 871 structure and then the twinning effects must be considered for 872 refinement. Obviously all Type 1 crystals are <span class=SpellE>noncentrosymmetric</span>. 873 For Type 2 the space group may be centrosymmetric from within a choice of just 874 55 possible space groups. However, the diffraction pattern may display apparent 875 higher symmetry especially if the twin components are all equally present in 876 the crystal. Note that menu entries and user input are shown in bold face 877 below as <b><span style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>, 878 which lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>) 880 exactly superimpose so that if Friedels law is obeyed the twin <span 881 class=GramE>components</span> have the same value of |F|<sup>2</sup> (the 882 twinning is undetectable!). However, in the presence of resonant scattering the 883 |F|<sup>2</sup> components differ and if the twin components have unequal 884 volumes then the Bragg intensities will differ from that obtained from the <span 885 class=SpellE>untwinned</span> structure and then the twinning effects must be 886 considered for refinement. Obviously all Type 1 crystals are <span 887 class=SpellE>noncentrosymmetric</span>. For Type 2 the space group may be 888 centrosymmetric from within a choice of just 55 possible space groups. However, 889 the diffraction pattern may display apparent higher symmetry especially if the 890 twin components are all equally present in the crystal. Note that menu 891 entries and user input are shown in bold face below as <b><span 892 style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>, which 893 lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>) 879 894 and second the name of the entry in the menu (here <b><span style='font-family: 880 "Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so 881 already,start GSAS-II.</p>895 "Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so already, 896 start GSAS-II.</p> 882 897 883 898 <h2 style='margin-bottom:.25in'><span style='mso-fareast-font-family:"Times New Roman"'><o:p> </o:p></span></h2> … … 913 928 and you will see the General page for this phase</p> 914 929 915 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=403 height=310 916 id="_x0000_i1056" 917 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image007.png"></span></p> 930 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 931 id="Picture_x0020_1" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:468pt; 932 height:373.5pt;visibility:visible;mso-wrap-style:square'> 933 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image005.png" 934 o:title=""/> 935 </v:shape><![endif]--><![if !vml]><img width=624 height=498 936 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_1"><![endif]></span></p> 918 937 919 938 <p class=MsoNormal>Next do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure 920 Factor/from CIF file</span></b> (that is the format of a <span class=SpellE>fcf</span> 921 file); a file selection dialog box will appear with the previously selected 922 directory chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>; 923 a popup window will appear</p> 924 925 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=447 height=249 926 id="_x0000_i1055" 927 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image008.png"></span></p> 928 929 <p class=MsoNormal>Select <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>; 939 Factor/from CIF file</span></b> (that is the format of <span class=GramE>a</span> 940 <span class=SpellE>fcf</span> file); a file selection dialog box will appear 941 with the previously selected directory chosen. Select <b><span 942 style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>; a popup window will 943 appear</p> 944 945 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 946 id="Picture_x0020_3" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:274.5pt; 947 height:208.5pt;visibility:visible;mso-wrap-style:square'> 948 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image008.png" 949 o:title=""/> 950 </v:shape><![endif]--><![if !vml]><img width=366 height=278 951 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_3"><![endif]></span></p> 952 953 <p class=MsoNormal>Select <span class=GramE><b><span style='font-family:"Calibri",sans-serif'>Yes</span></b></span>; 930 954 a new popup window allowing you to change the name</p> 931 955 932 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=336 height=137 933 id="_x0000_i1054" 934 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image009.png"></span></p> 956 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 957 id="Picture_x0020_4" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:259.5pt; 958 height:117pt;visibility:visible;mso-wrap-style:square'> 959 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image021.png" 960 o:title=""/> 961 </v:shape><![endif]--><![if !vml]><img width=346 height=156 962 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_4"><![endif]></span></p> 935 963 936 964 <p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; 937 965 after a pause and some activity a popup window will appear</p> 938 966 939 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=320 height=310 940 id="_x0000_i1053" 941 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image010.png"></span></p> 967 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 968 id="Picture_x0020_5" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:233.25pt; 969 height:228.75pt;visibility:visible;mso-wrap-style:square'> 970 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image023.png" 971 o:title=""/> 972 </v:shape><![endif]--><![if !vml]><img width=311 height=305 973 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_5"><![endif]></span></p> 942 974 943 975 <p class=MsoNormal>This makes the connection between the data set and the … … 959 991 GSAS-II data tree.</p> 960 992 961 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=522 height=301 962 id="_x0000_i1052" 963 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.png"></span></p> 993 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 994 id="Picture_x0020_6" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt; 995 height:209.25pt;visibility:visible;mso-wrap-style:square'> 996 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png" 997 o:title=""/> 998 </v:shape><![endif]--><![if !vml]><img width=624 height=279 999 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_6"><![endif]></span></p> 964 1000 965 1001 <p class=MsoNormal>Change <b><span style='font-family:"Calibri",sans-serif'>Min … … 967 1003 "Calibri",sans-serif'>2.0</span></b>. Next, select the <b><span 968 1004 style='font-family:"Calibri",sans-serif'>Phases/C8 H25 Al0.84 Ga1.16</span></b> 969 <span class=GramE>entry</span> in the GSAS-II data tree and choose the <b><span 970 style='font-family:"Calibri",sans-serif'>Data</span></b> tab</p> 971 972 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=434 height=444 973 id="_x0000_i1051" 974 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image011.png"></span></p> 1005 entry in the GSAS-II data tree and choose the <b><span style='font-family:"Calibri",sans-serif'>Data</span></b> 1006 tab</p> 1007 1008 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1009 id="Picture_x0020_23" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt; 1010 height:261.75pt;visibility:visible;mso-wrap-style:square'> 1011 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image028.png" 1012 o:title=""/> 1013 </v:shape><![endif]--><![if !vml]><img width=624 height=349 1014 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_23"><![endif]></span></p> 975 1015 976 1016 <p class=MsoNormal>Notice that the <b><span style='font-family:"Calibri",sans-serif'>Scale … … 986 1026 lets test this; select the <b><span style='font-family:"Calibri",sans-serif'>Flack 987 1027 parameter</span></b> for refinement and do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> 988 from the main GSAS-II data tree menu. The structure will quickly refine to give 989 <span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable 990 improvement on Scale factor alone. The Flack parameter is now 0.452, meaning 991 that both hands somehow exist in the structure. This can happen if the crystal 992 is <span class=SpellE>merohedrally</span> inversion twinned.</p> 1028 from the main GSAS-II data tree menu. Youll be asked to save the project; pick 1029 a directory & a name I chose <b style='mso-bidi-font-weight:normal'><span 1030 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1031 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1b</span></b>. 1032 The structure will quickly refine to give <span class=SpellE>R<sub>w</sub></span>=2.155% 1033 which is a considerable improvement on Scale factor alone. The Flack parameter 1034 is now 0.433, meaning that both hands somehow exist in the structure. This can 1035 happen if the crystal is <span class=SpellE>merohedrally</span> inversion twinned.</p> 993 1036 994 1037 <p class=MsoNormal>To introduce this twin, press the <b><span style='font-family: 995 1038 "Calibri",sans-serif'>Add Twin Law</span></b> box; the window will be redrawn.</p> 996 1039 997 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=434 height=444 998 id="_x0000_i1050" 999 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image013.png"></span></p> 1000 1001 <p class=MsoNormal>Notice that two Twin Law matrices have been generated; one 1002 is the identity for the reference structure and the other by default is the 1040 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1041 id="_x0000_i1046" type="#_x0000_t75" style='width:468pt;height:334.5pt; 1042 visibility:visible;mso-wrap-style:square'> 1043 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image030.png" 1044 o:title=""/> 1045 </v:shape><![endif]--><![if !vml]><img width=624 height=446 1046 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="_x0000_i1046"><![endif]></span></p> 1047 1048 <p class=MsoNormal>Notice that two Twin Law matrices have been generated; one is 1049 the identity for the reference structure and the other by default is the 1003 1050 merohedral inverse. If some other twin law is desired, then the matrix elements 1004 1051 need to be changed. Moreover, the Flack parameter has vanished as it is no … … 1007 1054 fraction</span></b> and rerun the refinement. The Data window now has.</p> 1008 1055 1009 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=449 height=500 1010 id="_x0000_i1049" 1011 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.png"></span></p> 1056 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1057 id="Picture_x0020_42" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt; 1058 height:337.5pt;visibility:visible;mso-wrap-style:square'> 1059 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image032.png" 1060 o:title=""/> 1061 </v:shape><![endif]--><![if !vml]><img width=624 height=450 1062 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image062.gif" v:shapes="Picture_x0020_42"><![endif]></span></p> 1012 1063 1013 1064 <p class=MsoNormal>The refinement quickly converged to where it was before but … … 1055 1106 you want.</p> 1056 1107 1057 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=410 height=262 1058 id="_x0000_i1048" 1059 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image012.png"></span></p> 1060 1061 <p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>; 1108 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1109 id="Picture_x0020_43" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:314.25pt; 1110 height:159pt;visibility:visible;mso-wrap-style:square'> 1111 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image034.png" 1112 o:title=""/> 1113 </v:shape><![endif]--><![if !vml]><img width=419 height=212 1114 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image063.gif" v:shapes="Picture_x0020_43"><![endif]></span></p> 1115 1116 <p class=MsoNormal>Press <span class=GramE><b><span style='font-family:"Calibri",sans-serif'>Yes</span></b></span>; 1062 1117 a Read Warning will appear.</p> 1063 1118 1064 1119 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1065 id="Picture_x0020_ 39" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:371.25pt;1066 height:17 6.25pt;visibility:visible;mso-wrap-style:square'>1067 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 01.png"1068 o:title=""/> 1069 </v:shape><![endif]--><![if !vml]><img width= 495 height=2351070 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 02.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>1120 id="Picture_x0020_44" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:378.75pt; 1121 height:177pt;visibility:visible;mso-wrap-style:square'> 1122 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image036.png" 1123 o:title=""/> 1124 </v:shape><![endif]--><![if !vml]><img width=505 height=236 1125 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image064.gif" v:shapes="Picture_x0020_44"><![endif]></span></p> 1071 1126 1072 1127 <p class=MsoNormal>There are two significant warnings concerning <span … … 1085 1140 the General tab for this phase is shown. </p> 1086 1141 1087 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=336 1088 id="_x0000_i1046" 1089 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image027.png"></span></p> 1142 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1143 id="Picture_x0020_45" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt; 1144 height:206.25pt;visibility:visible;mso-wrap-style:square'> 1145 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image038.png" 1146 o:title=""/> 1147 </v:shape><![endif]--><![if !vml]><img width=624 height=275 1148 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image065.gif" v:shapes="Picture_x0020_45"><![endif]></span></p> 1090 1149 1091 1150 <p class=MsoNormal>Change the Space group to <b><span style='font-family:"Calibri",sans-serif'>P … … 1094 1153 Atoms</span></b>.</p> 1095 1154 1096 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=478 height=358 1097 id="_x0000_i1045" 1098 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image028.jpg"></span></p> 1155 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1156 id="Picture_x0020_47" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt; 1157 height:405pt;visibility:visible;mso-wrap-style:square'> 1158 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image040.png" 1159 o:title=""/> 1160 </v:shape><![endif]--><![if !vml]><img width=624 height=540 1161 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image066.gif" v:shapes="Picture_x0020_47"><![endif]></span></p> 1099 1162 1100 1163 <p class=MsoNormal> </p> … … 1108 1171 from the file dialog box; a popup will appear showing a few lines.</p> 1109 1172 1110 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=366 height=262 1111 id="_x0000_i1044" 1112 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image022.png"></span></p> 1173 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1174 id="Picture_x0020_48" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:274.5pt; 1175 height:186pt;visibility:visible;mso-wrap-style:square'> 1176 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image042.png" 1177 o:title=""/> 1178 </v:shape><![endif]--><![if !vml]><img width=366 height=248 1179 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_48"><![endif]></span></p> 1113 1180 1114 1181 <p class=MsoNormal>This is the right file; a <span class=SpellE>Shelx</span> 1115 HKLF 4 file consists of records with just <span class=SpellE><span class=GramE>h,k</span>,l</span>, 1116 F<sup>2</sup> and <span style='font-family:Symbol'>s</span>(F<sup>2</sup>). 1117 Press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> and <b><span 1118 style='font-family:"Calibri",sans-serif'>OK</span></b> on the next one (well 1119 keep the name as it is). Choose the phase with the long name on the next popup 1120 and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a 2D 1121 display of the hk0 zone is plotted.</p> 1122 1123 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=535 1124 id="_x0000_i1043" 1125 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image029.png"></span></p> 1126 1127 <p class=MsoNormal>The size of the green circles <span class=GramE>are</span> 1128 proportional to <span class=SpellE>Fo</span> (after a structure factor 1182 HKLF 4 file consists of records with just <span class=SpellE>h<span 1183 class=GramE>,k,l</span></span>, F<sup>2</sup> and <span style='font-family: 1184 Symbol'>s</span>(F<sup>2</sup>). Press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> 1185 and <b><span style='font-family:"Calibri",sans-serif'>OK</span></b> on the next 1186 one (well keep the name as it is). Choose the phase with the long name on the 1187 next popup and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; 1188 select the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1189 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1190 minor-latin;mso-bidi-theme-font:minor-latin'>Structure factors</span></b> tab, a 1191 2D display of the hk0 zone is plotted.</p> 1192 1193 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1194 id="Picture_x0020_49" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt; 1195 height:401.25pt;visibility:visible;mso-wrap-style:square'> 1196 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image044.png" 1197 o:title=""/> 1198 </v:shape><![endif]--><![if !vml]><img width=624 height=535 1199 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image068.gif" v:shapes="Picture_x0020_49"><![endif]></span></p> 1200 1201 <p class=MsoNormal>The size of the green circles are proportional to <span 1202 class=SpellE><span class=GramE>Fo</span></span> (after a structure factor 1129 1203 calculation blue rings will appear for Fc).</p> 1130 1204 … … 1145 1219 GSAS-II data tree.</p> 1146 1220 1147 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=522 height=301 1148 id="_x0000_i1042" 1149 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.png"></span></p> 1221 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1222 id="Picture_x0020_50" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt; 1223 height:215.25pt;visibility:visible;mso-wrap-style:square'> 1224 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image046.png" 1225 o:title=""/> 1226 </v:shape><![endif]--><![if !vml]><img width=624 height=287 1227 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image069.gif" v:shapes="Picture_x0020_50"><![endif]></span></p> 1150 1228 1151 1229 <p class=MsoNormal>Change <b><span style='font-family:"Calibri",sans-serif'>Min … … 1158 1236 1159 1237 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=507 height=444 1160 id="_x0000_i10 41"1238 id="_x0000_i1037" 1161 1239 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image030.png"></span></p> 1162 1240 … … 1164 1242 factor</span></b> is selected for refinement by default. If you refine it, you 1165 1243 will get an <span class=SpellE>R<sub>w</sub></span>~ 25% which is terrible. If 1166 you try refining atom positions & thermal parameters you could possibly <span 1167 class=GramE>lower</span> it to ~15% (still terrible) and the resulting 1168 structure would not be very satisfactory. However, we have suspected from the 1169 equivalence of <span style='position:relative;top:3pt'><span style='mso-no-proof: 1170 yes'><img width=9 height=19 id="_x0000_i1040" 1171 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image031.png"></span> and 1172 <span style='position:relative;top:3pt'><span style='mso-no-proof:yes'><img 1173 width=9 height=19 id="_x0000_i1039" 1174 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1 1244 you try refining atom positions & thermal parameters you could possibly 1245 lower it to ~15% (still terrible) and the resulting structure would not be very 1246 satisfactory. However, we have suspected from the equivalence of <span 1247 style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:bar><m:barPr><m:pos 1248 m:val="top"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family: 1249 "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic; 1250 mso-bidi-font-style:normal'><m:ctrlPr></m:ctrlPr></span></m:barPr><m:e><i 1251 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>3</m:r></span></i></m:e></m:bar></m:oMath><![endif]--><![if !msEquation]><span 1252 style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family: 1253 "Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative; 1254 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 1255 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 1256 type="#_x0000_t75" style='width:6.75pt;height:15.75pt'> 1257 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image048.png" 1258 o:title="" chromakey="white"/> 1259 </v:shape><![endif]--><![if !vml]><img width=9 height=21 1260 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image070.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]> and 1261 <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:bar><m:barPr><m:pos 1262 m:val="top"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family: 1263 "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic; 1264 mso-bidi-font-style:normal'><m:ctrlPr></m:ctrlPr></span></m:barPr><m:e><i 1265 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>3</m:r></span></i></m:e></m:bar></m:oMath><![endif]--><![if !msEquation]><span 1266 style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family: 1267 "Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative; 1268 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 1269 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 1270 type="#_x0000_t75" style='width:6.75pt;height:15.75pt'> 1271 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image048.png" 1272 o:title="" chromakey="white"/> 1273 </v:shape><![endif]--><![if !vml]><img width=9 height=21 1274 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image070.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>m1 1175 1275 Laue data symmetries that there is twinning so dont bother trying to make it 1176 1276 better by refining the structure. To determine the possible twin law we refer 1177 1277 to Table 1.3.4.2 of the International Tables for Crystallography Vol C. and see 1178 that indeed Laue <span style='position:relative;top:3pt'><span 1179 style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1038" 1180 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1 1278 that indeed Laue <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:bar><m:barPr><m:pos 1279 m:val="top"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family: 1280 "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic; 1281 mso-bidi-font-style:normal'><m:ctrlPr></m:ctrlPr></span></m:barPr><m:e><i 1282 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>3</m:r></span></i></m:e></m:bar></m:oMath><![endif]--><![if !msEquation]><span 1283 style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family: 1284 "Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative; 1285 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 1286 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 1287 type="#_x0000_t75" style='width:6.75pt;height:15.75pt'> 1288 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image048.png" 1289 o:title="" chromakey="white"/> 1290 </v:shape><![endif]--><![if !vml]><img width=9 height=21 1291 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image070.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>m1 1181 1292 as P3<sub>2</sub>21 can be simulated by twinned Laue <span style='position: 1182 relative;top:3pt'><span style='mso-no-proof:yes'><img width=9 height=19 1183 id="_x0000_i1037" 1184 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span> crystals 1293 relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:bar><m:barPr><m:pos 1294 m:val="top"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family: 1295 "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic; 1296 mso-bidi-font-style:normal'><m:ctrlPr></m:ctrlPr></span></m:barPr><m:e><i 1297 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>3</m:r></span></i></m:e></m:bar></m:oMath><![endif]--><![if !msEquation]><span 1298 style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family: 1299 "Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative; 1300 top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language: 1301 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 1302 type="#_x0000_t75" style='width:6.75pt;height:15.75pt'> 1303 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image048.png" 1304 o:title="" chromakey="white"/> 1305 </v:shape><![endif]--><![if !vml]><img width=9 height=21 1306 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image070.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]> crystals 1185 1307 in P3<sub>2</sub>; the possible operator is shown in Table 1.3.4.1 (reproduced 1186 above) as either a mirror or a 2-fold. The detailed symbolism in the table (m.<span1187 class=GramE>., ..</span>2/.2.) indicates (perhaps obscurely) the operator 1188 specifics. See P3m1 and P3<sub>2</sub>21 space groups in International Tables 1189 for Crystallography, Vol A for the operations m as <span style='position:relative; 1190 top:3pt'><span style='mso-no-proof:yes'>-y-xz</span> or 2 as <span 1191 style='position:relative;top:3pt'><span style='mso-no-proof:yes'>yx-z</span>; 1192 we will use the 2-fold since the m inverts the structure which we are not 1193 sensitive to in thisexperiment.</p>1308 above) as either a mirror or a 2-fold. The detailed symbolism in the table 1309 (m.., ..2/.2.) indicates (perhaps obscurely) the operator specifics. See P3m1 1310 and P3<sub>2</sub>21 space groups in International Tables for Crystallography, 1311 Vol A for the operations m as <span style='position:relative;top:3pt'><span 1312 style='mso-no-proof:yes'>-y-xz</span> or 2 as <span style='position:relative; 1313 top:3pt'><span style='mso-no-proof:yes'>yx-z</span>; we will use the 2-fold 1314 since the m inverts the structure which we are not sensitive to in this 1315 experiment.</p> 1194 1316 1195 1317 <p class=MsoNormal>Select <b><span style='font-family:"Calibri",sans-serif'>Add … … 1199 1321 box. It should look like.</p> 1200 1322 1201 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=507 height=500 1202 id="_x0000_i1036" 1203 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image034.png"></span></p> 1323 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1324 id="Picture_x0020_51" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt; 1325 height:352.5pt;visibility:visible;mso-wrap-style:square'> 1326 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image050.png" 1327 o:title=""/> 1328 </v:shape><![endif]--><![if !vml]><img width=624 height=470 1329 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image071.gif" v:shapes="Picture_x0020_51"><![endif]></span></p> 1204 1330 1205 1331 <p class=MsoNormal>Now do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; 1206 there will be an immediate improvement in the fit to <span class=SpellE>Rw</span>=5.05% 1207 and the twin fractions will be ~50/50. Clearly this crystal is Type 2 <span 1208 class=SpellE>merohedrally</span> twinned; we cannot determine if there is any 1209 Type 1 twinning because we lack sufficient resonant scattering to see it. This 1210 ends the second example; you can save the project file.</p> 1332 youll have to save the project. Pick a directory & file name - I used <b 1333 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1334 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: 1335 minor-latin'>2b</span></b>. <span class=GramE>there</span> will be an immediate 1336 improvement in the fit to <span class=SpellE>Rw</span>=5.05% and the twin 1337 fractions will be ~50/50. Clearly this crystal is Type 2 <span class=SpellE>merohedrally</span> 1338 twinned; we cannot determine if there is any Type 1 twinning because we lack 1339 sufficient resonant scattering to see it. This ends the second example; you can 1340 save the project file.</p> 1211 1341 1212 1342 <h2><span style='mso-fareast-font-family:"Times New Roman"'>Example 3. A Type 1 1213 & 2 merohedraltwin <span class=SpellE>Cp</span>*Cs(NC<sub>5</sub>H<sub>5</sub>)<o:p></o:p></span></h2>1343 & 2 <span class=SpellE>merohedral</span> twin <span class=SpellE>Cp</span>*Cs(NC<sub>5</sub>H<sub>5</sub>)<o:p></o:p></span></h2> 1214 1344 1215 1345 <p class=MsoNormal>This <span class=SpellE>ecample</span> is very similar to … … 1237 1367 you want.</p> 1238 1368 1239 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=366 height=262 1240 id="_x0000_i1035" 1241 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image035.png"></span></p> 1369 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1370 id="Picture_x0020_52" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:274.5pt; 1371 height:174.75pt;visibility:visible;mso-wrap-style:square'> 1372 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image072.png" 1373 o:title=""/> 1374 </v:shape><![endif]--><![if !vml]><img width=366 height=233 1375 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image073.gif" v:shapes="Picture_x0020_52"><![endif]></span></p> 1242 1376 1243 1377 <p class=MsoNormal>It is; press the <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> … … 1248 1382 61</span></b>; the General tab will be redrawn after showing you the operators.</p> 1249 1383 1250 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=467 1251 id="_x0000_i1034" 1252 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image036.png"></span></p> 1384 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1385 id="Picture_x0020_53" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt; 1386 height:234.75pt;visibility:visible;mso-wrap-style:square'> 1387 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image074.png" 1388 o:title=""/> 1389 </v:shape><![endif]--><![if !vml]><img width=624 height=313 1390 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image075.gif" v:shapes="Picture_x0020_53"><![endif]></span></p> 1253 1391 1254 1392 <p class=MsoNormal>Next do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure … … 1265 1403 class=SpellE>Shelx</span>.</p> 1266 1404 1267 <p class=MsoNormal>You now have loaded all that is needed for the third 1268 example. The structure had previously been solved and refined with <span 1269 class=SpellE>Shelx</span> so you need not trouble about those steps. You can 1270 try to solve the structure in GSAS-II via charge flipping but this is not part 1271 of this exercise (it isnt easy because of the twinning; charge flipping will 1272 readily give the Cs position & most of the rest. It can be completed via 1273 difference Fourier techniques); we will only explore the twin analysis features 1274 of GSAS-II.</p> 1405 <p class=MsoNormal>You now have loaded all that is needed for the third example. 1406 The structure had previously been solved and refined with <span class=SpellE>Shelx</span> 1407 so you need not trouble about those steps. You can try to solve the structure 1408 in GSAS-II via charge flipping but this is not part of this exercise (it isnt 1409 easy because of the twinning; charge flipping will readily give the Cs position 1410 & most of the rest. It can be completed via difference Fourier techniques); 1411 we will only explore the twin analysis features of GSAS-II.</p> 1275 1412 1276 1413 <h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Refinement … … 1278 1415 1279 1416 <p class=MsoNormal>Before beginning the refinement, it usually the practice to 1280 eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub> <1281 2<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span1417 eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub> 1418 < 2<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span 1282 1419 style='font-family:"Calibri",sans-serif'>Controls</span></b> entry from the 1283 1420 GSAS-II data tree.</p> 1284 1421 1285 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=522 height=301 1286 id="_x0000_i1033" 1287 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.png"></span></p> 1422 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1423 id="Picture_x0020_54" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt; 1424 height:205.5pt;visibility:visible;mso-wrap-style:square'> 1425 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image076.png" 1426 o:title=""/> 1427 </v:shape><![endif]--><![if !vml]><img width=624 height=274 1428 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image077.gif" v:shapes="Picture_x0020_54"><![endif]></span></p> 1288 1429 1289 1430 <p class=MsoNormal>Change <b><span style='font-family:"Calibri",sans-serif'>Min … … 1295 1436 tab.</p> 1296 1437 1297 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=434 height=444 1298 id="_x0000_i1032" 1299 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image037.png"></span></p> 1438 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1439 id="Picture_x0020_55" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt; 1440 height:303.75pt;visibility:visible;mso-wrap-style:square'> 1441 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image078.png" 1442 o:title=""/> 1443 </v:shape><![endif]--><![if !vml]><img width=624 height=405 1444 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image079.gif" v:shapes="Picture_x0020_55"><![endif]></span></p> 1300 1445 1301 1446 <p class=MsoNormal>Notice that the <b><span style='font-family:"Calibri",sans-serif'>Scale … … 1303 1448 will get an <span class=SpellE>R<sub>w</sub></span>~ 17% which is terrible. It 1304 1449 doesnt change much if you add the Flack parameter (~0.36). If you try refining 1305 atom positions & thermal parameters you could possibly <span class=GramE>lower</span>1306 it but the resulting structure would not be very satisfactory. However, we have 1307 suspected from the equivalence of 6/m and 6/mmm Laue data symmetries that there 1308 is twinning so dont bother trying to make it better by refining the structure. 1309 To determine the possible twin <span class=GramE>laws</span> we again refer to 1310 Table 1.3.4.2 of the International Tables for Crystallography Vol C. and see 1311 that indeed Laue 6/mmm as P6<sub>1</sub>22 can be simulated by twinned Laue 6/m 1312 crystals in P6<sub>1</sub>; the possible operator is shown in Table 1.3.4.1 1313 (reproduced above) as either a mirror or a 2-fold. The detailed symbolism in the 1314 table (m.., ..2/.2.) indicates (perhaps obscurely) the operator specifics; 1315 they are m as <spanstyle='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr1450 atom positions & thermal parameters you could possibly lower it but the 1451 resulting structure would not be very satisfactory. However, we have suspected 1452 from the equivalence of 6/m and 6/mmm Laue data symmetries that there is 1453 twinning so dont bother trying to make it better by refining the structure. To 1454 determine the possible twin laws we again refer to Table 1.3.4.2 of the 1455 International Tables for Crystallography Vol C. and see that indeed Laue 6/mmm 1456 as P6<sub>1</sub>22 can be simulated by twinned Laue 6/m crystals in P6<sub>1</sub>; 1457 the possible operator is shown in Table 1.3.4.1 (reproduced above) as either a 1458 mirror or a 2-fold. The detailed symbolism in the table (m.., ..2/.2.) 1459 indicates (perhaps obscurely) the operator specifics; they are m as <span 1460 style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr 1316 1461 m:val="̅"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family: 1317 1462 "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic; … … 1328 1473 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 1329 1474 type="#_x0000_t75" style='width:19.5pt;height:14.25pt'> 1330 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 04.png"1475 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image052.png" 1331 1476 o:title="" chromakey="white"/> 1332 1477 </v:shape><![endif]--><![if !vml]><img width=26 height=19 1333 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 05.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]> or1478 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image080.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]> or 1334 1479 2 as <!--[if gte msEquation 12]><m:oMath><i style='mso-bidi-font-style:normal'><span 1335 1480 style='font-family:"Cambria Math",serif'><span style='position:relative; … … 1344 1489 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" 1345 1490 type="#_x0000_t75" style='width:19.5pt;height:14.25pt'> 1346 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 06.png"1491 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image054.png" 1347 1492 o:title="" chromakey="white"/> 1348 1493 </v:shape><![endif]--><![if !vml]><img width=26 height=19 1349 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 08.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span1494 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image081.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span 1350 1495 style='font-family:"Cambria Math",serif'>; we will use the 2-fold, m and 1351 1496 inversion operators to fully test for presence of the 4 possible twin laws. … … 1356 1501 redrawn. When done you should see.<o:p></o:p></span></p> 1357 1502 1358 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=434 height=444 1359 id="_x0000_i1031" 1360 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image038.png"></span> </p> 1503 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1504 id="Picture_x0020_56" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt; 1505 height:405.75pt;visibility:visible;mso-wrap-style:square'> 1506 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image082.png" 1507 o:title=""/> 1508 </v:shape><![endif]--><![if !vml]><img width=624 height=541 1509 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image083.gif" v:shapes="Picture_x0020_56"><![endif]></span> </p> 1361 1510 1362 1511 <p class=MsoNormal>For the third and fourth matrix enter <b><span … … 1367 1516 style='font-family:"Calibri",sans-serif'>Refine</span></b> button and do <b><span 1368 1517 style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the 1369 main menu. The <span class=SpellE>Rw</span> will immediately drop to ~2.26% 1370 (RF~2.05%). The four twin element fractions will show various values.</p> 1371 1372 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1373 id="Picture_x0020_40" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:336.75pt; 1374 height:375pt;visibility:visible;mso-wrap-style:square'> 1375 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image007.png" 1376 o:title=""/> 1377 </v:shape><![endif]--><![if !vml]><img width=449 height=500 1378 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_40"><![endif]></span></p> 1379 1380 <p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is 1381 nonphysical and the 1<sup>st</sup> twin fraction is small. It is likely that 1382 the true space group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span> 1518 main menu; again youll have to save the project file I called it 3a. The <span 1519 class=SpellE>Rw</span> will immediately drop to ~2.26% (RF~2.05%). The four 1520 twin element fractions will show various values</p> 1521 1522 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1523 id="Picture_x0020_57" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt; 1524 height:405.75pt;visibility:visible;mso-wrap-style:square'> 1525 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image084.png" 1526 o:title=""/> 1527 </v:shape><![endif]--><![if !vml]><img width=624 height=541 1528 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image085.gif" v:shapes="Picture_x0020_57"><![endif]></span></p> 1529 1530 <p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is nonphysical 1531 and the 1<sup>st</sup> twin fraction is small. It is likely that the true space 1532 group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span> 1383 1533 twinned (twin fractions 2 & 4). We can improve it by refining the atom 1384 1534 positions and thermal parameters, but first we need to replace the hydrogen … … 1394 1544 o:title=""/> 1395 1545 </v:shape><![endif]--><![if !vml]><img width=700 height=300 1396 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 12.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>1546 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image086.gif" v:shapes="Picture_x0020_41"><![endif]></span></p> 1397 1547 1398 1548 <p class=MsoNormal>If you scroll down the page, youll see H-atoms with default … … 1407 1557 The H-atoms will be highlighted (and plotted in green). Do <b style='mso-bidi-font-weight: 1408 1558 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1409 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Delete atom</span></b> from 1410 the menu; the H-atoms will be deleted and the structure will be redrawn. Next 1411 double <span class=GramE>click</span> the <b style='mso-bidi-font-weight:normal'><span 1559 minor-latin;mso-hansi-theme-font:minor-latin'>Edit Atoms/On selected atoms 1560 /Delete 1561 atom</span></b> from the menu; the H-atoms will be deleted and the structure 1562 will be redrawn. Next double click the <b style='mso-bidi-font-weight:normal'><span 1412 1563 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1413 1564 mso-hansi-theme-font:minor-latin'>Type</span></b> column heading and select <b … … 1416 1567 all the C-atoms will be selected (and shown in green on the plot). Do <b 1417 1568 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1418 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Insert 1419 H atoms</span></b>; a Distance Angle Controls will appear. Occasionally these 1420 values may need to be changed but not this time; press <b style='mso-bidi-font-weight: 1421 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1422 minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>. The next popup is 1423 for the H atoms add controls.</p> 1424 1425 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1426 id="Picture_x0020_42" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:300pt; 1427 height:363.75pt;visibility:visible;mso-wrap-style:square'> 1428 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image011.png" 1429 o:title=""/> 1430 </v:shape><![endif]--><![if !vml]><img width=400 height=485 1431 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_42"><![endif]></span></p> 1569 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Atoms/On 1570 selected atoms 1571 /<span class=SpellE>Calc</span> H atoms</span></b>; a Distance 1572 Angle Controls will appear. Occasionally these values may need to be changed 1573 but not this time; press <b style='mso-bidi-font-weight:normal'><span 1574 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1575 mso-hansi-theme-font:minor-latin'>Ok</span></b>. The next popup is for the H 1576 atoms add controls.</p> 1577 1578 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1579 id="Picture_x0020_58" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:300pt; 1580 height:187.5pt;visibility:visible;mso-wrap-style:square'> 1581 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image087.png" 1582 o:title=""/> 1583 </v:shape><![endif]--><![if !vml]><img width=400 height=250 1584 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image088.gif" v:shapes="Picture_x0020_58"><![endif]></span></p> 1432 1585 1433 1586 <p class=MsoNormal>It specifies the expected geometry around each C-atom for … … 1440 1593 after their respective C-atom. Their positions and thermal parameters are tied 1441 1594 to the C-atoms so that after refinement of the structure they can be shifted to 1442 the <span class=SpellE>stereochemically</span> best positions. For the refinement, 1443 double click the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1444 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1445 minor-latin'>Refine</span></b> column heading and select <b style='mso-bidi-font-weight: 1446 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1447 minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> and <b 1595 the <span class=SpellE>stereochemically</span> best positions. For the 1596 refinement, double click the <b style='mso-bidi-font-weight:normal'><span 1597 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1598 mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading and select <b 1448 1599 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1600 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> 1601 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1449 1602 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> 1450 1603 from the popup; press <b style='mso-bidi-font-weight:normal'><span … … 1453 1606 with XU in every entry under Refine. Now do <b style='mso-bidi-font-weight: 1454 1607 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1455 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from1456 t he main GSASII data tree window; the <span class=SpellE>Rw</span> will drop to1457 ~1.92%. If you look at the <b style='mso-bidi-font-weight:normal'><span 1458 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;1459 mso- hansi-theme-font:minor-latin'>Data</span></b> tab the Twin element1460 fractions are much clearer.</p>1461 1462 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1463 id="Picture_x0020_ 43" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:336.75pt;1464 height:3 75pt;visibility:visible;mso-wrap-style:square'>1465 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 13.png"1466 o:title=""/> 1467 </v:shape><![endif]--><![if !vml]><img width= 449 height=5001468 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 16.gif" v:shapes="Picture_x0020_43"><![endif]></span><span1608 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (2-3 1609 times until convergence<span class=GramE>)from</span> the main GSASII data tree 1610 window; the <span class=SpellE>Rw</span> will drop to ~1.80%. If you look at 1611 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1612 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b> 1613 tab the Twin element fractions are much clearer.</p> 1614 1615 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1616 id="Picture_x0020_59" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt; 1617 height:342.75pt;visibility:visible;mso-wrap-style:square'> 1618 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image089.png" 1619 o:title=""/> 1620 </v:shape><![endif]--><![if !vml]><img width=624 height=457 1621 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image090.gif" v:shapes="Picture_x0020_59"><![endif]></span><span 1469 1622 style='mso-spacerun:yes'> </span></p> 1470 1623 … … 1483 1636 youll see the Operators popup (press <b style='mso-bidi-font-weight:normal'><span 1484 1637 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1485 mso-hansi-theme-font:minor-latin'>Ok</span></b>) and the General tab will be redrawn. 1486 Next select the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1487 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1488 minor-latin'>Atoms</span></b> tab; do <b style='mso-bidi-font-weight:normal'><span 1638 mso-hansi-theme-font:minor-latin'>Ok</span></b>) and the General tab will be 1639 redrawn. Next select the <b style='mso-bidi-font-weight:normal'><span 1489 1640 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1490 mso-hansi-theme-font:minor-latin'>Edit/Update H atoms</span></b> to put them in 1491 their best positions.<span style='mso-spacerun:yes'> </span>Next select all 1492 the atoms by double clicking the empty box in upper left corner of the table; 1493 all atoms will be highlighted & plotted green. Do <b style='mso-bidi-font-weight: 1641 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab; do <b style='mso-bidi-font-weight: 1494 1642 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1495 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>; 1496 a popup will appear.</p> 1497 1498 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1499 id="Picture_x0020_44" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:270pt; 1500 height:263.25pt;visibility:visible;mso-wrap-style:square'> 1501 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image015.png" 1502 o:title=""/> 1503 </v:shape><![endif]--><![if !vml]><img width=360 height=351 1504 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_44"><![endif]></span></p> 1643 minor-latin;mso-hansi-theme-font:minor-latin'>Edit Atoms/Update H atoms</span></b> 1644 to put them in their best positions.<span style='mso-spacerun:yes'> 1645 </span>Next select all the atoms by double clicking the empty box in upper left 1646 corner of the table; all atoms will be highlighted & plotted green. Do <b 1647 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1648 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit 1649 Atoms/On selected atoms 1650 /Transform atoms</span></b>; a popup will appear.</p> 1651 1652 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1653 id="Picture_x0020_60" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:270pt; 1654 height:264pt;visibility:visible;mso-wrap-style:square'> 1655 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image091.png" 1656 o:title=""/> 1657 </v:shape><![endif]--><![if !vml]><img width=360 height=352 1658 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image092.gif" v:shapes="Picture_x0020_60"><![endif]></span></p> 1505 1659 1506 1660 <p class=MsoNormal>Check the <b style='mso-bidi-font-weight:normal'><span … … 1517 1671 will both be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span 1518 1672 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1519 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>; the <span1673 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>2-3 times; the <span 1520 1674 class=SpellE>Rw</span> will drop back to where it was before and the <b 1521 1675 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; … … 1524 1678 1525 1679 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1526 id="Picture_x0020_ 46" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:336.75pt;1527 height: 375pt;visibility:visible;mso-wrap-style:square'>1528 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 17.png"1529 o:title=""/> 1530 </v:shape><![endif]--><![if !vml]><img width= 449 height=5001531 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 19.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>1680 id="Picture_x0020_61" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt; 1681 height:400.5pt;visibility:visible;mso-wrap-style:square'> 1682 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image093.png" 1683 o:title=""/> 1684 </v:shape><![endif]--><![if !vml]><img width=624 height=534 1685 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image094.gif" v:shapes="Picture_x0020_61"><![endif]></span></p> 1532 1686 1533 1687 <p class=MsoNormal>Now the identity Twin Law is ~2/3 and the 2-fold Twin Law is -
Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS_files/filelist.xml
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