Changeset 457 for trunk/help


Ignore:
Timestamp:
Jan 25, 2012 9:24:20 AM (10 years ago)
Author:
vondreele
Message:

begin distance angle calcs
move gpxfile routines from GSASIIstruct.py to GSASIIIO.py
move getVCov & ValEsd? to GSASIImath.py
add some text to help/gsasII.html

File:
1 edited

Legend:

Unmodified
Added
Removed

  • trunk/help/gsasII.html

    r449 r457  
    1010<meta name=Generator content="Microsoft Word 12">
    1111<meta name=Originator content="Microsoft Word 12">
    12 <link href="gsasIIfav.png" rel="SHORTCUT ICON" />
    1312<link rel=File-List href="gsasII_files/filelist.xml">
    1413<link rel=Edit-Time-Data href="gsasII_files/editdata.mso">
    … …  
    2625  <o:Author>Von Dreele</o:Author>
    2726  <o:LastAuthor>Von Dreele</o:LastAuthor>
    28   <o:Revision>24</o:Revision>
    29   <o:TotalTime>1589</o:TotalTime>
     27  <o:Revision>25</o:Revision>
     28  <o:TotalTime>1625</o:TotalTime>
    3029  <o:Created>2011-11-28T16:49:00Z</o:Created>
    31   <o:LastSaved>2011-11-30T16:07:00Z</o:LastSaved>
    32   <o:Pages>2</o:Pages>
    33   <o:Words>2017</o:Words>
    34   <o:Characters>11500</o:Characters>
     30  <o:LastSaved>2012-01-23T21:39:00Z</o:LastSaved>
     31  <o:Pages>5</o:Pages>
     32  <o:Words>2599</o:Words>
     33  <o:Characters>14815</o:Characters>
    3534  <o:Company>Argonne National Laboratory</o:Company>
    36   <o:Lines>95</o:Lines>
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     35  <o:Lines>123</o:Lines>
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    3938  <o:Version>12.00</o:Version>
    4039 </o:DocumentProperties>
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    9711009        mso-list-template-ids:-1051437922 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
    972 @list l6:level1
     1010@list l7:level1
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    9741012        mso-level-number-position:left;
    9751013        text-indent:-.25in;}
    976 @list l6:level2
     1014@list l7:level2
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    9781016        mso-level-number-position:left;
    9791017        text-indent:-.25in;}
    980 @list l6:level3
     1018@list l7:level3
    9811019        {mso-level-tab-stop:1.5in;
    9821020        mso-level-number-position:left;
    9831021        text-indent:-.25in;}
    984 @list l6:level4
     1022@list l7:level4
    9851023        {mso-level-tab-stop:2.0in;
    9861024        mso-level-number-position:left;
    9871025        text-indent:-.25in;}
    988 @list l6:level5
     1026@list l7:level5
    9891027        {mso-level-tab-stop:2.5in;
    9901028        mso-level-number-position:left;
    9911029        text-indent:-.25in;}
    992 @list l6:level6
     1030@list l7:level6
    9931031        {mso-level-tab-stop:3.0in;
    9941032        mso-level-number-position:left;
    9951033        text-indent:-.25in;}
    996 @list l6:level7
     1034@list l7:level7
    9971035        {mso-level-tab-stop:3.5in;
    9981036        mso-level-number-position:left;
    9991037        text-indent:-.25in;}
    1000 @list l6:level8
     1038@list l7:level8
    10011039        {mso-level-tab-stop:4.0in;
    10021040        mso-level-number-position:left;
    10031041        text-indent:-.25in;}
    1004 @list l6:level9
     1042@list l7:level9
    10051043        {mso-level-tab-stop:4.5in;
    10061044        mso-level-number-position:left;
    … …  
    10301068        font-family:"Times New Roman","serif";}
    10311069</style>
    1032 <![endif]--><!--[if gte mso 9]><xml>
    1033  <o:shapedefaults v:ext="edit" spidmax="6146"/>
     1070<![endif]-->
     1071<link href=gsasIIfav.png rel="SHORTCUT ICON">
     1072<!--[if gte mso 9]><xml>
     1073 <o:shapedefaults v:ext="edit" spidmax="7170"/>
    10341074</xml><![endif]--><!--[if gte mso 9]><xml>
    10351075 <o:shapelayout v:ext="edit">
    … …  
    10621102 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    10631103 <o:lock v:ext="edit" aspectratio="t"/>
    1064 </v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1035" type="#_x0000_t75"
     1104</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1036" type="#_x0000_t75"
    10651105 alt="GSAS-II logo" style='position:absolute;margin-left:56pt;margin-top:0;
    10661106 width:96pt;height:96pt;z-index:1;visibility:visible;mso-wrap-style:square;
    … …  
    10761116
    10771117<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1078 is where to find help on various GSAS-II windows and plots.
    1079 Note that GSAS-II operates with three windows: the main <a href="#Data_tree">
    1080 GSAS-II data tree</A> window, which provides a hierarchical view of
    1081   the current project; the <a href="#Data_Frame">
    1082 GSAS-II data editing</A> window, which shows the contents of a
    1083   particular section of the project, where values can be examined and
    1084 changed; and the <a href="#Plots">
    1085 GSAS-II Plots</A> window, which shows graphical representations of the results.
    1086   <o:p></o:p></span></p>
    1087 
    1088 <P><hr><hr>
    1089   <h2><a name="Data_tree"><span style='mso-fareast-font-family:"Times
    1090   New Roman"'>1. GSAS-II
    1091 data tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    1092 
    1093 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1094 is a hierarchical view of the data items in your GSAS-II project (name.gpx). Clicking
    1095 on any item in the window opens a view where information in that item can be
    1096 viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
     1118is where to find help on various GSAS-II windows and plots. Note that GSAS-II
     1119operates with three windows: the main <a href="#Data_tree">GSAS-II data tree</a>
     1120window, which provides a hierarchical view of the current project; the <a
     1121href="#Data_Frame">GSAS-II data editing</a> window, which shows the contents of
     1122a particular section of the project, where values can be examined and changed;
     1123and the <a href="#Plots">GSAS-II Plots</a> window, which shows graphical
     1124representations of the results. <o:p></o:p></span></p>
     1125
     1126<div class=MsoNormal align=center style='text-align:center'><span
     1127style='mso-fareast-font-family:"Times New Roman"'>
     1128
     1129<hr size=2 width="100%" align=center>
     1130
     1131</span></div>
     1132
     1133<div class=MsoNormal align=center style='text-align:center'><span
     1134style='mso-fareast-font-family:"Times New Roman"'>
     1135
     1136<hr size=2 width="100%" align=center>
     1137
     1138</span></div>
     1139
     1140<h2><a name="Data_tree"><span style='mso-fareast-font-family:"Times New Roman"'>1.
     1141GSAS-II data tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
     1142
     1143<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1144is a hierarchical view of the data items in your GSAS-II project (name.gpx).
     1145Clicking on any item in the window opens a view where information in that item
     1146can be viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
    10971147Parameters&quot;</a> item contains information about how data were collected,
    10981148such as the sample temperature <a href="#Sample_Parameters">(see below)</a>. <o:p></o:p></span></p>
    10991149
    11001150<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1101 The menus associated with this window provide access to many features
    1102 of GSAS-II, as outlined below:
    1103 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1151
     1152<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
     1153menus associated with this window provide access to many features of GSAS-II,
     1154as outlined below: <o:p></o:p></span></p>
     1155
     1156<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    11041157style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    11051158style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
    … …  
    11071160
    11081161<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1109 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1162auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11101163style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    11111164style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    11161169
    11171170<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1118 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1171auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11191172style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    11201173style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    11281181
    11291182<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1130 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1183auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11311184style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    11321185style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    11381191
    11391192<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1140 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1193auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11411194style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    11421195style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    11471200
    11481201<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1149 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1202auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11501203style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    11511204style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    11561209option) GSAS-II; useful for escaping from GSAS-II if needed.</span></p>
    11571210
    1158 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1211<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    11591212style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    11601213style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
    … …  
    11621215
    11631216<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1164 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1217auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11651218style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    11661219style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    11761229
    11771230<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1178 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1231auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11791232style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    11801233style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    1181 style='mso-bidi-font-weight:normal'>Read image data&#8230;</b> - </p>
    1182 
    1183 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1184 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1234style='mso-bidi-font-weight:normal'>Read image data&#8230;</b> - Read in 2-D
     1235powder diffraction images (multiple patterns can be selected). GSAS-II can read
     1236many different image file formats including MAR345 files, Quantum ADSC files,
     1237and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of these
     1238formats have data fields that should contain relevant information for the
     1239exposure (e.g. wavelength), these are rarely filled in correctly by the data
     1240acquisition software. Thus, you should have separately noted this information
     1241as it will be needed</p>
     1242
     1243<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1244auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11851245style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    11861246style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    1187 style='mso-bidi-font-weight:normal'>Read Powder Pattern Peaks&#8230;</b> - </p>
    1188 
    1189 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1190 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1247style='mso-bidi-font-weight:normal'>Read Powder Pattern Peaks&#8230;</b> - Read
     1248in a list of powder pattern peak positions as either a d-spacing table or a set
     1249of 2<span style='font-family:Symbol'>Q</span> positions; these can be used in
     1250GSAS-II powder pattern indexing. </p>
     1251
     1252<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     1253auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11911254style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    11921255style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    11941257
    11951258<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1196 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1259auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    11971260style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    11981261style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12001263
    12011264<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1202 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1265auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12031266style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    12041267style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12061269
    12071270<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1208 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1271auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12091272style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    12101273style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12121275
    12131276<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1214 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1277auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12151278style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
    12161279style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12181281
    12191282<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1220 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1283auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12211284style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
    12221285style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    12251288
    12261289<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1227 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1290auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12281291style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
    12291292style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    … …  
    12311294data</b> - </p>
    12321295
    1233 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1296<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    12341297style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    12351298style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
    … …  
    12371300
    12381301<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1239 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1302auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12401303style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    12411304style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12431306
    12441307<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1245 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1308auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12461309style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    12471310style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12501313
    12511314<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1252 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1315auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12531316style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    12541317style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12561319
    12571320<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1258 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1321auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12591322style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    12601323style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12621325
    12631326<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1264 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1327auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12651328style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    12661329style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    12671330style='mso-bidi-font-weight:normal'>Solve</b> - </p>
    12681331
    1269 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1332<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    12701333style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    12711334style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
    … …  
    12731336
    12741337<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1275 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1338auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12761339style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    12771340style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12791342
    12801343<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1281 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1344auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12821345style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    12831346style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12851348
    12861349<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1287 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1350auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12881351style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    12891352style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    12911354
    12921355<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1293 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1356auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    12941357style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    12951358style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    12961359style='mso-bidi-font-weight:normal'>Import HKLs&#8230;</b> - </p>
    12971360
    1298 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo2'><![if !supportLists]><span
     1361<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
    12991362style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    13001363style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
    … …  
    13021365
    13031366<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1304 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1367auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13051368style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    13061369style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    13081371
    13091372<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1310 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1373auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13111374style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    13121375style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    13141377
    13151378<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1316 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1379auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13171380style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    13181381style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    13201383
    13211384<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1322 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1385auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13231386style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    13241387style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    13261389
    13271390<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1328 auto;text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1391auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13291392style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
    13301393style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    13321395
    13331396<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    1334 text-indent:-.25in;mso-list:l3 level2 lfo2'><![if !supportLists]><span
     1397text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
    13351398style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    13361399style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    13371400style='mso-bidi-font-weight:normal'>Export CIF&#8230;</b> - </p>
    13381401
    1339 <P><hr><hr>
    1340 <h2><a name="Data_Frame"><span style='mso-fareast-font-family:"Times
    1341 New Roman"'>2. GSAS-II
    1342 Data Editing Window</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    1343 Different information is displayed in the Data Editing Window,
    1344 depending on which section of the <a href="#Data_tree">data tree</A>
    1345 is selected. For example, clicking on the "Notebook" entry of the tree
    1346 brings up the Notebook editing window described below.
     1402<div class=MsoNormal align=center style='text-align:center'><span
     1403style='mso-fareast-font-family:"Times New Roman"'>
     1404
     1405<hr size=2 width="100%" align=center>
     1406
     1407</span></div>
     1408
     1409<div class=MsoNormal align=center style='text-align:center'><span
     1410style='mso-fareast-font-family:"Times New Roman"'>
     1411
     1412<hr size=2 width="100%" align=center>
     1413
     1414</span></div>
     1415
     1416<h2><a name="Data_Frame"><span style='mso-fareast-font-family:"Times New Roman"'>2.
     1417GSAS-II Data Editing Window</span></a><span style='mso-fareast-font-family:
     1418"Times New Roman"'><o:p></o:p></span></h2>
     1419
     1420<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Different
     1421information is displayed in the Data Editing Window, depending on which section
     1422of the <a href="#Data_tree">data tree</a> is selected. For example, clicking on
     1423the &quot;Notebook&quot; entry of the tree brings up the Notebook editing
     1424window described below. <o:p></o:p></span></p>
    13471425
    13481426<h4><a name=Notebook><span style='mso-fareast-font-family:"Times New Roman"'>Notebook</span></a><span
    … …  
    13621440<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    13631441window provides the main controls for the major calculations in GSAS-II. At
    1364 present only Refinement Controls are presented.<o:p></o:p></span></p>
    1365 
    1366 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    1367 main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
     1442present only Refinement Controls are presented. <o:p></o:p></span></p>
     1443
     1444<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Two
     1445of the main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
    13681446MINPACK <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
    13691447algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
    1370 package. Their purpose is to </span>minimize the sum of the squares of M<span
    1371 style='mso-fareast-font-family:"Times New Roman"'> nonlinear functions in N
    1372 variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
    1373 algorithm as written by </span>Burton S. <span class=SpellE>Garbow</span>,
     1448package and a third one is a python version utilizing only the <span
     1449class=SpellE>numpy</span> package. The purpose is to </span>minimize the sum of
     1450the squares of M<span style='mso-fareast-font-family:"Times New Roman"'>
     1451nonlinear functions in N variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
     1452algorithm. The <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
     1453routines were written by </span>Burton S. <span class=SpellE>Garbow</span>,
    13741454Kenneth E. <span class=SpellE>Hillstrom</span>, <span class=GramE>Jorge</span>
    1375 J. <span class=GramE>More (Argonne National Laboratory, 1980).</span></p>
     1455J. <span class=GramE>More (Argonne National Laboratory, 1980).</span> The
     1456python/numpy version was developed by us based on the material in Numerical
     1457Recipes (Press, Flannery, <span class=SpellE><span class=GramE>Teulosky</span></span>
     1458&amp; <span class=SpellE>Vetterling</span>) for the <span class=SpellE>Levenberg</span>-Marquardt
     1459algorithm.<span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    13761460
    13771461<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    13781462
    1379 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1463<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
    13801464style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    13811465style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    13821466style='mso-fareast-font-family:"Times New Roman"'>Select whether the refinement
    1383 uses &#8216;analytic&#8217; or &#8216;numeric&#8217; derivatives. The latter is
    1384 slower and perhaps a bit less accurate, but may be needed if the analytic
    1385 functions are not fully developed. Generally use &#8216;analytic&#8217; for
    1386 routine work.<o:p></o:p></span></p>
    1387 
    1388 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1467uses &#8216;analytic <span class=SpellE>Jacobian</span>&#8217;, &#8216;analytic
     1468Hessian&#8217; or &#8216;numeric&#8217; derivatives. The latter is slower and
     1469perhaps a bit less accurate, but may be needed if the analytic functions are
     1470not fully developed. The <span class=SpellE>Jacobian</span> matrix is shaped N x
     1471M (parameters x observations) and is much larger than the Hessian matrix which
     1472is shaped M x M (parameters x parameters). Generally use &#8216;analytic
     1473Hessian&#8217; for routine work.<o:p></o:p></span></p>
     1474
     1475<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
    13891476style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    13901477style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    … …  
    13961483to 1.0.<o:p></o:p></span></p>
    13971484
    1398 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1485<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
    13991486style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    14001487style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1401 style='mso-fareast-font-family:"Times New Roman"'>Select &#8216;Initial shift
    1402 factor&#8217; for the first cycle of refinement. This value is modified by the
    1403 least squares routine. The allowed range is 10<sup>-5</sup> to 100. Smaller
    1404 values may be needed if your initial <span class=GramE>refinement</span> trials
    1405 immediately diverge, however make sure your starting parameter values are
    1406 &#8216;reasonable&#8217;. The selected default (=1.0) normally gives good
    1407 performance.<o:p></o:p></span></p>
    1408 
    1409 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l4 level1 lfo4'><![if !supportLists]><span
     1488style='mso-fareast-font-family:"Times New Roman"'>If &#8216;analytic Jacobean&#8217;
     1489is chosen then select &#8216;Initial shift factor&#8217; for the first cycle of
     1490refinement. This value is modified by the least squares routine. The allowed
     1491range is 10<sup>-5</sup> to 100. Smaller values may be needed if your initial <span
     1492class=GramE>refinement</span> trials immediately diverge, however make sure
     1493your starting parameter values are &#8216;reasonable&#8217;. The selected
     1494default (=1.0) normally gives good performance.<o:p></o:p></span></p>
     1495
     1496<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
    14101497style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
     1498style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
     1499style='mso-fareast-font-family:"Times New Roman"'>If &#8216;analytic Hessian&#8217;
     1500is chosen then select &#8216;Max cycles&#8217;, the maximum number of least
     1501squares cycles to be performed. Choices are given in the pull down selection;
     1502the default is 3 cycles.<o:p></o:p></span></p>
     1503
     1504<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
     1505style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    14111506style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    14121507style='mso-fareast-font-family:"Times New Roman"'>Select data for sequential
    … …  
    14381533<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    14391534
    1440 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l5 level1 lfo6'><![if !supportLists]><span
     1535<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l6 level1 lfo6'><![if !supportLists]><span
    14411536style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    14421537style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1443 style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the parameter
    1444 types you wish to constrain. Each will have the same possibilities in the
    1445 &#8216;Edit menu.<o:p></o:p></span></p>
    1446 
    1447 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo6'><![if !supportLists]><span
     1538style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the
     1539parameter types you wish to constrain. Each will have the same possibilities in
     1540the &#8216;Edit menu.<o:p></o:p></span></p>
     1541
     1542<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo6'><![if !supportLists]><span
    14481543style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    14491544style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    … …  
    14521547
    14531548<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1454 auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1549auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
    14551550style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    14561551style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    … …  
    14701565
    14711566<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1472 auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1567auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
    14731568style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    14741569style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    14891584
    14901585<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
    1491 auto;text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1586auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
    14921587style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    14931588style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    15011596the first one. Choose those and press OK. Cancel in either dialog will cancel
    15021597the operation. The equivalenced parameters will show as an equation of the form
    1503 M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the
    1504 multipliers M1, <span class=GramE>M2, &#8230;</span> and C can be changed via
    1505 the &#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
     1598M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the multipliers
     1599M1, <span class=GramE>M2, &#8230;</span> and C can be changed via the
     1600&#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
    15061601constraint. A Delete button can be used to remove it.<o:p></o:p></span></p>
    15071602
    15081603<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    1509 text-indent:-.25in;mso-list:l5 level2 lfo6'><![if !supportLists]><span
     1604text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
    15101605style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
    15111606style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    … …  
    15351630<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    15361631
    1537 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo8'><![if !supportLists]><span
     1632<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l1 level1 lfo8'><![if !supportLists]><span
    15381633style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    15391634style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    … …  
    15471642operation.<o:p></o:p></span></p>
    15481643
    1549 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo8'><![if !supportLists]><span
     1644<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo8'><![if !supportLists]><span
    15501645style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    15511646style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    … …  
    15581653new value.<o:p></o:p></span></p>
    15591654
    1560 
    15611655<h4><span style='mso-fareast-font-family:"Times New Roman"'>Texture Control
    15621656Window<o:p></o:p></span></h4>
    … …  
    16101704<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
    16111705
    1612 <H3>Phase Windows</H3>
    1613 When a phase is selected from the <a href="#Data_tree">data tree</A>,
    1614 parameters are show from that selected phase in a tabbed
    1615 window. Clicking on the tab raises the windows listed below.
    1616 <blockquote>
    1617 <A name="General"><H4><U>General</U> Phase Parameters</H4></A>
    1618 This is used for overall parameters describing the phase such as the
    1619 space group, the unit cell parameters and overall parameters for
    1620 the atom present in the phase.
    1621 <A name="Data"><H4>Sample <U>Data</U></H4></A>
    1622 <A name="Texture"><H4><U>Texture</U> Parameters</H4></A>
    1623 <A name="Atoms"><H4><U>Atom</U> Parameter<U>s</U></H4></A>
    1624 <A name="Draw_Options"><H4><U>Draw Options</U></H4></A>
    1625 <A name="Draw_Atoms"><H4><U>Draw Atoms</U></H4></A>
    1626 
    1627 </blockquote>
    1628 
    1629 <H3>Powder Histogram Windows</H3>
    1630 When a powder diffraction data set (histogram) is selected from the
    1631 <a href="#Data_tree">data tree</A>, a variety of subcategories in the
    1632 tree are shown. The items that are shown depend on the data set type.
    1633 Selecting a subcategory raises the window listed below.
    1634 <blockquote>
    1635 <A name=""><H4><U></U></H4></A>
    1636 <A name="Comments"><H4><U>Comments</U></H4></A>
    1637 
    1638 <h4><a name=Background><span style='mso-fareast-font-family:"Times New Roman"'>Background</span></a><span
    1639 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1640 
    1641 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1642 window shows the choice of background function and coefficients to be used in
    1643 fitting this powder pattern.<o:p></o:p></span></p>
    1644 
    1645 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1646 
    1647 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1648 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    1649 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1650 style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
    1651 style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211; <b
     1706<h3>Phase Windows</h3>
     1707
     1708<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>When
     1709a phase is selected from the <a href="#Data_tree">data tree</a>, parameters are
     1710show from that selected phase in a tabbed window. Clicking on the tab raises
     1711the windows listed below. <o:p></o:p></span></p>
     1712
     1713<h4><a name=General><u>General</u> Phase Parameters</a></h4>
     1714
     1715<span style='mso-bookmark:General'></span>
     1716
     1717<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     1718is used for overall parameters describing the phase such as the space group,
     1719the unit cell parameters and overall parameters for the atom present in the
     1720phase. <a name=Data><o:p></o:p></a></span></p>
     1721
     1722<h4><span style='mso-bookmark:Data'>Sample <u>Data</u></span></h4>
     1723
     1724<span style='mso-bookmark:Data'></span>
     1725
     1726<h4><a name=Texture><u>Texture</u> Parameters</a></h4>
     1727
     1728<h4><span style='mso-bookmark:Texture'><a name=Atoms><u>Atom</u> Parameter<u>s</u></a></span></h4>
     1729
     1730<span style='mso-bookmark:Atoms'></span>
     1731
     1732<h4><span style='mso-bookmark:Texture'><a name="Draw_Options"><u>Draw Options</u></a></span></h4>
     1733
     1734<span style='mso-bookmark:Draw_Options'></span>
     1735
     1736<h4><span style='mso-bookmark:Texture'><a name="Draw_Atoms"><u>Draw Atoms</u></a></span></h4>
     1737
     1738<span style='mso-bookmark:Draw_Atoms'></span>
     1739
     1740<h3><span style='mso-bookmark:Texture'>Powder Histogram Windows</span></h3>
     1741
     1742<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1743"Times New Roman"'>When a powder diffraction data set (histogram) is selected
     1744from the </span></span><a href="#Data_tree"><span style='mso-bookmark:Texture'><span
     1745style='mso-fareast-font-family:"Times New Roman"'>data tree</span></span><span
     1746style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
     1747style='mso-fareast-font-family:"Times New Roman"'>, a variety of subcategories
     1748in the tree are shown. The items that are shown depend on the data set type.
     1749Selecting a subcategory raises the window listed below. <o:p></o:p></span></span></p>
     1750
     1751<h4><span style='mso-bookmark:Texture'><a name=Comments></a><a name=""></a><span
     1752style='mso-bookmark:Comments'><u>Comments</u></span></span></h4>
     1753
     1754<span style='mso-bookmark:Comments'></span>
     1755
     1756<h4><span style='mso-bookmark:Texture'><a name=Background><span
     1757style='mso-fareast-font-family:"Times New Roman"'>Background</span></a></span><span
     1758style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1759
     1760<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1761"Times New Roman"'>This window shows the choice of background function and
     1762coefficients to be used in fitting this powder pattern.<o:p></o:p></span></span></p>
     1763
     1764<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1765"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     1766
     1767<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1768style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1769"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1770</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Menu
     1771&#8216;<b style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211; <b
    16521772style='mso-bidi-font-weight:normal'>Copy</b> &#8211; this copies the background
    16531773parameters shown to other selected powder patterns. If used, a dialog box (Copy
    … …  
    16551775copy the background parameters to any or all of them; select &#8216;All&#8217;
    16561776to copy them to all patterns. Then select &#8216;OK&#8217; to do the copy;
    1657 &#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></p>
    1658 
    1659 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1660 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    1661 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1662 style='mso-fareast-font-family:"Times New Roman"'>You can select a different
    1663 Background function from the pull down tab.<o:p></o:p></span></p>
    1664 
    1665 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1666 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
    1667 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1668 style='mso-fareast-font-family:"Times New Roman"'>You can choose to refine/not
    1669 refine the background coefficients.<o:p></o:p></span></p>
    1670 
    1671 <p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1672 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    1673 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1674 style='mso-fareast-font-family:"Times New Roman"'>You can select the number of
    1675 background coefficients to be used (1-36).<o:p></o:p></span></p>
    1676 
    1677 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l6 level1 lfo10'><![if !supportLists]><span
    1678 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
    1679 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1680 style='mso-fareast-font-family:"Times New Roman"'>You can change individual
    1681 background coefficient values. Enter the value then press Enter or click the
    1682 mouse elsewhere in the Background window. This will set the new value.<o:p></o:p></span></p>
    1683 
    1684 <h4><a name="Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
    1685 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1686 
    1687 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1688 window... <o:p></o:p></span></p>
    1689 
    1690 <h4><a name="Sample_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Sample
    1691 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1692 
    1693 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1694 window... <o:p></o:p></span></p>
    1695 
    1696 <h4><a name="Powder_Peaks"></a><a name="Peak_List"><span style='mso-bookmark:
    1697 Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></a><span
    1698 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1699 
    1700 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1701 window shows the list of peaks that will be used by the peak fitting refinement.
    1702 It is filled by picking peaks in the powder pattern displayed in the GSASII
    1703 Plots window as a sequence of &#8216;+&#8217; marks. See <a
    1704 href="#Powder_Patterns">Powder Patterns</a> below for details for what can be
    1705 done on this plot.<o:p></o:p></span></p>
    1706 
    1707 <h4><a name="Index_Peaks"><span style='mso-fareast-font-family:"Times New Roman"'>Index
    1708 Peak List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1709 
    1710 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1711 window shows the list of peaks that will be used for indexing (see </span><a
    1712 href="#Unit_Cells_List"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
    1713 Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'>).
     1777&#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></span></p>
     1778
     1779<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1780style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1781"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1782</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1783can select a different Background function from the pull down tab.<o:p></o:p></span></span></p>
     1784
     1785<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1786style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1787"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1788</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1789can choose to refine/not refine the background coefficients.<o:p></o:p></span></span></p>
     1790
     1791<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1792style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1793"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1794</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1795can select the number of background coefficients to be used (1-36).<o:p></o:p></span></span></p>
     1796
     1797<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
     1798style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1799"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1800</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1801can change individual background coefficient values. Enter the value then press
     1802Enter or click the mouse elsewhere in the Background window. This will set the
     1803new value.<o:p></o:p></span></span></p>
     1804
     1805<h4><span style='mso-bookmark:Texture'><a name="Instrument_Parameters"><span
     1806style='mso-fareast-font-family:"Times New Roman"'>Instrument Parameters</span></a></span><span
     1807style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1808
     1809<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1810"Times New Roman"'>This window... <o:p></o:p></span></span></p>
     1811
     1812<h4><span style='mso-bookmark:Texture'><a name="Sample_Parameters"><span
     1813style='mso-fareast-font-family:"Times New Roman"'>Sample Parameters</span></a></span><span
     1814style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1815
     1816<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1817"Times New Roman"'>This window... <o:p></o:p></span></span></p>
     1818
     1819<h4><span style='mso-bookmark:Texture'><a name="Peak_List"></a><a
     1820name="Powder_Peaks"><span style='mso-bookmark:Peak_List'><span
     1821style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></a></span><span
     1822style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1823
     1824<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1825"Times New Roman"'>This window shows the list of peaks that will be used by the
     1826peak fitting refinement. It is filled by picking peaks in the powder pattern
     1827displayed in the GSASII Plots window as a sequence of &#8216;+&#8217; marks.
     1828See </span></span><a href="#Powder_Patterns"><span style='mso-bookmark:Texture'><span
     1829style='mso-fareast-font-family:"Times New Roman"'>Powder Patterns</span></span><span
     1830style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
     1831style='mso-fareast-font-family:"Times New Roman"'> below for details for what
     1832can be done on this plot.<o:p></o:p></span></span></p>
     1833
     1834<h4><span style='mso-bookmark:Texture'><a name="Index_Peaks"><span
     1835style='mso-fareast-font-family:"Times New Roman"'>Index Peak List</span></a></span><span
     1836style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1837
     1838<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1839"Times New Roman"'>This window shows the list of peaks that will be used for
     1840indexing (see </span></span><a href="#Unit_Cells_List"><span style='mso-bookmark:
     1841Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Unit Cells
     1842List</span></span><span style='mso-bookmark:Texture'></span></a><span
     1843style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>).
    17141844It must be filled before indexing can proceed. When indexing is completed, this
    17151845display will show the resulting <span class=SpellE>hkl</span> values for every
    17161846indexed reflection along with the calculated d-spacing (&#8216;d-<span
    1717 class=SpellE>calc</span>&#8217;) for the selected unit cell in </span><a
    1718 href="#Unit_Cells_List"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
    1719 Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
     1847class=SpellE>calc</span>&#8217;) for the selected unit cell in </span></span><a
     1848href="#Unit_Cells_List"><span style='mso-bookmark:Texture'><span
     1849style='mso-fareast-font-family:"Times New Roman"'>Unit Cells List</span></span><span
     1850style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
     1851style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></span></p>
     1852
     1853<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1854"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     1855
     1856<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo12'><span
     1857style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1858"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1859</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Menu
     1860&#8216;<b style='mso-bidi-font-weight:normal'>Operations</b>&#8217; &#8211; <b
     1861style='mso-bidi-font-weight:normal'>Load/Reload</b> &#8211; loads the peak
     1862positions &amp; intensities from the </span></span><a href="#Peak_List"><span
     1863style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Peak
     1864List</span></span><span style='mso-bookmark:Texture'></span></a><span
     1865style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
     1866to make them available for the indexing routine. The d-<span class=SpellE>obs</span>
     1867is obtained from Bragg&#8217;s Law after applying the Zero correction shown on
     1868the </span></span><a href="#Instrument_Parameters"><span style='mso-bookmark:
     1869Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
     1870Parameters</span></span><span style='mso-bookmark:Texture'></span></a><span
     1871style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
     1872table to the position shown here.<o:p></o:p></span></span></p>
     1873
     1874<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l3 level1 lfo12'><span
     1875style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     1876"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     1877</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
     1878may deselect individual peaks from indexing by <span class=SpellE>unchecking</span>
     1879the corresponding &#8216;use&#8217; box.<o:p></o:p></span></span></p>
     1880
     1881<h4><span style='mso-bookmark:Texture'><a name="Cell_Indexing_Refine"><span
     1882style='mso-fareast-font-family:"Times New Roman"'>Unit Cells List</span></a></span><span
     1883style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1884
     1885<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1886"Times New Roman"'>This window... <o:p></o:p></span></span></p>
     1887
     1888<h4><span style='mso-bookmark:Texture'><a name="Reflection_List"><span
     1889style='mso-fareast-font-family:"Times New Roman"'>Reflection List</span></a></span><span
     1890style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1891
     1892<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1893"Times New Roman"'>This window... <o:p></o:p></span></span></p>
     1894
     1895<div class=MsoNormal align=center style='text-align:center'><span
     1896style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
     1897
     1898<hr size=2 width="100%" align=center>
     1899
     1900</span></span></div>
     1901
     1902<div class=MsoNormal align=center style='text-align:center'><span
     1903style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
     1904
     1905<hr size=2 width="100%" align=center>
     1906
     1907</span></span></div>
     1908
     1909<h2><span style='mso-bookmark:Texture'><a name=Plots><span style='mso-fareast-font-family:
     1910"Times New Roman"'>3. GSAS-II Plots Window</span></a></span><span
     1911style='mso-bookmark:Plots'></span><span style='mso-bookmark:Texture'><span
     1912style='mso-fareast-font-family:"Times New Roman";font-weight:normal'> </span></span><span
     1913style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h2>
     1914
     1915<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1916"Times New Roman"'>This window presents all the graphical material as a
     1917multipage tabbed set of plots utilizing the <span class=SpellE>matplotlib</span>
     1918python package. Each page has a tool bar (at bottom in Windows) with the
     1919controls<o:p></o:p></span></span></p>
     1920
     1921<p class=MsoNormal><span style='mso-bookmark:Texture'></span><span
     1922style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman";
     1923mso-no-proof:yes'><img border=0 width=225 height=31 id="_x0000_i1032"
     1924src=graphbar.jpg></span></span><span style='mso-bookmark:Texture'><span
     1925style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></p>
     1926
     1927<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1928"Times New Roman"'>These are Home, Back, Forward, Pan, Zoom, Save and Help,
     1929respectively. <o:p></o:p></span></span></p>
     1930
     1931<ul type=disc>
     1932 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1933     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1934     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Home:
     1935     returns the plot to the initial scaling <o:p></o:p></span></span></li>
     1936 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1937     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1938     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Back:
     1939     returns the plot to the previous scaling <o:p></o:p></span></span></li>
     1940 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1941     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1942     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Forward:
     1943     reverses the action in the previous press(es) of the Back button <o:p></o:p></span></span></li>
     1944 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1945     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1946     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Pan:
     1947     allows you to control panning across the plot (press left mouse button)
     1948     and zooming (press right mouse button), <o:p></o:p></span></span></li>
     1949 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1950     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1951     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Zoom:
     1952     allows you to select a portion of the plot (press right mouse button &amp;
     1953     drag for zoom box) for the next plot. <o:p></o:p></span></span></li>
     1954 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1955     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1956     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Save:
     1957     allows you to save the currently displayed plot in one of several
     1958     graphical formats suitable for printing or insertion in a document. The <o:p></o:p></span></span></li>
     1959 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
     1960     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
     1961     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Help:
     1962     accesses GSASII help on the specific plot type. <o:p></o:p></span></span></li>
     1963</ul>
     1964
     1965<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1966"Times New Roman"'><o:p>&nbsp;</o:p></span></span></p>
     1967
     1968<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1969"Times New Roman"'>Below the toolbar may be a status bar that on the left may
     1970show either an instruction for a keyed input or a pull down selection of keyed
     1971input; on the right may be displayed position dependent information that is
     1972updated as the mouse is moved over the plot region.<o:p></o:p></span></span></p>
     1973
     1974<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1975"Times New Roman"'><o:p>&nbsp;</o:p></span></span></p>
     1976
     1977<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1978"Times New Roman"'>The specific types of plots that are pages in the GSASII
     1979Plots windows are next.<o:p></o:p></span></span></p>
     1980
     1981<h4><span style='mso-bookmark:Texture'><a name="Powder_Patterns"><span
     1982style='mso-fareast-font-family:"Times New Roman"'>Powder Patterns</span></a></span><span
     1983style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1984
     1985<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1986"Times New Roman"'>The powder patterns that are part of your project are shown
     1987on this page. They can be displayed as a stack of powder patterns, just a
     1988single pattern or as a contour image of the peak intensities. What can be done
     1989here will depend on which is displayed and on which item in the GSAS-II data
     1990tree you have selected.<o:p></o:p></span></span></p>
     1991
     1992<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     1993"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     1994
     1995<h4><span style='mso-bookmark:Texture'><a name=Covariance><span
     1996style='mso-fareast-font-family:"Times New Roman"'>Covariance</span></a></span><span
     1997style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
     1998
     1999<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2000"Times New Roman"'>The variance-covariance matrix as a color coded array is
     2001shown on this page. The color bar to the right shows the range of <span
     2002class=SpellE>covariances</span> (-1 to 1) and corresponding colors. The
     2003parameter names are to the right and the parameter numbers are below the plot.<o:p></o:p></span></span></p>
     2004
     2005<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2006"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     2007
     2008<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo15'><span
     2009style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     2010"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     2011</span></span></span><![endif]>Move the mouse cursor across the plot. If on a
     2012diagonal cell, the parameter name, value and <span class=SpellE>esd</span> is
     2013shown both as a tool tip and in the right hand portion of the status bar. If
     2014the cursor is off the diagonal, the two parameter names and their covariance
     2015are shown in the tool tip and the status bar.</span></p>
     2016
     2017<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo15'><span
     2018style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
     2019"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     2020</span></span></span><![endif]><span class=GramE>Type &#8216;s&#8217;</span>
     2021&#8211; A color scheme selection dialog is shown. Select a color scheme and
     2022press <span class=GramE>OK,</span> the new color scheme will be plotted. The
     2023default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</span></p>
     2024
     2025<h4><span style='mso-bookmark:Texture'><a name="Structure_Factors"><span
     2026style='mso-fareast-font-family:"Times New Roman"'>Structure Factors </span></a></span></h4>
     2027
     2028<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2029"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
     2030
     2031<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2032"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     2033
     2034<h4><span style='mso-bookmark:Texture'><a name="Powder_Lines"><span
     2035style='mso-fareast-font-family:"Times New Roman"'>Powder Lines </span></a></span></h4>
     2036
     2037<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2038"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
     2039
     2040<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2041"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     2042
     2043<h4><span style='mso-bookmark:Texture'><a name="Peak_Widths"><span
     2044style='mso-fareast-font-family:"Times New Roman"'>Peak Widths </span></a></span></h4>
     2045
     2046<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2047"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
     2048
     2049<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2050"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
     2051
     2052<h4><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
     2053"Times New Roman"'>Texture </span></span></h4>
     2054
     2055<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2056plot shows... <o:p></o:p></span></p>
    17202057
    17212058<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    17222059
    1723 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo12'><![if !supportLists]><span
    1724 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    1725 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1726 style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
    1727 style='mso-bidi-font-weight:normal'>Operations</b>&#8217; &#8211; <b
    1728 style='mso-bidi-font-weight:normal'>Load/Reload</b> &#8211; loads the peak
    1729 positions &amp; intensities from the </span><a href="#Peak_List"><span
    1730 style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></a><span
    1731 style='mso-fareast-font-family:"Times New Roman"'> to make them available for
    1732 the indexing routine. The d-<span class=SpellE>obs</span> is obtained from
    1733 Bragg&#8217;s Law after applying the Zero correction shown on the </span><a
    1734 href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
    1735 Parameters</span></a><span style='mso-fareast-font-family:"Times New Roman"'>
    1736 table to the position shown here.<o:p></o:p></span></p>
    1737 
    1738 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo12'><![if !supportLists]><span
    1739 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    1740 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1741 style='mso-fareast-font-family:"Times New Roman"'>You may deselect individual
    1742 peaks from indexing by <span class=SpellE>unchecking</span> the corresponding
    1743 &#8216;use&#8217; box.<o:p></o:p></span></p>
    1744 
    1745 <h4><a name="Cell_Indexing_Refine"><span style='mso-fareast-font-family:"Times New Roman"'>Unit
    1746 Cells List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1747 
    1748 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1749 window... <o:p></o:p></span></p>
    1750 
    1751 <h4><a name="Reflection_List"><span style='mso-fareast-font-family:"Times New Roman"'>Reflection
    1752 List</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1753 
    1754 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1755 window... <o:p></o:p></span></p>
    1756 
    1757 </blockquote>
    1758 
    1759 <P><hr><hr>
    1760 <h2><a name=Plots><span style='mso-fareast-font-family:"Times New
    1761 Roman"'>3. GSAS-II
    1762 Plots Window</span></a><span style='mso-bookmark:Plots'></span><span style='mso-fareast-font-family:
    1763 "Times New Roman";font-weight:normal'> </span><span style='mso-fareast-font-family:
    1764 "Times New Roman"'><o:p></o:p></span></h2>
    1765 
    1766 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    1767 window presents all the graphical material as a multipage tabbed set of plots
    1768 utilizing the <span class=SpellE>matplotlib</span> python package. Each page
    1769 has a tool bar (at bottom in Windows) with the controls<o:p></o:p></span></p>
    1770 
    1771 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    1772 mso-no-proof:yes'><img border=0 width=225 height=31
    1773 src="graphbar.jpg" align="middle"></span><span
    1774 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    1775 
    1776 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>These
    1777 are Home, Back, Forward, Pan, Zoom, Save and Help, respectively.
    1778 <UL>
    1779   <LI>Home: returns the plot to the initial scaling
    1780   <LI>Back: returns the plot to the previous scaling
    1781   <LI>Forward: reverses the action in the previous press(es)
    1782   of the Back button
    1783   <LI>Pan: allows you to control panning across the plot (press left mouse button) and
    1784 zooming (press right mouse button),
    1785   <LI>Zoom: allows you to select a
    1786 portion of the plot (press right mouse button &amp; drag for zoom box) for the
    1787 next plot.
    1788   <LI>Save: allows you to save the currently displayed plot in one of
    1789 several graphical formats suitable for printing or insertion in a document. The
    1790   <LI>Help: accesses GSASII help on the specific plot type.
    1791 </UL>
    1792   <o:p></o:p></span></p>
    1793 
    1794 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Below
    1795 the toolbar may be a status bar that on the left may show either an instruction
    1796 for a keyed input or a pull down selection of keyed input; on the right may be
    1797 displayed position dependent information that is updated as the mouse is moved
    1798 over the plot region.<o:p></o:p></span></p>
    1799 
    1800 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
    1801 
    1802 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    1803 specific types of plots that are pages in the GSASII Plots windows are next.<o:p></o:p></span></p>
    1804 
    1805 <h4><a name="Powder_Patterns"><span style='mso-fareast-font-family:"Times New Roman"'>Powder
    1806 Patterns</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1807 
    1808 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    1809 powder patterns that are part of your project are shown on this page. They can
    1810 be displayed as a stack of powder patterns, just a single pattern or as a
    1811 contour image of the peak intensities. What can be done here will depend on
    1812 which is displayed and on which item in the GSAS-II data tree you have
    1813 selected.<o:p></o:p></span></p>
     2060<h4><a name="Sequential_refinement"><span style='mso-fareast-font-family:"Times New Roman"'>Sequential
     2061refinement </span></a></h4>
     2062
     2063<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2064plot shows... <o:p></o:p></span></p>
     2065
    18142066<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    18152067
    1816 <h4><a name=Covariance><span style='mso-fareast-font-family:"Times New Roman"'>Covariance</span></a><span
    1817 style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
    1818 
    1819 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    1820 variance-covariance matrix as a color coded array is shown on this page. The
    1821 color bar to the right shows the range of <span class=SpellE>covariances</span>
    1822 (-1 to 1) and corresponding colors. The parameter names are to the right and
    1823 the parameter numbers are below the plot.<o:p></o:p></span></p>
     2068<h4><a name="2D_Powder_Image"><span style='mso-fareast-font-family:"Times New Roman"'>2D
     2069Powder Image </span></a></h4>
     2070
     2071<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2072plot shows... <o:p></o:p></span></p>
    18242073
    18252074<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    18262075
    1827 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l1 level1 lfo14'><![if !supportLists]><span
    1828 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
    1829 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Move
    1830 the mouse cursor across the plot. If on a diagonal cell, the parameter name,
    1831 value and <span class=SpellE>esd</span> is shown both as a tool tip and in the
    1832 right hand portion of the status bar. If the cursor is off the diagonal, the
    1833 two parameter names and their covariance are shown in the tool tip and the
    1834 status bar.</p>
    1835 
    1836 <p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo14'><![if !supportLists]><span
    1837 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    1838 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    1839 class=GramE>Type &#8216;s&#8217;</span> &#8211; A color scheme selection dialog
    1840 is shown. Select a color scheme and press <span class=GramE>OK,</span> the new
    1841 color scheme will be plotted. The default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</p>
    1842 
    1843 <h4><a name="Structure_Factors">
    1844 <span style='mso-fareast-font-family:"Times New Roman"'>
    1845 Structure Factors
     2076<h4><a name="2D_Integration"><span style='mso-fareast-font-family:"Times New Roman"'>2D
     2077Integration </span></a></h4>
     2078
     2079<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2080plot shows... <o:p></o:p></span></p>
     2081
     2082<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     2083
     2084<h4><a name="2D_Transformed_Powder_Image"><span style='mso-fareast-font-family:
     2085"Times New Roman"'>2D Transformed Powder Image </span></a></h4>
     2086
     2087<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2088plot shows... <o:p></o:p></span></p>
     2089
     2090<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     2091
     2092<h4><a name=Mustrain><span style='mso-fareast-font-family:"Times New Roman"'>Mustrain
    18462093</span></a></h4>
    1847 This plot shows...
     2094
     2095<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2096plot shows... <o:p></o:p></span></p>
     2097
    18482098<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    18492099
    1850 <h4><a name="Powder_Lines">
    1851 <span style='mso-fareast-font-family:"Times New Roman"'>
    1852 Powder Lines
    1853 </span></a></h4>
    1854 This plot shows...
     2100<h4><a name=Size><span style='mso-fareast-font-family:"Times New Roman"'>Size </span></a></h4>
     2101
     2102<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2103plot shows... <o:p></o:p></span></p>
     2104
    18552105<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    18562106
    1857 
    1858 <h4><a name="Peak_Widths">
    1859 <span style='mso-fareast-font-family:"Times New Roman"'>
    1860 Peak Widths
    1861 </span></a></h4>
    1862 This plot shows...
     2107<h4><a name="Preferred_orientation"><span style='mso-fareast-font-family:"Times New Roman"'>Preferred
     2108Orientation </span></a></h4>
     2109
     2110<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     2111plot shows... <o:p></o:p></span></p>
     2112
    18632113<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1864 
    1865 
    1866 <h4><a name="Texture">
    1867 <span style='mso-fareast-font-family:"Times New Roman"'>
    1868 Texture
    1869 </span></a></h4>
    1870 This plot shows...
    1871 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1872 
    1873 
    1874 <h4><a name="Sequential_refinement">
    1875 <span style='mso-fareast-font-family:"Times New Roman"'>
    1876 Sequential refinement
    1877 </span></a></h4>
    1878 This plot shows...
    1879 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1880 
    1881 
    1882 <h4><a name="2D_Powder_Image">
    1883 <span style='mso-fareast-font-family:"Times New Roman"'>
    1884 2D Powder Image
    1885 </span></a></h4>
    1886 This plot shows...
    1887 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1888 
    1889 
    1890 <h4><a name="2D_Integration">
    1891 <span style='mso-fareast-font-family:"Times New Roman"'>
    1892 2D Integration
    1893 </span></a></h4>
    1894 This plot shows...
    1895 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1896 
    1897 
    1898 <h4><a name="2D_Transformed_Powder_Image">
    1899 <span style='mso-fareast-font-family:"Times New Roman"'>
    1900 2D Transformed Powder Image
    1901 </span></a></h4>
    1902 This plot shows...
    1903 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1904 
    1905 
    1906 <h4><a name="Mustrain">
    1907 <span style='mso-fareast-font-family:"Times New Roman"'>
    1908 Mustrain
    1909 </span></a></h4>
    1910 This plot shows...
    1911 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1912 
    1913 
    1914 <h4><a name="Size">
    1915 <span style='mso-fareast-font-family:"Times New Roman"'>
    1916 Size
    1917 </span></a></h4>
    1918 This plot shows...
    1919 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1920 
    1921 <h4><a name="Preferred_orientation">
    1922 <span style='mso-fareast-font-family:"Times New Roman"'>
    1923 Preferred Orientation
    1924 </span></a></h4>
    1925 This plot shows...
    1926 <h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
    1927 
    1928 
    19292114
    19302115<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
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