Changeset 1435


Ignore:
Timestamp:
Jul 23, 2014 12:46:23 PM (7 years ago)
Author:
vondreele
Message:

modify comments about use of Alt key

Location:
trunk/help
Files:
4 edited

Legend:

Unmodified
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  • trunk/help/Charge Flipping - sucrose.htm

    r1434 r1435  
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    2324  <o:Author>Von Dreele</o:Author>
    2425  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>2</o:Revision>
     26  <o:Revision>3</o:Revision>
    2627  <o:TotalTime>1434</o:TotalTime>
    2728  <o:Created>2014-07-21T14:45:00Z</o:Created>
    28   <o:LastSaved>2014-07-21T14:45:00Z</o:LastSaved>
     29  <o:LastSaved>2014-07-23T17:43:00Z</o:LastSaved>
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     31  <o:Words>3469</o:Words>
     32  <o:Characters>19775</o:Characters>
    3233  <o:Company>Argonne National Laboratory</o:Company>
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    483486        mso-hansi-font-family:Tahoma;
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    938947<p class=MsoNormal>If you have not done so already, <a
    939948href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file
    940 (I called it <b style='mso-bidi-font-weight:normal'><span style='font-family:
    941 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    942 minor-latin'>sucrose.gpx</span></b>) you saved from the third part of the <a
    943 href="Fit%20Peaks.htm#sucrose_peak_fit">peak fitting-indexing exercise</a>. If
    944 you didn’t do that exercise, do it now.</p>
     949(I called it <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     950style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     951mso-hansi-theme-font:minor-latin'>sucrose.gpx</span></b></span>) you saved from
     952the third part of the <a href="Fit%20Peaks.htm#sucrose_peak_fit">peak
     953fitting-indexing exercise</a>. If you didn’t do that exercise, do it now.</p>
    945954
    946955<h2>Step 1: Setup for Pawley refinement</h2>
     
    962971symbol;mso-symbol-font-family:Symbol'>Q</span></span>. There is an area
    963972relatively clear of peaks that makes a good place to end the calculations with
    964 a reflection set of d<sub>min</sub> ~1Å resolution needed for charge flipping.
    965 Enter <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    966 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>23.55</span></b>
    967 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    968 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b>
     973a reflection set of <span class=SpellE>d<sub>min</sub></span> ~1Å resolution
     974needed for charge flipping. Enter <b style='mso-bidi-font-weight:normal'><span
     975style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     976mso-hansi-theme-font:minor-latin'>23.55</span></b> for <span class=SpellE><b
     977style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     978mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
    969979as the upper limit and make a note of the exact d-spacing (1.0125Å) using the
    970980mouse cursor on the plot.</p>
     
    10161026mso-hansi-theme-font:minor-latin'>1.0125</span></b>) into the <b
    10171027style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1018 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>
    1019 box.</p>
     1028mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
     1029class=SpellE>dmin</span></span></b> box.</p>
    10201030
    10211031<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
     
    10791089<p class=MsoNormal>I’ve stretched the window slightly to see the entire
    10801090contents. This is the location for all the phase dependent parameters for this
    1081 histogram. Notice that it includes phase fraction, size &amp; mustrain as well
    1082 as preferred orientation, elastic strain and extinction corrections. The
    1083 Babinet correction is intended for protein work where a significant region of
    1084 the structure is disordered solvent. There are buttons for plotting size and
    1085 mustrain surfaces</p>
    1086 
    1087 <p class=MsoNormal>as well as preferred orientation correction curves.</p>
     1091histogram. Notice that it includes phase fraction, size &amp; <span
     1092class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
     1093and extinction corrections. The <span class=SpellE>Babinet</span> correction is
     1094intended for protein work where a significant region of the structure is
     1095disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
     1096surfaces</p>
     1097
     1098<p class=MsoNormal><span class=GramE>as</span> well as preferred orientation
     1099correction curves.</p>
    10881100
    10891101<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    10901102style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    10911103mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
    1092 empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
    1093 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1094 mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
    1095 makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
    1096 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1097 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table
    1098 should list reflections 0-781. Select and check the refine column using the
    1099 same technique you used for the peak list. </p>
     1104empty except for column headings. <span class=GramE>Do</span> <b
     1105style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1106mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
     1107create</span></b>; this makes the reflection set over the range covered by
     1108setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1109mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
     1110class=SpellE>dmin</span></span></b>. The table should list reflections 0-781.
     1111Select and check the refine column using the same technique you used for the
     1112peak list. </p>
    11001113
    11011114<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    11281141style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    11291142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1130 to make sure it has essentially minimized. My refinement completed with Rwp
    1131 ~26.3%; a dialog box appears asking if you wish to load the result. Press <b
    1132 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1133 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1134 To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
    1135 the width and height).</p>
     1143to make sure it has essentially minimized. My refinement completed with <span
     1144class=SpellE>Rwp</span> ~26.3%; a dialog box appears asking if you wish to load
     1145the result. Press <b style='mso-bidi-font-weight:normal'><span
     1146style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1147mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
     1148PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
    11361149
    11371150<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    11601173mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,<b
    11611174style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1162 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> X </span></b>&amp;<b
    1163 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1164 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Y</span></b>.
    1165 The go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1166 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
    1167 Parameters</span></b> and check <b style='mso-bidi-font-weight:normal'><span
    1168 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1169 mso-hansi-theme-font:minor-latin'>Sample X displ</span></b>.; make the <b
    1170 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1171 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer
    1172 radius</span></b> <b style='mso-bidi-font-weight:normal'><span
    1173 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1174 mso-hansi-theme-font:minor-latin'>1000</span></b> if you didn’t do this
    1175 earlier. Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1176 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1177 minor-latin'>Calculate/Refine </span></b>until converged; I obtained an
    1178 improved residual of ~9.05% with a much better fit at the high angle part of
    1179 the pattern but still not fit well for the lower part.</p>
     1175mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
     1176class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
     1177style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1178mso-hansi-theme-font:minor-latin'> Y</span></b>. The go to <b style='mso-bidi-font-weight:
     1179normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1180minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and
     1181check <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
     1183class=SpellE>displ</span></span></b>.; make the <b style='mso-bidi-font-weight:
     1184normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1185minor-latin;mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> <b
     1186style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1187mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
     1188if you didn’t do this earlier. Repeat <b style='mso-bidi-font-weight:normal'><span
     1189style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1190mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>until converged;
     1191I obtained an improved residual of ~9.05% with a much better fit at the high
     1192angle part of the pattern but still not fit well for the lower part.</p>
    11801193
    11811194<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    11891202diffuse scattering feature at ~5deg and there are some peak shape issues (which
    11901203may be a consequence of the poor background fit). We’d like the fit to be
    1191 better before trying charge flipping. First select <b style='mso-bidi-font-weight:
    1192 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1193 minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>, set <b
    1194 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1204better before trying charge flipping. First select <span class=GramE><b
     1205style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1206mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>,</span>
     1207set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    11951208mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peaks in
    11961209background: No. peaks</span></b> to <b style='mso-bidi-font-weight:normal'><span
     
    12001213
    12011214<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1202  id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366pt;
     1215 id="Picture_x0020_27" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:366.75pt;
    12031216 height:197.25pt;visibility:visible;mso-wrap-style:square'>
    12041217 <v:imagedata src="Charge%20Flipping%20-%20sucrose_files/image007.png" o:title=""/>
    1205 </v:shape><![endif]--><![if !vml]><img border=0 width=488 height=263
     1218</v:shape><![endif]--><![if !vml]><img border=0 width=489 height=263
    12061219src="Charge%20Flipping%20-%20sucrose_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span><span
    12071220style='mso-spacerun:yes'> </span></p>
     
    12091222<p class=MsoNormal>Enter <b style='mso-bidi-font-weight:normal'><span
    12101223style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1211 mso-hansi-theme-font:minor-latin'>5.0</span></b> for <b style='mso-bidi-font-weight:
    1212 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1213 minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b>, <b
    1214 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1224mso-hansi-theme-font:minor-latin'>5.0</span></b> for <span class=SpellE><b
     1225style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1226mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span>,
     1227<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    12151228mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
    1216 for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1217 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b>
    1218 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1229for <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1230style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1231mso-hansi-theme-font:minor-latin'>int</span></b></span> and <b
     1232style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    12191233mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>
    12201234for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    12221236(as appropriate for broad diffuse peaks) and then check all three refine boxes.
    12231237Also set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1224 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b>
    1225 pulldown to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1226 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1227 minor-latin'>5</span></b> for the chebyschev part of the background. The window
     1238mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
     1239class=SpellE>coeff</span>.</span></b> <span class=SpellE><span class=GramE>pulldown</span></span>
     1240to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1241mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>
     1242for the <span class=SpellE>chebyschev</span> part of the background. The window
    12281243should look like</p>
    12291244
     
    12641279new negatives that may appear. Then set all the Pawley refinement flags back on
    12651280(excluding any that lead to a singular matrix) and repeat the refinement. After
    1266 refinement, mine converged to ~5.7% with very few negatives and and the plot
    1267 looked like</p>
     1281refinement, mine converged to ~5.7% with very few negatives and <span
     1282class=SpellE>and</span> the plot looked like</p>
    12681283
    12691284<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14741489position:absolute;z-index:251662336;margin-left:315px;margin-top:308px;
    14751490width:16px;height:35px'><img width=16 height=35
    1476 src="Charge%20Flipping%20-%20sucrose_files/image011.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
     1491src="Charge%20Flipping%20-%20sucrose_files/image052.png" v:shapes="Group_x0020_39 Arc_x0020_37 Arc_x0020_38"></span><![endif]><span
    14771492style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
    14781493 o:spid="_x0000_i1054" type="#_x0000_t75" style='width:502.5pt;height:431.25pt;
     
    14811496  croptop="3005f" cropbottom="25112f" cropleft="36677f" cropright="13798f"/>
    14821497</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=575
    1483 src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
     1498src="Charge%20Flipping%20-%20sucrose_files/image053.jpg" v:shapes="Picture_x0020_32"><![endif]></span></p>
    14841499
    14851500<p class=MsoNormal>The result looks very promising! Charge flipping operates
     
    15211536  croptop="635f" cropbottom="27738f" cropleft="37732f" cropright="12675f"/>
    15221537</v:shape><![endif]--><![if !vml]><img border=0 width=667 height=566
    1523 src="Charge%20Flipping%20-%20sucrose_files/image015.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
     1538src="Charge%20Flipping%20-%20sucrose_files/image054.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
    15241539
    15251540<h2>Step 4: Obtain solution from charge flip result</h2>
     
    15281543the map and make atoms out of them. The map peak list is initially sorted by
    15291544peak magnitude; you can change the sorting to be along any of the column
    1530 headings in the table by a single click on the desired heading. The <b
    1531 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1532 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>
    1533 column gives the distance of each peak from the origin. The menu items under
    1534 Map peaks give you several tools to aid in the peak selection process; we will
    1535 just use a couple in this example. I have chosen to proceed by sorting the
    1536 atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1537 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>,
    1538 selecting all and then finding the unique ones. </p>
     1545headings in the table by a single click on the desired heading. The <span
     1546class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1547"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1548minor-latin'>dzero</span></b></span> column gives the distance of each peak from
     1549the origin. The menu items under Map peaks give you several tools to aid in the
     1550peak selection process; we will just use a couple in this example. I have
     1551chosen to proceed by sorting the atoms by <b style='mso-bidi-font-weight:normal'><span
     1552style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1553mso-hansi-theme-font:minor-latin'>z</span></b>, selecting all and then finding
     1554the unique ones. </p>
    15391555
    15401556<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    15791595  croptop="610f" cropbottom="27878f" cropleft="37728f" cropright="12806f"/>
    15801596</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=572
    1581 src="Charge%20Flipping%20-%20sucrose_files/image018.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1597src="Charge%20Flipping%20-%20sucrose_files/image055.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
    15821598
    15831599<p class=MsoNormal>Notice that in my case one atom is in a neighboring
     
    16051621  croptop="735f" cropbottom="27738f" cropleft="37833f" cropright="12817f"/>
    16061622</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=578
    1607 src="Charge%20Flipping%20-%20sucrose_files/image020.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
     1623src="Charge%20Flipping%20-%20sucrose_files/image056.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
    16081624
    16091625<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16231639them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
    16241640style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1625 mso-hansi-theme-font:minor-latin'>Alt</span></b> key down and then selecting a
    1626 position in the table with the <b style='mso-bidi-font-weight:normal'><span
    1627 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1628 mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. After sorting
    1629 by magnitude, my list is now </p>
     1641mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
     1642normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1643minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
     1644and then selecting a position in the table with the <b style='mso-bidi-font-weight:
     1645normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1646minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
     1647Linux machines the <b style='mso-bidi-font-weight:normal'><span
     1648style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1649mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
     1650the operating system; use <b style='mso-bidi-font-weight:normal'><span
     1651style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1652mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. After
     1653sorting by magnitude, my list is now </p>
    16301654
    16311655<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16551679  croptop="4281f" cropbottom="26429f" cropleft="44874f" cropright="5786f"/>
    16561680</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=541
    1657 src="Charge%20Flipping%20-%20sucrose_files/image024.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
     1681src="Charge%20Flipping%20-%20sucrose_files/image057.jpg" v:shapes="Picture_x0020_18"><![endif]></span></p>
    16581682
    16591683<p class=MsoNormal>The original charge flipping solution is still visible and
     
    16781702style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    16791703mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
    1680 charge flip map (do <b style='mso-bidi-font-weight:normal'><span
    1681 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1682 mso-hansi-theme-font:minor-latin'>Clear map</span></b> in the <b
     1704charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1705style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1706mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
     1707normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1708minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
    16831709style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    16841710mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     
    17391765style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    17401766mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> table for the
    1741 selections and make note of the <b style='mso-bidi-font-weight:normal'><span
    1742 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1743 mso-hansi-theme-font:minor-latin'>Sym Op</span></b> for each one. In my case
    1744 they were “<b style='mso-bidi-font-weight:normal'><span style='font-family:
     1767selections and make note of the <span class=SpellE><b style='mso-bidi-font-weight:
     1768normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1769minor-latin;mso-hansi-theme-font:minor-latin'>Sym</span></b></span><b
     1770style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1771mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Op</span></b>
     1772for each one. In my case they were “<b style='mso-bidi-font-weight:normal'><span
     1773style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1774mso-hansi-theme-font:minor-latin'>2+1<span class=GramE>,0,0</span></span></b>”
     1775for O(4) and “<b style='mso-bidi-font-weight:normal'><span style='font-family:
    17451776"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1746 minor-latin'>2+1,0,0</span></b>” for O(4) and “<b style='mso-bidi-font-weight:
    1747 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1748 minor-latin;mso-hansi-theme-font:minor-latin'>2+2,-1,1</span></b>” for O(3).
    1749 The first number is the symmetry operator number and the 3 numbers after the ‘<b
    1750 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1751 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’
    1752 are unit cell translations.</p>
     1777minor-latin'>2+2,-1,1</span></b>” for O(3). The first number is the symmetry
     1778operator number and the 3 numbers after the ‘<b style='mso-bidi-font-weight:
     1779normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1780minor-latin;mso-hansi-theme-font:minor-latin'>+</span></b>’ are unit cell
     1781translations.</p>
    17531782
    17541783<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    17631792"Times New Roman"'><span style='mso-list:Ignore'>8.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    17641793</span></span></span><![endif]>Select an atom in turn that needs to be moved,
    1765 e.g. in my case O(3) or O(4). </p>
     1794e.g. in my case <span class=GramE>O(</span>3) or O(4). </p>
    17661795
    17671796<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    17701799</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    17711800style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1772 mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>, select the
    1773 operator and unit cell translations, then press <b style='mso-bidi-font-weight:
     1801mso-hansi-theme-font:minor-latin'>Edit/Transform <span class=GramE>atoms<span
     1802style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
     1803select the operator and unit cell translations, then press <b style='mso-bidi-font-weight:
    17741804normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    17751805minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. The atom
     
    17831813
    17841814<p class=MsoNormal style='margin-left:.5in'>This will complete the molecule
    1785 with the extra atoms. Do <b style='mso-bidi-font-weight:normal'><span
    1786 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1787 mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> to see the
    1788 completed molecule. I’ve made it a balls &amp; sticks with names as labels.</p>
     1815with the extra atoms. <span class=GramE>Do</span> <b style='mso-bidi-font-weight:
     1816normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1817minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>
     1818to see the completed molecule. I’ve made it a balls &amp; sticks with names as
     1819labels.</p>
    17891820
    17901821<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17941825  cropbottom="28348f" cropleft="41090f" cropright="9483f"/>
    17951826</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=576
    1796 src="Charge%20Flipping%20-%20sucrose_files/image027.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     1827src="Charge%20Flipping%20-%20sucrose_files/image058.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    17971828
    17981829<p class=MsoNormal>Save the project file; the next step is to complete the
    1799 structure by finding H-atoms and then do the final Rietveld refinements.</p>
     1830structure by finding H-atoms and then do the final <span class=SpellE>Rietveld</span>
     1831refinements.</p>
    18001832
    18011833<h2>Step 5: Complete the structure</h2>
    18021834
    18031835<p class=MsoNormal>To complete the structure you will need to perform a
    1804 preliminary Rietveld refinement. This will make the atom positions more
    1805 accurate and prepare a set of calculated structure factors needed to generate a
    1806 difference Fourier map good enough to maybe reveal the H atoms. There are a
    1807 number of steps needed to set all the controls from the previous Pawley
    1808 refinement to get a successful start for the Rietveld refinement.</p>
     1836preliminary <span class=SpellE>Rietveld</span> refinement. This will make the
     1837atom positions more accurate and prepare a set of calculated structure factors
     1838needed to generate a difference Fourier map good enough to maybe reveal the H
     1839atoms. There are a number of steps needed to set all the controls from the
     1840previous Pawley refinement to get a successful start for the <span
     1841class=SpellE>Rietveld</span> refinement.</p>
    18091842
    18101843<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    18291862scale factor</span></b> box. This is the scale factor for the data set. Uncheck
    18301863the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1831 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X
    1832 displ</span></b>.</p>
     1864mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
     1865class=SpellE>displ</span></span></b>.</p>
    18331866
    18341867<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    18491882style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    18501883mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
    1851 GSAS-II data tree menu; only scale and background are refined. I got a Rwp
    1852 ~20%. The plot shows clear intensity differences; the atom positions obviously
    1853 need refinement.</p>
     1884GSAS-II data tree menu; only scale and background are refined. I got <span
     1885class=GramE>a</span> <span class=SpellE>Rwp</span> ~20%. The plot shows clear
     1886intensity differences; the atom positions obviously need refinement.</p>
    18541887
    18551888<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19031936mso-hansi-theme-font:minor-latin'>Edit/Add hold</span></b> and select ‘<b
    19041937style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1905 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0::dAy:0 for
    1906 O(1)</span></b>’ from the dialog box. This will fix the shift along y for the
    1907 O(1) atom.</p>
     1938mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0:<span
     1939class=GramE>:dAy:0</span> for O(1)</span></b>’ from the dialog box. This will
     1940fix the shift along y for the <span class=GramE>O(</span>1) atom.</p>
    19081941
    19091942<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19281961<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
    19291962style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1930 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my Rwp is
    1931 now ~10.3%. You can now safely refine lattice parameters (in the <b
    1932 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1933 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    1934 tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1963mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
     1964class=SpellE>Rwp</span> is now ~10.3%. You can now safely refine lattice
     1965parameters (in the <b style='mso-bidi-font-weight:normal'><span
     1966style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1967mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
     1968style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    19351969mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>),
    19361970the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    19481982mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
    19491983and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1950 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X
    1951 displ</span></b>. You can also include refinement of atom thermal motion (U<sub>iso</sub>)
    1952 parameters. My refinement improved slightly to Rwp~10.0%. Let’s see if a
    1953 difference Fourier map will show anything.<br>
     1984mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample X <span
     1985class=SpellE>displ</span></span></b>. You can also include refinement of atom
     1986thermal motion (<span class=SpellE>U<sub>iso</sub></span>) parameters. My
     1987refinement improved slightly to Rwp~10.0%. Let’s see if a difference Fourier
     1988map will show anything.<br>
    19541989Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    19551990mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose
     
    19621997mso-list:l3 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    19631998"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1964 </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
    1965 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1966 mso-hansi-theme-font:minor-latin'>delt-F</span></b> for the <b
    1967 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1999</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
     2000normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2001minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
     2002style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2003mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
     2004for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    19682005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
    19692006
     
    20142051  croptop="1958f" cropbottom="26321f" cropleft="41054f" cropright="9779f"/>
    20152052</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=581
    2016 src="Charge%20Flipping%20-%20sucrose_files/image034.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
    2017 
    2018 <p class=MsoNormal>What is drawn here are green dots whose size are
    2019 proportional to the electron density. There are peaks that might be H-atom
    2020 positions as well as features that suggest C &amp; O-atoms out of position.
    2021 Recall that the refinement was just done without any H-atoms; it will make the
    2022 best fit compensating for the missing H-atoms by displacing the C &amp; O atoms
    2023 in the direction of the missing H-atoms. </p>
     2053src="Charge%20Flipping%20-%20sucrose_files/image059.jpg" v:shapes="Picture_x0020_35"><![endif]></span></p>
     2054
     2055<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
     2056whose size are proportional to the electron density. There are peaks that might
     2057be H-atom positions as well as features that suggest C &amp; O-atoms out of
     2058position. Recall that the refinement was just done without any H-atoms; it will
     2059make the best fit compensating for the missing H-atoms by displacing the C
     2060&amp; O atoms in the direction of the missing H-atoms. </p>
    20242061
    20252062<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20282065</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
    20292066style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2030 mso-hansi-theme-font:minor-latin'>Phases/sucrose<span
    2031 style='mso-spacerun:yes'>  </span>Draw Atoms</span></b> tab.</p>
     2067mso-hansi-theme-font:minor-latin'>Phases/<span class=GramE>sucrose<span
     2068style='mso-spacerun:yes'>  </span>Draw</span> Atoms</span></b> tab.</p>
    20322069
    20332070<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20602097  croptop="1838f" cropbottom="26454f" cropleft="41090f" cropright="9589f"/>
    20612098</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=581
    2062 src="Charge%20Flipping%20-%20sucrose_files/image036.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
     2099src="Charge%20Flipping%20-%20sucrose_files/image060.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
    20632100
    20642101<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20822119  croptop="1151f" cropbottom="27433f" cropleft="41826f" cropright="8682f"/>
    20832120</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=570
    2084 src="Charge%20Flipping%20-%20sucrose_files/image038.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
     2121src="Charge%20Flipping%20-%20sucrose_files/image061.jpg" v:shapes="Picture_x0020_38"><![endif]></span></p>
    20852122
    20862123<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20952132style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    20962133mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    2097 there should be a drop in Rwp. Then repeat the <b style='mso-bidi-font-weight:
    2098 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2099 minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> in
    2100 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2101 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    2102 tab, adjust the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2103 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2104 minor-latin'>Contour level</span></b> and <b style='mso-bidi-font-weight:normal'><span
     2134there should be a drop in <span class=SpellE>Rwp</span>. Then repeat the <b
     2135style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2136mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
     2137map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
     2138style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2139mso-hansi-theme-font:minor-latin'>General</span></b> tab, adjust the <b
     2140style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2141mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
     2142level</span></b> and <b style='mso-bidi-font-weight:normal'><span
    21052143style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    21062144mso-hansi-theme-font:minor-latin'>Map radius</span></b> as desired. Look for
     
    21142152  croptop="1524f" cropbottom="27738f" cropleft="41826f" cropright="8801f"/>
    21152153</v:shape><![endif]--><![if !vml]><img border=0 width=670 height=562
    2116 src="Charge%20Flipping%20-%20sucrose_files/image040.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
     2154src="Charge%20Flipping%20-%20sucrose_files/image062.jpg" v:shapes="Picture_x0020_39"><![endif]></span></p>
    21172155
    21182156<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    21192157style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    21202158mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> to finish this
    2121 stage in the structure analysis. My Rwp was ~8.02% with all the H-atoms
    2122 included (but not refined). The fit looks pretty good</p>
     2159stage in the structure analysis. My <span class=SpellE>Rwp</span> was ~8.02%
     2160with all the H-atoms included (but not refined). The fit looks pretty good</p>
    21232161
    21242162<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21332171<p class=MsoNormal>Looking at the fit, there may be room for improvement and
    21342172we’d like to refine the H-atom positions. First we need to change the profile
    2135 model to include crystallite size and mustrain broadening. Go to <b
    2136 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2137 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    2138 Parameters</span></b>, set <b style='mso-bidi-font-weight:normal'><span
    2139 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2140 mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:
    2141 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    2142 minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> to <b
    2143 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2173model to include crystallite size and <span class=SpellE>mustrain</span>
     2174broadening. Go to <b style='mso-bidi-font-weight:normal'><span
     2175style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2176mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b>, set <b
     2177style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
     2179and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2180mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
     2181to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    21442182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>zero</span></b>
    21452183and uncheck the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     
    21552193style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    21562194mso-hansi-theme-font:minor-latin'>Show</span></b> box is checked. Check the
    2157 boxes for both <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2158 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2159 minor-latin'>Cryst. size</span></b> and <b style='mso-bidi-font-weight:normal'><span
    2160 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2161 mso-hansi-theme-font:minor-latin'>microstrain</span></b>.</p>
     2195boxes for both <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2196style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2197mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b style='mso-bidi-font-weight:
     2198normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2199minor-latin;mso-hansi-theme-font:minor-latin'>. <span class=GramE>size</span></span></b>
     2200and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2201style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2202mso-hansi-theme-font:minor-latin'>microstrain</span></b></span>.</p>
    21622203
    21632204<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21702211<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    21712212style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2172 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will
    2173 start out high but should converge to where it was before this change. I got
    2174 8.08% and the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2175 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2176 minor-latin'>Data tab</span></b> looked like</p>
     2213mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
     2214class=SpellE>Rwp</span> will start out high but should converge to where it was
     2215before this change. I got 8.08% and the <b style='mso-bidi-font-weight:normal'><span
     2216style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2217mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like</p>
    21772218
    21782219<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21852226<p class=MsoNormal>Next select <b style='mso-bidi-font-weight:normal'><span
    21862227style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2187 mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <b
    2188 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2189 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain
    2190 model</span></b>; this is the Stephens phenomenological model for microstrain
    2191 which has 9 terms for monoclinic structures. Check all the boxes for it.</p>
     2228mso-hansi-theme-font:minor-latin'>Generalized</span></b> for the <span
     2229class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     2230"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2231minor-latin'>Mustrain</span></b></span><b style='mso-bidi-font-weight:normal'><span
     2232style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2233mso-hansi-theme-font:minor-latin'> model</span></b>; this is the Stephens
     2234phenomenological model for <span class=SpellE>microstrain</span> which has 9
     2235terms for monoclinic structures. Check all the boxes for it.</p>
    21922236
    21932237<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22002244<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    22012245style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2202 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the Rwp will
    2203 start out high but should converge lower than where it was before this change.
    2204 I got 7.65% and the <b style='mso-bidi-font-weight:normal'><span
    2205 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2206 mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like. If you check
    2207 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2208 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Mustrain</span></b>
    2209 button in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2210 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2211 minor-latin'>Select plot type</span></b> box, you will see the interesting
    2212 mustrain surface plot for ground sucrose.</p>
     2246mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
     2247class=SpellE>Rwp</span> will start out high but should converge lower than
     2248where it was before this change. I got 7.65% and the <b style='mso-bidi-font-weight:
     2249normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     2250minor-latin;mso-hansi-theme-font:minor-latin'>Data tab</span></b> looked like.
     2251If you check the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2252style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2253mso-hansi-theme-font:minor-latin'>Mustrain</span></b></span> button in the <b
     2254style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2255mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select plot
     2256type</span></b> box, you will see the interesting <span class=SpellE>mustrain</span>
     2257surface plot for ground sucrose.</p>
    22132258
    22142259<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22352280no bond restraints for sucrose. Do <b style='mso-bidi-font-weight:normal'><span
    22362281style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2237 mso-hansi-theme-font:minor-latin'>Edit/Add restraints</span></b>, a dialog box
    2238 will appear asking for the origin atom for the bond. </p>
     2282mso-hansi-theme-font:minor-latin'>Edit/Add <span class=GramE>restraints<span
     2283style='font-family:"Times New Roman","serif";font-weight:normal'>,</span></span></span></b>
     2284a dialog box will appear asking for the origin atom for the bond. </p>
    22392285
    22402286<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    23442390style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    23452391mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>, the console will
    2346 list progress on the “Penalty function” (i.e. the restraints) and the Rwp drops
    2347 in my case to ~7.05%. One can increase the <b style='mso-bidi-font-weight:normal'><span
    2348 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    2349 mso-hansi-theme-font:minor-latin'>Restraint weight factors</span></b> to
    2350 tighten them up at some expense in Rwp. In the end I chose <b style='mso-bidi-font-weight:
     2392list progress on the “Penalty function” (i.e. the restraints) and the <span
     2393class=SpellE>Rwp</span> drops in my case to ~7.05%. One can increase the <b
     2394style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2395mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Restraint
     2396weight factors</span></b> to tighten them up at some expense in <span
     2397class=SpellE>Rwp</span>. In the end I chose <b style='mso-bidi-font-weight:
    23512398normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    23522399minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b> for both <b
     
    23552402and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    23562403mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Angle</span></b>
    2357 restraints to give a final Rwp ~7.1%. NB: the H-atom positions may not be
    2358 correct even though the refinement apparently succeeded. You should check that
    2359 the OH ones all give reasonable H-bonds to neighboring O-atoms. As this is
    2360 powder data such changes will hardly affect the fit but will be more
    2361 satisfying. At present such checking is outside the scope of GSAS-II.</p>
     2404restraints to give a final <span class=SpellE>Rwp</span> ~7.1%. NB: the H-atom
     2405positions may not be correct even though the refinement apparently succeeded.
     2406You should check that the OH ones all give reasonable H-bonds to neighboring
     2407O-atoms. As this is powder data such changes will hardly affect the fit but
     2408will be more satisfying. At present such checking is outside the scope of
     2409GSAS-II.</p>
    23622410
    23632411<p class=MsoNormal><o:p>&nbsp;</o:p></p>
  • trunk/help/Charge Flipping - sucrose_files/filelist.xml

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  • trunk/help/Charge Flipping in GSAS.htm

    r1434 r1435  
    2323  <o:Author>vondreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
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    12261234
    12271235<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
    1228 GSAS-II - jadarite<o:p></o:p></span></h1>
     1236GSAS-II - <span class=SpellE>jadarite</span><o:p></o:p></span></h1>
    12291237
    12301238<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
    12311239
    12321240<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
    1233 of jadarite (aka “kryptonite”) from powder diffraction data via charge flipping.
    1234 This structure was originally solved by Pam Whitfield from laboratory powder
    1235 data in the space group P2<sub>1</sub>/c. </p>
     1241of <span class=SpellE>jadarite</span> (aka “kryptonite”) from powder
     1242diffraction data via charge flipping. This structure was originally solved by
     1243Pam Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p>
    12361244
    12371245<p class=MsoNormal>If you have not done so already, <a
    12381246href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file
    1239 (I called it jadarite.gpx) you saved from the second part of the <a
    1240 href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing exercise</a>.
    1241 If you didn’t do that exercise, do it now.</p>
    1242 
    1243 <h2>Step 1. Setup for Pawley refinement</h2>
     1247(I called it <span class=SpellE>jadarite.gpx</span>) you saved from the second
     1248part of the <a href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing
     1249exercise</a>. If you didn’t do that exercise, do it now.</p>
     1250
     1251<h2><span class=GramE>Step 1.</span> Setup for Pawley refinement</h2>
    12441252
    12451253<p class=MsoNormal>There are a number of steps that must be done in preparation
     
    12611269set of ~1Å resolution as needed for charge flipping. Enter <b style='mso-bidi-font-weight:
    12621270normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1263 minor-latin;mso-hansi-theme-font:minor-latin'>24</span></b> for <b
    1264 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1265 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b>
    1266 as the upper limit and make a note of the exact d-spacing (0.9945Å) using the
    1267 mouse cursor on the plot.</p>
     1271minor-latin;mso-hansi-theme-font:minor-latin'>24</span></b> for <span
     1272class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1273"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1274minor-latin'>Tmax</span></b></span> as the upper limit and make a note of the
     1275exact d-spacing (0.9945Å) using the mouse cursor on the plot.</p>
    12681276
    12691277<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
     
    12891297style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    12901298<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1291 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>
    1292 and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span
    1293 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1294 mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
     1299mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
     1300Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
     1301normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1302minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
    12951303
    12961304<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
     
    13061314box and enter the d-spacing (0.9945) into the <b style='mso-bidi-font-weight:
    13071315normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1308 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b> box.</p>
     1316minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
     1317box.</p>
    13091318
    13101319<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
     
    13681377<p class=MsoNormal>I’ve stretched the window slightly to see the entire
    13691378contents. This is the location for all the phase dependent parameters for this
    1370 histogram. Notice that it includes phase fraction, size &amp; mustrain as well
    1371 as preferred orientation, elastic strain and extinction corrections. The
    1372 Babinet correction is intended for protein work where a significant region of
    1373 the structure is disordered solvent. There are buttons for plotting size and
    1374 mustrain surfaces</p>
    1375 
    1376 <p class=MsoNormal>and preferred orientation correction curves.</p>
     1379histogram. Notice that it includes phase fraction, size &amp; <span
     1380class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
     1381and extinction corrections. The <span class=SpellE>Babinet</span> correction is
     1382intended for protein work where a significant region of the structure is
     1383disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
     1384surfaces</p>
     1385
     1386<p class=MsoNormal><span class=GramE>and</span> preferred orientation
     1387correction curves.</p>
    13771388
    13781389<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    13791390style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    13801391mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
    1381 empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
    1382 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1383 mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
    1384 makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
    1385 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1386 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table
    1387 should list reflections 0-629. Select and check the <b style='mso-bidi-font-weight:
    1388 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1389 minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column using
    1390 the same technique you used for the peak list. </p>
     1392empty except for column headings. <span class=GramE>Do</span> <b
     1393style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1394mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
     1395create</span></b>; this makes the reflection set over the range covered by
     1396setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1397mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
     1398class=SpellE>dmin</span></span></b>. The table should list reflections 0-629.
     1399Select and check the <b style='mso-bidi-font-weight:normal'><span
     1400style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1401mso-hansi-theme-font:minor-latin'>refine</span></b> column using the same
     1402technique you used for the peak list. </p>
    13911403
    13921404<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14081420file is made; the name will be jadarite.bck0.gpx. It can be used to recover
    14091421from a bad refinement. A progress dialog box will appear showing the residual
    1410 as the refinement proceeds. My refinement completed with Rwp ~15.5%; a dialog
    1411 box appears asking if you wish to load the result. Press <b style='mso-bidi-font-weight:
    1412 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1413 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot
    1414 select the PWDR line in the GSAS-II data tree (I’ve adjusted the width and
    1415 height).</p>
     1422as the refinement proceeds. My refinement completed with <span class=SpellE>Rwp</span>
     1423~15.5%; a dialog box appears asking if you wish to load the result. Press <b
     1424style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1425mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
     1426To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted the
     1427width and height).</p>
    14161428
    14171429<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1418  id="Picture_x0020_7" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
    1419  height:450pt;visibility:visible;mso-wrap-style:square'>
     1430 id="_x0000_i1043" type="#_x0000_t75" style='width:525pt;height:450pt;
     1431 visibility:visible;mso-wrap-style:square'>
    14201432 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image009.png" o:title=""/>
    14211433</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1422 src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1434src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="_x0000_i1043"><![endif]></span></p>
    14231435
    14241436<p class=MsoNormal>It is evident from examining the plot that improvement can
     
    14441456mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> W</span></b>,<b
    14451457style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1446 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> X </span></b>&amp;<b
    1447 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1448 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Y</span></b>.
    1449 Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1450 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    1451 I obtained an improved residual of 9.7% with a much better fit at the high
    1452 angle part of the pattern.</p>
     1458mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
     1459class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
     1460style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1461mso-hansi-theme-font:minor-latin'> Y</span></b>. Repeat <b style='mso-bidi-font-weight:
     1462normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1463minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I
     1464obtained an improved residual of 9.7% with a much better fit at the high angle
     1465part of the pattern.</p>
    14531466
    14541467<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15351548
    15361549<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1537  id="_x0000_i1041" type="#_x0000_t75" style='width:337.5pt;height:225pt;
    1538  visibility:visible;mso-wrap-style:square'>
     1550 id="Picture_x0020_7" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:337.5pt;
     1551 height:225pt;visibility:visible;mso-wrap-style:square'>
    15391552 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image013.png" o:title=""/>
    15401553</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
    1541 src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="_x0000_i1041"><![endif]></span></p>
     1554src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
    15421555
    15431556<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15841597the map and make atoms out of them. The map peak list is sorted with the
    15851598highest peak first; you can change the sorting to be along any of the column
    1586 headings in the table by a single click on the desired heading. The <b
    1587 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1588 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>
    1589 column gives the distance of each peak from the origin. The menu items under
    1590 Map peaks give you several tools to aid in the peak selection process, we will
    1591 just use a couple in this example. I have chosen to proceed by sorting the
    1592 atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1593 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>,
    1594 selecting all and then finding the unique ones. </p>
     1599headings in the table by a single click on the desired heading. The <span
     1600class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1601"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1602minor-latin'>dzero</span></b></span> column gives the distance of each peak
     1603from the origin. The menu items under Map peaks give you several tools to aid
     1604in the peak selection <span class=GramE>process,</span> we will just use a
     1605couple in this example. I have chosen to proceed by sorting the atoms by <span
     1606class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1607"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1608minor-latin'>dzero</span></b></span>, selecting all and then finding the unique
     1609ones. </p>
    15951610
    15961611<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    15971612mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
    15981613"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1599 </span></span></span><![endif]>Do a single click on the <b style='mso-bidi-font-weight:
    1600 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1601 minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b> column heading.
    1602 This will sort the peaks in increasing distance from the origin.</p>
     1614</span></span></span><![endif]>Do a single click on the <span class=SpellE><b
     1615style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1616mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b></span>
     1617column heading. This will sort the peaks in increasing distance from the origin.</p>
    16031618
    16041619<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    16531668identification (M100 for the largest in the <b style='mso-bidi-font-weight:
    16541669normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1655 minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
    1656 may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
     1670minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which may
     1671not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
    16571672style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    16581673mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
    16591674them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
    16601675style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1661 mso-hansi-theme-font:minor-latin'>Alt</span></b> key down and then selecting a
    1662 position in the table with the <b style='mso-bidi-font-weight:normal'><span
    1663 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1664 mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. My list is now
    1665 </p>
     1676mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
     1677normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1678minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
     1679and then selecting a position in the table with the <b style='mso-bidi-font-weight:
     1680normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1681minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
     1682Linux machines the <b style='mso-bidi-font-weight:normal'><span
     1683style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1684mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
     1685the operating system; use <b style='mso-bidi-font-weight:normal'><span
     1686style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1687mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. My
     1688list is now </p>
    16661689
    16671690<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17391762style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    17401763mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
    1741 charge flip map (do <b style='mso-bidi-font-weight:normal'><span
    1742 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1743 mso-hansi-theme-font:minor-latin'>Clear map</span></b> in the <b
     1764charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1765style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1766mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
     1767normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1768minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
    17441769style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    17451770mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     
    17571782
    17581783<p class=MsoNormal>Save the project file; the next step is to complete the
    1759 structure by finding the Li and H atoms and then doing the Rietveld refinement
    1760 on the completed structure.</p>
     1784structure by finding the Li and H atoms and then doing the <span class=SpellE>Rietveld</span>
     1785refinement on the completed structure.</p>
    17611786
    17621787<h2>Step 5 Complete the structure</h2>
    17631788
    17641789<p class=MsoNormal>To complete the structure you will need to perform a
    1765 preliminary Rietveld refinement. This will make the atom positions more
    1766 accurate and prepare a set of calculated structure factors needed to generate a
    1767 difference Fourier map good enough to reveal the Li atom position and maybe the
    1768 H-atom as well. There are a number of steps needed to set all the controls from
    1769 the previous Pawley refinement to get a successful start for the Rietveld
    1770 refinement.</p>
     1790preliminary <span class=SpellE>Rietveld</span> refinement. This will make the
     1791atom positions more accurate and prepare a set of calculated structure factors
     1792needed to generate a difference Fourier map good enough to reveal the Li atom
     1793position and maybe the H-atom as well. There are a number of steps needed to
     1794set all the controls from the previous Pawley refinement to get a successful
     1795start for the <span class=SpellE>Rietveld</span> refinement.</p>
    17711796
    17721797<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    18151840style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    18161841mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
    1817 GSAS-II data tree menu; all that was refined is scale and background. I got a
    1818 Rwp ~31%. The plot shows clear intensity differences; the atom positions
    1819 obviously need refinement.</p>
     1842GSAS-II data tree menu; all that was refined is scale and background. I got <span
     1843class=GramE>a</span> <span class=SpellE>Rwp</span> ~31%. The plot shows clear
     1844intensity differences; the atom positions obviously need refinement.</p>
    18201845
    18211846<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18531878<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
    18541879style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1855 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my Rwp is
    1856 now ~15%. You can now safely refine lattice parameters (in the <b
    1857 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1858 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    1859 tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1880mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
     1881class=SpellE>Rwp</span> is now ~15%. You can now safely refine lattice
     1882parameters (in the <b style='mso-bidi-font-weight:normal'><span
     1883style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1884mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
     1885style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18601886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>)
    18611887and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    18681894style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18691895mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
    1870 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1871 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    1872 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1896<span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1897style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1898mso-hansi-theme-font:minor-latin'>X</span></b></span> &amp; <b
     1899style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18731900mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>.
    18741901My refinement improved slightly to Rwp~14.5%. Let’s see if a difference Fourier
     
    18761903Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18771904mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite
    1878 General</span></b> tab ; the <b style='mso-bidi-font-weight:normal'><span
    1879 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1880 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
    1881 down the window.</p>
     1905General</span></b> <span class=GramE>tab ;</span> the <b style='mso-bidi-font-weight:
     1906normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1907minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b>
     1908are midway down the window.</p>
    18821909
    18831910<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    18841911mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    18851912"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1886 </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
    1887 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1888 mso-hansi-theme-font:minor-latin'>delt-F</span></b> for the <b
    1889 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1913</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
     1914normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1915minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
     1916style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1917mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
     1918for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18901919mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
    18911920
     
    19421971src="Charge%20Flipping%20in%20GSAS_files/image038.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    19431972
    1944 <p class=MsoNormal>What is drawn here are green dots whose size are
    1945 proportional to the electron density. These are the Li atom positions. There
    1946 are several ways within GSAS-II to add it to the atom list. One is to do <b
    1947 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1948 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Search
    1949 map</span></b> in the <b style='mso-bidi-font-weight:normal'><span
    1950 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1951 mso-hansi-theme-font:minor-latin'>General</span></b> tab and then find them in
    1952 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1953 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
    1954 tab much the same way we did earlier in this exercise. Another is to get the
    1955 atom position directly from the map, we will do that now.</p>
     1973<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
     1974whose size are proportional to the electron density. These are the Li atom
     1975positions. There are several ways within GSAS-II to add it to the atom list.
     1976One is to do <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1977"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1978minor-latin'>Compute/Search map</span></b> in the <b style='mso-bidi-font-weight:
     1979normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1980minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab and then
     1981find them in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1982"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1983minor-latin'>Map peaks</span></b> tab much the same way we did earlier in this
     1984exercise. Another is to get the atom position directly from the map, we will do
     1985that now.</p>
    19561986
    19571987<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20282058style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    20292059mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
    2030 GSAS-II data tree window. My residual Rwp dropped to ~11.3%. Next set all <b
    2031 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    2032 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
    2033 flags to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     2060GSAS-II data tree window. My residual <span class=SpellE>Rwp</span> dropped to
     2061~11.3%. Next set all <b style='mso-bidi-font-weight:normal'><span
     2062style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2063mso-hansi-theme-font:minor-latin'>refine</span></b> flags to <b
     2064style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    20342065mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>XU</span></b>
    20352066and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
    20362067"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2037 minor-latin'>Calculate/Refine</span></b>. My residual is now Rwp ~10.8%. Maybe
    2038 we can find the H-atom.</p>
     2068minor-latin'>Calculate/Refine</span></b>. My residual is now <span
     2069class=SpellE>Rwp</span> ~10.8%. Maybe we can find the H-atom.</p>
    20392070
    20402071<p class=MsoNormal>From the <b style='mso-bidi-font-weight:normal'><span
     
    20722103style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    20732104mso-hansi-theme-font:minor-latin'>UNK</span></b>). Repeat the Calculate/Refine
    2074 without varying any of the H-atom parameters; my final Rwp = 10.69% (you don’t
    2075 get much improvement for adding an H-atom to an oxide structure).</p>
     2105without varying any of the H-atom parameters; my final <span class=SpellE>Rwp</span>
     2106= 10.69% (you don’t get much improvement for adding an H-atom to an oxide
     2107structure).</p>
    20762108
    20772109</div>
  • trunk/help/Charge Flipping in GSAS_files/props053.xml

    r1425 r1435  
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