Changeset 1197


Ignore:
Timestamp:
Jan 13, 2014 1:49:36 PM (8 years ago)
Author:
vondreele
Message:

fix a couple of typos in tutorial

Location:
trunk/help
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/help/Strain fitting of 2D data in GSAS-II.htm

    r1196 r1197  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>5</o:Revision>
    28   <o:TotalTime>372</o:TotalTime>
     27  <o:Revision>7</o:Revision>
     28  <o:TotalTime>379</o:TotalTime>
    2929  <o:Created>2014-01-13T15:39:00Z</o:Created>
    30   <o:LastSaved>2014-01-13T19:33:00Z</o:LastSaved>
     30  <o:LastSaved>2014-01-13T19:49:00Z</o:LastSaved>
    3131  <o:Pages>6</o:Pages>
    32   <o:Words>888</o:Words>
    33   <o:Characters>5066</o:Characters>
     32  <o:Words>890</o:Words>
     33  <o:Characters>5078</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
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    3636  <o:Paragraphs>11</o:Paragraphs>
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    3939 </o:DocumentProperties>
     
    972972<h1>Strain fitting of 2D data in GSAS-II</h1>
    973973
    974 <p class=MsoNormal>For this demo, data was collected with a MAR2300 area
     974<p class=MsoNormal>For this demo, data were collected with a MAR2300 area
    975975detector at APS 1-ID-C with a wavelength 0.12398 Å (100<span style='font-family:
    976 Symbol'>m</span>m diameter beam) from a 1.5mm square hot rolled steel test
    977 specimen; the front surface has been dusted with some CeO<sub>2</sub> to aid in
     976Symbol'>m</span>m diameter beam) from a 1.5mm square hot rolled steel test specimen;
     977the front surface has been dusted with some CeO<sub>2</sub> to aid in
    978978calibration. Two images are used here; one is with no load on the sample and
    979979the other is with the sample under tension along the y-axis (vertical). The
     
    10161016Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>.<span
    10171017style='mso-no-proof:yes'> Select the 1<sup>st</sup> image (001) from the
    1018 GSAS-II data tree and select Image Controls; adjust the Max intensity so that the
    1019 CeO2 rings are visible (~1500 will suffice). You should see:<o:p></o:p></span></p>
     1018GSAS-II data tree and select Image Controls; adjust the Max intensity so that
     1019the CeO2 rings are visible (~1500 will suffice). You should see:<o:p></o:p></span></p>
    10201020
    10211021<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    10631063
    10641064<p class=MsoNormal>This image is a superposition of three diffraction patterns;
    1065 CeO<sub>2</sub> <span class=SpellE>calibrant</span>, ferrite (BCC iron) and austenite
    1066 (FCC iron). Consequently the calibration needs to be done with some care; the
    1067 steps are as follows:</p>
     1065CeO<sub>2</sub> <span class=SpellE>calibrant</span>, ferrite (BCC iron) and
     1066austenite (FCC iron). Consequently the calibration needs to be done with some
     1067care; the steps are as follows:</p>
    10681068
    10691069<p class=MsoNormal>Set the wavelength to <b style='mso-bidi-font-weight:normal'><span
     
    12361236
    12371237<p class=MsoNormal>We are now ready for the first strain fit; do Operations/Fit
    1238 stress/strain. Each ring will be fitted to the three strain tensor elements (&#949;<sub>11</sub>,
    1239 &#949;<sub>12</sub> &amp; &#949;<sub>22</sub>) that can be determined from a single
    1240 2D diffraction ring. The resulting Strain plot now shows curves calculated from
    1241 the fitted tensor elements; these are very nearly straight lines as expected
    1242 from an unloaded sample.<span style='mso-spacerun:yes'>  </span>In particular
    1243 the austenite 111 line (~2.08Å) is much flatter than the ferrite 200 line (~2.03Å);
    1244 this reflects the sample history (hot rolled steel). The tensor elements with <span
    1245 class=SpellE>esds</span> are shown on the console and in the data window</p>
     1238stress/strain. Each ring will be fitted to the three strain tensor elements
     1239(&#949;<sub>11</sub>, &#949;<sub>12</sub> &amp; &#949;<sub>22</sub>) that can
     1240be determined from a single 2D diffraction ring. The resulting Strain plot now
     1241shows curves calculated from the fitted tensor elements; these are very nearly
     1242straight lines as expected from an unloaded sample.<span
     1243style='mso-spacerun:yes'>  </span>In particular the austenite 111 line (~2.08Å)
     1244is much flatter than the ferrite 200 line (~2.03Å); this reflects the sample
     1245history (hot rolled steel). The tensor elements with <span class=SpellE>esds</span>
     1246are shown on the console and in the data window</p>
    12461247
    12471248<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    13161317
    13171318<p class=MsoNormal>I only show the bottom of the listing. The strain plot gives
    1318 (I zoomed in on just one line).</p>
     1319(I zoomed in on just one line; ferrite 211).</p>
    13191320
    13201321<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    13291330<p class=MsoNormal>When you look at the other lines, you should notice that the
    13301331ones at ca. 3.13Å, 1.91Å, and 1.63Å remain straight lines; these are from CeO<sub>2</sub>
    1331 and should be unchanged under load.<o:p></o:p></p>
     1332and should be unchanged under load.</p>
    13321333
    13331334<p class=MsoNormal><o:p>&nbsp;</o:p></p>
  • trunk/help/gsasII.html

    r1132 r1197  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>133</o:Revision>
    28   <o:TotalTime>3974</o:TotalTime>
     27  <o:Revision>134</o:Revision>
     28  <o:TotalTime>3975</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2013-07-12T10:17:00Z</o:LastSaved>
     30  <o:LastSaved>2014-01-13T19:41:00Z</o:LastSaved>
    3131  <o:Pages>27</o:Pages>
    32   <o:Words>10727</o:Words>
    33   <o:Characters>61145</o:Characters>
     32  <o:Words>10790</o:Words>
     33  <o:Characters>61503</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>509</o:Lines>
    36   <o:Paragraphs>143</o:Paragraphs>
    37   <o:CharactersWithSpaces>71729</o:CharactersWithSpaces>
     35  <o:Lines>512</o:Lines>
     36  <o:Paragraphs>144</o:Paragraphs>
     37  <o:CharactersWithSpaces>72149</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
    464464        font-style:italic;}
    465465h5
    466         {mso-style-priority:9;
     466        {mso-style-noshow:yes;
     467        mso-style-priority:9;
    467468        mso-style-qformat:yes;
    468469        mso-style-link:"Heading 5 Char";
     
    611612        mso-font-kerning:14.0pt;}
    612613a:link, span.MsoHyperlink
    613         {mso-style-noshow:yes;
    614         mso-style-priority:99;
     614        {mso-style-priority:99;
    615615        color:blue;
    616616        text-decoration:underline;
     
    850850span.Heading5Char
    851851        {mso-style-name:"Heading 5 Char";
     852        mso-style-noshow:yes;
    852853        mso-style-priority:9;
    853854        mso-style-unhide:no;
     
    23052306
    23062307<h2><a name=Programmers><strong>Programmers documentation</strong></a><strong>:<o:p></o:p></strong></h2>
    2307 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>
    2308 The routines and classes used within GSAS-II are documented in a set of
    2309 <a href="../sphinxdocs/build/html/index.html">web pages</a>
    2310 and in a <a href="../sphinxdocs/build/latex/GSASIIdoc.pdf">PDF document</a>.
    2311 This documentation is created from the Python source code files using
    2312 Sphinx. </span></p>
     2308
     2309<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
     2310routines and classes used within GSAS-II are documented in a set of <a
     2311href="../sphinxdocs/build/html/index.html">web pages</a> and in a <a
     2312href="../sphinxdocs/build/latex/GSASIIdoc.pdf">PDF document</a>. This
     2313documentation is created from the Python source code files using Sphinx. </span></p>
    23132314
    23142315<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     
    23402341href="Integration%20of%20area%20detector%20data%20in%20GSAS.htm"><span
    23412342style='font-weight:normal'>2-D Image integration</span></a><o:p></o:p></strong></p>
     2343
     2344<p class=MsoNormal><strong><a href="Strain%20fitting%20of%202D%20data%20in%20GSAS-II.htm"><span
     2345style='font-weight:normal'>2-D Strain data fitting</span></a><o:p></o:p></strong></p>
    23422346
    23432347<p class=MsoNormal><strong>Synchrotron X-ray powder pattern Rietveld refinement<o:p></o:p></strong></p>
     
    23472351class=SpellE><span style='font-weight:normal'>jadarite</span></span></a> &amp; <a
    23482352href="Charge%20Flipping%20-%20sucrose.htm"><span style='font-weight:normal'>sucrose</span></a><o:p></o:p></strong></p>
     2353
     2354<p class=MsoNormal><strong><o:p>&nbsp;</o:p></strong></p>
    23492355
    23502356<p class=MsoNormal><strong><o:p>&nbsp;</o:p></strong></p>
     
    23732379Parameters&quot;</a> item under a &#8216;PWDR&#8217; entry contains information
    23742380about how data were collected, such as the sample temperature <a
    2375 href="#Sample_Parameters">(see below)</a>. The arrow keys (up &amp; down) move
    2376 the selection to successive entries in the data tree; both the data window and
    2377 the associated plot (if any) will change.<o:p></o:p></span></p>
     2381href="#Sample_Parameters">(see below)</a>. The arrow keys (up &amp; down) move the
     2382selection to successive entries in the data tree; both the data window and the
     2383associated plot (if any) will change.<o:p></o:p></span></p>
    23782384
    23792385<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     
    25372543pair distribution function (PDF) controls for each powder pattern selected in
    25382544the dialog box. See <b style='mso-bidi-font-weight:normal'><span
    2539 style='color:#4F81BD;mso-themecolor:accent1'><a href="#PDF_Controls">PDF Controls</a></span></b>
    2540 for further directions.</p>
     2545style='color:#4F81BD;mso-themecolor:accent1'><a href="#PDF_Controls">PDF
     2546Controls</a></span></b> for further directions.</p>
    25412547
    25422548<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25962602style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    25972603class=GramE><b style='mso-bidi-font-weight:normal'>from</b></span><b
    2598 style='mso-bidi-font-weight:normal'> GSAS .EXP file - </b>This reads one phase
    2599 from a GSAS experiment file (name.EXP). The file name is found in a directory
     2604style='mso-bidi-font-weight:normal'> GSAS .EXP file - </b>This reads one phase from
     2605a GSAS experiment file (name.EXP). The file name is found in a directory
    26002606dialog; you can change directories as needed. Only .EXP (or .exp) file names
    26012607are shown. If the selected file has more than one phase, a dialog is shown with
     
    27442750normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F**2 HKL file </b>This
    27452751reads structure factors (as F**2) and sig(F**2) from a SHELX format .<span
    2746 class=SpellE>hkl</span> file. The file names are found in a directory dialog;
    2747 you can change directories as needed. You must know this is the content of this
     2752class=SpellE>hkl</span> file. The file names are found in a directory dialog; you
     2753can change directories as needed. You must know this is the content of this
    27482754file as it will have no internal indication of its contents.<b
    27492755style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
     
    27682774normal'>from</b></span><b style='mso-bidi-font-weight:normal'> CIF file</b>
    27692775This reads structure factors (as F**2 or F) and sig(F**2 or F) from a .CIF (or
    2770 .<span class=SpellE>cif</span>) or .FCF (or .<span class=SpellE>fcf</span>) format
    2771 file. The file names are found in a directory dialog; you can change
     2776.<span class=SpellE>cif</span>) or .FCF (or .<span class=SpellE>fcf</span>)
     2777format file. The file names are found in a directory dialog; you can change
    27722778directories as needed. The internal structure of this file indicates in which
    27732779form the structure factors are used.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
     
    31263132&#8211; this takes you through a sequence of dialog boxes which ask for the
    31273133identities of the atoms involved in the restraint and the value to be assigned
    3128 to the restraint. The <span class=SpellE>esd</span> is given a default value which
    3129 can be changed after the restraints are created.<o:p></o:p></span></p>
     3134to the restraint. The <span class=SpellE>esd</span> is given a default value
     3135which can be changed after the restraints are created.<o:p></o:p></span></p>
    31303136
    31313137<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    31853191style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Delete
    31863192restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    3187 &#8211; this deletes selected restraints from the list. A single click in the
    3188 blank box in the upper left corner of the table will select/deselect all
    3189 restraints.<o:p></o:p></span></p>
     3193&#8211; this deletes selected restraints from the list. A single click in the blank
     3194box in the upper left corner of the table will select/deselect all restraints.<o:p></o:p></span></p>
    31903195
    31913196<h4><a name="Rigid_bodies"><span style='mso-fareast-font-family:"Times New Roman"'>Rigid
     
    33313336<h3>Histograms</h3>
    33323337
    3333 <p class=MsoNormal>These are shown in the data tree with a prefix of &#8216;PWDR&#8217;,
    3334 &#8217;HKLF&#8217;, &#8216;IMG&#8217;, or &#8216;PDF&#8217; and usually a file
    3335 name. These constitute the data sets (&#8216;Histograms&#8217;) to be used by
    3336 GSAS-II for analysis. Selection of these items does not produce any information
    3337 in the data window but does display the data in the Plots Window. They are
    3338 described below.</p>
     3338<p class=MsoNormal>These are shown in the data tree with a prefix of
     3339&#8216;PWDR&#8217;, &#8217;HKLF&#8217;, &#8216;IMG&#8217;, or &#8216;PDF&#8217;
     3340and usually a file name. These constitute the data sets
     3341(&#8216;Histograms&#8217;) to be used by GSAS-II for analysis. Selection of
     3342these items does not produce any information in the data window but does
     3343display the data in the Plots Window. They are described below.</p>
    33393344
    33403345<h3><a name="PWD_Analysis"></a>Powder Histograms - PWDR</h3>
     
    33633368style='mso-bookmark:Comments'><span style='mso-fareast-font-family:"Times New Roman"'>
    33643369&#8211; this produces a &#8216;normal probability&#8217; plot for the
    3365 refinement result as bounded by the limits. The slope and intercept of the curve
    3366 in the central region (-1 &lt; </span></span><span style='mso-bookmark:Comments'><span
    3367 style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span></span><span
     3370refinement result as bounded by the limits. The slope and intercept of the
     3371curve in the central region (-1 &lt; </span></span><span style='mso-bookmark:
     3372Comments'><span style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span></span><span
    33683373style='mso-bookmark:Comments'><span style='mso-fareast-font-family:"Times New Roman"'>/</span></span><span
    33693374style='mso-bookmark:Comments'><span style='font-family:Symbol;mso-fareast-font-family:
     
    33983403style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    33993404style='mso-fareast-font-family:"Times New Roman"'>You can change <span
    3400 class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span> in the &#8216;changed&#8217;
    3401 row as needed. Use the mouse to select the value to be changed (the background
    3402 on the box will be blue or have a black border or a vertical bar will appear in
    3403 the value), then enter the new value and press Enter or click the mouse
    3404 elsewhere in the Limits window. This will set the new value.<o:p></o:p></span></p>
     3405class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span> in the
     3406&#8216;changed&#8217; row as needed. Use the mouse to select the value to be
     3407changed (the background on the box will be blue or have a black border or a
     3408vertical bar will appear in the value), then enter the new value and press
     3409Enter or click the mouse elsewhere in the Limits window. This will set the new
     3410value.<o:p></o:p></span></p>
    34053411
    34063412<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo9'><![if !supportLists]><span
     
    35773583style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span
    35783584style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3579 style='mso-fareast-font-family:"Times New Roman"'>You can introduce single Bragg
    3580 peaks into the background. For each you should specify at least the position.
    3581 Select parameters to refine; usually start with the &#8216;<span class=SpellE>int</span>&#8217;
    3582 coefficients.<o:p></o:p></span></p>
     3585style='mso-fareast-font-family:"Times New Roman"'>You can introduce single
     3586Bragg peaks into the background. For each you should specify at least the
     3587position. Select parameters to refine; usually start with the &#8216;<span
     3588class=SpellE>int</span>&#8217; coefficients.<o:p></o:p></span></p>
    35833589
    35843590<h4><a name="Instrument_Parameters"><u><span style='mso-fareast-font-family:
     
    36583664style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b><span
    36593665style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
    3660 instrument parameters shown to other selected powder patterns. If used, a dialog
    3661 box (Copy parameters) will appear showing the list of available powder
    3662 patterns, you can copy the instrument parameters to any or all of them; select
    3663 &#8216;All&#8217; to copy them to all patterns. Then select &#8216;OK&#8217; to
    3664 do the copy; &#8216;Cancel&#8217; to cancel the operation. The copy will only
    3665 work for instrument parameters that are commensurate with the one that is
    3666 shown, e.g. single radiation patterns will not be updated from K</span><sub><span
     3666instrument parameters shown to other selected powder patterns. If used, a
     3667dialog box (Copy parameters) will appear showing the list of available powder
     3668patterns, you can copy the instrument parameters to any or all of them; select &#8216;All&#8217;
     3669to copy them to all patterns. Then select &#8216;OK&#8217; to do the copy;
     3670&#8216;Cancel&#8217; to cancel the operation. The copy will only work for
     3671instrument parameters that are commensurate with the one that is shown, e.g.
     3672single radiation patterns will not be updated from K</span><sub><span
    36673673style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    36683674style='mso-fareast-font-family:"Times New Roman"'>1</span></sub><span
     
    36833689style='mso-fareast-font-family:"Times New Roman"'>- &#8211; this copies the
    36843690instrument parameter refinement flags shown to other selected powder patterns.
    3685 If used, a dialog box (Copy refinement flags) will appear showing the list of
    3686 available powder patterns, you can copy the instrument parameter refinement
    3687 flags to any or all of them; select &#8216;All&#8217; to copy them to all
    3688 patterns. Then select &#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217; to
    3689 cancel the operation. The copy will only work for instrument parameters that
    3690 are commensurate with the one that is shown, e.g. single radiation patterns
    3691 will not be updated from K</span><sub><span style='font-family:Symbol;
    3692 mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    3693 style='mso-fareast-font-family:"Times New Roman"'>1</span></sub><span
    3694 style='mso-fareast-font-family:"Times New Roman"'>/K</span><sub><span
     3691If used, a dialog box (Copy refinement flags) will appear showing the list of available
     3692powder patterns, you can copy the instrument parameter refinement flags to any
     3693or all of them; select &#8216;All&#8217; to copy them to all patterns. Then
     3694select &#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217; to cancel the
     3695operation. The copy will only work for instrument parameters that are
     3696commensurate with the one that is shown, e.g. single radiation patterns will
     3697not be updated from K</span><sub><span style='font-family:Symbol;mso-fareast-font-family:
     3698"Times New Roman"'>a</span></sub><sub><span style='mso-fareast-font-family:
     3699"Times New Roman"'>1</span></sub><span style='mso-fareast-font-family:"Times New Roman"'>/K</span><sub><span
    36953700style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    36963701style='mso-fareast-font-family:"Times New Roman"'>2</span></sub><span
     
    38133818- &#8211; this copies the sample parameter refinement flags shown to other
    38143819selected powder patterns. If used, a dialog box (Copy refinement flags) will
    3815 appear showing the list of available powder patterns, you can copy the sample parameter
    3816 refinement flags to any or all of them; select &#8216;All&#8217; to copy them
    3817 to all patterns. Then select &#8216;OK&#8217; to do the copy;
     3820appear showing the list of available powder patterns, you can copy the sample
     3821parameter refinement flags to any or all of them; select &#8216;All&#8217; to
     3822copy them to all patterns. Then select &#8216;OK&#8217; to do the copy;
    38183823&#8216;Cancel&#8217; to cancel the operation. <span class=MsoHyperlink><span
    38193824style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
     
    38613866color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> &#8211; this
    38623867fills the table with peak positions. These are selected based on peak tops that
    3863 are substantially above background. Noisy data will give spurious peaks and
    3864 small peaks or shoulders will not be found. Examine results &amp; modify as
    3865 needed.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    3866 none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
     3868are substantially above background. Noisy data will give spurious peaks and small
     3869peaks or shoulders will not be found. Examine results &amp; modify as needed.<span
     3870class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     3871text-underline:none'><o:p></o:p></span></span></span></span></h5>
    38673872
    38683873<h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l11 level2 lfo15;
     
    38913896style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    38923897normal;mso-bidi-font-weight:bold'> &#8211; perform a least squares fit of the
    3893 peaks in Peak List to the data. Any peak parameters, background parameters and instrument
    3894 parameters with refine checked will be varied in this refinement. The
    3895 refinement will proceed until convergence. We suggest you vary the intensity
    3896 along with the background first (the default), then vary the position and
    3897 instrument parameters after. The order will depend on how poor is the initial
     3898peaks in Peak List to the data. Any peak parameters, background parameters and
     3899instrument parameters with refine checked will be varied in this refinement.
     3900The refinement will proceed until convergence. We suggest you vary the
     3901intensity along with the background first (the default), then vary the position
     3902and instrument parameters after. The order will depend on how poor is the initial
    38983903estimate of the instrument parameters (U, V, W, X, Y &amp; SH/L). To determine
    38993904how to proceed, examine in detail the powder pattern difference curve displayed
     
    39153920none;text-underline:none'><span style='mso-list:Ignore'>d.<span
    39163921style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    3917 style='mso-fareast-font-family:"Times New Roman";color:windowtext'>LSQ one
    3918 cycle </span></span><span style='mso-bookmark:Index_Peaks'><span
    3919 style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    3920 normal;mso-bidi-font-weight:bold'>&#8211; perform a single cycle of least
    3921 squares refinement. This can be used in difficult cases to get a refinement
    3922 started toward convergence.<span class=MsoHyperlink><span style='color:windowtext;
    3923 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
     3922style='mso-fareast-font-family:"Times New Roman";color:windowtext'>LSQ one cycle
     3923</span></span><span style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:
     3924"Times New Roman";color:windowtext;font-weight:normal;mso-bidi-font-weight:
     3925bold'>&#8211; perform a single cycle of least squares refinement. This can be
     3926used in difficult cases to get a refinement started toward convergence.<span
     3927class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     3928text-underline:none'><o:p></o:p></span></span></span></span></h5>
    39243929
    39253930<h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l11 level2 lfo15;
     
    40774082<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    40784083window shows the controls and results from indexing of the peaks in the <a
    4079 href="#Index_Peak_List"><span style='color:windowtext;text-decoration:none;
    4080 text-underline:none'>Index_Peak_List</span></a></span><!--[if supportFields]><span
     4084href="#Index_Peak_List"><span class=SpellE><span style='color:windowtext;
     4085text-decoration:none;text-underline:none'>Index_Peak_List</span></span></a></span><!--[if supportFields]><span
    40814086style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element:
    40824087field-begin'></span> REF Index_Peak_List \h </span><![endif]--><span
     
    41924197style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Index
    41934198Cell</span></b></span><span style='mso-bookmark:Reflection_List'><span
    4194 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this starts the
    4195 indexing process. Output will appear on the console and a progress bar dialog
    4196 will appear which tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b>
     4199style='mso-fareast-font-family:"Times New Roman"'> &#8211; this starts the indexing
     4200process. Output will appear on the console and a progress bar dialog will
     4201appear which tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b>
    41974202button will terminate indexing; it may need to be pressed more than once to
    41984203fully terminate the indexing process. Console output shows possible solutions
     
    42454250style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Make
    42464251new phase</span></b></span><span style='mso-bookmark:Reflection_List'><span
    4247 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this creates a new
    4248 phase from the selected unit cell and chosen space group. A dialog box will
    4249 appear asking for a name for this phase. See the new entry under Phases and the
    4250 new lattice parameters will be in the </span></span><a href="#General"><span
     4252style='mso-fareast-font-family:"Times New Roman"'> &#8211; this creates a new phase
     4253from the selected unit cell and chosen space group. A dialog box will appear
     4254asking for a name for this phase. See the new entry under Phases and the new
     4255lattice parameters will be in the </span></span><a href="#General"><span
    42514256style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman";
    4252 color:windowtext;text-decoration:none;text-underline:none'>General</span></span></a><span
    4253 style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman"'>
    4254 window for that phase.<span class=MsoHyperlink><span style='color:windowtext;
    4255 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
     4257color:windowtext;text-decoration:none;text-underline:none'>General</span></span><span
     4258style='mso-bookmark:Reflection_List'></span></a><span style='mso-bookmark:Reflection_List'><span
     4259style='mso-fareast-font-family:"Times New Roman"'> window for that phase.<span
     4260class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     4261text-underline:none'><o:p></o:p></span></span></span></span></p>
    42564262
    42574263<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l16 level1 lfo17'><span
     
    42644270&#8211; </span></b></span><span style='mso-bookmark:Reflection_List'><span
    42654271style='mso-fareast-font-family:"Times New Roman"'>the plot will show (red
    4266 dashed lines) the<b style='mso-bidi-font-weight:normal'> </b>generated reflection
    4267 positions for the choice; compare them to the peak positions (blue lines) and
    4268 any unfitted peaks for conformation.<span class=MsoHyperlink><span
     4272dashed lines) the<b style='mso-bidi-font-weight:normal'> </b>generated
     4273reflection positions for the choice; compare them to the peak positions (blue
     4274lines) and any unfitted peaks for conformation.<span class=MsoHyperlink><span
    42694275style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    42704276
     
    44114417
    44124418<p class=MsoNormal>This window shows whatever comment lines found in a
    4413 &#8220;metadata&#8221; file when the image data file was read by GSAS-II. If
    4414 you are lucky, there will be useful information here (e.g. sample name, date
     4419&#8220;metadata&#8221; file when the image data file was read by GSAS-II. If you
     4420are lucky, there will be useful information here (e.g. sample name, date
    44154421collected, wavelength used, etc.). If not, this window will be blank. The text
    44164422is read-only.</p>
     
    45684574</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    45694575style='mso-fareast-font-family:"Times New Roman"'>Space group</span></b><span
    4570 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this should be set
    4571 when the phase is initialized; it can be changed later. Be careful about the
    4572 impact on Atom site symmetry and multiplicity if you do. GSAS-II will recognize
    4573 any legal space group symbol using the short Hermann-Mauguin forms; put a space
     4576style='mso-fareast-font-family:"Times New Roman"'> &#8211; this should be set when
     4577the phase is initialized; it can be changed later. Be careful about the impact
     4578on Atom site symmetry and multiplicity if you do. GSAS-II will recognize any
     4579legal space group symbol using the short Hermann-Mauguin forms; put a space
    45744580between the axial fields (e.g. &#8216;F d 3 m&#8217; not &#8216;Fd3m&#8217;).
    45754581For space groups with a choice of origin (e.g. F d 3 m), GSAS-II always uses
     
    47014707style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    47024708</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    4703 "Times New Roman"'>If there are entries in the Atoms page then the Elements
    4704 table is shown next on the General page; you may select the isotope (only
    4705 relevant for neutron diffraction experiments). The density (just above the
    4706 Elements) is computed depending on this choice, the unit cell volume and the
    4707 atom fractions/site multiplicities in the entries on the Atoms page.<span
     4709"Times New Roman"'>If there are entries in the Atoms page then the Elements table
     4710is shown next on the General page; you may select the isotope (only relevant
     4711for neutron diffraction experiments). The density (just above the Elements) is
     4712computed depending on this choice, the unit cell volume and the atom
     4713fractions/site multiplicities in the entries on the Atoms page.<span
    47084714class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    47094715
     
    47264732to perform a Pawley refinement as opposed to a Rietveld refinement for this
    47274733phase. <b style='mso-bidi-font-weight:normal'>NB:</b> you probably should clear
    4728 the <b style='mso-bidi-font-weight:normal'>Histogram scale factor</b>
    4729 refinement flag (found in <b style='mso-bidi-font-weight:normal'>Sample
    4730 parameters</b> for the powder data set) as it cannot be refined simultaneously
    4731 with the Pawley reflection intensities.<span class=MsoHyperlink><span
    4732 style='color:windowtext'><o:p></o:p></span></span></span></p>
     4734the <b style='mso-bidi-font-weight:normal'>Histogram scale factor</b> refinement
     4735flag (found in <b style='mso-bidi-font-weight:normal'>Sample parameters</b> for
     4736the powder data set) as it cannot be refined simultaneously with the Pawley
     4737reflection intensities.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    47334738
    47344739<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    48264831class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
    48274832"Times New Roman"'>k-Factor</span></b></span><span style='mso-fareast-font-family:
    4828 "Times New Roman"'> &#8211; This is the threshold on the density map, all
    4829 densities below this are charge flipped.</span></p>
     4833"Times New Roman"'> &#8211; This is the threshold on the density map, all densities
     4834below this are charge flipped.</span></p>
    48304835
    48314836<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    48804885color:windowtext;text-decoration:none;text-underline:none'>MC/SA algorithm</span></b></span><span
    48814886class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    4882 color:windowtext;text-decoration:none;text-underline:none'> &#8211; This selects
    4883 the type of jump to be used for each MC/SA trial.<o:p></o:p></span></span></p>
     4887color:windowtext;text-decoration:none;text-underline:none'> &#8211; This
     4888selects the type of jump to be used for each MC/SA trial.<o:p></o:p></span></span></p>
    48844889
    48854890<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    49634968</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    49644969style='mso-fareast-font-family:"Times New Roman"'>Shift LMB</span></b><span
    4965 style='mso-fareast-font-family:"Times New Roman"'> &#8211; on a row number
    4966 selects all atoms from last selection to the selected row (or top is none
    4967 previously selected).<span class=MsoHyperlink><span style='color:windowtext;
    4968 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     4970style='mso-fareast-font-family:"Times New Roman"'> &#8211; on a row number selects
     4971all atoms from last selection to the selected row (or top is none previously
     4972selected).<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     4973none;text-underline:none'><o:p></o:p></span></span></span></p>
    49694974
    49704975<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    49874992style='mso-fareast-font-family:"Times New Roman"'>Alt LMB</span></b><span
    49884993style='mso-fareast-font-family:"Times New Roman"'> &#8211; on a row number
    4989 selects that atom for moving; the status line at bottom of window will show
    4990 name of atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b>
    4991 again to select a target row for this atom; insertion will be before this row
    4992 and the table will be updated to show the change. NB: the <b style='mso-bidi-font-weight:
     4994selects that atom for moving; the status line at bottom of window will show name
     4995of atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b> again
     4996to select a target row for this atom; insertion will be before this row and the
     4997table will be updated to show the change. NB: the <b style='mso-bidi-font-weight:
    49934998normal'>Draw Atoms</b> list is not updated by this change.<span
    49944999class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     
    51115116style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
    51125117&#8216;<b style='mso-bidi-font-weight:normal'>Edit&#8217; - </b>The edit menu
    5113 shows operations that can be performed on your selected atoms. You must select one
    5114 or more atoms before using many of the menu items.</p>
     5118shows operations that can be performed on your selected atoms. You must select
     5119one or more atoms before using many of the menu items.</p>
    51155120
    51165121<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    51725177atoms according to position in table (e.g. Na(1) for Na atom as 1<sup>st</sup>
    51735178atom in list in row &#8216;0&#8217;). <b style='mso-bidi-font-weight:normal'>Type</b>
    5174 will give periodic table popup; selected element valence will be used for all selected
    5175 atoms and atoms names will be changed. <b style='mso-bidi-font-weight:normal'>I/A</b>
    5176 will give popup with choices to be used for all selected atoms. <b
    5177 style='mso-bidi-font-weight:normal'>x,y,z</b> will give popup for shift to be
    5178 applied to the parameter for all selected atoms. <span class=SpellE><b
     5179will give periodic table popup; selected element valence will be used for all
     5180selected atoms and atoms names will be changed. <b style='mso-bidi-font-weight:
     5181normal'>I/A</b> will give popup with choices to be used for all selected atoms.
     5182<b style='mso-bidi-font-weight:normal'>x,y,z</b> will give popup for shift to
     5183be applied to the parameter for all selected atoms. <span class=SpellE><b
    51795184style='mso-bidi-font-weight:normal'>Uiso</b></span> and <span class=SpellE><b
    51805185style='mso-bidi-font-weight:normal'>frac</b></span> will give popup for new
     
    52355240style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    52365241style='mso-bidi-font-weight:normal'>Atom Selection from table</b>: select
    5237 individual atoms by a left click of the mouse when pointed at the left most
    5238 column (atom numbers) of the atom display; hold down the Ctrl key to add to
    5239 your selection; a previously selected atom will be deselected; hold down Shift
    5240 key to select from last in list selected to current selection. A selected atom
    5241 will be highlighted (in grey) and the atoms will be shown in green on the plot.
     5242individual atoms by a left click of the mouse when pointed at the left most column
     5243(atom numbers) of the atom display; hold down the Ctrl key to add to your
     5244selection; a previously selected atom will be deselected; hold down Shift key
     5245to select from last in list selected to current selection. A selected atom will
     5246be highlighted (in grey) and the atoms will be shown in green on the plot.
    52425247Selection without the Ctrl key will clear previous selections. A double left
    52435248click in the (empty) upper left box will select or deselect all atoms.</p>
     
    52625267style='mso-bidi-font-weight:normal'>Double left click a Name, Type and Sym Op
    52635268column heading</b>: a dialog box is shown that allows you to select all atoms
    5264 with that characteristic. For example, selecting the Type column will show all the
    5265 atom types; your choice will then cause all those atoms to be selected.</p>
     5269with that characteristic. For example, selecting the Type column will show all
     5270the atom types; your choice will then cause all those atoms to be selected.</p>
    52665271
    52675272<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span
     
    54085413Microsoft Word). Shown are the atom coordinates transformed to Cartesian best
    54095414plane coordinates where the largest range is over the X-axis and the smallest
    5410 is over the Z-axis with the origin at the unweighted center of the selection. Root
    5411 mean square displacements along each axis for the best plane are also listed.
    5412 The Z-axis RMS value indicates the flatness of the proposed plane. <b
     5415is over the Z-axis with the origin at the unweighted center of the selection.
     5416Root mean square displacements along each axis for the best plane are also
     5417listed. The Z-axis RMS value indicates the flatness of the proposed plane. <b
    54135418style='mso-bidi-font-weight:normal'>NB</b>: if you select (e.g. all) atoms then
    54145419Best plane will give Cartesian coordinates for these atoms with respect to a
     
    54645469"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    54655470</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Peak
    5466 Selection from table</b>: select individual atoms by a left click of the mouse
    5467 when pointed at the left most column (atom numbers) of the atom display; hold
    5468 down the Ctrl key to add to your selection; a previously selected atom will be
     5471Selection from table</b>: select individual atoms by a left click of the mouse when
     5472pointed at the left most column (atom numbers) of the atom display; hold down
     5473the Ctrl key to add to your selection; a previously selected atom will be
    54695474deselected; hold down Shift key to select from last in list selected to current
    54705475selection. A selected atom will be highlighted (in grey) and the atoms will be
     
    55365541are selected, this calculates the distance between them. If 3 peaks are
    55375542selected this calculates the angle between them; NB: selection order matters.
    5538 If selection is not 2 or 3 peaks this is ignored. Output is on the console window.</span></p>
     5543If selection is not 2 or 3 peaks this is ignored. Output is on the console
     5544window.</span></p>
    55395545
    55405546<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    56235629clicking on the box or by selecting one and then selecting the column (a single
    56245630click on the column heading). Then type &#8216;y&#8217; to set the refine flags
    5625 or &#8216;n&#8217; to clear the flags. You should deselect those reflections
    5626 that fall below the lower limit or above the upper limit of the powder pattern
     5631or &#8216;n&#8217; to clear the flags. You should deselect those reflections that
     5632fall below the lower limit or above the upper limit of the powder pattern
    56275633otherwise you may have a singular matrix error in your Pawley refinement.</span></p>
    56285634
     
    56605666
    56615667<p class=MsoNormal align=center style='text-align:center'><span
     5668style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
     5669
     5670<p class=MsoNormal align=center style='text-align:center'><span
    56625671style='mso-bookmark:Pawley'><span class=MsoHyperlink><span style='color:windowtext;
    56635672text-decoration:none;text-underline:none'><o:p>&nbsp;</o:p></span></span></span></p>
     
    56765685
    56775686</span></span></a></div>
     5687
     5688<p class=MsoNormal align=center style='text-align:center'><span
     5689style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    56785690
    56795691<p class=MsoNormal align=center style='text-align:center'><span
     
    58515863"Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    58525864</span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    5853 normal'>d</b></span><b style='mso-bidi-font-weight:normal'>: offset down</b> -
    5854 for a waterfall plot of multiple powder profiles, increase the offset down.
    5855 Does not apply if only one pattern.</span></p>
     5865normal'>d</b></span><b style='mso-bidi-font-weight:normal'>: offset down</b> - for
     5866a waterfall plot of multiple powder profiles, increase the offset down. Does
     5867not apply if only one pattern.</span></p>
    58565868
    58575869<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    62346246
    62356247<p class=MsoNormal><span style='mso-bookmark:Pawley'>This plot shows the atoms
    6236 of the crystal structure. The atoms are displayed according to the controls in
    6237 the </span><a href="gsasII.html"><span style='mso-bookmark:Pawley'><span
     6248of the crystal structure. The atoms are displayed according to the controls in the
     6249</span><a href="gsasII.html"><span style='mso-bookmark:Pawley'><span
    62386250style='color:windowtext;text-decoration:none;text-underline:none'>Draw Options</span></span></a><span
    62396251style='mso-bookmark:Pawley'> page.</span></p>
     
    62566268
    62576269</span></span></a></div>
     6270
     6271<p class=MsoNormal align=center style='text-align:center'><span
     6272style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    62586273
    62596274<p class=MsoNormal align=center style='text-align:center'><span
  • trunk/help/gsasII_files/props011.xml

    r988 r1197  
    11<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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