Changeset 608 for trunk/help/gsasII.html


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Timestamp:
May 9, 2012 11:13:49 AM (10 years ago)
Author:
vondreele
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  • trunk/help/gsasII.html

    r599 r608  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>86</o:Revision>
     27  <o:Revision>87</o:Revision>
    2828  <o:TotalTime>2820</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2012-05-07T19:57:00Z</o:LastSaved>
     30  <o:LastSaved>2012-05-08T16:10:00Z</o:LastSaved>
    3131  <o:Pages>8</o:Pages>
    32   <o:Words>7204</o:Words>
    33   <o:Characters>41065</o:Characters>
     32  <o:Words>7207</o:Words>
     33  <o:Characters>41080</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    3535  <o:Lines>342</o:Lines>
    3636  <o:Paragraphs>96</o:Paragraphs>
    37   <o:CharactersWithSpaces>48173</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>48191</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
    605605        mso-font-kerning:14.0pt;}
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    609608        color:blue;
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    19641963 <o:lock v:ext="edit" aspectratio="t"/>
    19651964</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1026" type="#_x0000_t75"
    1966  alt="Description: Description: Description: Description: Description: Description: Description: GSAS-II logo"
     1965 alt="Description: Description: Description: Description: Description: Description: Description: Description: GSAS-II logo"
    19671966 style='position:absolute;margin-left:44.8pt;margin-top:0;width:96pt;height:96pt;
    19681967 z-index:251657728;visibility:visible;mso-wrap-style:square;
     
    19771976</v:shape><![endif]--><![if !vml]><img width=128 height=128 src=gsas2logo.png
    19781977align=right
    1979 alt="Description: Description: Description: Description: Description: Description: Description: GSAS-II logo"
     1978alt="Description: Description: Description: Description: Description: Description: Description: Description: GSAS-II logo"
    19801979v:shapes="Picture_x0020_2"><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Help
    19811980for GSAS-II<o:p></o:p></span></h1>
     
    20092008normal'>Powder pattern peak picking, fitting and indexing</span></a><o:p></o:p></strong></p>
    20102009
    2011 <p class=MsoNormal><strong>Lab X-ray powder pattern Rietveld refinement
    2012 (future)<o:p></o:p></strong></p>
     2010<p class=MsoNormal><strong><a href="Laboratory%20X.htm"><span style='font-weight:
     2011normal'>Lab X-ray powder patt</span><span style='font-weight:normal'>ern
     2012Rietveld refinement</span></a><o:p></o:p></strong></p>
    20132013
    20142014<p class=MsoNormal><strong><a href="Neutron%20CW%20Powder%20Data.htm"><span
     
    20162016constraints</span></a><o:p></o:p></strong></p>
    20172017
    2018 <p class=MsoNormal><strong>Synchrotron X-ray powder pattern Rietveld refinement
    2019 (future)<o:p></o:p></strong></p>
     2018<p class=MsoNormal><strong>Synchrotron X-ray powder pattern Rietveld refinement<o:p></o:p></strong></p>
    20202019
    20212020<p class=MsoNormal><span class=GramE><strong>Crystal structure drawing (balls
     
    21322131style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    21332132style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in
    2134 powder diffraction patterns (multiple patterns can be selected). GSAS-II can
    2135 read most of the old GSAS powder format files with the position in <span
     2133powder diffraction patterns (multiple patterns can be selected). GSAS-II can read
     2134most of the old GSAS powder format files with the position in <span
    21362135class=SpellE>centidegrees</span> 2-theta. It can also read &#8220;<span
    21372136class=SpellE>xye</span>&#8221; format files used by <span class=SpellE>topas</span>
     
    21472146style='mso-bidi-font-weight:normal'>Read image data&#8230;</b> - Read in 2-D
    21482147powder diffraction images (multiple patterns can be selected). GSAS-II can read
    2149 many different image file formats including MAR345 files, Quantum ADSC files,
    2150 and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of these
    2151 formats have data fields that should contain relevant information for the
    2152 exposure (e.g. wavelength), these are rarely filled in correctly by the data
    2153 acquisition software. Thus, you should have separately noted this information
    2154 as it will be needed</p>
     2148many different image file formats including MAR345 files, Quantum ADSC files, and
     2149tiff files from Perkin-Elmer, Pilatus, and GE. Although many of these formats
     2150have data fields that should contain relevant information for the exposure
     2151(e.g. wavelength), these are rarely filled in correctly by the data acquisition
     2152software. Thus, you should have separately noted this information as it will be
     2153needed</p>
    21552154
    21562155<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    22292228pair distribution function (PDF) controls for each powder pattern selected in
    22302229the dialog box. See <b style='mso-bidi-font-weight:normal'><span
    2231 style='color:#4F81BD;mso-themecolor:accent1'><a href="#PDF_Controls">PDF
    2232 Controls</a></span></b> for further directions.</p>
     2230style='color:#4F81BD;mso-themecolor:accent1'><a href="#PDF_Controls">PDF Controls</a></span></b>
     2231for further directions.</p>
    22332232
    22342233<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    30133012fixed. All values can be changed in this window.<o:p></o:p></span></p>
    30143013
    3015 <h5><a name="Peak_List"></a><a name="Powder_Peaks"><span style='mso-bookmark:
    3016 Peak_List'><span style='mso-fareast-font-family:"Times New Roman"'>What can I
    3017 do here?</span></span></a><span style='mso-bookmark:Powder_Peaks'><span
    3018 style='mso-bookmark:Peak_List'><span style='mso-fareast-font-family:"Times New Roman";
     3014<h5><a name="Powder_Peaks"></a><a name="Peak_List"><span style='mso-bookmark:
     3015Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>What can
     3016I do here?</span></span></a><span style='mso-bookmark:Peak_List'><span
     3017style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    30193018color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'><o:p></o:p></span></span></span></h5>
    30203019
    30213020<h5 style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo11'><span
    3022 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
     3021style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
    30233022style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30243023normal;mso-bidi-font-weight:bold'><span style='mso-list:Ignore'>1.<span
     
    30263025style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30273026normal;mso-bidi-font-weight:bold'>Menu &#8216;</span></span></span><span
    3028 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
     3027style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    30293028style='mso-fareast-font-family:"Times New Roman";color:windowtext'>File&#8217;</span></span></span><span
    3030 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
     3029style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    30313030style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    30323031normal;mso-bidi-font-weight:bold'> &#8211; <o:p></o:p></span></span></span></h5>
     
    30343033<p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto;
    30353034text-indent:-.25in;mso-list:l6 level2 lfo11;tab-stops:list 1.0in'><span
    3036 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
     3035style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
    30373036style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    30383037style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    30393038style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy</span></b></span></span><span
    3040 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
     3039style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    30413040style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
    30423041sample parameters shown to other selected powder patterns. If used, a dialog
     
    30483047<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
    30493048text-indent:-.25in;mso-list:l6 level2 lfo11;tab-stops:list 1.0in'><span
    3050 style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><![if !supportLists]><span
     3049style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><![if !supportLists]><span
    30513050style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
    30523051style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    30533052style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy
    3054 flags</span></b></span></span><span style='mso-bookmark:Powder_Peaks'><span
    3055 style='mso-bookmark:Peak_List'><span style='mso-fareast-font-family:"Times New Roman"'>
     3053flags</span></b></span></span><span style='mso-bookmark:Peak_List'><span
     3054style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman"'>
    30563055- &#8211; this copies the sample parameter refinement flags shown to other
    30573056selected powder patterns. If used, a dialog box (Copy refinement flags) will
     
    30613060&#8216;Cancel&#8217; to cancel the operation. <o:p></o:p></span></span></span></p>
    30623061
    3063 <h4><span style='mso-bookmark:Powder_Peaks'><span style='mso-bookmark:Peak_List'><span
     3062<h4><span style='mso-bookmark:Peak_List'><span style='mso-bookmark:Powder_Peaks'><span
    30643063style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></span><span
    30653064style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
     
    33963395style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Refine
    33973396unit cell</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    3398 &#8211; set this flag to refine the unit cell parameters in a Rietveld or
    3399 Pawley refinement. The actual parameters refined are the symmetry allowed terms
    3400 (A<sub>0</sub>-A<sub>5</sub>) in the expression</span><i style='mso-bidi-font-style:
    3401 normal'><span style='font-family:"Cambria Math","serif";mso-fareast-font-family:
    3402 "Times New Roman"'><br>
     3397&#8211; set this flag to refine the unit cell parameters in a Rietveld or Pawley
     3398refinement. The actual parameters refined are the symmetry allowed terms (A<sub>0</sub>-A<sub>5</sub>)
     3399in the expression</span><i style='mso-bidi-font-style:normal'><span
     3400style='font-family:"Cambria Math","serif";mso-fareast-font-family:"Times New Roman"'><br>
    34033401</span></i><!--[if gte msEquation 12]><m:oMathPara><m:oMath><m:sSup><m:sSupPr><span
    34043402    style='font-family:"Cambria Math","serif";mso-ascii-font-family:"Cambria Math";
     
    35543552rendered as lines, van der Waals radii balls, sticks, balls &amp; sticks,
    35553553ellipsoids &amp; sticks or <span class=SpellE>polyhedra</span>. There are two
    3556 menus for this tab; Edit allows modification of the list of atoms to be rendered
    3557 and Compute gives some options for geometric characterization of selected
    3558 atoms.</p>
     3554menus for this tab; Edit allows modification of the list of atoms to be
     3555rendered and Compute gives some options for geometric characterization of
     3556selected atoms.</p>
    35593557
    35603558<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    38053803
    38063804<p class=MsoNormal>This gives the list (magnitude, x y &amp; z) of all peaks
    3807 found within the unit cell from the last Fourier map search sorted in order of decreasing
    3808 peak magnitude. The crystal structure plot shows each peak position as a white
    3809 3-D cross.</p>
     3805found within the unit cell from the last Fourier map search sorted in order of
     3806decreasing peak magnitude. The crystal structure plot shows each peak position
     3807as a white 3-D cross.</p>
    38103808
    38113809<h5>What can I do here?</h5>
     
    38723870mso-no-proof:yes'><img border=0 width=225 height=31 id="_x0000_i1032"
    38733871src=graphbar.jpg
    3874 alt="Description: Description: Description: Description: Description: Description: Description: D:\pyGSAS\help\graphbar.jpg"></span><span
     3872alt="Description: Description: Description: Description: Description: Description: Description: Description: D:\pyGSAS\help\graphbar.jpg"></span><span
    38753873style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    38763874
     
    39233921
    39243922<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    3925 powder patterns that are part of your project are shown on this page. They can
    3926 be displayed as a stack of powder patterns, just a single pattern or as a
    3927 contour image of the peak intensities. What can be done here will depend on
    3928 which is displayed and on which item in the GSAS-II data tree you have
    3929 selected.<o:p></o:p></span></p>
     3923powder patterns that are part of your project are shown on this page. They can be
     3924displayed as a stack of powder patterns, just a single pattern or as a contour
     3925image of the peak intensities. What can be done here will depend on which is
     3926displayed and on which item in the GSAS-II data tree you have selected.<o:p></o:p></span></p>
    39303927
    39313928<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    39463943style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>On
    39473944the plot status line<b style='mso-bidi-font-weight:normal'> &#8216;key
    3948 press&#8217; </b>&#8211; you can either press the key on the key board or
    3949 select from the pull down menu. For line plots:</p>
     3945press&#8217; </b>&#8211; you can either press the key on the key board or select
     3946from the pull down menu. For line plots:</p>
    39503947
    39513948<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    41504147style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Move
    41514148the mouse cursor across the plot. If on a diagonal cell, the parameter name,
    4152 value and <span class=SpellE>esd</span> is shown both as a tool tip and in the
    4153 right hand portion of the status bar. If the cursor is off the diagonal, the
    4154 two parameter names and their covariance are shown in the tool tip and the
    4155 status bar.</p>
     4149value and <span class=SpellE>esd</span> is shown both as a tool tip and in the right
     4150hand portion of the status bar. If the cursor is off the diagonal, the two
     4151parameter names and their covariance are shown in the tool tip and the status
     4152bar.</p>
    41564153
    41574154<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo23'><![if !supportLists]><span
     
    42024199<span class=GramE>q(</span>=2</span><span style='font-family:Symbol;mso-fareast-font-family:
    42034200"Times New Roman"'>p</span><span style='mso-fareast-font-family:"Times New Roman"'>/d)
    4204 from the Gaussian and Lorentzian parts of the profile function. The computed curves
    4205 are based on the values of U, V, W, X and Y shown in the Instrument Parameters
    4206 window in parentheses. These are the values for the instrument contribution
    4207 that were set when the powder pattern was first read in to GSAS-II. If
    4208 individual peak fitting has been performed, the values of &#8216;sig&#8217;
    4209 &amp; &#8216;gam&#8217; for the peaks are plotted as &#8216;+&#8217;; these are
    4210 computed from the fitted values of U, V, W, X and Y as well as any sig or gam
    4211 individually refined.<o:p></o:p></span></p>
     4201from the Gaussian and Lorentzian parts of the profile function. The computed
     4202curves are based on the values of U, V, W, X and Y shown in the Instrument
     4203Parameters window in parentheses. These are the values for the instrument
     4204contribution that were set when the powder pattern was first read in to
     4205GSAS-II. If individual peak fitting has been performed, the values of
     4206&#8216;sig&#8217; &amp; &#8216;gam&#8217; for the peaks are plotted as
     4207&#8216;+&#8217;; these are computed from the fitted values of U, V, W, X and Y
     4208as well as any sig or gam individually refined.<o:p></o:p></span></p>
    42124209
    42134210<h4><span style='mso-fareast-font-family:"Times New Roman"'>Texture </span></h4>
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