Changeset 5481


Ignore:
Timestamp:
Jan 26, 2023 7:53:10 AM (10 months ago)
Author:
vondreele
Message:

fix help

Location:
trunk/help
Files:
46 added
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/help/gsasII.html

    r5480 r5481  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele, Robert B.</o:LastAuthor>
    27   <o:Revision>228</o:Revision>
    28   <o:TotalTime>8353</o:TotalTime>
     27  <o:Revision>229</o:Revision>
     28  <o:TotalTime>8356</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2022-10-06T18:08:00Z</o:LastSaved>
     30  <o:LastSaved>2023-01-26T14:53:00Z</o:LastSaved>
    3131  <o:Pages>44</o:Pages>
    3232  <o:Words>18360</o:Words>
    33   <o:Characters>104655</o:Characters>
     33  <o:Characters>104656</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    3535  <o:Lines>872</o:Lines>
    3636  <o:Paragraphs>245</o:Paragraphs>
    37   <o:CharactersWithSpaces>122770</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>122771</o:CharactersWithSpaces>
    3838  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
     
    4747 <w:WordDocument>
    4848  <w:View>Print</w:View>
     49  <w:Zoom>148</w:Zoom>
    4950  <w:TrackMoves>false</w:TrackMoves>
    5051  <w:TrackFormatting/>
     
    51365137<p class=MsoNormal>This is where to find help on various GSAS-II windows and
    51375138plots. Note that GSAS-II operates with three windows: the main <a
    5138 href="#_1._GSAS-II_Data">GSAS-II data tree</a> section, which provides a
    5139 hierarchical view of the current project on the left and the <a
    5140 href="#Data_Frame">GSAS-II data editing</a> section, which shows the contents
    5141 of a particular section of the project, where values can be examined and
    5142 changed; The second is the <a href="#_3._GSAS-II_Plots">GSAS-II Plots</a>
    5143 window, which shows graphical representations of the results. The third is a
    5144 console window, which has printout information that can be selected, cut &amp;
    5145 pasted into a document. </p>
     5139href="#_1._GSAS-II_Data">GSAS-II data tree</a> section, which provides a hierarchical
     5140view of the current project on the left and the <a href="#Data_Frame">GSAS-II
     5141data editing</a> section, which shows the contents of a particular section of
     5142the project, where values can be examined and changed; The second is the <a
     5143href="#_3._GSAS-II_Plots">GSAS-II Plots</a> window, which shows graphical
     5144representations of the results. The third is a console window, which has
     5145printout information that can be selected, cut &amp; pasted into a document. </p>
    51465146
    51475147<h2><a name=Index><span style='mso-fareast-font-family:"Times New Roman"'>Help
     
    52405240Window</span></span><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
    52415241
    5242 <p class=MsoNormal>This window presents all the graphical material as a
    5243 multipage tabbed set of plots utilizing the matplotlib python package. Each
    5244 page containing a graph or plot has a tool bar with the controls</p>
     5242<p class=MsoNormal>This window presents all the graphical material as a multipage
     5243tabbed set of plots utilizing the matplotlib python package. Each page
     5244containing a graph or plot has a tool bar with the controls</p>
     5245
     5246<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    52455247
    52465248<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    52505252  cropbottom="2353f" cropleft="535f" cropright="28388f"/>
    52515253</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=24
    5252 src="gsasII_files/image003.png" alt="GSAS-II plots: NiTi-C.gpx" v:shapes="Picture_x0020_1"><![endif]></span><span
     5254src="gsasII_files/image002.png" alt="GSAS-II plots: NiTi-C.gpx" v:shapes="Picture_x0020_1"><![endif]></span><span
    52535255class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    52545256mso-fareast-theme-font:minor-fareast;color:windowtext;text-decoration:none;
     
    53025304style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    53035305Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5304 </span></span></span><![endif]>Save - allows you to save the currently displayed
    5305 plot in one of several graphical formats suitable for printing or insertion in
    5306 a document. </p>
     5306</span></span></span><![endif]>Save - allows you to save the currently
     5307displayed plot in one of several graphical formats suitable for printing or
     5308insertion in a document. </p>
    53075309
    53085310<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l19 level1 lfo1'><![if !supportLists]><span
     
    60146016style='font-size:10.0pt'>.partials</span></tt> where <tt><i><span
    60156017style='font-size:10.0pt'>project</span></i></tt> is the GSAS-II project (.gpx)
    6016 name. This file is intended for internal use in GSAS-II and will be deleted if additional
    6017 refinements are performed (making the information in them obsolete; use this
    6018 menu command to recreate them if needed.) When the <tt><span style='font-size:
    6019 10.0pt'>.partials</span></tt> file is created, the user can optionally choose
    6020 to export the intensity information in a series of ASCII files named <tt><i><span
    6021 style='font-size:10.0pt'>prefix</span></i></tt><tt><span style='font-size:10.0pt'>_part_</span></tt><i>N</i><tt><span
    6022 style='font-size:10.0pt'>.csv</span></tt>, which can be read by spreadsheets
    6023 and most scientific software. </p>
     6018name. This file is intended for internal use in GSAS-II and will be deleted if
     6019additional refinements are performed (making the information in them obsolete;
     6020use this menu command to recreate them if needed.) When the <tt><span
     6021style='font-size:10.0pt'>.partials</span></tt> file is created, the user can
     6022optionally choose to export the intensity information in a series of ASCII
     6023files named <tt><i><span style='font-size:10.0pt'>prefix</span></i></tt><tt><span
     6024style='font-size:10.0pt'>_part_</span></tt><i>N</i><tt><span style='font-size:
     602510.0pt'>.csv</span></tt>, which can be read by spreadsheets and most scientific
     6026software. </p>
    60246027
    60256028<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo5'><![if !supportLists]><span
     
    62876290
    62886291<p class=MsoListParagraphCxSpLast style='margin-left:.75in;mso-add-space:auto'><span
    6289 style='mso-bookmark:FPAinput'>Description of the Topas-style fundamental parameters
    6290 used as FPA input for GSAS-II</span> </p>
     6292style='mso-bookmark:FPAinput'>Description of the Topas-style fundamental
     6293parameters used as FPA input for GSAS-II</span> </p>
    62916294
    62926295<div align=center>
     
    67476750  mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;
    67486751  mso-border-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
    6749   <p class=MsoNormal>Width of transition region from high-intensity, roughly flat
    6750   region of the x-ray tube output to the to the tube tails region as a fraction
    6751   of the IBM bandwidth</p>
     6752  <p class=MsoNormal>Width of transition region from high-intensity, roughly
     6753  flat region of the x-ray tube output to the to the tube tails region as a
     6754  fraction of the IBM bandwidth</p>
    67526755  </td>
    67536756 </tr>
     
    68166819style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    68176820Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    6818 </span></span></span><![endif]><b>Structure Factor</b> - Reads single crystal input
    6819 from a variety of file types. Results are placed in the GSAS-II data tree as
    6820 ‘HKLF file name’ </p>
     6821</span></span></span><![endif]><b>Structure Factor</b> - Reads single crystal
     6822input from a variety of file types. Results are placed in the GSAS-II data tree
     6823as ‘HKLF file name’ </p>
    68216824
    68226825<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     
    68246827style='font-family:"Courier New";mso-fareast-font-family:"Courier New"'><span
    68256828style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    6826 </span></span></span><![endif]><b>F**2 HKL file</b> - This reads squared
    6827 structure factors (as F**2) and sig(F**2) from a SHELX format .hkl file. The
    6828 file names are found in a directory dialog; you can change directories as
    6829 needed. You must know the file contains structure factors (as F**2) as the file
    6830 itself has no internal indication of this. </p>
     6829</span></span></span><![endif]><b>F**2 HKL file</b> - This reads squared structure
     6830factors (as F**2) and sig(F**2) from a SHELX format .hkl file. The file names
     6831are found in a directory dialog; you can change directories as needed. You must
     6832know the file contains structure factors (as F**2) as the file itself has no
     6833internal indication of this. </p>
    68316834
    68326835<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     
    68616864the correct format from the list.</p>
    68626865
    6863 <p class=MsoNormal style='margin-left:.25in;text-indent:.25in'>There are
    6864 specific importers for incommensurate or twinned single crystal data as well as
    6865 data from specific neutron diffractometers.</p>
     6866<p class=MsoNormal style='margin-left:.25in;text-indent:.25in'>There are specific
     6867importers for incommensurate or twinned single crystal data as well as data
     6868from specific neutron diffractometers.</p>
    68666869
    68676870<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l48 level1 lfo13'><![if !supportLists]><span
     
    69176920auto'>GSAS-II uses separate routines to write out files with information inside
    69186921GSAS-II. These routines can be created and customized easily. See the <a
    6919 href="https://gsas-ii.readthedocs.io/en/latest/exports.html">GSAS-II Export Modules
    6920 section</a> of the <a href="#Programmers"><strong>Programmers documentation</strong></a>
    6921 for more information on this. Since it is easy to support new formats, the
    6922 documentation below may not list all supported formats. <span style='mso-fareast-font-family:
    6923 "Times New Roman";mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
     6922href="https://gsas-ii.readthedocs.io/en/latest/exports.html">GSAS-II Export
     6923Modules section</a> of the <a href="#Programmers"><strong>Programmers
     6924documentation</strong></a> for more information on this. Since it is easy to
     6925support new formats, the documentation below may not list all supported
     6926formats. <span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
     6927minor-fareast'><o:p></o:p></span></p>
    69246928
    69256929<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l30 level1 lfo14'><![if !supportLists]><span
     
    72467250style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    72477251Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7248 </span></span></span><![endif]><b>Min extinct.</b> – Reflections with extinction
    7249 corrections larger than this value are ignored.</p>
     7252</span></span></span><![endif]><b>Min extinct.</b> – Reflections with
     7253extinction corrections larger than this value are ignored.</p>
    72507254
    72517255<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l27 level1 lfo19'><![if !supportLists]><span
     
    72537257Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    72547258</span></span></span><![endif]><b>Max delt-F/sig</b> - Removes reflections that
    7255 are very poorly fit. Should be used only with extreme care, since poorly-fit reflections
    7256 could be an indication that the structure is wrong. </p>
     7259are very poorly fit. Should be used only with extreme care, since poorly-fit
     7260reflections could be an indication that the structure is wrong. </p>
    72577261
    72587262<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l27 level1 lfo19'><![if !supportLists]><span
     
    73227326<p style='margin-left:.25in;text-indent:-.25in;mso-list:l23 level1 lfo16'><![if !supportLists]><span
    73237327style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7324 </span></span><![endif]><b><u>Global Settings</u></b><u>:</u> This is a location
    7325 for parameters that apply to an entire project. At present there is only one. <span
    7326 style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast'><o:p></o:p></span></p>
     7328</span></span><![endif]><b><u>Global Settings</u></b><u>:</u> This is a
     7329location for parameters that apply to an entire project. At present there is
     7330only one. <span style='mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:
     7331minor-fareast'><o:p></o:p></span></p>
    73277332
    73287333<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l22 level1 lfo21'><![if !supportLists]><span
     
    74047409</span></span></span><![endif]>those pertaining to quantities in each phase
    74057410(naming pattern &quot;<tt><i><span style='font-size:10.0pt'>p</span></i></tt><tt><span
    7406 style='font-size:10.0pt'>::<i>name</i></span></tt>&quot;); examples include
    7407 atom coordinates, thermal motion and site fraction parameters; </p>
     7411style='font-size:10.0pt'>::<i>name</i></span></tt>&quot;); examples include atom
     7412coordinates, thermal motion and site fraction parameters; </p>
    74087413
    74097414<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l26 level1 lfo22;
     
    74387443style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    74397444Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7440 </span></span></span><![endif]><b>Holds</b> - Use this to prevent a parameter
    7441 from being refined. Most valuable when refinement of a parameter is selected in
    7442 a group for refinement (such as x, y &amp; z for an atom or unit cell
    7443 parameters) and one must be fixed. For example, if the space group for a phase
    7444 has a polar axis (e.g., the <i>b</i>-axis in P2<sub>1</sub>), then the origin
    7445 with respect to <i>b</i> is arbitrary and it is not possible to refine the y
    7446 coordinates for all atoms. Place a Hold on any one atom y coordinate to keep
    7447 the structure from drifting up or down the y-axis during refinement. </p>
     7445</span></span></span><![endif]><b>Holds</b> - Use this to prevent a parameter from
     7446being refined. Most valuable when refinement of a parameter is selected in a
     7447group for refinement (such as x, y &amp; z for an atom or unit cell parameters)
     7448and one must be fixed. For example, if the space group for a phase has a polar
     7449axis (e.g., the <i>b</i>-axis in P2<sub>1</sub>), then the origin with respect
     7450to <i>b</i> is arbitrary and it is not possible to refine the y coordinates for
     7451all atoms. Place a Hold on any one atom y coordinate to keep the structure from
     7452drifting up or down the y-axis during refinement. </p>
    74487453
    74497454<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l43 level1 lfo23'><![if !supportLists]><span
     
    75337538OK. Cancel in either dialog will cancel the operation. The equivalenced
    75347539parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0;
    7535 usually M1=1.0 and M2=-1.0 but can be changed via the ‘Edit’ button. The equation(s)
    7536 are shown in the window tagged by ‘EQUIV’ to mark it as an equivalence
    7537 assignment. </p>
     7540usually M1=1.0 and M2=-1.0 but can be changed via the ‘Edit’ button. The
     7541equation(s) are shown in the window tagged by ‘EQUIV’ to mark it as an
     7542equivalence assignment. </p>
    75387543
    75397544<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo24'><![if !supportLists]><span
     
    76077612constraints have been processed, a series of relationships are developed to
    76087613determine new variables from the current parameters and &quot;inverse&quot;
    7609 equations that determine dependent parameters from the new variables and
    7610 independent parameters. This shows the resulting relationships, as well as any
     7614equations that determine dependent parameters from the new variables and independent
     7615parameters. This shows the resulting relationships, as well as any
    76117616&quot;Hold&quot; variables. </p>
    76127617
     
    77387743style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    77397744</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Add
    7740 restraints</b> – this takes you through a sequence of dialog boxes which ask for
    7741 the identities of the atoms involved in the restraint and the value to be
     7745restraints</b> – this takes you through a sequence of dialog boxes which ask
     7746for the identities of the atoms involved in the restraint and the value to be
    77427747assigned to the restraint. The esd is given a default value which can be
    77437748changed after the restraints are created.</p>
     
    78377842</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Add rigid
    78387843body</b> – (Vector rigid bodies) this creates a vector description of a rigid
    7839 body. A dialog box asks the number of atoms (&gt;2) and the number of vectors required
    7840 to create the rigid body. An entry will be created showing a magnitude with the
    7841 vector set to be applied for each vector needed to develop the rigid body.<b
    7842 style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
     7844body. A dialog box asks the number of atoms (&gt;2) and the number of vectors
     7845required to create the rigid body. An entry will be created showing a magnitude
     7846with the vector set to be applied for each vector needed to develop the rigid
     7847body.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
    78437848
    78447849<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    79267931style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;
    79277932</span></span></span><![endif]><b>Set used</b> – this allows you to select in a
    7928 dialog which entries to use; those not used are not plotted or used in further
    7929 processing.</p>
     7933dialog which entries to use; those not used are not plotted or used in further processing.</p>
    79307934
    79317935<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    82058209style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    82068210Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    8207 </span></span></span><![endif]><b>Select datasets</b> – this brings up a selection
    8208 tool for PWDR (&amp; PDF, if present) entries in the GSAS-II data tree. Your
    8209 selection must be either PWDR or PDF data; otherwise, there is no check on data
    8210 similarity so be careful with your selections. Multi-bank TOF data should not
    8211 be mixed for cluster analysis nor should laboratory and synchrotron data.
    8212 Cluster analysis on fewer than 5-10 data sets is probably not useful but should
    8213 be used when you have dozens or even hundreds of data sets.</p>
     8211</span></span></span><![endif]><b>Select datasets</b> – this brings up a
     8212selection tool for PWDR (&amp; PDF, if present) entries in the GSAS-II data
     8213tree. Your selection must be either PWDR or PDF data; otherwise, there is no
     8214check on data similarity so be careful with your selections. Multi-bank TOF
     8215data should not be mixed for cluster analysis nor should laboratory and
     8216synchrotron data. Cluster analysis on fewer than 5-10 data sets is probably not
     8217useful but should be used when you have dozens or even hundreds of data sets.</p>
    82148218
    82158219<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l39 level1 lfo31'><![if !supportLists]><span
     
    84608464mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
    84618465mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape
    8462  id="_x0000_i1025" type="#_x0000_t75" style='width:118.5pt;height:14.25pt'>
     8466 id="_x0000_i1025" type="#_x0000_t75" style='width:118.65pt;height:14.2pt'>
    84638467 <v:imagedata src="gsasII_files/image008.png" o:title="" chromakey="white"/>
    84648468</v:shape><![endif]--><![if !vml]><img width=158 height=19
     
    89598963distance data; it shows the location of each data set in this space. Clusters
    89608964may be evident from this plot; variable temperature scans tend to show a
    8961 complex path of distance points with cluster grouping corresponding to phases. Since
    8962 data sets may be in a series, a plot of the serial distances across the suite
    8963 of data is shown; spikes in a temperature series may indicate phase changes. The
    8964 GUI will be extended to show more steps in cluster analysis.<o:p></o:p></span></p>
     8965complex path of distance points with cluster grouping corresponding to phases.
     8966Since data sets may be in a series, a plot of the serial distances across the
     8967suite of data is shown; spikes in a temperature series may indicate phase changes.
     8968The GUI will be extended to show more steps in cluster analysis.<o:p></o:p></span></p>
    89658969
    89668970<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l28 level1 lfo32'><![if !supportLists]><span
     
    89758979single cluster is obtained. A dendrogram is displayed showing the progression
    89768980of this clustering. Each cluster is given a mean position, <i>s</i> or <i>t</i>,
    8977 to compare to the others. The linkage methods for calculating the distance (using
    8978 the distance method, <i>dist</i>, as selected above) between each pair of
    8979 clusters are:<o:p></o:p></span></p>
     8981to compare to the others. The linkage methods for calculating the distance
     8982(using the distance method, <i>dist</i>, as selected above) between each pair
     8983of clusters are:<o:p></o:p></span></p>
    89808984
    89818985<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     
    91729176"Times New Roman";mso-ansi-language:EN-US;mso-fareast-language:EN-US;
    91739177mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    9174  style='width:103.5pt;height:14.25pt'>
     9178 style='width:103.45pt;height:14.2pt'>
    91759179 <v:imagedata src="gsasII_files/image028.png" o:title="" chromakey="white"/>
    91769180</v:shape><![endif]--><![if !vml]><img width=138 height=19
     
    93459349"Times New Roman";mso-ansi-language:EN-US;mso-fareast-language:EN-US;
    93469350mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025" type="#_x0000_t75"
    9347  style='width:350.25pt;height:42.75pt'>
     9351 style='width:350.2pt;height:42.75pt'>
    93489352 <v:imagedata src="gsasII_files/image032.png" o:title="" chromakey="white"/>
    93499353</v:shape><![endif]--><![if !vml]><img width=467 height=57
     
    93569360linkage method results in an automatic recalculation of the hierarchical
    93579361clustering; a Compute button is provided for convenience. The result of this
    9358 calculation is shown as a dendrogram in the same plot tab; the 4<sup>th</sup>
    9359 plot shows the percentage contribution of the leading terms in the PCA to the
     9362calculation is shown as a dendrogram in the same plot tab; the 4<sup>th</sup> plot
     9363shows the percentage contribution of the leading terms in the PCA to the
    93609364distance data. Usually, 2-3 terms are sufficient to describe the distribution.<o:p></o:p></span></p>
    93619365
     
    96049608with a prefix of ‘PWDR’, ’HKLF’, ‘PDF’, ‘IMG’, ‘PKS’, ‘SASD’, ‘REFD’ or and
    96059609usually a file name. These constitute the data sets (‘Histograms’) to be used
    9606 by GSAS-II for analysis. Selection of these items does not produce much
    9607 information in the data window but does display the data in the Plots Window.
    9608 They are described below.</span><span style='mso-fareast-font-family:"Times New Roman";
     9610by GSAS-II for analysis. Selection of these items does not produce much information
     9611in the data window but does display the data in the Plots Window. They are
     9612described below.</span><span style='mso-fareast-font-family:"Times New Roman";
    96099613mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    96109614
     
    96369640refinement result as bounded by the limits. The slope and intercept of the
    96379641curve in the central region (-1 &lt; / &lt; 1) are shown on the plot status
    9638 line. The slope is the GOF for the best fit set of data points (~68% of the
    9639 data).<o:p></o:p></span></p>
     9642line. The slope is the GOF for the best fit set of data points (~68% of the data).<o:p></o:p></span></p>
    96409643
    96419644<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
     
    96439646Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    96449647</span></span></span><![endif]><b><span style='color:#4A4A4A'>Merge HKLs </span></b><span
    9645 style='color:#4A4A4A'>– this combines equivalent/duplicate reflections according
    9646 to space group and some options to make a unique and averaged set of structure
    9647 factors.<o:p></o:p></span></p>
     9648style='color:#4A4A4A'>– this combines equivalent/duplicate reflections
     9649according to space group and some options to make a unique and averaged set of
     9650structure factors.<o:p></o:p></span></p>
    96489651
    96499652<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l34 level1 lfo34'><![if !supportLists]><span
     
    96729675<h4><a name="HKLF_Instrument_Parameters">Instrument Parameters</a></h4>
    96739676
    9674 <p class=MsoNormal><span style='color:#4A4A4A'>This window shows the histogram type
    9675 (SXC or SNC) and the wavelength. You may change the wavelength or source type
    9676 but rarely will need to do so.<o:p></o:p></span></p>
     9677<p class=MsoNormal><span style='color:#4A4A4A'>This window shows the histogram
     9678type (SXC or SNC) and the wavelength. You may change the wavelength or source
     9679type but rarely will need to do so.<o:p></o:p></span></p>
    96779680
    96789681<h4><a name="HKLF_Reflection_List"></a><span style='mso-fareast-font-family:
     
    97759778PDF data tree item displays the same window as the PDF Controls, below. A PDF
    97769779entry can also be imported as G(R) from a file. When this item is selected, the
    9777 <a href="#PDF_S_Q">S(Q) function</a> or <a href="#PDF_G_R">G(R) function</a>
    9778 (if imported) is plotted, see below. <o:p></o:p></span></p>
     9780<a href="#PDF_S_Q">S(Q) function</a> or <a href="#PDF_G_R">G(R) function</a> (if
     9781imported) is plotted, see below. <o:p></o:p></span></p>
    97799782
    97809783<h4><a name="PDF_Controls">PDF Controls</a></h4>
     
    98979900style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    98989901</span></span></span><![endif]><b><span style='color:#4A4A4A'>m</span></b><span
    9899 style='color:#4A4A4A'>: toggle multiple plot - for multiple PDFs, this will show
    9900 only the one selected from the data tree. The offset options are not active. Or
    9901 all selected items will be plotted on a single axis. <o:p></o:p></span></p>
     9902style='color:#4A4A4A'>: toggle multiple plot - for multiple PDFs, this will
     9903show only the one selected from the data tree. The offset options are not
     9904active. Or all selected items will be plotted on a single axis. <o:p></o:p></span></p>
    99029905
    99039906<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
     
    99359938style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    99369939</span></span></span><![endif]><b><span style='color:#4A4A4A'>l</span></b><span
    9937 style='color:#4A4A4A'>: offset left - for a waterfall plot of multiple powder
    9938 profiles, increase the offset so that later plots are shifted more to the left
    9939 relative to previous plots. <o:p></o:p></span></p>
     9940style='color:#4A4A4A'>: offset left - for a waterfall plot of multiple powder profiles,
     9941increase the offset so that later plots are shifted more to the left relative
     9942to previous plots. <o:p></o:p></span></p>
    99409943
    99419944<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
     
    99459948style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    99469949</span></span></span><![endif]><b><span style='color:#4A4A4A'>r</span></b><span
    9947 style='color:#4A4A4A'>: offset right - for a waterfall plot of multiple powder profiles,
    9948 increase the offset to the right (or decrease the left offset.) <o:p></o:p></span></p>
     9950style='color:#4A4A4A'>: offset right - for a waterfall plot of multiple powder
     9951profiles, increase the offset to the right (or decrease the left offset.) <o:p></o:p></span></p>
    99499952
    99509953<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l57 level1 lfo37;
     
    1003210035listed values (caution: you do need to know what their true value is), you can
    1003310036determine the x-ray bean polarization and create a gain map for your detector.
    10034 Both require this image to from a purely isotropic amorphous sample (a glass
    10035 slide mounted perpendicular to the incident beam is recommended) with the
    10036 detector close to the sample so that the scattering angle at the edge of the
    10037 detector is at least 35° 2</span><span style='font-family:Symbol;mso-ascii-font-family:
     10037Both require this image to from a purely isotropic amorphous sample (a glass slide
     10038mounted perpendicular to the incident beam is recommended) with the detector
     10039close to the sample so that the scattering angle at the edge of the detector is
     10040at least 35° 2</span><span style='font-family:Symbol;mso-ascii-font-family:
    1003810041"Times New Roman";mso-hansi-font-family:"Times New Roman";color:#4A4A4A;
    1003910042mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
     
    1008610089style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1008710090</span></span></span><![endif]><b><span style='color:#4A4A4A'>Make gain map … -
    10088 </span></b><span style='color:#4A4A4A'>This uses the same image (from a glass slide)
    10089 used for polarization analysis to determine a gain map for the detector. The
    10090 process uses the result of an integration of the glass pattern to normalize the
    10091 entire detector pixel array. The result (~1.0 for all pixels) is the scaled by
    10092 1000, converted to integers and stored as a GSAS-II image file (NB: this is a
    10093 python pickle file and thus not usable by other programs) and entered in the
     10091</span></b><span style='color:#4A4A4A'>This uses the same image (from a glass
     10092slide) used for polarization analysis to determine a gain map for the detector.
     10093The process uses the result of an integration of the glass pattern to normalize
     10094the entire detector pixel array. The result (~1.0 for all pixels) is the scaled
     10095by 1000, converted to integers and stored as a GSAS-II image file (NB: this is
     10096a python pickle file and thus not usable by other programs) and entered in the
    1009410097GSAS-II data tree. You can view it to see what the map looks like (select its
    1009510098IMG entry). The gain map file can be imported into other projects using the
     
    1014210145style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1014310146</span></span></span><![endif]><b><span style='color:#4A4A4A'>Ring masks</span></b><span
    10144 style='color:#4A4A4A'>: occludes a specific Bragg reflection (a ring placed
    10145 relative to the image center). The location and thickness of the ring are
    10146 specified in degrees 2-theta. <o:p></o:p></span></p>
     10147style='color:#4A4A4A'>: occludes a specific Bragg reflection (a ring placed relative
     10148to the image center). The location and thickness of the ring are specified in
     10149degrees 2-theta. <o:p></o:p></span></p>
    1014710150
    1014810151<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l41 level1 lfo39;
     
    1017110174style='color:#4A4A4A'>: occludes an arbitrary region created by line segments
    1017210175joining a series of points specified in image coordinates (mm). Typically, a
    10173 point is placed near each corner of the image. Only pixels inside the frame mask
    10174 are used for integration. Only one frame mask can be defined. <o:p></o:p></span></p>
     10176point is placed near each corner of the image. Only pixels inside the frame
     10177mask are used for integration. Only one frame mask can be defined. <o:p></o:p></span></p>
    1017510178
    1017610179<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?</span></h5>
     
    1030310306
    1030410307<p><b><span style='color:#4A4A4A'>Edit Arc mask thickness or range</span></b><span
    10305 style='color:#4A4A4A'> by <a href="#Mac_rightclick">right-clicking*</a> either
    10306 on the inner or outer circle and drag the the circle change spacing between the
     10308style='color:#4A4A4A'> by <a href="#Mac_rightclick">right-clicking*</a> either on
     10309the inner or outer circle and drag the the circle change spacing between the
    1030710310inner and outer circle. Alternately, <a href="#Mac_rightclick">right-click*</a>
    1030810311on the upper or lower arc limit (the straight lines) and drag them to change
     
    1038110384examine the results as a series of diffraction line d-spacings vs azimuth
    1038210385angle; if no strain these are straight, otherwise they will show a single
    10383 sinusoidal variation with maxima at the maximum strain direction (90° &amp; 270°)
    10384 for a tension load. The signs are reversed for a compression load. One can also
    10385 examine the local intensity variation as multiples of a random distribution
     10386sinusoidal variation with maxima at the maximum strain direction (90° &amp;
     10387270°) for a tension load. The signs are reversed for a compression load. One
     10388can also examine the local intensity variation as multiples of a random distribution
    1038610389(MRD) due to texture. Before embarking on this analysis be sure that your
    1038710390detector is carefully calibrated for orientation and position; you are looking
     
    1042410427style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1042510428Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    10426 </span></span></span><![endif]><b><span style='color:#4A4A4A'>Save intensity distribution</span></b><span
    10427 style='color:#4A4A4A'> – this saves the intensity distribution curves as a
    10428 simple text file<o:p></o:p></span></p>
     10429</span></span></span><![endif]><b><span style='color:#4A4A4A'>Save intensity
     10430distribution</span></b><span style='color:#4A4A4A'> – this saves the intensity
     10431distribution curves as a simple text file<o:p></o:p></span></p>
    1042910432
    1043010433<p style='margin-left:.5in;text-indent:-.25in;mso-list:l6 level1 lfo42'><![if !supportLists]><span
     
    1047610479here?<o:p></o:p></span></h5>
    1047710480
    10478 <p class=MsoNormal><span style='color:#4A4A4A'>The Strain plot shows the
    10479 variation of d-spacing for each selected ring with azimuth angle. If there is
    10480 no strain the points will scatter about a straight line. If there is strain,
    10481 the points will describe a negative “cosine” curve if the sample is under
    10482 tension or a positive “cosine” curve if the sample is under compression. If the
    10483 fit has been done, a calculated curve will be shown along with a dashed black
    10484 line for the fitted average d-spacing of the calculated curve. This average is
    10485 either the mean (“Poisson mean” = False) or the Poisson mean which is ¼ or ¾ of
    10486 the interval from d-min to d-max depending on the comparison between ε<sub>11</sub>
     10481<p class=MsoNormal><span style='color:#4A4A4A'>The Strain plot shows the variation
     10482of d-spacing for each selected ring with azimuth angle. If there is no strain
     10483the points will scatter about a straight line. If there is strain, the points
     10484will describe a negative “cosine” curve if the sample is under tension or a
     10485positive “cosine” curve if the sample is under compression. If the fit has been
     10486done, a calculated curve will be shown along with a dashed black line for the
     10487fitted average d-spacing of the calculated curve. This average is either the
     10488mean (“Poisson mean” = False) or the Poisson mean which is ¼ or ¾ of the
     10489interval from d-min to d-max depending on the comparison between ε<sub>11</sub>
    1048710490&amp; ε<sub>22</sub>. Detector calibration errors will distort these curves.<o:p></o:p></span></p>
    1048810491
     
    1049510498
    1049610499<p class=MsoNormal><span style='color:#4A4A4A'>The Strain plot is best examined
    10497 line by line by zooming in on each. The deviations are quite small and can not
    10498 be discerned over the full d-spacing range. You should examine the calibration
     10500line by line by zooming in on each. The deviations are quite small and can not be
     10501discerned over the full d-spacing range. You should examine the calibration
    1049910502lines to ensure they are straight.<o:p></o:p></span></p>
    1050010503
     
    1051110514style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
    1051210515Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    10513 </span></span></span><![endif]><span style='color:#4A4A4A'>Key ‘<b>r</b>’ –
    10514 this progressively shifts the RMD lines to the right<o:p></o:p></span></p>
     10516</span></span></span><![endif]><span style='color:#4A4A4A'>Key ‘<b>r</b>’ – this
     10517progressively shifts the RMD lines to the right<o:p></o:p></span></p>
    1051510518
    1051610519<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo43'><![if !supportLists]><span
     
    1055310556<h4><span style='mso-fareast-font-family:"Times New Roman"'>Comments<o:p></o:p></span></h4>
    1055410557
    10555 <p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever
    10556 comment lines (preceded by “#”) found when the peaks data file was read by
    10557 GSAS-II. If you are lucky, there will be useful information here (e.g. sample
    10558 name, date collected, wavelength used, etc.). If not, this window will be
    10559 blank. The text is read-only.</span><span style='mso-fareast-font-family:"Times New Roman";
     10558<p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever comment
     10559lines (preceded by “#”) found when the peaks data file was read by GSAS-II. If
     10560you are lucky, there will be useful information here (e.g. sample name, date
     10561collected, wavelength used, etc.). If not, this window will be blank. The text
     10562is read-only.</span><span style='mso-fareast-font-family:"Times New Roman";
    1056010563mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    1056110564
     
    1056410567<p class=MsoNormal><span style='color:#4A4A4A'>This window shows the limits in
    1056510568position to be used in indexing from these peak positions. The ‘original’
    10566 values are obtained from the minimum &amp; maximum 1<sup>st</sup> &amp; last position.
    10567 The ‘new’ values determine the range of data that will be used in fitting.
    10568 Units are 2</span><span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
    10569 mso-hansi-font-family:"Times New Roman";color:#4A4A4A;mso-char-type:symbol;
    10570 mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
    10571 Symbol'>Q</span></span><span style='color:#4A4A4A'>.<o:p></o:p></span></p>
     10569values are obtained from the minimum &amp; maximum 1<sup>st</sup> &amp; last
     10570position. The ‘new’ values determine the range of data that will be used in
     10571fitting. Units are 2</span><span style='font-family:Symbol;mso-ascii-font-family:
     10572"Times New Roman";mso-hansi-font-family:"Times New Roman";color:#4A4A4A;
     10573mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
     10574symbol;mso-symbol-font-family:Symbol'>Q</span></span><span style='color:#4A4A4A'>.<o:p></o:p></span></p>
    1057210575
    1057310576<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    1066810671dialog box (Copy parameters) will appear showing the list of available powder
    1066910672patterns, you can copy the instrument parameters to any or all of them; select
    10670 ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’
    10671 to cancel the operation. <o:p></o:p></span></span></p>
     10673‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy; ‘Cancel’ to
     10674cancel the operation. <o:p></o:p></span></span></p>
    1067210675
    1067310676<p class=MsoListParagraphCxSpLast style='margin-left:.25in;mso-add-space:auto;
     
    1073710740style='mso-bookmark:PKS_Unit_Cells_List'>Index Peak List</span><span
    1073810741style='mso-bookmark:PKS_Unit_Cells_List'></span></a><span style='mso-bookmark:
    10739 PKS_Unit_Cells_List'><span style='color:#4A4A4A'> are used. Select one or more Bravais
    10740 lattice types to use and use the &quot;Cell Index/Refine&quot;/&quot;Index
    10741 Cell&quot; menu command to start indexing. Output will appear on the console
    10742 and a progress bar dialog will appear which tracks trial volume. A <b
    10743 style='mso-bidi-font-weight:normal'>Cancel</b> button will terminate indexing;
    10744 it may need to be pressed more than once to fully terminate the indexing
    10745 process. Console output shows possible solutions with a computed <b>M20</b> for
    10746 each; good solutions are indicated by high <b>M20</b> values. <b
    10747 style='mso-bidi-font-weight:normal'>X20</b> gives number of unindexed lines out
    10748 of the 1<sup>st</sup> 20 lines and <b>Nc</b> gives total number of reflections
    10749 generated for each solution. <o:p></o:p></span></span></p>
     10742PKS_Unit_Cells_List'><span style='color:#4A4A4A'> are used. Select one or more
     10743Bravais lattice types to use and use the &quot;Cell
     10744Index/Refine&quot;/&quot;Index Cell&quot; menu command to start indexing.
     10745Output will appear on the console and a progress bar dialog will appear which
     10746tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b> button
     10747will terminate indexing; it may need to be pressed more than once to fully
     10748terminate the indexing process. Console output shows possible solutions with a
     10749computed <b>M20</b> for each; good solutions are indicated by high <b>M20</b>
     10750values. <b style='mso-bidi-font-weight:normal'>X20</b> gives number of
     10751unindexed lines out of the 1<sup>st</sup> 20 lines and <b>Nc</b> gives total
     10752number of reflections generated for each solution. <o:p></o:p></span></span></p>
    1075010753
    1075110754<p class=MsoNormal><span style='mso-bookmark:PKS_Unit_Cells_List'><span
     
    1078310786</span></span></span><![endif]><span style='color:#4A4A4A'>Select
    1078410787&quot;keep&quot; in the table for a cell that should be preserved when an
    10785 additional indexing run is tried; all without that are erased before the
    10786 indexing trial begins. <o:p></o:p></span></span></p>
     10788additional indexing run is tried; all without that are erased before the indexing
     10789trial begins. <o:p></o:p></span></span></p>
    1078710790
    1078810791<p class=MsoNormal><span style='mso-bookmark:PKS_Unit_Cells_List'><b><span
     
    1079210795PKS_Unit_Cells_List'>list below</span><span style='mso-bookmark:PKS_Unit_Cells_List'></span></a><span
    1079310796style='mso-bookmark:PKS_Unit_Cells_List'><span style='color:#4A4A4A'>),
    10794 optionally select a space group (by default the highest symmetry space group for
    10795 the class is selected) and enter the unit cell parameters. Or use the
     10797optionally select a space group (by default the highest symmetry space group
     10798for the class is selected) and enter the unit cell parameters. Or use the
    1079610799&quot;Cell Index/Refine&quot;/&quot;Load Phase&quot; menu command to read this
    1079710800information from a phase that has been read into a project or from a file (such
     
    1089810901<h4><span style='mso-fareast-font-family:"Times New Roman"'>Comments<o:p></o:p></span></h4>
    1089910902
    10900 <p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever comment
    10901 lines found above the QIE table when the small angle data file was read by
    10902 GSAS-II. If you are lucky, there will be useful information here (e.g. sample
    10903 name, date collected, wavelength used, etc.). If not, this window will be
    10904 blank. The text is read-only.</span><span style='mso-fareast-font-family:"Times New Roman";
    10905 mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
     10903<p class=MsoNormal><span style='color:#4A4A4A'>This window shows whatever
     10904comment lines found above the QIE table when the small angle data file was read
     10905by GSAS-II. If you are lucky, there will be useful information here (e.g.
     10906sample name, date collected, wavelength used, etc.). If not, this window will
     10907be blank. The text is read-only.</span><span style='mso-fareast-font-family:
     10908"Times New Roman";mso-fareast-theme-font:minor-fareast;color:#4A4A4A'><o:p></o:p></span></p>
    1090610909
    1090710910<h4><a name="SASD_Limits">Limits</a></h4>
     
    1093410937Symbol;color:#4A4A4A'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    1093510938</span></span></span><![endif]><b><span style='color:#4A4A4A'>Copy - </span></b><span
    10936 style='color:#4A4A4A'>this copies the limits shown to other selected small angle
    10937 patterns. If used, a dialog box (Copy Parameters) will appear showing the list
    10938 of available small angle patterns, you can copy the limits parameters to any or
    10939 all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do
    10940 the copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></span></p>
     10939style='color:#4A4A4A'>this copies the limits shown to other selected small
     10940angle patterns. If used, a dialog box (Copy Parameters) will appear showing the
     10941list of available small angle patterns, you can copy the limits parameters to
     10942any or all of them; select ‘All’ to copy them to all patterns. Then select ‘OK’
     10943to do the copy; ‘Cancel’ to cancel the operation. <o:p></o:p></span></span></p>
    1094110944
    1094210945<span style='mso-bookmark:SASD_Limits'></span>
     
    1102411027</span></span></span><![endif]><b><span style='color:#4A4A4A'>Add substance</span></b><span
    1102511028style='color:#4A4A4A'> – this allows one to enter a new substance that is not
    11026 among the previously defined ones. Give it a name, element composition and volume/density;
    11027 GSAS-II will compute the scattering contrast data for it.<o:p></o:p></span></span></p>
     11029among the previously defined ones. Give it a name, element composition and
     11030volume/density; GSAS-II will compute the scattering contrast data for it.<o:p></o:p></span></span></p>
    1102811031
    1102911032<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo53;
     
    1106211065style='mso-bookmark:SASD_Substances'><![if !supportLists]><span
    1106311066style='color:#4A4A4A'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    11064 </span></span></span><![endif]><span style='color:#4A4A4A'>You can edit the composition
    11065 by changing the number of each kind of element and change the sum of atomic
    11066 volumes or the material density.<o:p></o:p></span></span></p>
     11067</span></span></span><![endif]><span style='color:#4A4A4A'>You can edit the
     11068composition by changing the number of each kind of element and change the sum
     11069of atomic volumes or the material density.<o:p></o:p></span></span></p>
    1106711070
    1106811071<span style='mso-bookmark:SASD_Substances'></span>
     
    1107711080last three parameters (named FreePrm<i>X</i>, <i>X</i>=1,2,3) have labels that
    1107811081can be changed. If changed in one histogram, the same label is used for all
    11079 histograms. When a label is changed, the Comments tree item for each SASD histogram
    11080 is searched for a matching &quot;Label=value&quot; pair (differences in letter
    11081 case between the two label strings is ignored). When found, the value is
    11082 converted to a float and saved as the appropriate Sample Parameter. The last
     11082histograms. When a label is changed, the Comments tree item for each SASD
     11083histogram is searched for a matching &quot;Label=value&quot; pair (differences
     11084in letter case between the two label strings is ignored). When found, the value
     11085is converted to a float and saved as the appropriate Sample Parameter. The last
    1108311086two items define the two components of a small angle scattering sample. One
    1108411087comprises the objects of interest while the other is the marix they are
     
    1118311186spaced by at least one delimiter. The first column in the table is used to look
    1118411187up SASD entries where the initial space-delimited string after the SASD tag
    11185 (&quot;myfile&quot; in &quot;SASD myfile AZM=180...&quot;) must match the table.
    11186 Subsequent columns can then be mapped to sample parameters or can be ignored,
    11187 using a dialog window. <o:p></o:p></span></span></p>
     11188(&quot;myfile&quot; in &quot;SASD myfile AZM=180...&quot;) must match the
     11189table. Subsequent columns can then be mapped to sample parameters or can be
     11190ignored, using a dialog window. <o:p></o:p></span></span></p>
    1118811191
    1118911192<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l50 level1 lfo54;
     
    1143811441style='color:#4A4A4A'> – select from a suite of various substance predefined by
    1143911442GSAS-II as defined in <b>GSASII/Substances.py</b>. You may add to this list by
    11440 adding a file, UserSubstances.py, by following the substance format as described
    11441 in Substances.py. Place your UserSubstances.py in the GSAS-II directory.<o:p></o:p></span></span></p>
     11443adding a file, UserSubstances.py, by following the substance format as
     11444described in Substances.py. Place your UserSubstances.py in the GSAS-II
     11445directory.<o:p></o:p></span></span></p>
    1144211446
    1144311447<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l20 level1 lfo59;
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