Changeset 1258


Ignore:
Timestamp:
Mar 20, 2014 4:34:09 PM (8 years ago)
Author:
vondreele
Message:

Added new tutorial for size distribution from SASD.

Location:
trunk/help
Files:
19 added
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/help/gsasII.html

    r1197 r1258  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>134</o:Revision>
    28   <o:TotalTime>3975</o:TotalTime>
     27  <o:Revision>135</o:Revision>
     28  <o:TotalTime>3979</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2014-01-13T19:41:00Z</o:LastSaved>
     30  <o:LastSaved>2014-03-20T17:00:00Z</o:LastSaved>
    3131  <o:Pages>27</o:Pages>
    32   <o:Words>10790</o:Words>
    33   <o:Characters>61503</o:Characters>
     32  <o:Words>10804</o:Words>
     33  <o:Characters>61589</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>512</o:Lines>
     35  <o:Lines>513</o:Lines>
    3636  <o:Paragraphs>144</o:Paragraphs>
    37   <o:CharactersWithSpaces>72149</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>72249</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
    23422342style='font-weight:normal'>2-D Image integration</span></a><o:p></o:p></strong></p>
    23432343
    2344 <p class=MsoNormal><strong><a href="Strain%20fitting%20of%202D%20data%20in%20GSAS-II.htm"><span
     2344<p class=MsoNormal><strong><a
     2345href="Strain%20fitting%20of%202D%20data%20in%20GSAS-II.htm"><span
    23452346style='font-weight:normal'>2-D Strain data fitting</span></a><o:p></o:p></strong></p>
    23462347
     
    23512352class=SpellE><span style='font-weight:normal'>jadarite</span></span></a> &amp; <a
    23522353href="Charge%20Flipping%20-%20sucrose.htm"><span style='font-weight:normal'>sucrose</span></a><o:p></o:p></strong></p>
     2354
     2355<p class=MsoNormal><strong><span style='font-weight:normal;mso-bidi-font-weight:
     2356bold'><a href="Small%20Angle%20Size%20Distribution.htm"><span style='mso-bidi-font-weight:
     2357normal'>Small angle X-ray data size distribution</span></a><o:p></o:p></span></strong></p>
    23532358
    23542359<p class=MsoNormal><strong><o:p>&nbsp;</o:p></strong></p>
     
    23792384Parameters&quot;</a> item under a &#8216;PWDR&#8217; entry contains information
    23802385about how data were collected, such as the sample temperature <a
    2381 href="#Sample_Parameters">(see below)</a>. The arrow keys (up &amp; down) move the
    2382 selection to successive entries in the data tree; both the data window and the
    2383 associated plot (if any) will change.<o:p></o:p></span></p>
     2386href="#Sample_Parameters">(see below)</a>. The arrow keys (up &amp; down) move
     2387the selection to successive entries in the data tree; both the data window and
     2388the associated plot (if any) will change.<o:p></o:p></span></p>
    23842389
    23852390<h4><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h4>
     
    25882593&#8216;<b style='mso-bidi-font-weight:normal'>Import</b>&#8217; &#8211; A sub
    25892594menu appears with choices for import of data. Each entry when selected with the
    2590 mouse shows further submenus with specific imports that are available. Any of
    2591 these files can be accessed from a zip file.</p>
     2595mouse shows further submenus with specific imports that are available. Any of these
     2596files can be accessed from a zip file.</p>
    25922597
    25932598<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    26022607style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    26032608class=GramE><b style='mso-bidi-font-weight:normal'>from</b></span><b
    2604 style='mso-bidi-font-weight:normal'> GSAS .EXP file - </b>This reads one phase from
    2605 a GSAS experiment file (name.EXP). The file name is found in a directory
     2609style='mso-bidi-font-weight:normal'> GSAS .EXP file - </b>This reads one phase
     2610from a GSAS experiment file (name.EXP). The file name is found in a directory
    26062611dialog; you can change directories as needed. Only .EXP (or .exp) file names
    26072612are shown. If the selected file has more than one phase, a dialog is shown with
     
    27502755normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F**2 HKL file </b>This
    27512756reads structure factors (as F**2) and sig(F**2) from a SHELX format .<span
    2752 class=SpellE>hkl</span> file. The file names are found in a directory dialog; you
    2753 can change directories as needed. You must know this is the content of this
     2757class=SpellE>hkl</span> file. The file names are found in a directory dialog;
     2758you can change directories as needed. You must know this is the content of this
    27542759file as it will have no internal indication of its contents.<b
    27552760style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
     
    29142919style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    29152920style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    2916 style='mso-fareast-font-family:"Times New Roman"'>Select &#8216;Min
    2917 delta-M/M&#8217; for convergence; the refinement will stop when the change in
    2918 the minimization function is less than this value. Set Min delta-M/M = 1.0 to
    2919 force just a single cycle to be performed. A value less than 10<sup>-4</sup>
    2920 (the default) generally gives no better result. The allowed range is 10<sup>-9</sup>
    2921 to 1.0.<o:p></o:p></span></p>
     2921style='mso-fareast-font-family:"Times New Roman"'>Select &#8216;Min delta-M/M&#8217;
     2922for convergence; the refinement will stop when the change in the minimization
     2923function is less than this value. Set Min delta-M/M = 1.0 to force just a
     2924single cycle to be performed. A value less than 10<sup>-4</sup> (the default)
     2925generally gives no better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
    29222926
    29232927<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span
     
    29372941style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    29382942style='mso-fareast-font-family:"Times New Roman"'>If &#8216;analytic
    2939 Hessian&#8217; is chosen then select &#8216;Max cycles&#8217;, the maximum
    2940 number of least squares cycles to be performed. Least squares cycles are
    2941 determined by the number of times a new Hessian matrix is computes; the <span
    2942 class=SpellE>Levenberg</span>-Marquardt algorithm may compute the function
    2943 several times between cycles as it finds the optimal value of the Marquardt
    2944 coefficient. Choices are given in the pull down selection; the default is 3
    2945 cycles.<o:p></o:p></span></p>
     2943Hessian&#8217; is chosen then select &#8216;Max cycles&#8217;, the maximum number
     2944of least squares cycles to be performed. Least squares cycles are determined by
     2945the number of times a new Hessian matrix is computes; the <span class=SpellE>Levenberg</span>-Marquardt
     2946algorithm may compute the function several times between cycles as it finds the
     2947optimal value of the Marquardt coefficient. Choices are given in the pull down
     2948selection; the default is 3 cycles.<o:p></o:p></span></p>
    29462949
    29472950<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span
     
    30163019&#8211; select a list of parameters that should have the same value (possibly
    30173020with a non-unitary multiplier for some). Examples are a list of atoms with the
    3018 same thermal motion <span class=SpellE>Uiso</span>, sets of profile
    3019 coefficients U<span class=GramE>,V,W</span> across multiple data sets. If
    3020 selected, a dialog box will appear with a list of the available parameters.
    3021 Select one and press OK; a second dialog box will appear with only those
    3022 parameters that can be made equivalent to the first one. Choose those and press
    3023 OK. Cancel in either dialog will cancel the operation. The equivalenced
    3024 parameters 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;
    3025 usually M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217;
    3026 button. The keyword &#8216;EQUIV&#8217; marks it as <span class=GramE>an
    3027 equivalence</span>. A Delete button can be used to remove it.<o:p></o:p></span></p>
     3021same thermal motion <span class=SpellE>Uiso</span>, sets of profile coefficients
     3022U<span class=GramE>,V,W</span> across multiple data sets. If selected, a dialog
     3023box will appear with a list of the available parameters. Select one and press
     3024OK; a second dialog box will appear with only those parameters that can be made
     3025equivalent to the first one. Choose those and press OK. Cancel in either dialog
     3026will cancel the operation. The equivalenced parameters will show as an equation
     3027of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0; usually
     3028M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217; button. The
     3029keyword &#8216;EQUIV&#8217; marks it as <span class=GramE>an equivalence</span>.
     3030A Delete button can be used to remove it.<o:p></o:p></span></p>
    30283031
    30293032<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    30933096style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
    30943097style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    3095 style='mso-fareast-font-family:"Times New Roman"'>You can change the search
    3096 range used to find the bonds/angles that meet your criteria for restraint.<o:p></o:p></span></p>
     3098style='mso-fareast-font-family:"Times New Roman"'>You can change the search range
     3099used to find the bonds/angles that meet your criteria for restraint.<o:p></o:p></span></p>
    30973100
    30983101<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span
     
    31913194style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Delete
    31923195restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
    3193 &#8211; this deletes selected restraints from the list. A single click in the blank
    3194 box in the upper left corner of the table will select/deselect all restraints.<o:p></o:p></span></p>
     3196&#8211; this deletes selected restraints from the list. A single click in the
     3197blank box in the upper left corner of the table will select/deselect all
     3198restraints.<o:p></o:p></span></p>
    31953199
    31963200<h4><a name="Rigid_bodies"><span style='mso-fareast-font-family:"Times New Roman"'>Rigid
     
    32293233</span></span></span></b><![endif]><b style='mso-bidi-font-weight:normal'><span
    32303234style='mso-fareast-font-family:"Times New Roman"'>Add rigid body</span></b><span
    3231 style='mso-fareast-font-family:"Times New Roman"'> &#8211; (Vector rigid
    3232 bodies) this creates a vector description of a rigid body. A dialog box asks
    3233 the number of atoms (&gt;2) and the number of vectors required to create the
    3234 rigid body. An entry will be created showing a magnitude with the vector set to
    3235 be applied for each vector needed to develop the rigid body.<b
    3236 style='mso-bidi-font-weight:normal'><o:p></o:p></b></span></p>
     3235style='mso-fareast-font-family:"Times New Roman"'> &#8211; (Vector rigid bodies)
     3236this creates a vector description of a rigid body. A dialog box asks the number
     3237of atoms (&gt;2) and the number of vectors required to create the rigid body.
     3238An entry will be created showing a magnitude with the vector set to be applied
     3239for each vector needed to develop the rigid body.<b style='mso-bidi-font-weight:
     3240normal'><o:p></o:p></b></span></p>
    32373241
    32383242<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    33303334style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    33313335normal;mso-bidi-font-weight:bold'> &#8211; this will create a text file of
    3332 selected columns with values and corresponding <span class=SpellE>esds</span>.
    3333 A file dialog box will appear; give a suitable file name; you may change
     3336selected columns with values and corresponding <span class=SpellE>esds</span>. A
     3337file dialog box will appear; give a suitable file name; you may change
    33343338directory if desired.<o:p></o:p></span></h5>
    33353339
     
    33383342<p class=MsoNormal>These are shown in the data tree with a prefix of
    33393343&#8216;PWDR&#8217;, &#8217;HKLF&#8217;, &#8216;IMG&#8217;, or &#8216;PDF&#8217;
    3340 and usually a file name. These constitute the data sets
    3341 (&#8216;Histograms&#8217;) to be used by GSAS-II for analysis. Selection of
    3342 these items does not produce any information in the data window but does
    3343 display the data in the Plots Window. They are described below.</p>
     3344and usually a file name. These constitute the data sets (&#8216;Histograms&#8217;)
     3345to be used by GSAS-II for analysis. Selection of these items does not produce
     3346any information in the data window but does display the data in the Plots
     3347Window. They are described below.</p>
    33443348
    33453349<h3><a name="PWD_Analysis"></a>Powder Histograms - PWDR</h3>
     
    36653669style='mso-fareast-font-family:"Times New Roman"'> &#8211; this copies the
    36663670instrument parameters shown to other selected powder patterns. If used, a
    3667 dialog box (Copy parameters) will appear showing the list of available powder
    3668 patterns, you can copy the instrument parameters to any or all of them; select &#8216;All&#8217;
    3669 to 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
    3671 instrument parameters that are commensurate with the one that is shown, e.g.
    3672 single radiation patterns will not be updated from K</span><sub><span
     3671dialog box (Copy parameters) will appear showing the list of available powder patterns,
     3672you can copy the instrument parameters to any or all of them; select
     3673&#8216;All&#8217; to copy them to all patterns. Then select &#8216;OK&#8217; to
     3674do the copy; &#8216;Cancel&#8217; to cancel the operation. The copy will only
     3675work for instrument parameters that are commensurate with the one that is
     3676shown, e.g. single radiation patterns will not be updated from K</span><sub><span
    36733677style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    36743678style='mso-fareast-font-family:"Times New Roman"'>1</span></sub><span
     
    36893693style='mso-fareast-font-family:"Times New Roman"'>- &#8211; this copies the
    36903694instrument parameter refinement flags shown to other selected powder patterns.
    3691 If used, a dialog box (Copy refinement flags) will appear showing the list of available
    3692 powder patterns, you can copy the instrument parameter refinement flags to any
    3693 or all of them; select &#8216;All&#8217; to copy them to all patterns. Then
    3694 select &#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217; to cancel the
    3695 operation. The copy will only work for instrument parameters that are
    3696 commensurate with the one that is shown, e.g. single radiation patterns will
    3697 not 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
     3695If used, a dialog box (Copy refinement flags) will appear showing the list of
     3696available powder patterns, you can copy the instrument parameter refinement
     3697flags to any or all of them; select &#8216;All&#8217; to copy them to all
     3698patterns. Then select &#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217; to
     3699cancel the operation. The copy will only work for instrument parameters that
     3700are commensurate with the one that is shown, e.g. single radiation patterns
     3701will not be updated from K</span><sub><span style='font-family:Symbol;
     3702mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
     3703style='mso-fareast-font-family:"Times New Roman"'>1</span></sub><span
     3704style='mso-fareast-font-family:"Times New Roman"'>/K</span><sub><span
    37003705style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>a</span></sub><sub><span
    37013706style='mso-fareast-font-family:"Times New Roman"'>2</span></sub><span
     
    38663871color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> &#8211; this
    38673872fills the table with peak positions. These are selected based on peak tops that
    3868 are substantially above background. Noisy data will give spurious peaks and small
    3869 peaks or shoulders will not be found. Examine results &amp; modify as needed.<span
    3870 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    3871 text-underline:none'><o:p></o:p></span></span></span></span></h5>
     3873are substantially above background. Noisy data will give spurious peaks and
     3874small peaks or shoulders will not be found. Examine results &amp; modify as
     3875needed.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     3876none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
    38723877
    38733878<h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l11 level2 lfo15;
     
    39003905The refinement will proceed until convergence. We suggest you vary the
    39013906intensity along with the background first (the default), then vary the position
    3902 and instrument parameters after. The order will depend on how poor is the initial
    3903 estimate of the instrument parameters (U, V, W, X, Y &amp; SH/L). To determine
    3904 how to proceed, examine in detail the powder pattern difference curve displayed
    3905 in the GSASII Plots window. If individual peaks show peak widths that are
    3906 widely different, their individual sigma and gamma parameters may be refined.
    3907 If the refinement results in negative peak coefficients, these will be
     3907and instrument parameters after. The order will depend on how poor is the
     3908initial estimate of the instrument parameters (U, V, W, X, Y &amp; SH/L). To
     3909determine how to proceed, examine in detail the powder pattern difference curve
     3910displayed in the GSASII Plots window. If individual peaks show peak widths that
     3911are widely different, their individual sigma and gamma parameters may be
     3912refined. If the refinement results in negative peak coefficients, these will be
    39083913highlighted in red. If this happens, you should </span></span><span
    39093914style='mso-bookmark:Index_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
     
    39203925none;text-underline:none'><span style='mso-list:Ignore'>d.<span
    39213926style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    3922 style='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:
    3925 bold'>&#8211; perform a single cycle of least squares refinement. This can be
    3926 used in difficult cases to get a refinement started toward convergence.<span
    3927 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    3928 text-underline:none'><o:p></o:p></span></span></span></span></h5>
     3927style='mso-fareast-font-family:"Times New Roman";color:windowtext'>LSQ one
     3928cycle </span></span><span style='mso-bookmark:Index_Peaks'><span
     3929style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
     3930normal;mso-bidi-font-weight:bold'>&#8211; perform a single cycle of least
     3931squares refinement. This can be used in difficult cases to get a refinement
     3932started toward convergence.<span class=MsoHyperlink><span style='color:windowtext;
     3933text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
    39293934
    39303935<h5 style='margin-left:1.0in;text-indent:-.25in;mso-list:l11 level2 lfo15;
     
    41594164style='mso-fareast-font-family:"Times New Roman"'>Max <span class=SpellE>Nc</span>/Nobs
    41604165</span></b></span><span style='mso-bookmark:Reflection_List'><span
    4161 style='mso-fareast-font-family:"Times New Roman"'>&#8211; this controls the
    4162 extent of the search for the correct indexing. This may need to be increased if
    4163 an indexing trial terminates too quickly. It rarely needs to be changed.<span
     4166style='mso-fareast-font-family:"Times New Roman"'>&#8211; this controls the extent
     4167of the search for the correct indexing. This may need to be increased if an
     4168indexing trial terminates too quickly. It rarely needs to be changed.<span
    41644169class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    41654170text-underline:none'><o:p></o:p></span></span></span></span></p>
     
    41974202style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Index
    41984203Cell</span></b></span><span style='mso-bookmark:Reflection_List'><span
    4199 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this starts the indexing
    4200 process. Output will appear on the console and a progress bar dialog will
    4201 appear which tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b>
     4204style='mso-fareast-font-family:"Times New Roman"'> &#8211; this starts the
     4205indexing process. Output will appear on the console and a progress bar dialog
     4206will appear which tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b>
    42024207button will terminate indexing; it may need to be pressed more than once to
    42034208fully terminate the indexing process. Console output shows possible solutions
     
    42504255style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Make
    42514256new phase</span></b></span><span style='mso-bookmark:Reflection_List'><span
    4252 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this creates a new phase
    4253 from the selected unit cell and chosen space group. A dialog box will appear
    4254 asking for a name for this phase. See the new entry under Phases and the new
    4255 lattice parameters will be in the </span></span><a href="#General"><span
     4257style='mso-fareast-font-family:"Times New Roman"'> &#8211; this creates a new
     4258phase from the selected unit cell and chosen space group. A dialog box will
     4259appear asking for a name for this phase. See the new entry under Phases and the
     4260new lattice parameters will be in the </span></span><a href="#General"><span
    42564261style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman";
    42574262color:windowtext;text-decoration:none;text-underline:none'>General</span></span><span
     
    44174422
    44184423<p class=MsoNormal>This window shows whatever comment lines found in a
    4419 &#8220;metadata&#8221; file when the image data file was read by GSAS-II. If you
    4420 are lucky, there will be useful information here (e.g. sample name, date
     4424&#8220;metadata&#8221; file when the image data file was read by GSAS-II. If
     4425you are lucky, there will be useful information here (e.g. sample name, date
    44214426collected, wavelength used, etc.). If not, this window will be blank. The text
    44224427is read-only.</p>
     
    45644569style='mso-fareast-font-family:"Times New Roman"'>Phase type &#8211; </span></b><span
    45654570style='mso-fareast-font-family:"Times New Roman"'>this can only be set when
    4566 there are no atoms in the Atoms page for this phase. Select it when the phase
    4567 is initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
     4571there are no atoms in the Atoms page for this phase. Select it when the phase is
     4572initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    45684573
    45694574<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    45744579</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    45754580style='mso-fareast-font-family:"Times New Roman"'>Space group</span></b><span
    4576 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this should be set when
    4577 the phase is initialized; it can be changed later. Be careful about the impact
    4578 on Atom site symmetry and multiplicity if you do. GSAS-II will recognize any
    4579 legal space group symbol using the short Hermann-Mauguin forms; put a space
     4581style='mso-fareast-font-family:"Times New Roman"'> &#8211; this should be set
     4582when the phase is initialized; it can be changed later. Be careful about the
     4583impact on Atom site symmetry and multiplicity if you do. GSAS-II will recognize
     4584any legal space group symbol using the short Hermann-Mauguin forms; put a space
    45804585between the axial fields (e.g. &#8216;F d 3 m&#8217; not &#8216;Fd3m&#8217;).
    45814586For space groups with a choice of origin (e.g. F d 3 m), GSAS-II always uses
     
    47074712style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    47084713</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    4709 "Times New Roman"'>If there are entries in the Atoms page then the Elements table
    4710 is shown next on the General page; you may select the isotope (only relevant
    4711 for neutron diffraction experiments). The density (just above the Elements) is
    4712 computed depending on this choice, the unit cell volume and the atom
    4713 fractions/site multiplicities in the entries on the Atoms page.<span
     4714"Times New Roman"'>If there are entries in the Atoms page then the Elements
     4715table is shown next on the General page; you may select the isotope (only
     4716relevant for neutron diffraction experiments). The density (just above the
     4717Elements) is computed depending on this choice, the unit cell volume and the
     4718atom fractions/site multiplicities in the entries on the Atoms page.<span
    47144719class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    47154720
     
    47324737to perform a Pawley refinement as opposed to a Rietveld refinement for this
    47334738phase. <b style='mso-bidi-font-weight:normal'>NB:</b> you probably should clear
    4734 the <b style='mso-bidi-font-weight:normal'>Histogram scale factor</b> refinement
    4735 flag (found in <b style='mso-bidi-font-weight:normal'>Sample parameters</b> for
    4736 the powder data set) as it cannot be refined simultaneously with the Pawley
    4737 reflection intensities.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
     4739the <b style='mso-bidi-font-weight:normal'>Histogram scale factor</b>
     4740refinement flag (found in <b style='mso-bidi-font-weight:normal'>Sample
     4741parameters</b> for the powder data set) as it cannot be refined simultaneously
     4742with the Pawley reflection intensities.<span class=MsoHyperlink><span
     4743style='color:windowtext'><o:p></o:p></span></span></span></p>
    47384744
    47394745<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    48314837class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
    48324838"Times New Roman"'>k-Factor</span></b></span><span style='mso-fareast-font-family:
    4833 "Times New Roman"'> &#8211; This is the threshold on the density map, all densities
    4834 below this are charge flipped.</span></p>
     4839"Times New Roman"'> &#8211; This is the threshold on the density map, all
     4840densities below this are charge flipped.</span></p>
    48354841
    48364842<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    48854891color:windowtext;text-decoration:none;text-underline:none'>MC/SA algorithm</span></b></span><span
    48864892class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    4887 color:windowtext;text-decoration:none;text-underline:none'> &#8211; This
    4888 selects the type of jump to be used for each MC/SA trial.<o:p></o:p></span></span></p>
     4893color:windowtext;text-decoration:none;text-underline:none'> &#8211; This selects
     4894the type of jump to be used for each MC/SA trial.<o:p></o:p></span></span></p>
    48894895
    48904896<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    49684974</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    49694975style='mso-fareast-font-family:"Times New Roman"'>Shift LMB</span></b><span
    4970 style='mso-fareast-font-family:"Times New Roman"'> &#8211; on a row number selects
    4971 all atoms from last selection to the selected row (or top is none previously
    4972 selected).<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    4973 none;text-underline:none'><o:p></o:p></span></span></span></p>
     4976style='mso-fareast-font-family:"Times New Roman"'> &#8211; on a row number
     4977selects all atoms from last selection to the selected row (or top is none
     4978previously selected).<span class=MsoHyperlink><span style='color:windowtext;
     4979text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    49744980
    49754981<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    49924998style='mso-fareast-font-family:"Times New Roman"'>Alt LMB</span></b><span
    49934999style='mso-fareast-font-family:"Times New Roman"'> &#8211; on a row number
    4994 selects that atom for moving; the status line at bottom of window will show name
    4995 of atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b> again
    4996 to select a target row for this atom; insertion will be before this row and the
    4997 table will be updated to show the change. NB: the <b style='mso-bidi-font-weight:
     5000selects that atom for moving; the status line at bottom of window will show
     5001name of atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b>
     5002again to select a target row for this atom; insertion will be before this row
     5003and the table will be updated to show the change. NB: the <b style='mso-bidi-font-weight:
    49985004normal'>Draw Atoms</b> list is not updated by this change.<span
    49995005class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     
    51645170style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
    51655171style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    5166 style='mso-bidi-font-weight:normal'>Set atom refinement flags</b> &#8211; A
    5167 popup dialog box appears; select refinement flags to apply to all selected
    5168 atoms.</p>
     5172style='mso-bidi-font-weight:normal'>Set atom refinement flags</b> &#8211; A popup
     5173dialog box appears; select refinement flags to apply to all selected atoms.</p>
    51695174
    51705175<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    52405245style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    52415246style='mso-bidi-font-weight:normal'>Atom Selection from table</b>: select
    5242 individual 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
    5244 selection; a previously selected atom will be deselected; hold down Shift key
    5245 to select from last in list selected to current selection. A selected atom will
    5246 be highlighted (in grey) and the atoms will be shown in green on the plot.
     5247individual atoms by a left click of the mouse when pointed at the left most
     5248column (atom numbers) of the atom display; hold down the Ctrl key to add to
     5249your selection; a previously selected atom will be deselected; hold down Shift
     5250key to select from last in list selected to current selection. A selected atom
     5251will be highlighted (in grey) and the atoms will be shown in green on the plot.
    52475252Selection without the Ctrl key will clear previous selections. A double left
    52485253click in the (empty) upper left box will select or deselect all atoms.</p>
     
    53875392style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    53885393style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    5389 style='mso-bidi-font-weight:normal'>View pt. dist.</b> - this calculates
    5390 distance from view point to all selected draw atoms; result is given on the
    5391 console window.</p>
     5394style='mso-bidi-font-weight:normal'>View pt. dist.</b> - this calculates distance
     5395from view point to all selected draw atoms; result is given on the console
     5396window.</p>
    53925397
    53935398<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    54595464(magnitude, x y &amp; z) of all peaks found within the unit cell from the last
    54605465Fourier/charge flip map search sorted in order of decreasing peak magnitude.
    5461 The crystal structure plot shows each peak position as a white to dark gray
    5462 cross; the shade is determined from the magnitude for the peak relative to the
    5463 maximum peak magnitude.</span></p>
     5466The crystal structure plot shows each peak position as a white to dark gray cross;
     5467the shade is determined from the magnitude for the peak relative to the maximum
     5468peak magnitude.</span></p>
    54645469
    54655470<h5><span style='mso-bookmark:Pawley'>What can I do here?</span></h5>
     
    54695474"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    54705475</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Peak
    5471 Selection from table</b>: select individual atoms by a left click of the mouse when
    5472 pointed at the left most column (atom numbers) of the atom display; hold down
    5473 the Ctrl key to add to your selection; a previously selected atom will be
     5476Selection from table</b>: select individual atoms by a left click of the mouse
     5477when pointed at the left most column (atom numbers) of the atom display; hold
     5478down the Ctrl key to add to your selection; a previously selected atom will be
    54745479deselected; hold down Shift key to select from last in list selected to current
    54755480selection. A selected atom will be highlighted (in grey) and the atoms will be
     
    55795584class=MsoHyperlink><span style='color:#4F81BD;mso-themecolor:accent1'><o:p></o:p></span></span></span></h4>
    55805585
    5581 <p class=MsoNormal><span style='mso-bookmark:Pawley'>This gives the list of
    5582 reflections used in a Pawley refinement and can only be seen if the phase type
    5583 is &#8216;Pawley&#8217; (see </span><a href="#General"><span style='mso-bookmark:
     5586<p class=MsoNormal><span style='mso-bookmark:Pawley'>This gives the list of reflections
     5587used in a Pawley refinement and can only be seen if the phase type is
     5588&#8216;Pawley&#8217; (see </span><a href="#General"><span style='mso-bookmark:
    55845589Pawley'><span style='color:windowtext;text-decoration:none;text-underline:none'>General</span></span></a><span
    55855590style='mso-bookmark:Pawley'>).</span></p>
     
    56295634clicking on the box or by selecting one and then selecting the column (a single
    56305635click on the column heading). Then type &#8216;y&#8217; to set the refine flags
    5631 or &#8216;n&#8217; to clear the flags. You should deselect those reflections that
    5632 fall below the lower limit or above the upper limit of the powder pattern
     5636or &#8216;n&#8217; to clear the flags. You should deselect those reflections
     5637that fall below the lower limit or above the upper limit of the powder pattern
    56335638otherwise you may have a singular matrix error in your Pawley refinement.</span></p>
    56345639
     
    56695674
    56705675<p class=MsoNormal align=center style='text-align:center'><span
     5676style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
     5677
     5678<p class=MsoNormal align=center style='text-align:center'><span
    56715679style='mso-bookmark:Pawley'><span class=MsoHyperlink><span style='color:windowtext;
    56725680text-decoration:none;text-underline:none'><o:p>&nbsp;</o:p></span></span></span></p>
     
    56855693
    56865694</span></span></a></div>
     5695
     5696<p class=MsoNormal align=center style='text-align:center'><span
     5697style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    56875698
    56885699<p class=MsoNormal align=center style='text-align:center'><span
     
    58225833none;text-underline:none'><span style='mso-list:Ignore'>1.<span
    58235834style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><![endif]><span
    5824 style='mso-fareast-font-family:"Times New Roman"'>Move the mouse cursor across
    5825 the plot, the plot status line will show the cursor position in 2</span></span><span
     5835style='mso-fareast-font-family:"Times New Roman"'>Move the mouse cursor across the
     5836plot, the plot status line will show the cursor position in 2</span></span><span
    58265837style='mso-bookmark:Pawley'><span style='font-family:Symbol;mso-fareast-font-family:
    58275838"Times New Roman"'>Q</span></span><span style='mso-bookmark:Pawley'><span
     
    58635874"Times New Roman"'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    58645875</span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    5865 normal'>d</b></span><b style='mso-bidi-font-weight:normal'>: offset down</b> - for
    5866 a waterfall plot of multiple powder profiles, increase the offset down. Does
    5867 not apply if only one pattern.</span></p>
     5876normal'>d</b></span><b style='mso-bidi-font-weight:normal'>: offset down</b> -
     5877for a waterfall plot of multiple powder profiles, increase the offset down.
     5878Does not apply if only one pattern.</span></p>
    58685879
    58695880<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    58735884</span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    58745885normal'>u</b></span><b style='mso-bidi-font-weight:normal'>: offset up</b> -
    5875 for a waterfall plot of multiple powder profiles, increase the offset up. Does
    5876 not apply if only one pattern.</span></p>
     5886for a waterfall plot of multiple powder profiles, increase the offset up. Does not
     5887apply if only one pattern.</span></p>
    58775888
    58785889<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    60206031style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>:
    60216032contour off/on</span></b></span><span style='mso-bookmark:Pawley'><span
    6022 style='mso-fareast-font-family:"Times New Roman"'> &#8211; this turns off
    6023 contouring and returns to a waterfall plot with any offsets applied.<span
     6033style='mso-fareast-font-family:"Times New Roman"'> &#8211; this turns off contouring
     6034and returns to a waterfall plot with any offsets applied.<span
    60246035class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    60256036text-underline:none'><o:p></o:p></span></span></span></span></p>
     
    62456256none'><o:p></o:p></span></span></span></span></h4>
    62466257
    6247 <p class=MsoNormal><span style='mso-bookmark:Pawley'>This plot shows the atoms
    6248 of the crystal structure. The atoms are displayed according to the controls in the
     6258<p class=MsoNormal><span style='mso-bookmark:Pawley'>This plot shows the atoms of
     6259the crystal structure. The atoms are displayed according to the controls in the
    62496260</span><a href="gsasII.html"><span style='mso-bookmark:Pawley'><span
    62506261style='color:windowtext;text-decoration:none;text-underline:none'>Draw Options</span></span></a><span
     
    62686279
    62696280</span></span></a></div>
     6281
     6282<p class=MsoNormal align=center style='text-align:center'><span
     6283style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    62706284
    62716285<p class=MsoNormal align=center style='text-align:center'><span
  • trunk/help/gsasII_files/props011.xml

    r1197 r1258  
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