Changeset 1336


Ignore:
Timestamp:
May 7, 2014 3:09:02 PM (8 years ago)
Author:
vondreele
Message:

Add Small angle seq. fit to tutorial menu

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/help/gsasII.html

    r1330 r1336  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>140</o:Revision>
    28   <o:TotalTime>3991</o:TotalTime>
     27  <o:Revision>141</o:Revision>
     28  <o:TotalTime>3992</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2014-05-06T14:17:00Z</o:LastSaved>
     30  <o:LastSaved>2014-05-07T18:53:00Z</o:LastSaved>
    3131  <o:Pages>28</o:Pages>
    32   <o:Words>10836</o:Words>
    33   <o:Characters>61767</o:Characters>
     32  <o:Words>10847</o:Words>
     33  <o:Characters>61830</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>514</o:Lines>
    36   <o:Paragraphs>144</o:Paragraphs>
    37   <o:CharactersWithSpaces>72459</o:CharactersWithSpaces>
     35  <o:Lines>515</o:Lines>
     36  <o:Paragraphs>145</o:Paragraphs>
     37  <o:CharactersWithSpaces>72532</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
    22432243<meta name=Title content="Help for GSAS-II">
    22442244<meta name=Keywords content="">
    2245 <link href="gsasIIfav.png"
    2246 rel="SHORTCUT ICON">
     2245<link href=gsasIIfav.png rel="SHORTCUT ICON">
    22472246<!--[if gte mso 9]><xml>
    22482247 <o:shapedefaults v:ext="edit" spidmax="1027"/>
     
    22782277 <o:lock v:ext="edit" aspectratio="t"/>
    22792278</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1026" type="#_x0000_t75"
    2280  alt="Description: GSAS-II logo"
    2281  style='position:absolute;margin-left:44.8pt;margin-top:0;width:96pt;height:96pt;
    2282  z-index:251657728;visibility:visible;mso-wrap-style:square;
    2283  mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:0;
    2284  mso-wrap-distance-top:0;mso-wrap-distance-right:0;mso-wrap-distance-bottom:0;
    2285  mso-position-horizontal:right;mso-position-horizontal-relative:text;
    2286  mso-position-vertical:absolute;mso-position-vertical-relative:line;
    2287  mso-width-percent:0;mso-height-percent:0;mso-width-relative:page;
    2288  mso-height-relative:page' o:allowoverlap="f">
     2279 alt="Description: GSAS-II logo" style='position:absolute;margin-left:44.8pt;
     2280 margin-top:0;width:96pt;height:96pt;z-index:251657728;visibility:visible;
     2281 mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0;
     2282 mso-wrap-distance-left:0;mso-wrap-distance-top:0;mso-wrap-distance-right:0;
     2283 mso-wrap-distance-bottom:0;mso-position-horizontal:right;
     2284 mso-position-horizontal-relative:text;mso-position-vertical:absolute;
     2285 mso-position-vertical-relative:line;mso-width-percent:0;mso-height-percent:0;
     2286 mso-width-relative:page;mso-height-relative:page' o:allowoverlap="f">
    22892287 <v:imagedata src="gsas2logo.png"/>
    22902288 <w:wrap type="square" anchory="line"/>
    2291 </v:shape><![endif]--><![if !vml]><img width=128 height=128
    2292 src="gsas2logo.png"
    2293 align=right
    2294 alt="Description: GSAS-II logo"
    2295 v:shapes="Picture_x0020_2"><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Help
    2296 for GSAS-II<o:p></o:p></span></h1>
     2289</v:shape><![endif]--><![if !vml]><img width=128 height=128 src=gsas2logo.png
     2290align=right alt="Description: GSAS-II logo" v:shapes="Picture_x0020_2"><![endif]><span
     2291style='mso-fareast-font-family:"Times New Roman"'>Help for GSAS-II<o:p></o:p></span></h1>
    22972292
    22982293<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     
    23372332<p class=MsoNormal><strong><span style='font-weight:normal'><a
    23382333href="Calibration%20of%20an%20area%20detector%20in%20GSAS.htm">2-D Image
    2339 calibration<o:p></o:p></a></span></strong></p>
     2334calibration</a></span></strong><span class=MsoHyperlink><o:p></o:p></span></p>
    23402335
    23412336<p class=MsoNormal><strong><a
     
    23432338style='font-weight:normal'>2-D Image integration</span></a><o:p></o:p></strong></p>
    23442339
    2345 <p class=MsoNormal><strong><a href="Strain%20fitting%20of%202D%20data%20in%20GSAS-II.htm"><span
     2340<p class=MsoNormal><strong><a
     2341href="Strain%20fitting%20of%202D%20data%20in%20GSAS-II.htm"><span
    23462342style='font-weight:normal'>2-D Strain data fitting</span></a><o:p></o:p></strong></p>
    23472343
     
    23652361bold'><a href="Fitting%20Small%20Angle%20Scattering%20Data.htm"><span
    23662362style='mso-bidi-font-weight:normal'>Fitting Small Angle Scattering Data</span></a><o:p></o:p></span></strong></p>
     2363
     2364<p class=MsoNormal><strong><span style='font-weight:normal;mso-bidi-font-weight:
     2365bold'><a href="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data.htm"><span
     2366style='mso-bidi-font-weight:normal'>Sequential Refinement of Small Angle
     2367Scattering Data</span></a></span><o:p></o:p></strong></p>
     2368
     2369<p class=MsoNormal><strong><span style='font-weight:normal;mso-bidi-font-weight:
     2370bold'><o:p>&nbsp;</o:p></span></strong></p>
    23672371
    23682372<p class=MsoNormal><strong><o:p>&nbsp;</o:p></strong></p>
     
    24932497style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    24942498style='mso-bidi-font-weight:normal'>Sum powder data</b> – Form the sum of
    2495 previously read powder patterns; each with a multiplier. Can be used to
    2496 accumulate data, subtract background or empty container patterns, etc. Patterns
    2497 used to form the sum must be of identical range and step size. Result is a new
    2498 PWDR entry in the GSAS-II data tree.</p>
     2499previously read powder patterns; each with a multiplier. Can be used to accumulate
     2500data, subtract background or empty container patterns, etc. Patterns used to
     2501form the sum must be of identical range and step size. Result is a new PWDR
     2502entry in the GSAS-II data tree.</p>
    24992503
    25002504<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25532557style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
    25542558style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2555 style='mso-bidi-font-weight:normal'>Make new PDFs</b> – This creates the pair
    2556 distribution function (PDF) controls for each powder pattern selected in the
    2557 dialog box. See <b style='mso-bidi-font-weight:normal'><span style='color:#4F81BD;
    2558 mso-themecolor:accent1'><a href="#PDF_Controls">PDF Controls</a></span></b> for
    2559 further directions.</p>
     2559style='mso-bidi-font-weight:normal'>Make new PDFs</b> – This creates the pair distribution
     2560function (PDF) controls for each powder pattern selected in the dialog box. See
     2561<b style='mso-bidi-font-weight:normal'><span style='color:#4F81BD;mso-themecolor:
     2562accent1'><a href="#PDF_Controls">PDF Controls</a></span></b> for further
     2563directions.</p>
    25602564
    25612565<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    26272631style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    26282632class=GramE><b style='mso-bidi-font-weight:normal'>from</b></span><b
    2629 style='mso-bidi-font-weight:normal'> PDB file</b> - This reads the
    2630 macromolecular phase information from a Protein Data Base file (name.PDB or
    2631 name.ENT). The file name is found in a directory dialog; you can change
    2632 directories as needed. Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT
    2633 (or .<span class=SpellE>ent</span>) file names are shown. Be careful that the
    2634 space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II
    2635 conventions (e.g. with spaces between axial fields). A dialog box is shown with
    2636 the proposed phase name. You can change it if desired.</p>
     2633style='mso-bidi-font-weight:normal'> PDB file</b> - This reads the macromolecular
     2634phase information from a Protein Data Base file (name.PDB or name.ENT). The
     2635file name is found in a directory dialog; you can change directories as needed.
     2636Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT (or .<span class=SpellE>ent</span>)
     2637file names are shown. Be careful that the space group symbol on the ‘CRYST1’
     2638record in the PDB file follows the GSAS-II conventions (e.g. with spaces
     2639between axial fields). A dialog box is shown with the proposed phase name. You
     2640can change it if desired.</p>
    26372641
    26382642<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     
    27032707</span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    27042708normal'>from</b></span><b style='mso-bidi-font-weight:normal'> GSAS-II <span
    2705 class=SpellE>gpx</span> file</b> This reads powder patterns from a previously
    2706 created GSAS-II <span class=SpellE>gpx</span> project file. If the selected
    2707 file has more than one powder pattern, a dialog is shown with the choices; one
    2708 or more can be selected. It will ask for an appropriate instrument parameter
    2709 file to go with the selected powder data sets. <b style='mso-bidi-font-weight:
    2710 normal'><o:p></o:p></b></p>
     2709class=SpellE>gpx</span> file</b> This reads powder patterns from a previously created
     2710GSAS-II <span class=SpellE>gpx</span> project file. If the selected file has
     2711more than one powder pattern, a dialog is shown with the choices; one or more
     2712can be selected. It will ask for an appropriate instrument parameter file to go
     2713with the selected powder data sets. <b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
    27112714
    27122715<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     
    27952798style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    27962799</span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    2797 normal'>guess</b></span><b style='mso-bidi-font-weight:normal'> format from
    2798 file</b> This attempts to read one set of single crystal structure factors from
    2799 a file trying the formats as described above. One should not use this for SHELX
    2800 format files as the form of the structure factors is not indicated from within
    2801 the file.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
     2800normal'>guess</b></span><b style='mso-bidi-font-weight:normal'> format from file</b>
     2801This attempts to read one set of single crystal structure factors from a file
     2802trying the formats as described above. One should not use this for SHELX format
     2803files as the form of the structure factors is not indicated from within the
     2804file.<b style='mso-bidi-font-weight:normal'><o:p></o:p></b></p>
    28022805
    28032806<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l14 level1 lfo1'><![if !supportLists]><span
     
    28192822style='mso-bidi-font-weight:normal'>Export All Peak Lists…</b> - This writes
    28202823the contents of the Peak List for all PWDR data onto a simple text file. There
    2821 will be a heading for each PWDR GSAS-II tree item and columns of values for
    2822 position, intensity, sigma and gamma follow.</p>
     2824will be a heading for each PWDR GSAS-II tree item and columns of values for position,
     2825intensity, sigma and gamma follow.</p>
    28232826
    28242827<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    29232926style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    29242927style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’ for
    2925 convergence; the refinement will stop when the change in the minimization
    2926 function is less than this value. Set Min delta-M/M = 1.0 to force just a
    2927 single cycle to be performed. A value less than 10<sup>-4</sup> (the default)
    2928 generally gives no better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
     2928convergence; the refinement will stop when the change in the minimization function
     2929is less than this value. Set Min delta-M/M = 1.0 to force just a single cycle
     2930to be performed. A value less than 10<sup>-4</sup> (the default) generally
     2931gives no better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
    29292932
    29302933<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span
     
    31293132style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
    31303133restraints</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    3131 this takes you through a sequence of dialog boxes which ask for the identities
    3132 of the atoms involved in the restraint and the value to be assigned to the
     3134this takes you through a sequence of dialog boxes which ask for the identities of
     3135the atoms involved in the restraint and the value to be assigned to the
    31333136restraint. The <span class=SpellE>esd</span> is given a default value which can
    31343137be changed after the restraints are created.<o:p></o:p></span></p>
     
    32623265style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Import
    32633266residues</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    3264 (Residue rigid bodies) this reads a predetermined macro file that contains standard
    3265 (<span class=SpellE>Engh</span> &amp; Huber) coordinates for the amino acids
    3266 found in natural proteins along with predetermined variable torsion angle
     3267(Residue rigid bodies) this reads a predetermined macro file that contains
     3268standard (<span class=SpellE>Engh</span> &amp; Huber) coordinates for the amino
     3269acids found in natural proteins along with predetermined variable torsion angle
    32673270definitions.<o:p></o:p></span></p>
    32683271
     
    33773380
    33783381<p class=MsoNormal><span style='mso-bookmark:Comments'>This window shows
    3379 whatever comment lines (preceded by “#”) found when the powder data file was read
    3380 by GSAS-II. If you are lucky, there will be useful information here (e.g.
     3382whatever comment lines (preceded by “#”) found when the powder data file was
     3383read by GSAS-II. If you are lucky, there will be useful information here (e.g.
    33813384sample name, date collected, wavelength used, etc.). If not, this window will
    33823385be blank. The text is read-only.</span></p>
     
    34993502
    35003503<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>3).
    3501 A set of individual Bragg peaks using the pseudo-Voigt profile function as their
    3502 shapes. Their parameters are ‘<span class=SpellE>pos</span>’, ’<span
     3504A set of individual Bragg peaks using the pseudo-Voigt profile function as
     3505their shapes. Their parameters are ‘<span class=SpellE>pos</span>’, ’<span
    35033506class=SpellE>int</span>’, ‘sig’ &amp; ‘gam’; each can be selected for
    35043507refinement. The default values for sig &amp; gam (=0.10) are for very sharp
     
    35333536flags </span></b><span style='mso-fareast-font-family:"Times New Roman"'>– this
    35343537copies only the refinement flags shown to other selected powder patterns. If
    3535 used, a dialog box (Copy Refinement Flags) will appear showing the list of
    3536 available powder patterns, you can copy the refinement flags to any or all of
    3537 them; select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the
    3538 copy; ‘Cancel’ to cancel the operation.<o:p></o:p></span></p>
     3538used, a dialog box (Copy Refinement Flags) will appear showing the list of available
     3539powder patterns, you can copy the refinement flags to any or all of them;
     3540select ‘All’ to copy them to all patterns. Then select ‘OK’ to do the copy;
     3541‘Cancel’ to cancel the operation.<o:p></o:p></span></p>
    35393542
    35403543<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l23 level1 lfo10'><![if !supportLists]><span
     
    38173820
    38183821<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    3819 window shows the list of peaks that will be used by the peak fitting
    3820 refinement. It is filled by picking peaks in the powder pattern displayed in
    3821 the GSASII Plots window as a sequence of ‘+’ marks.<span class=MsoHyperlink><span
     3822window shows the list of peaks that will be used by the peak fitting refinement.
     3823It is filled by picking peaks in the powder pattern displayed in the GSASII
     3824Plots window as a sequence of ‘+’ marks.<span class=MsoHyperlink><span
    38223825style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    38233826
     
    41394142</span></b></span><span style='mso-bookmark:Reflection_List'><span
    41404143style='mso-fareast-font-family:"Times New Roman"'>– this controls the extent of
    4141 the search for the correct indexing. This may need to be increased if an
    4142 indexing trial terminates too quickly. It rarely needs to be changed.<span
     4144the search for the correct indexing. This may need to be increased if an indexing
     4145trial terminates too quickly. It rarely needs to be changed.<span
    41434146class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    41444147text-underline:none'><o:p></o:p></span></span></span></span></p>
     
    41954198style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy
    41964199Cell</span></b></span><span style='mso-bookmark:Reflection_List'><span
    4197 style='mso-fareast-font-family:"Times New Roman"'> – this copies selected
    4198 solution to the Unit cell values; attention is paid to the Bravais lattice
    4199 shown for the choice and you may select a <b style='mso-bidi-font-weight:normal'>Space
    4200 group</b> from the pull down box. Press <b style='mso-bidi-font-weight:normal'>Show
    4201 hkl positions</b> to give the allowed peaks; to confirm the indexing compare
    4202 these to peak positions and any unfitted peaks in the pattern.<span
     4200style='mso-fareast-font-family:"Times New Roman"'> – this copies selected solution
     4201to the Unit cell values; attention is paid to the Bravais lattice shown for the
     4202choice and you may select a <b style='mso-bidi-font-weight:normal'>Space group</b>
     4203from the pull down box. Press <b style='mso-bidi-font-weight:normal'>Show hkl
     4204positions</b> to give the allowed peaks; to confirm the indexing compare these
     4205to peak positions and any unfitted peaks in the pattern.<span
    42034206class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    42044207text-underline:none'><o:p></o:p></span></span></span></span></p>
     
    44684471name="Map_peaks"></a><a href="gsasII.html"><span style='mso-bookmark:Map_peaks'><span
    44694472style='color:windowtext;text-decoration:none;text-underline:none'>Map peaks</span></span></a><span
    4470 style='mso-bookmark:Map_peaks'></span>’ page. This page will immediately be
    4471 shown and the peaks will be shown on the structure drawing for this phase as
    4472 white 3-D crosses.<span class=MsoHyperlink><span style='color:windowtext;
    4473 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     4473style='mso-bookmark:Map_peaks'></span>’ page. This page will immediately be shown
     4474and the peaks will be shown on the structure drawing for this phase as white
     44753-D crosses.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     4476none;text-underline:none'><o:p></o:p></span></span></span></p>
    44744477
    44754478<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    45474550</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    45484551style='mso-fareast-font-family:"Times New Roman"'>Space group</span></b><span
    4549 style='mso-fareast-font-family:"Times New Roman"'> – this should be set when
    4550 the phase is initialized; it can be changed later. Be careful about the impact
    4551 on Atom site symmetry and multiplicity if you do. GSAS-II will recognize any
    4552 legal space group symbol using the short Hermann-Mauguin forms; put a space
    4553 between the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’). For space groups with a
    4554 choice of origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup> setting
    4555 where the center of inversion is located at the origin. The choice of space
    4556 group will set the available unit cell parameters.<span class=MsoHyperlink><span
     4552style='mso-fareast-font-family:"Times New Roman"'> – this should be set when the
     4553phase is initialized; it can be changed later. Be careful about the impact on
     4554Atom site symmetry and multiplicity if you do. GSAS-II will recognize any legal
     4555space group symbol using the short Hermann-Mauguin forms; put a space between
     4556the axial fields (e.g. ‘F d 3 m’ not ‘Fd3m’). For space groups with a choice of
     4557origin (e.g. F d 3 m), GSAS-II always uses the 2<sup>nd</sup> setting where the
     4558center of inversion is located at the origin. The choice of space group will
     4559set the available unit cell parameters.<span class=MsoHyperlink><span
    45574560style='color:windowtext'><o:p></o:p></span></span></span></p>
    45584561
     
    46514654    "Times New Roman"'><m:r>5</m:r></span></i></m:sub></m:sSub><i
    46524655  style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math","serif";
    4653   mso-fareast-font-family:"Times New Roman"'><m:r>k&#55349;&#56409;</m:r></span></i></m:oMath></m:oMathPara><![endif]--><![if !msEquation]><span
     4656  mso-fareast-font-family:"Times New Roman"'><m:r>kl</m:r></span></i></m:oMath></m:oMathPara><![endif]--><![if !msEquation]><span
    46544657style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family:
    46554658"Times New Roman";mso-fareast-theme-font:minor-fareast;mso-ansi-language:EN-US;
     
    47764779</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    47774780style='mso-fareast-font-family:"Times New Roman"'>Normalizing element </span></b><span
    4778 style='mso-fareast-font-family:"Times New Roman"'>– This is an element form
    4779 factor chosen to normalize the structure factors before charge flipping. <b
     4781style='mso-fareast-font-family:"Times New Roman"'>– This is an element form factor
     4782chosen to normalize the structure factors before charge flipping. <b
    47804783style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from
    47814784the lower right of the Periodic Table display shown when this is selected.<span
     
    48304833set from</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    48314834This is the source of structure factors to be used in a charge flip
    4832 calculation. These may be either a single crystal data set, or structure
    4833 factors extracted from a powder pattern via a Pawley refinement or a Rietveld
     4835calculation. These may be either a single crystal data set, or structure factors
     4836extracted from a powder pattern via a Pawley refinement or a Rietveld
    48344837refinement.<o:p></o:p></span></p>
    48354838
     
    49384941</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    49394942style='mso-fareast-font-family:"Times New Roman"'>Shift LMB</span></b><span
    4940 style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects
    4941 all atoms from last selection to the selected row (or top is none previously
     4943style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects all
     4944atoms from last selection to the selected row (or top is none previously
    49424945selected).<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    49434946none;text-underline:none'><o:p></o:p></span></span></span></p>
     
    49624965style='mso-fareast-font-family:"Times New Roman"'>Alt LMB</span></b><span
    49634966style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects
    4964 that atom for moving; the status line at bottom of window will show name of
    4965 atom selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b> again to
     4967that atom for moving; the status line at bottom of window will show name of atom
     4968selected. Use <b style='mso-bidi-font-weight:normal'>Alt LMB</b> again to
    49664969select a target row for this atom; insertion will be before this row and the
    49674970table will be updated to show the change. NB: the <b style='mso-bidi-font-weight:
     
    49964999</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    49975000style='mso-fareast-font-family:"Times New Roman"'>Atom data item editing tools</span></b><span
    4998 style='mso-fareast-font-family:"Times New Roman"'> – These are controlled by
    4999 the mouse (<b style='mso-bidi-font-weight:normal'>Alt</b> ignored, <b
     5001style='mso-fareast-font-family:"Times New Roman"'> – These are controlled by the
     5002mouse (<b style='mso-bidi-font-weight:normal'>Alt</b> ignored, <b
    50005003style='mso-bidi-font-weight:normal'>Shift</b> &amp; <b style='mso-bidi-font-weight:
    50015004normal'>Ctrl</b> allow selection of multiple cells but no use is made of them).
     
    50365039</span></span></span></span><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    50375040normal'><span style='mso-fareast-font-family:"Times New Roman"'>refine</span></b></span><span
    5038 style='mso-fareast-font-family:"Times New Roman"'> – shows a pulldown of
    5039 allowed refinement flag choices to be shown; select one (top entry is blank for
    5040 no refinement).<span class=MsoHyperlink><span style='color:windowtext;
    5041 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     5041style='mso-fareast-font-family:"Times New Roman"'> – shows a pulldown of allowed
     5042refinement flag choices to be shown; select one (top entry is blank for no
     5043refinement).<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     5044none;text-underline:none'><o:p></o:p></span></span></span></p>
    50425045
    50435046<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    53935396mso-themecolor:accent1;mso-themeshade:191;mso-style-textfill-fill-color:#376092;
    53945397mso-style-textfill-fill-themecolor:accent1;mso-style-textfill-fill-alpha:100.0%;
    5395 mso-style-textfill-fill-colortransforms:lumm=75000'><a
    5396 href="#Rigid_bodies"><!--[if supportFields]><span
     5398mso-style-textfill-fill-colortransforms:lumm=75000'><a href="#Rigid_bodies"><!--[if supportFields]><span
    53975399style='color:black;mso-style-textfill-fill-color:black;mso-style-textfill-fill-alpha:
    53985400100.0%'><span style='mso-element:field-begin'></span></span><span
     
    54255427(magnitude, x y &amp; z) of all peaks found within the unit cell from the last
    54265428Fourier/charge flip map search sorted in order of decreasing peak magnitude.
    5427 The crystal structure plot shows each peak position as a white to dark gray cross;
    5428 the shade is determined from the magnitude for the peak relative to the maximum
    5429 peak magnitude.</span></p>
     5429The crystal structure plot shows each peak position as a white to dark gray
     5430cross; the shade is determined from the magnitude for the peak relative to the
     5431maximum peak magnitude.</span></p>
    54305432
    54315433<h5><span style='mso-bookmark:Pawley'>What can I do here?</span></h5>
     
    54545456"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    54555457</span></span></span><![endif]>Select the <span class=SpellE><b
    5456 style='mso-bidi-font-weight:normal'>dzero</b></span> column – the entries will
    5457 be sorted with the smallest (distance from origin) at the top.</span></p>
     5458style='mso-bidi-font-weight:normal'>dzero</b></span> column – the entries will be
     5459sorted with the smallest (distance from origin) at the top.</span></p>
    54585460
    54595461<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l28 level1 lfo24'><span
     
    55425544class=MsoHyperlink><span style='color:#4F81BD;mso-themecolor:accent1'><o:p></o:p></span></span></span></h4>
    55435545
    5544 <p class=MsoNormal><span style='mso-bookmark:Pawley'>This gives the list of reflections
    5545 used in a Pawley refinement and can only be seen if the phase type is ‘Pawley’
    5546 (see </span><a href="#General"><span style='mso-bookmark:Pawley'><span
     5546<p class=MsoNormal><span style='mso-bookmark:Pawley'>This gives the list of
     5547reflections used in a Pawley refinement and can only be seen if the phase type
     5548is ‘Pawley’ (see </span><a href="#General"><span style='mso-bookmark:Pawley'><span
    55475549style='color:windowtext;text-decoration:none;text-underline:none'>General</span></span></a><span
    55485550style='mso-bookmark:Pawley'>).</span></p>
     
    55615563style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    55625564</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Pawley
    5563 create</b> – this creates a new set of Pawley reflections, over writing any preexisting
    5564 Pawley set. They are generated with d-spacings larger than the limit set as
    5565 ‘Pawley dmin’ in the General tab for this phase. By default the refine flags
    5566 are not set and the <span class=SpellE><span class=GramE>Fsq</span></span><span
     5565create</b> – this creates a new set of Pawley reflections, over writing any
     5566preexisting Pawley set. They are generated with d-spacings larger than the
     5567limit set as ‘Pawley dmin’ in the General tab for this phase. By default the
     5568refine flags are not set and the <span class=SpellE><span class=GramE>Fsq</span></span><span
    55675569class=GramE>(</span><span class=SpellE>hkl</span>) = 100.0.</span></p>
    55685570
     
    55925594click on the column heading). Then type ‘y’ to set the refine flags or ‘n’ to
    55935595clear the flags. You should deselect those reflections that fall below the
    5594 lower limit or above the upper limit of the powder pattern otherwise you may
    5595 have a singular matrix error in your Pawley refinement.</span></p>
     5596lower limit or above the upper limit of the powder pattern otherwise you may have
     5597a singular matrix error in your Pawley refinement.</span></p>
    55965598
    55975599<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo25'><span
     
    56435645
    56445646<p class=MsoNormal align=center style='text-align:center'><span
     5647style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
     5648
     5649<p class=MsoNormal align=center style='text-align:center'><span
    56455650style='mso-bookmark:Pawley'><span class=MsoHyperlink><span style='color:windowtext;
    56465651text-decoration:none;text-underline:none'><o:p>&nbsp;</o:p></span></span></span></p>
     
    56595664
    56605665</span></span></a></div>
     5666
     5667<p class=MsoNormal align=center style='text-align:center'><span
     5668style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    56615669
    56625670<p class=MsoNormal align=center style='text-align:center'><span
     
    57015709style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:"Times New Roman";
    57025710mso-no-proof:yes'><img border=0 width=227 height=33 id="_x0000_i1032"
    5703 src="graphbar.jpg"
    5704 alt="Description: toolbar on plots"></span></span><span
     5711src=graphbar.jpg alt="Description: toolbar on plots"></span></span><span
    57055712style='mso-bookmark:Pawley'><span class=MsoHyperlink><span style='mso-fareast-font-family:
    57065713"Times New Roman";color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     
    60036010style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>:
    60046011contour off/on</span></b></span><span style='mso-bookmark:Pawley'><span
    6005 style='mso-fareast-font-family:"Times New Roman"'> – this turns off contouring
    6006 and returns to a waterfall plot with any offsets applied.<span
    6007 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    6008 text-underline:none'><o:p></o:p></span></span></span></span></p>
     6012style='mso-fareast-font-family:"Times New Roman"'> – this turns off contouring and
     6013returns to a waterfall plot with any offsets applied.<span class=MsoHyperlink><span
     6014style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    60096015
    60106016<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo28'><span
     
    60266032style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Limits</span></b></span><span
    60276033style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:"Times New Roman"'>
    6028 - Modify the values of ‘changed’; this can be done on the plot by dragging the limit
    6029 bars (left – vertical green dashed line, right – vertical red dashed line) into
    6030 position. A left or right mouse click on a data point on the plot will set the
    6031 associated limit. In either case the appropriate value on the ‘changed’ row
    6032 will be updated immediately.<span class=MsoHyperlink><span style='color:windowtext;
    6033 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
     6034- Modify the values of ‘changed’; this can be done on the plot by dragging the
     6035limit bars (left – vertical green dashed line, right – vertical red dashed
     6036line) into position. A left or right mouse click on a data point on the plot
     6037will set the associated limit. In either case the appropriate value on the
     6038‘changed’ row will be updated immediately.<span class=MsoHyperlink><span
     6039style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    60346040
    60356041<h4><span style='mso-bookmark:Pawley'><a name=Covariance><span
     
    60436049"Times New Roman"'>The variance-covariance matrix as a color coded array is
    60446050shown on this page. The color bar to the right shows the range of covariances
    6045 (-1 to 1) and corresponding colors. The parameter names are to the right and the
    6046 parameter numbers are below the plot.<span class=MsoHyperlink><span
     6051(-1 to 1) and corresponding colors. The parameter names are to the right and
     6052the parameter numbers are below the plot.<span class=MsoHyperlink><span
    60476053style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    60486054
     
    60566062</span></span></span><![endif]>Move the mouse cursor across the plot. If on a
    60576063diagonal cell, the parameter name, value and esd is shown both as a tool tip
    6058 and in the right hand portion of the status bar. If the cursor is off the
    6059 diagonal, the two parameter names and their covariance are shown in the tool
    6060 tip and the status bar.</span></p>
     6064and in the right hand portion of the status bar. If the cursor is off the diagonal,
     6065the two parameter names and their covariance are shown in the tool tip and the
     6066status bar.</span></p>
    60616067
    60626068<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo29'><span
     
    62266232none'><o:p></o:p></span></span></span></span></h4>
    62276233
    6228 <p class=MsoNormal><span style='mso-bookmark:Pawley'>This plot shows the atoms of
    6229 the crystal structure. The atoms are displayed according to the controls in the
    6230 </span><a href="gsasII.html"><span style='mso-bookmark:Pawley'><span
     6234<p class=MsoNormal><span style='mso-bookmark:Pawley'>This plot shows the atoms
     6235of the crystal structure. The atoms are displayed according to the controls in
     6236the </span><a href="gsasII.html"><span style='mso-bookmark:Pawley'><span
    62316237style='color:windowtext;text-decoration:none;text-underline:none'>Draw Options</span></span></a><span
    62326238style='mso-bookmark:Pawley'> page.</span></p>
     
    62496255
    62506256</span></span></a></div>
     6257
     6258<p class=MsoNormal align=center style='text-align:center'><span
     6259style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    62516260
    62526261<p class=MsoNormal align=center style='text-align:center'><span
Note: See TracChangeset for help on using the changeset viewer.