Ignore:
Timestamp:
Aug 22, 2014 1:09:47 PM (8 years ago)
Author:
vondreele
Message:

add MCSA tutorial to main gsasII.html web page
change difB tern from d3 to 1/d - works much better
make all TOF/2-theta to dsp & vv conversions with G2lat.Pos2dsp & Dsp2pos routines.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/help/gsasII.html

    r1347 r1475  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>144</o:Revision>
    28   <o:TotalTime>3995</o:TotalTime>
     27  <o:Revision>145</o:Revision>
     28  <o:TotalTime>3997</o:TotalTime>
    2929  <o:Created>2011-11-28T16:49:00Z</o:Created>
    30   <o:LastSaved>2014-05-15T15:02:00Z</o:LastSaved>
    31   <o:Pages>2</o:Pages>
    32   <o:Words>10871</o:Words>
    33   <o:Characters>61971</o:Characters>
     30  <o:LastSaved>2014-08-22T13:28:00Z</o:LastSaved>
     31  <o:Pages>28</o:Pages>
     32  <o:Words>10888</o:Words>
     33  <o:Characters>62064</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    35   <o:Lines>516</o:Lines>
     35  <o:Lines>517</o:Lines>
    3636  <o:Paragraphs>145</o:Paragraphs>
    37   <o:CharactersWithSpaces>72697</o:CharactersWithSpaces>
     37  <o:CharactersWithSpaces>72807</o:CharactersWithSpaces>
    3838  <o:Version>14.00</o:Version>
    3939 </o:DocumentProperties>
     
    23582358href="Charge%20Flipping%20-%20sucrose.htm"><span style='font-weight:normal'>sucrose</span></a><o:p></o:p></strong></p>
    23592359
     2360<p class=MsoNormal><strong><span style='font-weight:normal;mso-bidi-font-weight:
     2361bold'>Monte Carlo/Simulated Annealing structure solution – <o:p></o:p></span></strong></p>
     2362
     2363<p class=MsoNormal style='text-indent:.5in'><strong><span style='font-weight:
     2364normal'><a href="MCSA%20in%20GSAS.htm">MCSA in GSAS-II<o:p></o:p></a></span></strong></p>
     2365
    23602366<p class=MsoNormal><strong><a href="Small%20Angle%20Image%20Processing.htm"><span
    23612367style='font-weight:normal'>Small angle image processing</span></a><o:p></o:p></strong></p>
     
    24002406
    24012407<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    2402 is a hierarchical view of the data items in your GSAS-II project (name.gpx).
    2403 Clicking on any item in the tree opens a window where information in that item
    2404 can be viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
     2408is a hierarchical view of the data items in your GSAS-II project (name.gpx). Clicking
     2409on any item in the tree opens a window where information in that item can be
     2410viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
    24052411Parameters&quot;</a> item under a ‘PWDR’ entry contains information about how
    24062412data were collected, such as the sample temperature <a href="#Sample_Parameters">(see
     
    24302436class=SpellE>gpx</span> file (e.g. name.bak3.gpx) to recover a previous version
    24312437of your project. Remember to <b style='mso-bidi-font-weight:normal'>Save As</b>…
    2432 to e.g. name.gpx to overwrite the current version. Otherwise you will get
    2433 backups of your backup file (e.g. name.bak3.bak0.gpx, etc.).</p>
     2438to e.g. name.gpx to overwrite the current version. Otherwise you will get backups
     2439of your backup file (e.g. name.bak3.bak0.gpx, etc.).</p>
    24342440
    24352441<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    24412447style='mso-fareast-font-family:"Times New Roman"'>, it will be saved there.
    24422448Otherwise, you will be prompted for a new name in a file dialog (you may change
    2443 directory as well). If the file exists, you will be asked if it OK to overwrite.</span></p>
     2449directory as well). If the file exists, you will be asked if it OK to
     2450overwrite.</span></p>
    24442451
    24452452<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25032510style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    25042511style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2505 style='mso-bidi-font-weight:normal'>Sum powder data</b> – Form the sum of previously
    2506 read powder patterns; each with a multiplier. Can be used to accumulate data,
    2507 subtract background or empty container patterns, etc. Patterns used to form the
    2508 sum must be of identical range and step size. Result is a new PWDR entry in the
    2509 GSAS-II data tree.</p>
     2512style='mso-bidi-font-weight:normal'>Sum powder data</b> – Form the sum of
     2513previously read powder patterns; each with a multiplier. Can be used to
     2514accumulate data, subtract background or empty container patterns, etc. Patterns
     2515used to form the sum must be of identical range and step size. Result is a new
     2516PWDR entry in the GSAS-II data tree.</p>
    25102517
    25112518<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25272534box for a name to be assigned to the new phase. Then the <b style='mso-bidi-font-weight:
    25282535normal'><a href="#General">General</a></b> tab is opened for this phase; you
    2529 should first select the phase type, enter the space group symbol and then
    2530 lattice parameters. Note that nonstandard space group symbols are permitted; there
    2531 must be spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’).</p>
     2536should first select the phase type, enter the space group symbol and then lattice
     2537parameters. Note that nonstandard space group symbols are permitted; there must
     2538be spaces between the axial fields (e.g. use ‘P n a 21’ not ‘Pna21’).</p>
    25322539
    25332540<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    25432550style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
    25442551style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    2545 style='mso-bidi-font-weight:normal'>Rename data</b> – This might be a bad idea!!
    2546 Don’t use this unless the data to be renamed has not been used anywhere in
    2547 GSAS-II, e.g. only rename freshly read data.</p>
     2552style='mso-bidi-font-weight:normal'>Rename data</b> – This might be a bad
     2553idea!! Don’t use this unless the data to be renamed has not been used anywhere
     2554in GSAS-II, e.g. only rename freshly read data.</p>
    25482555
    25492556<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    26392646style='mso-bidi-font-weight:normal'> PDB file</b> - This reads the
    26402647macromolecular phase information from a Protein Data Base file (name.PDB or
    2641 name.ENT). The file name is found in a directory dialog; you can change
    2642 directories as needed. Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT
    2643 (or .<span class=SpellE>ent</span>) file names are shown. Be careful that the
    2644 space group symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II
    2645 conventions (e.g. with spaces between axial fields). A dialog box is shown with
    2646 the proposed phase name. You can change it if desired.</p>
     2648name.ENT). The file name is found in a directory dialog; you can change directories
     2649as needed. Only .PDB (or .<span class=SpellE>pdb</span>) or .ENT (or .<span
     2650class=SpellE>ent</span>) file names are shown. Be careful that the space group
     2651symbol on the ‘CRYST1’ record in the PDB file follows the GSAS-II conventions
     2652(e.g. with spaces between axial fields). A dialog box is shown with the
     2653proposed phase name. You can change it if desired.</p>
    26472654
    26482655<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     
    27812788style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    27822789</span></span></span></b><![endif]><span class=GramE><b style='mso-bidi-font-weight:
    2783 normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F HKL file</b> This
    2784 reads structure factors (as F) and sig(F) from a SHELX format .<span
     2790normal'>from</b></span><b style='mso-bidi-font-weight:normal'> F HKL file</b>
     2791This reads structure factors (as F) and sig(F) from a SHELX format .<span
    27852792class=SpellE>hkl</span> file. The file names are found in a directory dialog;
    27862793you can change directories as needed. You must know this is the content of this
     
    28882895
    28892896<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    2890 window provides a place for you to enter whatever text commentary you wish.
    2891 Each time you enter this window, a date/time entry is provided for you. A
    2892 possibly useful technique is to select a portion of the <span class=SpellE>project.lst</span>
     2897window provides a place for you to enter whatever text commentary you wish. Each
     2898time you enter this window, a date/time entry is provided for you. A possibly
     2899useful technique is to select a portion of the <span class=SpellE>project.lst</span>
    28932900file after a refinement completes (it will contain refinement results with
    28942901residuals, new values &amp; <span class=SpellE>esds</span>) and paste it into
     
    29322939style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    29332940style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    2934 style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’ for convergence;
    2935 the refinement will stop when the change in the minimization function is less
    2936 than this value. Set Min delta-M/M = 1.0 to force just a single cycle to be
    2937 performed. A value less than 10<sup>-4</sup> (the default) generally gives no
    2938 better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
     2941style='mso-fareast-font-family:"Times New Roman"'>Select ‘Min delta-M/M’ for
     2942convergence; the refinement will stop when the change in the minimization
     2943function is less than this value. Set Min delta-M/M = 1.0 to force just a
     2944single cycle to be performed. A value less than 10<sup>-4</sup> (the default)
     2945generally gives no better result. The allowed range is 10<sup>-9</sup> to 1.0.<o:p></o:p></span></p>
    29392946
    29402947<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l18 level1 lfo2'><![if !supportLists]><span
     
    30343041will cancel the operation. The equivalenced parameters will show as an equation
    30353042of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0; usually
    3036 M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The keyword
    3037 ‘EQUIV’ marks it as <span class=GramE>an equivalence</span>. A Delete button
    3038 can be used to remove it.<o:p></o:p></span></p>
     3043M1=1.0 and M2=-1.0, but can be changed via the ‘Edit’ button. The keyword ‘EQUIV’
     3044marks it as <span class=GramE>an equivalence</span>. A Delete button can be
     3045used to remove it.<o:p></o:p></span></p>
    30393046
    30403047<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    31103117style='mso-fareast-font-family:"Times New Roman"'>You can examine the table of
    31113118restraints and change individual values; grayed out regions cannot be changed.
    3112 The ‘<span class=SpellE>calc</span>’ values are determined from the atom
    3113 positions in your structure, ‘<span class=SpellE>obs</span>’ values are the
    3114 target values for the restraint and ‘<span class=SpellE>esd</span>’ is the
    3115 uncertainty used to weight the restraint in the refinement (multiplied by the
    3116 weight factor).<o:p></o:p></span></p>
     3119The ‘<span class=SpellE>calc</span>’ values are determined from the atom positions
     3120in your structure, ‘<span class=SpellE>obs</span>’ values are the target values
     3121for the restraint and ‘<span class=SpellE>esd</span>’ is the uncertainty used
     3122to weight the restraint in the refinement (multiplied by the weight factor).<o:p></o:p></span></p>
    31173123
    31183124<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l12 level1 lfo4'><![if !supportLists]><span
     
    31813187style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Change
    31823188value</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – this
    3183 changes the ‘<span class=SpellE>obsd</span>’ value for selected restraints; a dialog
    3184 box will appear asking for the new value. <o:p></o:p></span></p>
     3189changes the ‘<span class=SpellE>obsd</span>’ value for selected restraints; a
     3190dialog box will appear asking for the new value. <o:p></o:p></span></p>
    31853191
    31863192<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    33373343style='mso-fareast-font-family:"Times New Roman";color:windowtext;font-weight:
    33383344normal;mso-bidi-font-weight:bold'> – this will create a text file of selected
    3339 columns with values and corresponding <span class=SpellE>esds</span>. A file dialog
    3340 box will appear; give a suitable file name; you may change directory if
     3345columns with values and corresponding <span class=SpellE>esds</span>. A file
     3346dialog box will appear; give a suitable file name; you may change directory if
    33413347desired.<o:p></o:p></span></h5>
    33423348
     
    33993405<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
    34003406window shows the limits in position to be used in any fitting for this powder
    3401 pattern. The ‘original’ values are obtained from the minimum &amp; maximum
    3402 values in the powder pattern. You can modify ‘changed’ as needed.<o:p></o:p></span></p>
     3407pattern. The ‘original’ values are obtained from the minimum &amp; maximum values
     3408in the powder pattern. You can modify ‘changed’ as needed.<o:p></o:p></span></p>
    34033409
    34043410<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
     
    37833789style='mso-fareast-font-family:"Times New Roman";color:windowtext'>Save</span></span><span
    37843790style='mso-bookmark:Powder_Peaks'><span style='mso-fareast-font-family:"Times New Roman";
    3785 color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this saves the
    3786 sample parameters to a file with the extension ’.samprm’. A file dialog box
     3791color:windowtext;font-weight:normal;mso-bidi-font-weight:bold'> – this saves
     3792the sample parameters to a file with the extension ’.samprm’. A file dialog box
    37873793will appear to ask for the file name.<span class=MsoHyperlink><span
    37883794style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></h5>
     
    40484054</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    40494055"Times New Roman"'>Menu ‘<b style='mso-bidi-font-weight:normal'>Operations</b>’
    4050 – <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads the peak
    4051 positions &amp; intensities from the </span><a href="#Peak_List"><span
    4052 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
    4053 none;text-underline:none'>Peak List</span></a><span style='mso-fareast-font-family:
    4054 "Times New Roman"'> to make them available for the indexing routine. The d-obs is
    4055 obtained from Bragg’s Law after applying the Zero correction shown on the </span><a
     4056– <b style='mso-bidi-font-weight:normal'>Load/Reload</b> – loads the peak positions
     4057&amp; intensities from the </span><a href="#Peak_List"><span style='mso-fareast-font-family:
     4058"Times New Roman";color:windowtext;text-decoration:none;text-underline:none'>Peak
     4059List</span></a><span style='mso-fareast-font-family:"Times New Roman"'> to make
     4060them available for the indexing routine. The d-obs is obtained from Bragg’s Law
     4061after applying the Zero correction shown on the </span><a
    40564062href="#Instrument_Parameters"><span style='mso-fareast-font-family:"Times New Roman";
    40574063color:windowtext;text-decoration:none;text-underline:none'>Instrument
     
    41724178style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    41734179</span></span></span></span><![endif]><span style='mso-fareast-font-family:
    4174 "Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Cell Index/Refine’
    4175 </b>– <span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    4176 none;text-underline:none'><o:p></o:p></span></span></span></span></p>
     4180"Times New Roman"'>Menu<b style='mso-bidi-font-weight:normal'> ‘Cell
     4181Index/Refine’ </b>– <span class=MsoHyperlink><span style='color:windowtext;
     4182text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    41774183
    41784184<p class=MsoListParagraphCxSpMiddle style='margin-left:.75in;mso-add-space:
     
    43354341style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    43364342style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select
    4337 the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> – select
    4338 between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p>
     4343the zone</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
     4344select between 100, 010 or 001; plot axes will be labeled accordingly.<o:p></o:p></span></p>
    43394345
    43404346<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo19'><![if !supportLists]><span
     
    44744480style='mso-fareast-font-family:"Times New Roman"'>Search maps </span></b><span
    44754481style='mso-fareast-font-family:"Times New Roman"'>– search the computed Fourier
    4476 map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this
    4477 procedure; they will be printed on the console and will be shown in the ‘<a
     4482map. Peaks that are above ‘Peak cutoff’ % of the maximum will be found in this procedure;
     4483they will be printed on the console and will be shown in the ‘<a
    44784484name="Map_peaks"></a><a href="gsasII.html"><span style='mso-bookmark:Map_peaks'><span
    44794485style='color:windowtext;text-decoration:none;text-underline:none'>Map peaks</span></span></a><span
     
    44924498style='mso-fareast-font-family:"Times New Roman"'>– This performs a charge
    44934499flipping <i style='mso-bidi-font-style:normal'>ab initio</i> structure solution
    4494 using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You will
    4495 need to select a source for the reflection set and perhaps select an element
    4496 for normalization by its form factor, a resolution limit (usually 0.5A) and a
    4497 charge flip threshold (usually 0.1); these are found at the bottom of the <b
    4498 style='mso-bidi-font-weight:normal'>General</b> window. A progress bar showing
    4499 the charge flip residual is shown while the charge flip is in operation. When
    4500 the residual is no longer decreasing (be patient – it doesn’t necessarily fall
    4501 continuously), press the <b style='mso-bidi-font-weight:normal'>Cancel</b>
     4500using the method of Oszlanyi &amp; Suto (Acta Cryst. A60, 134-141, 2004). You
     4501will need to select a source for the reflection set and perhaps select an
     4502element for normalization by its form factor, a resolution limit (usually 0.5A)
     4503and a charge flip threshold (usually 0.1); these are found at the bottom of the
     4504<b style='mso-bidi-font-weight:normal'>General</b> window. A progress bar
     4505showing the charge flip residual is shown while the charge flip is in
     4506operation. When the residual is no longer decreasing (be patient – it doesn’t
     4507necessarily fall continuously), press the <b style='mso-bidi-font-weight:normal'>Cancel</b>
    45024508button to stop the charge flipping. The resulting map will be positioned to
    45034509properly place symmetry operators (NB: depends on the quality of the resulting
     
    45464552</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    45474553style='mso-fareast-font-family:"Times New Roman"'>Phase type – </span></b><span
    4548 style='mso-fareast-font-family:"Times New Roman"'>this can only be set when
    4549 there are no atoms in the Atoms page for this phase. Select it when the phase
    4550 is initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
     4554style='mso-fareast-font-family:"Times New Roman"'>this can only be set when there
     4555are no atoms in the Atoms page for this phase. Select it when the phase is
     4556initialized.<span class=MsoHyperlink><span style='color:windowtext'><o:p></o:p></span></span></span></p>
    45514557
    45524558<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    47734779</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    47744780style='mso-fareast-font-family:"Times New Roman"'>Reflection set from</span></b><span
    4775 style='mso-fareast-font-family:"Times New Roman"'> – This is the source of structure
    4776 factors to be used in a charge flip calculation. These may be either a single
    4777 crystal data set, or structure factors extracted from a powder pattern via a
    4778 Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span
     4781style='mso-fareast-font-family:"Times New Roman"'> – This is the source of
     4782structure factors to be used in a charge flip calculation. These may be either
     4783a single crystal data set, or structure factors extracted from a powder pattern
     4784via a Pawley refinement or a Rietveld refinement.<span class=MsoHyperlink><span
    47794785style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
    47804786
     
    47864792</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    47874793style='mso-fareast-font-family:"Times New Roman"'>Normalizing element </span></b><span
    4788 style='mso-fareast-font-family:"Times New Roman"'>– This is an element form factor
    4789 chosen to normalize the structure factors before charge flipping. <b
     4794style='mso-fareast-font-family:"Times New Roman"'>– This is an element form
     4795factor chosen to normalize the structure factors before charge flipping. <b
    47904796style='mso-bidi-font-weight:normal'>None</b> (the default) can be selected from
    47914797the lower right of the Periodic Table display shown when this is selected.<span
     
    48294835style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>7.<span
    48304836style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
    4831 style='mso-fareast-font-family:"Times New Roman"'>Monte Carlo/Simulated Annealing
    4832 controls are at the bottom of the window. (Future capability &amp; under
    4833 development).<o:p></o:p></span></p>
     4837style='mso-fareast-font-family:"Times New Roman"'>Monte Carlo/Simulated
     4838Annealing controls are at the bottom of the window. (Future capability &amp;
     4839under development).<o:p></o:p></span></p>
    48344840
    48354841<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    48404846set from</span></b><span style='mso-fareast-font-family:"Times New Roman"'> –
    48414847This is the source of structure factors to be used in a charge flip
    4842 calculation. These may be either a single crystal data set, or structure factors
    4843 extracted from a powder pattern via a Pawley refinement or a Rietveld
     4848calculation. These may be either a single crystal data set, or structure
     4849factors extracted from a powder pattern via a Pawley refinement or a Rietveld
    48444850refinement.<o:p></o:p></span></p>
    48454851
     
    49104916text-underline:none'><o:p></o:p></span></span></h4>
    49114917
    4912 <p class=MsoNormal>This is the table of parameters for the atoms in this
    4913 crystal structure model. The menu controls allow manipulation of the values,
    4914 refinement flags as well as initiate calculations of geometrical values
    4915 (distances &amp; angles) among the atoms.</p>
     4918<p class=MsoNormal>This is the table of parameters for the atoms in this crystal
     4919structure model. The menu controls allow manipulation of the values, refinement
     4920flags as well as initiate calculations of geometrical values (distances &amp;
     4921angles) among the atoms.</p>
    49164922
    49174923<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
     
    49604966</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span
    49614967style='mso-fareast-font-family:"Times New Roman"'>Ctrl LMB</span></b><span
    4962 style='mso-fareast-font-family:"Times New Roman"'> – on a row number
    4963 selects/deselects the atom.<span class=MsoHyperlink><span style='color:windowtext;
    4964 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p>
     4968style='mso-fareast-font-family:"Times New Roman"'> – on a row number selects/deselects
     4969the atom.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
     4970none;text-underline:none'><o:p></o:p></span></span></span></p>
    49654971
    49664972<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    49854991style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    49864992</span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Double
    4987 left click a Type column heading</b>: a dialog box is shown that allows you to select
    4988 all atoms with that type. <span class=MsoHyperlink><span style='mso-fareast-font-family:
    4989 "Times New Roman";color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></p>
     4993left click a Type column heading</b>: a dialog box is shown that allows you to
     4994select all atoms with that type. <span class=MsoHyperlink><span
     4995style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration:
     4996none;text-underline:none'><o:p></o:p></span></span></p>
    49904997
    49914998<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l3 level1 lfo21'><![if !supportLists]><span
     
    51605167be applied to the parameter for all selected atoms. <span class=SpellE><b
    51615168style='mso-bidi-font-weight:normal'>Uiso</b></span> and <span class=SpellE><b
    5162 style='mso-bidi-font-weight:normal'>frac</b></span> will give popup for new
    5163 value to be used for all selected atoms. </p>
     5169style='mso-bidi-font-weight:normal'>frac</b></span> will give popup for new value
     5170to be used for all selected atoms. </p>
    51645171
    51655172<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    51905197style='mso-bidi-font-weight:normal'>Distances &amp; Angles – </b>compute
    51915198distances and angles with esds (if possible) for selected atoms. A popup dialog
    5192 box will appear with distance angle controls. NB: if atoms have been added or
    5193 their type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b>
     5199box will appear with distance angle controls. NB: if atoms have been added or their
     5200type changed, you may need to do a <b style='mso-bidi-font-weight:normal'>Reset</b>
    51945201of this dialog box before proceeding.</p>
    51955202
     
    52045211
    52055212<p class=MsoNormal>This gives a list of the atoms and bonds that are to be
    5206 rendered as lines, van der Waals radii balls, sticks, balls &amp; sticks,
    5207 ellipsoids &amp; sticks or polyhedra. There are two menus for this tab; Edit
    5208 allows modification of the list of atoms to be rendered and Compute gives some
    5209 options for geometric characterization of selected atoms.</p>
     5213rendered as lines, van der Waals radii balls, sticks, balls &amp; sticks, ellipsoids
     5214&amp; sticks or polyhedra. There are two menus for this tab; Edit allows
     5215modification of the list of atoms to be rendered and Compute gives some options
     5216for geometric characterization of selected atoms.</p>
    52105217
    52115218<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<span
     
    52365243the selection list. <b style='mso-bidi-font-weight:normal'>NB</b>: beware of
    52375244atoms that are hiding behind the one you are trying to select, they may be
    5238 selected inadvertently. You can rotate the structure anytime during the selection
    5239 process.</p>
     5245selected inadvertently. You can rotate the structure anytime during the
     5246selection process.</p>
    52405247
    52415248<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l13 level1 lfo22'><![if !supportLists]><span
     
    53275334style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
    53285335style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    5329 style='mso-bidi-font-weight:normal'>Fill CN-sphere</b> – using the atoms
    5330 currently in the draw atom table, find all atoms that belong in the
    5331 coordination sphere around the selected atoms via unit cell translations. NB:
    5332 symmetry operations are not used in this search.</p>
     5336style='mso-bidi-font-weight:normal'>Fill CN-sphere</b> – using the atoms currently
     5337in the draw atom table, find all atoms that belong in the coordination sphere
     5338around the selected atoms via unit cell translations. NB: symmetry operations
     5339are not used in this search.</p>
    53335340
    53345341<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
     
    53835390style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
    53845391style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
    5385 style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms are
    5386 selected, a best plane is determined for them. The result is shown on the
    5387 console window; it may be cut &amp; pasted to another application (e.g. Microsoft
    5388 Word). Shown are the atom coordinates transformed to Cartesian best plane
    5389 coordinates where the largest range is over the X-axis and the smallest is over
    5390 the Z-axis with the origin at the unweighted center of the selection. Root mean
    5391 square displacements along each axis for the best plane are also listed. The
    5392 Z-axis RMS value indicates the flatness of the proposed plane. <b
    5393 style='mso-bidi-font-weight:normal'>NB</b>: if you select (e.g. all) atoms then
    5394 Best plane will give Cartesian coordinates for these atoms with respect to a
    5395 coordinate system where the X-axis is along the longest axis of the atom
    5396 grouping and the Z-axis is along the shortest distance. The origin is at the
    5397 unweighted center of the selected atoms.</p>
     5392style='mso-bidi-font-weight:normal'>Best plane</b> – when 4 or more atoms are selected,
     5393a best plane is determined for them. The result is shown on the console window;
     5394it may be cut &amp; pasted to another application (e.g. Microsoft Word). Shown
     5395are the atom coordinates transformed to Cartesian best plane coordinates where
     5396the largest range is over the X-axis and the smallest is over the Z-axis with
     5397the origin at the unweighted center of the selection. Root mean square
     5398displacements along each axis for the best plane are also listed. The Z-axis
     5399RMS value indicates the flatness of the proposed plane. <b style='mso-bidi-font-weight:
     5400normal'>NB</b>: if you select (e.g. all) atoms then Best plane will give
     5401Cartesian coordinates for these atoms with respect to a coordinate system where
     5402the X-axis is along the longest axis of the atom grouping and the Z-axis is
     5403along the shortest distance. The origin is at the unweighted center of the
     5404selected atoms.</p>
    53985405
    53995406<h4>RB Models</h4>
     
    55965603style='mso-bookmark:Pawley'><![if !supportLists]><span style='mso-fareast-font-family:
    55975604"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    5598 </span></span></span><![endif]>You can change the refine flags either by clicking
    5599 on the box or by selecting one and then selecting the column (a single click on
    5600 the column heading). Then type ‘y’ to set the refine flags or ‘n’ to clear the
    5601 flags. You should deselect those reflections that fall below the lower limit or
    5602 above the upper limit of the powder pattern otherwise you may have a singular
    5603 matrix error in your Pawley refinement.</span></p>
     5605</span></span></span><![endif]>You can change the refine flags either by
     5606clicking on the box or by selecting one and then selecting the column (a single
     5607click on the column heading). Then type ‘y’ to set the refine flags or ‘n’ to
     5608clear the flags. You should deselect those reflections that fall below the
     5609lower limit or above the upper limit of the powder pattern otherwise you may
     5610have a singular matrix error in your Pawley refinement.</span></p>
    56045611
    56055612<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo25'><span
     
    56575664
    56585665<p class=MsoNormal align=center style='text-align:center'><span
     5666style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
     5667
     5668<p class=MsoNormal align=center style='text-align:center'><span
    56595669style='mso-bookmark:Pawley'><span class=MsoHyperlink><span style='color:windowtext;
    56605670text-decoration:none;text-underline:none'><o:p>&nbsp;</o:p></span></span></span></p>
     
    56735683
    56745684</span></span></a></div>
     5685
     5686<p class=MsoNormal align=center style='text-align:center'><span
     5687style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    56755688
    56765689<p class=MsoNormal align=center style='text-align:center'><span
     
    60226035style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>:
    60236036contour off/on</span></b></span><span style='mso-bookmark:Pawley'><span
    6024 style='mso-fareast-font-family:"Times New Roman"'> – this turns off contouring
    6025 and returns to a waterfall plot with any offsets applied.<span
    6026 class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
    6027 text-underline:none'><o:p></o:p></span></span></span></span></p>
     6037style='mso-fareast-font-family:"Times New Roman"'> – this turns off contouring and
     6038returns to a waterfall plot with any offsets applied.<span class=MsoHyperlink><span
     6039style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    60286040
    60296041<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo28'><span
     
    60616073<p class=MsoNormal><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:
    60626074"Times New Roman"'>The variance-covariance matrix as a color coded array is
    6063 shown on this page. The color bar to the right shows the range of covariances (-1
    6064 to 1) and corresponding colors. The parameter names are to the right and the
    6065 parameter numbers are below the plot.<span class=MsoHyperlink><span
     6075shown on this page. The color bar to the right shows the range of covariances
     6076(-1 to 1) and corresponding colors. The parameter names are to the right and
     6077the parameter numbers are below the plot.<span class=MsoHyperlink><span
    60666078style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p>
    60676079
     
    60756087</span></span></span><![endif]>Move the mouse cursor across the plot. If on a
    60766088diagonal cell, the parameter name, value and esd is shown both as a tool tip
    6077 and in the right hand portion of the status bar. If the cursor is off the
    6078 diagonal, the two parameter names and their covariance are shown in the tool
    6079 tip and the status bar.</span></p>
     6089and in the right hand portion of the status bar. If the cursor is off the diagonal,
     6090the two parameter names and their covariance are shown in the tool tip and the
     6091status bar.</span></p>
    60806092
    60816093<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l9 level1 lfo29'><span
     
    61386150style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>p</span></span><span
    61396151style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:"Times New Roman"'>/d)
    6140 from the Gaussian and Lorentzian parts of the profile function. The computed
    6141 curves are based on the values of U, V, W, X and Y shown in the Instrument
    6142 Parameters window in parentheses. These are the values for the instrument
    6143 contribution that were set when the powder pattern was first read in to
    6144 GSAS-II. If individual peak fitting has been performed, the values of ‘sig’
    6145 &amp; ‘gam’ for the peaks are plotted as ‘+’; these are computed from the
    6146 fitted values of U, V, W, X and Y as well as any sig or gam individually
    6147 refined.<span class=MsoHyperlink><span style='color:windowtext;text-decoration:
    6148 none;text-underline:none'><o:p></o:p></span></span></span></span></p>
     6152from the Gaussian and Lorentzian parts of the profile function. The computed curves
     6153are based on the values of U, V, W, X and Y shown in the Instrument Parameters
     6154window in parentheses. These are the values for the instrument contribution
     6155that were set when the powder pattern was first read in to GSAS-II. If
     6156individual peak fitting has been performed, the values of ‘sig’ &amp; ‘gam’ for
     6157the peaks are plotted as ‘+’; these are computed from the fitted values of U,
     6158V, W, X and Y as well as any sig or gam individually refined.<span
     6159class=MsoHyperlink><span style='color:windowtext;text-decoration:none;
     6160text-underline:none'><o:p></o:p></span></span></span></span></p>
    61496161
    61506162<h4><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:
     
    62996311style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
    63006312
     6313<p class=MsoNormal align=center style='text-align:center'><span
     6314style='mso-bookmark:Pawley'><o:p>&nbsp;</o:p></span></p>
     6315
    63016316<p class=MsoNormal><span style='mso-bookmark:Pawley'><!-- hhmts start --></span><a
    63026317href="gsasII.html"><span style='mso-bookmark:Pawley'><span style='mso-fareast-font-family:
Note: See TracChangeset for help on using the changeset viewer.