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Timestamp:
Aug 19, 2012 1:14:18 PM (9 years ago)
Author:
toby
Message:

update sandbox docs

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  • branches/sandbox/doc/expgui6.html

    r1150 r1217  
    2222<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
    2323<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    24 </TH><TH><A Href="expgui6A.html">Next page</A>
     24</TH><TH><A Href="expgui6R.html">Next page</A>
    2525</TH><TH><A Href="expgui5.html">Previous page</A>
    2626</TH></TR></TABLE><BR CLEAR=ALL>
     
    3232</h1></center>
    3333
    34 <h3>A.6 Re/Constraints panel</h3>
    35 <DL><DL>
    36 GSAS offers two types of restraints that can be included in a model.
    37 So called "soft constraints" or "restraints" penalize the fit if
    38 aspects of a model (for example, bond lengths) differ from selected values.
    39 So called "hard constraints" reduce the actual number of
     34<h3>A.6 Constraints panel</h3>
     35<DL><DL>
     36GSAS offers two ways to limit changes to parameters that are based rules
     37  created by a crystallographer to create what is felt to be the most
     38  reasonable model.
     39So called "soft constraints", which are better described as "restraints"
     40  penalize the fit if
     41aspects of a model (for example, bond lengths) differ from selected
     42  values. They are now located on the on the <A Href="expgui6R.html">Restraints panel</A>.
     43Actual constraints, which are sometimes called "hard constraints", are
     44  on panel described here. They reduce the actual number of
    4045parameters in a model,
    4146by grouping parameters so that a single shift (possibly scaled) is
    4247applied to each parameter in the group.
    43 The Re/Constraints panel is used to set these "hard constraints" or in
    44   the case of bond distances, "restraints".
    4548At this time the only constraints that can be set in EXPGUI are on atomic
    46 and profile profile (others can be set in EXPEDT). EXPEDT offers many
     49and profile profile (others can be set in EXPEDT).
     50  EXPEDT offers many
    4751  other types of restraints as well.
    4852<P>
     
    5155if two atoms
    5256are constrained so that the shift on their occupancy is the same, but
    53 the initial occupancies differ, the in occupancy difference will not change
    54 as the values refine.
     57the initial occupancies differ, the difference in their occupancies
     58  will not change as the values are refined.
    5559<P>
    5660Due to the way GSAS implements constraints, a parameter can be included
    5761in only one constraint. Should one or more parameters be constrained twice,
    58 the refinement results are unpredictable.
     62the refinement results are unpredictable, so EXPGUI will not allow
     63  this (EXPEDT will). One can sometimes bypass
     64  this problem by defining redundant parameters. For example to
     65  constrain the occupancy of site A to B and site A to C, one can
     66  create two atom A sites: A<sub>1</sub> & A<sub>2</sub>. Then one can create two
     67  constraints, for site A<sub>1</sub> to B and site A<sub>2</sub> to C. The actual occupancy
     68  of site A is then that of A<sub>1</sub> plus A<sub>2</sub>
    5969
    6070</DL></DL>
     
    6676variable by clicking on the buttons at the top of the panel.
    6777<P>
    68 To delete one or more constraints, click on the appropriate checkbuttons in the <B>Delete</B> column and the press the Delete button, below.
     78To delete one or more constraints, click on the appropriate
     79  checkbuttons
     80  in the <B>Delete</B> column and the press the Delete button, below.
    6981</DL></DL>
    7082<img SRC="mc.gif" align=TEXTTOP  alt="EXPGUI Screen snapshot">
     
    214226usually make sense and EXPGUI does not allow it.
    215227</DL></DL>
    216 <a name="DistanceRestraints"></a>
    217 <H4>Distance Restraints</H4>
    218 <DL><DL>
    219   When the distance restraints tab is first selected, the active
    220   distance restraints for the selected phase are shown. The <B>Atom 1</B> and
    221   <B>Atom 2</B> buttons can be used to sort this list.
    222   <P>
    223   The <B>Restraint Weight</B> parameter is very important. As this
    224   determines how strongly the distance restraints will be used in the
    225   refinement relative to the diffraction data. This value is sometimes
    226   set as high as 500,000 in the initial stages of a fit, but should be
    227   lowered as much as is possible in the final stages of the fit, as
    228   needed to obtain chemically plausible interatomic distances. For
    229   some refinements, a value of 0.0 is possible for the Restraint
    230   Weight in the final stages. This removes any restraint effect.
    231 
    232   To see how restraints are affecting the refinement, one can look at
    233   the ratio of the "Sum(w*d**2)" (shown in the .LST file) for the
    234   diffraction histograms vs. the restraint histogram.
    235 <P>
    236   The <B>Active Restraints Editor</B> can be used to select distances
    237   to be restrained or edit the restraints. If there are too many
    238   distances shown, the options at the top of the window can be used to
    239   select a distance range, or specific atoms to include. Likewise,
    240   only restrained or unrestrained distances can be selected. The
    241   changes are applied when the <B>Filter</B> button is pressed.
    242 <P>
    243   The bottom section of the window shows individual interatomic
    244   distances. A <B>Restraint</B> and <B>Tolerance</B> value is needed to restrain
    245   that distance. The quantity minimized is
    246 <blockquote>
    247 <blockquote>
    248  "Restraint Weight" * SUM{  [ (Distance - Restraint) / Tolerance ]**2 }
    249 </blockquote>
    250 </blockquote>
    251 thus the "Tolerance" provides individual weighting for each
    252   restraint.
    253 <P>
    254   To set a large number of restraints at the same time, select the
    255   check button next to the distance(s), or use the <B>Check
    256   All</B>. Then use the section above to enter a global
    257   <B>Restraint</B> and <B>Tolerance</B> value. These values are set
    258   when the <B>Set Checked</B> button is used.  The <B>Delete
    259   Checked</B> button removes restraints from all selected distances.
    260 <P>
    261 The entered restraint information will be used onlt when the <B>Save
    262   Changes</B> button is pressed. The <B>Cancel</B> button will reverse
    263   any changes made while the window is open. Closing the window has
    264   the same effect as "Cancel."
    265   <P>
    266   Note that the interatomic distances that are shown are determined by
    267   the parameters to program DISAGL. These are controlled with the
    268   <B>Edit Search Distance Parameters</B> button.
    269 
    270 </DL></DL>
    271228<hr>
    272229<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
    273230<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    274 </TH><TH><A Href="expgui6A.html">Next page</A>
     231</TH><TH><A Href="expgui6R.html">Next page</A>
    275232</TH><TH><A Href="expgui5.html">Previous page</A>
    276233</TH></TR></TABLE>
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