Changeset 1217 for branches/sandbox


Ignore:
Timestamp:
Aug 19, 2012 1:14:18 PM (8 years ago)
Author:
toby
Message:

update sandbox docs

Location:
branches/sandbox/doc
Files:
6 added
5 edited

Legend:

Unmodified
Added
Removed
  • branches/sandbox/doc/expgui.html

    r1157 r1217  
    5151<P>
    5252<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=CENTER>
    53 <TR><TH BGCOLOR="#F0F0F0" rowspan=3>GUI Sections</TH>
     53<TR><TH BGCOLOR="#F0F0F0" rowspan=4>GUI Sections</TH>
    5454<TH><A Href="expgui1.html">Least Squares</A></TH>
    5555<TH><A Href="expgui2.html">Phase info</A></TH>
     
    5959<TH><A Href="expgui4.html">Scaling info</A></TH>
    6060<TH><A Href="expgui5.html">Profile terms</A></TH>
    61 <TH><A Href="expgui6.html">Constraints & Restraints</A></TH>
     61<TH><A Href="expgui6.html">Constraints</A></TH>
    6262</TR>
    6363<TR>
     64<TH><A Href="expgui6R.html">Restraints</A></TH>
    6465<TH><A Href="expgui6A.html">Rigid Bodies</A></TH>
    6566<TH><A Href="expgui7.html">Preferred Orientation</A></TH>
     67</TR>
     68<TR>
    6669<TH><A Href="expguic.html">Menus</A></TH>
     70<TH>&nbsp;</TH>
    6771<TH>&nbsp;</TH>
    6872</TR>
  • 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>
  • branches/sandbox/doc/expgui6A.html

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    r1173 r1217  
    2323<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    2424</TH><TH><A Href="expgui7.html">Next page</A>
    25 </TH><TH><A Href="expgui6.html">Previous page</A>
     25</TH><TH><A Href="expgui6R.html">Previous page</A>
    2626</TH></TR></TABLE><BR CLEAR=ALL>
    2727
    2828<center><h1>
    2929<HR noshade width="75%" size="2" align="center">
    30 EXPGUI, part 7
     30EXPGUI, part 8
    3131<HR noshade width="75%" size="2" align="center">
    3232</h1></center>
    3333
    34 <h3>A.7 Rigid Body Introduction</h3>
     34<h3>A.8 Rigid Body Introduction</h3>
    3535<DL><DL>
    3636GSAS Rigid bodies are another way to constrain relative atomic
     
    108108</OL> 
    109109</DL></DL>
    110 <H3>A.7.a Main Rigid Body Panel</H3>
     110<H3>A.8.a Main Rigid Body Panel</H3>
    111111<DL><DL>
    112112The main panel for rigid bodies presents a interface where bodies can
     
    156156  </UL>
    157157 
    158  <H4>A.7.a1 Manual rigid body definition</H4>
     158 <H4>A.8.a1 Manual rigid body definition</H4>
    159159<DL>
    160160  The manual definition window allows input of coordinates and
     
    167167  <BR><img src="rb002.jpg" alt="Manual RB creation window">
    168168</DL>
    169  <H4>A.7.a2 Cartesian coordinates from ASCII text file</H4>
     169 <H4>A.8.a2 Cartesian coordinates from ASCII text file</H4>
    170170<DL>
    171171Cartesian coordinates
     
    184184</DL>
    185185
    186   <H4>A.7.a3 Cartesian coordinates from a Z-matrix</H4>
     186  <H4>A.8.a3 Cartesian coordinates from a Z-matrix</H4>
    187187<DL>
    188188Cartesian coordinates
     
    196196</DL>
    197197<A name="fromEXP">
    198 <H4>A.7.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4>
     198<H4>A.8.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4>
    199199</A>
    200200<DL>
     
    217217button) for later use. More commonly, the "Save and Map
    218218Rigid Body" button is used; this creates a new rigid body type and
    219   maps that body (<A href="#MapBody">see A.7.b2</A>) to the selected atoms in the phase.
     219  maps that body (<A href="#MapBody">see A.8.b2</A>) to the selected atoms in the phase.
    220220 <BR><img src="rb005.jpg" alt="Fraction Coords RB input window">
    221221</DL>
    222222
    223223</DL></DL>
    224 <H3>A.7.b Rigid Body Panel</H3>
     224<H3>A.8.b Rigid Body Panel</H3>
    225225<DL><DL>
    226226 As each rigid body is
     
    235235  <BR><img src="rb006.jpg" alt="RB edit panel">
    236236
    237   <H4>A.7.b1 Plot Rigid Body</H4>
     237  <H4>A.8.b1 Plot Rigid Body</H4>
    238238<DL>
    239239  <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A>
     
    249249</DL>
    250250<A name="MapBody">
    251  <H4>A.7.b2 Map Rigid Body</H4>
     251 <H4>A.8.b2 Map Rigid Body</H4>
    252252</A><DL>
    253253The rigid body must be mapped to the
     
    256256  <BR><img src="rb008.png" alt="Map RB"><BR>
    257257Note that when a rigid body is created from atoms already in the .EXP
    258   file (<A href="#fromEXP">see A.7.a4</A>), the "Save and Map" command
     258  file (<A href="#fromEXP">see A.8.a4</A>), the "Save and Map" command
    259259  performs this step automatically.
    260260  <P>
     
    291291<BR Clear="all">
    292292  </DL>
    293  <H4>A.7.b3 Edit Rigid Body</H4>
     293 <H4>A.8.b3 Edit Rigid Body</H4>
    294294  <DL>
    295295
     
    313313
    314314</DL></DL>
    315 <H3>A.7.c Setting Rigid Body Refinement Flags</H3>
     315<H3>A.8.c Setting Rigid Body Refinement Flags</H3>
    316316<DL><DL>
    317317 The "Refinement Flags" button opens a window that allows the
     
    362362<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    363363</TH><TH><A Href="expgui7.html">Next page</A>
    364 </TH><TH><A Href="expgui6.html">Previous page</A>
     364</TH><TH><A Href="expgui6R.html">Previous page</A>
    365365</TH></TR></TABLE>
    366366
  • branches/sandbox/doc/expgui7.html

    r1164 r1217  
    2828<center><h1>
    2929<HR noshade width="75%" size="2" align="center">
    30 EXPGUI, part 8
     30EXPGUI, part 9
    3131<HR noshade width="75%" size="2" align="center">
    3232</h1></center>
    3333
    34 <h3>A.8 Preferential Orientation Panel</h3></a>
     34<h3>A.9 Preferential Orientation Panel</h3></a>
    3535<DL><DL>
    3636The Preferential Orientation Panel is used to control parameters related
     
    4343</DL></DL>
    4444<a name="MD"></a>
    45 <h4>A.8.a March-Dollase</H4>
     45<h4>A.9.a March-Dollase</H4>
    4646<DL><DL>
    4747In this model one or more axes are designated
     
    6767</DL></DL>
    6868<a name="ODF"></a>
    69 <H4>A.8.b Spherical harmonic</H4>
     69<H4>A.9.b Spherical harmonic</H4>
    7070<DL><DL>
    7171The spherical harmonic formulation, also referred to as an "orientation
  • branches/sandbox/doc/mc.gif

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