Changeset 1217 for branches

Timestamp:

Aug 19, 2012 1:14:18 PM (13 years ago)

Author:

toby

Message:

update sandbox docs

Location:

branches/sandbox/doc

Files:

• chem0.png (added)
• chem1.png (added)
• chem2.png (added)
• dist1.png (added)
• dist2.png (added)
• expgui.html (modified) (2 diffs)
• expgui6.html (modified) (5 diffs)
• expgui6A.html (modified) (13 diffs, 1 prop)
• expgui6R.html (added)
• expgui7.html (modified) (3 diffs)
• mc.gif (modified) (1 prop) (previous)

branches/sandbox/doc/expgui.html ¶

@@ -51 +51 @@
 <P>
 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=CENTER>
-<TR><TH BGCOLOR="#F0F0F0" rowspan=3>GUI Sections</TH>
+<TR><TH BGCOLOR="#F0F0F0" rowspan=4>GUI Sections</TH>
 <TH><A Href="expgui1.html">Least Squares</A></TH>
 <TH><A Href="expgui2.html">Phase info</A></TH>
@@ -59 +59 @@
 <TH><A Href="expgui4.html">Scaling info</A></TH>
 <TH><A Href="expgui5.html">Profile terms</A></TH>
-<TH><A Href="expgui6.html">Constraints & Restraints</A></TH>
+<TH><A Href="expgui6.html">Constraints</A></TH>
 </TR>
 <TR>
+<TH><A Href="expgui6R.html">Restraints</A></TH>
 <TH><A Href="expgui6A.html">Rigid Bodies</A></TH>
 <TH><A Href="expgui7.html">Preferred Orientation</A></TH>
+</TR>
+<TR>
 <TH><A Href="expguic.html">Menus</A></TH>
+<TH>&nbsp;</TH>
 <TH>&nbsp;</TH>
 </TR>

branches/sandbox/doc/expgui6.html ¶

@@ -22 +22 @@
 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
 <TR><TH><A  Href="expgui.html">EXPGUI top</A> 
-</TH><TH><A Href="expgui6A.html">Next page</A>
+</TH><TH><A Href="expgui6R.html">Next page</A>
 </TH><TH><A Href="expgui5.html">Previous page</A>
 </TH></TR></TABLE><BR CLEAR=ALL>
@@ -32 +32 @@
 </h1></center>
 
-<h3>A.6 Re/Constraints panel</h3>
-<DL><DL>
-GSAS offers two types of restraints that can be included in a model. 
-So called "soft constraints" or "restraints" penalize the fit if 
-aspects of a model (for example, bond lengths) differ from selected values.
-So called "hard constraints" reduce the actual number of 
+<h3>A.6 Constraints panel</h3>
+<DL><DL>
+GSAS offers two ways to limit changes to parameters that are based rules
+  created by a crystallographer to create what is felt to be the most
+  reasonable model.
+So called "soft constraints", which are better described as "restraints"
+  penalize the fit if 
+aspects of a model (for example, bond lengths) differ from selected
+  values. They are now located on the on the <A Href="expgui6R.html">Restraints panel</A>. 
+Actual constraints, which are sometimes called "hard constraints", are
+  on panel described here. They reduce the actual number of 
 parameters in a model,
 by grouping parameters so that a single shift (possibly scaled) is 
 applied to each parameter in the group.
-The Re/Constraints panel is used to set these "hard constraints" or in
-  the case of bond distances, "restraints".
 At this time the only constraints that can be set in EXPGUI are on atomic
-and profile profile (others can be set in EXPEDT). EXPEDT offers many
+and profile profile (others can be set in EXPEDT).
+  EXPEDT offers many
   other types of restraints as well.
 <P>
@@ -51 +55 @@
 if two atoms 
 are constrained so that the shift on their occupancy is the same, but 
-the initial occupancies differ, the in occupancy difference will not change 
-as the values refine.
+the initial occupancies differ, the difference in their occupancies
+  will not change as the values are refined.
 <P>
 Due to the way GSAS implements constraints, a parameter can be included 
 in only one constraint. Should one or more parameters be constrained twice,
-the refinement results are unpredictable.
+the refinement results are unpredictable, so EXPGUI will not allow
+  this (EXPEDT will). One can sometimes bypass
+  this problem by defining redundant parameters. For example to
+  constrain the occupancy of site A to B and site A to C, one can
+  create two atom A sites: A<sub>1</sub> & A<sub>2</sub>. Then one can create two
+  constraints, for site A<sub>1</sub> to B and site A<sub>2</sub> to C. The actual occupancy
+  of site A is then that of A<sub>1</sub> plus A<sub>2</sub>
 
 </DL></DL>
@@ -66 +76 @@
 variable by clicking on the buttons at the top of the panel.
 <P>
-To delete one or more constraints, click on the appropriate checkbuttons in the <B>Delete</B> column and the press the Delete button, below.
+To delete one or more constraints, click on the appropriate
+  checkbuttons
+  in the <B>Delete</B> column and the press the Delete button, below.
 </DL></DL>
 <img SRC="mc.gif" align=TEXTTOP  alt="EXPGUI Screen snapshot">
@@ -214 +226 @@
 usually make sense and EXPGUI does not allow it.
 </DL></DL>
-<a name="DistanceRestraints"></a>
-<H4>Distance Restraints</H4>
-<DL><DL>
-  When the distance restraints tab is first selected, the active
-  distance restraints for the selected phase are shown. The <B>Atom 1</B> and
-  <B>Atom 2</B> buttons can be used to sort this list.
-  <P>
-  The <B>Restraint Weight</B> parameter is very important. As this
-  determines how strongly the distance restraints will be used in the
-  refinement relative to the diffraction data. This value is sometimes
-  set as high as 500,000 in the initial stages of a fit, but should be
-  lowered as much as is possible in the final stages of the fit, as
-  needed to obtain chemically plausible interatomic distances. For
-  some refinements, a value of 0.0 is possible for the Restraint
-  Weight in the final stages. This removes any restraint effect.
-
-  To see how restraints are affecting the refinement, one can look at
-  the ratio of the "Sum(w*d**2)" (shown in the .LST file) for the
-  diffraction histograms vs. the restraint histogram.
-<P>
-  The <B>Active Restraints Editor</B> can be used to select distances
-  to be restrained or edit the restraints. If there are too many
-  distances shown, the options at the top of the window can be used to
-  select a distance range, or specific atoms to include. Likewise,
-  only restrained or unrestrained distances can be selected. The
-  changes are applied when the <B>Filter</B> button is pressed.
-<P>
-  The bottom section of the window shows individual interatomic
-  distances. A <B>Restraint</B> and <B>Tolerance</B> value is needed to restrain
-  that distance. The quantity minimized is
-<blockquote>
-<blockquote>
- "Restraint Weight" * SUM{  [ (Distance - Restraint) / Tolerance ]**2 } 
-</blockquote>
-</blockquote>
-thus the "Tolerance" provides individual weighting for each
-  restraint.
-<P>
-  To set a large number of restraints at the same time, select the
-  check button next to the distance(s), or use the <B>Check
-  All</B>. Then use the section above to enter a global
-  <B>Restraint</B> and <B>Tolerance</B> value. These values are set
-  when the <B>Set Checked</B> button is used.  The <B>Delete
-  Checked</B> button removes restraints from all selected distances.
-<P>
-The entered restraint information will be used onlt when the <B>Save
-  Changes</B> button is pressed. The <B>Cancel</B> button will reverse
-  any changes made while the window is open. Closing the window has
-  the same effect as "Cancel."
-  <P>
-  Note that the interatomic distances that are shown are determined by
-  the parameters to program DISAGL. These are controlled with the
-  <B>Edit Search Distance Parameters</B> button. 
-
-</DL></DL>
 <hr>
 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
 <TR><TH><A  Href="expgui.html">EXPGUI top</A> 
-</TH><TH><A Href="expgui6A.html">Next page</A>
+</TH><TH><A Href="expgui6R.html">Next page</A>
 </TH><TH><A Href="expgui5.html">Previous page</A>
 </TH></TR></TABLE>

branches/sandbox/doc/expgui6A.html ¶

@@ -23 +23 @@
 <TR><TH><A  Href="expgui.html">EXPGUI top</A> 
 </TH><TH><A Href="expgui7.html">Next page</A>
-</TH><TH><A Href="expgui6.html">Previous page</A>
+</TH><TH><A Href="expgui6R.html">Previous page</A>
 </TH></TR></TABLE><BR CLEAR=ALL>
 
 <center><h1>
 <HR noshade width="75%" size="2" align="center">
-EXPGUI, part 7
+EXPGUI, part 8
 <HR noshade width="75%" size="2" align="center">
 </h1></center>
 
-<h3>A.7 Rigid Body Introduction</h3>
+<h3>A.8 Rigid Body Introduction</h3>
 <DL><DL>
 GSAS Rigid bodies are another way to constrain relative atomic
@@ -108 +108 @@
 </OL>  
 </DL></DL>
-<H3>A.7.a Main Rigid Body Panel</H3>
+<H3>A.8.a Main Rigid Body Panel</H3>
 <DL><DL>
 The main panel for rigid bodies presents a interface where bodies can
@@ -156 +156 @@
   </UL>
   
- <H4>A.7.a1 Manual rigid body definition</H4>
+ <H4>A.8.a1 Manual rigid body definition</H4>
 <DL>
   The manual definition window allows input of coordinates and
@@ -167 +167 @@
   <BR><img src="rb002.jpg" alt="Manual RB creation window">
 </DL>
- <H4>A.7.a2 Cartesian coordinates from ASCII text file</H4>
+ <H4>A.8.a2 Cartesian coordinates from ASCII text file</H4>
 <DL>
 Cartesian coordinates
@@ -184 +184 @@
 </DL>
 
-  <H4>A.7.a3 Cartesian coordinates from a Z-matrix</H4>
+  <H4>A.8.a3 Cartesian coordinates from a Z-matrix</H4>
 <DL>
 Cartesian coordinates
@@ -196 +196 @@
 </DL>
 <A name="fromEXP">
-<H4>A.7.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4>
+<H4>A.8.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4>
 </A>
 <DL>
@@ -217 +217 @@
 button) for later use. More commonly, the "Save and Map
 Rigid Body" button is used; this creates a new rigid body type and
-  maps that body (<A href="#MapBody">see A.7.b2</A>) to the selected atoms in the phase.
+  maps that body (<A href="#MapBody">see A.8.b2</A>) to the selected atoms in the phase.
  <BR><img src="rb005.jpg" alt="Fraction Coords RB input window">
 </DL>
 
 </DL></DL>
-<H3>A.7.b Rigid Body Panel</H3>
+<H3>A.8.b Rigid Body Panel</H3>
 <DL><DL>
  As each rigid body is
@@ -235 +235 @@
   <BR><img src="rb006.jpg" alt="RB edit panel">
 
-  <H4>A.7.b1 Plot Rigid Body</H4>
+  <H4>A.8.b1 Plot Rigid Body</H4>
 <DL>
   <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A>
@@ -249 +249 @@
 </DL>
 <A name="MapBody">
- <H4>A.7.b2 Map Rigid Body</H4>
+ <H4>A.8.b2 Map Rigid Body</H4>
 </A><DL>
 The rigid body must be mapped to the
@@ -256 +256 @@
   <BR><img src="rb008.png" alt="Map RB"><BR> 
 Note that when a rigid body is created from atoms already in the .EXP
-  file (<A href="#fromEXP">see A.7.a4</A>), the "Save and Map" command
+  file (<A href="#fromEXP">see A.8.a4</A>), the "Save and Map" command
   performs this step automatically.
   <P>
@@ -291 +291 @@
 <BR Clear="all">
   </DL>
- <H4>A.7.b3 Edit Rigid Body</H4>
+ <H4>A.8.b3 Edit Rigid Body</H4>
   <DL>
 
@@ -313 +313 @@
 
 </DL></DL>
-<H3>A.7.c Setting Rigid Body Refinement Flags</H3>
+<H3>A.8.c Setting Rigid Body Refinement Flags</H3>
 <DL><DL>
  The "Refinement Flags" button opens a window that allows the
@@ -362 +362 @@
 <TR><TH><A  Href="expgui.html">EXPGUI top</A> 
 </TH><TH><A Href="expgui7.html">Next page</A>
-</TH><TH><A Href="expgui6.html">Previous page</A>
+</TH><TH><A Href="expgui6R.html">Previous page</A>
 </TH></TR></TABLE>
 

branches/sandbox/doc/expgui7.html ¶

@@ -28 +28 @@
 <center><h1>
 <HR noshade width="75%" size="2" align="center">
-EXPGUI, part 8
+EXPGUI, part 9
 <HR noshade width="75%" size="2" align="center">
 </h1></center>
 
-<h3>A.8 Preferential Orientation Panel</h3></a>
+<h3>A.9 Preferential Orientation Panel</h3></a>
 <DL><DL>
 The Preferential Orientation Panel is used to control parameters related
@@ -43 +43 @@
 </DL></DL>
 <a name="MD"></a>
-<h4>A.8.a March-Dollase</H4>
+<h4>A.9.a March-Dollase</H4>
 <DL><DL>
 In this model one or more axes are designated
@@ -67 +67 @@
 </DL></DL>
 <a name="ODF"></a>
-<H4>A.8.b Spherical harmonic</H4>
+<H4>A.9.b Spherical harmonic</H4>
 <DL><DL>
 The spherical harmonic formulation, also referred to as an "orientation