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1<html>
2<head>
3   <title>EXPGUI</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
5   GSAS, EXPGUI">
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15
16<?
17   include("/var/www/include/navigation.inc");
18   include("/var/www/include/utility.inc");
19?>
20<blockquote><font face="arial, helvetica, sans-serif">
21
22<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
23<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
24</TH><TH><A Href="expgui6A.html">Next page</A>
25</TH><TH><A Href="expgui5.html">Previous page</A>
26</TH></TR></TABLE><BR CLEAR=ALL>
27
28<center><h1>
29<HR noshade width="75%" size="2" align="center">
30EXPGUI, part 6
31<HR noshade width="75%" size="2" align="center">
32</h1></center>
33
34<h3>A.6 Re/Constraints panel</h3>
35<DL><DL>
36GSAS offers two types of restraints that can be included in a model.
37So called "soft constraints" or "restraints" penalize the fit if
38aspects of a model (for example, bond lengths) differ from selected values.
39So called "hard constraints" reduce the actual number of
40parameters in a model,
41by grouping parameters so that a single shift (possibly scaled) is
42applied to each parameter in the group.
43The Re/Constraints panel is used to set these "hard constraints" or in
44  the case of bond distances, "restraints".
45At this time the only constraints that can be set in EXPGUI are on atomic
46and profile profile (others can be set in EXPEDT). EXPEDT offers many
47  other types of restraints as well.
48<P>
49Note that these constraints are only applied to shifts, but not to the
50actual values. This means that, for example,
51if two atoms
52are constrained so that the shift on their occupancy is the same, but
53the initial occupancies differ, the in occupancy difference will not change
54as the values refine.
55<P>
56Due to the way GSAS implements constraints, a parameter can be included
57in only one constraint. Should one or more parameters be constrained twice,
58the refinement results are unpredictable.
59
60</DL></DL>
61<a name="AtomConstraints"></a>
62<H4>Atom Constraints</H4>
63<DL><DL>
64The atom constraints editing panel appears below. Note that constraints can
65be listed sorted by constraint number, phase number, lowest atom number or
66variable by clicking on the buttons at the top of the panel.
67<P>
68To delete one or more constraints, click on the appropriate checkbuttons in the <B>Delete</B> column and the press the Delete button, below.
69</DL></DL>
70<img SRC="mc.gif" align=TEXTTOP  alt="EXPGUI Screen snapshot">
71<DL><DL>
72<a name="AtomConstraintsError"></a>
73Should parameters be included in more than one constraint,
74an error message is displayed, as shown below.
75Note that the constraint number is displayed as red on the main
76atomic constraints window (see above), if the
77constraint contains a parameter referenced elsewhere.
78Negative contraint values are highlighted with a beige background
79to make them more visible.
80
81</DL></DL>
82<img SRC="mcerr.gif" align=TEXTTOP  alt="EXPGUI Screen snapshot">
83<DL><DL>
84<a name="EditAtomConstraints"></a>
85<P>
86<img SRC="mcedit.gif" align=LEFT  alt="EXPGUI Screen snapshot">
87<img SRC="mcvar.gif" align=RIGHT alt="EXPGUI Screen snapshot">
88When the edit button for a constraint is pressed, the constraint is
89opened for editing. Controls are available to select the phase, variable,
90multiplier and atom(s). Note that for atom selection, use of the control key
91and the left mouse button allow individual atoms to be selected or deselected.
92Shift and the left mouse button allow ranges of atoms to be selected and the
93right mouse button selects all atoms
94<A href="expgui.html#mouseactions">(see Mouse Actions)</A>.
95<P>
96Note that it is inappropriate
97to constrain different types of parameters together, for example X and Uiso.
98The left-most variable button is the "master" which
99determines what variable are allowed in the
100other variable buttons.
101<P>
102When the "New Constraint" button is pressed, a blank constraint editing
103window is opened. Note that any variable to the right may then be selected,
104including three special codes, Uxx, XYZU and XYZU+-F.
105<UL><LI>
106XYZU creates
107four constraints,
108requiring the shifts on x, y, z and Uiso to be the same for all the selected
109atoms.
110<LI> 
111Uxx does the same for the six anisotropic displacement parameters.
112<LI>
113<a name="XYZUF"></a>XYZU+-F is used for pairs of atoms where
114the shifts on x, y, z and Uiso are required to be equal, but the shifts
115on Frac are opposite.
116</UL>
117These special codes are valuable for atoms that share a site or are
118otherwise grouped together.
119<P>
120<a name="AtomConstraintsMax"></a>
121Note that only 100 parameters may be included in a single atomic constraint,
122with one exception. When shifts for Uiso
123are constrained to the same value for all atoms in a phase,
124this counts as a single parameter. If more than 500
125parameters are entered for a constraint, an error message is shown.
126Up to 2000 total atomic constraints may be entered.
127EXPGUI does not warn if you exceed this limit.
128</DL></DL>
129
130<a name="MMConstraints"></a>
131<H4>Macromolecular Constraints</H4>
132<DL><DL>
133Constraints for a macromolecular phase can be entered on a
134panel similar to the Atomic Constraints, except that the phase number
135does not appear anywhere (since the macromolecular phase must
136be phase #1). The variables that can be constrained for
137a macromolecular phase are the coordinates, x, y, & z as well as
138the occupancy, FRA and the atomic displacement parameter, UIS.
139The special constraint, XYZU, is used to constrain all coordinates
140and the displacement parameter.
141</DL></DL>
142
143<a name="ProfileConstraints"></a>
144<H4>Profile Constraints</H4>
145<DL><DL>
146The profile constraints editing panel appears below. Profile constraints
147are used to relate the shifts applied to profile terms for different
148phase/histogram combinations. Profile terms are identified by number,
149so while EXPEDT allows one to constrain the first profile term for
150a TOF histogram to a the first term in a CW histogram, EXPGUI attempts to
151make this impossible.
152<P>
153To delete one or more constraints, click on the appropriate checkbuttons
154in the <B>Delete</B> column and the press the Delete button, below.
155</DL></DL>
156<img SRC="pc.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
157<DL><DL>
158
159<a name="ProfileConstraintErr"></a>
160<img SRC="pcerr.gif" align=LEFT alt="EXPGUI Screen snapshot">
161Should parameters be included in more than one constraint,
162an error message is displayed, as shown below.
163Note that the constraint number is displayed as red on the main
164profile constraints window (see above), if the
165constraint contains a parameter referenced elsewhere.
166
167<BR CLEAR=LEFT>
168<P>
169<a name="EditProfileConstraints"></a>
170When the edit button for a constraint is pressed, the constraint is
171opened for editing, as shown below.
172Listboxes contain the available phases and histograms.
173Only the histograms of the same data type (TOF, CW or ED) are included,
174but no check is made to ensure that the
175selected phase/histogram combinations
176all have the same profile type.
177Note that for phase and histogram selection, use of the control key
178and the left mouse button allow individual items to be selected or deselected.
179Shift and the left mouse button allow ranges of items to be selected and the
180right mouse button selects all phases or histograms.
181<A href="expgui.html#mouseactions">(see Mouse Actions)</A>.
182<P>
183<img SRC="pcedit.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
184<P>
185</DL></DL>
186<a name="NewProfileConstraints"></a>
187<img SRC="pcnew1.gif" align=LEFT alt="EXPGUI Screen snapshot">
188When the "New Constraint" button is pressed, a window is opened to select
189the histogram and profile function type to be constrained. Note that
190only for profile function #4, where the number of terms depends on the
191phase symmetry, does it matter what phase you select. The available profile
192terms are displayed on the bottom of the window and more than
193one can be selected.
194<BR CLEAR=LEFT>
195<P>
196<DL><DL>
197<img SRC="pcnew2.gif" align=LEFT alt="EXPGUI Screen snapshot">
198
199After the "Continue" button is pressed, a constraint
200edit window is opened, as shown to the left.
201Listboxes contain the available phases and histograms and
202only the histograms of the selected data type are included, as before.
203Also, for phase and histogram selection, use of the control or shift key
204and the left mouse button allow individual items to be selected or deselected
205and the right mouse button selects all phases or histograms.
206Note that if more than one profile term was selected on the previous window,
207the same set of constraints are for each term.
208<BR CLEAR=LEFT>
209<P>
210<a name="ProfileConstraintsMax"></a>
211Note that only 27 terms can be included in a single profile constraint.
212Also, only like profile terms can be constrained. While GSAS does allow
213different types of profile terms to be constrained together, this does not
214usually make sense and EXPGUI does not allow it.
215</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>
251thus 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>
261The 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>
271<hr>
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273<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
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