Changeset 1218


Ignore:
Timestamp:
Aug 19, 2012 1:17:28 PM (8 years ago)
Author:
toby
Message:

update main docs

Location:
trunk/doc
Files:
6 added
5 edited

Legend:

Unmodified
Added
Removed

  • trunk/doc/expgui.html

    r1166 r1218  
    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>

  • trunk/doc/expgui6.html

    r1166 r1218  
    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>

  • trunk/doc/expgui6A.html

    r1184 r1218  
    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
    … …  
    195195 <BR><img src="rb004.jpg" alt="Z-matrix RB input window">
    196196</DL>
    197   <H4>A.7.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4>
    198 <DL>
    199   Cartesian coordinates
    200 can also be determined from atoms in the EXP file.
    201   In order to generate Cartesian
    202 coordinates, the number of sites in the rigid body framework must be specified
    203 as well as the starting atom (remember rigid bodies are mapped consecutively).
     197<A name="fromEXP">
     198<H4>A.8.a4 Compute Cartesian coordinates from EXP file (fractional coordinates)</H4>
     199</A>
     200<DL>
     201  A rigid body can also be created directly by computing Cartesian coordinates
     202for atoms in the current EXP file.
     203  In order to do this, the number of atom sites in the rigid body framework must be specified
     204as well as the starting atom number (remember rigid bodies are mapped
     205  consecutively) using the window shown below.
    204206  Once the number of atoms in the body is
    205207set, the "Choose Start Atom" button is pressed. This creates buttons for
    206 all possible choices for the first atom to define the body. Once the starting
    207 atom is selected by pressing one of these button(s), the atoms to be used to
    208 define the rigid body framework have been determined. The user must than select
     208all possible choices for the first atom to define the body. The starting
     209atom is selected by pressing one of these button(s) and this defines
     210  the atoms to be used in the rigid body framework. The user must then
     211  select
    209212which atoms will be used to define the origin (the origin will be at the
    210 centroid of the atoms chosen) and must define the axes that will be used to
    211 generate the x-axis and the xy plane.
    212 The Cartesian coordinates can then be generated.
    213 Either the defined body can be determined and mapped (with the "Save and Map
    214 Rigid Body" button), or the Cartesian coordinates can exported to an
     213centroid of the atoms chosen) as well as define the axes that will be used to
     214generate the x-axis and the xy plane for the Cartesian coordinate system.
     215The Cartesian coordinates for the body that are generated can be exported to an
    215216ASCII text file (with the "Export Cartesian Coordinates"
    216 button).
    217   <BR><img src="rb005.jpg" alt="Fraction Coords RB input window">
     217button) for later use. More commonly, the "Save and Map
     218Rigid Body" button is used; this creates a new rigid body type and
     219  maps that body (<A href="#MapBody">see A.8.b2</A>) to the selected atoms in the phase.
     220 <BR><img src="rb005.jpg" alt="Fraction Coords RB input window">
    218221</DL>
    219222
    220223</DL></DL>
    221 <H3>A.7.b Rigid Body Panel</H3>
     224<H3>A.8.b Rigid Body Panel</H3>
    222225<DL><DL>
    223226 As each rigid body is
    … …  
    232235  <BR><img src="rb006.jpg" alt="RB edit panel">
    233236
    234   <H4>A.7.b1 Plot Rigid Body</H4>
     237  <H4>A.8.b1 Plot Rigid Body</H4>
    235238<DL>
    236239  <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A>
    … …  
    238241EXPGUI can invoke, if installed. It
    239242allows for the viewing of the rigid body to ensure it is correct before mapping
    240 and matches the ordering of the atoms in the EXP file. The plot below
    241   was obtained from the "Plot Rigid Body" button.
     243and matches the ordering of the atoms in the EXP file. Note that plots
     244  to not display atom types, since there is no type information
     245  associated with position in a rigid body. Atom types are determined
     246  by the atoms when the body is mapped. A sample plot
     247  obtained from the "Plot Rigid Body" button is shown below.
    242248  <BR><img src="rb007.png" alt="DRAWxtl screen">
    243249</DL>
    244 
    245  <H4>A.7.b2 Map Rigid Body</H4>
    246 <DL>
     250<A name="MapBody">
     251 <H4>A.8.b2 Map Rigid Body</H4>
     252</A><DL>
    247253The rigid body must be mapped to the
    248254crystal structure to define the constraint. This is done by pressing
    249255  the "Map Rigid Body" button, which raises the window below.
    250256  <BR><img src="rb008.png" alt="Map RB"><BR>
     257Note that when a rigid body is created from atoms already in the .EXP
     258  file (<A href="#fromEXP">see A.8.a4</A>), the "Save and Map" command
     259  performs this step automatically.
     260  <P>
    251261  In order to map the rigid body the user
    252262will need to specify the phase and the sequence number of the first atom in the
    … …  
    281291<BR Clear="all">
    282292  </DL>
    283  <H4>A.7.b3 Edit Rigid Body</H4>
     293 <H4>A.8.b3 Edit Rigid Body</H4>
    284294  <DL>
    285295
    … …  
    303313
    304314</DL></DL>
    305 <H3>A.7.c Setting Rigid Body Refinement Flags</H3>
     315<H3>A.8.c Setting Rigid Body Refinement Flags</H3>
    306316<DL><DL>
    307317 The "Refinement Flags" button opens a window that allows the
    … …  
    345355 These flags were set automatically when
    346356the rigid body position parameter were set to be refined. If these flags are
    347 turned off, it is likely that GENLES will crash.
    348 
     357turned off, it is likely that GENLES will crash. Note that atoms in a
     358  rigid body are now tagged with the letter "r" in the atom listings.
    349359  </DL></DL>
    350360<hr>
    … …  
    352362<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    353363</TH><TH><A Href="expgui7.html">Next page</A>
    354 </TH><TH><A Href="expgui6.html">Previous page</A>
     364</TH><TH><A Href="expgui6R.html">Previous page</A>
    355365</TH></TR></TABLE>
    356366

  • trunk/doc/expgui7.html

    r1166 r1218  
    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
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