Changeset 1150 for branches/sandbox

Jul 6, 2011 3:35:40 PM (12 years ago)

update documentation

1 added
1 deleted
19 edited


  • branches/sandbox/addcmds.tcl

    r1141 r1150  
    20322032     #puts "$coord before: $status_fixed $status_unfixed"
    20332033     foreach i $numberList {
    2034             set temp [info exists ::fix_param($phase,$i,$coord)]
    2035              puts "::fix_param($phase,$i,$coord) is variable present?: $temp"
    2036             if {$temp != 0} {set status_fixed 1}
    2037             if {$temp == 0} {set status_unfixed 1}
     2034        set temp [info exists ::fix_param($phase,$i,$coord)]
     2035         #puts "::fix_param($phase,$i,$coord) is variable present?: $temp"
     2036        if {$temp != 0} {set status_fixed 1}
     2037        if {$temp == 0} {set status_unfixed 1}
    20382038     }
    20392039     #puts "$coord after $status_fixed $status_unfixed"
  • branches/sandbox/doc/excledt.html

    r971 r1150  
    285 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    286 <font size=-1><? lastmod(); ?> </font>
    287 <br>$Revision$ $Date$
  • branches/sandbox/doc/expgui.html

    r1115 r1150  
    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</A></TH>
     61<TH><A Href="expgui6.html">Constraints & Restraints</A></TH>
     64<TH><A Href="expgui6A.html">Rigid Bodies</A></TH>
    6465<TH><A Href="expgui7.html">Preferred Orientation</A></TH>
    6566<TH><A Href="expguic.html">Menus</A></TH>
  • branches/sandbox/doc/expgui0.html

    r971 r1150  
    46 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    47 <font size=-1><? lastmod(); ?> </font>
    48 <br>$Revision$ $Date$
    49 </blockquote>
  • branches/sandbox/doc/expgui1.html

    r971 r1150  
    188 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    189 <font size=-1><? lastmod(); ?> </font>
    190 <br>$Revision$ $Date$
  • branches/sandbox/doc/expgui2.html

    r971 r1150  
    8181<a name="xform"></a>
    82 <h4>A.2.2 Transform Coordinates</h4>
    83 <DL><DL>
    84 <img SRC="2a.gif" align=RIGHT alt="EXPGUI Screen snapshot">
    85 If one or more atoms have been selected
    86 <A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
    87 to make changes to those atoms by pressing the "Xform atom(s)" button.
    88 This raises the window shown to the right.
    89 Note that no changes are actually made, until the
    90 "Transform Coordinates", "Set Occupancies",... buttons are pressed.
    91 <P>
    92 This window can be used
    93 to transform the coordinates coordinates of the selected atoms,
    94 globally set occupancy or Uiso (Uequiv)
    95 values for the selected atoms, or erase the selected atoms. by pressing the
    96 It is also possible to transform the selected atoms
    97 from isotropic to anisotropic, or the reverse.
    98 <P>
    99 <IMG SRC="new.gif" alt="New!">
    100 The "Xform Origin 1 to Origin 2" button is only available for those
     82<h4>A.2.2 Modify Atom</h4>
     84<img SRC="2a.jpg" align=RIGHT alt="EXPGUI Screen snapshot">
     85The "Modify Atom" button ("Modify Atoms" when multiple atoms are
     86  selected) provides access to additional options that can
     87  transform or modify the selected atom(s) from the phase panel 
     88<A href="expgui.html#mouseactions">(see Mouse Actions</A> for
     89  information on selecting atoms); this opens the menu window shown to
     90  the right.
     91Note that changes are made to the coordinates when the buttons on this
     92  window (such as
     93"Transform Coordinates", "Set Occupancies",...) are pressed.
     94<P><B>Modify Coordinates:</B>
     95  This is used
     96to transform the coordinates coordinates of the selected atoms using a
     97set of  transformation relationships.
     99<P><B>Reset Multiplicities:</B>
     100 When atom positions are edited in EXPGUI, they may be moved off from
     101  or onto special positions in the cell, changing the site
     102  multiplicity -- but this will not be reflected in the phase
     103  display. When atoms are subsequently refined, GENLES will update the
     104  multiplcities. Pressing the  "Reset Multiplicities" button cases
     105  this to be done right away (I think this may not work if there are no
     106  histograms present).
     108<P><B>Xform Origin 1 to Origin 2:</B> This button is only available for those
    101109orthorhombic, tetragonal and cubic space groups that are listed in the
    102110International Tables with two origin settings. (These space groups have
    106114of symmetry. GSAS only uses the origin 2 settings.)
    107115If coordinates have been entered in the origin 1 setting, they may be
    108 transformed to the origin 2 setting using this button.
     116transformed to the origin 2 setting using this button. It is important
     117  to select all atoms in the asymmetric unit before using this button.
     119  <P><B>Modify Occupancies:</B>
     120 This allows the occupancy to be set for one or more atoms. It is
     121  most convenient for when many atoms will have their occupancy
     122  changed at one time.
     124<P><B>Modify Displacement Parameters:</B>
     125  This allows one to set Uiso (or Uequiv) values for the selected
     126  atoms (<B>Set U</B>). To change the flag that determines if the
     127  selected atom(s) are represented as Isotropic or Anisotropic, press
     128  the <B>Set Isotropic</B> or <B>Set Anisotropic</B> buttons.
     130<P><B>Erase Atoms:</B>
     131  The "Erase Atoms" removes the selected atoms from the phase. I
     132  usually set the occupancy to 0. instead.
     134<P><B>Fix Atom Coordinates:</B>
     135When an atom is refined in GSAS, only the coordinates that are not
     136defined by site symmetry are refined. However, in some space groups,
     137it is necessary to not refine additional coordinates. The most common
     138example are polar space groups (P1, P2, P2<sub>1</sub>, C2,  P4, P4<sub>1</sub>, P
     1394<sub>2</sub>, P4<sub>3</sub>, I4, I4<sub>1</sub>, P3, P3<sub>1</sub>, P3<sub>2</sub>, R3, P6, P6<sub>1</sub>, P6<sub>5</sub>, P6<sub>2</sub>, P6<sub>4</sub> and
     140P6<sub>3</sub> - from
     141<a href=""> Bernard Rupp's
     142web site,</A>) where
     143one or more coordinates of the origin are not defined by symmetry. In
     144these space groups an appropriate number of coordinates must be fixed
     145to define the origin. As an example, in P1, one x, one y and one z
     146coordinate must not be refined; in space group P2<sub>1</sub>, the
     1472<sub>1</sub> screw axis defines the origin at (0,0,z) so one z
     148coordinate cannot be varied.
     150Occasionally, while symmetry may allow
     151atom coordinates to be varied, a crystallographer may choose to
     152simplify or constrain the representation to fix the atom in a
     153particular location and not refine with all allowed degrees of freedom.
     155<IMG SRC="new.gif" alt="New!">
     156 The "Fix Atom Coordinates" buttons allows a flag to be set (or
     157cleared) for an atom
     158to prevent refinement of selected coordinates, even when the X
     159refinement flag is set. Note the addition of an "F" for the x and z
     160coordinates of the first atom as shown in the phase panel, above. This
     161indicates that x & z have been fixed. When the atom position is
     162varied, only y will be optimized.
    110164<br clear=all>
    250 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    251 <font size=-1><? lastmod(); ?> </font>
    252 <br>$Revision$ $Date$
  • branches/sandbox/doc/expgui3.html

    r971 r1150  
    3131<HR noshade width="75%" size="2" align="center">
    33 <h3>A.3 Histogram panel</h3>
    34 <DL><DL>
    35 The histogram panel is used to edit background
    36 and diffractometer constants for a histogram, as well as
     33<h3>A.3 Powder panel</h3>
     35The Powder (was histogram) panel is used to edit background
     36and diffractometer constants for powder histogram(s), as well as
    3737set damping and refinement flags for these parameters.
    290 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    291 <font size=-1><? lastmod(); ?> </font>
    292 <br>$Revision$ $Date$
  • branches/sandbox/doc/expgui4.html

    r971 r1150  
    62 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    63 <font size=-1><? lastmod(); ?> </font>
    64 <br>$Revision$ $Date$
  • branches/sandbox/doc/expgui5.html

    r971 r1150  
    120 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    121 <font size=-1><? lastmod(); ?> </font>
    122 <br>$Revision$ $Date$
  • branches/sandbox/doc/expgui6.html

    r971 r1150  
    2323<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    24 </TH><TH><A Href="expgui7.html">Next page</A>
     24</TH><TH><A Href="expgui6A.html">Next page</A>
    2525</TH><TH><A Href="expgui5.html">Previous page</A>
    2626</TH></TR></TABLE><BR CLEAR=ALL>
    34 <h3>A.6 Constraints panel</h3>
     34<h3>A.6 Re/Constraints panel</h3>
    3636GSAS offers two types of restraints that can be included in a model.
    4141by grouping parameters so that a single shift (possibly scaled) is
    4242applied to each parameter in the group.
    43 The constraints panel is used to set these "hard constraints."
     43The Re/Constraints panel is used to set these "hard constraints" or in
     44  the case of bond distances, "restraints".
    4445At this time the only constraints that can be set in EXPGUI are on atomic
    45 and profile profile (others can be set in EXPEDT).
     46and profile profile (others can be set in EXPEDT). EXPEDT offers many
     47  other types of restraints as well.
    4749Note that these constraints are only applied to shifts, but not to the
    212214usually make sense and EXPGUI does not allow it.
     216<a name="DistanceRestraints"></a>
     217<H4>Distance Restraints</H4>
     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.
     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.
     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.
     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
     248 "Restraint Weight" * SUM{  [ (Distance - Restraint) / Tolerance ]**2 }
     251thus the "Tolerance" provides individual weighting for each
     252  restraint.
     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.
     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.
    216273<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    217 </TH><TH><A Href="expgui7.html">Next page</A>
     274</TH><TH><A Href="expgui6A.html">Next page</A>
    218275</TH><TH><A Href="expgui5.html">Previous page</A>
    221 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    222 <font size=-1><? lastmod(); ?> </font>
    223 <br>$Revision$ $Date$
  • branches/sandbox/doc/expgui7.html

    r971 r1150  
    2323<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    2424</TH><TH><A Href="expguic.html">Next page (Menus)</A>
    25 </TH><TH><A Href="expgui6.html">Previous page</A>
     25</TH><TH><A Href="expgui6A.html">Previous page</A>
    2626</TH></TR></TABLE><BR CLEAR=ALL>
    9898<TR><TH><A  Href="expgui.html">EXPGUI top</A>
    9999</TH><TH><A Href="expguic.html">Next page (Menus)</A>
    100 </TH><TH><A Href="expgui6.html">Previous page</A>
     100</TH><TH><A Href="expgui6A.html">Previous page</A>
    103 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    104 <font size=-1><? lastmod(); ?> </font>
    105 <br>$Revision$ $Date$
  • branches/sandbox/doc/gsas2cif.html

    r971 r1150  
    3434to export
    35 <A Href="">
    36 GSAS</A>
     35<A Href="">GSAS</A>
    3837<HR noshade width="75%" size="2" align="center">
    577 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    578 <font size=-1><? lastmod(); ?></font>
    579 $Revision$ $Date$
  • branches/sandbox/doc/liveplot.html

    r1144 r1150  
    682682<B>Combining LIVEPLOT with CMPR & LOGIC</B>
    683683If you have the
    684 <A HREF="">
    685 CMPR/LOGIC</A>
    686 programs installed on your computer, you can use superimpose on the
     684<A HREF="">CMPR</A>
     685program installed on your computer, you can use superimpose on the
    687686GSAS results the peaks for an arbitrary unit cell.
    688 If you have an old version of the
    689 <A HREF="">
    690 ICDD-JCPDS PDF-2 powder diffraction database</a>,
    691 (when distributed as an AIDS*83 format flat file)
    692 you can also superimpose entries from this database on the
    693 GSAS results displayed in LIVEPLOT.
    694 <P>
    695 When the CMPR/LOGIC program is installed in the same location
     688When the CMPR program is installed in the same location
    696689as the GSAS package (<i>e.g.</i>
    697690<font face="courier">/home/gsas</font> &
    721714software is located. The
    722715"Display a cell" option produces a window similar to the
    723 <A href="">
     716<A href="">
    724717Edit Cell feature in CMPR</A>
    725718where allowed reflection positions are displayed for a set of unit cell
    726719parameters and optionally a space group or extinction conditions.
    727 The "Plot ICDD Entry" provides a window similar to the
    728 <A href="">
    729 LOGIC interface in CMPR</A>
    730 where ICDD searches may be conducted. From the resulting list of matches,
    731 selected entries may be displayed.
    733721Note that these routines display peak positions in units of 2Theta, Q or
    749 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    750 <font size=-1><? lastmod(); ?> </font>
    751 <br>
    752 $Revision$ $Date$
  • branches/sandbox/doc/revlog.html

    r971 r1150  
    3232    </h1></center>
    3333    <P>
    34     This page describes all revisions logged for changes to the EXPGUI source
     34    This page has been superceeded by the Trac registry, see
     35    <A HREF="">
     37    <HR><HR>
     38    Below is information on older revisions logged for changes to the EXPGUI source
    3539    files, sorted by date.
    36     See the <A HREF="wishlist.html">EXPGUI Wish List</A> for a more
    37     descriptive listing.
     40    See the
     41    <A HREF="">
     42    View Tickets</A> section of the Trac site for active and closed
     43    projects. There is some older information on the
     44    <A HREF="wishlist.html">EXPGUI Wish List</A>.
    3946<h2>since 1-Jun-2009</h2><DL><DL>
    16331640    </TH><TH><A Href="wishlist.html">Past and Planned<BR>Updates</A> 
    16341641    </TH></TR></TABLE>
    1635     <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    1636     <font size=-1><? lastmod(); ?> </font>
    1637     <br>
    1638     </blockquote>
     1642   </blockquote>
    16401644Created Fri Jul 03 20:35:34 CDT 2009
  • branches/sandbox/doc/win_old_notes.html

    r971 r1150  
    4343Nonetheless, please report problems, including improvements on
    4444these instructions to
    45 <A HREF="">Brian Toby</A>.
     45<A HREF="">Brian Toby</A>.
    4646Otherwise, Windows-specific issues are unlikely to be addressed or repaired.
    59 <A Href="">
    60 GSAS</A> from one of the following sites:
     59<A Href="">GSAS</A>
     60from one of the following sites:
    296296<A HREF=""></A>
    297297<P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research,
    298 <A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A>
     298<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>
    299299with help from Jonathan Wasserman.
    327 <P><font size=-1><A HREF=" page <?=$PHP_SELF?>">Comments, corrections or questions:</A></font><BR>
    328 <font size=-1><? lastmod(); ?> </font>
    329 <br>
    330 $Revision$ $Date$
  • branches/sandbox/doc/wishlist.html

    r971 r1150  
    3131<HR noshade width="75%" size="2" align="center">
     34Information on desired (and completed) development tasks for EXPGUI
     35are now captured as "Tickets" in the
     36    <A HREF="">
     37EXPGUI Trac system</A>. In particular, see the
     38    <A HREF="">
     39    timeline of changes</A> and the
     40   <A HREF="">
     41    reports on Tickets</A>. Any other information on this page is no
     42longer being updated -- though there are still some good ideas for
     43development here.
    3450This page describes recent features added to EXPGUI or that are being
  • branches/sandbox/expgui

    r1131 r1150  
    33073307            DisplayHistogram \
    33083308            1  expgui3.html ""}
    3309     {singFrame   Single \
    3310             "source  [file join $expgui(scriptdir) single.tcl]; MakeSinglePane" \
    3311             DisplaySingle \
    3312             1  expguiSing.html ""}
    33133309    {fracFrame    Scaling \
    33143310            MakeScalingPane \
    33363332            0  expgui7.html ODF}
     3335# future expansion: single crystal panel goes here -- if present
     3336catch {
     3337   source  [file join $expgui(scriptdir) single.tcl]
     3338   set expgui(notebookpagelist) [linsert $expgui(notebookpagelist) 3 \
     3339       {singFrame   Single \
     3340       "MakeSinglePane" \
     3341       DisplaySingle \
     3342       1  expguiSing.html ""}]
     3343} err
    33393346pack [NoteBook .n -bd 2] -expand yes -fill both
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