Changeset 1166 for trunk/doc


Ignore:
Timestamp:
Aug 17, 2011 6:17:04 PM (9 years ago)
Author:
toby
Message:

bring sandbox changes over to main release

Location:
trunk/doc
Files:
20 added
1 deleted
19 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/excledt.html

    r971 r1166  
    283283</TH></TR></TABLE>
    284284
    285 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    286 <font size=-1><? lastmod(); ?> </font>
    287 <br>$Revision$ $Date$
    288285</blockquote>
    289286</body>
  • trunk/doc/expgui.html

    r973 r1166  
    1616EXPGUI<BR>
    1717A Graphical User Interface for
    18 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
     18<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
    1919GSAS</A>
    2020<HR noshade width="75%" size="2" align="center">
     
    3434<P><P>
    3535EXPGUI is a graphical interface for the
    36 Los Alamos
    37 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
    38 GSAS</A> package.
     36<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
     37package, developed at Los Alamos and maintained now at Argonne.
    3938EXPGUI does two things:
    4039it can be used to directly modify the GSAS
     
    6059<TH><A Href="expgui4.html">Scaling info</A></TH>
    6160<TH><A Href="expgui5.html">Profile terms</A></TH>
    62 <TH><A Href="expgui6.html">Constraints</A></TH>
     61<TH><A Href="expgui6.html">Constraints & Restraints</A></TH>
    6362</TR>
    6463<TR>
     64<TH><A Href="expgui6A.html">Rigid Bodies</A></TH>
    6565<TH><A Href="expgui7.html">Preferred Orientation</A></TH>
    6666<TH><A Href="expguic.html">Menus</A></TH>
     
    117117A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)",
    118118Los Alamos National Laboratory Report LAUR 86-748 (2000).
    119 <A HREF="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/GSASManual.pdf">
     119<A
     120  HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
    120121[link to PDF copy of manual]
    121122</A>
     
    154155are used. The File/Save operation is done automatically before any GSAS
    155156programs, such as GENLES or EXPEDT, are run.
     157<P>
     158<A name="badexp">
     159The GSAS refinement program, GENLES, will sometimes "blow up", where the
     160  program changes varied parameters to values very far from their
     161  correct values. This occurs when parameters are highly correlated,
     162  are refining to values that are not allowed, or some of the refined parameters have
     163  very little impact on the quality of the fit. When this happens,
     164  invalid values are written to the GSAS experiment file that contain
     165  either asterisks (****) or the string "NAN" (not a number). Such
     166  files cannot be used for additional GENLES runs.
     167  <P>
     168  When EXPGUI reads a .EXP file it scans it for evidence of a previous
     169  failure of a GENLES refinement and warns if a problem is
     170  noted. Please note that this scan is not perfect and occasionally
     171  you may be warned in cases where the file is fine (if possible,
     172  please send such .EXP file to Brian Toby so this scan can be improved.)
     173  When such a "bad" .EXP file is located, one can "revert" to an
     174  archived copy of a previous experiment file (with suffix .Oxx). This
     175  can be done with the Revert menu item in the File menu. Note that
     176clicking on a file in the file selection window causes it to be
     177scanned and shows the status of that refinement. Also note that
     178usually the last good archived file has settings that will produce the same bad
     179refinement, so it is necessary to either revert further back, or to
     180change the refinement options before running GENLES.
    156181<P>
    157182
     
    475500
    476501The INSTEDIT utility is used to edit or create an instrument parameter file.
    477 At this time it can only be used to edit files for
    478 constant-wavelength data. The utility can be started from the "Edit File"
    479 button in the
     502The utility can be started from the "Edit File" button in the
    480503<A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the
    481 the "instedit" option in the Powder menu. In the latter case, the user
    482 is given the chance to select an input file. If no file is selected,
    483 a new, empty, file is created. An example INSTEDIT window appears below.
     504the "instedit" option in the Powder menu. Alternately, to create a new
     505  instrument parameter file, choose Powder menu option "New InstParm
     506  file". (It is also possible
     507  to create a new file using the standard instedit by selecting
     508  "Cancel" when asked for an input file.)
     509An example INSTEDIT window appears below.
    484510<P>
    485511<img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
     
    593619records can slow the GSAS programs
    594620(this is less of a problem on faster computers). For these reasons, it may be
    595 a good idea to prune the older history records from the file. If more than 100
    596 history records are found in an experiment file, EXPGUI suggests that the
    597 older history entries be deleted. Alternately the File/EraseHistory command
    598 can be used to invoke the this option.
     621a good idea to prune the older history records from the file.
     622The File/EraseHistory command can be used to invoke the this option.
    599623<P>
    600624On the dialog the number of history records to be retained is specified.
     
    681705<A name=tcltk>
    682706<H2>
    683 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
     707<A Href="http://www.tcl.tk">
    684708Tcl/Tk</A></H2>
    685709The
    686 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
     710<A Href="http://www.tcl.tk">
    687711Tcl/Tk program</A> is a platform-independent scripting language that is
    688712used to implement most of EXPGUI. This software is available for free
    689 and must be loaded in order to use EXPGUI. See the
    690 installation notes for
    691 <A HREF="expgui_Win_readme.html">Windows</A>,
    692 and for
    693 <A HREF="expgui_Unix_readme.html">UNIX</A> for information on how to do this.
     713and must be loaded in order to use EXPGUI. A somewhat out of date
     714version of Tcl/Tk (8.4) is distributed with EXPGUI (ncnrpack.exe, etc.) but
     715more recent versions can be used, but note that the BLT package (see
     716below) is needed for all features of EXPGUI.
    694717While learning Tcl/Tk is a great thing to do, it is not a requirement
    695718for using or installing EXPGUI.
    696 
    697 <A name=winexec>
    698 <H3>
    699 WINEXEC</H3>
    700 <UL>
    701 The WINEXEC package is needed under Windows-95 and its offspring
    702 (-98 and -ME). See the <A HREF="expgui_Win_readme.html">Windows installation
    703 notes</A> for more details.
    704 </UL>
    705719
    706720<A name=blt>
     
    715729If this is the case, a message,
    716730"BLT Setup Error: could not access a Blt_ routine...", will be displayed.
    717 This is most common in UNIX and is discussed further in the
    718 <A HREF="expgui_Unix_readme.html">UNIX installation notes</A>. Also see
    719 <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
    720 http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
    721 </A> for more information on installation of BLT.
     731Use of the ncnrpack file distributed with EXPGUI usually avoids this problem.
    722732</UL>
    723733
     
    727737<UL>
    728738The
    729 <A HREF="www.hume.com">Hume
     739<A HREF="http://www.hume.com">Hume
    730740</A>
    731741Linear Algebra Tcl Package,
    732 <A HREF="www.hume.com">
     742<A HREF="http://www.hume.com/la/la.html">
    733743La</A>,
    734744is used by the BKGEDIT
     
    739749should not happen, since the package is included with the EXPGUI files.
    740750So if get this error you probably have an incomplete installation.
    741 Note that the La package requires Tcl/Tk version 8.1 or higher, so that if
    742 you are using an older version of Tcl/Tk, you will need to upgrade.
    743 See the installation instructions for
    744 <A HREF="expgui_Win_readme.html">Windows</A>,
    745 and for
    746 <A HREF="expgui_Unix_readme.html">UNIX</A> for more information on Tcl/Tk.
     751</UL>
     752
     753<A name=winexec>
     754<H3>
     755WINEXEC</H3>
     756<UL>
     757The WINEXEC package was needed under Windows-95 and its offspring
     758(-98 and -ME). It was found in older versions of EXPGUI, but is no
     759  longer included.
    747760</UL>
    748761
     
    750763Acknowledgments</H2>
    751764Praise to Larson and
    752 Von Dreele for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A>
     765Von Dreele for GSAS, <A HREF="http://home.pacbell.net/ouster/">John Ousterhout</A>
    753766for Tcl/Tk,
    754 Przemek Klosowski</A>
     767Przemek Klosowski
    755768for convincing me to learn Tcl/Tk
    756 and Jonathan Wasserman for helping get this project started.
    757 Thanks also to
     769and Jonathan Wasserman for helping me get this project started.
     770Thanks also to
     771Charles Lake of Indiana University of PA for working on many recent additions to EXPGUI, including the
     772bond-distance restraints module and the (soon to come) rigid body editor;
    758773Pamela Whitfield of the NRC (Canada) for writing large
    759774sections of the
     
    763778code and to John Cowgill for the "Export to GRACE" code.
    764779<P>
    765 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
     780<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
    766781GSAS</A>
    767782is written by Allen C. Larson and Robert B. Von Dreele while at
     
    770785<A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
    771786EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
    772 <A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>
    773 with help from Jonathan Wasserman.
     787<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>.
    774788
    775789<P><hr><blockquote>
     
    786800software.
    787801
    788 <P>The author of EXPGUI is a U.S. Government employee which means that
     802<P>EXPGUI was written by a U.S. Government employee, which means that
    789803EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write
    790804new sections and make them available to the rest of the world.
     
    793807expressed or implied, or assumes any liability or responsibility
    794808for the use of this information or the software described
    795 here. Brand names cited herein are used for
    796 identification purposes and do not constitute an endorsement by NIST.
     809here.
    797810</blockquote>
    798811
  • trunk/doc/expgui0.html

    r971 r1166  
    4444</TH></TR></TABLE>
    4545
    46 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    47 <font size=-1><? lastmod(); ?> </font>
    48 <br>$Revision$ $Date$
    49 </blockquote>
     46/blockquote>
    5047</body>
    5148</html>
  • trunk/doc/expgui1.html

    r971 r1166  
    186186</TH></TR></TABLE>
    187187
    188 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    189 <font size=-1><? lastmod(); ?> </font>
    190 <br>$Revision$ $Date$
    191188</blockquote>
    192189</body>
  • trunk/doc/expgui2.html

    r971 r1166  
    8080<P>
    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>
     83<DL><DL>
     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.
     98 
     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).
     107
     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.
     118
     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.
     123
     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.
     129
     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.
     133 
     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="http://www.ruppweb.org/Xray/comp/space_instr.htm"> Bernard Rupp's
     142web site, http://www.ruppweb.org/Xray/comp/space_instr.htm</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.
     149
     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.
     154
     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.
    109163
    110164<br clear=all>
     
    248302</TH></TR></TABLE>
    249303
    250 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    251 <font size=-1><? lastmod(); ?> </font>
    252 <br>$Revision$ $Date$
    253304</blockquote>
    254305</body>
  • trunk/doc/expgui3.html

    r971 r1166  
    3131<HR noshade width="75%" size="2" align="center">
    3232</h1></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>
     34<DL><DL>
     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.
    3838<P>
     
    288288</TH></TR></TABLE>
    289289
    290 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    291 <font size=-1><? lastmod(); ?> </font>
    292 <br>$Revision$ $Date$
    293290</blockquote>
    294291</body>
  • trunk/doc/expgui4.html

    r971 r1166  
    6060</TH></TR></TABLE>
    6161
    62 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    63 <font size=-1><? lastmod(); ?> </font>
    64 <br>$Revision$ $Date$
    6562</blockquote>
    6663</body>
  • trunk/doc/expgui5.html

    r971 r1166  
    118118</TH></TR></TABLE>
    119119
    120 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    121 <font size=-1><? lastmod(); ?> </font>
    122 <br>$Revision$ $Date$
    123120</blockquote>
    124121</body>
  • trunk/doc/expgui6.html

    r971 r1166  
    2222<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
    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>
     
    3232</h1></center>
    3333
    34 <h3>A.6 Constraints panel</h3>
     34<h3>A.6 Re/Constraints panel</h3>
    3535<DL><DL>
    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.
    4648<P>
    4749Note that these constraints are only applied to shifts, but not to the
     
    212214usually make sense and EXPGUI does not allow it.
    213215</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>
    214271<hr>
    215272<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
    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>
    219276</TH></TR></TABLE>
    220277
    221 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    222 <font size=-1><? lastmod(); ?> </font>
    223 <br>$Revision$ $Date$
    224278</blockquote>
    225279</body>
  • trunk/doc/expgui7.html

    r971 r1166  
    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>
    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 Preferential Orientation Panel</h3></a>
     34<h3>A.8 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.7.a March-Dollase</H4>
     45<h4>A.8.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.7.b Spherical harmonic</H4>
     69<H4>A.8.b Spherical harmonic</H4>
    7070<DL><DL>
    7171The spherical harmonic formulation, also referred to as an "orientation
     
    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>
    101101</TH></TR></TABLE>
    102102
    103 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    104 <font size=-1><? lastmod(); ?> </font>
    105 <br>$Revision$ $Date$
    106103</blockquote>
    107104</body>
  • trunk/doc/expgui_intro.html

    r971 r1166  
    7070Customization notes</A>
    7171<LI>
    72 <A HREF="tutorial3/index.html">
     72<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
    7373A well-annotated CW neutron tutorial (Alumina).</A>
    7474<B><I>A very good place to start!</I></B>
    7575<LI>
    76 <A HREF="tutorial1/index.html">
     76<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">
    7777A TOF Tutorial Example (Nickel)</A>
    7878<LI>
    79 <A HREF="tutorial2/index.html">
     79<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">
    8080A CW Neutron Tutorial Example (Garnet)</A>
    8181</UL>
     
    164164<p><br><B>Who is to blame for EXPGUI?</B>
    165165<blockquote>The initial version of the GUI part of EXPGUI was created by
    166 Jonathan Wasserman (thanks Jon!) <a href="http://www.ncnr.nist.gov/staff/toby/">Brian
     166Jonathan Wasserman (thanks Jon!) Brian
    167167Toby</a> is irresponsible for the rest.</blockquote>
    168168
     
    170170<blockquote>Gee, you want to add some features... Great! You have all the
    171171EXPGUI sources and
    172 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">Tcl/Tk</A>
    173 is free. Oh, you want me to do it. Well, please
     172Tcl/Tk is free. Oh, you want me to do it. Well, please
    174173ask and I will try. In particular, I am looking for good ideas on
    175174how to design GUI's for different aspects of experiment editing,
     
    177176
    178177<p><br><B>Mailing List</B>
    179 <blockquote>If you would like to get news about EXPGUI, please send
    180 <a href="mailto:brian.toby@anl.gov?subject=EXPGUI Mailing List">Brian.Toby@ANL.GOV</a> e-mail. The mailing list is not active at present, but
    181 I hope to use it again to provide
     178<blockquote>If you would like to get news about EXPGUI, please
     179<a href="http://www.aps.anl.gov/mailman/listinfo/expgui">see this
     180link</a>.
     181The mailing list is used only to provide
    182182information about updates and bug fixes.
    183183</blockquote>
  • trunk/doc/expguic.html

    r971 r1166  
    4949        experiment file from scratch.
    5050<DT>expnam<DD>
    51 Equivalent to Open, included since this is the command used in other
    52 GSAS shells to select GSAS experiments.
     51Equivalent to Open (included for historical reasons.)
     52
    5353<DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S).
    5454<DT>Save As<DD>Saves modifications to the current experiment file to disk
     
    6060  offers the program user the option to update these files. The update
    6161  will fail if the user does not have permission to change the EXPGUI
    62   or GSAS files. In this case, a system administrator may be needed.
     62  or GSAS files. In this case, a system administrator may be needed.
     63  <DT>revert<DD>Used to load an <a href="#archive">archived</A>
     64    (backup) version of the current .EXP file.
    6365<DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
    64 <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
     66<DT>convert<DD>Convert a standard ASCII file to the direct access
     67  format used by GSAS (and for UNIX, the reverse) -- this is not
     68  likely to be needed, as GSAS now does most conversions automatically.
    6569<DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
    6670</DL>
     
    99103revised .EXP file, which means that you reject the last set of changes.
    100104This is useful if
    101 GENLES blows up or you have done something wrong. The advantage
    102 of turning "autoload EXP" on is
     105GENLES blows up or you have done something wrong. The reason to
     106turning "autoload EXP" on is
    103107that there is one less thing to do when running GSAS programs.
    104108Note that it is still possible to reverse changes, if
    105 <a href="#archive">archive files</A>, but this may require more effort.
    106 
     109<a href="#archive">archive files</A>, but this may require more
     110  effort. See the File/revert menu entry.
    107111<a name="execprompt"></a>
    108112<DT>Prompt after GSAS run<DD>
     
    121125screen cluttered with EXPGUI when it can't be used,
    122126but this is an option so that the mode can be turned off by those people
    123 who find this behavior annoying.
     127who find this behavior annoying. It appears this option causes
     128  problems on Windows 7.
    124129
    125130<a name="AutostartGRWND"></a>
     
    225230<DT>rawplot<DD>Plot powder data
    226231<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
    227 <DT>tofnorm<DD>Normalize a TOF spectrum
    228232<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
    229233<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
     
    233237to set the upper and lower limits for a histogram, as well as
    234238edit excluded regions.
     239<DT>seqgsas<DD>Invokes the sequential GSAS refinement program to run
     240  GENLES on a set of very similar data files.
     241<DT>mustrplot<DD>Plot microstrain results
     242<DT><a HREF="expgui.html#INSTEDIT">instedit</A><DD>Invokes the <a HREF="expgui.html#INSTEDIT">instedit</A>
     243  to edit an instrument parameter file.
     244<DT>New InstParm file<DD>Creates a new instrument parameter file using
     245  <a HREF="expgui.html#INSTEDIT">instedit</A>.
     246
     247
    235248</DL>
    236249<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
     
    238251
    239252<a name="4"></a>
    240 <h3>C.4 Single Crystal Menu</h3>
     253<h3>C.4 Xtal (Single Crystal) Menu</h3>
    241254<BLOCKQUOTE>
    242255This menu contains links to GSAS programs used for
     
    268281<DT>fourier<DD>Generate Fourier map
    269282<DT>forsrh<DD>Search Fourier map for peaks
     283<DT>gsas2map<DD>Exports a Fourier map in formats used by other
     284  programs (for example Fox and DRAWxtl).
    270285<DT><a HREF="liveplot.html#liveplot">liveplot</a>
    271286<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
     
    274289<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
    275290<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
     291<DT><a HREF="expgui.html#ABSPLT">absplt</A>
     292<DD>The <a HREF="expgui.html#ABSPLT">absplt</A> program displays the
     293  absorption/reflectivity correction curve for values used in a histogram.
     294<DT>mustrplot<DD>Plot microstrain results
     295<DT>seqplot<DD>Plot results from seqgsas
    276296</DL>
    277297<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
     
    287307<DT>bijcalc<DD>Thermal parameter analysis
    288308<DT>disagl<DD>Distance/angle calculations
     309<DT>disaglviewer<DD>Display results from distance/angle calculations
     310  in a graphical browser.
    289311<DT>reflist<DD>List reflection data
    290312<DT>geometry<DD>Molecular geometry calculations
     
    297319<DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
    298320chains, for use in restraints.
     321<DT>seqplot<DD>Plot results from seqgsas
    299322</DL>
    300323<img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
     
    307330<DL>
    308331<DT>cllchg<DD>Transform unit cell
    309 <DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
     332<DT>composition<DD>Computes the chemical composition of a unit cell
     333accounting for site multiplicies and occupancies
    310334<DT>rducll<DD>Unit cell reduction
    311335<DT>spcgroup<DD>Space group symbol interpreter
     336<DT>seqgsas<DD>Invokes the sequential GSAS refinement program to run
     337  GENLES on a set of very similar data files.
     338<DT>seqplot<DD>Plot results from seqgsas
    312339<DT>unimol<DD>Unique molecule assembler
    313340</DL>
     
    315342</BLOCKQUOTE>
    316343
    317 <a name="8"></a>
    318 <h3>C.8 Import/Export Menu</h3>
    319 <BLOCKQUOTE>
    320 This menu contains utilities for importing information into GSAS and
    321 exporting.
    322 <DL>
    323 <DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
    324 file is used in MSI software such as Cerius and InsightII.
    325 <DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
    326 <DT>hklsort<DD>Prepare HKL tables
    327 <DT>pubtable<DD>Prepare atom parameter tables
    328 <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
    329 <DT>cad4rd<DD>Prepare CAD4 single crystal data
    330 <DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
    331 <DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
    332 <DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
    333 <DT>sxtldata<DD>Prepare generic single crystal data
    334 <DT>gsas2pdb<DD>
    335 Import (using GSAS2PDB & EXPEDT) and export coordinates (for
    336 macromolecular phases) to/from Protein Data Base files
    337 <DT>ref2asc<DD>
    338 Exports a GSAS reflection file to ASCII for use in non-GSAS programs
    339 <DT>ref2bin<DD>
    340 Imports an ASCII reflection file to the GSAS binary format
    341 </DL>
    342 <img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
    343 </BLOCKQUOTE>
    344 
    345344<a name="9"></a>
    346 <h3>C.9 Macro Menu
     345<h3>C.8 Macro Menu
    347346<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
    348347</h3>
     
    402401</DL>
    403402</BLOCKQUOTE>
     403
     404<a name="8"></a>
     405<h3>C.9 Import/Export Menu</h3>
     406<BLOCKQUOTE>
     407This menu contains utilities for importing information into GSAS and
     408exporting it to other programs.
     409<DL>
     410<DT>Coord Export<DD>This provides a series of routines that are used
     411to write coordinates and possibly other information to files:<P>
     412<DL>
     413<DT>gsas2cif<DD>Prepares IUCr crystallographic information (CIF) file
     414that documents the current refinement. The CIF contains the
     415coordinates for all phases as well as the observed and computed
     416diffraction patterns. The templates used by GSAS2CIF can be customized
     417to provide a detailed description of the experimental measurements and
     418results for use in documenting analysis for publication or
     419deposition.
     420<DT>coords-only CIF<DD>For export of intermediate results to another
     421program, CIF can be a useful exchange format. This routine provides a
     422CIF with the current coordinates from one phase and not much else.
     423<DT>export to DRAWxtl<DD>This writes a .STR file used in the DRAWxtl
     424program and optionally launches DRAWxtl.
     425<DT>export to SHELX<DD>This writes coordinates for a selected phase in
     426the .INS format used by SHELX and several other programs.
     427<DT>export to PLATON<DD>This writes coordinates for a selected phase in
     428the .SPF format used by PLATON
     429<DT>export test format<DD>This demonstrates how a coordinate export
     430routine can be added to EXPGUI. See the <A
     431HREF="expgui_cfg.html#export">documentation on this</A> for further
     432information.
     433<DT>export to FOX<DD>This prepares a XML file with coordinates for use
     434in the FOX program
     435<DT>MSI .xtl<DD>Prepare a .XTL format file of atomic positions. This
     436file is used in older Accelrys software such as Cerius and
     437Insight-II. It may no longer be of value.
     438</DL>
     439
     440<DT>CIF Export<DD>This provides a series of routines that are used
     441to prepare CIF files:<P>
     442<DL>
     443<DT>gsas2cif<DD>Prepares IUCr crystallographic information (CIF) file
     444that documents the current refinement. The CIF contains the
     445coordinates for all phases as well as the observed and computed
     446diffraction patterns. The templates used by GSAS2CIF can be customized
     447to provide a detailed description of the experimental measurements and
     448results for use in documenting analysis for publication or
     449deposition.
     450<DT>FillTemplate<DD>Used to edit the CIF template files used in GSAS2CIF
     451<DT>CIFselect<DD>Used to select interatomic distances and angles to be
     452included in the CIF created by GSAS2CIF.
     453</DL>
     454
     455<DT>hklsort<DD>Prepare HKL tables
     456<DT>pubtable<DD>Prepare atom parameter tables
     457<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
     458<DT>cad4rd<DD>Prepare CAD4 single crystal data
     459<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
     460<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
     461<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
     462<DT>sxtldata<DD>Prepare generic single crystal data
     463<DT>gsas2pdb<DD>
     464Import (using GSAS2PDB & EXPEDT) and export coordinates (for
     465macromolecular phases) to/from Protein Data Base files
     466<DT>ref2asc<DD>
     467Exports a GSAS reflection file to ASCII for use in non-GSAS programs
     468<DT>ref2bin<DD>
     469Imports an ASCII reflection file to the GSAS binary format
     470<DT>gsas2map<DD>Exports a Fourier map in formats used by other
     471  programs (for example Fox and DRAWxtl).
     472</DL>
     473<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
     474</BLOCKQUOTE>
     475
    404476<hr>
    405477<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
  • trunk/doc/gsas2cif.html

    r971 r1166  
    3333<BR>
    3434to export
    35 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
    36 GSAS</A>
     35<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
    3736results
    3837<HR noshade width="75%" size="2" align="center">
     
    575574</BLOCKQUOTE>
    576575
    577 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    578 <font size=-1><? lastmod(); ?></font>
    579 $Revision$ $Date$
    580576</font>
    581577</BLOCKQUOTE>
  • trunk/doc/liveplot.html

    r971 r1166  
    4040<P>
    4141Both LIVEPLOT and BKGEDIT get the current diffraction information
    42 by running the GSAS TCLDUMP program, if installed, or
    43 the GSAS HSTDUMP otherwise. The TCLDUMP program has been optimized for use
    44 with LIVEPLOT and allows LIVEPLOT to offer a number of extra
    45 options that are not available when HSTDUMP is used. Since TCLDUMP has been
    46 included in GSAS since April of 2000, the following documentation assumes
    47 that TCLDUMP is installed.
     42by running the GSAS TCLDUMP program. (In GSAS/EXPGUI before 2001, the
     43GSAS HSTDUMP program was used, which was less powerful. This code has
     44not been removed, but will not be used if TCLDUMP is present.)
    4845
    4946<a name="liveplot"></a>
     
    5451Some of the features available in LIVEPLOT are:
    5552<UL>
    56 <LI>The plot is updated automatically after each refinement run
     53<LI><IMG SRC="new.gif" alt="New!">
     54Regions of the plot can be magnified to show more detail, for example
     55  in regions at high Q.
     56<LI><IMG SRC="new.gif" alt="New!">
     57Plots can be <a href="#export">exported to obtain publication-quality
     58graphics </a> -- <B><I>now on all platforms</I></B>.
     59<LI><IMG SRC="new.gif" alt="New!"> Intensity can be displayed as I/sigma(I)
     60 <LI>The plot is updated automatically after each refinement run
    5761<LI>The plot can be "zoomed-in", by clicking on the corners of the
    5862area to be magnified and "zoomed-out" using the
     
    6165The units used for plotting histograms can be selected. Choices are:
    6266native units (2Theta/TOF/KeV); d-space (A) or Q (A<sup>-1</sup>)
    63 <LI>
    64 The background (fixed plus fitted) can be plotted or can be subtracted.
     67 <LI>
     68  The background (fixed plus fitted) can be plotted or can be subtracted.
    6569<LI>
    6670Reflection tickmarks can be displayed in a variety of formats
     
    7377<LI>
    7478The cumulative chi<sup>2</sup> function or
    75 <IMG SRC="new.gif" alt="New!"> (obs-calc)/sigma can be plotted.
     79 (obs-calc)/sigma can be plotted.
    7680<LI>
    7781The cursor position can be displayed
    78 <LI>
    79 Plots can be <a href="#export">exported to obtain publication-quality
    80 graphics.</a>
    8182</UL>
    8283
     
    285286<P>
    286287<a name="zoomshift"></a>
    287 <IMG SRC="new.gif" alt="New!">
    288288To shift the zoom region around,
    289289the right and left arrow keys can be used to shift the
     
    363363<br clear=all>
    364364<P>
     365<a name="magnification"></a>
     366<B>Plot Magnification</B>
     367Sections of the plot can be magnified through use of options in the
     368Magnification menu or by using control-1 through control-9.
     369<img SRC="magreg.png" align=RIGHT alt="LIVEPLOT Screen snapshot">
     370<UL>
     371<LI>The Magnification/Add region menu item requests a location in the
     372  pattern (2Theta/TOF/KeV/d-space/Q) and a multiplier. Data where the
     373  scan variable (2Theta...) is of that value or higher, up to the
     374  next region or end of the pattern are multiplied by that factor. The
     375  factor, must be >0.
     376<LI>Magnification/Edit regions brings up a menu (see below) where the previously
     377 defined regions can be changed. The region boundaries can be moved
     378  and the multiplier values can be changed. If a multiplier is set to
     379  zero (or negative) that region is removed.
     380<LI>Magnification/Clear deletes all previously defined regions
     381<LI>Pressing control plus a positive digit (1,2,3,...9) also adds a
     382  magnification region. The digit determines the magnification
     383  multiplier. Data where the
     384  scan variable (2Theta...) from the mouse position up to the
     385  next region or end of the pattern are multiplied by that factor.
     386<img SRC="editreg.png" align=RIGHT alt="LIVEPLOT menu">
     387</UL>
     388 <br clear=all>
     389<P>
    365390<a name="export"></a>
    366391<B>Export plot options</B>
    367392<UL><LI>
    368 The plot can be exported to
     393<IMG SRC="new.gif" alt="New!">
     394The LIVEPLOT program can export plots to to a <I>high quality</I> PDF
     395  file for presentations or publications using <A
     396  HREF="http://www.gnuplot.info/">gnuplot</A>.
     397  The PDF will match what is is shown on fairly
     398  closely with respect to colors, <A href="#plotfont">font sizes</a>
     399  and <a href="#zoom">zoom</a>. The new <A href="#magnification">plot magnification</a> to show detail in
     400  the fit and for publication increase the
     401  <A href="#plotfont">plot font</a> so that the figure size can be
     402  reduced to the standard Rietveld postage stamp, required by so many
     403  Journals -- allowing the text to be discerned, even if the problems in the
     404  fit cannot.
     405  <P>Starting August
     406  2011, windows and Mac versions of gnuplot are included with the GSAS
     407  binaries; gnuplot is easily
     408  installed on Linux with standard tools such as yum (Redhat),
     409  apt-get (ubuntu) or zypper (openSuse).
     410
     411<P><LI>  The plot can be exported to
    369412<A HREF="http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows
    370 that produces publication-quality graphics. Many UNIX users know
    371 this program under a previous name, xmgr.
    372 The export is implemented
    373 by producing an ASCII file with instructions that
    374 creates a plot with similar formatting to what appears on the
    375 screen in LIVEPLOT/BKGEDIT. However, the output quality from
    376 Grace is much higher quality. Further, Grace
    377 can be used to enhanced and annotate the plot further.
    378 <LI>
     413that produces publication-quality graphics that appear very similar to
     414  what is seen in LIVEPLOT/BKGEDIT. Further, Grace
     415  can be used to enhance the plot, for example by editing captions,
     416  figure display options and even annotate the plot.
     417  Grace runs well on Linux and Mac computers; Many UNIX users know
     418  this program under a previous name, xmgr.
     419  For Windows,
     420  installation of <A HREF="http://cygwin.com/">Cygwin</A> is required.
     421  <P><LI>
    379422For use in many other graphics programs, LIVEPLOT will produce a
    380423"comma separated variable" data file with the data displayed on the screen.
     
    382425set line styles and scaling, etc., but this does provide an option for
    383426generating high-quality graphics for presentations and publications.
    384 <LI>LIVEPLOT will produce PostScript versions of the plot on the screen,
     427<P><LI>LIVEPLOT will produce PostScript versions of the plot on the screen,
    385428but the quality is rather low (this is a limitation of the BLT graphics
    386429package).
     430  <P><LI>LIVEPLOT/BKGFIT can also be used to prepare input for FOX (Free
     431  Objects for Xtallography).
     432 
    387433</UL>
    388434
     
    408454<DT><a href="#zoomshift">arrow keys</A>
    409455<DD>Moves zoom region around in plot
     456<DT><a href="#mag">Control+1, 2,...</a>
     457<DD>Defines a <a href="#magnification">magnification region</A> at the
     458  cursor location.
    410459</DL>
    411460
     
    438487<DT>Export Plot
    439488<DD>This offers options for exporting the plot in multiple formats.
    440 I am hoping to add more export formats eventually.
    441 <DL><DL>
     489<DL><DL>
     490<DT>to PDF
     491 <IMG SRC="new.gif" alt="New!">
     492<DD>Creates a <I>high quality</I> PDF file that may be useful for
     493  presentations or publications. Note that you may wish to use
     494  <A href="#magnification">plot magnification</a> to show detail in
     495  the fit and for publication increase the
     496  <A href="#plotfont">plot font</a> so that the figure size can be
     497  reduced.
     498
    442499<DT>to PostScript
    443500<DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT
     
    446503On Windows, a program such ghostview may be needed to translate the
    447504PostScript to a format that can be viewed or printed.
    448 <A name="grace">
     505
     506  <A name="grace">
    449507<DT>to Grace
    450508<IMG SRC="note.gif" alt="Note!">
     
    454512After the plot is exported, it can be further
    455513enhanced and annotated in grace.
     514
     515<DT>to .csv file
     516  <DD>Creates a "comma separated variable" file. This contains all the
     517  diffraction data shown in the plot. It can be used to produce a plot
     518  in some other graphics program.
     519  <DT>Fox XML
     520  <DD>The Fox program provides structure solution capabilities. This
     521  option can be used to write data in the XML format that Fox uses.
    456522</DL></DL>
    457523<DT>Quit
     
    505571<DT>Y units
    506572<DD>The intensity values can be normalized by the incident spectrum
    507 (for energy dispersive methods).
     573(for energy dispersive methods) or
     574  <IMG SRC="new.gif" alt="New!"> can be displayed as a ratio with the
     575  experimental uncertainty [I<sub>obs</sub>/sigma(I<sub>obs</sub>),
     576  I<sub>calc</sub>/sigma(I<sub>obs</sub>) and their difference].
    508577</DL></DL>
    509578<br clear=all>
     
    535604<DT>Set screen font
    536605<DD>This option is used to control the font used for menus, graphics and
    537 other aspects of windows.
     606other aspects of windows. This value can be saved as a default value.
     607<A name="plotfont">
     608  <DT>Set plot font
     609<DD>This option is used to change the font used in the plot
     610  window. This has a similar effect to changing the screen font, but
     611  can be changed over a wider range and only affects the
     612  graph. Changing the font size either way will change the font used
     613  in the exported .PDF.
    538614<DT>Raise on update
    539615<DD>This causes the plot to be placed on top of other windows, if partially
     
    650726<P>
    651727<hr><H2>Interfacing External Programs</H2>
    652 <IMG SRC="new.gif" alt="New!">
    653728<B>Combining LIVEPLOT with CMPR & LOGIC</B>
    654729If you have the
    655 <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">
    656 CMPR/LOGIC</A>
    657 programs installed on your computer, you can use superimpose on the
     730<A HREF="https://subversion.xor.aps.anl.gov/trac/CMPR">CMPR</A>
     731program installed on your computer, you can use superimpose on the
    658732GSAS results the peaks for an arbitrary unit cell.
    659 If you have an old version of the
    660 <A HREF="http://www.icdd.com/products/overview.htm">
    661 ICDD-JCPDS PDF-2 powder diffraction database</a>,
    662 (when distributed as an AIDS*83 format flat file)
    663 you can also superimpose entries from this database on the
    664 GSAS results displayed in LIVEPLOT.
    665 <P>
    666 When the CMPR/LOGIC program is installed in the same location
     733<P>
     734When the CMPR program is installed in the same location
    667735as the GSAS package (<i>e.g.</i>
    668736<font face="courier">/home/gsas</font> &
     
    692760software is located. The
    693761"Display a cell" option produces a window similar to the
    694 <A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell">
     762<A href="https://subversion.xor.aps.anl.gov/CMPR/trunk/doc/cmprdoc.html#editcell">
    695763Edit Cell feature in CMPR</A>
    696764where allowed reflection positions are displayed for a set of unit cell
    697765parameters and optionally a space group or extinction conditions.
    698 The "Plot ICDD Entry" provides a window similar to the
    699 <A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell">
    700 LOGIC interface in CMPR</A>
    701 where ICDD searches may be conducted. From the resulting list of matches,
    702 selected entries may be displayed.
    703766<P>
    704767Note that these routines display peak positions in units of 2Theta, Q or
     
    718781</TH></TR></TABLE>
    719782
    720 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    721 <font size=-1><? lastmod(); ?> </font>
    722 <br>
    723 $Revision$ $Date$
    724783</blockquote>
    725784</body>
  • trunk/doc/revlog.html

    r971 r1166  
    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="https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline">
     36    https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline</A>.
     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.
    38 
     40    See the
     41    <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/report">
     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>.
     45   
    3946<h2>since 1-Jun-2009</h2><DL><DL>
    4047</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="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    1636     <font size=-1><? lastmod(); ?> </font>
    1637     <br>
    1638     </blockquote>
     1642   </blockquote>
    16391643
    16401644Created Fri Jul 03 20:35:34 CDT 2009
  • trunk/doc/win_old_notes.html

    r971 r1166  
    4343Nonetheless, please report problems, including improvements on
    4444these instructions to
    45 <A HREF="mailto:brian.toby@nist.gov">Brian Toby</A>.
     45<A HREF="mailto:brian.toby@anl.gov">Brian Toby</A>.
    4646Otherwise, Windows-specific issues are unlikely to be addressed or repaired.
    4747</EM>
     
    5757<P>
    5858<LI>Get
    59 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
    60 GSAS</A> from one of the following sites:
     59<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
     60from one of the following sites:
    6161<DL><P>
    6262<DT>UK<DD>
     
    296296<A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</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.
    300300
     
    325325</TH></TR></TABLE>
    326326
    327 <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
    328 <font size=-1><? lastmod(); ?> </font>
    329 <br>
    330 $Revision$ $Date$
    331327</blockquote>
    332328</body>
  • trunk/doc/wishlist.html

    r971 r1166  
    3131<HR noshade width="75%" size="2" align="center">
    3232</h1></center>
     33<I><blockquote><blockquote>
     34Information on desired (and completed) development tasks for EXPGUI
     35are now captured as "Tickets" in the
     36    <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/">
     37EXPGUI Trac system</A>. In particular, see the
     38    <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline">
     39    timeline of changes</A> and the
     40   <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/report">
     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.
     44</blockquote></blockquote></I>
     45<P>
     46<hr><hr>
     47
     48
    3349<P>
    3450This page describes recent features added to EXPGUI or that are being
Note: See TracChangeset for help on using the changeset viewer.