Changeset 1225 for trunk/doc


Ignore:
Timestamp:
Nov 8, 2012 1:42:25 PM (8 years ago)
Author:
toby
Message:

update to latest, with Fourier & f'/f

Location:
trunk/doc
Files:
16 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/expgui.html

    r1218 r1225  
    1616EXPGUI<BR>
    1717A Graphical User Interface for
    18 <A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
     18<A Href="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
    1919GSAS</A>
    2020<HR noshade width="75%" size="2" align="center">
     
    2424<blockquote>
    2525For the impatient, see download/installation instructions for:
    26 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows">
     26<A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows">
    2727Windows</A>,
    28 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallOSX">
     28<A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallOSX">
    2929Mac (OS X)</A>, or
    30 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallLinux">
     30<A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallLinux">
    3131Linux</A>
    3232</blockquote>
     
    3434<P><P>
    3535EXPGUI is a graphical interface for the
    36 <A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
     36<A Href="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
    3737package, developed at Los Alamos and maintained now at Argonne.
    3838EXPGUI does two things:
     
    9696<TH>&nbsp;</TH>
    9797</TR>
    98 <TR><TH BGCOLOR="#F0F0F0">Tutorials:</TH>
    99 <TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
     98<TR><TH BGCOLOR="#F0F0F0" rowspan=2>Tutorials:</TH>
     99<TH><A Href="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
    100100NIST<BR>Neutron data</A></TH>
    101 <TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH>
    102 <TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH>
     101<TH><A Href="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH>
     102<TH><A Href="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH>
     103</TR>
     104<TR>
     105<TH><A Href="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial4/FapatitleExample.htm">
     106Lab x-ray data<BR>(Fluoroapatite)</A></TH>
     107<TH>&nbsp;</TH>
     108<TH>&nbsp;</TH>
    103109</TR>
    104110<TR><TH BGCOLOR="#F0F0F0">Messages:</TH>
     
    122128Los Alamos National Laboratory Report LAUR 86-748 (2000).
    123129<A
    124   HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
     130  HREF="https://subversion.xray.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
    125131[link to PDF copy of manual]
    126132</A>
     
    782788code and to John Cowgill for the "Export to GRACE" code.
    783789<P>
    784 <A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
     790<A Href="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
    785791GSAS</A>
    786792is written by Allen C. Larson and Robert B. Von Dreele while at
  • trunk/doc/expgui3.html

    r1166 r1225  
    3333<h3>A.3 Powder panel</h3>
    3434<DL><DL>
    35 The Powder (was histogram) panel is used to edit background
     35The Powder panel (previously called the Histogram panel) is used to edit background
    3636and diffractometer constants for powder histogram(s), as well as
    3737set damping and refinement flags for these parameters.
     
    280280<img SRC="3a.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
    281281<blockquote>
    282 <br clear=all>
     282
     283<h3>A.3.8 Setting Resonant Scattering (Anomolous Dispersion) terms</h3>
     284<DL><DL>
     285<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     286The button on the lower left of the Powder Panel, labeled "Edit
     287  (Delta) f' and f''" is used to enter the anomolous dispersion
     288  terms for x-rays.
     289  These terms are automatically defined for elements near
     290  standard x-ray tube wavelengths (Cu Kalpha, etc), but need to be
     291  entered for synchrotron datasets when significant.
     292<P>
     293  They can be estimated from <A HREF="http://it.iucr.org/C/">
     294  Volume C of the International Tables</A>. Alternately,
     295  a Python program,
     296  <A HREF="https://subversion.xray.aps.anl.gov/trac/pyFprime/">
     297  pyFPRIME</A>, for estimating
     298  these terms at arbitrary wavelengths can be run with a <A
     299  href="http://11bm.xray.aps.anl.gov/absorb/absorb.php">web
     300  interface</A> or can be downloaded and installed.
     301<img SRC="3g1.png" align=TEXTTOP alt="EXPGUI Screen snapshot">
     302</DL></DL>
     303
    283304<hr>
    284305<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
  • trunk/doc/expgui6.html

    r1218 r1225  
    4646by grouping parameters so that a single shift (possibly scaled) is
    4747applied to each parameter in the group.
    48 At this time the only constraints that can be set in EXPGUI are on atomic
    49 and profile profile (others can be set in EXPEDT).
    50   EXPEDT offers many
    51   other types of restraints as well.
    52 <P>
    53 Note that these constraints are only applied to shifts, but not to the
     48At this time the only constraints that can be set in EXPGUI are on
     49<a href="#AtomConstraints"><B>Atom Constraints</B></A> for normal phases,
     50<a href="#MMConstraints"><B>Macromolecular Atom Constraints</B></A>
     51  when a macromolecular phase is present, or
     52<a href="#ProfileConstraints"><B>Peak Profile Constraints</B></A>.
     53GSAS offers many other types of restraints, but these must be
     54  accessed in EXPEDT.
     55<P>
     56Note that in GSAS these constraints are only applied to shifts, but not to the
    5457actual values. This means that, for example,
    5558if two atoms
     
    7073</DL></DL>
    7174<a name="AtomConstraints"></a>
    72 <H4>Atom Constraints</H4>
     75<H4>A.6.1 Atom Constraints</H4>
    7376<DL><DL>
    7477The atom constraints editing panel appears below. Note that constraints can
     
    141144
    142145<a name="MMConstraints"></a>
    143 <H4>Macromolecular Constraints</H4>
     146<H4>A.6.2 Macromolecular Constraints</H4>
    144147<DL><DL>
    145148Constraints for a macromolecular phase can be entered on a
     
    154157
    155158<a name="ProfileConstraints"></a>
    156 <H4>Profile Constraints</H4>
     159<H4>A.6.3 Profile Constraints</H4>
    157160<DL><DL>
    158161The profile constraints editing panel appears below. Profile constraints
  • trunk/doc/expgui6R.html

    r1218 r1225  
    6060applied to each parameter in the group.
    6161<P>
    62   The Restraints panel at present can be used to set up restraints on
    63 interatomic distances and atomic composition.  EXPEDT offers many
    64   other types of restraints as well.
     62  The Restraints panel can be used to set up restraints on
     63  <a href="#DistanceRestraints"><B>Interatomic Distances</B></A> and
     64  on <a href="#Chemical Restraints"><B>Atomic Composition</B></A>. Note
     65  that the atomic composition constraints can be used to establish
     66  quite complex constraints that account for charge balance or even
     67  segregation of elements between phases. GSAS offers many other types
     68  of restraints, but EXPEDT must be used to access them.
    6569</DL></DL>
    6670
    6771<a name="DistanceRestraints"></a>
    68 <H4>Distance Restraints</H4>
     72<H4>A.7.1 Distance Restraints</H4>
    6973<DL><DL>
    7074 When the distance restraints tab is first selected, the active
     
    130134</DL></DL>
    131135<a name="Chemical Restraints"></a>
    132 <H4>Chemical (or Compositional) Restraints</H4>
     136<H4>A.7.2 Chemical (or Compositional) Restraints</H4>
    133137<DL><DL>
    134138  Chemical constraints allow a model to be penalized if it moves away
  • trunk/doc/expgui_Unix_readme.html

    r973 r1225  
    2929<B>Please note:</B>
    3030A new mechanism for installing GSAS & EXPGUI is now recommended. See
    31 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallLinux">
     31<A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallLinux">
    3232this link</a>. If this method is used, EXPGUI or a python script can
    3333be used to update GSAS & EXPGUI quickly and easily. The information
  • trunk/doc/expgui_Win_readme.html

    r973 r1225  
    3636<B>Please note:</B>
    3737A new mechanism for installing GSAS & EXPGUI is now recommended. See
    38 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows">
     38<A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows">
    3939this link</a>. If this method is used, EXPGUI or a batch file can
    4040be used to update GSAS & EXPGUI quickly and easily.
     
    5757<a href="http://www.ncnr.nist.gov/xtal/software/gsas.html">GSAS (General Structure Analysis System)</a>
    5858and
    59 <a href="https://subversion.xor.aps.anl.gov/EXPGUI/trunk/doc/expgui.html">EXPGUI</a>
     59<a href="https://subversion.xray.aps.anl.gov/EXPGUI/trunk/doc/expgui.html">EXPGUI</a>
    6060will do so by downloading a single file that installs the GSAS programs,
    6161the Tcl/Tk package (with some extensions), the EXPGUI scripts, as well as
     
    9393gsas+expgui.exe
    9494from
    95 <a href="http://11bm.xor.aps.anl.gov/downloads/gsas/windows/">Argonne</a>
    96 (http://11bm.xor.aps.anl.gov/downloads/gsas/windows/)
     95<a href="http://11bm.xray.aps.anl.gov/downloads/gsas/windows/">Argonne</a>
     96(http://11bm.xray.aps.anl.gov/downloads/gsas/windows/)
    9797or
    9898<a href="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/windows/">
     
    162162a lot of testing)
    163163is found as a .tar or .zip file in
    164 <A HREF="http://11bm.xor.aps.anl.gov/downloads/gsas/">
    165   http://11bm.xor.aps.anl.gov/downloads/gsas/</A>.
     164<A HREF="http://11bm.xray.aps.anl.gov/downloads/gsas/">
     165  http://11bm.xray.aps.anl.gov/downloads/gsas/</A>.
    166166On the newest versions of Windows, support for .zip files is built in, but
    167167for older versions, you will need an unzip program, such as WinZip or pkZip.
     
    176176is distributed as
    177177<DL>
    178 <A HREF="http://11bm.xor.aps.anl.gov/downloads/gsas/">
    179   http://11bm.xor.aps.anl.gov/downloads/gsas/</A>.
     178<A HREF="http://11bm.xray.aps.anl.gov/downloads/gsas/">
     179  http://11bm.xray.aps.anl.gov/downloads/gsas/</A>.
    180180</DL><P>
    181181 and unpack it to subdirectory <tt>...\gsas\expgui\</tt>.
  • trunk/doc/expgui_intro.html

    r1166 r1225  
    7070Customization notes</A>
    7171<LI>
    72 <A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
     72<A HREF="https://subversion.xray.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="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">
     76<A HREF="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial4/FapatitleExample.htm">
     77A well-annotated Lab data tutorial (Fluoroapatite).</A>
     78<B><I>Also a good place to start!</I></B>
     79<LI>
     80<A HREF="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">
    7781A TOF Tutorial Example (Nickel)</A>
    7882<LI>
    79 <A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">
     83<A HREF="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">
    8084A CW Neutron Tutorial Example (Garnet)</A>
    8185</UL>
  • trunk/doc/expguic.html

    r1166 r1225  
    273273programs used for graphical display of data and results.
    274274<DL>
     275<DT>Fourier<DD>Provides an interface to set up computation of
     276  Fourier maps and compute them using program Fourier.
     277  Also see the <A HREF="#DRAWxtl">Export to DRAWxtl</A> interface,
     278  which can be used to set up, compute, export and display Fourier
     279  maps. Note that a Fourier map can be set up for only one phase
     280  at a time.
     281<DT>forsrh<DD>Search Fourier map for peaks
    275282<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
    276283        and then compute with FOURIER
     
    279286<DT>ortep<DD>Draw crystal structure
    280287<DT>rawplot<DD>Plot powder data
    281 <DT>fourier<DD>Generate Fourier map
    282 <DT>forsrh<DD>Search Fourier map for peaks
    283288<DT>gsas2map<DD>Exports a Fourier map in formats used by other
    284289  programs (for example Fox and DRAWxtl).
     
    421426program, CIF can be a useful exchange format. This routine provides a
    422427CIF 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
    424 program and optionally launches DRAWxtl.
     428<a name="DRAWxtl"></a>
     429<DT>export to DRAWxtl<DD>
     430  <A HREF="http://www.lwfinger.net/drawxtl/">DRAWxtl</A>
     431  is a very useful free program for display of structures and
     432maps. This writes a .STR input file used in the DRAWxtl
     433program and optionally launches DRAWxtl, if installed.
     434While the control options offered by EXPGUI are relatively
     435modest (display of polyhedra,
     436selection for bonds to be drawn, display of Fourier contours),
     437once the DRAWxtl program is launched, the full range of DRAWxtl
     438options can be accessed from that program's GUI. When a Fourier map
     439contour is included, the Fourier parameters are set, the map is
     440computed (program fourier) and is converted to the format needed by
     441DRAWxtl (program gsas2map) automatically.
    425442<DT>export to SHELX<DD>This writes coordinates for a selected phase in
    426443the .INS format used by SHELX and several other programs.
  • trunk/doc/gsas+expgui.html

    r973 r1225  
    2121<B>Please note:</B>
    2222A new mechanism for installing GSAS & EXPGUI is now recommended. See
    23 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows">
     23<A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows">
    2424this link</a>. If this method is used, EXPGUI or a batch file can
    2525be used to update GSAS & EXPGUI quickly and easily.
     
    3333<a href="http://www.ncnr.nist.gov/xtal/software/gsas.html">GSAS (General Structure Analysis System)</a>
    3434and
    35 <a href="https://subversion.xor.aps.anl.gov/EXPGUI/trunk/doc/expgui.html">EXPGUI</a>
     35<a href="https://subversion.xray.aps.anl.gov/EXPGUI/trunk/doc/expgui.html">EXPGUI</a>
    3636is available. This program uncompresses itself, copies the required files
    3737(including the Tcl/Tk files used in EXPGUI)
     
    4242<P>
    4343The self-installer can be downloaded as file gsas+expgui.exe from
    44 <a href="http://11bm.xor.aps.anl.gov/downloads/gsas/windows/">Argonne</a>
    45 (http://11bm.xor.aps.anl.gov/downloads/gsas/windows/)
     44<a href="http://11bm.xray.aps.anl.gov/downloads/gsas/windows/">Argonne</a>
     45(http://11bm.xray.aps.anl.gov/downloads/gsas/windows/)
    4646or
    4747<a href="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/windows/">
  • trunk/doc/gsas2cif.html

    r1166 r1225  
    3333<BR>
    3434to export
    35 <A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
     35<A Href="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
    3636results
    3737<HR noshade width="75%" size="2" align="center">
  • trunk/doc/liveplot.html

    r1181 r1225  
    455455can be done in Windows by following these
    456456<A
    457 HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows#shortcut">instructions
     457HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows#shortcut">instructions
    458458to make a short cut</A>, but reference file <tt>.../expgui/liveplot</tt>
    459459rather than file <tt>.../expgui/expgui</tt>. Similar things can be
     
    755755<B>Combining LIVEPLOT with CMPR & LOGIC</B>
    756756If you have the
    757 <A HREF="https://subversion.xor.aps.anl.gov/trac/CMPR">CMPR</A>
     757<A HREF="https://subversion.xray.aps.anl.gov/trac/CMPR">CMPR</A>
    758758program installed on your computer, you can use superimpose on the
    759759GSAS results the peaks for an arbitrary unit cell.
     
    787787software is located. The
    788788"Display a cell" option produces a window similar to the
    789 <A href="https://subversion.xor.aps.anl.gov/CMPR/trunk/doc/cmprdoc.html#editcell">
     789<A href="https://subversion.xray.aps.anl.gov/CMPR/trunk/doc/cmprdoc.html#editcell">
    790790Edit Cell feature in CMPR</A>
    791791where allowed reflection positions are displayed for a set of unit cell
  • trunk/doc/osx.html

    r973 r1225  
    2727  <B>Please note:</B>
    2828A new mechanism for installing GSAS & EXPGUI is now recommended. See
    29 <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallOSX">
     29<A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallOSX">
    3030this link</a>. If this method is used, EXPGUI or a python script can
    3131be used to update GSAS & EXPGUI quickly and easily.
     
    8484for the CPU type of your computer (to find out what you have
    8585click on the "About This Mac" item in the Apple menu) from
    86 <a href="http://11bm.xor.aps.anl.gov/downloads/gsas/macOSX/">
    87   http://11bm.xor.aps.anl.gov/downloads/gsas/macOSX/</A>
     86<a href="http://11bm.xray.aps.anl.gov/downloads/gsas/macOSX/">
     87  http://11bm.xray.aps.anl.gov/downloads/gsas/macOSX/</A>
    8888<P>
    8989<DL><UL>
  • trunk/doc/revlog.html

    r1166 r1225  
    3333    <P>
    3434    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>.
     35    <A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/timeline">
     36    https://subversion.xray.aps.anl.gov/trac/EXPGUI/timeline</A>.
    3737    <HR><HR>
    3838    Below is information on older revisions logged for changes to the EXPGUI source
    3939    files, sorted by date.
    4040    See the
    41     <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/report">
     41    <A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/report">
    4242    View Tickets</A> section of the Trac site for active and closed
    4343    projects. There is some older information on the
  • trunk/doc/win_old_notes.html

    r1166 r1225  
    11<HTML>
    22<HEAD>
    3    <TITLE>Windows Installation Notes for EXPGUI</TITLE>
     3   <TITLE>OLD Windows Installation Notes for EXPGUI</TITLE>
    44   <meta name="keywords" content="crystallography, Rietveld, diffraction,
    55   GSAS, EXPGUI, Windows">
     
    2626<CENTER><H1>
    2727<HR noshade width="75%" size="2" align="center">
    28 Windows installation notes for
     28Old, out of date, Windows installation notes for
    2929<A HREF="expgui.html">EXPGUI</A>
    3030<HR noshade width="75%" size="2" align="center">
     
    5757<P>
    5858<LI>Get
    59 <A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
     59<A Href="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
    6060from one of the following sites:
    6161<DL><P>
  • trunk/doc/wishlist.html

    r1166 r1225  
    3434Information on desired (and completed) development tasks for EXPGUI
    3535are now captured as "Tickets" in the
    36     <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/">
     36    <A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/">
    3737EXPGUI Trac system</A>. In particular, see the
    38     <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/timeline">
     38    <A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/timeline">
    3939    timeline of changes</A> and the
    40    <A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/report">
     40   <A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/report">
    4141    reports on Tickets</A>. Any other information on this page is no
    4242longer being updated -- though there are still some good ideas for
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