Ignore:
Timestamp:
Jul 26, 2011 12:47:57 PM (10 years ago)
Author:
toby
Message:

liveplot: export to gnuplot; plot I/sigma(I); change title & size of labels; improve tick location; make autoticks standard; expgui: new menu item to create InstParm? file; InstEdit?: bug fixes; remove fprime since not in GSAS anymore; fix 2Theta max bug for CW instruments; updates to doc files

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  • branches/sandbox/doc/expguic.html

    r971 r1157  
    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>
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