Changeset 1157 for branches/sandbox/doc


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

Location:
branches/sandbox/doc
Files:
3 edited

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  • branches/sandbox/doc/expgui.html

    r1150 r1157  
    500500
    501501The INSTEDIT utility is used to edit or create an instrument parameter file.
    502 At this time it can only be used to edit files for
    503 constant-wavelength data. The utility can be started from the "Edit File"
    504 button in the
     502The utility can be started from the "Edit File" button in the
    505503<A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the
    506 the "instedit" option in the Powder menu. In the latter case, the user
    507 is given the chance to select an input file. If no file is selected,
    508 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.
    509510<P>
    510511<img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
     
    618619records can slow the GSAS programs
    619620(this is less of a problem on faster computers). For these reasons, it may be
    620 a good idea to prune the older history records from the file. If more than 100
    621 history records are found in an experiment file, EXPGUI suggests that the
    622 older history entries be deleted. Alternately the File/EraseHistory command
    623 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.
    624623<P>
    625624On the dialog the number of history records to be retained is specified.
  • 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>
  • branches/sandbox/doc/liveplot.html

    r1150 r1157  
    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><IMG SRC="new.gif" alt="New!">
    64 Regions of the plot can be magnified to show more detail, for example
    65   in regions at high Q.
    66   <LI>
    67 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.
    6869<LI>
    6970Reflection tickmarks can be displayed in a variety of formats
     
    7980<LI>
    8081The cursor position can be displayed
    81 <LI>
    82 Plots can be <a href="#export">exported to obtain publication-quality
    83 graphics.</a>
    8482</UL>
    8583
     
    393391<B>Export plot options</B>
    394392<UL><LI>
    395 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
    396412<A HREF="http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows
    397 that produces publication-quality graphics. Many UNIX users know
    398 this program under a previous name, xmgr.
    399 The export is implemented
    400 by producing an ASCII file with instructions that
    401 creates a plot with similar formatting to what appears on the
    402 screen in LIVEPLOT/BKGEDIT. However, the output quality from
    403 Grace is much higher quality. Further, Grace
    404 can be used to enhanced and annotate the plot further.
    405 <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>
    406422For use in many other graphics programs, LIVEPLOT will produce a
    407423"comma separated variable" data file with the data displayed on the screen.
     
    409425set line styles and scaling, etc., but this does provide an option for
    410426generating high-quality graphics for presentations and publications.
    411 <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,
    412428but the quality is rather low (this is a limitation of the BLT graphics
    413429package).
     430  <P><LI>LIVEPLOT/BKGFIT can also be used to prepare input for FOX (Free
     431  Objects for Xtallography).
     432 
    414433</UL>
    415434
     
    468487<DT>Export Plot
    469488<DD>This offers options for exporting the plot in multiple formats.
    470 I am hoping to add more export formats eventually.
    471 <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
    472499<DT>to PostScript
    473500<DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT
     
    476503On Windows, a program such ghostview may be needed to translate the
    477504PostScript to a format that can be viewed or printed.
    478 <A name="grace">
     505
     506  <A name="grace">
    479507<DT>to Grace
    480508<IMG SRC="note.gif" alt="Note!">
     
    484512After the plot is exported, it can be further
    485513enhanced 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.
    486522</DL></DL>
    487523<DT>Quit
     
    535571<DT>Y units
    536572<DD>The intensity values can be normalized by the incident spectrum
    537 (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].
    538577</DL></DL>
    539578<br clear=all>
     
    565604<DT>Set screen font
    566605<DD>This option is used to control the font used for menus, graphics and
    567 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.
    568614<DT>Raise on update
    569615<DD>This causes the plot to be placed on top of other windows, if partially
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