Changeset 226


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Timestamp:
Dec 4, 2009 5:02:30 PM (14 years ago)
Author:
toby
Message:

# on 2000/07/03 21:44:27, toby did:
make into multiple pages

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1 edited

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  • trunk/doc/expgui.html

    • Property rcs:date changed from 2000/06/09 03:53:28 to 2000/07/03 21:44:27
    • Property rcs:lines changed from +145 -101 to +45 -328
    • Property rcs:rev changed from 1.12 to 1.13
    r202 r226  
    6666<br><img SRC="panebar1.gif"  BORDER=3 >
    6767</center></B>
    68 
    69 <P>
     68More information about each pane can be found using the links below.
     69
     70<A Href="expgui1.html">
    7071<h3>A.1 Least Squares (LS) Controls Pane</h3>
    71 <DL><DL>
    72 <p>The LS Controls pane shows information about the
    73 current experiment, typically found in the EXPEDT "Least
    74 Squares Controls" options.
    75 <P>
    76 Note that the order that histograms appear in this
    77 pane is determined by the
    78 <a href="http:#sorthist">"Sort histograms by"</a> option in
    79 the Options Menu.
    80 <img SRC="1.gif" align=TEXTTOP>
    81 </DL></DL>
    82 
    83 <P>
     72</A><A Href="expgui2.html">
    8473<h3>A.2 Phase Pane</h3>
    85 <DL><DL>
    86 The phase pane is used to edit information
    87 about the structural model(s) found in the experiment
    88 file. The flags for refining the unit cell and atomic parameters,
    89 as well as ther damping values,
    90 can be set  on this pane. Note that if a
    91 single atom is selected using the mouse, the information
    92 for that atom can be edited. If a group of atoms is
    93 selected
    94 <A href="#mouseactions">(see Mouse Actions)</A>
    95 the damping and refinement flags
    96 for all the selected atoms are changed.
    97 <P>
    98 If the EXPTOOL program
    99 <A href="#installation">(see the installation instructions)</A>
    100 is installed, buttons for adding phases and atoms will
    101 appear on this pane, as seen below. If the
    102 program is not properly installed, no errors occur, but the buttons
    103 do not appear.
    104 <P>
    105 Note that the order that atoms appear in this pane is
    106 determined by the
    107 <a href="http:#sortatoms">"Sort Atoms by"</a> option in the Options Menu.
    108 <img SRC="2.gif" align=TEXTTOP>
    109 </DL></DL>
    110 
     74</A><A Href="expgui3.html">
    11175<h3>A.3 Histogram pane</h3>
    112 <DL><DL>
    113 The histogram pane is used to edit background
    114 and diffractometer constants for a histogram, as well as
    115 set damping and refinement flags for these parameters.
    116 <P>
    117 If
    118 <A href="#multiplehistogram">
    119 "Multiple Histogram Selection" mode</A> is set to "All",
    120 this pane is disabled. For other settings of this mode,
    121 groups of histograms can be selected and modified
    122 collectively.
    123 <P>
    124 If the EXPTOOL program
    125 <A href="#installation">(see the installation instructions)</A>
    126 is installed, a button for adding histograms will
    127 appear on the bottom right on this pane, as seen below. If the
    128 program is not properly installed, no errors occur, but the button
    129 does not appear.
    130 <P>
    131 Note that the order that histograms appear in this
    132 pane is determined by the <a href="http:#sorthist">"Sort histograms by"</a> option in
    133 the Options Menu.
    134 <img SRC="3.gif" align=TEXTTOP>
    135 </DL></DL>
    136 
     76</A><A Href="expgui4.html">
    13777<h3>A.4 Scaling pane</h3>
    138 <DL><DL>
    139 The Scaling pane is used to edit the scale factor for a
    140 histogram as well as the phase fractions for each phase
    141 present in that histogram. Damping and refinement flags
    142 for the scaling terms can also be set here.
    143 <P>
    144 If
    145 <A href="#multiplehistogram">
    146 "Multiple Histogram Selection" mode</A> is set to
    147 any value other than "Off,"
    148 groups of histograms can be selected and modified
    149 collectively.
    150 <P>
    151 Note that the order that histograms appear in this
    152 pane is determined by the <a href="http:#sorthist">"Sort histograms by"</a> option in
    153 the Options Menu.
    154 <img SRC="4.gif" align=TEXTTOP>
    155 </DL></DL>
    156 
     78</A><A Href="expgui5.html">
    15779<h3>A.5 Profile pane</h3>
    158 <DL><DL>
    159 The Profile pane is used to edit the profile values for
    160 each phase present in a histogram as well as set
    161 the refinement flags and a damping value for each phase.
    162 <P>
    163 If
    164 <A href="#multiplehistogram">
    165 "Multiple Histogram Selection" mode</A> is set to "All",
    166 this pane is disabled. For other settings of this mode,
    167 profile values and settings can be collectively
    168 modified for groups of histograms.
    169 <P>
    170 Note that the order that histograms appear in this
    171 pane is determined by the
    172 <a href="http:#sorthist">"Sort histograms by"</a> option in
    173 the Options Menu.
    174 <img SRC="5.gif" align=TEXTTOP>
    175 </DL></DL>
    176 
     80</A><A Href="expgui6.html">
    17781<h3>A.6 Constraints pane</h3>
    178 <DL><DL>
    179 GSAS offers two types of restraints that can be included in a model.
    180 So called "soft constraints" or "restraints" penalize the fit if
    181 aspects of a model (for example, bond lengths) differ from selected values.
    182 So called "hard constraints" reduce the actual number of
    183 parameters in a model,
    184 by grouping parameters so that a single shift (possibly scaled) is
    185 applied to each parameter in the group.
    186 The constraints pane is used to set these "hard constraints."
    187 At this time the only constraints that can be set in EXPGUI are on atomic
    188 parameters (others can be set in EXPEDT).
    189 <P>
    190 Note that these constraints are only applied to shifts but not to the
    191 actual values. This means that, for example,
    192 if two atoms
    193 are constrained so that the shift on their occupancy is the same, but
    194 the initial occupancies differ, the in occupancy difference will not change
    195 as the values refine.
    196 <P>
    197 <H4>Atom Constraints</H4>
    198 The atom constraints editing pane appears below. Note that constraints can
    199 be listed sorted by constraint number, phase number, lowest atom number or
    200 variable by clicking on the buttons at the top of the pane.
    201 <P>
    202 To delete one or more constraints, click on the appropriate checkbuttons in the <B>Delete</B> column and the press the Delete button, below.
    203 <img SRC="mc.gif" align=TEXTTOP>
    204 Due to the way GSAS implements these constraints, a parameter can be included
    205 in only one constraint. Should one or more parameters be constrained twice,
    206 an error message is shown as shown below.
    207 Note that the constraint number is displayed as red, for constraints that
    208 have conflicts in the constraints editing pane (see above.)
    209 <img SRC="mcerr.gif" align=TEXTTOP>
    210 <P>
    211 <img SRC="mcedit.gif" align=LEFT>
    212 <img SRC="mcvar.gif" align=RIGHT>
    213 When the edit button for a constraint is pressed, the constraint is
    214 opened for editing. Controls are available to select the phase, variable,
    215 multiplier and atom(s). Note that for atom selection, use of the control key
    216 and the left mouse button allow individual atoms to be selected or deselected.
    217 Shift and the left mouse button allow ranges of atoms to be selected and the
    218 right mouse button selects all atoms
    219 <A href="#mouseactions">(see Mouse Actions)</A>.
    220 <P>
    221 Note that it is inappropriate
    222 to constrain different types of parameters together, for example X and Uiso.
    223 The left-most variable button is the "master" which
    224 determines what variable are allowed in the
    225 other variable buttons.
    226 <P>
    227 When the "New Constraint" button is pressed, a blank constraint editing
    228 window is opened. Note that any variable to the right may then be selected,
    229 including two special codes, Uxx and XYZU. XYZU creates four constraints,
    230 requiring the shifts on x, y, z and Uiso to be the same for all the selected
    231 atoms. Uxx does the same for the six anisotropic displacement parameters.
    232 These special codes are valuable for atoms that share a site.
    233 <P>
    234 Note that only 100 parameters may be included in a constraint,
    235 with one exception. When shifts for Uiso for all atoms in a phase
    236 are constrained, this counts as a single parameter. If more than 100
    237 parameters are entered for a constraint, an error message is shown.
    238 Up to 2000 atomic constraints may be entered.
    239 EXPGUI does not warn if you exceed this limit.
    240 </DL></DL>
    241 
    242 <P>
     82</A><A Href="expgui7.html">
    24383<h3>A.7 Preferential Orientation Pane</h3></a>
    244 The Preferential Orientation Pane is used to control parameters related
    245 to fitting parameters using the March-Dollase formulation
    246 for preferred orientation. In this model one or more axes are designated
    247 as directions [designated by (<i>hkl</i>)] where crystallites are over
    248 (Ratio > 1) or underrepresented (Ratio < 1).
    249 The checkbox to the right of the Ratio value determines if it will
    250 be refined.
    251 <img SRC="po1.gif" align=TEXTTOP>
    252 If more than one axis is present, one must define the relative fraction
    253 of preferred orientation for each direction. These fractions are normalized,
    254 so do not vary the fractions for all directions in a phase.
    255 <img SRC="po2.gif" align=TEXTTOP>
    256 If
    257 <A href="#multiplehistogram">
    258 "Multiple Histogram Selection" mode</A> is set to any value other than
    259 "Off", all terms are displayed for all selected histograms.
    260 No attempt is made to group terms or flags.
    261 <P>
    262 Note that the other model for treating preferred orientation -- the orientation
    263 distribution function (spherical harmonics) is not yet implemented
    264 in EXPGUI and must be accessed from EXPEDT.
    265 
     84</A>
    26685<P>
    26786<h2>B. Shortcuts</h2></a>
    … …  
    27796to be selected and modified.
    27897<A href="#mouseactions">(see Mouse Actions)</A>.
    279 
     98<P>
    28099It does not make sense, however, to globally modify
    281100instrument-related parameters and flags for different
    … …  
    288107<P>
    289108The setting for "Multiple Histogram Selection" mode is
     109displayed above each histogram selection box and is
    290110selected using the "Multiple Hist. Selection" item on the
    291 Options menu to create a submenu. Also on this submenu is an option
    292 "Group Phases Together" that controls how EXPGUI treats phases having
    293 the same profile type when multiple histograms are selected. If
     111Options menu to create a submenu or by clicking on the display.
     112Note that another option in this "Multiple Hist. Selection"
     113submenu is an option "Group Phases Together" that controls how
     114EXPGUI treats phases having
     115the same profile type that is used when multiple histograms are selected. If
    294116the "Group Phases Together" option is on, then the refinement flags for
    295117all phases with the same histogram types are grouped together, when possible.
    296118If this option is off, phases are treated separately.
     119<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     120If the left mouse button is used to click on the selection mode display,
     121the mode is cycled between the available modes. If the right mouse
     122button is used, the mode is reset, to disable multiple histogram selection.
    297123<p>
    298124<a name="mouseactions">
    … …  
    328154</center></B>
    329155
    330 A description of the EXPGUI menus follows along with a very
     156A description of the EXPGUI menus follows. Use the links to obtain
     157more information, including a very
    331158brief description of the function of each menu option.
    332159Note that an option may appear under more than one menu.
     160
     161<DL><DL>
     162
     163<A Href="expguic.html#1">
    333164<H3>C.1 File Menu</H3>
     165</A>
    334166<DL><DL>
    335167The options on the File menu as is the custom contains the commands
    336168for reading and writing experiment files, as well as starting
    337169and ending the program.
    338 <DL>
    339 <DT>expnam<DD>
    340         Select an existing GSAS experiment to be used. If a name is entered
    341         that does not exists, it is possible to create a new
    342         experiment file from scratch.
    343 <DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S).
    344 <DT>Save As<DD>Saves modifications to the current experiment file to disk
    345         under a new file name
    346 <DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
    347 <DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
    348 <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
    349 <DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
    350 </DL>
    351 <img SRC="m1.gif" BORDER=3 >
    352 </DL></DL>
    353 
     170</DL></DL>
     171
     172<A Href="expguic.html#2">
    354173<h3>C.2 Options Menu</h3>
     174</A>
    355175<DL><DL>
    356176This menu contains options that determine how EXPGUI runs.
    357 <DL>
    358 <DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are
    359         saved prior to each save or run of expedt in a file named
    360         [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX)
    361         or in a file named [expnam].ZIP or  [expnam].xxx (Windows)
    362 <DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are
    363          shown in a separate window. When it is not set, the results are
    364         written in the .LST file.
    365 <a name="sortatoms"></a><DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
    366         Atoms may be displayed sorted by atom number, atom type,
    367         or by x, y or z
    368 
    369 <a name="sorthist"></a><DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
    370         Histogram, Scaling and Profile panes
    371 
    372         Histograms may be sorted by histogram number, histogram type,
    373         original bank number, or diffraction angle/wavelength
    374 <DT><A href="#multiplehistogram">Multiple hist. selection</A><DD>
    375         When this mode is off, it is possible to modify parameters
    376         and refinement flags for only a single histogram. For other settings,
    377         it is possible to modify parameters and flags for groups of
    378         histograms (see help for Mouse actions).
    379 
    380         It does not make sense, however, to globally modify
    381         instrument-related parameters and flags for different histogram types.
    382         So global actions can be limited to a single class of histogram types
    383         (e.g. TOF, CW Neutron,...), which allows these parameters to be set
    384         for groups of similar histograms. Thus, if this mode is set to "All"
    385         the Histogram and Profile panes are disabled.
    386 <DT>Override backspace<DD>This option is available in UNIX only, as there are different
    387         ways that backspace can be implemented. When option is set
    388         as "On," the backspace key is overridden to send a "delete"
    389         character. If backspace does not work in a program such as
    390         EXPEDT, change try the other setting for this option.
    391 <DT>Autoupdate EXP<DD>Normally EXPGUI prompts before rereading the EXP
    392 file when GENLES, POWPREF,... are run (this is so that one can change
    393 the experiment file and rerun with the current input). If this option is
    394 set, the new file is automatically read without a prompt.
    395 This option is not available in Windows.
    396 
    397 <DT>SaveOptions<DD>Save the current values for "Override backspace",
    398         <a href="http:#sortatoms">"Sort atoms by"</a>,
    399         <a href="http:#sorthist">"Sort histograms by"</a> and "archive EXP"
    400         in file ~/.gsas_config (c:\.gsas_config on Windows).
    401 <DT>liveplot_options<DD>Used to set options for liveplot,
    402 for example, the histogram to be plotted
    403 </DL>
    404 <img SRC="m2.gif"  BORDER=3>
    405 </DL></DL>
    406 
     177</DL></DL>
     178
     179<A Href="expguic.html#3">
    407180<h3>C.3 Powder Menu</h3>
     181</A>
    408182<DL><DL>
    409183This menu contains links to GSAS programs used for powder diffraction
    410184analysis.
    411 <DL>
    412 <DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
    413 <DT>powpref<DD>Powder data preparation (shortcut Alt-P)
    414 <DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
    415 <DT>powplot<DD>Display powder patterns
    416 <DT>rawplot<DD>Plot powder data
    417 <DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
    418 <DT>tofnorm<DD>Normalize a TOF spectrum
    419 </DL>
    420 <img SRC="m3.gif"  BORDER=3>
    421 </DL></DL>
    422 
     185</DL></DL>
     186
     187<A Href="expguic.html#4">
    423188<h3>C.4 Single Crystal Menu</h3>
     189</A>
    424190<DL><DL>
    425191This menu contains links to GSAS programs used for
    426 single-rystal diffraction analysis.
    427 <DL>
    428 <DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
    429 <DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
    430 <DT>scabs<DD>Single crystal absorption
    431 <DT>scmerge<DD>Sort and merge single crystal data
    432 <DT>sxtldata<DD>Prepare generic single crystal data
    433 </DL>
    434 <img SRC="m4.gif"  BORDER=3>
    435 </DL></DL>
    436 
     192single-crystal diffraction analysis.
     193</DL></DL>
     194
     195<A Href="expguic.html#5">
    437196<h3>C.5 Graphics Menu</h3>
     197</A>
    438198<DL><DL>
    439199This menu contains links to several GSAS and
    440200two non-GSAS (liveplot and widplt)
    441201programs used for graphical display of data and results.
    442 <DL>
    443 <DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
    444         and then compute with FOURIER
    445 <DT>polfplot<DD>Display polefigures
    446 <DT>powplot<DD>Display powder patterns
    447 <DT>ortep<DD>Draw crystal structure
    448 <DT>rawplot<DD>Plot powder data
    449 <DT>fourier<DD>Generate Fourier map
    450 <DT>forsrh<DD>Search Fourier map for peaks
    451 <DT>liveplot<DD>Create a plot of powder data
    452 with zooming, automatic update and other nice features.
    453 <DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
    454 <DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
    455 </DL>
    456 <img SRC="m5.gif"  BORDER=3>
    457 </DL></DL>
    458 
     202</DL></DL>
     203
     204<A Href="expguic.html#6">
    459205<h3>C.6 Results Menu</h3>
     206</A>
    460207<DL><DL>
    461208This menu contains links to several GSAS and
    462209one non-GSAS (lstview)
    463210programs used for analysis of results.
    464 <DL>
    465 <DT>bijcalc<DD>Thermal parameter analysis
    466 <DT>disagl<DD>Distance/angle calculations
    467 <DT>reflist<DD>List reflection data
    468 <DT>geometry<DD>Molecular geometry calculations
    469 <DT>hstdmp<DD>List powder histogram data
    470 <DT>istats<DD>HKL Intensity statistics
    471 <DT>rcalc<DD>Compute reflection resuduals
    472 <DT>composition<DD>Computes the chemical composition of a unit cell
    473 accounting for site multiplicies and occupancies
    474 <DT>lstview<DD>Create a box with scrollbars containing the current .LST file
    475 </DL>
    476 <img SRC="m6.gif"  BORDER=3>
    477 </DL></DL>
    478 
     211</DL></DL>
     212
     213<A Href="expguic.html#7">
    479214<h3>C.7 Calculations Menu</h3>
     215</A>
    480216<DL><DL>
    481217This menu contains programs for useful crystallographic computations.
    482 <DL>
    483 <DT>cllchg<DD>Transform unit cell
    484 <DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
    485 <DT>rducll<DD>Unit cell reduction
    486 <DT>spcgroup<DD>Space group symbol interpreter
    487 <DT>unimol<DD>Unique molecule assembler
    488 </DL>
    489 <img SRC="m7.gif" BORDER=3>
    490 </DL></DL>
    491 
     218</DL></DL>
     219
     220<A Href="expguic.html#8">
    492221<h3>C.8 Import/Export Menu</h3>
     222</A>
    493223<DL><DL>
    494224This menu contains utilities for importing information into GSAS and
    495225exporting.
    496 <DL>
    497 <DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
    498 file is used in MSI software such as Cerius and InsightII.
    499 <DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
    500 <DT>hklsort<DD>Prepare HKL tables
    501 <DT>pubtable<DD>Prepare atom parameter tables
    502 <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
    503 <DT>cad4rd<DD>Prepare CAD4 single crystal data
    504 <DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
    505 <DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
    506 <DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
    507 <DT>sxtldata<DD>Prepare generic single crystal data
    508 </DL>
    509 <img SRC="m8.gif"  BORDER=3>
     226</DL></DL>
    510227</DL></DL>
    511228
    … …  
    603320
    604321<P>EXPGUI is not subject to copyright. Have fun with it. Modify it. Write
    605 new sections and make them available to the reset of the world.
     322new sections and make them available to the rest of the world.
    606323
    607324<p>Neither the U.S. Government nor any author makes any warranty,
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