Changeset 1222

Sep 22, 2012 7:13:29 PM (11 years ago)

Add more documentation

1 added
7 edited


  • branches/sandbox/anomal.tcl

    r1206 r1222  
    1515     set ::anom_wave [histinfo $histlbl lam1]
    1616     foreach test $::expmap(powderlist) {
    17              puts "[histinfo $test lam1] versus $::anom_wave"
     17             #puts "[histinfo $test lam1] versus $::anom_wave"
    1818             if {[histinfo $test lam1] == $::anom_wave} {
    1919                lappend ::anom_list $test
    4242             set ::anom_fp($::anom_atomcount) [lindex $temp 1]
    4343             set ::anom_f2p($::anom_atomcount) [lindex $temp 2]
    44              puts "$::anom_lbl($::anom_atomcount) $::anom_fp($::anom_atomcount) $::anom_f2p($::anom_atomcount)"
     44             #puts "$::anom_lbl($::anom_atomcount) $::anom_fp($::anom_atomcount) $::anom_f2p($::anom_atomcount)"
    4545     }
    5757     grid [frame $anomal.list -bd 2 -relief groove] -row 0 -column 0 -sticky news
    58      grid [label $anomal.list.lbl1 -text "The anomalous dispersion terms will be set for the following histograms\n with wavelength $::anom_wave angstroms:"] -row 0 -column 0
     58     grid [label $anomal.list.lbl1 -text "The anomalous dispersion terms will be set for x-ray histograms\n with wavelength $::anom_wave angstroms:"] -row 0 -column 0
    5959     grid [label $anomal.list.lbl1a -text "$::anom_list"] -row 1 -column 0
    6161     grid [frame $anomal.con -bd 2 -relief groove] -row 5  -column 0 -sticky news
    6262     grid [button $  -width 8 -text "Save"  -command {anomalous_save}] -column 0 -row 4 -padx 3
    63      grid [button $anomal.con.abort -width 8 -text "abort" -command {anomalous_abort}] -column 1 -row 4 -padx 3
     63     grid [button $anomal.con.abort -width 8 -text "Cancel" -command {anomalous_abort}] -column 1 -row 4 -padx 3
    6565     grid [frame $anomal.warning -bd 2 -relief groove] -row 7 -column 0 -sticky news
    8686proc anomalous_save {args} {
    8787     set histnum $::expgui(curhist)
    88      puts $histnum
     88     #puts $histnum
    8989     set histlbl [lindex $::expmap(powderlist) $histnum]
    90      puts $histlbl
     90     #puts $histlbl
    9191     set x ""
    9292     set atomcount 0
    9595             lappend x "$::anom_lbl($atomcount) $::anom_fp($atomcount) $::anom_f2p($atomcount)"
    9696     }
    97      puts $x
     97     #puts $x
    9898     foreach test $::anom_list {
    9999          histinfo $test anomff set $x
  • branches/sandbox/doc/expgui3.html

    r1150 r1222  
    3333<h3>A.3 Powder panel</h3>
    35 The Powder (was histogram) panel is used to edit background
     35The Powder panel (previously call 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">
    282 <br clear=all>
     283<h3>A.3.8 Setting Resonant Scattering (Anomolous Dispersion) terms</h3>
     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.
     293  They can be estimated from <A HREF="">
     294  Volume C of the International Tables</A>. Alternately,
     295  a Python program,
     296  <A HREF="">
     297  pyFPRIME</A>, for estimating
     298  these terms at arbitrary wavelengths can be run with a <A
     299  href="">web
     300  interface</A> or can be downloaded and installed.
     301<img SRC="3g1.png" align=TEXTTOP alt="EXPGUI Screen snapshot">
  • branches/sandbox/doc/expgui6.html

    r1217 r1222  
    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.
     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
    7174<a name="AtomConstraints"></a>
    72 <H4>Atom Constraints</H4>
     75<H4>A.6.1 Atom Constraints</H4>
    7477The atom constraints editing panel appears below. Note that constraints can
    142145<a name="MMConstraints"></a>
    143 <H4>Macromolecular Constraints</H4>
     146<H4>A.6.2 Macromolecular Constraints</H4>
    145148Constraints for a macromolecular phase can be entered on a
    155158<a name="ProfileConstraints"></a>
    156 <H4>Profile Constraints</H4>
     159<H4>A.6.3 Profile Constraints</H4>
    158161The profile constraints editing panel appears below. Profile constraints
  • branches/sandbox/doc/expgui6R.html

    r1217 r1222  
    6060applied to each parameter in the group.
    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.
    6771<a name="DistanceRestraints"></a>
    68 <H4>Distance Restraints</H4>
     72<H4>A.7.1 Distance Restraints</H4>
    7074 When the distance restraints tab is first selected, the active
    131135<a name="Chemical Restraints"></a>
    132 <H4>Chemical (or Compositional) Restraints</H4>
     136<H4>A.7.2 Chemical (or Compositional) Restraints</H4>
    134138  Chemical constraints allow a model to be penalized if it moves away
  • branches/sandbox/doc/expguic.html

    r1157 r1222  
    273273programs used for graphical display of data and results.
     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="">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.
  • branches/sandbox/expgui

    r1221 r1222  
    33443344            "source [file join $expgui(scriptdir) atomcons.tcl]; MakeRestraintsPane" \
    33453345            DisplayRestraintsPane \
    3346             0  expgui6.html ""}
     3346            0  expgui6R.html ""}
    33473347    {rbFrame   "Rigid Body" \
    33483348            "source  [file join $expgui(scriptdir) rigid.tcl]; MakeRBPane" \
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