Changeset 3126


Ignore:
Timestamp:
Oct 6, 2017 6:52:07 PM (4 years ago)
Author:
toby
Message:

proxy fix; document Phase/Data? tab in help

Location:
trunk
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIImpsubs.py

    r3049 r3126  
    9797            sInt += icod[1]
    9898        elif icod == -1:
    99             res.append((None,iref))
     99            resList.append((None,iref))
    100100        elif icod == -2:
    101101            break
  • trunk/GSASIIpath.py

    r3125 r3126  
    134134        if not host.strip(): return '',''
    135135        return host,port
    136     return None,None
     136    return '',''
    137137
    138138def setsvnProxy(host,port):
     
    600600    sys.excepthook = savehook # reset IPython's change to the exception hook
    601601
     602from IPython.core import ultratb
    602603def exceptHook(*args):
    603604    '''A routine to be called when an exception occurs. It prints the traceback
     
    607608    This routine is only used when debug=True is set in config.py   
    608609    '''
    609     from IPython.core import ultratb
     610    #from IPython.core import ultratb
    610611    if 'win' in sys.platform:
    611612        ultratb.FormattedTB(call_pdb=False,color_scheme='NoColor')(*args)
  • trunk/help/gsasII.html

    r3102 r3126  
    64366436class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman";
    64376437color:windowtext;text-decoration:none;text-underline:none'> – This selects the
    6438 type of jump to be used for each MC/SA trial.<o:p></o:p></span></span></p>
     6438type of jump to be used for each MC/SA trial.</span></span></p>
    64396439
    64406440<p class=MsoListParagraphCxSpMiddle style='margin-left:1.5in;mso-add-space:
     
    64636463algorithm is chosen these determine the jump components for each trial.<o:p></o:p></span></span></p>
    64646464
    6465 <h4 style='margin-left:0.25in'><a name=Data></a><u><span style='mso-fareast-font-family:
    6466 "Times New Roman"'>Data<span class=MsoHyperlink><span style='color:#5B9BD5;
    6467 mso-themecolor:accent1'><o:p></o:p></span></span></span></u></h4>
     6465<h4 style='margin-left:0.25in'><a name=Data></a><u>Data</u></h4>
     6466
     6467<p class=MsoNormal style='margin-left:.5in'>
     6468This tab serves serveral
     6469purposes. It is used to link histograms to the selected phase and it
     6470allows the values and refinement flags to be set for the parameters
     6471that are defined for each histogram-phase pair, labeled as HAP
     6472parameters.
     6473[Note that some GSAS-II parameters are defined for each phase (atomic positions, for example),
     6474other parameters are defined for each histogram (scale factors and
     6475instrumental constants, for example) but the HAP parameters have
     6476values for each histogram in each phase.] It can also be used to show
     6477a graphical representation of an HAP parameter set.</p>
     6478<P></P>
     6479<p class=MsoNormal style='margin-left:.5in'>
     6480The HAP parameters include: the phase fraction; the sample contribution to peak broadening:
     6481microstrain and crystallite size; a LeBail intensity extraction flag;
     6482hydrostatic/elastic strain shifts to
     6483lattice parameters; corrections to peak intensities due to
     6484experimental effects (preferred orientation, extinction and disordered
     6485solvents).</p>
     6486<DL style='margin-left:.5in'>
     6487<dt><B>Use flag</B><dd>
     6488  When the Use flag is selected, the currently selected
     6489  phase is used to compute intensities as a contribution to the selected
     6490  histogram (single-crystal histograms can have only one phase; powder
     6491  histograms can have any number of associated phases). When not set,
     6492  the phase is not present in the selected histogram.
     6493
     6494<dt><B>Phase fraction</B><dd> used in powder histograms: a multiplier
     6495  that determines the relative amount of the selected phase to a
     6496  histogram. Note that when the histogram scale factor is varied,
     6497  these values are on a relative scale. Conventional practice it to
     6498  vary the scale factor and to not vary the phase fraction for one
     6499  phase in a histogram. Do not refine the scale factor and all phase
     6500  fractions unless a constraint is defined so the phase
     6501  fractions add to 1.
     6502<dt><B>Crystallite size peak broadening</B><dd>is computed from size
     6503  factor(s) in microns (10<sup>-6</sup> m), with the Scherrer constant
     6504  assumed as unity. Sizes can be computed in three ways: isotropic,
     6505  uniaxial and ellipsoidal. In isotropic broadening, crystallites are
     6506  assumed to average as uniform in all directions and a single size
     6507  value is supplied; with uniaxial broadening, a preferred direction
     6508  (as a crystallographic axis, such as 0,0,1 is supplied) -- note that
     6509  for most
     6510  crystal systems only one axis makes sense -- and two size parameters
     6511  are defined, one for along the axis and one for in the perpendicular
     6512  plane; with ellipsoidal, six terms are used to define a broadening
     6513  tensor that mak have arbitrary orientation -- this model may require
     6514  constraints and is seldomly needed.
     6515  Note that size broadening is usually Lorentzian, which corresponds to
     6516  a LGmix value of 1.0; if this value is between 0. and 1., both
     6517  Gaussian and Lorentz size broadening is modeled and a value of 0.0
     6518  is pure Gaussian. Values less than 0. or greater than 1. make no
     6519  physical sense.
     6520 
     6521<dt><B>Microstrain peak broadening </B><dd>
     6522  is computed as unitless fraction of delta d-space/d-space (or equivalently delta-Q/Q)
     6523  times 10<sup>6</sup>. Microstrain can be computed in three ways: isotropic,
     6524  uniaxial and generalized. In isotropic broadening, microstrain
     6525  broadening assumed to be the same in all crystallographic directions and a single
     6526  value is supplied; with uniaxial broadening, a preferred direction
     6527  (as a crystallographic axis, such as 0,0,1) is supplied -- note that
     6528  for most
     6529  crystal systems only one axis makes sense -- and two microstrain parameters
     6530  are defined, one for along the axis and one for in the perpendicular
     6531  plane; with generalized, the Peter Stephens second-order expansion
     6532  model is used and the number of terms will depend on the crystal
     6533  system. It is typicall possible to refine all terms when signficant
     6534  anisotropic strain broadening is present.
     6535  Note that microstrain broadening is usually Lorentzian, which corresponds to
     6536  a LGmix value of 1.0; if this value is between 0. and 1., both
     6537  Gaussian and Lorentz broadening is modeled and a value of 0.0
     6538  is pure Gaussian. Values less than 0. or greater than 1. make no
     6539  physical sense.
     6540
     6541<dt><B>LeBail intensity extraction </B><dd>When this is selected,
     6542  intensities are set to values that are best-fit using the LeBail
     6543  intensity determination method rather than are computed from the
     6544  atomic information for the phase.
     6545<dt><B>Hydrostatic/elastic strain</B><dd>shifts the lattice constants
     6546  for the contribution of a phase into a histogram (powder diffraction
     6547  only). The values are added to the
     6548  <A href="http://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#gsasiilattice-unit-cells">
     6549  reciprocal lattice parameter tensor terms</A>. They must be refined
     6550  in sequential refinements or where the lattice constants are
     6551  slightly different in different histograms (as an example see the
     6552   <a
     6553  href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWCombined/Combined%20refinement.htm">Combined
     6554  X-ray/CW-neutron refinement of PbSO4 tutorial</a>.
     6555
     6556<dt><B>Preferred orientation</B><dd> is treated in one of two
     6557  ways. Intensity corrections can be added to the model here or a full
     6558  texture model is possible with the "texture" tab (which usually
     6559  requires multiple histograms at different sample or detector
     6560  settings). The approaches available here are March-Dollase, which
     6561  requires a definition of a unique axis (in crystallographic
     6562  coordinates) and the relative amount of excess or depletion of
     6563  crystallites in that direction; or Spherical Harmonics, where the
     6564  selection of an order determines the shape of the probability
     6565  surface (which is always constrained to match the symmetry of the
     6566  crystal system).
     6567
     6568<dt><B>Extinction </B><dd>can occur when crystals/crystallites have
     6569  minimal mosaic character, which results in lowering of diffraction
     6570  intensities for the most intense reflections. This is not commonly
     6571  seen in powder diffraction.
     6572 
     6573<dt><B>Disordered solvent</B><dd>This correction, using the Babinet model, is typically used to
     6574  treat scattering from water that is not well-ordered in protein
     6575  structures. It probably makes no sense in any other application.
     6576  </DL>
     6577
    64686578
    64696579<h5 style='margin-left:.5in'><span style='mso-fareast-font-family:"Times New Roman"'>What
    6470 can I do here?</span><i style='mso-bidi-font-style:normal'><span
    6471 style='font-family:"Cambria Math",serif;mso-fareast-font-family:"Times New Roman"'><br
    6472 style='mso-special-character:line-break'>
    6473 <![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
    6474 <![endif]></span></i><span class=MsoHyperlink><span style='color:windowtext;
    6475 font-weight:normal;text-decoration:none;text-underline:none'><o:p></o:p></span></span></h5>
     6580can I do here?</span></h5>
     6581
     6582  <OL style='margin-left:0.5in'>
     6583    <LI>
     6584  In this tab, menu items allow copying values or refinement flags to
     6585  histograms/phases and selection of which histograms are used in the
     6586  current phase.
     6587    <LI>
     6588  The plot selection items allow for three dimensional representations
     6589   of the microstrain or crystallite size distributions (which are
     6590    spheres for isotropic treatments); preferred orientation can be
     6591    plotted as a Psi scan (a plot of relative crystallite abundance
     6592    for a particular reflection as a function of azimuthal angle)
     6593    or as an inverse pole figure (which shows in a stereographic projection
     6594    the probability distribution for different reciprocal lattice
     6595    directions for a particular sample orientation).
     6596</OL>
    64766597
    64776598<h4 style='margin-left:0.25in'><a name=Atoms></a><u>Atoms</u><span
     
    72747395<hr size=2 width="100%" align=center>
    72757396
    7276 <!-- hhmts start -->Last modified: Thu Sep 28 11:14:02 CDT 2017 <!-- hhmts end -->
     7397<!-- hhmts start -->Last modified: Fri Oct  6 18:46:54 CDT 2017 <!-- hhmts end -->
    72777398
    72787399</div>
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