Changeset 990


Ignore:
Timestamp:
Jul 15, 2013 1:47:25 PM (10 years ago)
Author:
toby
Message:

mac fix for gltext; update docs

Location:
trunk
Files:
14 edited

Legend:

Unmodified
Added
Removed

  • trunk/GSASIIstrMath.py

    r989 r990  
    15851585
    15861586def dervRefine(values,HistoPhases,parmDict,varylist,calcControls,pawleyLookup,dlg):
    1587     'Needs a doc string'
     1587    '''Loop over histograms and compute derivatives of the fitting
     1588    model (M) with respect to all parameters.  Results are returned in
     1589    a Jacobian matrix (aka design matrix) of dimensions (n by m) where
     1590    n is the number of parameters and m is the number of data
     1591    points. This can exceed memory when m gets large. This routine is
     1592    used when refinement derivatives are selected as "analtytic
     1593    Jacobian" in Controls.
     1594
     1595    :returns: Jacobian numpy.array dMdv for all histograms concatinated
     1596    '''
    15881597    parmDict.update(zip(varylist,values))
    15891598    G2mv.Dict2Map(parmDict,varylist)
    … …  
    16981707
    16991708def HessRefine(values,HistoPhases,parmDict,varylist,calcControls,pawleyLookup,dlg):
     1709    '''Loop over histograms and compute derivatives of the fitting
     1710    model (M) with respect to all parameters.  For each histogram, the
     1711    Jacobian matrix, dMdv, with dimensions (n by m) where n is the
     1712    number of parameters and m is the number of data points *in the
     1713    histogram*. The (n by n) Hessian is computed from each Jacobian
     1714    and it is returned.  This routine is used when refinement
     1715    derivatives are selected as "analtytic Hessian" in Controls.
     1716
     1717    :returns: Vec,Hess where Vec is the least-squares vector and Hess is the Hessian
     1718    '''
    17001719    'Needs a doc string'
    17011720    parmDict.update(zip(varylist,values))

  • trunk/exports/G2cif.py

    r989 r990  
    216216                    s += s1
    217217            return s
     218        def FormatBackground(bkg):
     219            '''Display the Background information as a descriptive text string.
     220           
     221            TODO: this needs to be expanded to show the diffuse peak and
     222            Debye term information as well.
     223
     224            :returns: the text description (str)
     225            '''
     226            fxn, bkgdict = bkg
     227            terms = fxn[2]
     228            txt = 'Background function: "'+fxn[0]+'" function with '+str(terms)+' terms:\n'
     229            l = "   "
     230            for v in fxn[3:]:
     231                if len(l) > 60:
     232                    txt += l + '\n'
     233                    l = '   '
     234                l += G2mth.ValEsd(v,-.009)+', '
     235            txt += l
     236            return txt
    218237
    219238        def FormatInstProfile(instparmdict):
    … …  
    586605            refprx = '_refln_' # normal
    587606
    588             WriteCIFitem('\n# SCATTERING FACTOR INFO')
    589607            if 'Lam1' in inst:
    590608                ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1])
    … …  
    645663                            )
    646664
    647             # this will need help from Bob
     665            # TODO: this will need help from Bob
    648666            # WriteCIFitem('_pd_proc_ls_prof_R_factor','?')
    649667            # WriteCIFitem('_pd_proc_ls_prof_wR_factor','?')
    … …  
    651669            # WriteCIFitem('_refine_ls_R_Fsqd_factor','?')
    652670
     671            print histblk['Instrument Parameters'][0]['Type']
     672           
     673            if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
     674                WriteCIFitem('_diffrn_radiation_probe','x-ray')
     675                pola = histblk['Instrument Parameters'][0].get('Polariz.')
     676                if pola:
     677                    pfx = ':' + str(hId) + ':'
     678                    sig = self.sigDict.get(pfx+'Polariz.',-0.0009)
     679                    txt = G2mth.ValEsd(pola[1],sig)
     680                    WriteCIFitem('_diffrn_radiation_polarisn_ratio',txt)
     681            elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
     682                WriteCIFitem('_diffrn_radiation_probe','neutron')
     683            # TOF (note that this may not be defined)
     684            #if histblk['Instrument Parameters'][0]['Type'][1][2] == 'T':
     685            #    WriteCIFitem('_pd_meas_2theta_fixed',text)
     686           
     687
     688            # TODO: this will need help from Bob
     689            #if not oneblock:
     690            #WriteCIFitem('\n# SCATTERING FACTOR INFO')
     691            #WriteCIFitem('loop_  _atom_type_symbol')
     692            #if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
     693            #    WriteCIFitem('      _atom_type_scat_dispersion_real')
     694            #    WriteCIFitem('      _atom_type_scat_dispersion_imag')
     695            #    for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'):
     696            #        WriteCIFitem('      _atom_type_scat_Cromer_Mann_'+lbl)
     697            #elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
     698            #    WriteCIFitem('      _atom_type_scat_length_neutron')
     699            #WriteCIFitem('      _atom_type_scat_source')
     700
     701            WriteCIFitem('_pd_proc_ls_background_function',FormatBackground(histblk['Background']))
     702
     703            #WriteCIFitem('_exptl_absorpt_process_details','?')
     704            #WriteCIFitem('_exptl_absorpt_correction_T_min','?')
     705            #WriteCIFitem('_exptl_absorpt_correction_T_max','?')
     706            #C extinction
     707            #WRITE(IUCIF,'(A)') '# Extinction correction'
     708            #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10))
     709            #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20))
     710
     711            if not oneblock:
     712                # instrumental profile terms go here
     713                WriteCIFitem('_pd_proc_ls_profile_function','?')
     714
     715            raise Exception, "testing"
    653716            phasenam = self.Phases.keys()[0]
    654717            for key in self.Phases[phasenam]['Histograms']:
    … …  
    656719                print '------------'
    657720                print self.Phases[phasenam]['Histograms'][key]
    658             raise Exception, "testing"
    659721            print histblk.keys()
    660722            for key in histblk:
    … …  
    663725            #print self.parmDict.keys()
    664726            #print self.sigDict.keys()
    665            
    666             #WriteCIFitem('_pd_meas_2theta_fixed',text)
    667             WriteCIFitem('_diffrn_radiation_probe','x-ray')
    668             WriteCIFitem('_diffrn_radiation_probe','neutron')
    669             WriteCIFitem('_diffrn_radiation_polarisn_ratio','?')
    670            
    671             WriteCIFitem('loop_  _atom_type_symbol')
    672             if oneblock:
    673                 WriteCIFitem('       _atom_type_number_in_cell')
    674             #IF (HTYP(2:2) .eq. 'X' .AND. HTYP(3:3) .ne. 'E') THEN
    675             WriteCIFitem('      _atom_type_scat_dispersion_real')
    676             WriteCIFitem('      _atom_type_scat_dispersion_imag')
    677             for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'):
    678                 WriteCIFitem('      _atom_type_scat_Cromer_Mann_'+lbl)
    679             #ELSEIF (HTYP(2:2) .eq. 'N') THEN
    680             WriteCIFitem('      _atom_type_scat_length_neutron')
    681             #ENDIF
    682             WriteCIFitem('      _atom_type_scat_source')
    683 
    684             #C document the background function used
    685             WriteCIFitem('_pd_proc_ls_background_function','?')
    686 
    687             WriteCIFitem('_exptl_absorpt_process_details','?')
    688             WriteCIFitem('_exptl_absorpt_correction_T_min','?')
    689             WriteCIFitem('_exptl_absorpt_correction_T_max','?')
    690             #C extinction
    691             #WRITE(IUCIF,'(A)') '# Extinction correction'
    692             #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10))
    693             #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20))
    694 
    695             if not oneblock:
    696                 # instrumental profile terms go here
    697                 WriteCIFitem('_pd_proc_ls_profile_function','?')
    698727
    699728            #print 'Data'

  • trunk/gltext.py

    r987 r990  
    147147        texture. If you see any optimizations that could save time PLEASE CREATE A PATCH!!!
    148148        """
    149         # get a memory dc
     149        # get a memory dc and assign a temporary bitmap
    150150        dc = wx.MemoryDC()
     151        dc.SelectObject(wx.EmptyBitmap(100, 100))
    151152       
    152153        # set our font

  • trunk/sphinxdocs/build/html/GSASII.html

    r957 r990  
    227227<dl class="method">
    228228<dt id="GSASII.GSASII.OnFileOpen">
    229 <tt class="descclassname">GSASII.</tt><tt class="descname">OnFileOpen</tt><big>(</big><em>event</em><big>)</big><a class="reference internal" href="_modules/GSASII.html#GSASII.OnFileOpen"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASII.GSASII.OnFileOpen" title="Permalink to this definition">¶</a></dt>
     229<tt class="descclassname">GSASII.</tt><tt class="descname">OnFileOpen</tt><big>(</big><em>event</em>, <em>filename=None</em><big>)</big><a class="reference internal" href="_modules/GSASII.html#GSASII.OnFileOpen"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASII.GSASII.OnFileOpen" title="Permalink to this definition">¶</a></dt>
    230230<dd><p>Reads in a GSAS-II .gpx project file in response to the
    231231File/Open Project menu button</p>
    … …  
    479479<p>Creates a wx frame (self.main) which contains the display of the
    480480data tree.</p>
     481<dl class="method">
     482<dt id="GSASII.GSASIImain.MacOpenFile">
     483<tt class="descname">MacOpenFile</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#GSASII.GSASIImain.MacOpenFile" title="Permalink to this definition">¶</a></dt>
     484<dd><p>Called on Mac every time a file is dropped on the app when it is running,
     485treat this like a File/Open project menu action.
     486Should be ignored on other platforms</p>
     487</dd></dl>
     488
    481489<dl class="method">
    482490<dt id="GSASII.GSASIImain.OnInit">

  • trunk/sphinxdocs/build/html/GSASIIGUIr.html

    r957 r990  
    248248</dd></dl>
    249249
     250<dl class="method">
     251<dt id="GSASIIgrid.MyHelp.OnSelectVersion">
     252<tt class="descname">OnSelectVersion</tt><big>(</big><em>event</em><big>)</big><a class="headerlink" href="#GSASIIgrid.MyHelp.OnSelectVersion" title="Permalink to this definition">¶</a></dt>
     253<dd><p>Allow the user to select a specific version of GSAS-II</p>
     254</dd></dl>
     255
    250256</dd></dl>
    251257
    … …  
    679685</tbody>
    680686</table>
     687</dd></dl>
     688
     689</dd></dl>
     690
     691<dl class="class">
     692<dt id="GSASIIgrid.downdate">
     693<em class="property">class </em><tt class="descclassname">GSASIIgrid.</tt><tt class="descname">downdate</tt><big>(</big><em>parent=None</em><big>)</big><a class="headerlink" href="#GSASIIgrid.downdate" title="Permalink to this definition">¶</a></dt>
     694<dd><p>Dialog to allow a user to select a version of GSAS-II to install</p>
     695<dl class="method">
     696<dt id="GSASIIgrid.downdate.getVersion">
     697<tt class="descname">getVersion</tt><big>(</big><big>)</big><a class="headerlink" href="#GSASIIgrid.downdate.getVersion" title="Permalink to this definition">¶</a></dt>
     698<dd><p>Get the version number in the dialog</p>
    681699</dd></dl>
    682700

  • trunk/sphinxdocs/build/html/GSASIImapvars.html

    r957 r990  
    267267<li><strong>derivDict</strong> (<em>dict</em>) &#8211; a dict containing derivatives for parameter values keyed by the
    268268parameter names.</li>
    269 <li><strong>dMdv</strong> (<em>dict</em>) &#8211; a dict containing derivatives for dependent parameter computed from
    270 derivDict</li>
     269<li><strong>dMdv</strong> (<em>list</em>) &#8211; a Jacobian, as a list of np.array containing derivatives for dependent
     270parameter computed from derivDict</li>
    271271</ul>
    272272</td>

  • trunk/sphinxdocs/build/html/GSASIImath.html

    r957 r990  
    338338<dl class="function">
    339339<dt id="GSASIImath.HessianLSQ">
    340 <tt class="descclassname">GSASIImath.</tt><tt class="descname">HessianLSQ</tt><big>(</big><em>func</em>, <em>x0</em>, <em>Hess</em>, <em>args=()</em>, <em>ftol=1.49012e-08</em>, <em>xtol=1.49012e-08</em>, <em>maxcyc=0</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#HessianLSQ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.HessianLSQ" title="Permalink to this definition">¶</a></dt>
     340<tt class="descclassname">GSASIImath.</tt><tt class="descname">HessianLSQ</tt><big>(</big><em>func</em>, <em>x0</em>, <em>Hess</em>, <em>args=()</em>, <em>ftol=1.49012e-08</em>, <em>xtol=1.49012e-08</em>, <em>maxcyc=0</em>, <em>Print=False</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#HessianLSQ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.HessianLSQ" title="Permalink to this definition">¶</a></dt>
    341341<dd><p>Minimize the sum of squares of a function (<span class="math">\(f\)</span>) evaluated on a series of
    342342values (y): <span class="math">\(\sum_{y=0}^{N_{obs}} f(y,{args})\)</span></p>
    … …  
    362362<li><strong>maxcyc</strong> (<em>int</em>) &#8211; The maximum number of cycles of refinement to execute, if -1 refine
    363363until other limits are met (ftol, xtol)</li>
     364<li><strong>Print</strong> (<em>bool</em>) &#8211; True for printing results (residuals &amp; times) by cycle</li>
    364365</ul>
    365366</td>

  • trunk/sphinxdocs/build/html/GSASIIobj.html

    r957 r990  
    222222</table>
    223223</div>
    224 <div class="section" id="phase-tree-item">
    225 <h2>Phase Tree Item<a class="headerlink" href="#phase-tree-item" title="Permalink to this headline">¶</a></h2>
     224<div class="section" id="phase-tree-items">
     225<h2>Phase Tree Items<a class="headerlink" href="#phase-tree-items" title="Permalink to this headline">¶</a></h2>
    226226<span class="target" id="phase-table"></span><p id="index-3">Phase information is stored in the GSAS-II data tree as children of the
    227227Phases item in a dict with keys:</p>
    … …  
    245245<tr class="row-odd"><td></td>
    246246<td>AtomPtrs</td>
    247 <td>? (list)</td>
     247<td>list of four locations to use to pull info
     248from the atom records (list)</td>
    248249</tr>
    249250<tr class="row-even"><td></td>
    … …  
    375376<td></td>
    376377<td>Atoms in phase as a list of lists. The outer list
    377 is for each atom, the inner list contains 18
    378 items:
    379 0) atom label, 1) the atom type,
    380 2) the refinement flags, 3-6) x, y, z, frac
    381 7) site symmetry, 8) site multiplicity,
    382 9) &#8216;I&#8217; or &#8216;A&#8217; for iso/anisotropic,
    383 10) Uiso, 10-16) Uij, 16) unique Id #.
     378is for each atom, the inner list contains varying
     379items depending on the type of phase, see
     380the <a class="reference internal" href="#atoms-table"><em>Atom Records</em></a> description.
    384381(list of lists)</td>
    385382</tr>
    … …  
    567564Asymmetric unit coordinates [X is (x,y,z)]
    568565are transformed using
    569 <span class="math">\(X\prime = M_n*X+T_n\)</span></td>
     566<span class="math">\(X^\prime = M_n*X+T_n\)</span></td>
    570567</tr>
    571568<tr class="row-odd"><td>SGSys</td>
    … …  
    583580</tbody>
    584581</table>
     582</div>
     583<div class="section" id="atom-records">
     584<h2>Atom Records<a class="headerlink" href="#atom-records" title="Permalink to this headline">¶</a></h2>
     585<span class="target" id="atoms-table"></span><p id="index-5">If <tt class="docutils literal"><span class="pre">phasedict</span></tt> points to the phase information in the data tree, then
     586atoms are contained in a list of atom records (list) in
     587<tt class="docutils literal"><span class="pre">phasedict['Atoms']</span></tt>. Also needed to read atom information
     588are four pointers, <tt class="docutils literal"><span class="pre">cx,ct,cs,cia</span> <span class="pre">=</span> <span class="pre">phasedict['General']['AtomPtrs']</span></tt>,
     589which define locations in the atom record, as shown below.</p>
     590<table border="1" class="docutils">
     591<colgroup>
     592<col width="21%" />
     593<col width="79%" />
     594</colgroup>
     595<thead valign="bottom">
     596<tr class="row-odd"><th class="head">location</th>
     597<th class="head">explanation</th>
     598</tr>
     599</thead>
     600<tbody valign="top">
     601<tr class="row-even"><td>cx,cx+1,cx+2</td>
     602<td>the x,y and z coordinates</td>
     603</tr>
     604<tr class="row-odd"><td>cx+3</td>
     605<td>fractional occupancy (also cs-1)</td>
     606</tr>
     607<tr class="row-even"><td>ct-1</td>
     608<td>atom label</td>
     609</tr>
     610<tr class="row-odd"><td>ct</td>
     611<td>atom type</td>
     612</tr>
     613<tr class="row-even"><td>ct+1</td>
     614<td>refinement flags</td>
     615</tr>
     616<tr class="row-odd"><td>cs</td>
     617<td>site symmetry string</td>
     618</tr>
     619<tr class="row-even"><td>cs+1</td>
     620<td>site multiplicity</td>
     621</tr>
     622<tr class="row-odd"><td>cia</td>
     623<td>ADP flag: Isotropic (&#8216;I&#8217;) or Anisotropic (&#8216;A&#8217;)</td>
     624</tr>
     625<tr class="row-even"><td>cia+1</td>
     626<td>Uiso</td>
     627</tr>
     628<tr class="row-odd"><td>cia+2...cia+6</td>
     629<td>U11, U22, U33, U12, U13, U23</td>
     630</tr>
     631</tbody>
     632</table>
     633</div>
     634<div class="section" id="powder-diffraction-tree-items">
     635<h2>Powder Diffraction Tree Items<a class="headerlink" href="#powder-diffraction-tree-items" title="Permalink to this headline">¶</a></h2>
     636<span class="target" id="powder-table"></span><p id="index-6">Every powder diffraction histogram is stored in the GSAS-II data tree
     637with a top-level entry named beginning with the string &#8220;PWDR &#8221;. The
     638diffraction data for that information are directly associated with
     639that tree item and there are a series of children to that item. The
     640routine <a class="reference internal" href="GSASII.html#GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree" title="GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree"><tt class="xref py py-func docutils literal"><span class="pre">GetUsedHistogramsAndPhasesfromTree()</span></tt></a> will
     641load this information into a dictionary where the child tree name is
     642used as a key, and the information in the main entry is assigned
     643a key of <tt class="docutils literal"><span class="pre">Data</span></tt>, as outlined below.</p>
     644<table border="1" class="docutils">
     645<colgroup>
     646<col width="25%" />
     647<col width="17%" />
     648<col width="58%" />
     649</colgroup>
     650<thead valign="bottom">
     651<tr class="row-odd"><th class="head">key</th>
     652<th class="head">sub-key</th>
     653<th class="head">explanation</th>
     654</tr>
     655</thead>
     656<tbody valign="top">
     657<tr class="row-even"><td>Limits</td>
     658<td></td>
     659<td>A list of two two element lists, as [[Ld,Hd],[L,H]]
     660where L and Ld are the current and default lowest
     661two-theta value to be used and
     662where H and Hd are the current and default highest
     663two-theta value to be used.</td>
     664</tr>
     665<tr class="row-odd"><td>Reflection Lists</td>
     666<td></td>
     667<td>A dict with an entry for each phase in the
     668histogram. The contents of each dict item
     669is a list or reflections as described in the
     670<a class="reference internal" href="#powderrefl-table"><em>Powder Reflections</em></a>
     671description.</td>
     672</tr>
     673<tr class="row-even"><td>Instrument Parameters</td>
     674<td></td>
     675<td>A list containing two dicts where the possible
     676keys in each dict are listed below. The value
     677for each item is a list containing three values:
     678the initial value, the current value and a
     679refinement flag which can have a value of
     680True, False or 0 where 0 indicates a value that
     681cannot be refined. The first and second
     682values are floats unless otherwise noted.
     683Items in the first dict are noted as [1]</td>
     684</tr>
     685<tr class="row-odd"><td></td>
     686<td>Lam</td>
     687<td>Specifies a wavelength in Angstroms [1]</td>
     688</tr>
     689<tr class="row-even"><td></td>
     690<td>Lam1</td>
     691<td>Specifies the primary wavelength in
     692Angstrom, when an alpha1, alpha2
     693source is used [1]</td>
     694</tr>
     695<tr class="row-odd"><td></td>
     696<td><p class="first">Lam2</p>
     697<p class="last">I(L2)/I(L1)</p>
     698</td>
     699<td>Specifies the secondary wavelength in
     700Angstrom, when an alpha1, alpha2
     701source is used [1]
     702Ratio of Lam2 to Lam1 [1]</td>
     703</tr>
     704<tr class="row-even"><td></td>
     705<td>Type</td>
     706<td><dl class="first last docutils">
     707<dt>Histogram type (str) [1]:</dt>
     708<dd><ul class="first last simple">
     709<li>&#8216;PXC&#8217; for constant wavelength x-ray</li>
     710<li>&#8216;PNC&#8217; for constant wavelength neutron</li>
     711<li>&#8216;PNT&#8217; for time of flight neutron</li>
     712</ul>
     713</dd>
     714</dl>
     715</td>
     716</tr>
     717<tr class="row-odd"><td></td>
     718<td>Zero</td>
     719<td>Two-theta zero correction in <em>degrees</em> [1]</td>
     720</tr>
     721<tr class="row-even"><td></td>
     722<td>Azimuth</td>
     723<td>Azimuthal setting angle for data recorded
     724with differing setting angles [1]</td>
     725</tr>
     726<tr class="row-odd"><td></td>
     727<td>U, V, W</td>
     728<td>Cagliotti profile coefficients
     729for Gaussian instrumental broadening, where the
     730FWHM goes as
     731<span class="math">\(U \tan^2\theta + V \tan\theta + W\)</span> [1]</td>
     732</tr>
     733<tr class="row-even"><td></td>
     734<td>X, Y</td>
     735<td>Cauchy (Lorentzian) instrumental broadening
     736coefficients [1]</td>
     737</tr>
     738<tr class="row-odd"><td></td>
     739<td>SH/L</td>
     740<td>Variant of the Finger-Cox-Jephcoat asymmetric
     741peak broadening ratio. Note that this is the
     742average between S/L and H/L where S is
     743sample height, H is the slit height and
     744L is the goniometer diameter. [1]</td>
     745</tr>
     746<tr class="row-even"><td></td>
     747<td>Polariz.</td>
     748<td>Polarization coefficient. [1]</td>
     749</tr>
     750<tr class="row-odd"><td>wtFactor</td>
     751<td></td>
     752<td>A weighting factor to increase or decrease
     753the leverage of data in the histogram (float).
     754A value of 1.0 weights the data with their
     755standard uncertainties and a larger value
     756increases the weighting of the data (equivalent
     757to decreasing the uncertainties).</td>
     758</tr>
     759<tr class="row-even"><td>Sample Parameters</td>
     760<td></td>
     761<td>Specifies a dict with parameters that describe how
     762the data were collected, as listed
     763below. Refinable parameters are a list containing
     764a float and a bool, where the second value
     765specifies if the value is refined, otherwise
     766the value is a float unless otherwise noted.</td>
     767</tr>
     768<tr class="row-odd"><td></td>
     769<td>Scale</td>
     770<td>The histogram scale factor (refinable)</td>
     771</tr>
     772<tr class="row-even"><td></td>
     773<td>Absorption</td>
     774<td>The sample absorption coefficient as
     775<span class="math">\(\mu r\)</span> where r is the radius
     776(refinable).</td>
     777</tr>
     778<tr class="row-odd"><td></td>
     779<td>DisplaceX,
     780DisplaceY</td>
     781<td>Sample displacement from goniometer center
     782where Y is along the beam direction and
     783X is perpendicular. Units are <span class="math">\(\mu m\)</span>
     784(refinable).</td>
     785</tr>
     786<tr class="row-even"><td></td>
     787<td>Phi, Chi,
     788Omega</td>
     789<td>Goniometer sample setting angles, in degrees.</td>
     790</tr>
     791<tr class="row-odd"><td></td>
     792<td>Gonio. radius</td>
     793<td>Radius of the diffractometer in mm</td>
     794</tr>
     795<tr class="row-even"><td></td>
     796<td>InstrName</td>
     797<td>A name for the instrument, used in preparing
     798a CIF (str).</td>
     799</tr>
     800<tr class="row-odd"><td></td>
     801<td>Force,
     802Temperature,
     803Humidity,
     804Pressure,
     805Voltage</td>
     806<td>Variables that describe how the measurement
     807was performed. Not used directly in
     808any computations.</td>
     809</tr>
     810<tr class="row-even"><td></td>
     811<td>ranId</td>
     812<td>The random-number Id for the histogram
     813(same value as where top-level key is ranId)</td>
     814</tr>
     815<tr class="row-odd"><td></td>
     816<td>Type</td>
     817<td>Type of diffraction data, may be &#8216;Debye-Scherrer&#8217;
     818or &#8216;Bragg-Brentano&#8217; (str).</td>
     819</tr>
     820<tr class="row-even"><td></td>
     821<td>Diffuse</td>
     822<td>not in use?</td>
     823</tr>
     824<tr class="row-odd"><td>hId</td>
     825<td></td>
     826<td>The number assigned to the histogram when
     827the project is loaded or edited (can change)</td>
     828</tr>
     829<tr class="row-even"><td>ranId</td>
     830<td></td>
     831<td>A random number id for the histogram
     832that does not change</td>
     833</tr>
     834<tr class="row-odd"><td>Background</td>
     835<td></td>
     836<td>The background is stored as a list with where
     837the first item in the list is list and the second
     838item is a dict. The list contains the background
     839function and its coefficients; the dict contains
     840Debye diffuse terms and background peaks.
     841(TODO: this needs to be expanded.)</td>
     842</tr>
     843<tr class="row-even"><td>Data</td>
     844<td></td>
     845<td><p class="first">The data consist of a list of 6 np.arrays
     846containing in order:</p>
     847<blockquote class="last">
     848<div><ol class="arabic simple">
     849<li>the x-postions (two-theta in degrees),</li>
     850<li>the intensity values (Yobs),</li>
     851<li>the weights for each Yobs value</li>
     852<li>the computed intensity values (Ycalc)</li>
     853<li>the background values</li>
     854<li>Yobs-Ycalc</li>
     855</ol>
     856</div></blockquote>
     857</td>
     858</tr>
     859</tbody>
     860</table>
     861</div>
     862<div class="section" id="powder-reflection-data-structure">
     863<h2>Powder Reflection Data Structure<a class="headerlink" href="#powder-reflection-data-structure" title="Permalink to this headline">¶</a></h2>
     864<span class="target" id="powderrefl-table"></span><p id="index-7">For every phase in a histogram, the <tt class="docutils literal"><span class="pre">Reflection</span> <span class="pre">Lists</span></tt> value is a list of
     865reflections. The items in that list are documented below.</p>
     866<table border="1" class="docutils">
     867<colgroup>
     868<col width="16%" />
     869<col width="84%" />
     870</colgroup>
     871<thead valign="bottom">
     872<tr class="row-odd"><th class="head">index</th>
     873<th class="head">explanation</th>
     874</tr>
     875</thead>
     876<tbody valign="top">
     877<tr class="row-even"><td>0,1,2</td>
     878<td>h,k,l (float)</td>
     879</tr>
     880<tr class="row-odd"><td>3</td>
     881<td>multiplicity</td>
     882</tr>
     883<tr class="row-even"><td>4</td>
     884<td>d-space, Angstrom</td>
     885</tr>
     886<tr class="row-odd"><td>5</td>
     887<td>pos, two-theta</td>
     888</tr>
     889<tr class="row-even"><td>6</td>
     890<td>sig, Gaussian width</td>
     891</tr>
     892<tr class="row-odd"><td>7</td>
     893<td>gam, Lorenzian width</td>
     894</tr>
     895<tr class="row-even"><td>8</td>
     896<td>Fobs**2</td>
     897</tr>
     898<tr class="row-odd"><td>9</td>
     899<td>Fcalc**2</td>
     900</tr>
     901<tr class="row-even"><td>10</td>
     902<td>reflection phase, in degrees</td>
     903</tr>
     904<tr class="row-odd"><td>11</td>
     905<td>the equivalent reflections as a (m x 3)
     906np.array, where m is 0.5 * multiplicity. Note
     907that Freidel pairs, (-h,-k-,l), are not
     908included.</td>
     909</tr>
     910<tr class="row-even"><td>12</td>
     911<td>phase shift for each of the equivalent
     912reflections as a length (m) array</td>
     913</tr>
     914<tr class="row-odd"><td>13</td>
     915<td>intensity correction for reflection, this times
     916Fobs**2 or Fcalc**2 gives Iobs or Icalc</td>
     917</tr>
     918<tr class="row-even"><td>14</td>
     919<td>dict with the form factor (f or b) by atom type
     920symbol at the reflection position.</td>
     921</tr>
     922</tbody>
     923</table>
     924</div>
     925<div class="section" id="classes-and-routines">
     926<h2><em>Classes and routines</em><a class="headerlink" href="#classes-and-routines" title="Permalink to this headline">¶</a></h2>
    585927<dl class="function">
    586928<dt id="GSASIIobj.LoadHistogramIDs">
    … …  
    6911033<li><a class="reference internal" href="#constraints-tree-item">Constraints Tree Item</a></li>
    6921034<li><a class="reference internal" href="#covariance-tree-item">Covariance Tree Item</a></li>
    693 <li><a class="reference internal" href="#phase-tree-item">Phase Tree Item</a></li>
     1035<li><a class="reference internal" href="#phase-tree-items">Phase Tree Items</a></li>
    6941036<li><a class="reference internal" href="#space-group-objects">Space Group Objects</a></li>
     1037<li><a class="reference internal" href="#atom-records">Atom Records</a></li>
     1038<li><a class="reference internal" href="#powder-diffraction-tree-items">Powder Diffraction Tree Items</a></li>
     1039<li><a class="reference internal" href="#powder-reflection-data-structure">Powder Reflection Data Structure</a></li>
     1040<li><a class="reference internal" href="#classes-and-routines"><em>Classes and routines</em></a></li>
    6951041</ul>
    6961042</li>

  • trunk/sphinxdocs/build/html/GSASIIstruc.html

    r957 r990  
    233233<dt id="GSASIIstrMath.HessRefine">
    234234<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">HessRefine</tt><big>(</big><em>values</em>, <em>HistoPhases</em>, <em>parmDict</em>, <em>varylist</em>, <em>calcControls</em>, <em>pawleyLookup</em>, <em>dlg</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#HessRefine"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.HessRefine" title="Permalink to this definition">¶</a></dt>
    235 <dd><p>Needs a doc string</p>
     235<dd><p>Loop over histograms and compute derivatives of the fitting
     236model (M) with respect to all parameters.  For each histogram, the
     237Jacobian matrix, dMdv, with dimensions (n by m) where n is the
     238number of parameters and m is the number of data points <em>in the
     239histogram</em>. The (n by n) Hessian is computed from each Jacobian
     240and it is returned.  This routine is used when refinement
     241derivatives are selected as &#8220;analtytic Hessian&#8221; in Controls.</p>
     242<table class="docutils field-list" frame="void" rules="none">
     243<col class="field-name" />
     244<col class="field-body" />
     245<tbody valign="top">
     246<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Vec,Hess where Vec is the least-squares vector and Hess is the Hessian</td>
     247</tr>
     248</tbody>
     249</table>
    236250</dd></dl>
    237251
    … …  
    307321<dt id="GSASIIstrMath.dervRefine">
    308322<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">dervRefine</tt><big>(</big><em>values</em>, <em>HistoPhases</em>, <em>parmDict</em>, <em>varylist</em>, <em>calcControls</em>, <em>pawleyLookup</em>, <em>dlg</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#dervRefine"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.dervRefine" title="Permalink to this definition">¶</a></dt>
    309 <dd><p>Needs a doc string</p>
     323<dd><p>Loop over histograms and compute derivatives of the fitting
     324model (M) with respect to all parameters.  Results are returned in
     325a Jacobian matrix (aka design matrix) of dimensions (n by m) where
     326n is the number of parameters and m is the number of data
     327points. This can exceed memory when m gets large. This routine is
     328used when refinement derivatives are selected as &#8220;analtytic
     329Jacobian&#8221; in Controls.</p>
     330<table class="docutils field-list" frame="void" rules="none">
     331<col class="field-name" />
     332<col class="field-body" />
     333<tbody valign="top">
     334<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Jacobian numpy.array dMdv for all histograms concatinated</td>
     335</tr>
     336</tbody>
     337</table>
    310338</dd></dl>
    311339
    … …  
    449477<dl class="function">
    450478<dt id="GSASIIstrIO.GetHistogramPhaseData">
    451 <tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetHistogramPhaseData</tt><big>(</big><em>Phases</em>, <em>Histograms</em>, <em>Print=True</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetHistogramPhaseData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetHistogramPhaseData" title="Permalink to this definition">¶</a></dt>
    452 <dd><p>needs a doc string</p>
     479<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetHistogramPhaseData</tt><big>(</big><em>Phases</em>, <em>Histograms</em>, <em>Print=True</em>, <em>pFile=None</em>, <em>resetRefList=True</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetHistogramPhaseData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetHistogramPhaseData" title="Permalink to this definition">¶</a></dt>
     480<dd><p>Loads the HAP histogram/phase information into dicts</p>
     481<table class="docutils field-list" frame="void" rules="none">
     482<col class="field-name" />
     483<col class="field-body" />
     484<tbody valign="top">
     485<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     486<li><strong>Phases</strong> (<em>dict</em>) &#8211; phase information</li>
     487<li><strong>Histograms</strong> (<em>dict</em>) &#8211; Histogram information</li>
     488<li><strong>Print</strong> (<em>bool</em>) &#8211; prints information as it is read</li>
     489<li><strong>pFile</strong> (<em>file</em>) &#8211; file object to print to (the default, None causes printing to the console)</li>
     490<li><strong>resetRefList</strong> (<em>bool</em>) &#8211; Should the contents of the Reflection List be initialized
     491on loading. The default, True, initializes the Reflection List as it is loaded.</li>
     492</ul>
     493</td>
     494</tr>
     495<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(hapVary,hapDict,controlDict)
     496* hapVary: list of refined variables
     497* hapDict: dict with refined variables and their values
     498* controlDict: dict with computation controls (?)</p>
     499</td>
     500</tr>
     501</tbody>
     502</table>
    453503</dd></dl>
    454504
    … …  
    551601<dt id="GSASIIstrIO.ProcessConstraints">
    552602<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">ProcessConstraints</tt><big>(</big><em>constList</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#ProcessConstraints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.ProcessConstraints" title="Permalink to this definition">¶</a></dt>
    553 <dd><p>interpret constraints</p>
     603<dd><p>Interpret the constraints in the constList input into a dictionary, etc.</p>
     604<table class="docutils field-list" frame="void" rules="none">
     605<col class="field-name" />
     606<col class="field-body" />
     607<tbody valign="top">
     608<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>constList</strong> (<em>list</em>) &#8211; <p>a list of lists where each item in the outer list
     609specifies a constraint of some form. The last item in each inner list
     610determines which of the four constraints types has been input:</p>
     611<blockquote>
     612<div><ul class="simple">
     613<li>h (hold): a single variable that will not be varied. It
     614will be removed from the varyList later.</li>
     615<li>c (constraint): specifies a linear relationship that
     616can be varied as a new grouped variable
     617a fixed value.</li>
     618<li>f (fixed): specifies a linear relationship that is assigned
     619a fixed value.</li>
     620<li>e (equivalence): specifies a series of variables where the
     621first variable in the last can be used to generate the
     622values for all the remaining variables.</li>
     623</ul>
     624</div></blockquote>
     625</td>
     626</tr>
     627<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a tuple of (constDict,fixedList,ignored) where:<ul class="simple">
     628<li>constDict (list) contains the constraint relationships</li>
     629<li>fixedList (list) contains the fixed values for type
     630of constraint.</li>
     631<li>ignored (int) counts the number of invalid constraint items
     632(should always be zero!)</li>
     633</ul>
     634</td>
     635</tr>
     636</tbody>
     637</table>
    554638</dd></dl>
    555639
    … …  
    630714<dt id="GSASIIstrIO.cellFill">
    631715<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">cellFill</tt><big>(</big><em>pfx</em>, <em>SGData</em>, <em>parmDict</em>, <em>sigDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#cellFill"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.cellFill" title="Permalink to this definition">¶</a></dt>
    632 <dd><p>needs a doc string</p>
     716<dd><p>Returns the filled-out reciprocal cell (A) terms and their uncertainties
     717from the parameter and sig dictionaries.</p>
     718<table class="docutils field-list" frame="void" rules="none">
     719<col class="field-name" />
     720<col class="field-body" />
     721<tbody valign="top">
     722<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     723<li><strong>pfx</strong> (<em>str</em>) &#8211; parameter prefix (&#8220;n::&#8221;, where n is a phase number)</li>
     724<li><strong>SGdata</strong> (<em>dict</em>) &#8211; a symmetry object</li>
     725<li><strong>parmDict</strong> (<em>dict</em>) &#8211; a dictionary of parameters</li>
     726<li><strong>sigDict</strong> (<em>dict</em>) &#8211; a dictionary of uncertainties on parameters</li>
     727</ul>
     728</td>
     729</tr>
     730<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A,sigA where each is a list of six terms with the A terms</p>
     731</td>
     732</tr>
     733</tbody>
     734</table>
    633735</dd></dl>
    634736

  • trunk/sphinxdocs/build/html/GSASIIutil.html

    r957 r990  
    110110<col class="field-body" />
    111111<tbody valign="top">
    112 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>RevString</strong> (<em>str</em>) &#8211; something like &#8220;$Revision: 939 $&#8221;
     112<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>RevString</strong> (<em>str</em>) &#8211; something like &#8220;$Revision: 989 $&#8221;
    113113that is set by subversion when the file is retrieved from subversion.</td>
    114114</tr>
    115115</tbody>
    116116</table>
    117 <p>Place <tt class="docutils literal"><span class="pre">GSASIIpath.SetVersionNumber(&quot;$Revision:</span> <span class="pre">939</span> <span class="pre">$&quot;)</span></tt> in every python
     117<p>Place <tt class="docutils literal"><span class="pre">GSASIIpath.SetVersionNumber(&quot;$Revision:</span> <span class="pre">989</span> <span class="pre">$&quot;)</span></tt> in every python
    118118file.</p>
    119119</dd></dl>
    … …  
    139139
    140140<dl class="function">
     141<dt id="GSASIIpath.svnGetLog">
     142<tt class="descclassname">GSASIIpath.</tt><tt class="descname">svnGetLog</tt><big>(</big><em>fpath='/Users/toby/software/G2/GSASII'</em>, <em>version=None</em><big>)</big><a class="headerlink" href="#GSASIIpath.svnGetLog" title="Permalink to this definition">¶</a></dt>
     143<dd><p>Get the revision log information for a specific version of the</p>
     144<table class="docutils field-list" frame="void" rules="none">
     145<col class="field-name" />
     146<col class="field-body" />
     147<tbody valign="top">
     148<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     149<li><strong>fpath</strong> (<em>str</em>) &#8211; path to repository dictionary, defaults to directory where
     150the current file is located.</li>
     151<li><strong>version</strong> (<em>int</em>) &#8211; the version number to be looked up or None (default)
     152for the latest version.</li>
     153</ul>
     154</td>
     155</tr>
     156<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">a dictionary with keys (one hopes) &#8216;author&#8217;, &#8216;date&#8217;, &#8216;msg&#8217;, and &#8216;revision&#8217;</p>
     157</td>
     158</tr>
     159</tbody>
     160</table>
     161</dd></dl>
     162
     163<dl class="function">
    141164<dt id="GSASIIpath.svnGetRev">
    142165<tt class="descclassname">GSASIIpath.</tt><tt class="descname">svnGetRev</tt><big>(</big><em>fpath='/Users/toby/software/G2/GSASII'</em>, <em>local=True</em><big>)</big><a class="reference internal" href="_modules/GSASIIpath.html#svnGetRev"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIpath.svnGetRev" title="Permalink to this definition">¶</a></dt>
    143 <dd><p>This obtains the version number for the either the latest local last update
     166<dd><p>Obtain the version number for the either the last update of the local version
    144167or contacts the subversion server to get the latest update version (# of Head).</p>
    145168<table class="docutils field-list" frame="void" rules="none">
    … …  
    148171<tbody valign="top">
    149172<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
    150 <li><strong>fpath</strong> &#8211; path to repository dictionary, defaults to directory where
     173<li><strong>fpath</strong> (<em>str</em>) &#8211; path to repository dictionary, defaults to directory where
    151174the current file is located</li>
    152 <li><strong>local</strong> &#8211; determines the type of version number, where
     175<li><strong>local</strong> (<em>bool</em>) &#8211; determines the type of version number, where
    153176True (default): returns the latest installed update
    154177False: returns the version number of Head on the server</li>
    … …  
    167190<dl class="function">
    168191<dt id="GSASIIpath.svnUpdateDir">
    169 <tt class="descclassname">GSASIIpath.</tt><tt class="descname">svnUpdateDir</tt><big>(</big><em>fpath='/Users/toby/software/G2/GSASII'</em><big>)</big><a class="reference internal" href="_modules/GSASIIpath.html#svnUpdateDir"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIpath.svnUpdateDir" title="Permalink to this definition">¶</a></dt>
     192<tt class="descclassname">GSASIIpath.</tt><tt class="descname">svnUpdateDir</tt><big>(</big><em>fpath='/Users/toby/software/G2/GSASII'</em>, <em>version=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIpath.html#svnUpdateDir"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIpath.svnUpdateDir" title="Permalink to this definition">¶</a></dt>
    170193<dd><p>This performs an update of the files in a local directory from a server.</p>
    171194<table class="docutils field-list" frame="void" rules="none">
    … …  
    173196<col class="field-body" />
    174197<tbody valign="top">
    175 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fpath</strong> &#8211; path to repository dictionary, defaults to directory where
    176 the current file is located</td>
    177 </tr>
    178 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A dictionary with the files that have been changed/added and
    179 a code describing how they have been updated (see changetype) ro
     198<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
     199<li><strong>fpath</strong> (<em>str</em>) &#8211; path to repository dictionary, defaults to directory where
     200the current file is located</li>
     201<li><strong>version</strong> &#8211; the number of the version to be loaded. Used only
     202cast as a string, but should be an integer or something that corresponds to a
     203string representation of an integer value when cast. A value of None (default)
     204causes the latest version on the server to be used.</li>
     205</ul>
     206</td>
     207</tr>
     208<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A dictionary with the files that have been changed/added and
     209a code describing how they have been updated (see changetype) or
    180210None if there is a subversion error (likely because the path is
    181 not a repository or svn is not found)</td>
     211not a repository or svn is not found)</p>
     212</td>
    182213</tr>
    183214</tbody>
    … …  
    195226<col class="field-body" />
    196227<tbody valign="top">
    197 <tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">None if svn is not found.</td>
     228<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">None if svn is not found or an absolute path to the subversion
     229executable file.</td>
    198230</tr>
    199231</tbody>
    … …  
    431463<dl class="function">
    432464<dt id="GSASIIElem.getFFvalues">
    433 <tt class="descclassname">GSASIIElem.</tt><tt class="descname">getFFvalues</tt><big>(</big><em>FFtables</em>, <em>SQ</em><big>)</big><a class="reference internal" href="_modules/GSASIIElem.html#getFFvalues"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIElem.getFFvalues" title="Permalink to this definition">¶</a></dt>
     465<tt class="descclassname">GSASIIElem.</tt><tt class="descname">getFFvalues</tt><big>(</big><em>FFtables</em>, <em>SQ</em>, <em>ifList=False</em><big>)</big><a class="reference internal" href="_modules/GSASIIElem.html#getFFvalues"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIElem.getFFvalues" title="Permalink to this definition">¶</a></dt>
    434466<dd><p>Needs a doc string</p>
    435467</dd></dl>
    … …  
    439471<h2><em>GSASIIlattice: Unit cells</em><a class="headerlink" href="#gsasiilattice-unit-cells" title="Permalink to this headline">¶</a></h2>
    440472<p>Perform lattice-related computations</p>
     473<p>Note that <em>g</em> is the reciprocal lattice tensor, and <em>G</em> is its inverse,
     474<span class="math">\(G = g^{-1}\)</span>, where</p>
     475<blockquote>
     476<div><div class="math">
     477\[\begin{split}G = \left( \begin{matrix}
     478a^2 &amp; a b\cos\gamma &amp; a c\cos\beta \\
     479a b\cos\gamma &amp; b^2 &amp; b c \cos\alpha \\
     480a c\cos\beta &amp;  b c \cos\alpha &amp; c^2
     481\end{matrix}\right)\end{split}\]</div>
     482</div></blockquote>
     483<p>The &#8220;<em>A</em> tensor&#8221; terms are defined as
     484<span class="math">\(A = (\begin{matrix} G_{11} &amp; G_{22} &amp; G_{33} &amp; 2G_{12} &amp; 2G_{13} &amp; 2G_{23}\end{matrix})\)</span> and <em>A</em> can be used in this fashion:
     485<span class="math">\(d^* = \sqrt {A_1 h^2 + A_2 k^2 + A_3 l^2 + A_4 hk + A_5 hl + A_6 kl}\)</span>, where
     486<em>d</em> is the d-spacing, and <span class="math">\(d^*\)</span> is the reciprocal lattice spacing,
     487<span class="math">\(Q = 2 \pi d^* = 2 \pi / d\)</span></p>
    441488<dl class="function">
    442489<dt id="GSASIIlattice.A2Gmat">
    443490<tt class="descclassname">GSASIIlattice.</tt><tt class="descname">A2Gmat</tt><big>(</big><em>A</em>, <em>inverse=True</em><big>)</big><a class="reference internal" href="_modules/GSASIIlattice.html#A2Gmat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIlattice.A2Gmat" title="Permalink to this definition">¶</a></dt>
    444 <dd><p>Fill real &amp; reciprocal metric tensor (G) from A</p>
     491<dd><p>Fill real &amp; reciprocal metric tensor (G) from A.</p>
    445492<table class="docutils field-list" frame="void" rules="none">
    446493<col class="field-name" />
    … …  
    796843
    797844<dl class="function">
     845<dt id="GSASIIlattice.Uij2Ueqv">
     846<tt class="descclassname">GSASIIlattice.</tt><tt class="descname">Uij2Ueqv</tt><big>(</big><em>Uij</em>, <em>GS</em>, <em>Amat</em><big>)</big><a class="headerlink" href="#GSASIIlattice.Uij2Ueqv" title="Permalink to this definition">¶</a></dt>
     847<dd><p>returns 1/3 trace of diagonalized U matrix</p>
     848</dd></dl>
     849
     850<dl class="function">
    798851<dt id="GSASIIlattice.Uij2betaij">
    799852<tt class="descclassname">GSASIIlattice.</tt><tt class="descname">Uij2betaij</tt><big>(</big><em>Uij</em>, <em>G</em><big>)</big><a class="reference internal" href="_modules/GSASIIlattice.html#Uij2betaij"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIlattice.Uij2betaij" title="Permalink to this definition">¶</a></dt>
    … …  
    894947
    895948<dl class="function">
     949<dt id="GSASIIlattice.cell2GS">
     950<tt class="descclassname">GSASIIlattice.</tt><tt class="descname">cell2GS</tt><big>(</big><em>cell</em><big>)</big><a class="headerlink" href="#GSASIIlattice.cell2GS" title="Permalink to this definition">¶</a></dt>
     951<dd><p>returns Uij to betaij conversion matrix</p>
     952</dd></dl>
     953
     954<dl class="function">
    896955<dt id="GSASIIlattice.cell2Gmat">
    897956<tt class="descclassname">GSASIIlattice.</tt><tt class="descname">cell2Gmat</tt><big>(</big><em>cell</em><big>)</big><a class="reference internal" href="_modules/GSASIIlattice.html#cell2Gmat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIlattice.cell2Gmat" title="Permalink to this definition">¶</a></dt>
    … …  
    10441103<dl class="data">
    10451104<dt id="GSASIIlattice.selftestlist">
    1046 <tt class="descclassname">GSASIIlattice.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x17e346f0&gt;, &lt;function test1 at 0x17e34730&gt;, &lt;function test2 at 0x17e34770&gt;, &lt;function test3 at 0x17e347b0&gt;, &lt;function test4 at 0x17e347f0&gt;, &lt;function test5 at 0x17e34830&gt;, &lt;function test6 at 0x17e34870&gt;, &lt;function test7 at 0x17e348b0&gt;, &lt;function test8 at 0x17e348f0&gt;, &lt;function test9 at 0x17e34930&gt;]</em><a class="headerlink" href="#GSASIIlattice.selftestlist" title="Permalink to this definition">¶</a></dt>
     1105<tt class="descclassname">GSASIIlattice.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x279ea70&gt;, &lt;function test1 at 0x279eab0&gt;, &lt;function test2 at 0x279eaf0&gt;, &lt;function test3 at 0x279eb30&gt;, &lt;function test4 at 0x279eb70&gt;, &lt;function test5 at 0x279ebb0&gt;, &lt;function test6 at 0x279ebf0&gt;, &lt;function test7 at 0x279ec30&gt;, &lt;function test8 at 0x279ec70&gt;, &lt;function test9 at 0x279ecb0&gt;]</em><a class="headerlink" href="#GSASIIlattice.selftestlist" title="Permalink to this definition">¶</a></dt>
    10471106<dd><p>Defines a list of self-tests</p>
    10481107</dd></dl>
    … …  
    11411200<dt id="GSASIIspc.AllOps">
    11421201<tt class="descclassname">GSASIIspc.</tt><tt class="descname">AllOps</tt><big>(</big><em>SGData</em><big>)</big><a class="headerlink" href="#GSASIIspc.AllOps" title="Permalink to this definition">¶</a></dt>
    1143 <dd><p>Returns a list of all operators for a space group, including those for centering and a center of symmetry</p>
     1202<dd><p>Returns a list of all operators for a space group, including those for
     1203centering and a center of symmetry</p>
    11441204<table class="docutils field-list" frame="void" rules="none">
    11451205<col class="field-name" />
    … …  
    11481208<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>SGData</strong> &#8211; from <a class="reference internal" href="#GSASIIspc.SpcGroup" title="GSASIIspc.SpcGroup"><tt class="xref py py-func docutils literal"><span class="pre">SpcGroup()</span></tt></a></td>
    11491209</tr>
    1150 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">list of strings of formatted symmetry operators</td>
     1210<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">(SGTextList,offsetList,symOpList,G2oprList) where<ul class="simple">
     1211<li>SGTextList: a list of strings with formatted and normalized
     1212symmetry operators.</li>
     1213<li>offsetList: a tuple of (dx,dy,dz) offsets that relate the GSAS-II
     1214symmetry operation to the operator in SGTextList and symOpList.
     1215these dx (etc.) values are added to the GSAS-II generated
     1216positions to provide the positions that are generated
     1217by the normalized symmetry operators.</li>
     1218<li>symOpList: a list of tuples with the normalized symmetry
     1219operations as (M,T) values
     1220(see <tt class="docutils literal"><span class="pre">SGOps</span></tt> in the <a class="reference internal" href="GSASIIobj.html#sgdata-table"><em>Space Group object</em></a>)</li>
     1221<li>G2oprList: The GSAS-II operations for each symmetry operation as
     1222a tuple with (center,mult,opnum), where center is (0,0,0), (0.5,0,0),
     1223(0.5,0.5,0.5),...; where mult is 1 or -1 for the center of symmetry
     1224and opnum is the number for the symmetry operation, in <tt class="docutils literal"><span class="pre">SGOps</span></tt>
     1225(starting with 0).</li>
     1226</ul>
     1227</td>
    11511228</tr>
    11521229</tbody>
    … …  
    12191296<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><p>iabsnt,mulp,Uniq,phi</p>
    12201297<ul class="simple">
    1221 <li>iabsnt = True is reflection is forbidden by symmetry</li>
     1298<li>iabsnt = True if reflection is forbidden by symmetry</li>
    12221299<li>mulp = reflection multiplicity including Friedel pairs</li>
    12231300<li>Uniq = numpy array of equivalent hkl in descending order of h,k,l</li>
    … …  
    14741551<dl class="data">
    14751552<dt id="GSASIIspc.selftestlist">
    1476 <tt class="descclassname">GSASIIspc.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x17e36430&gt;, &lt;function test1 at 0x17e36630&gt;, &lt;function test2 at 0x17e36530&gt;, &lt;function test3 at 0x17e364b0&gt;]</em><a class="headerlink" href="#GSASIIspc.selftestlist" title="Permalink to this definition">¶</a></dt>
     1553<tt class="descclassname">GSASIIspc.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x27b6630&gt;, &lt;function test1 at 0x27b6670&gt;, &lt;function test2 at 0x27b66b0&gt;, &lt;function test3 at 0x27b66f0&gt;]</em><a class="headerlink" href="#GSASIIspc.selftestlist" title="Permalink to this definition">¶</a></dt>
    14771554<dd><p>Defines a list of self-tests</p>
    14781555</dd></dl>

  • trunk/sphinxdocs/build/html/genindex.html

    r957 r990  
    151151
    152152     
     153  <dt><a href="GSASIIobj.html#index-5">Atoms record description</a>
     154  </dt>
     155
     156     
    153157  <dt><a href="GSASIImath.html#GSASIImath.AtomTLS2UIJ">AtomTLS2UIJ() (in module GSASIImath)</a>
    154158  </dt>
    … …  
    266270     
    267271  <dt><a href="GSASIIutil.html#GSASIIlattice.cell2Gmat">cell2Gmat() (in module GSASIIlattice)</a>
     272  </dt>
     273
     274     
     275  <dt><a href="GSASIIutil.html#GSASIIlattice.cell2GS">cell2GS() (in module GSASIIlattice)</a>
    268276  </dt>
    269277
    … …  
    389397      <dd><dl>
    390398       
     399  <dt><a href="GSASIIobj.html#index-5">Atoms record</a>
     400  </dt>
     401
     402       
    391403  <dt><a href="GSASIIobj.html#index-1">Constraint Definition</a>
    392404  </dt>
    … …  
    405417
    406418       
     419  <dt><a href="GSASIIobj.html#index-6">Powder Data</a>
     420  </dt>
     421
     422       
     423  <dt><a href="GSASIIobj.html#index-7">Powder Reflections</a>
     424  </dt>
     425
     426       
    407427  <dt><a href="GSASIIobj.html#index-4">SGData</a>
    408428  </dt>
    … …  
    433453  </dt>
    434454
    435   </dl></td>
    436   <td style="width: 33%" valign="top"><dl>
    437455     
    438456  <dt><a href="GSASIIpwd.html#GSASIIpwd.Dict2Values">Dict2Values() (in module GSASIIpwd)</a>
    … …  
    445463
    446464      </dl></dd>
     465  </dl></td>
     466  <td style="width: 33%" valign="top"><dl>
    447467     
    448468  <dt><a href="GSASIIGUIr.html#GSASIIgrid.DisAglDialog">DisAglDialog (class in GSASIIgrid)</a>
    … …  
    463483     
    464484  <dt><a href="GSASIIpwd.html#GSASIIpwd.DoPeakFit">DoPeakFit() (in module GSASIIpwd)</a>
     485  </dt>
     486
     487     
     488  <dt><a href="GSASIIGUIr.html#GSASIIgrid.downdate">downdate (class in GSASIIgrid)</a>
    465489  </dt>
    466490
    … …  
    10371061  </dt>
    10381062
    1039   </dl></td>
    1040   <td style="width: 33%" valign="top"><dl>
    10411063     
    10421064  <dt><a href="GSASIIpwd.html#GSASIIpwd.getPeakProfileDerv">getPeakProfileDerv() (in module GSASIIpwd)</a>
    10431065  </dt>
    10441066
     1067  </dl></td>
     1068  <td style="width: 33%" valign="top"><dl>
    10451069     
    10461070  <dt><a href="GSASII.html#GSASII.GSASII.GetPhaseData">GetPhaseData() (GSASII.GSASII method)</a>
    … …  
    12341258
    12351259     
     1260  <dt><a href="GSASIIGUIr.html#GSASIIgrid.downdate.getVersion">getVersion() (GSASIIgrid.downdate method)</a>
     1261  </dt>
     1262
     1263     
    12361264  <dt><a href="GSASIIutil.html#GSASIIpath.GetVersionNumber">GetVersionNumber() (in module GSASIIpath)</a>
    12371265  </dt>
    … …  
    15821610  <td style="width: 33%" valign="top"><dl>
    15831611     
     1612  <dt><a href="GSASII.html#GSASII.GSASIImain.MacOpenFile">MacOpenFile() (GSASII.GSASIImain method)</a>
     1613  </dt>
     1614
     1615     
    15841616  <dt><a href="GSASII.html#GSASII.main">main() (in module GSASII)</a>
    15851617  </dt>
    … …  
    18761908
    18771909     
     1910  <dt><a href="GSASIIGUIr.html#GSASIIgrid.MyHelp.OnSelectVersion">OnSelectVersion() (GSASIIgrid.MyHelp method)</a>
     1911  </dt>
     1912
     1913     
    18781914  <dt><a href="GSASII.html#GSASII.GSASII.OnSeqRefine">OnSeqRefine() (GSASII.GSASII method)</a>
    18791915  </dt>
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    19932029  </dt>
    19942030
    1995   </dl></td>
    1996   <td style="width: 33%" valign="top"><dl>
    19972031     
    19982032  <dt><a href="GSASIIplot.html#GSASIIplot.PlotSizeStrainPO">PlotSizeStrainPO() (in module GSASIIplot)</a>
    19992033  </dt>
    20002034
     2035  </dl></td>
     2036  <td style="width: 33%" valign="top"><dl>
    20012037     
    20022038  <dt><a href="GSASIIplot.html#GSASIIplot.PlotSngl">PlotSngl() (in module GSASIIplot)</a>
    … …  
    20372073     
    20382074  <dt><a href="GSASIIGUIr.html#GSASIIgrid.DataFrame.PostfillDataMenu">PostfillDataMenu() (GSASIIgrid.DataFrame method)</a>
     2075  </dt>
     2076
     2077     
     2078  <dt><a href="GSASIIobj.html#index-6">Powder data object description</a>
     2079  </dt>
     2080
     2081     
     2082  <dt><a href="GSASIIobj.html#index-7">Powder reflection object description</a>
    20392083  </dt>
    20402084
    … …  
    23312375  </dt>
    23322376
    2333   </dl></td>
    2334   <td style="width: 33%" valign="top"><dl>
    23352377     
    23362378  <dt><a href="GSASIIsolve.html#GSASIIsolve.ShowBanner">ShowBanner() (in module GSASIIsolve)</a>
    … …  
    23432385
    23442386      </dl></dd>
     2387  </dl></td>
     2388  <td style="width: 33%" valign="top"><dl>
    23452389     
    23462390  <dt><a href="GSASIIsolve.html#GSASIIsolve.ShowControls">ShowControls() (in module GSASIIsolve)</a>
    … …  
    24422486
    24432487     
     2488  <dt><a href="GSASIIutil.html#GSASIIpath.svnGetLog">svnGetLog() (in module GSASIIpath)</a>
     2489  </dt>
     2490
     2491     
    24442492  <dt><a href="GSASIIutil.html#GSASIIpath.svnGetRev">svnGetRev() (in module GSASIIpath)</a>
    24452493  </dt>
    … …  
    25892637     
    25902638  <dt><a href="GSASIIutil.html#GSASIIlattice.Uij2betaij">Uij2betaij() (in module GSASIIlattice)</a>
     2639  </dt>
     2640
     2641     
     2642  <dt><a href="GSASIIutil.html#GSASIIlattice.Uij2Ueqv">Uij2Ueqv() (in module GSASIIlattice)</a>
    25912643  </dt>
    25922644

  • trunk/sphinxdocs/build/html/index.html

    r957 r990  
    6060<li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#constraints-tree-item">Constraints Tree Item</a></li>
    6161<li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#covariance-tree-item">Covariance Tree Item</a></li>
    62 <li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#phase-tree-item">Phase Tree Item</a></li>
     62<li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#phase-tree-items">Phase Tree Items</a></li>
    6363<li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#space-group-objects">Space Group Objects</a></li>
     64<li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#atom-records">Atom Records</a></li>
     65<li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#powder-diffraction-tree-items">Powder Diffraction Tree Items</a></li>
     66<li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#powder-reflection-data-structure">Powder Reflection Data Structure</a></li>
     67<li class="toctree-l2"><a class="reference internal" href="GSASIIobj.html#classes-and-routines"><em>Classes and routines</em></a></li>
    6468</ul>
    6569</li>

  • trunk/sphinxdocs/build/html/searchindex.js

    r957 r990  
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