Changeset 941


Ignore:
Timestamp:
Jun 4, 2013 11:53:16 PM (9 years ago)
Author:
toby
Message:

fix Matts mac bug on switching phase tabs; start doc of phase contents; get major CIF data names (but not yet values) into export

Location:
trunk
Files:
2 added
10 edited

Legend:

Unmodified
Added
Removed
  • trunk/GSASIIIO.py

    r938 r941  
    15951595                    if self.GroupedParms.get(key) is None:
    15961596                        self.GroupedParms[key] = {}
     1597                    if self.GroupedParms[key].get(name):
     1598                        print("Aborting export: Histogram name repeated"+str(name))
     1599                        return
    15971600                    self.GroupedParms[key][name] = {}
    15981601                    self.GroupedParms[key][name][None] = G2frame.PatternTree.GetItemPyData(item)
     
    16001603                while item2:
    16011604                    name = G2frame.PatternTree.GetItemText(item2)
     1605                    if d.get(name):
     1606                        print("Aborting export: phase name repeated"+str(name))
     1607                        return
    16021608                    d[name] = G2frame.PatternTree.GetItemPyData(item2)
    16031609                    item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)                           
  • trunk/GSASIIphsGUI.py

    r940 r941  
    1717such as GSASIIddata.)
    1818
     19Phase information is stored in the GSAS-II data tree as children of the
     20Phases item in a dict with keys:
     21
     22.. tabularcolumns:: |l|l|p{4in}|
     23
     24==========  ===============  ====================================================
     25  key         sub-key        explaination
     26==========  ===============  ====================================================
     27General         \            Overall information for the phase (dict)
     28  \         AtomPtrs         ? (list)
     29  \         F000X            x-ray F(000) intensity (float)
     30  \         F000N            neutron F(000) intensity (float)
     31  \         Mydir            directory of current .gpx file (str)
     32  \         MCSA controls    ?
     33  \         Cell             List with 7 items: cell refinement flag (bool)
     34                             a, b, c, (Angstrom, float)
     35                             alpha, beta & gamma (degrees, float)
     36  \         Type             for now 'nuclear' (str)
     37  \         Map              dict of map parameters
     38  \         SH Texture       dict of spherical harmonic preferred orientation
     39                             parameters
     40  \         Isotope          dict of isotopes for each atom type
     41  \         Isotopes         dict of scattering lengths for each isotope
     42                             combination for each element in phase 
     43  \         Name             phase name (str)
     44  \         SGData           Space group details,
     45                             as defined in :mod:`GSASIIspc`
     46  \         Pawley neg wt    Restraint value for negative Pawley intensities
     47                             (float)
     48  \         Flip             Charge flip controls dict?
     49  \         Data plot type   ?
     50  \         Mass             Mass of unit cell contents in g/mm**3
     51  \         POhkl            March-Dollase preferred orientation direction
     52  \         Z                ?
     53  \         vdWRadii         ?
     54  \         Color            Colors for atoms (list of (r,b,g) triplets)
     55  \         AtomTypes        List of atom types
     56  \         AtomMass         List of masses for atoms
     57  \         doPawley         Flag for Pawley intensity extraction (bool)
     58  \         NoAtoms          Number of atoms per unit cell of each type (dict)
     59  \         Pawley dmin      maximum Q (as d-space) to use for Pawley
     60                             extraction (float)
     61  \         BondRadii        Radius for each atom used to compute
     62                             interatomic distances (list of floats)
     63  \         AngleRadii       Radius for each atom used to compute
     64                             interatomic angles (list of floats)
     65ranId           \            unique random number Id for phase (int)
     66pId             \            ? (int)
     67Atoms           \            Atoms in phase as a list of lists. The outer list
     68                             is for each atom, the inner list contains 18
     69                             items:
     70                             0) atom label, 1) the atom type,
     71                             2) the refinement flags, 3-6) x, y, z, frac
     72                             7) site symmetry, 8) site multiplicity,
     73                             9) 'I' or 'A' for iso/anisotropic,
     74                             10) Uiso, 10-16) Uij, 16) unique Id #.
     75                             (list of lists)
     76Drawing         \            Display parameters (dict)
     77\           ballScale        Size of spheres in ball-and-stick display (float)
     78\           bondList         dict with bonds
     79\           contourLevel     ? (float)
     80\           showABC          Flag to show view point triplet (bool). True=show.
     81\           viewDir          cartesian viewing direction (np.array with three
     82                             elements)
     83\           Zclip            clipping distance in A (float)
     84\           backColor        background for plot as and R,G,B triplet
     85                             (default = [0, 0, 0], black).
     86                             (list with three atoms)
     87\           selectedAtoms    List of selected atoms (list of int values)
     88\           showRigidBodies  Flag to highlight rigid body placement
     89\           sizeH            Size ratio for H atoms (float)
     90\           bondRadius       Size of binds in A (float)
     91\           atomPtrs         ? (list)
     92\           viewPoint        list of lists. First item in list is [x,y,z]
     93                             in fractional coordinates for the center of
     94                             the plot. Second item ?.
     95\           showHydrogen     Flag to control plotting of H atoms.
     96\           unitCellBox      Flag to control display of the unit cell.
     97\           ellipseProb      Probability limit for display of thermal
     98                             ellipsoids in % (float).
     99\           vdwScale         Multiplier of van der Waals radius for
     100                             display of vdW spheres.
     101\           Atoms            A list of lists with an entry for each atom
     102                             that is plotted.
     103\           Zstep            Step to de/increase Z-clip (float)
     104\           Quaternion       Viewing quaternion (4 element np.array)
     105\           radiusFactor     Distance ratio for searching for bonds. ? Bonds
     106                             are located that are within r(Ra+Rb) and (Ra+Rb)/r
     107                             where Ra and Rb are the atomic radii.
     108\           oldxy            ? (list with two floats)
     109\           cameraPos        Viewing position in A for plot (float)
     110\           depthFog         ? (bool)
     111RBModels        \            Rigid body assignments (note Rigid body definitions
     112                             are stored in their own main top-level tree entry.)
     113Pawley ref      \            Pawley reflections
     114Histograms      \            A dict of dicts. The key for the outer dict is
     115                             the histograms tied to this phase. The inner
     116                             dict contains the combined phase/histogram
     117                             parameters for items such as scale factors,
     118                             size and strain parameters. (dict)
     119MCSA            \            Monte-Carlo simulated annealing parameters
     120==========  ===============  ====================================================
    19121'''
    20122import wx
     
    96198    G2frame.dataFrame.CreateStatusBar()
    97199    G2frame.dataDisplay = G2gd.GSNoteBook(parent=G2frame.dataFrame,size=G2frame.dataFrame.GetClientSize())
    98 
     200    G2frame.dataDisplay.gridList = [] # list of all grids in notebook
     201   
    99202    def SetupGeneral():
    100203        generalData = data['General']
     
    9611064                   
    9621065        def ChangeAtomCell(event):
    963            
     1066
    9641067            def chkUij(Uij,CSI): #needs to do something!!!
    9651068                return Uij
     
    19522055        else:
    19532056            G2frame.dataFrame.Update()
    1954        
     2057
    19552058        FindBondsDraw()
    19562059        drawAtoms.ClearSelection()
     
    48334936        on a Phase data item window
    48344937        '''
     4938        for page in G2frame.dataDisplay.gridList: # clear out all grids, forcing edits in progress to complete
     4939            page.ClearGrid()
    48354940        wx.Frame.Unbind(G2frame.dataFrame,wx.EVT_SIZE) # ignore size events during this routine
    48364941        page = event.GetSelection()
     
    48514956            for id in G2frame.dataFrame.ReImportMenuId:     #loop over submenu items
    48524957                G2frame.dataFrame.Bind(wx.EVT_MENU, OnReImport, id=id)
    4853            
     4958               
    48544959            FillAtomsGrid(Atoms)
    48554960        elif text == 'General':
     
    49435048       
    49445049    wx.Frame.Unbind(G2frame.dataFrame,wx.EVT_SIZE) # ignore size events during this routine
     5050    G2frame.dataDisplay.gridList = []
    49455051    General = wx.ScrolledWindow(G2frame.dataDisplay)
    49465052    G2frame.dataDisplay.AddPage(General,'General')
     
    49485054    G2frame.dataDisplay.AddPage(DData,'Data')
    49495055    Atoms = G2gd.GSGrid(G2frame.dataDisplay)
     5056    G2frame.dataDisplay.gridList.append(Atoms)
    49505057    G2frame.dataDisplay.AddPage(Atoms,'Atoms')
    49515058    drawOptions = wx.ScrolledWindow(G2frame.dataDisplay)
    49525059    G2frame.dataDisplay.AddPage(drawOptions,'Draw Options')
    49535060    drawAtoms = G2gd.GSGrid(G2frame.dataDisplay)
     5061    G2frame.dataDisplay.gridList.append(drawAtoms)
    49545062    G2frame.dataDisplay.AddPage(drawAtoms,'Draw Atoms')
    49555063    RigidBodies = wx.ScrolledWindow(G2frame.dataDisplay)
    49565064    G2frame.dataDisplay.AddPage(RigidBodies,'RB Models')
    49575065    MapPeaks = G2gd.GSGrid(G2frame.dataDisplay)
     5066    G2frame.dataDisplay.gridList.append(MapPeaks)   
    49585067    G2frame.dataDisplay.AddPage(MapPeaks,'Map peaks')
    49595068    MCSA = wx.ScrolledWindow(G2frame.dataDisplay)
     
    49625071    G2frame.dataDisplay.AddPage(Texture,'Texture')
    49635072    G2frame.PawleyRefl = G2gd.GSGrid(G2frame.dataDisplay)
     5073    G2frame.dataDisplay.gridList.append(G2frame.PawleyRefl)
    49645074    G2frame.dataDisplay.AddPage(G2frame.PawleyRefl,'Pawley reflections')
    49655075   
  • trunk/GSASIIspc.py

    r939 r941  
    11# -*- coding: utf-8 -*-
    2 '''
     2"""
    33*GSASIIspc: Space group module*
    44-------------------------------
    55
    6 Space group interpretion routines
    7 '''
     6Space group interpretation routines.
     7
     8Space groups are interpreted and the information is placed in a SGdata object,
     9which is a dict with these keys:
     10
     11.. tabularcolumns:: |l|p{4.5in}|
     12
     13==========  ====================================================
     14  key         explaination
     15==========  ====================================================
     16SpGrp       space group symbol (str)
     17Laue        one of the following 14 Laue classes:
     18            -1, 2/m, mmm, 4/m, 4/mmm, 3R,
     19            3mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)
     20SGInv       True if centrosymmetric, False if not (bool)
     21SGLatt      Lattice centering type. Will be one of
     22            P, A, B, C, I, F, R (str)
     23SGUniq      unique axis if monoclinic. Will be
     24            a, b, or c for monoclinic space groups.
     25            Will be blank for non-monoclinic. (str)
     26SGCen       Symmetry cell centering vectors. A (n,3) np.array
     27            of centers. Will always have at least one row:
     28            ``np.array([[0, 0, 0]])``
     29SGOps       symmetry operations as a list in form
     30            [[M1,T1],[M2,T2,...] where Mn is a 3x3 np.array
     31            and T is a length 3 np.array.
     32            Atom coordinates are transformed where the
     33            Asymmetric unit coordinates [X=(x,y,z)] are
     34            transformed using ``M*X+T ==> X'``
     35SGSys       symmetry unit cell: type one of
     36            'triclinic', 'monoclinic', 'orthorhombic',
     37            'tetragonal', 'rhombohedral', 'trigonal',
     38            'hexagonal', 'cubic' (str)
     39SGPolax     Axes for space group polarity. Will be one of
     40            '', 'x', 'y', 'x y', 'z', 'x z', 'y z',
     41            'xyz'. In the case where axes are arbitrary
     42            '111' is used (P 1, and ?).
     43==========  ====================================================
     44
     45
     46"""
    847########### SVN repository information ###################
    948# $Date$
  • trunk/exports/G2cif.py

    r938 r941  
    2525        def WriteCIFitem(name,value=''):
    2626            if value:
    27                 if "\n" in value or len(value)+len(name)+4 > 70:
     27                if "\n" in value or len(value)> 70:
    2828                    if name.strip(): print name
    2929                    print '; '+value
    3030                    print '; '
    3131                elif " " in value:
    32                     print name,'  ','"' + str(value) + '"'
     32                    if len(name)+len(value) > 65:
     33                        print name,'\n   ','"' + str(value) + '"'
     34                    else:
     35                        print name,'  ','"' + str(value) + '"'
    3336                else:
    34                     print name,'  ',value
     37                    if len(name)+len(value) > 65:
     38                        print name,'\n   ',value
     39                    else:
     40                        print name,'  ',value
    3541            else:
    3642                print name
     
    4854            '''TODO: Write out overall refinement information
    4955            '''
     56            WriteCIFitem('_pd_proc_info_datetime', self.CIFdate)
     57            WriteCIFitem('_pd_calc_method', 'Rietveld Refinement')
    5058            #WriteCIFitem('_refine_ls_shift/su_max',DAT1)
    5159            #WriteCIFitem('_refine_ls_shift/su_mean',DAT2)
     
    6371            # _refine_ls_restrained_S_all
    6472            # _refine_ls_restrained_S_obs
     73
    6574            # include an overall profile r-factor, if there is more than one powder histogram
    6675            if self.npowder > 1:
    67                 WriteCIFitem('# Overall powder R-factors')
     76                WriteCIFitem('\n# OVERALL POWDER R-FACTORS')
    6877                #WriteCIFitem('_pd_proc_ls_prof_R_factor',TEXT(11:20))
    6978                #WriteCIFitem('_pd_proc_ls_prof_wR_factor',TEXT(1:10))
     
    96105
    97106        def WritePhaseInfo(phasenam):
     107            # see writepha.for
    98108            print 'TODO: phase info for',phasenam,'goes here'
    99             phasedict = self.GroupedParms['Phases'][phasenam] # pointer to current phase info
    100             print phasedict.keys()
    101             # see WRITEPHASE
     109            # THINK: how to select publication flags for distances/angles?
     110            phasedict = self.GroupedParms['Phases'][phasenam] # pointer to current phase info           
     111            WriteCIFitem('_pd_phase_name', phasenam)
     112            text = '?'
     113            for lbl in 'a','b','c':
     114                WriteCIFitem('_cell_length_'+lbl,text)
     115            for lbl in 'alpha','beta ','gamma':
     116                WriteCIFitem('_cell_angle_'+lbl,text)
     117
     118            WriteCIFitem('_cell_volume',text)
     119
     120            #print phasedict['Histograms']
     121#            for key in phasedict['General']:
     122#                print key,'=',phasedict['General'][key]
     123#            print phasedict['pId']
     124
     125            #NSYS = (1,2,3,4,4,5,5,5,5,5,6,6,7,7)
     126            #SYST = ('','triclinic','monoclinic','orthorhombic','tetragonal','trigonal ','hexagonal','cubic')
     127
     128            WriteCIFitem('_symmetry_cell_setting',
     129                         phasedict['General']['SGData']['SGSys'])
     130
     131            spacegroup = phasedict['General']['SGData']['SpGrp'].strip()
     132            # regularize capitalization and remove trailing H/R
     133            spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ')
     134            WriteCIFitem('_symmetry_space_group_name_H-M',spacegroup)
     135            # generate symmetry operations including centering and center of symmetry
     136            WriteCIFitem('loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz')
     137
     138            # loop over histogram(s) used in this phase
     139            if not oneblock:
     140                # pointers to histograms used in this phase
     141                histlist = []
     142                for hist in self.GroupedParms['Phases'][phasenam]['Histograms']:
     143                    if self.GroupedParms['Phases'][phasenam]['Histograms'][hist]['Use']:
     144                        if phasebyhistDict.get(hist):
     145                            phasebyhistDict[hist].append(phasenam)
     146                        else:
     147                            phasebyhistDict[hist] = [phasenam,]
     148                        blockid = datablockidDict.get(hist)
     149                        if not blockid:
     150                            print "Internal error: no block for data. Phase "+str(
     151                                phasenam)+" histogram "+str(hist)
     152                            histlist = []
     153                            break
     154                        histlist.append(blockid)
     155
     156                if len(histlist) == 0:
     157                    WriteCIFitem('# Note: phase has no associated data')
     158                else:
     159                    WriteCIFitem('loop_  _pd_block_diffractogram_id')
     160                    for hist in histlist:
     161                        WriteCIFitem('',hist)
     162                        # TODO: sample/histogram profile information and other "HAP" info should be
     163                        # reported in this loop, such as
     164                        # _pd_proc_ls_pref_orient_corr
     165                        # _pd_proc_ls_profile_function
     166                        #txt = ' Spherical Harmonic ODF' + '\n spherical harmonic order='+'?'
     167                        #IF ( ISAMSYM.EQ.1 ) THEN
     168                        #txt += '\n No sample symmetry'
     169                #ELSE IF ( ISAMSYM.EQ.2 ) THEN
     170                #txt += ' The sample symmetry is: 2/m (shear texture)'
     171                #ELSE IF ( ISAMSYM.EQ.3 ) THEN
     172                #txt += ' The sample symmetry is: mmm (rolling texture)'
     173                #ELSE IF ( ISAMSYM.EQ.0 ) THEN
     174                #txt += ' The sample symmetry is: cylindrical (fiber texture)'
     175                #WriteCIFitem('_pd_proc_ls_pref_orient_corr',txt)
     176            else:
     177                # report all profile information here (include instrumental)
     178                # _pd_proc_ls_pref_orient_corr
     179                # _pd_proc_ls_profile_function
     180                pass
     181           
     182            WriteCIFitem('\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS')
     183     
     184            WriteCIFitem('loop_ '+
     185                         '\n\t_atom_site_type_symbol'+
     186                         '\n\t_atom_site_label'+
     187                         '\n\t_atom_site_fract_x'+
     188                         '\n\t_atom_site_fract_y'+
     189                         '\n\t_atom_site_fract_z'+
     190                         '\n\t_atom_site_occupancy'+
     191                         '\n\t_atom_site_thermal_displace_type'+
     192                         '\n\t_atom_site_U_iso_or_equiv'+
     193                         '\n\t_atom_site_symmetry_multiplicity')
     194
     195            WriteCIFitem('loop_' + '\n\t_atom_site_aniso_label' +
     196                         '\n\t_atom_site_aniso_U_11' + '\n\t_atom_site_aniso_U_12' +
     197                         '\n\t_atom_site_aniso_U_13' + '\n\t_atom_site_aniso_U_22' +
     198                         '\n\t_atom_site_aniso_U_23' + '\n\t_atom_site_aniso_U_33')
     199
     200            # process the chemical formula: pick a Z value & generate molecular weight
     201            # find the maximum possible Z value
     202
     203            # order the elements in "Hill" order: C, H, D, T & alphabetical or alphabetical
     204            if not oneblock: # in single block, this is combined with the scattering factors
     205                WriteCIFitem('loop_  _atom_type_symbol _atom_type_number_in_cell')
     206
     207            WriteCIFitem('# If you change Z, be sure to change all 3 of the following')
     208            WriteCIFitem( '_chemical_formula_sum',text)
     209            #WRITE(TEXT,'(F15.2)') ATMASS
     210            WriteCIFitem( '_chemical_formula_weight',text)
     211            #WRITE(TEXT,'(I4)') Z
     212            WriteCIFitem( '_cell_formula_units_Z',text)
     213
     214            #C now loop over interatomic distances for this phase
     215            WriteCIFitem('\n# MOLECULAR GEOMETRY')
     216            WriteCIFitem('loop_' +
     217                         '\n\t_geom_bond_atom_site_label_1' +
     218                         '\n\t_geom_bond_atom_site_label_2' +
     219                         '\n\t_geom_bond_distance' +
     220                         '\n\t_geom_bond_site_symmetry_1' +
     221                         '\n\t_geom_bond_site_symmetry_2' +
     222                         '\n\t_geom_bond_publ_flag')
     223
     224            #C now loop over interatomic angles for this phase
     225            WriteCIFitem('loop_' +
     226                         '\n\t_geom_angle_atom_site_label_1' +
     227                         '\n\t_geom_angle_atom_site_label_2' +
     228                         '\n\t_geom_angle_atom_site_label_3' +
     229                         '\n\t_geom_angle' +
     230                         '\n\t_geom_angle_site_symmetry_1' +
     231                         '\n\t_geom_angle_site_symmetry_2' +
     232                         '\n\t_geom_angle_site_symmetry_3' +
     233                         '\n\t_geom_angle_publ_flag')
    102234
    103235        def WritePowderData(histlbl):
     236            text = '?'
    104237            histblk = self.GroupedParms['PWDR'][histlbl]
    105238            print 'TODO: powder here data for',histblk["Sample Parameters"]['InstrName']
    106             # see WRPOWDHIST & WRREFLIST
    107 
     239            # see wrpowdhist.for & wrreflist.for
     240           
     241            refprx = '_refln.' # mm
     242            refprx = '_refln_' # normal
     243
     244            if not oneblock:
     245                if not phasebyhistDict.get(histlbl):
     246                    WriteCIFitem('\n# No phases associated with this data set')
     247                else:
     248                    WriteCIFitem('\n# PHASE TABLE')
     249                    WriteCIFitem('loop_' +
     250                                 '\n\t_pd_phase_id' +
     251                                 '\n\t_pd_phase_block_id' +
     252                                 '\n\t_pd_phase_mass_%')
     253                    for phasenam in phasebyhistDict.get(histlbl):
     254                        pass
     255
     256            WriteCIFitem('\n# SCATTERING FACTOR INFO')
     257            WriteCIFitem('_diffrn_radiation_wavelength' ,text)
     258            #WriteCIFitem('_diffrn_radiation_type',text)
     259            #C always assume Ka1 & Ka2 if two wavelengths are present
     260            #WriteCIFitem('loop_' +
     261            #             '\n\t_diffrn_radiation_wavelength' +
     262            #             '\n\t_diffrn_radiation_wavelength_wt' +
     263            #             '\n\t_diffrn_radiation_type' +
     264            #             '\n\t_diffrn_radiation_wavelength_id')
     265            #WRITE LAM1,1.0,'K\\a~1~',1, LAM2,ratio,'K\\a~2~',2
     266
     267            WriteCIFitem('_pd_proc_ls_prof_R_factor','?')
     268            WriteCIFitem('_pd_proc_ls_prof_wR_factor','?')
     269            WriteCIFitem('_pd_proc_ls_prof_wR_expected','?')
     270            WriteCIFitem('_refine_ls_R_Fsqd_factor','?')
     271           
     272            #WriteCIFitem('_pd_meas_2theta_fixed',text)
     273            WriteCIFitem('_diffrn_radiation_probe','x-ray')
     274            WriteCIFitem('_diffrn_radiation_probe','neutron')
     275            WriteCIFitem('_diffrn_radiation_polarisn_ratio','?')
     276           
     277            WriteCIFitem('loop_  _atom_type_symbol')
     278            if oneblock:
     279                WriteCIFitem('       _atom_type_number_in_cell')
     280            #IF (HTYP(2:2) .eq. 'X' .AND. HTYP(3:3) .ne. 'E') THEN
     281            WriteCIFitem('      _atom_type_scat_dispersion_real')
     282            WriteCIFitem('      _atom_type_scat_dispersion_imag')
     283            for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'):
     284                WriteCIFitem('      _atom_type_scat_Cromer_Mann_'+lbl)
     285            #ELSEIF (HTYP(2:2) .eq. 'N') THEN
     286            WriteCIFitem('      _atom_type_scat_length_neutron')
     287            #ENDIF
     288            WriteCIFitem('      _atom_type_scat_source')
     289
     290            #C document the background function used
     291            WriteCIFitem('_pd_proc_ls_background_function','?')
     292
     293            WriteCIFitem('_exptl_absorpt_process_details','?')
     294            WriteCIFitem('_exptl_absorpt_correction_T_min','?')
     295            WriteCIFitem('_exptl_absorpt_correction_T_max','?')
     296            #C extinction
     297            #WRITE(IUCIF,'(A)') '# Extinction correction'
     298            #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10))
     299            #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20))
     300
     301            if not oneblock:
     302                # instrumental profile terms go here
     303                WriteCIFitem('_pd_proc_ls_profile_function','?')
     304
     305            WriteCIFitem('\n# STRUCTURE FACTOR TABLE')           
     306            WriteCIFitem('loop_' +
     307                         '\n\t' + refprx + 'index_h' +
     308                         '\n\t' + refprx + 'index_k' +
     309                         '\n\t' + refprx + 'index_l' +
     310                         '\n\t_pd_refln_wavelength_id' +
     311                         '\n\t_pd_refln_phase_id' +
     312                         '\n\t' + refprx + 'status' +
     313                         '\n\t' + refprx + 'F_squared_meas' +
     314                         '\n\t' + refprx + 'F_squared_sigma' +
     315                         '\n\t' + refprx + 'F_squared_calc' +
     316                         '\n\t' + refprx + 'phase_calc' +
     317                         '\n\t_pd_refln_d_spacing' +
     318                         '\n\t_gsas_i100_meas')
     319
     320            WriteCIFitem('_reflns_number_total', text)
     321            WriteCIFitem('_reflns_limit_h_min', text)
     322            WriteCIFitem('_reflns_limit_h_max', text)
     323            WriteCIFitem('_reflns_limit_k_min', text)
     324            WriteCIFitem('_reflns_limit_k_max', text)
     325            WriteCIFitem('_reflns_limit_l_min', text)
     326            WriteCIFitem('_reflns_limit_l_max', text)
     327            WriteCIFitem('_reflns_d_resolution_high', text)
     328            WriteCIFitem('_reflns_d_resolution_low', text)
     329           
     330            WriteCIFitem('\n# POWDER DATA TABLE')
     331            # is data fixed step?
     332            fixedstep = False
     333            # are ESDs sqrt(I)
     334            countsdata = False
     335            zero = 0.01
     336            if fixedstep:
     337                WriteCIFitem('_pd_meas_2theta_range_min', text)
     338                WriteCIFitem('_pd_meas_2theta_range_max', text)
     339                WriteCIFitem('_pd_meas_2theta_range_inc', text)
     340                # zero correct
     341                if zero != 0.0:
     342                    WriteCIFitem('_pd_proc_2theta_range_min', text)
     343                    WriteCIFitem('_pd_proc_2theta_range_max', text)
     344                    WriteCIFitem('_pd_proc_2theta_range_inc', text)
     345            WriteCIFitem('loop_' +
     346                         '\n\t_pd_proc_d_spacing')
     347                         #'_pd_meas_time_of_flight'
     348            if not fixedstep:
     349                if zero != 0.0:
     350                    WriteCIFitem('\t_pd_proc_2theta_corrected')
     351                else:
     352                    WriteCIFitem('\t_pd_meas_2theta_scan')
     353            if countsdata:
     354                WriteCIFitem('\t_pd_meas_counts_total')
     355            else:
     356                WriteCIFitem('\t_pd_meas_intensity_total')
     357            WriteCIFitem('\t_pd_proc_ls_weight')
     358            WriteCIFitem('\t_pd_proc_intensity_bkg_calc')
     359            WriteCIFitem('\t_pd_calc_intensity_total')
     360            if zero != 0.0:
     361                WriteCIFitem('_pd_proc_number_of_points', text)
     362            else:
     363                WriteCIFitem('_pd_meas_number_of_points', text)
     364                         
    108365        def WriteSingleXtalData(histlbl):
    109366            histblk = self.GroupedParms['HKLF'][histlbl]
    110367            print 'TODO: single xtal here data for',histblk["Instrument Parameters"][0]['InstrName']
    111             # see WRREFLIST
    112 
     368            # see wrreflist.for
     369            refprx = '_refln.' # mm
     370            refprx = '_refln_' # normal
     371           
     372            WriteCIFitem('\n# STRUCTURE FACTOR TABLE')           
     373            WriteCIFitem('loop_' +
     374                         '\n\t' + refprx + 'index_h' +
     375                         '\n\t' + refprx + 'index_k' +
     376                         '\n\t' + refprx + 'index_l' +
     377                         '\n\t' + refprx + 'status' +
     378                         '\n\t' + refprx + 'F_squared_meas' +
     379                         '\n\t' + refprx + 'F_squared_sigma' +
     380                         '\n\t' + refprx + 'F_squared_calc' +
     381                         '\n\t' + refprx + 'phase_calc')
     382            WriteCIFitem('_reflns_number_total', text)
     383            WriteCIFitem('_reflns_number_observed', text)
     384            WriteCIFitem('_reflns_limit_h_min', text)
     385            WriteCIFitem('_reflns_limit_h_max', text)
     386            WriteCIFitem('_reflns_limit_k_min', text)
     387            WriteCIFitem('_reflns_limit_k_max', text)
     388            WriteCIFitem('_reflns_limit_l_min', text)
     389            WriteCIFitem('_reflns_limit_l_max', text)
     390            WriteCIFitem('_reflns_d_resolution_high', text)
     391            WriteCIFitem('_reflns_d_resolution_low', text)
     392
     393        #============================================================
    113394        # the export process starts here
    114395        self.loadTree()
     
    273554            WriteCIFitem('data_'+str(self.CIFname)+'_overall')
    274555            WriteOverall()
    275             WriteCIFitem('# pointers to phase and histogram blocks')
    276             # loop over future phase blocks
     556            #============================================================
     557            WriteCIFitem('# POINTERS TO PHASE AND HISTOGRAM BLOCKS')
     558            datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!)
     559            # loop over phase blocks
    277560            if self.nphase > 1:
    278561                loopprefix = ''
     
    280563            else:
    281564                loopprefix = '_pd_phase_block_id'
     565           
    282566            for i,phasenam in enumerate(sorted(self.GroupedParms['Phases'].keys())):
    283                 WriteCIFitem(loopprefix,
    284                              str(self.CIFdate) + "|" + str(self.CIFname) + "|" +
    285                              'phase_'+ str(i) + '|' + str(self.shortauthorname))
    286             # loop over future data blocks, create and save block names
     567                datablockidDict[phasenam] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" +
     568                             'phase_'+ str(i+1) + '|' + str(self.shortauthorname))
     569                WriteCIFitem(loopprefix,datablockidDict[phasenam])
     570            # loop over data blocks
    287571            i = 0
    288             datablockidDict = {}
    289572            if self.npowder + self.nsingle > 1:
    290573                loopprefix = ''
    291                 WriteCIFitem('loop_   _pd_block_diffractogramphase_id')
     574                WriteCIFitem('loop_   _pd_block_diffractogram_id')
    292575            else:
    293576                loopprefix = '_pd_block_diffractogram_id'
     
    302585                        instnam = histblk["Instrument Parameters"][0]['InstrName']
    303586                    instnam = instnam.replace(' ','')
     587                    if datablockidDict.get(key1):
     588                        print "Error: histogram name is duplicated: ",key1
     589                        return
    304590                    datablockidDict[key1] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" +
    305591                                             str(self.shortauthorname) + "|" +
     
    307593                    WriteCIFitem(loopprefix,datablockidDict[key1])
    308594            #============================================================
    309             # export phase information
    310             for i,phasenam in enumerate(sorted(self.GroupedParms['Phases'].keys())):
     595            # loop over phases, exporting them
     596            phasebyhistDict = {} # create a cross-reference to phases by histogram
     597            for j,phasenam in enumerate(sorted(self.GroupedParms['Phases'].keys())):
     598                i = j + 1
    311599                WriteCIFitem('\ndata_'+self.CIFname+"_phase_"+str(i))
    312600                print "debug, processing ",phasenam
    313601                WriteCIFitem('# Information for phase '+str(i))
    314                 WriteCIFitem('_pd_block_id',
    315                              str(self.CIFdate) + "|" + str(self.CIFname) + "|" +
    316                              'phase_'+ str(i) + '|' + str(self.shortauthorname))
    317                 # pointers to histograms used in this phase
    318                 histlist = []
    319                 for hist in self.GroupedParms['Phases'][phasenam]['Histograms']:
    320                     if self.GroupedParms['Phases'][phasenam]['Histograms'][hist]['Use']:
    321                         blockid = datablockidDict.get(hist)
    322                         if not blockid:
    323                             print "Internal error: no block for data. Phase "+str(
    324                                 phasenam)+" histogram "+str(hist)
    325                             histlist = []
    326                             break
    327                         histlist.append(blockid)
    328                 if len(histlist) == 0:
    329                     WriteCIFitem('# Note: phase has no associated data')
    330                 elif len(histlist) == 1:
    331                     WriteCIFitem('_pd_block_diffractogram_id',histlist[0])
    332                 else:
    333                     WriteCIFitem('loop_  _pd_block_diffractogram_id')
    334                     for hist in histlist:
    335                         WriteCIFitem('',hist)
     602                WriteCIFitem('_pd_block_id',datablockidDict[phasenam])
    336603                # report the phase
    337604                WritePhaseTemplate()
     
    339606
    340607            #============================================================
    341             # loop over histograms
     608            # loop over histograms, exporting them
     609            i = 0
    342610            for key in self.GroupedParms:
    343611                if key == 'Phases': continue
     
    346614                    histblk = self.GroupedParms[key][key1]
    347615                    if key == "PWDR":
    348                         WriteCIFitem('\ndata_'+self.CIFname+"_p_"+str(i))
     616                        WriteCIFitem('\ndata_'+self.CIFname+"_pwd_"+str(i))
    349617                    elif key == "HKLF":
    350                         WriteCIFitem('\ndata_'+self.CIFname+"_s_"+str(i))
     618                        WriteCIFitem('\ndata_'+self.CIFname+"_sx_"+str(i))
    351619                    WriteCIFitem('# Information for histogram '+str(i)+': '+
    352620                                 key1)
     
    358626                        WriteSnglXtalTemplate()
    359627                        WriteSingleXtalData(key1)
     628
     629        # TODO: how to report _pd_proc_ls_peak_cutoff?
    360630        WriteCIFitem('#--' + 15*'eof--' + '#')
     631
  • trunk/sphinxdocs/build/html/GSASIIGUI.html

    r939 r941  
    6363(pages displayed in response to some phase tabs are done in other modules,
    6464such as GSASIIddata.)</p>
     65<p>Phase information is stored in the GSAS-II data tree as children of the
     66Phases item in a dict with keys:</p>
     67<table border="1" class="docutils">
     68<colgroup>
     69<col width="13%" />
     70<col width="19%" />
     71<col width="68%" />
     72</colgroup>
     73<thead valign="bottom">
     74<tr class="row-odd"><th class="head">key</th>
     75<th class="head">sub-key</th>
     76<th class="head">explaination</th>
     77</tr>
     78</thead>
     79<tbody valign="top">
     80<tr class="row-even"><td>General</td>
     81<td></td>
     82<td>Overall information for the phase (dict)</td>
     83</tr>
     84<tr class="row-odd"><td></td>
     85<td>AtomPtrs</td>
     86<td>? (list)</td>
     87</tr>
     88<tr class="row-even"><td></td>
     89<td>F000X</td>
     90<td>x-ray F(000) intensity (float)</td>
     91</tr>
     92<tr class="row-odd"><td></td>
     93<td>F000N</td>
     94<td>neutron F(000) intensity (float)</td>
     95</tr>
     96<tr class="row-even"><td></td>
     97<td>Mydir</td>
     98<td>directory of current .gpx file (str)</td>
     99</tr>
     100<tr class="row-odd"><td></td>
     101<td>MCSA controls</td>
     102<td>?</td>
     103</tr>
     104<tr class="row-even"><td></td>
     105<td>Cell</td>
     106<td>List with 7 items: cell refinement flag (bool)
     107a, b, c, (Angstrom, float)
     108alpha, beta &amp; gamma (degrees, float)</td>
     109</tr>
     110<tr class="row-odd"><td></td>
     111<td>Type</td>
     112<td>for now &#8216;nuclear&#8217; (str)</td>
     113</tr>
     114<tr class="row-even"><td></td>
     115<td>Map</td>
     116<td>dict of map parameters</td>
     117</tr>
     118<tr class="row-odd"><td></td>
     119<td>SH Texture</td>
     120<td>dict of spherical harmonic preferred orientation
     121parameters</td>
     122</tr>
     123<tr class="row-even"><td></td>
     124<td>Isotope</td>
     125<td>dict of isotopes for each atom type</td>
     126</tr>
     127<tr class="row-odd"><td></td>
     128<td>Isotopes</td>
     129<td>dict of scattering lengths for each isotope
     130combination for each element in phase</td>
     131</tr>
     132<tr class="row-even"><td></td>
     133<td>Name</td>
     134<td>phase name (str)</td>
     135</tr>
     136<tr class="row-odd"><td></td>
     137<td>SGData</td>
     138<td>Space group details,
     139as defined in <a class="reference internal" href="GSASIIutil.html#module-GSASIIspc" title="GSASIIspc"><tt class="xref py py-mod docutils literal"><span class="pre">GSASIIspc</span></tt></a></td>
     140</tr>
     141<tr class="row-even"><td></td>
     142<td>Pawley neg wt</td>
     143<td>Restraint value for negative Pawley intensities
     144(float)</td>
     145</tr>
     146<tr class="row-odd"><td></td>
     147<td>Flip</td>
     148<td>Charge flip controls dict?</td>
     149</tr>
     150<tr class="row-even"><td></td>
     151<td>Data plot type</td>
     152<td>?</td>
     153</tr>
     154<tr class="row-odd"><td></td>
     155<td>Mass</td>
     156<td>Mass of unit cell contents in g/mm**3</td>
     157</tr>
     158<tr class="row-even"><td></td>
     159<td>POhkl</td>
     160<td>March-Dollase preferred orientation direction</td>
     161</tr>
     162<tr class="row-odd"><td></td>
     163<td>Z</td>
     164<td>?</td>
     165</tr>
     166<tr class="row-even"><td></td>
     167<td>vdWRadii</td>
     168<td>?</td>
     169</tr>
     170<tr class="row-odd"><td></td>
     171<td>Color</td>
     172<td>Colors for atoms (list of (r,b,g) triplets)</td>
     173</tr>
     174<tr class="row-even"><td></td>
     175<td>AtomTypes</td>
     176<td>List of atom types</td>
     177</tr>
     178<tr class="row-odd"><td></td>
     179<td>AtomMass</td>
     180<td>List of masses for atoms</td>
     181</tr>
     182<tr class="row-even"><td></td>
     183<td>doPawley</td>
     184<td>Flag for Pawley intensity extraction (bool)</td>
     185</tr>
     186<tr class="row-odd"><td></td>
     187<td>NoAtoms</td>
     188<td>Number of atoms per unit cell of each type (dict)</td>
     189</tr>
     190<tr class="row-even"><td></td>
     191<td>Pawley dmin</td>
     192<td>maximum Q (as d-space) to use for Pawley
     193extraction (float)</td>
     194</tr>
     195<tr class="row-odd"><td></td>
     196<td>BondRadii</td>
     197<td>Radius for each atom used to compute
     198interatomic distances (list of floats)</td>
     199</tr>
     200<tr class="row-even"><td></td>
     201<td>AngleRadii</td>
     202<td>Radius for each atom used to compute
     203interatomic angles (list of floats)</td>
     204</tr>
     205<tr class="row-odd"><td>ranId</td>
     206<td></td>
     207<td>unique random number Id for phase (int)</td>
     208</tr>
     209<tr class="row-even"><td>pId</td>
     210<td></td>
     211<td>? (int)</td>
     212</tr>
     213<tr class="row-odd"><td>Atoms</td>
     214<td></td>
     215<td>Atoms in phase as a list of lists. The outer list
     216is for each atom, the inner list contains 18
     217items:
     2180) atom label, 1) the atom type,
     2192) the refinement flags, 3-6) x, y, z, frac
     2207) site symmetry, 8) site multiplicity,
     2219) &#8216;I&#8217; or &#8216;A&#8217; for iso/anisotropic,
     22210) Uiso, 10-16) Uij, 16) unique Id #.
     223(list of lists)</td>
     224</tr>
     225<tr class="row-even"><td>Drawing</td>
     226<td></td>
     227<td>Display parameters (dict)</td>
     228</tr>
     229<tr class="row-odd"><td></td>
     230<td>ballScale</td>
     231<td>Size of spheres in ball-and-stick display (float)</td>
     232</tr>
     233<tr class="row-even"><td></td>
     234<td>bondList</td>
     235<td>dict with bonds</td>
     236</tr>
     237<tr class="row-odd"><td></td>
     238<td>contourLevel</td>
     239<td>? (float)</td>
     240</tr>
     241<tr class="row-even"><td></td>
     242<td>showABC</td>
     243<td>Flag to show view point triplet (bool). True=show.</td>
     244</tr>
     245<tr class="row-odd"><td></td>
     246<td>viewDir</td>
     247<td>cartesian viewing direction (np.array with three
     248elements)</td>
     249</tr>
     250<tr class="row-even"><td></td>
     251<td>Zclip</td>
     252<td>clipping distance in A (float)</td>
     253</tr>
     254<tr class="row-odd"><td></td>
     255<td>backColor</td>
     256<td>background for plot as and R,G,B triplet
     257(default = [0, 0, 0], black).
     258(list with three atoms)</td>
     259</tr>
     260<tr class="row-even"><td></td>
     261<td>selectedAtoms</td>
     262<td>List of selected atoms (list of int values)</td>
     263</tr>
     264<tr class="row-odd"><td></td>
     265<td>showRigidBodies</td>
     266<td>Flag to highlight rigid body placement</td>
     267</tr>
     268<tr class="row-even"><td></td>
     269<td>sizeH</td>
     270<td>Size ratio for H atoms (float)</td>
     271</tr>
     272<tr class="row-odd"><td></td>
     273<td>bondRadius</td>
     274<td>Size of binds in A (float)</td>
     275</tr>
     276<tr class="row-even"><td></td>
     277<td>atomPtrs</td>
     278<td>? (list)</td>
     279</tr>
     280<tr class="row-odd"><td></td>
     281<td>viewPoint</td>
     282<td>list of lists. First item in list is [x,y,z]
     283in fractional coordinates for the center of
     284the plot. Second item ?.</td>
     285</tr>
     286<tr class="row-even"><td></td>
     287<td>showHydrogen</td>
     288<td>Flag to control plotting of H atoms.</td>
     289</tr>
     290<tr class="row-odd"><td></td>
     291<td>unitCellBox</td>
     292<td>Flag to control display of the unit cell.</td>
     293</tr>
     294<tr class="row-even"><td></td>
     295<td>ellipseProb</td>
     296<td>Probability limit for display of thermal
     297ellipsoids in % (float).</td>
     298</tr>
     299<tr class="row-odd"><td></td>
     300<td>vdwScale</td>
     301<td>Multiplier of van der Waals radius for
     302display of vdW spheres.</td>
     303</tr>
     304<tr class="row-even"><td></td>
     305<td>Atoms</td>
     306<td>A list of lists with an entry for each atom
     307that is plotted.</td>
     308</tr>
     309<tr class="row-odd"><td></td>
     310<td>Zstep</td>
     311<td>Step to de/increase Z-clip (float)</td>
     312</tr>
     313<tr class="row-even"><td></td>
     314<td>Quaternion</td>
     315<td>Viewing quaternion (4 element np.array)</td>
     316</tr>
     317<tr class="row-odd"><td></td>
     318<td>radiusFactor</td>
     319<td>Distance ratio for searching for bonds. ? Bonds
     320are located that are within r(Ra+Rb) and (Ra+Rb)/r
     321where Ra and Rb are the atomic radii.</td>
     322</tr>
     323<tr class="row-even"><td></td>
     324<td>oldxy</td>
     325<td>? (list with two floats)</td>
     326</tr>
     327<tr class="row-odd"><td></td>
     328<td>cameraPos</td>
     329<td>Viewing position in A for plot (float)</td>
     330</tr>
     331<tr class="row-even"><td></td>
     332<td>depthFog</td>
     333<td>? (bool)</td>
     334</tr>
     335<tr class="row-odd"><td>RBModels</td>
     336<td></td>
     337<td>Rigid body assignments (note Rigid body definitions
     338are stored in their own main top-level tree entry.)</td>
     339</tr>
     340<tr class="row-even"><td>Pawley ref</td>
     341<td></td>
     342<td>Pawley reflections</td>
     343</tr>
     344<tr class="row-odd"><td>Histograms</td>
     345<td></td>
     346<td>A dict of dicts. The key for the outer dict is
     347the histograms tied to this phase. The inner
     348dict contains the combined phase/histogram
     349parameters for items such as scale factors,
     350size and strain parameters. (dict)</td>
     351</tr>
     352<tr class="row-even"><td>MCSA</td>
     353<td></td>
     354<td>Monte-Carlo simulated annealing parameters</td>
     355</tr>
     356</tbody>
     357</table>
    65358<dl class="function">
    66359<dt id="GSASIIphsGUI.UpdatePhaseData">
  • trunk/sphinxdocs/build/html/GSASIImath.html

    r939 r941  
    5959<p>Routines for least-squares minimization and other stuff</p>
    6060<dl class="function">
    61 <dt id="GSASIImath.AV2Q">
    62 <tt class="descclassname">GSASIImath.</tt><tt class="descname">AV2Q</tt><big>(</big><em>A</em>, <em>V</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#AV2Q"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.AV2Q" title="Permalink to this definition">¶</a></dt>
    63 <dd><p>convert angle (radians) &amp; vector to quaternion
    64 q=r+ai+bj+ck</p>
    65 </dd></dl>
    66 
    67 <dl class="function">
    68 <dt id="GSASIImath.AVdeg2Q">
    69 <tt class="descclassname">GSASIImath.</tt><tt class="descname">AVdeg2Q</tt><big>(</big><em>A</em>, <em>V</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#AVdeg2Q"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.AVdeg2Q" title="Permalink to this definition">¶</a></dt>
    70 <dd><p>convert angle (degrees) &amp; vector to quaternion
    71 q=r+ai+bj+ck</p>
    72 </dd></dl>
    73 
    74 <dl class="function">
    75 <dt id="GSASIImath.AtomTLS2UIJ">
    76 <tt class="descclassname">GSASIImath.</tt><tt class="descname">AtomTLS2UIJ</tt><big>(</big><em>atomData</em>, <em>atPtrs</em>, <em>Amat</em>, <em>rbObj</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#AtomTLS2UIJ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.AtomTLS2UIJ" title="Permalink to this definition">¶</a></dt>
    77 <dd><p>Needs a doc string; not used anywhere</p>
    78 </dd></dl>
    79 
    80 <dl class="function">
    81 <dt id="GSASIImath.AtomUij2TLS">
    82 <tt class="descclassname">GSASIImath.</tt><tt class="descname">AtomUij2TLS</tt><big>(</big><em>atomData</em>, <em>atPtrs</em>, <em>Amat</em>, <em>Bmat</em>, <em>rbObj</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#AtomUij2TLS"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.AtomUij2TLS" title="Permalink to this definition">¶</a></dt>
    83 <dd><p>Needs a doc string; unfinished &amp; not used</p>
    84 </dd></dl>
    85 
    86 <dl class="function">
    87 <dt id="GSASIImath.ChargeFlip">
    88 <tt class="descclassname">GSASIImath.</tt><tt class="descname">ChargeFlip</tt><big>(</big><em>data</em>, <em>reflData</em>, <em>pgbar</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#ChargeFlip"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.ChargeFlip" title="Permalink to this definition">¶</a></dt>
    89 <dd><p>Needs a doc string</p>
    90 </dd></dl>
    91 
    92 <dl class="function">
    93 <dt id="GSASIImath.FillAtomLookUp">
    94 <tt class="descclassname">GSASIImath.</tt><tt class="descname">FillAtomLookUp</tt><big>(</big><em>atomData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#FillAtomLookUp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.FillAtomLookUp" title="Permalink to this definition">¶</a></dt>
    95 <dd><p>Needs a doc string</p>
    96 </dd></dl>
    97 
    98 <dl class="function">
    99 <dt id="GSASIImath.FindAtomIndexByIDs">
    100 <tt class="descclassname">GSASIImath.</tt><tt class="descname">FindAtomIndexByIDs</tt><big>(</big><em>atomData</em>, <em>IDs</em>, <em>Draw=True</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#FindAtomIndexByIDs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.FindAtomIndexByIDs" title="Permalink to this definition">¶</a></dt>
    101 <dd><p>Needs a doc string</p>
    102 </dd></dl>
    103 
    104 <dl class="function">
    105 <dt id="GSASIImath.FourierMap">
    106 <tt class="descclassname">GSASIImath.</tt><tt class="descname">FourierMap</tt><big>(</big><em>data</em>, <em>reflData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#FourierMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.FourierMap" title="Permalink to this definition">¶</a></dt>
    107 <dd><p>Needs a doc string</p>
    108 </dd></dl>
    109 
    110 <dl class="function">
    111 <dt id="GSASIImath.GetAngleSig">
    112 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetAngleSig</tt><big>(</big><em>Oatoms</em>, <em>Atoms</em>, <em>Amat</em>, <em>SGData</em>, <em>covData={}</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetAngleSig"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetAngleSig" title="Permalink to this definition">¶</a></dt>
    113 <dd><p>Needs a doc string</p>
    114 </dd></dl>
    115 
    116 <dl class="function">
    117 <dt id="GSASIImath.GetAtomCoordsByID">
    118 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetAtomCoordsByID</tt><big>(</big><em>pId</em>, <em>parmDict</em>, <em>AtLookup</em>, <em>indx</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetAtomCoordsByID"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetAtomCoordsByID" title="Permalink to this definition">¶</a></dt>
    119 <dd><p>Needs a doc string</p>
    120 </dd></dl>
    121 
    122 <dl class="function">
    123 <dt id="GSASIImath.GetAtomItemsById">
    124 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetAtomItemsById</tt><big>(</big><em>atomData</em>, <em>atomLookUp</em>, <em>IdList</em>, <em>itemLoc</em>, <em>numItems=1</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetAtomItemsById"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetAtomItemsById" title="Permalink to this definition">¶</a></dt>
    125 <dd><p>Needs a doc string</p>
    126 </dd></dl>
    127 
    128 <dl class="function">
    129 <dt id="GSASIImath.GetAtomsById">
    130 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetAtomsById</tt><big>(</big><em>atomData</em>, <em>atomLookUp</em>, <em>IdList</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetAtomsById"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetAtomsById" title="Permalink to this definition">¶</a></dt>
    131 <dd><p>Needs a doc string</p>
    132 </dd></dl>
    133 
    134 <dl class="function">
    135 <dt id="GSASIImath.GetDATSig">
    136 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetDATSig</tt><big>(</big><em>Oatoms</em>, <em>Atoms</em>, <em>Amat</em>, <em>SGData</em>, <em>covData={}</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetDATSig"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetDATSig" title="Permalink to this definition">¶</a></dt>
    137 <dd><p>Needs a doc string</p>
    138 </dd></dl>
    139 
    140 <dl class="function">
    141 <dt id="GSASIImath.GetDistSig">
    142 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetDistSig</tt><big>(</big><em>Oatoms</em>, <em>Atoms</em>, <em>Amat</em>, <em>SGData</em>, <em>covData={}</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetDistSig"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetDistSig" title="Permalink to this definition">¶</a></dt>
    143 <dd><p>Needs a doc string</p>
    144 </dd></dl>
    145 
    146 <dl class="function">
    147 <dt id="GSASIImath.GetSHCoeff">
    148 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetSHCoeff</tt><big>(</big><em>pId</em>, <em>parmDict</em>, <em>SHkeys</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetSHCoeff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetSHCoeff" title="Permalink to this definition">¶</a></dt>
    149 <dd><p>Needs a doc string</p>
    150 </dd></dl>
    151 
    152 <dl class="function">
    153 <dt id="GSASIImath.GetTorsionSig">
    154 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetTorsionSig</tt><big>(</big><em>Oatoms</em>, <em>Atoms</em>, <em>Amat</em>, <em>SGData</em>, <em>covData={}</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetTorsionSig"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetTorsionSig" title="Permalink to this definition">¶</a></dt>
    155 <dd><p>Needs a doc string</p>
    156 </dd></dl>
    157 
    158 <dl class="function">
    159 <dt id="GSASIImath.GetXYZDist">
    160 <tt class="descclassname">GSASIImath.</tt><tt class="descname">GetXYZDist</tt><big>(</big><em>xyz</em>, <em>XYZ</em>, <em>Amat</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#GetXYZDist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.GetXYZDist" title="Permalink to this definition">¶</a></dt>
    161 <dd><p>gets distance from position xyz to all XYZ, xyz &amp; XYZ are np.array
    162 and are in crystal coordinates; Amat is crystal to Cart matrix</p>
    163 </dd></dl>
    164 
    165 <dl class="function">
    166 <dt id="GSASIImath.HessianLSQ">
    167 <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>
    168 <dd><p>Minimize the sum of squares of a set of equations.</p>
    169 <div class="highlight-python"><pre>            Nobs
    170 x = arg min(sum(func(y)**2,axis=0))
    171             y=0</pre>
    172 </div>
    173 <table class="docutils field-list" frame="void" rules="none">
    174 <col class="field-name" />
    175 <col class="field-body" />
    176 <tbody valign="top">
    177 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
    178 <li><strong>func</strong> (<em>function</em>) &#8211; callable method or function
    179 should take at least one (possibly length N vector) argument and
    180 returns M floating point numbers.</li>
    181 <li><strong>x0</strong> (<em>np.ndarray</em>) &#8211; The starting estimate for the minimization of length N</li>
    182 <li><strong>Hess</strong> (<em>function</em>) &#8211; callable method or function
    183 A required function or method to compute the weighted vector and Hessian for func.
    184 It must be a symmetric NxN array</li>
    185 <li><strong>args</strong> (<em>tuple</em>) &#8211; Any extra arguments to func are placed in this tuple.</li>
    186 <li><strong>ftol</strong> (<em>float</em>) &#8211; Relative error desired in the sum of squares.</li>
    187 <li><strong>xtol</strong> (<em>float</em>) &#8211; Relative error desired in the approximate solution.</li>
    188 <li><strong>maxcyc</strong> (<em>int</em>) &#8211; The maximum number of cycles of refinement to execute, if -1 refine
    189 until other limits are met (ftol, xtol)</li>
    190 </ul>
    191 </td>
    192 </tr>
    193 <tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body"><p class="first">(x,cov_x,infodict) where</p>
    194 <ul class="last">
    195 <li><p class="first">x : ndarray
    196 The solution (or the result of the last iteration for an unsuccessful
    197 call).</p>
    198 </li>
    199 <li><p class="first">cov_x : ndarray
    200 Uses the fjac and ipvt optional outputs to construct an
    201 estimate of the jacobian around the solution.  <tt class="docutils literal"><span class="pre">None</span></tt> if a
    202 singular matrix encountered (indicates very flat curvature in
    203 some direction).  This matrix must be multiplied by the
    204 residual standard deviation to get the covariance of the
    205 parameter estimates &#8211; see curve_fit.</p>
    206 </li>
    207 <li><p class="first">infodict : dict
    208 a dictionary of optional outputs with the keys:</p>
    209 <blockquote>
    210 <div><ul class="simple">
    211 <li>&#8216;fvec&#8217; : the function evaluated at the output</li>
    212 <li>&#8216;num cyc&#8217;:</li>
    213 <li>&#8216;nfev&#8217;:</li>
    214 <li>&#8216;lamMax&#8217;:</li>
    215 <li>&#8216;psing&#8217;:</li>
    216 </ul>
    217 </div></blockquote>
    218 </li>
    219 </ul>
    220 </td>
    221 </tr>
    222 </tbody>
    223 </table>
    224 </dd></dl>
    225 
    226 <dl class="function">
    227 <dt id="GSASIImath.OmitMap">
    228 <tt class="descclassname">GSASIImath.</tt><tt class="descname">OmitMap</tt><big>(</big><em>data</em>, <em>reflData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#OmitMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.OmitMap" title="Permalink to this definition">¶</a></dt>
    229 <dd><p>Needs a doc string</p>
    230 </dd></dl>
    231 
    232 <dl class="function">
    233 <dt id="GSASIImath.PeaksEquiv">
    234 <tt class="descclassname">GSASIImath.</tt><tt class="descname">PeaksEquiv</tt><big>(</big><em>data</em>, <em>Ind</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#PeaksEquiv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.PeaksEquiv" title="Permalink to this definition">¶</a></dt>
    235 <dd><p>Needs a doc string</p>
    236 </dd></dl>
    237 
    238 <dl class="function">
    239 <dt id="GSASIImath.PeaksUnique">
    240 <tt class="descclassname">GSASIImath.</tt><tt class="descname">PeaksUnique</tt><big>(</big><em>data</em>, <em>Ind</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#PeaksUnique"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.PeaksUnique" title="Permalink to this definition">¶</a></dt>
    241 <dd><p>Needs a doc string</p>
    242 </dd></dl>
    243 
    244 <dl class="function">
    245 <dt id="GSASIImath.Q2AV">
    246 <tt class="descclassname">GSASIImath.</tt><tt class="descname">Q2AV</tt><big>(</big><em>Q</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#Q2AV"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.Q2AV" title="Permalink to this definition">¶</a></dt>
    247 <dd><p>convert quaternion to angle (radians 0-2pi) &amp; normalized vector
    248 q=r+ai+bj+ck</p>
    249 </dd></dl>
    250 
    251 <dl class="function">
    252 <dt id="GSASIImath.Q2AVdeg">
    253 <tt class="descclassname">GSASIImath.</tt><tt class="descname">Q2AVdeg</tt><big>(</big><em>Q</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#Q2AVdeg"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.Q2AVdeg" title="Permalink to this definition">¶</a></dt>
    254 <dd><p>convert quaternion to angle (degrees 0-360) &amp; normalized vector
    255 q=r+ai+bj+ck</p>
    256 </dd></dl>
    257 
    258 <dl class="function">
    259 <dt id="GSASIImath.Q2Mat">
    260 <tt class="descclassname">GSASIImath.</tt><tt class="descname">Q2Mat</tt><big>(</big><em>Q</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#Q2Mat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.Q2Mat" title="Permalink to this definition">¶</a></dt>
    261 <dd><p>make rotation matrix from quaternion
    262 q=r+ai+bj+ck</p>
    263 </dd></dl>
    264 
    265 <dl class="function">
    266 <dt id="GSASIImath.SearchMap">
    267 <tt class="descclassname">GSASIImath.</tt><tt class="descname">SearchMap</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#SearchMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.SearchMap" title="Permalink to this definition">¶</a></dt>
    268 <dd><p>Needs a doc string</p>
    269 </dd></dl>
    270 
    271 <dl class="function">
    272 <dt id="GSASIImath.SetMolCent">
    273 <tt class="descclassname">GSASIImath.</tt><tt class="descname">SetMolCent</tt><big>(</big><em>model</em>, <em>RBData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#SetMolCent"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.SetMolCent" title="Permalink to this definition">¶</a></dt>
    274 <dd><p>Needs a doc string</p>
    275 </dd></dl>
    276 
    277 <dl class="function">
    278 <dt id="GSASIImath.TLS2Uij">
    279 <tt class="descclassname">GSASIImath.</tt><tt class="descname">TLS2Uij</tt><big>(</big><em>xyz</em>, <em>g</em>, <em>Amat</em>, <em>rbObj</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#TLS2Uij"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.TLS2Uij" title="Permalink to this definition">¶</a></dt>
    280 <dd><p>Needs a doc string; not used anywhere</p>
    281 </dd></dl>
    282 
    283 <dl class="function">
    284 <dt id="GSASIImath.UpdateMCSAxyz">
    285 <tt class="descclassname">GSASIImath.</tt><tt class="descname">UpdateMCSAxyz</tt><big>(</big><em>Bmat</em>, <em>MCSA</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#UpdateMCSAxyz"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.UpdateMCSAxyz" title="Permalink to this definition">¶</a></dt>
    286 <dd><p>Needs a doc string</p>
    287 </dd></dl>
    288 
    289 <dl class="function">
    290 <dt id="GSASIImath.UpdateRBUIJ">
    291 <tt class="descclassname">GSASIImath.</tt><tt class="descname">UpdateRBUIJ</tt><big>(</big><em>Bmat</em>, <em>Cart</em>, <em>RBObj</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#UpdateRBUIJ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.UpdateRBUIJ" title="Permalink to this definition">¶</a></dt>
    292 <dd><p>Returns atom I/A, Uiso or UIJ for atoms at XYZ as described by RBObj</p>
    293 </dd></dl>
    294 
    295 <dl class="function">
    296 <dt id="GSASIImath.UpdateRBXYZ">
    297 <tt class="descclassname">GSASIImath.</tt><tt class="descname">UpdateRBXYZ</tt><big>(</big><em>Bmat</em>, <em>RBObj</em>, <em>RBData</em>, <em>RBType</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#UpdateRBXYZ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.UpdateRBXYZ" title="Permalink to this definition">¶</a></dt>
    298 <dd><p>Returns crystal coordinates for atoms described by RBObj</p>
    299 </dd></dl>
    300 
    301 <dl class="function">
    302 <dt id="GSASIImath.ValEsd">
    303 <tt class="descclassname">GSASIImath.</tt><tt class="descname">ValEsd</tt><big>(</big><em>value</em>, <em>esd=0</em>, <em>nTZ=False</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#ValEsd"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.ValEsd" title="Permalink to this definition">¶</a></dt>
    304 <dd><p>Format a floating point number with a given level of precision or
    305 with in crystallographic format with a &#8220;esd&#8221;, as value(esd)
    306 e.g. value=1.2345; esd=0.003 is formatted as 1.234(3)</p>
    307 <table class="docutils field-list" frame="void" rules="none">
    308 <col class="field-name" />
    309 <col class="field-body" />
    310 <tbody valign="top">
    311 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
    312 <li><strong>value</strong> (<em>float</em>) &#8211; number to be formatted</li>
    313 <li><strong>esd</strong> (<em>float</em>) &#8211; uncertainty or if esd &lt; 0, specifies level of
    314 precision to be shown e.g. esd=-0.01 gives 2 places beyond decimal</li>
    315 <li><strong>nTZ</strong> (<em>bool</em>) &#8211; True to remove trailing zeros (default is False)</li>
    316 </ul>
    317 </td>
    318 </tr>
    319 <tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">value(esd) or value as a string</p>
    320 </td>
    321 </tr>
    322 </tbody>
    323 </table>
    324 </dd></dl>
    325 
    326 <dl class="function">
    327 <dt id="GSASIImath.adjHKLmax">
    328 <tt class="descclassname">GSASIImath.</tt><tt class="descname">adjHKLmax</tt><big>(</big><em>SGData</em>, <em>Hmax</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#adjHKLmax"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.adjHKLmax" title="Permalink to this definition">¶</a></dt>
    329 <dd><p>Needs a doc string</p>
    330 </dd></dl>
    331 
    332 <dl class="function">
    333 <dt id="GSASIImath.calcRamaEnergy">
    334 <tt class="descclassname">GSASIImath.</tt><tt class="descname">calcRamaEnergy</tt><big>(</big><em>phi</em>, <em>psi</em>, <em>Coeff=</em><span class="optional">[</span><span class="optional">]</span><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#calcRamaEnergy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.calcRamaEnergy" title="Permalink to this definition">¶</a></dt>
    335 <dd><p>Needs a doc string</p>
    336 </dd></dl>
    337 
    338 <dl class="function">
    339 <dt id="GSASIImath.calcTorsionEnergy">
    340 <tt class="descclassname">GSASIImath.</tt><tt class="descname">calcTorsionEnergy</tt><big>(</big><em>TOR</em>, <em>Coeff=</em><span class="optional">[</span><span class="optional">]</span><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#calcTorsionEnergy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.calcTorsionEnergy" title="Permalink to this definition">¶</a></dt>
    341 <dd><p>Needs a doc string</p>
    342 </dd></dl>
    343 
    344 <dl class="function">
    345 <dt id="GSASIImath.findOffset">
    346 <tt class="descclassname">GSASIImath.</tt><tt class="descname">findOffset</tt><big>(</big><em>SGData</em>, <em>A</em>, <em>Fhkl</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#findOffset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.findOffset" title="Permalink to this definition">¶</a></dt>
    347 <dd><p>Needs a doc string</p>
    348 </dd></dl>
    349 
    350 <dl class="function">
    351 <dt id="GSASIImath.getAngSig">
    352 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getAngSig</tt><big>(</big><em>VA</em>, <em>VB</em>, <em>Amat</em>, <em>SGData</em>, <em>covData={}</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getAngSig"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getAngSig" title="Permalink to this definition">¶</a></dt>
    353 <dd><p>Needs a doc string</p>
    354 </dd></dl>
    355 
    356 <dl class="function">
    357 <dt id="GSASIImath.getAtomXYZ">
    358 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getAtomXYZ</tt><big>(</big><em>atoms</em>, <em>cx</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getAtomXYZ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getAtomXYZ" title="Permalink to this definition">¶</a></dt>
    359 <dd><p>Needs a doc string; not used anywhere</p>
    360 </dd></dl>
    361 
    362 <dl class="function">
    363 <dt id="GSASIImath.getDensity">
    364 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getDensity</tt><big>(</big><em>generalData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getDensity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getDensity" title="Permalink to this definition">¶</a></dt>
    365 <dd><p>Computes density of unit cell contents</p>
    366 </dd></dl>
    367 
    368 <dl class="function">
    369 <dt id="GSASIImath.getDistDerv">
    370 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getDistDerv</tt><big>(</big><em>Oxyz</em>, <em>Txyz</em>, <em>Amat</em>, <em>Tunit</em>, <em>Top</em>, <em>SGData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getDistDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getDistDerv" title="Permalink to this definition">¶</a></dt>
    371 <dd><p>Needs a doc string</p>
    372 </dd></dl>
    373 
    374 <dl class="function">
    375 <dt id="GSASIImath.getMass">
    376 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getMass</tt><big>(</big><em>generalData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getMass"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getMass" title="Permalink to this definition">¶</a></dt>
    377 <dd><p>Computes mass of unit cell contents</p>
    378 </dd></dl>
    379 
    380 <dl class="function">
    381 <dt id="GSASIImath.getRamaDeriv">
    382 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRamaDeriv</tt><big>(</big><em>XYZ</em>, <em>Amat</em>, <em>Coeff</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRamaDeriv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRamaDeriv" title="Permalink to this definition">¶</a></dt>
    383 <dd><p>Needs a doc string</p>
    384 </dd></dl>
    385 
    386 <dl class="function">
    387 <dt id="GSASIImath.getRestAngle">
    388 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestAngle</tt><big>(</big><em>XYZ</em>, <em>Amat</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestAngle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestAngle" title="Permalink to this definition">¶</a></dt>
    389 <dd><p>Needs a doc string</p>
    390 </dd></dl>
    391 
    392 <dl class="function">
    393 <dt id="GSASIImath.getRestChiral">
    394 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestChiral</tt><big>(</big><em>XYZ</em>, <em>Amat</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestChiral"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestChiral" title="Permalink to this definition">¶</a></dt>
    395 <dd><p>Needs a doc string</p>
    396 </dd></dl>
    397 
    398 <dl class="function">
    399 <dt id="GSASIImath.getRestDeriv">
    400 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestDeriv</tt><big>(</big><em>Func</em>, <em>XYZ</em>, <em>Amat</em>, <em>ops</em>, <em>SGData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestDeriv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestDeriv" title="Permalink to this definition">¶</a></dt>
    401 <dd><p>Needs a doc string</p>
    402 </dd></dl>
    403 
    404 <dl class="function">
    405 <dt id="GSASIImath.getRestDist">
    406 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestDist</tt><big>(</big><em>XYZ</em>, <em>Amat</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestDist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestDist" title="Permalink to this definition">¶</a></dt>
    407 <dd><p>Needs a doc string</p>
    408 </dd></dl>
    409 
    410 <dl class="function">
    411 <dt id="GSASIImath.getRestPlane">
    412 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestPlane</tt><big>(</big><em>XYZ</em>, <em>Amat</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestPlane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestPlane" title="Permalink to this definition">¶</a></dt>
    413 <dd><p>Needs a doc string</p>
    414 </dd></dl>
    415 
    416 <dl class="function">
    417 <dt id="GSASIImath.getRestPolefig">
    418 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestPolefig</tt><big>(</big><em>ODFln</em>, <em>SamSym</em>, <em>Grid</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestPolefig"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestPolefig" title="Permalink to this definition">¶</a></dt>
    419 <dd><p>Needs a doc string</p>
    420 </dd></dl>
    421 
    422 <dl class="function">
    423 <dt id="GSASIImath.getRestPolefigDerv">
    424 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestPolefigDerv</tt><big>(</big><em>HKL</em>, <em>Grid</em>, <em>SHCoeff</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestPolefigDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestPolefigDerv" title="Permalink to this definition">¶</a></dt>
    425 <dd><p>Needs a doc string</p>
    426 </dd></dl>
    427 
    428 <dl class="function">
    429 <dt id="GSASIImath.getRestRama">
    430 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestRama</tt><big>(</big><em>XYZ</em>, <em>Amat</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestRama"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestRama" title="Permalink to this definition">¶</a></dt>
    431 <dd><p>Needs a doc string</p>
    432 </dd></dl>
    433 
    434 <dl class="function">
    435 <dt id="GSASIImath.getRestTorsion">
    436 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getRestTorsion</tt><big>(</big><em>XYZ</em>, <em>Amat</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getRestTorsion"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getRestTorsion" title="Permalink to this definition">¶</a></dt>
    437 <dd><p>Needs a doc string</p>
    438 </dd></dl>
    439 
    440 <dl class="function">
    441 <dt id="GSASIImath.getSyXYZ">
    442 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getSyXYZ</tt><big>(</big><em>XYZ</em>, <em>ops</em>, <em>SGData</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getSyXYZ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getSyXYZ" title="Permalink to this definition">¶</a></dt>
    443 <dd><p>Needs a doc string</p>
    444 </dd></dl>
    445 
    446 <dl class="function">
    447 <dt id="GSASIImath.getTorsionDeriv">
    448 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getTorsionDeriv</tt><big>(</big><em>XYZ</em>, <em>Amat</em>, <em>Coeff</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getTorsionDeriv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getTorsionDeriv" title="Permalink to this definition">¶</a></dt>
    449 <dd><p>Needs a doc string</p>
    450 </dd></dl>
    451 
    452 <dl class="function">
    453 <dt id="GSASIImath.getVCov">
    454 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getVCov</tt><big>(</big><em>varyNames</em>, <em>varyList</em>, <em>covMatrix</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getVCov"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getVCov" title="Permalink to this definition">¶</a></dt>
    455 <dd><p>Needs a doc string</p>
    456 </dd></dl>
    457 
    458 <dl class="function">
    459 <dt id="GSASIImath.getWave">
    460 <tt class="descclassname">GSASIImath.</tt><tt class="descname">getWave</tt><big>(</big><em>Parms</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#getWave"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.getWave" title="Permalink to this definition">¶</a></dt>
    461 <dd><p>Needs a doc string</p>
    462 </dd></dl>
    463 
    464 <dl class="function">
    465 <dt id="GSASIImath.invQ">
    466 <tt class="descclassname">GSASIImath.</tt><tt class="descname">invQ</tt><big>(</big><em>Q</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#invQ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.invQ" title="Permalink to this definition">¶</a></dt>
    467 <dd><p>get inverse of quaternion
    468 q=r+ai+bj+ck; q* = r-ai-bj-ck</p>
    469 </dd></dl>
    470 
    471 <dl class="function">
    472 <dt id="GSASIImath.makeQuat">
    473 <tt class="descclassname">GSASIImath.</tt><tt class="descname">makeQuat</tt><big>(</big><em>A</em>, <em>B</em>, <em>C</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#makeQuat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.makeQuat" title="Permalink to this definition">¶</a></dt>
    474 <dd><p>Make quaternion from rotation of A vector to B vector about C axis</p>
    475 <table class="docutils field-list" frame="void" rules="none">
    476 <col class="field-name" />
    477 <col class="field-body" />
    478 <tbody valign="top">
    479 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>A,B,C</strong> (<em>np.array</em>) &#8211; Cartesian 3-vectors</td>
    480 </tr>
    481 <tr class="field-even field"><th class="field-name">Returns :</th><td class="field-body">quaternion &amp; rotation angle in radians q=r+ai+bj+ck</td>
    482 </tr>
    483 </tbody>
    484 </table>
    485 </dd></dl>
    486 
    487 <dl class="function">
    488 <dt id="GSASIImath.mcsaSearch">
    489 <tt class="descclassname">GSASIImath.</tt><tt class="descname">mcsaSearch</tt><big>(</big><em>data</em>, <em>reflType</em>, <em>reflData</em>, <em>covData</em>, <em>pgbar</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#mcsaSearch"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.mcsaSearch" title="Permalink to this definition">¶</a></dt>
    490 <dd><p>Needs a doc string</p>
    491 </dd></dl>
    492 
    493 <dl class="function">
    494 <dt id="GSASIImath.normQ">
    495 <tt class="descclassname">GSASIImath.</tt><tt class="descname">normQ</tt><big>(</big><em>QA</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#normQ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.normQ" title="Permalink to this definition">¶</a></dt>
    496 <dd><p>get length of quaternion &amp; normalize it
    497 q=r+ai+bj+ck</p>
    498 </dd></dl>
    499 
    500 <dl class="function">
    501 <dt id="GSASIImath.printRho">
    502 <tt class="descclassname">GSASIImath.</tt><tt class="descname">printRho</tt><big>(</big><em>SGLaue</em>, <em>rho</em>, <em>rhoMax</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#printRho"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.printRho" title="Permalink to this definition">¶</a></dt>
    503 <dd><p>Needs a doc string</p>
    504 </dd></dl>
    505 
    506 <dl class="function">
    507 <dt id="GSASIImath.prodQQ">
    508 <tt class="descclassname">GSASIImath.</tt><tt class="descname">prodQQ</tt><big>(</big><em>QA</em>, <em>QB</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#prodQQ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.prodQQ" title="Permalink to this definition">¶</a></dt>
    509 <dd><p>Grassman quaternion product
    510 QA,QB quaternions; q=r+ai+bj+ck</p>
    511 </dd></dl>
    512 
    513 <dl class="function">
    514 <dt id="GSASIImath.prodQVQ">
    515 <tt class="descclassname">GSASIImath.</tt><tt class="descname">prodQVQ</tt><big>(</big><em>Q</em>, <em>V</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#prodQVQ"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.prodQVQ" title="Permalink to this definition">¶</a></dt>
    516 <dd><p>compute the quaternion vector rotation qvq-1 = v&#8217;
    517 q=r+ai+bj+ck</p>
    518 </dd></dl>
    519 
    520 <dl class="function">
    521 <dt id="GSASIImath.setPeakparms">
    522 <tt class="descclassname">GSASIImath.</tt><tt class="descname">setPeakparms</tt><big>(</big><em>Parms</em>, <em>Parms2</em>, <em>pos</em>, <em>mag</em>, <em>ifQ=False</em>, <em>useFit=False</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#setPeakparms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.setPeakparms" title="Permalink to this definition">¶</a></dt>
    523 <dd><p>Needs a doc string</p>
    524 </dd></dl>
    525 
    526 <dl class="function">
    527 <dt id="GSASIImath.sortArray">
    528 <tt class="descclassname">GSASIImath.</tt><tt class="descname">sortArray</tt><big>(</big><em>data</em>, <em>pos</em>, <em>reverse=False</em><big>)</big><a class="reference internal" href="_modules/GSASIImath.html#sortArray"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIImath.sortArray" title="Permalink to this definition">¶</a></dt>
    529 <dd><p>data is a list of items
    530 sort by pos in list; reverse if True</p>
     61<dt id="GSASIImath.anneal">
     62<tt class="descclassname">GSASIImath.</tt><tt class="descname">anneal</tt><big>(</big><em>func</em>, <em>x0</em>, <em>args=()</em>, <em>schedule='fast'</em>, <em>full_output=0</em>, <em>T0=None</em>, <em>Tf=1e-12</em>, <em>maxeval=None</em>, <em>maxaccept=None</em>, <em>maxiter=400</em>, <em>boltzmann=1.0</em>, <em>learn_rate=0.5</em>, <em>feps=1e-06</em>, <em>quench=1.0</em>, <em>m=1.0</em>, <em>n=1.0</em>, <em>lower=-100</em>, <em>upper=100</em>, <em>dwell=50</em>, <em>slope=0.9</em><big>)</big><a class="headerlink" href="#GSASIImath.anneal" title="Permalink to this definition">¶</a></dt>
     63<dd><p>Minimize a function using simulated annealing.</p>
     64<p>Schedule is a schedule class implementing the annealing schedule.
     65Available ones are &#8216;fast&#8217;, &#8216;cauchy&#8217;, &#8216;boltzmann&#8217;</p>
     66<dl class="docutils">
     67<dt>func <span class="classifier-delimiter">:</span> <span class="classifier">callable f(x, <a href="#id1"><span class="problematic" id="id2">*</span></a>args)</span></dt>
     68<dd>Function to be optimized.</dd>
     69<dt>x0 <span class="classifier-delimiter">:</span> <span class="classifier">ndarray</span></dt>
     70<dd>Initial guess.</dd>
     71<dt>args <span class="classifier-delimiter">:</span> <span class="classifier">tuple</span></dt>
     72<dd>Extra parameters to <cite>func</cite>.</dd>
     73<dt>schedule <span class="classifier-delimiter">:</span> <span class="classifier">base_schedule</span></dt>
     74<dd>Annealing schedule to use (a class).</dd>
     75<dt>full_output <span class="classifier-delimiter">:</span> <span class="classifier">bool</span></dt>
     76<dd>Whether to return optional outputs.</dd>
     77<dt>T0 <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     78<dd>Initial Temperature (estimated as 1.2 times the largest
     79cost-function deviation over random points in the range).</dd>
     80<dt>Tf <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     81<dd>Final goal temperature.</dd>
     82<dt>maxeval <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
     83<dd>Maximum function evaluations.</dd>
     84<dt>maxaccept <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
     85<dd>Maximum changes to accept.</dd>
     86<dt>maxiter <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
     87<dd>Maximum cooling iterations.</dd>
     88<dt>learn_rate <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     89<dd>Scale constant for adjusting guesses.</dd>
     90<dt>boltzmann <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     91<dd>Boltzmann constant in acceptance test
     92(increase for less stringent test at each temperature).</dd>
     93<dt>feps <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     94<dd>Stopping relative error tolerance for the function value in
     95last four coolings.</dd>
     96<dt>quench, m, n <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     97<dd>Parameters to alter fast_sa schedule.</dd>
     98<dt>lower, upper <span class="classifier-delimiter">:</span> <span class="classifier">float or ndarray</span></dt>
     99<dd>Lower and upper bounds on <cite>x</cite>.</dd>
     100<dt>dwell <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
     101<dd>The number of times to search the space at each temperature.</dd>
     102<dt>slope <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     103<dd>Parameter for log schedule</dd>
     104</dl>
     105<dl class="docutils">
     106<dt>xmin <span class="classifier-delimiter">:</span> <span class="classifier">ndarray</span></dt>
     107<dd>Point giving smallest value found.</dd>
     108<dt>Jmin <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     109<dd>Minimum value of function found.</dd>
     110<dt>T <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
     111<dd>Final temperature.</dd>
     112<dt>feval <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
     113<dd>Number of function evaluations.</dd>
     114<dt>iters <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
     115<dd>Number of cooling iterations.</dd>
     116<dt>accept <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
     117<dd>Number of tests accepted.</dd>
     118<dt>retval <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
     119<dd><p class="first">Flag indicating stopping condition:</p>
     120<div class="last highlight-python"><pre>0 : Points no longer changing
     1211 : Cooled to final temperature
     1222 : Maximum function evaluations
     1233 : Maximum cooling iterations reached
     1244 : Maximum accepted query locations reached
     1255 : Final point not the minimum amongst encountered points</pre>
     126</div>
     127</dd>
     128</dl>
     129<p>Simulated annealing is a random algorithm which uses no derivative
     130information from the function being optimized. In practice it has
     131been more useful in discrete optimization than continuous
     132optimization, as there are usually better algorithms for continuous
     133optimization problems.</p>
     134<p>Some experimentation by trying the difference temperature
     135schedules and altering their parameters is likely required to
     136obtain good performance.</p>
     137<p>The randomness in the algorithm comes from random sampling in numpy.
     138To obtain the same results you can call numpy.random.seed with the
     139same seed immediately before calling scipy.optimize.anneal.</p>
     140<p>We give a brief description of how the three temperature schedules
     141generate new points and vary their temperature. Temperatures are
     142only updated with iterations in the outer loop. The inner loop is
     143over loop over xrange(dwell), and new points are generated for
     144every iteration in the inner loop. (Though whether the proposed
     145new points are accepted is probabilistic.)</p>
     146<p>For readability, let d denote the dimension of the inputs to func.
     147Also, let x_old denote the previous state, and k denote the
     148iteration number of the outer loop. All other variables not
     149defined below are input variables to scipy.optimize.anneal itself.</p>
     150<p>In the &#8216;fast&#8217; schedule the updates are</p>
     151<div class="highlight-python"><pre>u ~ Uniform(0, 1, size=d)
     152y = sgn(u - 0.5) * T * ((1+ 1/T)**abs(2u-1) -1.0)
     153xc = y * (upper - lower)
     154x_new = x_old + xc
     155
     156c = n * exp(-n * quench)
     157T_new = T0 * exp(-c * k**quench)</pre>
     158</div>
     159<p>In the &#8216;cauchy&#8217; schedule the updates are</p>
     160<div class="highlight-python"><pre>u ~ Uniform(-pi/2, pi/2, size=d)
     161xc = learn_rate * T * tan(u)
     162x_new = x_old + xc
     163
     164T_new = T0 / (1+k)</pre>
     165</div>
     166<p>In the &#8216;boltzmann&#8217; schedule the updates are</p>
     167<div class="highlight-python"><pre>std = minimum( sqrt(T) * ones(d), (upper-lower) / (3*learn_rate) )
     168y ~ Normal(0, std, size=d)
     169x_new = x_old + learn_rate * y
     170
     171T_new = T0 / log(1+k)</pre>
     172</div>
    531173</dd></dl>
    532174
  • trunk/sphinxdocs/build/html/GSASIIutil.html

    r939 r941  
    109109<col class="field-body" />
    110110<tbody valign="top">
    111 <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: 772 $&#8221;
     111<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>RevString</strong> (<em>str</em>) &#8211; something like &#8220;$Revision: 939 $&#8221;
    112112that is set by subversion when the file is retrieved from subversion.</td>
    113113</tr>
    114114</tbody>
    115115</table>
    116 <p>Place <tt class="docutils literal"><span class="pre">GSASIIpath.SetVersionNumber(&quot;$Revision:</span> <span class="pre">$&quot;)</span></tt> in every python
     116<p>Place <tt class="docutils literal"><span class="pre">GSASIIpath.SetVersionNumber(&quot;$Revision:</span> <span class="pre">939</span> <span class="pre">$&quot;)</span></tt> in every python
    117117file.</p>
    118118</dd></dl>
     
    999999<dl class="data">
    10001000<dt id="GSASIIlattice.selftestlist">
    1001 <tt class="descclassname">GSASIIlattice.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x17cc0930&gt;, &lt;function test1 at 0x17cc0970&gt;, &lt;function test2 at 0x17cc09b0&gt;, &lt;function test3 at 0x17cc09f0&gt;, &lt;function test4 at 0x17cc0a30&gt;, &lt;function test5 at 0x17cc0a70&gt;, &lt;function test6 at 0x17cc0ab0&gt;, &lt;function test7 at 0x17cc0af0&gt;, &lt;function test8 at 0x17cc0b30&gt;, &lt;function test9 at 0x17cc0b70&gt;]</em><a class="headerlink" href="#GSASIIlattice.selftestlist" title="Permalink to this definition">¶</a></dt>
     1001<tt class="descclassname">GSASIIlattice.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0xc92aa30&gt;, &lt;function test1 at 0xc92aa70&gt;, &lt;function test2 at 0xc92aab0&gt;, &lt;function test3 at 0xc92aaf0&gt;, &lt;function test4 at 0xc92ab30&gt;, &lt;function test5 at 0xc92ab70&gt;, &lt;function test6 at 0xc92abb0&gt;, &lt;function test7 at 0xc92abf0&gt;, &lt;function test8 at 0xc92ac30&gt;, &lt;function test9 at 0xc92ac70&gt;]</em><a class="headerlink" href="#GSASIIlattice.selftestlist" title="Permalink to this definition">¶</a></dt>
    10021002<dd><p>Defines a list of self-tests</p>
    10031003</dd></dl>
     
    10911091<span class="target" id="module-GSASIIspc"></span><div class="section" id="gsasiispc-space-group-module">
    10921092<h2><em>GSASIIspc: Space group module</em><a class="headerlink" href="#gsasiispc-space-group-module" title="Permalink to this headline">¶</a></h2>
    1093 <p>Space group interpretion routines</p>
     1093<p>Space group interpretation routines.</p>
     1094<p>Space groups are interpreted and the information is placed in a SGdata object,
     1095which is a dict with these keys:</p>
     1096<table border="1" class="docutils">
     1097<colgroup>
     1098<col width="16%" />
     1099<col width="84%" />
     1100</colgroup>
     1101<thead valign="bottom">
     1102<tr class="row-odd"><th class="head">key</th>
     1103<th class="head">explaination</th>
     1104</tr>
     1105</thead>
     1106<tbody valign="top">
     1107<tr class="row-even"><td>SpGrp</td>
     1108<td>space group symbol (str)</td>
     1109</tr>
     1110<tr class="row-odd"><td>Laue</td>
     1111<td>one of the following 14 Laue classes:
     1112-1, 2/m, mmm, 4/m, 4/mmm, 3R,
     11133mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)</td>
     1114</tr>
     1115<tr class="row-even"><td>SGInv</td>
     1116<td>True if centrosymmetric, False if not (bool)</td>
     1117</tr>
     1118<tr class="row-odd"><td>SGLatt</td>
     1119<td>Lattice centering type. Will be one of
     1120P, A, B, C, I, F, R (str)</td>
     1121</tr>
     1122<tr class="row-even"><td>SGUniq</td>
     1123<td>unique axis if monoclinic. Will be
     1124a, b, or c for monoclinic space groups.
     1125Will be blank for non-monoclinic. (str)</td>
     1126</tr>
     1127<tr class="row-odd"><td>SGCen</td>
     1128<td>Symmetry cell centering vectors. A (n,3) np.array
     1129of centers. Will always have at least one row:
     1130<tt class="docutils literal"><span class="pre">np.array([[0,</span> <span class="pre">0,</span> <span class="pre">0]])</span></tt></td>
     1131</tr>
     1132<tr class="row-even"><td>SGOps</td>
     1133<td>symmetry operations as a list in form
     1134[[M1,T1],[M2,T2,...] where Mn is a 3x3 np.array
     1135and T is a length 3 np.array.
     1136Atom coordinates are transformed where the
     1137Asymmetric unit coordinates [X=(x,y,z)] are
     1138transformed using <tt class="docutils literal"><span class="pre">M*X+T</span> <span class="pre">==&gt;</span> <span class="pre">X'</span></tt></td>
     1139</tr>
     1140<tr class="row-odd"><td>SGSys</td>
     1141<td>symmetry unit cell: type one of
     1142&#8216;triclinic&#8217;, &#8216;monoclinic&#8217;, &#8216;orthorhombic&#8217;,
     1143&#8216;tetragonal&#8217;, &#8216;rhombohedral&#8217;, &#8216;trigonal&#8217;,
     1144&#8216;hexagonal&#8217;, &#8216;cubic&#8217; (str)</td>
     1145</tr>
     1146<tr class="row-even"><td>SGPolax</td>
     1147<td>Axes for space group polarity. Will be one of
     1148&#8216;&#8217;, &#8216;x&#8217;, &#8216;y&#8217;, &#8216;x y&#8217;, &#8216;z&#8217;, &#8216;x z&#8217;, &#8216;y z&#8217;,
     1149&#8216;xyz&#8217;. In the case where axes are arbitrary
     1150&#8216;111&#8217; is used (P 1, and ?).</td>
     1151</tr>
     1152</tbody>
     1153</table>
    10941154<dl class="function">
    10951155<dt id="GSASIIspc.ApplyStringOps">
     
    14121472<dl class="data">
    14131473<dt id="GSASIIspc.selftestlist">
    1414 <tt class="descclassname">GSASIIspc.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0x2376470&gt;, &lt;function test1 at 0x23764b0&gt;, &lt;function test2 at 0x23764f0&gt;, &lt;function test3 at 0x2376530&gt;]</em><a class="headerlink" href="#GSASIIspc.selftestlist" title="Permalink to this definition">¶</a></dt>
     1474<tt class="descclassname">GSASIIspc.</tt><tt class="descname">selftestlist</tt><em class="property"> = [&lt;function test0 at 0xbdfd7b0&gt;, &lt;function test1 at 0xbdfd930&gt;, &lt;function test2 at 0xbdfd9f0&gt;, &lt;function test3 at 0xbdfdb70&gt;]</em><a class="headerlink" href="#GSASIIspc.selftestlist" title="Permalink to this definition">¶</a></dt>
    14151475<dd><p>Defines a list of self-tests</p>
    14161476</dd></dl>
  • trunk/sphinxdocs/build/html/genindex.html

    r939 r941  
    6767 | <a href="#O"><strong>O</strong></a>
    6868 | <a href="#P"><strong>P</strong></a>
    69  | <a href="#Q"><strong>Q</strong></a>
    7069 | <a href="#R"><strong>R</strong></a>
    7170 | <a href="#S"><strong>S</strong></a>
     
    111110  </dt>
    112111
     112  </dl></td>
     113  <td style="width: 33%" valign="top"><dl>
    113114     
    114115  <dt><a href="GSASIIplot.html#GSASIIplot.G2PlotNoteBook.addMpl">addMpl() (GSASIIplot.G2PlotNoteBook method)</a>
     
    119120  </dt>
    120121
    121   </dl></td>
    122   <td style="width: 33%" valign="top"><dl>
    123      
    124   <dt><a href="GSASIImath.html#GSASIImath.adjHKLmax">adjHKLmax() (in module GSASIImath)</a>
     122     
     123  <dt><a href="GSASIImath.html#GSASIImath.anneal">anneal() (in module GSASIImath)</a>
    125124  </dt>
    126125
     
    139138     
    140139  <dt><a href="GSASIIstruc.html#GSASIIstrMath.ApplyXYZshifts">ApplyXYZshifts() (in module GSASIIstrMath)</a>
    141   </dt>
    142 
    143      
    144   <dt><a href="GSASIImath.html#GSASIImath.AtomTLS2UIJ">AtomTLS2UIJ() (in module GSASIImath)</a>
    145   </dt>
    146 
    147      
    148   <dt><a href="GSASIImath.html#GSASIImath.AtomUij2TLS">AtomUij2TLS() (in module GSASIImath)</a>
    149   </dt>
    150 
    151      
    152   <dt><a href="GSASIImath.html#GSASIImath.AV2Q">AV2Q() (in module GSASIImath)</a>
    153   </dt>
    154 
    155      
    156   <dt><a href="GSASIImath.html#GSASIImath.AVdeg2Q">AVdeg2Q() (in module GSASIImath)</a>
    157140  </dt>
    158141
     
    228211
    229212     
    230   <dt><a href="GSASIImath.html#GSASIImath.calcRamaEnergy">calcRamaEnergy() (in module GSASIImath)</a>
    231   </dt>
    232 
    233      
    234   <dt><a href="GSASIImath.html#GSASIImath.calcTorsionEnergy">calcTorsionEnergy() (in module GSASIImath)</a>
    235   </dt>
    236 
    237      
    238213  <dt><a href="GSASIIimage.html#GSASIIimage.calcZdisCosB">calcZdisCosB() (in module GSASIIimage)</a>
    239214  </dt>
     
    279254     
    280255  <dt><a href="GSASIIutil.html#GSASIIlattice.CentCheck">CentCheck() (in module GSASIIlattice)</a>
    281   </dt>
    282 
    283      
    284   <dt><a href="GSASIImath.html#GSASIImath.ChargeFlip">ChargeFlip() (in module GSASIImath)</a>
    285256  </dt>
    286257
     
    510481
    511482     
    512   <dt><a href="GSASIImath.html#GSASIImath.FillAtomLookUp">FillAtomLookUp() (in module GSASIImath)</a>
    513   </dt>
    514 
    515      
    516483  <dt><a href="GSASIIutil.html#GSASIIlattice.fillgmat">fillgmat() (in module GSASIIlattice)</a>
    517484  </dt>
     
    522489
    523490     
    524   <dt><a href="GSASIImath.html#GSASIImath.FindAtomIndexByIDs">FindAtomIndexByIDs() (in module GSASIImath)</a>
    525   </dt>
    526 
    527      
    528491  <dt><a href="GSASIIindex.html#GSASIIindex.findBestCell">findBestCell() (in module GSASIIindex)</a>
    529492  </dt>
    530493
    531494     
    532   <dt><a href="GSASIImath.html#GSASIImath.findOffset">findOffset() (in module GSASIImath)</a>
    533   </dt>
    534 
    535      
    536495  <dt><a href="GSASIIimage.html#GSASIIimage.FitCircle">FitCircle() (in module GSASIIimage)</a>
    537496  </dt>
     
    545504  </dt>
    546505
    547   </dl></td>
    548   <td style="width: 33%" valign="top"><dl>
    549506     
    550507  <dt><a href="GSASIIindex.html#GSASIIindex.FitHKL">FitHKL() (in module GSASIIindex)</a>
    551508  </dt>
    552509
     510  </dl></td>
     511  <td style="width: 33%" valign="top"><dl>
    553512     
    554513  <dt><a href="GSASIIindex.html#GSASIIindex.FitHKLZ">FitHKLZ() (in module GSASIIindex)</a>
     
    585544     
    586545  <dt><a href="GSASIIGUIr.html#GSASIIpy3.FormulaEval">FormulaEval() (in module GSASIIpy3)</a>
    587   </dt>
    588 
    589      
    590   <dt><a href="GSASIImath.html#GSASIImath.FourierMap">FourierMap() (in module GSASIImath)</a>
    591546  </dt>
    592547
     
    658613
    659614     
    660   <dt><a href="GSASIImath.html#GSASIImath.GetAngleSig">GetAngleSig() (in module GSASIImath)</a>
    661   </dt>
    662 
    663      
    664   <dt><a href="GSASIImath.html#GSASIImath.getAngSig">getAngSig() (in module GSASIImath)</a>
    665   </dt>
    666 
    667      
    668615  <dt><a href="GSASIIpwd.html#GSASIIpwd.GetAsfMean">GetAsfMean() (in module GSASIIpwd)</a>
    669616  </dt>
    670617
    671618     
    672   <dt><a href="GSASIImath.html#GSASIImath.GetAtomCoordsByID">GetAtomCoordsByID() (in module GSASIImath)</a>
    673   </dt>
    674 
    675      
    676619  <dt><a href="GSASIIstruc.html#GSASIIstrMath.GetAtomFXU">GetAtomFXU() (in module GSASIIstrMath)</a>
    677620  </dt>
     
    682625
    683626     
    684   <dt><a href="GSASIImath.html#GSASIImath.GetAtomItemsById">GetAtomItemsById() (in module GSASIImath)</a>
    685   </dt>
    686 
    687      
    688   <dt><a href="GSASIImath.html#GSASIImath.GetAtomsById">GetAtomsById() (in module GSASIImath)</a>
    689   </dt>
    690 
    691      
    692   <dt><a href="GSASIImath.html#GSASIImath.getAtomXYZ">getAtomXYZ() (in module GSASIImath)</a>
    693   </dt>
    694 
    695      
    696627  <dt><a href="GSASIIimage.html#GSASIIimage.GetAzm">GetAzm() (in module GSASIIimage)</a>
    697628  </dt>
     
    742673
    743674     
    744   <dt><a href="GSASIImath.html#GSASIImath.GetDATSig">GetDATSig() (in module GSASIImath)</a>
    745   </dt>
    746 
    747      
    748   <dt><a href="GSASIImath.html#GSASIImath.getDensity">getDensity() (in module GSASIImath)</a>
    749   </dt>
    750 
    751      
    752675  <dt><a href="GSASIImapvars.html#GSASIImapvars.GetDependentVars">GetDependentVars() (in module GSASIImapvars)</a>
    753676  </dt>
     
    770693
    771694     
    772   <dt><a href="GSASIImath.html#GSASIImath.getDistDerv">getDistDerv() (in module GSASIImath)</a>
    773   </dt>
    774 
    775      
    776   <dt><a href="GSASIImath.html#GSASIImath.GetDistSig">GetDistSig() (in module GSASIImath)</a>
    777   </dt>
    778 
    779      
    780695  <dt><a href="GSASIIindex.html#GSASIIindex.getDmax">getDmax() (in module GSASIIindex)</a>
    781696  </dt>
     
    930845
    931846     
    932   <dt><a href="GSASIImath.html#GSASIImath.getMass">getMass() (in module GSASIImath)</a>
    933   </dt>
    934 
    935      
    936847  <dt><a href="GSASIIstruc.html#GSASIIstrMath.GetNewCellParms">GetNewCellParms() (in module GSASIIstrMath)</a>
    937848  </dt>
     
    945856  </dt>
    946857
     858  </dl></td>
     859  <td style="width: 33%" valign="top"><dl>
    947860     
    948861  <dt><a href="GSASIIutil.html#GSASIIspc.GetOprPtrName">GetOprPtrName() (in module GSASIIspc)</a>
     
    957870  </dt>
    958871
    959   </dl></td>
    960   <td style="width: 33%" valign="top"><dl>
    961872     
    962873  <dt><a href="GSASIIstruc.html#GSASIIstrIO.GetPawleyConstr">GetPawleyConstr() (in module GSASIIstrIO)</a>
     
    1014925
    1015926     
    1016   <dt><a href="GSASIImath.html#GSASIImath.getRamaDeriv">getRamaDeriv() (in module GSASIImath)</a>
    1017   </dt>
    1018 
    1019      
    1020927  <dt><a href="GSASIIstruc.html#GSASIIstrMath.GetReflPos">GetReflPos() (in module GSASIIstrMath)</a>
    1021928  </dt>
     
    1026933
    1027934     
    1028   <dt><a href="GSASIImath.html#GSASIImath.getRestAngle">getRestAngle() (in module GSASIImath)</a>
    1029   </dt>
    1030 
    1031      
    1032   <dt><a href="GSASIImath.html#GSASIImath.getRestChiral">getRestChiral() (in module GSASIImath)</a>
    1033   </dt>
    1034 
    1035      
    1036   <dt><a href="GSASIImath.html#GSASIImath.getRestDeriv">getRestDeriv() (in module GSASIImath)</a>
    1037   </dt>
    1038 
    1039      
    1040   <dt><a href="GSASIImath.html#GSASIImath.getRestDist">getRestDist() (in module GSASIImath)</a>
    1041   </dt>
    1042 
    1043      
    1044   <dt><a href="GSASIImath.html#GSASIImath.getRestPlane">getRestPlane() (in module GSASIImath)</a>
    1045   </dt>
    1046 
    1047      
    1048   <dt><a href="GSASIImath.html#GSASIImath.getRestPolefig">getRestPolefig() (in module GSASIImath)</a>
    1049   </dt>
    1050 
    1051      
    1052   <dt><a href="GSASIImath.html#GSASIImath.getRestPolefigDerv">getRestPolefigDerv() (in module GSASIImath)</a>
    1053   </dt>
    1054 
    1055      
    1056935  <dt><a href="GSASIIstruc.html#GSASIIstrIO.GetRestraints">GetRestraints() (in module GSASIIstrIO)</a>
    1057936  </dt>
    1058937
    1059938     
    1060   <dt><a href="GSASIImath.html#GSASIImath.getRestRama">getRestRama() (in module GSASIImath)</a>
    1061   </dt>
    1062 
    1063      
    1064   <dt><a href="GSASIImath.html#GSASIImath.getRestTorsion">getRestTorsion() (in module GSASIImath)</a>
    1065   </dt>
    1066 
    1067      
    1068939  <dt><a href="GSASIIstruc.html#GSASIIstrIO.GetRigidBodies">GetRigidBodies() (in module GSASIIstrIO)</a>
    1069940  </dt>
     
    1082953
    1083954     
    1084   <dt><a href="GSASIImath.html#GSASIImath.GetSHCoeff">GetSHCoeff() (in module GSASIImath)</a>
    1085   </dt>
    1086 
    1087      
    1088   <dt><a href="GSASIImath.html#GSASIImath.getSyXYZ">getSyXYZ() (in module GSASIImath)</a>
    1089   </dt>
    1090 
    1091      
    1092955  <dt><a href="GSASIIGUIr.html#GSASIIIO.GetTifData">GetTifData() (in module GSASIIIO)</a>
    1093956  </dt>
    1094957
    1095958     
    1096   <dt><a href="GSASIImath.html#GSASIImath.getTorsionDeriv">getTorsionDeriv() (in module GSASIImath)</a>
    1097   </dt>
    1098 
    1099      
    1100   <dt><a href="GSASIImath.html#GSASIImath.GetTorsionSig">GetTorsionSig() (in module GSASIImath)</a>
    1101   </dt>
    1102 
    1103      
    1104959  <dt><a href="GSASIIimage.html#GSASIIimage.GetTth">GetTth() (in module GSASIIimage)</a>
    1105960  </dt>
     
    1126981
    1127982     
    1128   <dt><a href="GSASIImath.html#GSASIImath.getVCov">getVCov() (in module GSASIImath)</a>
    1129   </dt>
    1130 
    1131      
    1132983  <dt><a href="GSASIIutil.html#GSASIIpath.GetVersionNumber">GetVersionNumber() (in module GSASIIpath)</a>
    1133984  </dt>
    1134985
    1135986     
    1136   <dt><a href="GSASIImath.html#GSASIImath.getWave">getWave() (in module GSASIImath)</a>
    1137   </dt>
    1138 
    1139      
    1140987  <dt><a href="GSASIIpwd.html#GSASIIpwd.getWidthsCW">getWidthsCW() (in module GSASIIpwd)</a>
    1141988  </dt>
     
    1147994     
    1148995  <dt><a href="GSASIIutil.html#GSASIIElem.GetXsectionCoeff">GetXsectionCoeff() (in module GSASIIElem)</a>
    1149   </dt>
    1150 
    1151      
    1152   <dt><a href="GSASIImath.html#GSASIImath.GetXYZDist">GetXYZDist() (in module GSASIImath)</a>
    1153996  </dt>
    1154997
     
    13381181
    13391182     
    1340   <dt><a href="GSASIImath.html#GSASIImath.HessianLSQ">HessianLSQ() (in module GSASIImath)</a>
    1341   </dt>
    1342 
    1343      
    13441183  <dt><a href="GSASIIstruc.html#GSASIIstrMath.HessRefine">HessRefine() (in module GSASIIstrMath)</a>
    13451184  </dt>
    13461185
    1347   </dl></td>
    1348   <td style="width: 33%" valign="top"><dl>
    13491186     
    13501187  <dt><a href="GSASIIGUIr.html#GSASIIgrid.HorizontalLine">HorizontalLine() (in module GSASIIgrid)</a>
    13511188  </dt>
    13521189
     1190  </dl></td>
     1191  <td style="width: 33%" valign="top"><dl>
    13531192     
    13541193  <dt><a href="GSASIIutil.html#GSASIIspc.HStrainNames">HStrainNames() (in module GSASIIspc)</a>
     
    14251264     
    14261265  <dt><a href="GSASIIutil.html#GSASIIlattice.invpolfcal">invpolfcal() (in module GSASIIlattice)</a>
    1427   </dt>
    1428 
    1429      
    1430   <dt><a href="GSASIImath.html#GSASIImath.invQ">invQ() (in module GSASIImath)</a>
    14311266  </dt>
    14321267
     
    14961331
    14971332     
    1498   <dt><a href="GSASIImath.html#GSASIImath.makeQuat">makeQuat() (in module GSASIImath)</a>
    1499   </dt>
    1500 
    1501      
    15021333  <dt><a href="GSASIIimage.html#GSASIIimage.makeRing">makeRing() (in module GSASIIimage)</a>
    15031334  </dt>
     
    15161347
    15171348     
    1518   <dt><a href="GSASIImath.html#GSASIImath.mcsaSearch">mcsaSearch() (in module GSASIImath)</a>
    1519   </dt>
    1520 
    1521      
    15221349  <dt><a href="GSASIIindex.html#GSASIIindex.monoCellReduce">monoCellReduce() (in module GSASIIindex)</a>
    15231350  </dt>
    15241351
    1525   </dl></td>
    1526   <td style="width: 33%" valign="top"><dl>
    15271352     
    15281353  <dt><a href="GSASIIGUIr.html#GSASIIgrid.MovePatternTreeToGrid">MovePatternTreeToGrid() (in module GSASIIgrid)</a>
    15291354  </dt>
    15301355
     1356  </dl></td>
     1357  <td style="width: 33%" valign="top"><dl>
    15311358     
    15321359  <dt><a href="GSASIIutil.html#GSASIIspc.MoveToUnitCell">MoveToUnitCell() (in module GSASIIspc)</a>
     
    15831410  </dt>
    15841411
    1585      
    1586   <dt><a href="GSASIImath.html#GSASIImath.normQ">normQ() (in module GSASIImath)</a>
    1587   </dt>
    1588 
    15891412  </dl></td>
    15901413  <td style="width: 33%" valign="top"><dl>
     
    16091432     
    16101433  <dt><a href="GSASIIutil.html#GSASIIlattice.OdfChk">OdfChk() (in module GSASIIlattice)</a>
    1611   </dt>
    1612 
    1613      
    1614   <dt><a href="GSASIImath.html#GSASIImath.OmitMap">OmitMap() (in module GSASIImath)</a>
    16151434  </dt>
    16161435
     
    17861605
    17871606     
    1788   <dt><a href="GSASIImath.html#GSASIImath.PeaksEquiv">PeaksEquiv() (in module GSASIImath)</a>
    1789   </dt>
    1790 
    1791      
    1792   <dt><a href="GSASIImath.html#GSASIImath.PeaksUnique">PeaksUnique() (in module GSASIImath)</a>
    1793   </dt>
    1794 
    1795      
    17961607  <dt><a href="GSASIIstruc.html#GSASIIstrMath.penaltyDeriv">penaltyDeriv() (in module GSASIIstrMath)</a>
    17971608  </dt>
     
    18691680  </dt>
    18701681
     1682  </dl></td>
     1683  <td style="width: 33%" valign="top"><dl>
    18711684     
    18721685  <dt><a href="GSASIIplot.html#GSASIIplot.PlotSizeStrainPO">PlotSizeStrainPO() (in module GSASIIplot)</a>
    18731686  </dt>
    18741687
    1875   </dl></td>
    1876   <td style="width: 33%" valign="top"><dl>
    18771688     
    18781689  <dt><a href="GSASIIplot.html#GSASIIplot.PlotSngl">PlotSngl() (in module GSASIIplot)</a>
     
    19401751
    19411752     
    1942   <dt><a href="GSASIImath.html#GSASIImath.printRho">printRho() (in module GSASIImath)</a>
    1943   </dt>
    1944 
    1945      
    19461753  <dt><a href="GSASIIstruc.html#GSASIIstrIO.ProcessConstraints">ProcessConstraints() (in module GSASIIstrIO)</a>
    19471754  </dt>
    19481755
    19491756     
    1950   <dt><a href="GSASIImath.html#GSASIImath.prodQQ">prodQQ() (in module GSASIImath)</a>
    1951   </dt>
    1952 
    1953      
    1954   <dt><a href="GSASIImath.html#GSASIImath.prodQVQ">prodQVQ() (in module GSASIImath)</a>
    1955   </dt>
    1956 
    1957      
    19581757  <dt><a href="GSASIIGUIr.html#GSASIIIO.ProjFileOpen">ProjFileOpen() (in module GSASIIIO)</a>
    19591758  </dt>
     
    19651764     
    19661765  <dt><a href="GSASIIGUIr.html#GSASIIIO.PutG2Image">PutG2Image() (in module GSASIIIO)</a>
    1967   </dt>
    1968 
    1969   </dl></td>
    1970 </tr></table>
    1971 
    1972 <h2 id="Q">Q</h2>
    1973 <table style="width: 100%" class="indextable genindextable"><tr>
    1974   <td style="width: 33%" valign="top"><dl>
    1975      
    1976   <dt><a href="GSASIImath.html#GSASIImath.Q2AV">Q2AV() (in module GSASIImath)</a>
    1977   </dt>
    1978 
    1979      
    1980   <dt><a href="GSASIImath.html#GSASIImath.Q2AVdeg">Q2AVdeg() (in module GSASIImath)</a>
    1981   </dt>
    1982 
    1983   </dl></td>
    1984   <td style="width: 33%" valign="top"><dl>
    1985      
    1986   <dt><a href="GSASIImath.html#GSASIImath.Q2Mat">Q2Mat() (in module GSASIImath)</a>
    19871766  </dt>
    19881767
     
    20991878     
    21001879  <dt><a href="GSASIIGUIr.html#GSASIIgrid.ScrolledMultiEditor">ScrolledMultiEditor (class in GSASIIgrid)</a>
    2101   </dt>
    2102 
    2103      
    2104   <dt><a href="GSASIImath.html#GSASIImath.SearchMap">SearchMap() (in module GSASIImath)</a>
    21051880  </dt>
    21061881
     
    21481923
    21491924     
    2150   <dt><a href="GSASIImath.html#GSASIImath.SetMolCent">SetMolCent() (in module GSASIImath)</a>
    2151   </dt>
    2152 
    2153      
    21541925  <dt><a href="GSASIIGUIr.html#GSASIIIO.SetNewPhase">SetNewPhase() (in module GSASIIIO)</a>
    2155   </dt>
    2156 
    2157      
    2158   <dt><a href="GSASIImath.html#GSASIImath.setPeakparms">setPeakparms() (in module GSASIImath)</a>
    21591926  </dt>
    21601927
     
    22091976
    22101977      </dl></dd>
    2211   </dl></td>
    2212   <td style="width: 33%" valign="top"><dl>
    22131978     
    22141979  <dt><a href="GSASIIsolve.html#GSASIIsolve.ShowControls">ShowControls() (in module GSASIIsolve)</a>
     
    22211986
    22221987      </dl></dd>
     1988  </dl></td>
     1989  <td style="width: 33%" valign="top"><dl>
    22231990     
    22241991  <dt><a href="GSASIIGUIr.html#GSASIIgrid.ShowHelp">ShowHelp() (in module GSASIIgrid)</a>
     
    22632030     
    22642031  <dt><a href="GSASIIsolve.html#GSASIIsolve.Solve">Solve() (in module GSASIIsolve)</a>
    2265   </dt>
    2266 
    2267      
    2268   <dt><a href="GSASIImath.html#GSASIImath.sortArray">sortArray() (in module GSASIImath)</a>
    22692032  </dt>
    22702033
     
    24302193
    24312194     
    2432   <dt><a href="GSASIImath.html#GSASIImath.TLS2Uij">TLS2Uij() (in module GSASIImath)</a>
    2433   </dt>
    2434 
    2435      
    24362195  <dt><a href="GSASIIGUIr.html#GSASIIgrid.NumberValidator.TransferFromWindow">TransferFromWindow() (GSASIIgrid.NumberValidator method)</a>
    24372196  </dt>
     
    25132272  </dt>
    25142273
     2274  </dl></td>
     2275  <td style="width: 33%" valign="top"><dl>
    25152276     
    25162277  <dt><a href="GSASIIGUI.html#GSASIIimgGUI.UpdateMasks">UpdateMasks() (in module GSASIIimgGUI)</a>
    25172278  </dt>
    25182279
    2519   </dl></td>
    2520   <td style="width: 33%" valign="top"><dl>
    2521      
    2522   <dt><a href="GSASIImath.html#GSASIImath.UpdateMCSAxyz">UpdateMCSAxyz() (in module GSASIImath)</a>
    2523   </dt>
    2524 
    25252280     
    25262281  <dt><a href="GSASIIGUIr.html#GSASIIgrid.UpdateNotebook">UpdateNotebook() (in module GSASIIgrid)</a>
     
    25412296     
    25422297  <dt><a href="GSASIIGUIr.html#GSASIIgrid.UpdatePWHKPlot">UpdatePWHKPlot() (in module GSASIIgrid)</a>
    2543   </dt>
    2544 
    2545      
    2546   <dt><a href="GSASIImath.html#GSASIImath.UpdateRBUIJ">UpdateRBUIJ() (in module GSASIImath)</a>
    2547   </dt>
    2548 
    2549      
    2550   <dt><a href="GSASIImath.html#GSASIImath.UpdateRBXYZ">UpdateRBXYZ() (in module GSASIImath)</a>
    25512298  </dt>
    25522299
     
    25852332<table style="width: 100%" class="indextable genindextable"><tr>
    25862333  <td style="width: 33%" valign="top"><dl>
    2587      
    2588   <dt><a href="GSASIImath.html#GSASIImath.ValEsd">ValEsd() (in module GSASIImath)</a>
    2589   </dt>
    2590 
    25912334     
    25922335  <dt><a href="GSASIIGUIr.html#GSASIIgrid.ValidatedTxtCtrl">ValidatedTxtCtrl (class in GSASIIgrid)</a>
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    r939 r941  
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