Changeset 1161
- Timestamp:
- Dec 5, 2013 2:50:03 PM (9 years ago)
- Location:
- trunk
- Files:
-
- 3 edited
-
GSASIIgrid.py (modified) (2 diffs)
-
GSASIIphsGUI.py (modified) (5 diffs)
-
imports/G2phase_ISO.py (modified) (2 diffs)
Legend:
- Unmodified
- Added
- Removed
-
trunk/GSASIIgrid.py
r1160 r1161 1579 1579 num = len(varyList) 1580 1580 mainSizer.Add(wx.StaticText(self,wx.ID_ANY,'Number of refined variables: '+str(num))) 1581 num = len(fullVaryList)1582 mainSizer.Add(wx.StaticText(self,wx.ID_ANY,'Number dependent and refined variables: '+str(num)))1583 1581 if len(varyList) != len(fullVaryList): 1582 num = len(fullVaryList) - len(varyList) 1583 mainSizer.Add(wx.StaticText(self,wx.ID_ANY,' + '+str(num)+' parameters are varied via constraints')) 1584 1584 subSizer = wx.FlexGridSizer(rows=len(parmDict)+1,cols=4,hgap=2,vgap=2) 1585 1585 parmNames = parmDict.keys() … … 1624 1624 wx.StaticText(self,wx.ID_ANY, 1625 1625 '"R" indicates a refined variable\n'+ 1626 '"C" i s generated from a constraint'1626 '"C" indicates generated from a constraint' 1627 1627 ), 1628 1628 0, wx.ALL,0) -
trunk/GSASIIphsGUI.py
r1160 r1161 48 48 import GSASIIpwd as G2pwd 49 49 import GSASIIpy3 as G2py3 50 import GSASIIobj as G2obj 50 51 import numpy as np 51 52 import numpy.linalg as nl … … 1637 1638 only when Phase['ISODISTORT'] is defined. 1638 1639 ''' 1640 def _onClose(event): 1641 dlg.EndModal(wx.ID_CANCEL) 1642 def fmtHelp(item,fullname): 1643 helptext = "A new variable" 1644 if item[-3]: 1645 helptext += " named "+str(item[-3]) 1646 helptext += " is a linear combination of the following parameters:\n" 1647 first = True 1648 for term in item[:-3]: 1649 line = '' 1650 var = str(term[1]) 1651 m = term[0] 1652 if first: 1653 first = False 1654 line += ' = ' 1655 else: 1656 if m >= 0: 1657 line += ' + ' 1658 else: 1659 line += ' - ' 1660 m = abs(m) 1661 line += '%.3f*%s '%(m,var) 1662 varMean = G2obj.fmtVarDescr(var) 1663 helptext += "\n" + line + " ("+ varMean + ")" 1664 helptext += '\n\nISODISTORT full name: '+str(fullname) 1665 return helptext 1666 1639 1667 if 'ISODISTORT' not in data: 1640 1668 raise Exception,"Should not happen: 'ISODISTORT' not in data" … … 1645 1673 ) 1646 1674 return 1647 def _onClose(event):1648 dlg.EndModal(wx.ID_CANCEL)1649 1650 1675 Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() # init for constraint 1676 # make a lookup table for constraints 1677 sub = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Constraints') 1678 Constraints = G2frame.PatternTree.GetItemPyData(sub) 1679 constDict = {} 1680 for item in Constraints: 1681 if item.startswith('_'): continue 1682 for c in Constraints[item]: 1683 if c[-1] != 'f' or not c[-3]: continue 1684 constDict[c[-3]] = c 1685 1651 1686 ISO = data['ISODISTORT'] 1652 1687 parmDict,varyList = G2frame.MakeLSParmDict() 1653 deltaList = [] 1654 for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']): 1655 dvar = gv.varname() 1656 var = dvar.replace('::dA','::A') 1657 albl = Ilbl[:Ilbl.rfind('_')] 1658 v = Ilbl[Ilbl.rfind('_')+1:] 1659 pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)] 1660 if var in parmDict: 1661 cval = parmDict[var][0] 1662 else: 1663 G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var)) 1664 return 1665 deltaList.append(cval-pval) 1666 modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList) 1688 1667 1689 dlg = wx.Dialog(G2frame,wx.ID_ANY,'ISODISTORT mode values',#size=(630,400), 1668 1690 style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) … … 1679 1701 dlg, wx.ID_ANY,#size=(100,200), 1680 1702 style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER) 1681 subSizer2 = wx.FlexGridSizer(rows=1,cols=2,hgap=5,vgap=2) 1682 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'Parameter name')) 1683 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'value '),0,wx.ALIGN_RIGHT) 1684 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,' Mode name ')) 1685 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'value '),0,wx.ALIGN_RIGHT) 1703 subSizer2 = wx.FlexGridSizer(rows=1,cols=3,hgap=5,vgap=2) 1704 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'Parameter name ')) 1705 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT) 1706 subSizer2.Add((-1,-1)) 1707 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'Mode name ')) 1708 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT) 1686 1709 1687 for lbl,xyz,var,val in zip(ISO['IsoVarList'],deltaList,ISO['IsoModeList'],modeVals): 1688 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl))) 1689 try: 1690 value = G2py3.FormatValue(xyz) 1691 except TypeError: 1692 value = str(xyz) 1693 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) 1694 #subSizer.Add((10,-1)) 1695 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var))) 1696 try: 1697 value = G2py3.FormatValue(val) 1698 except TypeError: 1699 value = str(val) 1700 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) 1710 if 'G2VarList' in ISO: 1711 deltaList = [] 1712 for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']): 1713 dvar = gv.varname() 1714 var = dvar.replace('::dA','::A') 1715 albl = Ilbl[:Ilbl.rfind('_')] 1716 v = Ilbl[Ilbl.rfind('_')+1:] 1717 pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)] 1718 if var in parmDict: 1719 cval = parmDict[var][0] 1720 else: 1721 dlg.EndModal(wx.ID_CANCEL) 1722 G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var)) 1723 return 1724 deltaList.append(cval-pval) 1725 modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList) 1726 for lbl,xyz,var,val,G2var in zip(ISO['IsoVarList'],deltaList, 1727 ISO['IsoModeList'],modeVals,ISO['G2ModeList']): 1728 if G2var in constDict: 1729 ch = G2gd.HelpButton(panel2,fmtHelp(constDict[G2var],var)) 1730 subSizer2.Add(ch,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER,1) 1731 else: 1732 subSizer2.Add((-1,-1)) 1733 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl))) 1734 try: 1735 value = G2py3.FormatValue(xyz) 1736 except TypeError: 1737 value = str(xyz) 1738 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) 1739 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var))) 1740 try: 1741 value = G2py3.FormatValue(val) 1742 except TypeError: 1743 value = str(val) 1744 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) 1745 if 'G2OccVarList' in ISO: 1746 deltaList = [] 1747 for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']): 1748 var = gv.varname() 1749 albl = Ilbl[:Ilbl.rfind('_')] 1750 #v = Ilbl[Ilbl.rfind('_')+1:] 1751 pval = ISO['BaseOcc'][albl] 1752 if var in parmDict: 1753 cval = parmDict[var][0] 1754 else: 1755 dlg.EndModal(wx.ID_CANCEL) 1756 G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var)) 1757 return 1758 deltaList.append(cval-pval) 1759 modeVals = np.inner(ISO['Var2OccMatrix'],deltaList) 1760 for lbl,xyz,var,val,G2var in zip(ISO['OccVarList'],deltaList, 1761 ISO['OccModeList'],modeVals,ISO['G2OccModeList']): 1762 if G2var in constDict: 1763 ch = G2gd.HelpButton(panel2,fmtHelp(constDict[G2var],var)) 1764 subSizer2.Add(ch,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER,1) 1765 else: 1766 subSizer2.Add((-1,-1)) 1767 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl))) 1768 try: 1769 value = G2py3.FormatValue(xyz) 1770 except TypeError: 1771 value = str(xyz) 1772 subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) 1773 #subSizer.Add((10,-1)) 1774 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var))) 1775 try: 1776 value = G2py3.FormatValue(val) 1777 except TypeError: 1778 value = str(val) 1779 subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) 1780 1701 1781 # finish up ScrolledPanel 1702 1782 panel1.SetSizer(subSizer1) … … 1727 1807 dlg.ShowModal() 1728 1808 dlg.Destroy() 1729 1730 1809 1731 1810 def OnReImport(event): -
trunk/imports/G2phase_ISO.py
r1160 r1161 19 19 20 20 class ISODISTORTPhaseReader(G2IO.ImportPhase): 21 varLookup = {'dx':'dAx','dy':'dAy','dz':'dAz' }21 varLookup = {'dx':'dAx','dy':'dAy','dz':'dAz','do':'Afrac'} 22 22 def __init__(self): 23 23 super(self.__class__,self).__init__( # fancy way to say ImportPhase.__init__ … … 199 199 self.Phase['General']['Name'] = name.strip()[:20] 200 200 #---------------------------------------------------------------------- 201 # now read in the ISODISTORT modes201 # now read in the ISODISTORT displacement modes 202 202 #---------------------------------------------------------------------- 203 modelist = []204 shortmodelist = []205 for lbl in blk.get('_iso_displacivemode_label'):206 modelist.append(lbl)207 # assume lbl is of form SSSSS[x,y,z]AAAA(a,b,...)BBBBB208 # where SSSSS is the parent spacegroup, [x,y,z] is a location209 regexp = re.match(r'.*?\[.*?\](.*?)\(.*?\)(.*)',lbl)210 # this extracts the AAAAA and BBBBB parts of the string211 if regexp:212 lbl = regexp.expand(r'\1\2') # parse succeeded, make a short version213 G2obj.MakeUniqueLabel(lbl,shortmodelist) # make unique and add to list214 215 # read in the coordinate offset variables names and map them to G2 names/objects216 coordVarLbl = []217 G2varLbl = []218 G2varObj = []219 error = False220 for lbl in blk.get('_iso_deltacoordinate_label'):221 coordVarLbl.append(lbl)222 if '_' in lbl:223 albl = lbl[:lbl.rfind('_')]224 vlbl = lbl[lbl.rfind('_')+1:]225 else:226 self.warnings += ' ERROR: _iso_deltacoordinate_label not parsed: '+lbl227 error = True228 continue229 if albl not in atomlbllist:230 self.warnings += ' ERROR: _iso_deltacoordinate_label atom not found: '+lbl231 error = True232 continue233 else:234 anum = atomlbllist.index(albl)235 var = self.varLookup.get(vlbl)236 if not var:237 self.warnings += ' ERROR: _iso_deltacoordinate_label variable not found: '+lbl238 error = True239 continue240 G2varLbl.append('::'+var+':'+str(anum)) # variable name, less phase ID241 G2varObj.append(G2obj.G2VarObj(242 (self.Phase['ranId'],None,var,ranIdlookup[albl])243 ))244 if error:245 raise Exception,"Error decoding variable labels"246 247 if len(G2varObj) != len(modelist):248 print "non-square input"249 raise Exception,"Rank of _iso_displacivemode != _iso_deltacoordinate"250 251 error = False252 ParentCoordinates = {}253 for lbl,exp in zip(254 blk.get('_iso_coordinate_label'),255 blk.get('_iso_coordinate_formula'),256 ):257 if '_' in lbl:258 albl = lbl[:lbl.rfind('_')]259 vlbl = lbl[lbl.rfind('_')+1:]260 else:261 self.warnings += ' ERROR: _iso_coordinate_label not parsed: '+lbl262 error = True263 continue264 if vlbl not in 'xyz' or len(vlbl) != 1:265 self.warnings += ' ERROR: _iso_coordinate_label coordinate not parsed: '+lbl266 error = True267 continue268 i = 'xyz'.index(vlbl)269 if not ParentCoordinates.get(albl):270 ParentCoordinates[albl] = [None,None,None]271 if '+' in exp:272 val = exp.split('+')[0].strip()273 else:274 self.warnings += ' ERROR: _iso_coordinate_formula not parsed: '+lbl275 error = True276 continue277 val = G2p3.FormulaEval(val)278 if val is None:279 self.warnings += ' ERROR: _iso_coordinate_formula coordinate not interpreted: '+lbl280 error = True281 continue282 ParentCoordinates[albl][i] = val283 if error:284 raise Exception,"Error decoding variable labels"285 # get mapping of modes to atomic coordinate displacements286 displacivemodematrix = np.zeros((len(G2varObj),len(G2varObj)))287 for row,col,val in zip(288 blk.get('_iso_displacivemodematrix_row'),289 blk.get('_iso_displacivemodematrix_col'),290 blk.get('_iso_displacivemodematrix_value'),):291 displacivemodematrix[int(row)-1,int(col)-1] = float(val)292 # Invert to get mapping of atom displacements to modes293 displacivemodeInvmatrix = np.linalg.inv(displacivemodematrix)294 # create the constraints295 203 self.Constraints = [] 296 for i,row in enumerate(displacivemodeInvmatrix):297 constraint = []298 for j,(lbl,k) in enumerate(zip(coordVarLbl,row)):299 if k == 0: continue300 constraint.append([k,G2varObj[j]])301 constraint += [shortmodelist[i],False,'f']302 self.Constraints.append(constraint)303 # save the ISODISTORT info for "mode analysis"304 self.Phase['ISODISTORT'] = {305 'IsoModeList' : modelist,306 'G2ModeList' : shortmodelist,307 'IsoVarList' : coordVarLbl,308 'G2VarList' : G2varObj,309 'ParentStructure' : ParentCoordinates,310 'Var2ModeMatrix' : displacivemodeInvmatrix,311 'Mode2VarMatrix' : displacivemodematrix,312 }313 # make explaination dictionary314 204 explaination = {} 315 for mode,shortmode in zip(modelist,shortmodelist): 316 explaination[shortmode] = "ISODISTORT full name "+str(mode) 317 self.Constraints.append(explaination) 205 if blk.get('_iso_displacivemode_label'): 206 modelist = [] 207 shortmodelist = [] 208 for lbl in blk.get('_iso_displacivemode_label'): 209 modelist.append(lbl) 210 # assume lbl is of form SSSSS[x,y,z]AAAA(a,b,...)BBBBB 211 # where SSSSS is the parent spacegroup, [x,y,z] is a location 212 regexp = re.match(r'.*?\[.*?\](.*?)\(.*?\)(.*)',lbl) 213 # this extracts the AAAAA and BBBBB parts of the string 214 if regexp: 215 lbl = regexp.expand(r'\1\2') # parse succeeded, make a short version 216 G2obj.MakeUniqueLabel(lbl,shortmodelist) # make unique and add to list 217 # read in the coordinate offset variables names and map them to G2 names/objects 218 coordVarLbl = [] 219 G2varLbl = [] 220 G2varObj = [] 221 error = False 222 for lbl in blk.get('_iso_deltacoordinate_label'): 223 coordVarLbl.append(lbl) 224 if '_' in lbl: 225 albl = lbl[:lbl.rfind('_')] 226 vlbl = lbl[lbl.rfind('_')+1:] 227 else: 228 self.warnings += ' ERROR: _iso_deltacoordinate_label not parsed: '+lbl 229 error = True 230 continue 231 if albl not in atomlbllist: 232 self.warnings += ' ERROR: _iso_deltacoordinate_label atom not found: '+lbl 233 error = True 234 continue 235 else: 236 anum = atomlbllist.index(albl) 237 var = self.varLookup.get(vlbl) 238 if not var: 239 self.warnings += ' ERROR: _iso_deltacoordinate_label variable not found: '+lbl 240 error = True 241 continue 242 G2varLbl.append('::'+var+':'+str(anum)) # variable name, less phase ID 243 G2varObj.append(G2obj.G2VarObj( 244 (self.Phase['ranId'],None,var,ranIdlookup[albl]) 245 )) 246 if error: 247 raise Exception,"Error decoding variable labels" 248 249 if len(G2varObj) != len(modelist): 250 print "non-square input" 251 raise Exception,"Rank of _iso_displacivemode != _iso_deltacoordinate" 252 253 error = False 254 ParentCoordinates = {} 255 for lbl,exp in zip( 256 blk.get('_iso_coordinate_label'), 257 blk.get('_iso_coordinate_formula'), 258 ): 259 if '_' in lbl: 260 albl = lbl[:lbl.rfind('_')] 261 vlbl = lbl[lbl.rfind('_')+1:] 262 else: 263 self.warnings += ' ERROR: _iso_coordinate_label not parsed: '+lbl 264 error = True 265 continue 266 if vlbl not in 'xyz' or len(vlbl) != 1: 267 self.warnings += ' ERROR: _iso_coordinate_label coordinate not parsed: '+lbl 268 error = True 269 continue 270 i = 'xyz'.index(vlbl) 271 if not ParentCoordinates.get(albl): 272 ParentCoordinates[albl] = [None,None,None] 273 if '+' in exp: 274 val = exp.split('+')[0].strip() 275 val = G2p3.FormulaEval(val) 276 if val is None: 277 self.warnings += ' ERROR: _iso_coordinate_formula coordinate not interpreted: '+lbl 278 error = True 279 continue 280 ParentCoordinates[albl][i] = val 281 if error: 282 print self.warnings 283 raise Exception,"Error decoding variable labels" 284 # get mapping of modes to atomic coordinate displacements 285 displacivemodematrix = np.zeros((len(G2varObj),len(G2varObj))) 286 for row,col,val in zip( 287 blk.get('_iso_displacivemodematrix_row'), 288 blk.get('_iso_displacivemodematrix_col'), 289 blk.get('_iso_displacivemodematrix_value'),): 290 displacivemodematrix[int(row)-1,int(col)-1] = float(val) 291 # Invert to get mapping of atom displacements to modes 292 displacivemodeInvmatrix = np.linalg.inv(displacivemodematrix) 293 # create the constraints 294 for i,row in enumerate(displacivemodeInvmatrix): 295 constraint = [] 296 for j,(lbl,k) in enumerate(zip(coordVarLbl,row)): 297 if k == 0: continue 298 constraint.append([k,G2varObj[j]]) 299 constraint += [shortmodelist[i],False,'f'] 300 self.Constraints.append(constraint) 301 #---------------------------------------------------------------------- 302 # save the ISODISTORT info for "mode analysis" 303 if 'ISODISTORT' not in self.Phase: self.Phase['ISODISTORT'] = {} 304 self.Phase['ISODISTORT'].update({ 305 'IsoModeList' : modelist, 306 'G2ModeList' : shortmodelist, 307 'IsoVarList' : coordVarLbl, 308 'G2VarList' : G2varObj, 309 'ParentStructure' : ParentCoordinates, 310 'Var2ModeMatrix' : displacivemodeInvmatrix, 311 'Mode2VarMatrix' : displacivemodematrix, 312 }) 313 # make explaination dictionary 314 for mode,shortmode in zip(modelist,shortmodelist): 315 explaination[shortmode] = "ISODISTORT full name "+str(mode) 316 #---------------------------------------------------------------------- 317 # now read in the ISODISTORT occupancy modes 318 #---------------------------------------------------------------------- 319 if blk.get('_iso_occupancymode_label'): 320 modelist = [] 321 shortmodelist = [] 322 for lbl in blk.get('_iso_occupancymode_label'): 323 modelist.append(lbl) 324 # assume lbl is of form SSSSS[x,y,z]AAAA(a,b,...)BBBBB 325 # where SSSSS is the parent spacegroup, [x,y,z] is a location 326 regexp = re.match(r'.*?\[.*?\](.*?)\(.*?\)(.*)',lbl) 327 # this extracts the AAAAA and BBBBB parts of the string 328 if regexp: 329 lbl = regexp.expand(r'\1\2') # parse succeeded, make a short version 330 lbl = lbl.replace('order','o') 331 G2obj.MakeUniqueLabel(lbl,shortmodelist) # make unique and add to list 332 # read in the coordinate offset variables names and map them to G2 names/objects 333 occVarLbl = [] 334 G2varLbl = [] 335 G2varObj = [] 336 error = False 337 for lbl in blk.get('_iso_deltaoccupancy_label'): 338 occVarLbl.append(lbl) 339 if '_' in lbl: 340 albl = lbl[:lbl.rfind('_')] 341 vlbl = lbl[lbl.rfind('_')+1:] 342 else: 343 self.warnings += ' ERROR: _iso_deltaoccupancy_label not parsed: '+lbl 344 error = True 345 continue 346 if albl not in atomlbllist: 347 self.warnings += ' ERROR: _iso_deltaoccupancy_label atom not found: '+lbl 348 error = True 349 continue 350 else: 351 anum = atomlbllist.index(albl) 352 var = self.varLookup.get(vlbl) 353 if not var: 354 self.warnings += ' ERROR: _iso_deltaoccupancy_label variable not found: '+lbl 355 error = True 356 continue 357 G2varLbl.append('::'+var+':'+str(anum)) # variable name, less phase ID 358 G2varObj.append(G2obj.G2VarObj( 359 (self.Phase['ranId'],None,var,ranIdlookup[albl]) 360 )) 361 if error: 362 raise Exception,"Error decoding variable labels" 363 364 if len(G2varObj) != len(modelist): 365 print "non-square input" 366 raise Exception,"Rank of _iso_occupancymode != _iso_deltaoccupancy" 367 368 error = False 369 ParentCoordinates = {} 370 for lbl,exp in zip( 371 blk.get('_iso_occupancy_label'), 372 blk.get('_iso_occupancy_formula'), 373 ): 374 if '_' in lbl: 375 albl = lbl[:lbl.rfind('_')] 376 vlbl = lbl[lbl.rfind('_')+1:] 377 else: 378 self.warnings += ' ERROR: _iso_occupancy_label not parsed: '+lbl 379 error = True 380 continue 381 if vlbl != 'occ': 382 self.warnings += ' ERROR: _iso_occupancy_label coordinate not parsed: '+lbl 383 error = True 384 continue 385 if '+' in exp: 386 val = exp.split('+')[0].strip() 387 val = G2p3.FormulaEval(val) 388 if val is None: 389 self.warnings += ' ERROR: _iso_occupancy_formula coordinate not interpreted: '+lbl 390 error = True 391 continue 392 ParentCoordinates[albl] = val 393 if error: 394 raise Exception,"Error decoding occupancy labels" 395 # get mapping of modes to atomic coordinate displacements 396 occupancymodematrix = np.zeros((len(G2varObj),len(G2varObj))) 397 for row,col,val in zip( 398 blk.get('_iso_occupancymodematrix_row'), 399 blk.get('_iso_occupancymodematrix_col'), 400 blk.get('_iso_occupancymodematrix_value'),): 401 occupancymodematrix[int(row)-1,int(col)-1] = float(val) 402 # Invert to get mapping of atom displacements to modes 403 occupancymodeInvmatrix = np.linalg.inv(occupancymodematrix) 404 # create the constraints 405 for i,row in enumerate(occupancymodeInvmatrix): 406 constraint = [] 407 for j,(lbl,k) in enumerate(zip(occVarLbl,row)): 408 if k == 0: continue 409 constraint.append([k,G2varObj[j]]) 410 constraint += [shortmodelist[i],False,'f'] 411 self.Constraints.append(constraint) 412 #---------------------------------------------------------------------- 413 # save the ISODISTORT info for "mode analysis" 414 if 'ISODISTORT' not in self.Phase: self.Phase['ISODISTORT'] = {} 415 self.Phase['ISODISTORT'].update({ 416 'OccModeList' : modelist, 417 'G2OccModeList' : shortmodelist, 418 'OccVarList' : occVarLbl, 419 'G2OccVarList' : G2varObj, 420 'BaseOcc' : ParentCoordinates, 421 'Var2OccMatrix' : occupancymodeInvmatrix, 422 'Occ2VarMatrix' : occupancymodematrix, 423 }) 424 # make explaination dictionary 425 for mode,shortmode in zip(modelist,shortmodelist): 426 explaination[shortmode] = "ISODISTORT full name "+str(mode) 427 #---------------------------------------------------------------------- 428 # done with read 429 #---------------------------------------------------------------------- 430 if explaination: self.Constraints.append(explaination) 318 431 319 432 # # debug: show the mode var to mode relations
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