- Timestamp:
- Dec 26, 2020 12:25:59 AM (2 years ago)
- Location:
- trunk
- Files:
-
- 4 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/GSASIIdataGUI.py
r4680 r4682 5176 5176 text = 'Detailed results are in ' + lst + '.lst\n' 5177 5177 if 'GOF0' in Rvals and 'GOF' in Rvals: 5178 text += '\n Reduced Chi^2 before refinement={:.3f} and after={:.3f}\n'.format(5179 Rvals['GOF 0']**2,Rvals['GOF']**2)5178 text += '\nFinal Reduced Chi^2: {:.3f} (before ref: {:.3f})\n'.format( 5179 Rvals['GOF']**2,Rvals['GOF0']**2) 5180 5180 if 'Max shft/sig' in Rvals: 5181 5181 text += '\nMax shift/sigma={:.3f}\n'.format(Rvals['Max shft/sig']) … … 5187 5187 ' You should reconsider which parameters you refine' 5188 5188 dlg2 = wx.MessageDialog(self,text,'Refinement results, Rw =%.3f'%(Rw),wx.OK|wx.CANCEL) 5189 dlg2.CenterOnParent() 5189 5190 try: 5190 5191 if dlg2.ShowModal() == wx.ID_OK: … … 5195 5196 finally: 5196 5197 dlg2.Destroy() 5197 elif ' SingVars' in Rvals:5198 elif 'psing' in Rvals: 5198 5199 if 'msg' in Rvals: 5199 5200 msg = 'Refinement results:\n\n' … … 5202 5203 else: 5203 5204 msg = '' 5204 if len(Rvals['SingVars']) == 1:5205 h = 'This variable appears'5206 # that = 'that variable'5207 else:5208 h = 'These variables appear'5209 # that = 'those variables'5210 msg += h + ' to cause a singular matrix:\n\t'5211 for i,var in enumerate(Rvals['SingVars']):5212 if i: msg += ', '5213 msg += var5214 # msg += '\n\nRefine again with '+that+' frozen?'5205 # if len(Rvals['psing']) == 1: 5206 # h = 'This variable appears' 5207 # # that = 'that variable' 5208 # else: 5209 # h = 'These variables appear' 5210 # # that = 'those variables' 5211 # msg += h + ' to cause a singular matrix:\n\t' 5212 # for i,var in enumerate(Rvals['psing']): 5213 # if i: msg += ', ' 5214 # msg += varyList[var] 5215 # # msg += '\n\nRefine again with '+that+' frozen?' 5215 5216 result = wx.ID_NO 5216 5217 try: … … 5219 5220 dlg = wx.MessageDialog(self, msg,'Note singularities', 5220 5221 wx.OK) 5222 dlg.CenterOnParent() 5221 5223 dlg.SetSize((700,300)) # does not resize on Mac 5222 5224 result = dlg.ShowModal() … … 5230 5232 # Controls['parmFrozen']['FrozenList'] = [] 5231 5233 # Controls['parmFrozen']['FrozenList'] += [ 5232 # G2obj.G2VarObj( i) for i in Rvals['SingVars']]5234 # G2obj.G2VarObj(varyList[i]) for i in Rvals['plist']] 5233 5235 # wx.CallAfter(self.OnRefine,event) 5234 5236 else: … … 5384 5386 text += '\nLoad new result?' 5385 5387 dlg = wx.MessageDialog(self,text,'Refinement results',wx.OK|wx.CANCEL) 5388 dlg.CenterOnParent() 5386 5389 try: 5387 5390 if dlg.ShowModal() == wx.ID_OK: -
trunk/GSASIIstrMain.py
r4666 r4682 48 48 DEBUG = True 49 49 50 def ReportProblems(result,Rvals,varyList): 51 '''Create a message based results from the refinement 52 ''' 53 #report on SVD 0's and highly correlated variables 54 msg = '' 55 SVD0 = result[2].get('SVD0') 56 if SVD0 > 0: 57 msg += 'Warning: There were {} singularities in the Hessian'.format(SVD0) 58 # process singular variables 59 psing = result[2].get('psing',[]) 60 if psing: 61 if msg: msg += '\n' 62 msg += 'Parameters dropped due to singularities:' 63 for i,val in enumerate(psing): 64 if i == 0: 65 msg += '\n\t{}'.format(varyList[val]) 66 else: 67 msg += ', {}'.format(varyList[val]) 68 #report on highly correlated variables 69 Hcorr = result[2].get('Hcorr',[]) 70 for i,(v1,v2,corr) in enumerate(Hcorr): 71 if msg: msg += '\n' 72 if i == 0: 73 msg += 'Note highly correlated parameters:\n' 74 if corr > .95: 75 stars = '**' 76 else: 77 stars = ' ' 78 msg += ' {} {} and {} (@{:.2f}%)'.format( 79 stars,varyList[v1],varyList[v2],100.*corr) 80 if msg: 81 if 'msg' not in Rvals: Rvals['msg'] = '' 82 Rvals['msg'] += msg 83 50 84 def RefineCore(Controls,Histograms,Phases,restraintDict,rigidbodyDict,parmDict,varyList, 51 85 calcControls,pawleyLookup,ifSeq,printFile,dlg,refPlotUpdate=None): … … 60 94 # print 'current',varyList 61 95 # for item in parmDict: print item,parmDict[item] ######### show dict just before refinement 62 G2mv.Map2Dict(parmDict,varyList)63 96 ifPrint = True 64 97 if ifSeq: … … 67 100 chisq0 = None 68 101 while True: 102 G2mv.Map2Dict(parmDict,varyList) 69 103 begin = time.time() 70 104 values = np.array(G2stMth.Dict2Values(parmDict, varyList)) … … 95 129 ncyc = result[2]['num cyc']+1 96 130 Rvals['lamMax'] = result[2]['lamMax'] 131 if 'msg' in result[2]: 132 Rvals['msg'] = result[2]['msg'] 97 133 Controls['Marquardt'] = -3 #reset to default 98 134 if 'chisq0' in result[2] and chisq0 is None: … … 164 200 # table = dict(zip(varyList,zip(values,result[0],(result[0]-values)/sig))) 165 201 # for item in table: print item,table[item] #useful debug - are things shifting? 202 # report on refinement issues. Result in Rvals['msg'] 203 ReportProblems(result,Rvals,varyList) 166 204 break #refinement succeeded - finish up! 167 except TypeError: #result[1] is None on singular matrix or LinAlgError 205 except TypeError: 206 # if we get here, no result[1] (covar matrix) was returned or other calc error: refinement failed 168 207 IfOK = False 169 208 if not len(varyList): 170 209 covMatrix = [] 171 210 break 172 G2fil.G2Print ('**** Refinement failed - singular matrix ****',mode='error')173 211 if 'Hessian' in Controls['deriv type']: 212 SVD0 = result[2].get('SVD0') 213 if SVD0 == -1: 214 G2fil.G2Print ('**** Refinement failed - singular matrix ****',mode='error') 215 elif SVD0 == -2: 216 G2fil.G2Print ('**** Refinement failed - other problem ****',mode='error') 217 elif SVD0 > 0: 218 G2fil.G2Print ('**** Refinement failed with {} SVD singularities ****'.format(SVD0),mode='error') 219 else: 220 G2fil.G2Print ('**** Refinement failed ****',mode='error') 174 221 if result[1] is None: 175 222 IfOK = False 176 223 covMatrix = [] 177 224 sig = len(varyList)*[None,] 178 break 179 num = len(varyList)-1 180 for i,val in enumerate(np.flipud(result[2]['psing'])): 181 if val: 182 G2fil.G2Print ('Removing parameter: '+varyList[num-i]) 183 del(varyList[num-i]) 225 # report on highly correlated variables 226 ReportProblems(result,Rvals,varyList) 227 # process singular variables 228 psing = result[2].get('psing',[]) 229 if dlg: break # refining interactively 230 # non-interactive refinement 231 for val in sorted(psing,reverse=True): 232 G2fil.G2Print ('Removing parameter: '+varyList[val]) 233 del(varyList[val]) 234 if not psing: break # removed variable(s), try again 184 235 else: 236 G2fil.G2Print ('**** Refinement failed - singular matrix ****',mode='error') 185 237 Ipvt = result[2]['ipvt'] 186 238 for i,ipvt in enumerate(Ipvt): … … 196 248 197 249 def Refine(GPXfile,dlg=None,makeBack=True,refPlotUpdate=None): 198 'Global refinement -- refines to minimize against all histograms' 250 '''Global refinement -- refines to minimize against all histograms. 251 This can be called in one of three ways, from :meth:`GSASIIdataGUI.GSASII.OnRefine` in an 252 interactive refinement, where dlg will be a wx.ProgressDialog, or non-interactively from 253 :meth:`GSASIIscriptable.G2Project.refine` or from :func:`main`, where dlg will be None. 254 ''' 199 255 import GSASIImpsubs as G2mp 200 256 G2mp.InitMP() … … 217 273 G2fil.G2Print (' *** ERROR - you have no phases to refine! ***') 218 274 G2fil.G2Print (' *** Refine aborted ***') 219 return False, 'No phases'275 return False,{'msg':'No phases'} 220 276 if not Histograms: 221 277 G2fil.G2Print (' *** ERROR - you have no data to refine with! ***') 222 278 G2fil.G2Print (' *** Refine aborted ***') 223 return False, 'No data'279 return False,{'msg':'No data'} 224 280 rigidbodyDict = G2stIO.GetRigidBodies(GPXfile) 225 281 rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) … … 250 306 msg = G2mv.EvaluateMultipliers(constrDict,parmDict) 251 307 if msg: 252 return False, 'Unable to interpret multiplier(s): '+msg308 return False,{'msg':'Unable to interpret multiplier(s): '+msg} 253 309 try: 254 310 G2mv.GenerateConstraints(varyList,constrDict,fixedList,parmDict) … … 261 317 #print 'Errors',errmsg 262 318 #if warnmsg: print 'Warnings',warnmsg 263 return False, ' Constraint error'319 return False,{'msg':' Constraint error'} 264 320 # print G2mv.VarRemapShow(varyList) 265 321 … … 280 336 printFile.write('\n Refinement results:\n') 281 337 printFile.write(135*'-'+'\n') 338 Rvals = {} 282 339 try: 283 340 covData = {} … … 305 362 G2stIO.SetHistogramData(parmDict,sigDict,Histograms,calcControls,pFile=printFile) 306 363 if len(frozen): 364 if 'msg' in Rvals: 365 Rvals['msg'] += '\n' 366 else: 367 Rvals['msg'] = '' 307 368 msg = ('Warning: {} variable(s) refined outside limits and were frozen ({} total frozen)' 308 369 .format(len(frozen),len(parmFrozenList)) 309 370 ) 310 371 G2fil.G2Print(msg) 311 Rvals['msg'] = msg372 Rvals['msg'] += msg 312 373 elif len(parmFrozenList): 374 if 'msg' in Rvals: 375 Rvals['msg'] += '\n' 376 else: 377 Rvals['msg'] = '' 313 378 msg = ('Note: a total of {} variable(s) are frozen due to refining outside limits' 314 379 .format(len(parmFrozenList)) 315 380 ) 316 381 G2fil.G2Print('Note: ',msg) 317 Rvals['msg'] = msg382 Rvals['msg'] += msg 318 383 G2stIO.SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,rigidbodyDict,covData,parmFrozenList,makeBack) 319 384 printFile.close() … … 321 386 G2fil.G2Print (' ***** Refinement successful *****') 322 387 else: 323 G2fil.G2Print ('****ERROR - Refinement failed') 324 raise G2obj.G2Exception('****ERROR - Refinement failed') 388 G2fil.G2Print ('****ERROR - Refinement failed',mode='error') 389 if 'msg' in Rvals: 390 G2fil.G2Print ('Note refinement problem:',mode='warn') 391 G2fil.G2Print (Rvals['msg'],mode='warn') 392 raise G2obj.G2Exception('**** ERROR: Refinement failed ****') 325 393 except G2obj.G2RefineCancel as Msg: 326 394 printFile.close() 327 395 G2fil.G2Print (' ***** Refinement stopped *****') 328 return False,Msg.msg 329 except G2obj.G2Exception as Msg: # cell metric error, others? 396 if not hasattr(Msg,'msg'): Msg.msg = str(Msg) 397 if 'msg' in Rvals: 398 Rvals['msg'] += '\n' 399 Rvals['msg'] += Msg.msg 400 if not dlg: 401 G2fil.G2Print ('Note refinement problem:',mode='warn') 402 G2fil.G2Print (Rvals['msg'],mode='warn') 403 else: 404 Rvals['msg'] = Msg.msg 405 return False,Rvals 406 # except G2obj.G2Exception as Msg: # cell metric error, others? 407 except Exception as Msg: # cell metric error, others? 408 if GSASIIpath.GetConfigValue('debug'): 409 import traceback 410 print(traceback.format_exc()) 411 if not hasattr(Msg,'msg'): Msg.msg = str(Msg) 330 412 printFile.close() 331 413 G2fil.G2Print (' ***** Refinement error *****') 332 return False,Msg.msg 414 if 'msg' in Rvals: 415 Rvals['msg'] += '\n\n' 416 Rvals['msg'] += Msg.msg 417 if not dlg: 418 G2fil.G2Print ('Note refinement problem:',mode='warn') 419 G2fil.G2Print (Rvals['msg'],mode='warn') 420 else: 421 Rvals['msg'] = Msg.msg 422 return False,Rvals 333 423 334 424 #for testing purposes, create a file for testderiv … … 346 436 if dlg: 347 437 return True,Rvals 438 elif 'msg' in Rvals: 439 G2fil.G2Print ('Reported from refinement:',mode='warn') 440 G2fil.G2Print (Rvals['msg'],mode='warn') 348 441 349 442 def phaseCheck(phaseVary,Phases,histogram): … … 642 735 643 736 except G2obj.G2RefineCancel as Msg: 737 if not hasattr(Msg,'msg'): Msg.msg = str(Msg) 644 738 printFile.close() 645 739 G2fil.G2Print (' ***** Refinement stopped *****') 646 740 return False,Msg.msg 647 741 except G2obj.G2Exception as Msg: # cell metric error, others? 742 if not hasattr(Msg,'msg'): Msg.msg = str(Msg) 648 743 printFile.close() 649 744 G2fil.G2Print (' ***** Refinement error *****') … … 657 752 G2stIO.SetSeqResult(GPXfile,Histograms,SeqResult) 658 753 except Exception as msg: 659 print('Error reading Sequential results ')754 print('Error reading Sequential results\n',str(msg)) 660 755 if GSASIIpath.GetConfigValue('debug'): 661 756 import traceback -
trunk/GSASIIstrMath.py
r4672 r4682 3229 3229 #?? 3230 3230 Dij = GetDij(phfx,SGData,parmDict) 3231 A = [parmDict[pfx+'A%d'%(i)]+Dij[i] for i in range(6)] #TODO: need to do somet ing if Dij << 0.3231 A = [parmDict[pfx+'A%d'%(i)]+Dij[i] for i in range(6)] #TODO: need to do something if Dij << 0. 3232 3232 G,g = G2lat.A2Gmat(A) #recip & real metric tensors 3233 if np.any(np.diag(G)<0.) or np.any(np.isnan(A)): 3234 #G2obj.HowDidIgetHere() 3235 raise G2obj.G2Exception('Error in metric tensor refinement\nCheck for refinement of conflicting variables') 3236 GA,GB = G2lat.Gmat2AB(G) #Orthogonalization matricies 3233 if np.any(np.diag(G)<0.): 3234 msg = 'Invalid metric tensor for phase #{}\n ({})'.format( 3235 pId,Phase['General']['Name']) 3236 elif np.any(np.isnan(A)): 3237 msg = 'Infinite metric tensor for phase #{}\n ({})'.format( 3238 pId,Phase['General']['Name']) 3239 else: 3240 msg = None 3241 if msg: 3242 print('\nInvalid cell metric tensor for phase #{} ({})\n'.format( 3243 pId,Phase['General']['Name']), 3244 'values (A): {:.3f} {:.3f} {:.3f} {:.3f} {:.3f} {:.3f}\n' 3245 .format(*A)) 3246 raise G2obj.G2Exception('Error: '+msg+ 3247 ' See console.\nCheck for refinement of conflicting variables') 3248 GA,GB = G2lat.Gmat2AB(G) #Orthogonalization matrices 3237 3249 Vst = np.sqrt(nl.det(G)) #V* 3238 3250 if not Phase['General'].get('doPawley') and not parmDict[phfx+'LeBail']: -
trunk/help/gsasII.html
r4668 r4682 3179 3179 <LI><a href="#Phase">Phase </a>Data Tree headings</LI> 3180 3180 <LI><a href="#IMG">Image (IMG) </a>Data Tree headings</LI> 3181 <LI><a href="#PWDR">Powder histogram (PWDR) </a>Data Tree headings</LI> 3181 <LI><a href="#PWDR">Powder histogram (PWDR) </a>Data Tree 3182 headings</LI> 3183 <UL> 3184 <LI><a href="#PWDR_Comments">Comments</a></li> 3185 <LI><a href="#PWDR_Limits">Limits</a></li> 3186 <LI><a href="#PWDR_Background">Background</a></li> 3187 <LI><a href="#PWDR_Instrument_Parameters">Instrument Parameters</a></li> 3188 <LI><a href="#PWDR_Sample_Parameters">Sample Parameters</a></li> 3189 <LI><a href="#PWDR_Peak_List">Peak List</a></li> 3190 <LI><a href="#PWDR_Index_Peak_List">Index Peak List</a></li> 3191 <LI><a href="#PWDR_Unit_Cells_List">Unit Cells List</a></li> 3192 <LI><a href="#PWDR_Reflection_Lists">Reflection Lists</a></li> 3193 </UL> 3194 3182 3195 <LI><a href="#HKLF">Single Crystal histogram (HKLF)</a> Data Tree 3183 3196 headings</LI> 3184 3197 <UL> 3198 <LI><a href="#HKLF_Instrument_Parameters">Instrument Parameters</a></li> 3199 <LI><a href="#HKLF_HKL_Plot_Controls">HKL Plot Controls</a></li> 3200 <LI><a href="#HKLF_Reflection_List">Reflection List</a></li> 3201 </UL> 3185 3202 <LI><a href="#PDF">Pair Distribution Functions (PDF) </a>Data Tree headings</LI> 3186 3203 <LI><a href="#PKS">Powder Peaks (PKS) </a>Data Tree headings</LI> … … 4336 4353 below. Clicking on any of them produces changes in the plot and allows 4337 4354 access to different parameters associated with the dataset. 4338 </p> 4355 </p> 4356 <UL style='margin-left:0.75in'> 4357 <LI><a href="#PWDR_Comments">Comments</a></li> 4358 <LI><a href="#PWDR_Limits">Limits</a></li> 4359 <LI><a href="#PWDR_Background">Background</a></li> 4360 <LI><a href="#PWDR_Instrument_Parameters">Instrument Parameters</a></li> 4361 <LI><a href="#PWDR_Sample_Parameters">Sample Parameters</a></li> 4362 <LI><a href="#PWDR_Peak_List">Peak List</a></li> 4363 <LI><a href="#PWDR_Index_Peak_List">Index Peak List</a></li> 4364 <LI><a href="#PWDR_Unit_Cells_List">Unit Cells List</a></li> 4365 <LI><a href="#PWDR_Reflection_Lists">Reflection Lists</a></li> 4366 </UL> 4339 4367 4340 4368 <h5 style='margin-left:.5in'>What can I do here?</h5> … … 5223 5251 5224 5252 <p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family: 5225 "Times New Roman"'>This window shows the controls and results from indexing of 5226 the peaks in the <a href="#Index_Peak_List"><span class=SpellE><span 5227 style='color:windowtext;text-decoration:none;text-underline:none'>Index_Peak_List</span></span></a></span><!--[if supportFields]><span 5228 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 5229 field-begin'></span> REF Index_Peak_List \h </span><![endif]--><span 5230 style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 5231 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 5232 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 5233 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 5234 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 5235 field-begin'></span><span style='mso-spacerun:yes'> </span>REF Index_Peak_List 5236 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 5237 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 5238 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 5239 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 5240 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 5241 field-begin'></span><span style='mso-spacerun:yes'> </span>REF Index_Peak_List 5242 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 5243 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 5244 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 5245 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 5246 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 5247 field-begin'></span><span style='mso-spacerun:yes'> </span>REF Index_Peak_List 5248 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 5249 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 5250 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 5251 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 5252 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 5253 field-begin'></span><span style='mso-spacerun:yes'> </span>REF Index_Peak_List 5254 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 5255 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 5256 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 5257 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 5258 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 5259 field-begin'></span><span style='mso-spacerun:yes'> </span>REF Index_Peak_List 5260 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 5261 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 5262 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 5263 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><!--[if supportFields]><span 5264 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-element: 5265 field-begin'></span><span style='mso-spacerun:yes'> </span>REF Index_Peak_List 5266 \h </span><![endif]--><span style='mso-fareast-font-family:"Times New Roman"'><!--[if gte mso 9]><xml> 5267 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000001000000049006E006400650078005F005000650061006B005F004C006900730074000000</w:data> 5268 </xml><![endif]--></span><!--[if supportFields]><span style='mso-fareast-font-family: 5269 "Times New Roman"'><span style='mso-element:field-end'></span></span><![endif]--><span 5270 style='mso-fareast-font-family:"Times New Roman"'>. <span class=MsoHyperlink><span 5271 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></p> 5272 5273 <h5 style='margin-left:.5in'><a name="PWDR_Reflection_Lists"><span style='mso-fareast-font-family: 5253 "Times New Roman"'>This tree item has several purposes, it can be used to 5254 perform autoindexing and it can be used to show the positions of peaks 5255 from unit cells which may be results from autoindexing or may be 5256 entered from a phase or manually. It can be used to refine unit cell 5257 parameters. It can also be used to search for 5258 cells/symmetry settings related to a specified unit cell & space 5259 group. 5260 5261 <h5 style='margin-left:.5in'><span style='mso-fareast-font-family: 5274 5262 "Times New Roman"'>What can I do here?<span class=MsoHyperlink><span 5275 5263 style='color:#4F4FFF;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></a></h5> 5276 5264 5277 <p class=MsoListParagraphCxSpFirst style='margin-left:1.0in;mso-add-space:auto; 5278 text-indent:-.25in;mso-list:l20 level1 lfo24'><span style='mso-bookmark:Reflection_List'><![if !supportLists]><span 5279 class=MsoHyperlink><span style='mso-fareast-font-family:"Times New Roman"; 5280 color:windowtext;text-decoration:none;text-underline:none'><span 5281 style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 5282 </span></span></span></span><![endif]><b style='mso-bidi-font-weight:normal'><span 5283 style='mso-fareast-font-family:"Times New Roman"'>Select <span class=SpellE>Bravais</span> 5284 Lattices</span></b></span><span style='mso-bookmark:Reflection_List'><span 5285 style='mso-fareast-font-family:"Times New Roman"'> – the selected are tried for 5286 indexing the powder pattern. <span class=MsoHyperlink><span style='color:windowtext; 5287 text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p> 5288 5289 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5290 auto;text-indent:-.25in;mso-list:l20 level1 lfo24'><span style='mso-bookmark: 5291 Reflection_List'><![if !supportLists]><span class=MsoHyperlink><span 5292 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 5293 none;text-underline:none'><span style='mso-list:Ignore'>2.<span 5294 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 5295 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Max 5296 <span class=SpellE>Nc</span>/Nobs </span></b></span><span style='mso-bookmark: 5297 Reflection_List'><span style='mso-fareast-font-family:"Times New Roman"'>– this 5298 controls the extent of the search for the correct indexing. This may need to be 5299 increased if an indexing trial terminates too quickly. It rarely needs to be 5300 changed.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 5301 none;text-underline:none'><o:p></o:p></span></span></span></span></p> 5302 5303 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5304 auto;text-indent:-.25in;mso-list:l20 level1 lfo24'><span style='mso-bookmark: 5305 Reflection_List'><![if !supportLists]><span class=MsoHyperlink><span 5306 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 5307 none;text-underline:none'><span style='mso-list:Ignore'>3.<span 5308 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 5309 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Start 5310 Volume </span></b></span><span style='mso-bookmark:Reflection_List'><span 5311 style='mso-fareast-font-family:"Times New Roman"'>– this sets an initial unit 5312 cell volume for the indexing. It rarely needs to be changed.<span 5313 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 5314 text-underline:none'><o:p></o:p></span></span></span></span></p> 5315 5316 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5317 auto;text-indent:-.25in;mso-list:l20 level1 lfo24'><span style='mso-bookmark: 5318 Reflection_List'><![if !supportLists]><span class=MsoHyperlink><span 5319 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 5320 none;text-underline:none'><span style='mso-list:Ignore'>4.<span 5321 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><span 5322 style='mso-fareast-font-family:"Times New Roman"'>Menu<b style='mso-bidi-font-weight: 5323 normal'> ‘Cell Index/Refine’ </b>– <span class=MsoHyperlink><span 5324 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p> 5325 5326 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space: 5327 auto;text-indent:-.25in;mso-list:l20 level2 lfo24'><span style='mso-bookmark: 5328 Reflection_List'><![if !supportLists]><span class=MsoHyperlink><span 5329 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 5330 none;text-underline:none'><span style='mso-list:Ignore'>a.<span 5331 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 5332 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Index 5333 Cell</span></b></span><span style='mso-bookmark:Reflection_List'><span 5334 style='mso-fareast-font-family:"Times New Roman"'> – this starts the indexing 5335 process. Output will appear on the console and a progress bar dialog will 5265 <P class=MsoNormal style='margin-left:1.0in'> 5266 <B>For autoindexing</B>, the peaks in the 5267 <a href="#Index_Peak_List">Index Peak List</a> are used. Select one or 5268 more Bravais lattice types to use and use the "Cell 5269 Index/Refine"/"Index Cell" menu command to start indexing. 5270 Output will appear on the console and a progress bar dialog will 5336 5271 appear which tracks trial volume. A <b style='mso-bidi-font-weight:normal'>Cancel</b> 5337 5272 button will terminate indexing; it may need to be pressed more than once to 5338 5273 fully terminate the indexing process. Console output shows possible solutions 5339 with a computed <b style='mso-bidi-font-weight:normal'>M20</b> for each; good5340 solutions are indicated by high <b style='mso-bidi-font-weight:normal'>M20</b>5274 with a computed <b>M20</b> for each; good 5275 solutions are indicated by high <b>M20</b> 5341 5276 values. <b style='mso-bidi-font-weight:normal'>X20</b> gives number of 5342 unindexed lines out of the 1<sup>st</sup> 20 lines and <b style='mso-bidi-font-weight: 5343 normal'>Nc</b> gives total number of reflections generated for each solution.<span 5344 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 5345 text-underline:none'><o:p></o:p></span></span></span></span></p> 5346 5347 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space: 5348 auto;text-indent:-.25in;mso-list:l20 level2 lfo24'><span style='mso-bookmark: 5349 Reflection_List'><![if !supportLists]><span class=MsoHyperlink><span 5350 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 5351 none;text-underline:none'><span style='mso-list:Ignore'>b.<span 5352 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 5353 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Copy 5354 Cell</span></b></span><span style='mso-bookmark:Reflection_List'><span 5355 style='mso-fareast-font-family:"Times New Roman"'> – this copies selected 5356 solution to the Unit cell values; attention is paid to the Bravais lattice 5357 shown for the choice and you may select a <b style='mso-bidi-font-weight:normal'>Space 5358 group</b> from the pull down box. Press <b style='mso-bidi-font-weight:normal'>Show 5359 hkl positions</b> to give the allowed peaks; to confirm the indexing compare 5360 these to peak positions and any unfitted peaks in the pattern.<span 5361 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 5362 text-underline:none'><o:p></o:p></span></span></span></span></p> 5363 5364 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space: 5365 auto;text-indent:-.25in;mso-list:l20 level2 lfo24'><span style='mso-bookmark: 5366 Reflection_List'><![if !supportLists]><span class=MsoHyperlink><span 5367 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 5368 none;text-underline:none'><span style='mso-list:Ignore'>c.<span 5369 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 5370 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Refine 5371 cell</span></b></span><span style='mso-bookmark:Reflection_List'><span 5372 style='mso-fareast-font-family:"Times New Roman"'> – this refines the copied 5373 lattice parameters and optionally the <b style='mso-bidi-font-weight:normal'>Zero 5374 offset. </b>The results will be placed in the <b style='mso-bidi-font-weight: 5375 normal'>Indexing Result</b> table with ‘<b style='mso-bidi-font-weight:normal'>use’</b> 5376 selected.<span class=MsoHyperlink><span style='color:windowtext;text-decoration: 5377 none;text-underline:none'><o:p></o:p></span></span></span></span></p> 5378 5379 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.25in;mso-add-space: 5380 auto;text-indent:-.25in;mso-list:l20 level2 lfo24'><span style='mso-bookmark: 5381 Reflection_List'><![if !supportLists]><span class=MsoHyperlink><span 5382 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 5383 none;text-underline:none'><span style='mso-list:Ignore'>d.<span 5384 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 5385 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Make 5386 new phase</span></b></span><span style='mso-bookmark:Reflection_List'><span 5387 style='mso-fareast-font-family:"Times New Roman"'> – this creates a new phase 5277 unindexed lines out of the 1<sup>st</sup> 20 lines and <b>Nc</b> gives total number of reflections generated for each 5278 solution. 5279 </P><P class=MsoNormal style='margin-left:1.0in'> 5280 The "Copy Cell" menu commnd copies a selected 5281 solution to the Unit cell values; the Bravais lattice 5282 shown for the choice is copied. 5283 Press <b style='mso-bidi-font-weight:normal'>Show 5284 hkl positions</b> to generate the allowed reflection positions, which 5285 are visually superimposed on the displayed powder pattern to visually 5286 confirm the indexing. Pay particular attention to any unmatched 5287 peaks in the pattern. A 5288 <b style='mso-bidi-font-weight:normal'>Space 5289 group</b> can be from the pulldown box to remove reflections based on space 5290 group extinctions and visually eliminate possiblities. 5291 5292 <OL class=MsoNormal style='margin-left:1.2in'> 5293 <LI>Max Nc/Nobs: 5294 – this controls the extent of the search for the correct indexing. This may need to be 5295 increased if an indexing trial terminates too quickly. It rarely needs to be 5296 changed. 5297 <LI>Start Volume: 5298 – this sets an initial unit 5299 cell volume for the indexing. It rarely needs to be changed. 5300 <LI>Select "keep" in the table for a cell that should be preserved 5301 when an additional indexing run is tried; all without that 5302 are erased before the indexing trial begins. 5303 5304 </OL> 5305 5306 </P><P class=MsoNormal style='margin-left:1.0in'> 5307 <B>To display a unit cell</B>, optionally with space group extinctions, set a 5308 Bravais class to determine a unit cell type (see <a href="#Laue_List">list 5309 below</a>), optionally select a space 5310 group (by default the lowest symmetry space group for the class is 5311 selected) and enter the unit cell contents. Or use the "Cell 5312 Index/Refine"/"Load Phase" menu command to read this information from 5313 a phase that has been read into a project or from a file (such as a CIF) 5314 using the "Cell Index/Refine"/"Import Cell" menu command. 5315 5316 </P><P class=MsoNormal style='margin-left:1.0in'> 5317 <B>For symmetry exploration</B>, once a phase/cell has been loaded, 5318 use the "Run SUBGROUPS", "Cell Symmetry Search" or "Run k-SUBGROUPSMAG" 5319 commands from the "Cell Index/Refine" menu. These commands look for: 5320 subgroups, higher symmetry cells or magnetic subgroups, respectively. 5321 Also note the "Transform Cell" commnd in that menu that can perform 5322 namy common lattice transformations, apply a user-supplied cell 5323 transformation or create a magnetic phase. 5324 5325 </P><P class=MsoNormal style='margin-left:1.0in'> 5326 <B>To optimize a cell</B>, to fit the peaks in the 5327 <a href="#Index_Peak_List">Index Peak List</a>, use the 5328 "Cell Index/Refine"/"Refine Cell" menu command. 5329 The results will be placed in the <b>Indexing Result</b> table with ‘<b>use’</b> 5330 selected. 5331 5332 </P><P class=MsoNormal style='margin-left:1.0in'> 5333 <B>Other</B>: The "Make new phase" command creates a new phase 5388 5334 from the selected unit cell and chosen space group. A dialog box will appear 5389 5335 asking for a name for this phase. See the new entry under Phases and the new 5390 lattice parameters will be in the </span></span><a href="#General"><span 5391 style='mso-bookmark:Reflection_List'><span style='mso-fareast-font-family:"Times New Roman"; 5392 color:windowtext;text-decoration:none;text-underline:none'>General</span></span><span 5393 style='mso-bookmark:Reflection_List'></span></a><span style='mso-bookmark:Reflection_List'><span 5394 style='mso-fareast-font-family:"Times New Roman"'> window for that phase.<span 5395 class=MsoHyperlink><span style='color:windowtext;text-decoration:none; 5396 text-underline:none'><o:p></o:p></span></span></span></span></p> 5397 5398 <p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space: 5399 auto;text-indent:-.25in;mso-list:l20 level1 lfo24'><span style='mso-bookmark: 5400 Reflection_List'><![if !supportLists]><span class=MsoHyperlink><span 5401 style='mso-fareast-font-family:"Times New Roman";color:windowtext;text-decoration: 5402 none;text-underline:none'><span style='mso-list:Ignore'>5.<span 5403 style='font:7.0pt "Times New Roman"'> </span></span></span></span><![endif]><b 5404 style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Select 5405 another solution – </span></b></span><span style='mso-bookmark:Reflection_List'><span 5406 style='mso-fareast-font-family:"Times New Roman"'>the plot will show (red 5407 dashed lines) the<b style='mso-bidi-font-weight:normal'> </b>generated 5408 reflection positions for the choice; compare them to the peak positions (blue 5409 lines) and any unfitted peaks for conformation.<span class=MsoHyperlink><span 5410 style='color:windowtext;text-decoration:none;text-underline:none'><o:p></o:p></span></span></span></span></p> 5411 5412 <p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto; 5413 text-indent:-.25in;mso-list:l20 level1 lfo24'> 5414 6. 5415 Select ‘keep’ – 5416 this preserves this solution for a subsequent indexing run; otherwise all 5417 solutions are erased before the indexing trial begins. 5336 lattice parameters will be in the <a href="#General">General 5337 </a> window for that phase. 5418 5338 </p> 5339 5340 <A name="Laue_List"> 5341 <P style='margin-left:1.0in'><B>GSAS-II Laue classes</B> (note that some 5342 redundant entries are included for convenience.)</P></A> 5343 <UL style='margin-left:1.0in'> 5344 <LI>Cubic: Fm3m, Im3m & Pm3m 5345 <LI>Rhombohedral: R3-H (hexagonal axes) 5346 <LI>Hexagonal: P6/mmm 5347 <LI>Tetragonal: I4/mmm, P4/mmm 5348 <LI>Orthorhombic: Fmmm, Immm, Ammm, Bmmm, Cmmm, Pmmm 5349 <LI>Monoclinic: I2/m, C2/m, P2/m (b-unique) 5350 <LI>Triclinic: P1, C1 5351 </UL> 5352 </P><P> 5419 5353 5420 5354 <h4 style='margin-left:0.25in'><a name="PWDR_Reflection_Lists"></a><u> … … 5531 5465 the slider for upper layers for the selected zone.<o:p></o:p></span></p> 5532 5466 5467 <a name="HKLF_Reflection_List"></a> 5533 5468 <h4 style='margin-left:0.25in'><span style='mso-fareast-font-family:"Times New Roman"'>Reflection 5534 5469 List</span><span class=MsoHyperlink><span style='color:#5B9BD5;mso-themecolor: … … 7568 7503 <hr size=2 width="100%" align=center> 7569 7504 7570 <!-- hhmts start -->Last modified: Wed Dec 2 11:04:42CST 2020 <!-- hhmts end -->7505 <!-- hhmts start -->Last modified: Thu Dec 10 19:31:56 CST 2020 <!-- hhmts end --> 7571 7506 7572 7507 </div>
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