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source: trunk/GSASIIconstrGUI.py @ 3789

Last change on this file since 3789 was 3789, checked in by toby, 4 years ago
fix transpose error for lattice constraints
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1	# -- coding: utf-8 --
2	#GSASIIconstrGUI - constraint GUI routines
3	########### SVN repository information ###################
4	# $Date: 2019-01-20 02:38:49 +0000 (Sun, 20 Jan 2019) $
5	# $Author: toby $
6	# $Revision: 3789 $
7	# $URL: trunk/GSASIIconstrGUI.py $
8	# $Id: GSASIIconstrGUI.py 3789 2019-01-20 02:38:49Z toby $
9	########### SVN repository information ###################
10	'''
11	GSASIIconstrGUI: Constraint GUI routines
12	------------------------------------------
13
14	Used to define constraints and rigid bodies.
15
16	'''
17	from __future__ import division, print_function
18	import sys
19	import wx
20	import wx.grid as wg
21	import random as ran
22	import numpy as np
23	import numpy.ma as ma
24	import numpy.linalg as nl
25	import os.path
26	import GSASIIpath
27	GSASIIpath.SetVersionNumber("$Revision: 3789 $")
28	import GSASIIElem as G2elem
29	import GSASIIElemGUI as G2elemGUI
30	import GSASIIstrIO as G2stIO
31	import GSASIImapvars as G2mv
32	import GSASIImath as G2mth
33	import GSASIIlattice as G2lat
34	import GSASIIdataGUI as G2gd
35	import GSASIIctrlGUI as G2G
36	import GSASIIplot as G2plt
37	import GSASIIobj as G2obj
38	import GSASIIspc as G2spc
39	VERY_LIGHT_GREY = wx.Colour(235,235,235)
40
41	class ConstraintDialog(wx.Dialog):
42	'''Window to edit Constraint values
43	'''
44	def __init__(self,parent,title,text,data,separator='*',varname="",varyflag=False):
45	wx.Dialog.__init__(self,parent,-1,'Edit '+title,
46	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
47	self.data = data[:]
48	self.newvar = [varname,varyflag]
49	panel = wx.Panel(self)
50	mainSizer = wx.BoxSizer(wx.VERTICAL)
51	topLabl = wx.StaticText(panel,-1,text)
52	mainSizer.Add((10,10),1)
53	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.LEFT,10)
54	mainSizer.Add((10,10),1)
55	dataGridSizer = wx.FlexGridSizer(cols=3,hgap=2,vgap=2)
56	self.OkBtn = wx.Button(panel,wx.ID_OK)
57	for id in range(len(self.data)):
58	lbl1 = lbl = str(self.data[id][1])
59	if lbl[-1] != '=': lbl1 = lbl + ' ' + separator + ' '
60	name = wx.StaticText(panel,wx.ID_ANY,lbl1,
61	style=wx.ALIGN_RIGHT)
62	scale = G2G.ValidatedTxtCtrl(panel,self.data[id],0,
63	typeHint=float,
64	OKcontrol=self.DisableOK)
65	dataGridSizer.Add(name,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,5)
66	dataGridSizer.Add(scale,0,wx.RIGHT,3)
67	if ':' in lbl:
68	dataGridSizer.Add(
69	wx.StaticText(panel,-1,G2obj.fmtVarDescr(lbl)),
70	0,wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,3)
71	else:
72	dataGridSizer.Add((-1,-1))
73	if title == 'New Variable':
74	name = wx.StaticText(panel,wx.ID_ANY,"New variable's\nname (optional)",
75	style=wx.ALIGN_CENTER)
76	scale = G2G.ValidatedTxtCtrl(panel,self.newvar,0,
77	typeHint=str,notBlank=False)
78	dataGridSizer.Add(name,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,5)
79	dataGridSizer.Add(scale,0,wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,3)
80	self.refine = wx.CheckBox(panel,label='Refine?')
81	self.refine.SetValue(self.newvar[1]==True)
82	self.refine.Bind(wx.EVT_CHECKBOX, self.OnCheckBox)
83	dataGridSizer.Add(self.refine,0,wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL,3)
84
85	mainSizer.Add(dataGridSizer,0,wx.EXPAND)
86	self.OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
87	self.OkBtn.SetDefault()
88	cancelBtn = wx.Button(panel,wx.ID_CANCEL)
89	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
90	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
91	btnSizer.Add((20,20),1)
92	btnSizer.Add(self.OkBtn)
93	btnSizer.Add((20,20),1)
94	btnSizer.Add(cancelBtn)
95	btnSizer.Add((20,20),1)
96
97	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
98	panel.SetSizer(mainSizer)
99	panel.Fit()
100	self.Fit()
101	self.CenterOnParent()
102
103	def DisableOK(self,setting):
104	if setting:
105	self.OkBtn.Enable()
106	else:
107	self.OkBtn.Disable()
108
109	def OnCheckBox(self,event):
110	self.newvar[1] = self.refine.GetValue()
111
112	def OnOk(self,event):
113	parent = self.GetParent()
114	parent.Raise()
115	self.EndModal(wx.ID_OK)
116
117	def OnCancel(self,event):
118	parent = self.GetParent()
119	parent.Raise()
120	self.EndModal(wx.ID_CANCEL)
121
122	def GetData(self):
123	return self.data
124
125	################################################################################
126	##### Constraints
127	################################################################################
128
129	def UpdateConstraints(G2frame,data):
130	'''Called when Constraints tree item is selected.
131	Displays the constraints in the data window
132	'''
133
134	def FindEquivVarb(name,nameList):
135	'Creates a list of variables appropriate to constrain with name'
136	outList = []
137	#phlist = []
138	items = name.split(':')
139	namelist = [items[2],]
140	if 'dA' in name:
141	namelist = ['dAx','dAy','dAz']
142	elif 'AU' in name:
143	namelist = ['AUiso','AU11','AU22','AU33','AU12','AU13','AU23']
144	elif 'AM' in name:
145	namelist = ['AMx','AMy','AMz']
146	elif items[-1] in ['A0','A1','A2','A3','A4','A5']:
147	namelist = ['A0','A1','A2','A3','A4','A5']
148	elif items[-1] in ['D11','D22','D33','D12','D13','D23']:
149	namelist = ['D11','D22','D33','D12','D13','D23']
150	elif 'Tm' in name:
151	namelist = ['Tmin','Tmax']
152	elif 'RB' in name:
153	rbfx = 'RB'+items[2][2]
154	if 'T' in name and 'Tr' not in name:
155	namelist = [rbfx+'T11',rbfx+'T22',rbfx+'T33',rbfx+'T12',rbfx+'T13',rbfx+'T23']
156	if 'L' in name:
157	namelist = [rbfx+'L11',rbfx+'L22',rbfx+'L33',rbfx+'L12',rbfx+'L13',rbfx+'L23']
158	if 'S' in name:
159	namelist = [rbfx+'S12',rbfx+'S13',rbfx+'S21',rbfx+'S23',rbfx+'S31',rbfx+'S32',rbfx+'SAA',rbfx+'SBB']
160	if 'U' in name:
161	namelist = [rbfx+'U',]
162
163	for item in nameList:
164	keys = item.split(':')
165	#if keys[0] not in phlist:
166	# phlist.append(keys[0])
167	if items[1] == '*' and keys[2] in namelist: # wildcard -- select only sequential options
168	keys[1] = '*'
169	mitem = ':'.join(keys)
170	if mitem == name: continue
171	if mitem not in outList: outList.append(mitem)
172	elif keys[2] in namelist and item != name:
173	outList.append(item)
174	return outList
175
176	def SelectVarbs(page,FrstVarb,varList,legend,constType):
177	'''Select variables used in constraints after one variable has
178	been selected. This routine determines the appropriate variables to be
179	used based on the one that has been selected and asks for more to be added.
180
181	It then creates the constraint and adds it to the constraints list.
182
183	Called from OnAddEquivalence, OnAddFunction & OnAddConstraint (all but
184	OnAddHold)
185
186	:param list page: defines calling page -- type of variables to be used
187	:parm GSASIIobj.G2VarObj FrstVarb: reference to first selected variable
188	:param list varList: list of other appropriate variables to select from
189	:param str legend: header for selection dialog
190	:param str constType: type of constraint to be generated
191	:returns: a constraint, as defined in
192	:ref:`GSASIIobj <Constraint_definitions_table>`
193	'''
194	choices = [[i]+list(G2obj.VarDescr(i)) for i in varList]
195	meaning = G2obj.getDescr(FrstVarb.name)
196	if not meaning:
197	meaning = "(no definition found!)"
198	l = str(FrstVarb).split(':')
199	# make lists of phases & histograms to iterate over
200	phaselist = [l[0]]
201	if l[0]:
202	phaselbl = ['phase #'+l[0]]
203	if len(Phases) > 1:
204	phaselist += ['all']
205	phaselbl += ['all phases']
206	else:
207	phaselbl = ['']
208	histlist = [l[1]]
209	if l[1] == '*':
210	pass
211	elif l[1]:
212	histlbl = ['histogram #'+l[1]]
213	if len(Histograms) > 1:
214	histlist += ['all']
215	histlbl += ['all histograms']
216	typ = Histograms[G2obj.LookupHistName(l[1])[0]]['Instrument Parameters'][0]['Type'][1]
217	i = 0
218	for hist in Histograms:
219	if Histograms[hist]['Instrument Parameters'][0]['Type'][1] == typ: i += 1
220	if i > 1:
221	histlist += ['all='+typ]
222	histlbl += ['all '+typ+' histograms']
223	else:
224	histlbl = ['']
225	# make a list of equivalent parameter names
226	nameList = [FrstVarb.name]
227	for var in varList:
228	nam = var.split(":")[2]
229	if nam not in nameList: nameList += [nam]
230	# add "wild-card" names to the list of variables
231	if l[1] == '*':
232	pass
233	elif page[1] == 'phs':
234	if 'RB' in FrstVarb.name:
235	pass
236	elif FrstVarb.atom is None:
237	for nam in nameList:
238	for ph,plbl in zip(phaselist,phaselbl):
239	if plbl: plbl = 'For ' + plbl
240	var = ph+"::"+nam
241	if var == str(FrstVarb) or var in varList: continue
242	varList += [var]
243	choices.append([var,plbl,meaning])
244	else:
245	for nam in nameList:
246	for ph,plbl in zip(phaselist,phaselbl):
247	if plbl: plbl = ' in ' + plbl
248	for atype in ['']+TypeList:
249	if atype:
250	albl = "For "+atype+" atoms"
251	akey = "all="+atype
252	else:
253	albl = "For all atoms"
254	akey = "all"
255	var = ph+"::"+nam+":"+akey
256	if var == str(FrstVarb) or var in varList: continue
257	varList += [var]
258	choices.append([var,albl+plbl,meaning])
259	elif page[1] == 'hap':
260	if FrstVarb.name == "Scale":
261	meaning = "Phase fraction"
262	for nam in nameList:
263	for ph,plbl in zip(phaselist,phaselbl):
264	if plbl: plbl = 'For ' + plbl
265	for hst,hlbl in zip(histlist,histlbl):
266	if hlbl:
267	if plbl:
268	hlbl = ' in ' + hlbl
269	else:
270	hlbl = 'For ' + hlbl
271	var = ph+":"+hst+":"+nam
272	if var == str(FrstVarb) or var in varList: continue
273	varList += [var]
274	choices.append([var,plbl+hlbl,meaning])
275	elif page[1] == 'hst':
276	if FrstVarb.name == "Scale":
277	meaning = "Scale factor"
278	for nam in nameList:
279	for hst,hlbl in zip(histlist,histlbl):
280	if hlbl:
281	hlbl = 'For ' + hlbl
282	var = ":"+hst+":"+nam
283	if var == str(FrstVarb) or var in varList: continue
284	varList += [var]
285	choices.append([var,hlbl,meaning])
286	elif page[1] == 'glb' or page[1] == 'sym':
287	pass
288	else:
289	raise Exception('Unknown constraint page '+ page[1])
290	if len(choices):
291	l1 = l2 = 1
292	for i1,i2,i3 in choices:
293	l1 = max(l1,len(i1))
294	l2 = max(l2,len(i2))
295	fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
296	atchoices = [fmt.format(*i1) for i1 in choices] # reformat list as str with columns
297	dlg = G2G.G2MultiChoiceDialog(
298	G2frame,legend,
299	'Constrain '+str(FrstVarb)+' with...',atchoices,
300	toggle=False,size=(625,400),monoFont=True)
301	dlg.CenterOnParent()
302	res = dlg.ShowModal()
303	Selections = dlg.GetSelections()[:]
304	dlg.Destroy()
305	if res != wx.ID_OK: return []
306	if len(Selections) == 0:
307	dlg = wx.MessageDialog(
308	G2frame,
309	'No variables were selected to include with '+str(FrstVarb),
310	'No variables')
311	dlg.CenterOnParent()
312	dlg.ShowModal()
313	dlg.Destroy()
314	return []
315	else:
316	dlg = wx.MessageDialog(
317	G2frame,
318	'There are no appropriate variables to include with '+str(FrstVarb),
319	'No variables')
320	dlg.CenterOnParent()
321	dlg.ShowModal()
322	dlg.Destroy()
323	return []
324	# now process the variables provided by the user
325	varbs = [str(FrstVarb),] # list of selected variables
326	for sel in Selections:
327	var = varList[sel]
328	# phase(s) included
329	l = var.split(':')
330	if l[0] == "all":
331	phlist = [str(Phases[phase]['pId']) for phase in Phases]
332	else:
333	phlist = [l[0]]
334	# histogram(s) included
335	if l[1] == "all":
336	hstlist = [str(Histograms[hist]['hId']) for hist in Histograms]
337	elif '=' in l[1]:
338	htyp = l[1].split('=')[1]
339	hstlist = [str(Histograms[hist]['hId']) for hist in Histograms if
340	Histograms[hist]['Instrument Parameters'][0]['Type'][1] == htyp]
341	else:
342	hstlist = [l[1]]
343	if len(l) == 3:
344	for ph in phlist:
345	for hst in hstlist:
346	var = ph + ":" + hst + ":" + l[2]
347	if var in varbs: continue
348	varbs.append(var)
349	else: # constraints with atoms or rigid bodies
350	if len(l) == 5: # rigid body parameter
351	var = ':'.join(l)
352	if var in varbs: continue
353	varbs.append(var)
354	elif l[3] == "all":
355	for ph in phlist:
356	key = G2obj.LookupPhaseName(ph)[0]
357	for hst in hstlist: # should be blank
358	for iatm,at in enumerate(Phases[key]['Atoms']):
359	var = ph + ":" + hst + ":" + l[2] + ":" + str(iatm)
360	if var in varbs: continue
361	varbs.append(var)
362	elif '=' in l[3]:
363	for ph in phlist:
364	key = G2obj.LookupPhaseName(ph)[0]
365	cx,ct,cs,cia = Phases[key]['General']['AtomPtrs']
366	for hst in hstlist: # should be blank
367	atyp = l[3].split('=')[1]
368	for iatm,at in enumerate(Phases[key]['Atoms']):
369	if at[ct] != atyp: continue
370	var = ph + ":" + hst + ":" + l[2] + ":" + str(iatm)
371	if var in varbs: continue
372	varbs.append(var)
373	else:
374	for ph in phlist:
375	key = G2obj.LookupPhaseName(ph)[0]
376	for hst in hstlist: # should be blank
377	var = ph + ":" + hst + ":" + l[2] + ":" + l[3]
378	if var in varbs: continue
379	varbs.append(var)
380	if len(varbs) >= 1 or 'constraint' in constType:
381	constr = [[1.0,FrstVarb]]
382	for item in varbs[1:]:
383	constr += [[1.0,G2obj.G2VarObj(item)]]
384	if 'equivalence' in constType:
385	return [constr+[None,None,'e']]
386	elif 'function' in constType:
387	return [constr+[None,False,'f']]
388	elif 'constraint' in constType:
389	return [constr+[1.0,None,'c']]
390	else:
391	raise Exception('Unknown constraint type: '+str(constType))
392	else:
393	dlg = wx.MessageDialog(
394	G2frame,
395	'There are no selected variables to include with '+str(FrstVarb),
396	'No variables')
397	dlg.CenterOnParent()
398	dlg.ShowModal()
399	dlg.Destroy()
400	return []
401
402	def ConstraintsLoad(data,newcons=[]):
403	'''Load all constraints. Constraints based on symmetry (etc.)
404	are generated by running :func:`GSASIIstrIO.GetPhaseData`.
405	'''
406	G2mv.InitVars()
407	#Find all constraints
408	constraintSet = []
409	for key in data:
410	if key.startswith('_'): continue
411	constraintSet += data[key]
412	if newcons:
413	constraintSet = constraintSet + newcons
414	constDictList,fixedList,ignored = G2stIO.ProcessConstraints(constraintSet)
415	# generate symmetry constraints to check for conflicts
416	rigidbodyDict = G2frame.GPXtree.GetItemPyData(
417	G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies'))
418	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
419	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
420	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
421	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
422	return constDictList,phaseDict,fixedList
423
424	def ConstraintsCheck(data,newcons=[]):
425	'''Load constraints & check them for errors. Since error checking
426	can cause changes in constraints in case of repairable conflicts
427	between equivalences, reload the constraints again after the check.
428	This could probably be done more effectively, but only reloading when
429	needed, but the reload should be quick.
430	'''
431	constDictList,phaseDict,fixedList = ConstraintsLoad(data,newcons)
432	msg = G2mv.EvaluateMultipliers(constDictList,phaseDict)
433	if msg:
434	return 'Unable to interpret multiplier(s): '+msg,''
435	res = G2mv.CheckConstraints('',constDictList,fixedList)
436	# reload constraints in case any were merged in MoveConfEquiv
437	ConstraintsLoad(data,newcons)
438	return res
439
440	def CheckAddedConstraint(newcons):
441	'''Check a new constraint that has just been input.
442	If there is an error display a message and discard the last entry
443
444	Since the varylist is not available, no warning messages
445	should be generated here
446
447	:returns: True if constraint should be added
448	'''
449
450	errmsg,warnmsg = ConstraintsCheck(data,newcons)
451	if errmsg:
452	G2frame.ErrorDialog('Constraint Error',
453	'Error with newly added constraint:\n'+errmsg+
454	'\nIgnoring newly added constraint',parent=G2frame)
455	# reset error status
456	errmsg,warnmsg = ConstraintsCheck(data)
457	if errmsg:
458	print (errmsg)
459	print (G2mv.VarRemapShow([],True))
460	return False
461	elif warnmsg:
462	print ('Unexpected contraint warning:\n'+warnmsg)
463	return True
464
465	def CheckChangedConstraint():
466	'''Check all constraints after an edit has been made.
467	If there is an error display a message and reject the change.
468
469	Since the varylist is not available, no warning messages
470	should be generated.
471
472	:returns: True if the edit should be retained
473	'''
474	errmsg,warnmsg = ConstraintsCheck(data)
475	if errmsg:
476	G2frame.ErrorDialog('Constraint Error',
477	'Error after editing constraint:\n'+errmsg+
478	'\nDiscarding last constraint edit',parent=G2frame)
479	# reset error status
480	errmsg,warnmsg = ConstraintsCheck(data)
481	if errmsg:
482	print (errmsg)
483	print (G2mv.VarRemapShow([],True))
484	return False
485	elif warnmsg:
486	print ('Unexpected contraint warning:\n'+warnmsg)
487	return True
488
489	def PageSelection(page):
490	'Decode page reference'
491	if page[1] == "phs":
492	vartype = "phase"
493	varList = G2obj.removeNonRefined(phaseList) # remove any non-refinable prms from list
494	constrDictEnt = 'Phase'
495	elif page[1] == "hap":
496	vartype = "Histogram*Phase"
497	varList = G2obj.removeNonRefined(hapList) # remove any non-refinable prms from list
498	constrDictEnt = 'HAP'
499	elif page[1] == "hst":
500	vartype = "Histogram"
501	varList = G2obj.removeNonRefined(histList) # remove any non-refinable prms from list
502	constrDictEnt = 'Hist'
503	elif page[1] == "glb":
504	vartype = "Global"
505	varList = G2obj.removeNonRefined(globalList) # remove any non-refinable prms from list
506
507	constrDictEnt = 'Global'
508	elif page[1] == "sym":
509	return None,None,None
510	else:
511	raise Exception('Should not happen!')
512	return vartype,varList,constrDictEnt
513
514	def OnAddHold(event):
515	'''Create a new Hold constraint
516
517	Hold constraints allows the user to select one variable (the list of available
518	variables depends on which tab is currently active).
519	'''
520	page = G2frame.Page
521	vartype,varList,constrDictEnt = PageSelection(page)
522	if vartype is None: return
523	varList = G2obj.SortVariables(varList)
524	title1 = "Hold "+vartype+" variable"
525	if not varList:
526	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
527	parent=G2frame)
528	return
529	l2 = l1 = 1
530	for i in varList:
531	l1 = max(l1,len(i))
532	loc,desc = G2obj.VarDescr(i)
533	l2 = max(l2,len(loc))
534	fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
535	varListlbl = [fmt.format(i,*G2obj.VarDescr(i)) for i in varList]
536	#varListlbl = ["("+i+") "+G2obj.fmtVarDescr(i) for i in varList]
537	legend = "Select variables to hold (Will not be varied, even if vary flag is set)"
538	dlg = G2G.G2MultiChoiceDialog(G2frame,
539	legend,title1,varListlbl,toggle=False,size=(625,400),monoFont=True)
540	dlg.CenterOnParent()
541	if dlg.ShowModal() == wx.ID_OK:
542	for sel in dlg.GetSelections():
543	Varb = varList[sel]
544	VarObj = G2obj.G2VarObj(Varb)
545	newcons = [[[0.0,VarObj],None,None,'h']]
546	if CheckAddedConstraint(newcons):
547	data[constrDictEnt] += newcons
548	dlg.Destroy()
549	wx.CallAfter(OnPageChanged,None)
550
551	def OnAddEquivalence(event):
552	'''add an Equivalence constraint'''
553	page = G2frame.Page
554	vartype,varList,constrDictEnt = PageSelection(page)
555	if vartype is None: return
556	title1 = "Create equivalence constraint between "+vartype+" variables"
557	title2 = "Select additional "+vartype+" variable(s) to be equivalent with "
558	if not varList:
559	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
560	parent=G2frame)
561	return
562	# legend = "Select variables to make equivalent (only one of the variables will be varied when all are set to be varied)"
563	GetAddVars(page,title1,title2,varList,constrDictEnt,'equivalence')
564
565	def OnAddAtomEquiv(event):
566	''' Add equivalences between all parameters on atoms '''
567	page = G2frame.Page
568	vartype,varList,constrDictEnt = PageSelection(page)
569	if vartype is None: return
570	title1 = "Setup equivalent atom variables"
571	title2 = "Select additional atoms(s) to be equivalent with "
572	if not varList:
573	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
574	parent=G2frame)
575	return
576	# legend = "Select atoms to make equivalent (only one of the atom variables will be varied when all are set to be varied)"
577	GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'equivalence')
578
579	def OnAddRiding(event):
580	''' Add riding equivalences between all parameters on atoms '''
581	page = G2frame.Page
582	vartype,varList,constrDictEnt = PageSelection(page)
583	if vartype is None: return
584	title1 = "Setup riding atoms "
585	title2 = "Select additional atoms(s) to ride on "
586	if not varList:
587	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
588	parent=G2frame)
589	return
590	# legend = "Select atoms to ride (only one of the atom variables will be varied when all are set to be varied)"
591	GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'riding')
592
593	def OnAddFunction(event):
594	'''add a Function (new variable) constraint'''
595	page = G2frame.Page
596	vartype,varList,constrDictEnt = PageSelection(page)
597	if vartype is None: return
598	title1 = "Setup new variable based on "+vartype+" variables"
599	title2 = "Include additional "+vartype+" variable(s) to be included with "
600	if not varList:
601	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
602	parent=G2frame)
603	return
604	# legend = "Select variables to include in a new variable (the new variable will be varied when all included variables are varied)"
605	GetAddVars(page,title1,title2,varList,constrDictEnt,'function')
606
607	def OnAddConstraint(event):
608	'''add a constraint equation to the constraints list'''
609	page = G2frame.Page
610	vartype,varList,constrDictEnt = PageSelection(page)
611	if vartype is None: return
612	title1 = "Creating constraint on "+vartype+" variables"
613	title2 = "Select additional "+vartype+" variable(s) to include in constraint with "
614	if not varList:
615	G2frame.ErrorDialog('No variables','There are no variables of type '+vartype,
616	parent=G2frame)
617	return
618	# legend = "Select variables to include in a constraint equation (the values will be constrainted to equal a specified constant)"
619	GetAddVars(page,title1,title2,varList,constrDictEnt,'constraint')
620
621	def GetAddVars(page,title1,title2,varList,constrDictEnt,constType):
622	'''Get the variables to be added for OnAddEquivalence, OnAddFunction,
623	and OnAddConstraint. Then create and check the constraint.
624	'''
625	#varListlbl = ["("+i+") "+G2obj.fmtVarDescr(i) for i in varList]
626	if constType == 'equivalence':
627	omitVars = G2mv.GetDependentVars()
628	else:
629	omitVars = []
630	varList = G2obj.SortVariables([i for i in varList if i not in omitVars])
631	l2 = l1 = 1
632	for i in varList:
633	l1 = max(l1,len(i))
634	loc,desc = G2obj.VarDescr(i)
635	l2 = max(l2,len(loc))
636	fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}"
637	varListlbl = [fmt.format(i,*G2obj.VarDescr(i)) for i in varList]
638	dlg = G2G.G2SingleChoiceDialog(G2frame,'Select 1st variable:',
639	title1,varListlbl,monoFont=True,size=(625,400))
640	dlg.CenterOnParent()
641	if dlg.ShowModal() == wx.ID_OK:
642	if constType == 'equivalence':
643	omitVars = G2mv.GetDependentVars() + G2mv.GetIndependentVars()
644	sel = dlg.GetSelection()
645	FrstVarb = varList[sel]
646	VarObj = G2obj.G2VarObj(FrstVarb)
647	moreVarb = G2obj.SortVariables(FindEquivVarb(FrstVarb,[i for i in varList if i not in omitVars]))
648	newcons = SelectVarbs(page,VarObj,moreVarb,title2+FrstVarb,constType)
649	if len(newcons) > 0:
650	if CheckAddedConstraint(newcons):
651	data[constrDictEnt] += newcons
652	dlg.Destroy()
653	wx.CallAfter(OnPageChanged,None)
654
655	def FindNeighbors(phase,FrstName,AtNames):
656	General = phase['General']
657	cx,ct,cs,cia = General['AtomPtrs']
658	Atoms = phase['Atoms']
659	atNames = [atom[ct-1] for atom in Atoms]
660	Cell = General['Cell'][1:7]
661	Amat,Bmat = G2lat.cell2AB(Cell)
662	atTypes = General['AtomTypes']
663	Radii = np.array(General['BondRadii'])
664	AtInfo = dict(zip(atTypes,Radii)) #or General['BondRadii']
665	Orig = atNames.index(FrstName.split()[1])
666	OType = Atoms[Orig][ct]
667	XYZ = G2mth.getAtomXYZ(Atoms,cx)
668	Neigh = []
669	Dx = np.inner(Amat,XYZ-XYZ[Orig]).T
670	dist = np.sqrt(np.sum(Dx**2,axis=1))
671	sumR = AtInfo[OType]+0.5 #H-atoms only!
672	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
673	for j in IndB[0]:
674	if j != Orig:
675	Neigh.append(AtNames[j])
676	return Neigh
677
678	def GetAddAtomVars(page,title1,title2,varList,constrDictEnt,constType):
679	'''Get the atom variables to be added for OnAddAtomEquiv. Then create and
680	check the constraints. Riding for H atoms only.
681	'''
682	Atoms = {G2obj.VarDescr(i)[0]:[] for i in varList if 'Atom' in G2obj.VarDescr(i)[0]}
683	for item in varList:
684	atName = G2obj.VarDescr(item)[0]
685	if atName in Atoms:
686	Atoms[atName].append(item)
687	AtNames = list(Atoms.keys())
688	AtNames.sort()
689	dlg = G2G.G2SingleChoiceDialog(G2frame,'Select 1st atom:',
690	title1,AtNames,monoFont=True,size=(625,400))
691	dlg.CenterOnParent()
692	FrstAtom = ''
693	if dlg.ShowModal() == wx.ID_OK:
694	sel = dlg.GetSelection()
695	FrstAtom = AtNames[sel]
696	if 'riding' in constType:
697	phaseName = (FrstAtom.split(' in ')[1]).strip()
698	phase = Phases[phaseName]
699	AtNames = FindNeighbors(phase,FrstAtom,AtNames)
700	else:
701	AtNames.remove(FrstAtom)
702	dlg.Destroy()
703	if FrstAtom == '':
704	print ('no atom selected')
705	return
706	dlg = G2G.G2MultiChoiceDialog(
707	G2frame,title2+FrstAtom,
708	'Constrain '+str(FrstAtom)+' with...',AtNames,
709	toggle=False,size=(625,400),monoFont=True)
710	if dlg.ShowModal() == wx.ID_OK:
711	Selections = dlg.GetSelections()[:]
712	else:
713	print ('no target atom selected')
714	dlg.Destroy()
715	return
716	dlg.Destroy()
717	for name in Atoms[FrstAtom]:
718	newcons = []
719	constr = []
720	if 'riding' in constType:
721	if 'AUiso' in name:
722	constr = [[1.0,G2obj.G2VarObj(name)]]
723	elif 'AU11' in name:
724	pass
725	elif 'AU' not in name:
726	constr = [[1.0,G2obj.G2VarObj(name)]]
727	else:
728	constr = [[1.0,G2obj.G2VarObj(name)]]
729	pref = ':'+name.rsplit(':',1)[0].split(':',1)[1] #get stuff between phase id & atom id
730	for sel in Selections:
731	name2 = Atoms[AtNames[sel]][0]
732	pid = name2.split(':',1)[0] #get phase id for 2nd atom
733	id = name2.rsplit(':',1)[-1] #get atom no. for 2nd atom
734	if 'riding' in constType:
735	pref = pid+pref
736	if 'AUiso' in pref:
737	parts = pref.split('AUiso')
738	constr += [[1.2,G2obj.G2VarObj('%s:%s'%(parts[0]+'AUiso',id))]]
739	elif 'AU' not in pref:
740	constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pref,id))]]
741	else:
742	constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pid+pref,id))]]
743	if not constr:
744	continue
745	if 'frac' in pref and 'riding' not in constType:
746	newcons = [constr+[1.0,None,'c']]
747	else:
748	newcons = [constr+[None,None,'e']]
749	if len(newcons) > 0:
750	if CheckAddedConstraint(newcons):
751	data[constrDictEnt] += newcons
752	wx.CallAfter(OnPageChanged,None)
753
754	def MakeConstraintsSizer(name,pageDisplay):
755	'''Creates a sizer displaying all of the constraints entered of
756	the specified type.
757
758	:param str name: the type of constraints to be displayed ('HAP',
759	'Hist', 'Phase', 'Global', 'Sym-Generated')
760	:param wx.Panel pageDisplay: parent panel for sizer
761	:returns: wx.Sizer created by method
762	'''
763	if name == 'Sym-Generated': #show symmetry generated constraints
764	Sizer1 = wx.BoxSizer(wx.VERTICAL)
765	Sizer1.Add(wx.StaticText(pageDisplay,wx.ID_ANY,
766	'Equivalences generated based on cell/space group input'))
767	Sizer1.Add((-1,5))
768	Sizer = wx.FlexGridSizer(0,2,0,0)
769	Sizer1.Add(Sizer)
770	for sym in G2mv.GetSymEquiv():
771	Sizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,'EQUIV'),
772	0,wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER\|wx.RIGHT\|wx.LEFT,3)
773	Sizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,sym))
774	Sizer.Add((-1,-1))
775	Sizer.Add((-1,2))
776	return Sizer1
777	constSizer = wx.FlexGridSizer(0,6,0,0)
778	maxlen = 50 # characters before wrapping a constraint
779	for Id,item in enumerate(data[name]):
780	refineflag = False
781	helptext = ""
782	eqString = ['',]
783	problemItem = False
784	for term in item[:-3]:
785	if str(term[1]) in G2mv.problemVars:
786	problemItem = True
787	if item[-1] == 'h': # Hold on variable
788	constSizer.Add((-1,-1),0) # blank space for edit button
789	typeString = 'FIXED'
790	var = str(item[0][1])
791	varMean = G2obj.fmtVarDescr(var)
792	eqString[-1] = var +' '
793	helptext = "Prevents variable:\n"+ var + " ("+ varMean + ")\nfrom being changed"
794	elif item[-1] == 'f' or item[-1] == 'e' or item[-1] == 'c': # not true on original-style (2011?) constraints
795	constEdit = wx.Button(pageDisplay,wx.ID_ANY,'Edit',style=wx.BU_EXACTFIT)
796	constEdit.Bind(wx.EVT_BUTTON,OnConstEdit)
797	constSizer.Add(constEdit,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1) # edit button
798	Indx[constEdit.GetId()] = [Id,name]
799	if item[-1] == 'f':
800	helptext = "A new variable"
801	if item[-3]:
802	helptext += " named "+str(item[-3])
803	helptext += " is created from a linear combination of the following variables:\n"
804	for term in item[:-3]:
805	var = str(term[1])
806	if len(eqString[-1]) > maxlen:
807	eqString.append(' ')
808	m = term[0]
809	if eqString[-1] != '':
810	if m >= 0:
811	eqString[-1] += ' + '
812	else:
813	eqString[-1] += ' - '
814	m = abs(m)
815	eqString[-1] += '{:g}*{:} '.format(m,var)
816	varMean = G2obj.fmtVarDescr(var)
817	helptext += "\n" + var + " ("+ varMean + ")"
818	if '_Explain' in data:
819	if data['_Explain'].get(item[-3]):
820	helptext += '\n\n'
821	helptext += data['_Explain'][item[-3]]
822	# typeString = 'NEWVAR'
823	# if item[-3]:
824	# eqString[-1] += ' = '+item[-3]
825	# else:
826	# eqString[-1] += ' = New Variable'
827	if item[-3]:
828	typeString = item[-3] + ' = '
829	else:
830	typeString = 'New Variable = '
831	#print 'refine',item[-2]
832	refineflag = True
833	elif item[-1] == 'c':
834	helptext = "The following variables constrained to equal a constant:"
835	for term in item[:-3]:
836	var = str(term[1])
837	if len(eqString[-1]) > maxlen:
838	eqString.append(' ')
839	m = term[0]
840	if eqString[-1] != '':
841	if term[0] > 0:
842	eqString[-1] += ' + '
843	else:
844	eqString[-1] += ' - '
845	m = -term[0]
846	eqString[-1] += '{:g}*{:} '.format(m,var)
847	varMean = G2obj.fmtVarDescr(var)
848	helptext += "\n" + var + " ("+ varMean + ")"
849	typeString = 'CONST'
850	eqString[-1] += ' = '+str(item[-3])
851	elif item[-1] == 'e':
852	helptext = "The following variables are set to be equivalent, noting multipliers:"
853	normval = item[:-3][1][0]
854	for i,term in enumerate(item[:-3]):
855	var = str(term[1])
856	if term[0] == 0: term[0] = 1.0
857	if len(eqString[-1]) > maxlen:
858	eqString.append(' ')
859	if i == 0: # move independent variable to end
860	indepterm = term
861	continue
862	elif eqString[-1] != '':
863	eqString[-1] += ' = '
864	if normval/term[0] == 1:
865	eqString[-1] += '{:}'.format(var)
866	else:
867	eqString[-1] += '{:g}*{:} '.format(normval/term[0],var)
868	varMean = G2obj.fmtVarDescr(var)
869	helptext += "\n" + var + " ("+ varMean + ")"
870	if normval/indepterm[0] == 1:
871	eqString[-1] += ' = {:} '.format(indepterm[1])
872	else:
873	eqString[-1] += ' = {:g}*{:} '.format(normval/indepterm[0],str(indepterm[1]))
874	typeString = 'EQUIV'
875	else:
876	print ('Unexpected constraint'+item)
877
878	else:
879	print ('Removing old-style constraints')
880	data[name] = []
881	return constSizer
882	constDel = wx.Button(pageDisplay,wx.ID_ANY,'Delete',style=wx.BU_EXACTFIT)
883	constDel.Bind(wx.EVT_BUTTON,OnConstDel)
884	Indx[constDel.GetId()] = [Id,name]
885	constSizer.Add(constDel,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1) # delete button
886	if helptext:
887	ch = G2G.HelpButton(pageDisplay,helptext)
888	constSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1)
889	else:
890	constSizer.Add((-1,-1))
891	if refineflag:
892	ch = G2G.G2CheckBox(pageDisplay,'',item,-2)
893	constSizer.Add(ch,0,wx.LEFT\|wx.RIGHT\|wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER,1)
894	else:
895	constSizer.Add((-1,-1))
896	constSizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,typeString),
897	0,wx.ALIGN_CENTER_VERTICAL\|wx.ALIGN_CENTER\|wx.RIGHT\|wx.LEFT,3)
898	if problemItem: eqString[-1] += ' -- Conflict: see console'
899	if len(eqString) > 1:
900	Eq = wx.BoxSizer(wx.VERTICAL)
901	for s in eqString:
902	line = wx.StaticText(pageDisplay,wx.ID_ANY,s)
903	if problemItem: line.SetBackgroundColour(wx.YELLOW)
904	Eq.Add(line,0,wx.ALIGN_CENTER_VERTICAL)
905	Eq.Add((-1,4))
906	else:
907	Eq = wx.StaticText(pageDisplay,wx.ID_ANY,eqString[0])
908	if problemItem: Eq.SetBackgroundColour(wx.YELLOW)
909	constSizer.Add(Eq,1,wx.ALIGN_CENTER_VERTICAL)
910	return constSizer
911
912	def OnConstDel(event):
913	'Delete a constraint'
914	Obj = event.GetEventObject()
915	Id,name = Indx[Obj.GetId()]
916	del data[name][Id]
917	ConstraintsLoad(data)
918	wx.CallAfter(OnPageChanged,None)
919
920	def OnConstEdit(event):
921	'''Called to edit an individual contraint in response to a
922	click on its Edit button
923	'''
924	Obj = event.GetEventObject()
925	Id,name = Indx[Obj.GetId()]
926	if data[name][Id][-1] == 'f':
927	items = data[name][Id][:-3]
928	constType = 'New Variable'
929	if data[name][Id][-3]:
930	varname = data[name][Id][-3]
931	else:
932	varname = ""
933	lbl = 'Enter value for each term in constraint; sum = new variable'
934	dlg = ConstraintDialog(G2frame,constType,lbl,items,
935	varname=varname,varyflag=data[name][Id][-2])
936	elif data[name][Id][-1] == 'c':
937	items = data[name][Id][:-3]+[
938	[data[name][Id][-3],'fixed value =']]
939	constType = 'Constraint'
940	lbl = 'Edit value for each term in constant constraint sum'
941	dlg = ConstraintDialog(G2frame,constType,lbl,items)
942	elif data[name][Id][-1] == 'e':
943	items = data[name][Id][:-3]
944	constType = 'Equivalence'
945	lbl = 'The following terms are set to be equal:'
946	dlg = ConstraintDialog(G2frame,constType,lbl,items,'/')
947	else:
948	return
949	try:
950	prev = data[name][Id][:]
951	if dlg.ShowModal() == wx.ID_OK:
952	result = dlg.GetData()
953	for i in range(len(data[name][Id][:-3])):
954	if type(data[name][Id][i]) is tuple: # fix non-mutable construct
955	data[name][Id][i] = list(data[name][Id][i])
956	data[name][Id][i][0] = result[i][0]
957	if data[name][Id][-1] == 'c':
958	data[name][Id][-3] = str(result[-1][0])
959	elif data[name][Id][-1] == 'f':
960	# process the variable name to put in global form (::var)
961	varname = str(dlg.newvar[0]).strip().replace(' ','_')
962	if varname.startswith('::'):
963	varname = varname[2:]
964	varname = varname.replace(':',';')
965	if varname:
966	data[name][Id][-3] = varname
967	else:
968	data[name][Id][-3] = ''
969	data[name][Id][-2] = dlg.newvar[1]
970	if not CheckChangedConstraint():
971	data[name][Id] = prev
972	except:
973	import traceback
974	print (traceback.format_exc())
975	finally:
976	dlg.Destroy()
977	wx.CallAfter(OnPageChanged,None)
978
979	def UpdateConstraintPanel(panel,typ):
980	'''Update the contents of the selected Constraint
981	notebook tab. Called in :func:`OnPageChanged`
982	'''
983	if panel.GetSizer(): panel.GetSizer().Clear(True)
984	Siz = wx.BoxSizer(wx.VERTICAL)
985	Siz.Add((5,5),0)
986	Siz.Add(MakeConstraintsSizer(typ,panel),1,wx.EXPAND)
987	panel.SetSizer(Siz,True)
988	Size = Siz.GetMinSize()
989	Size[0] += 40
990	Size[1] = max(Size[1],450) + 20
991	panel.SetSize(Size)
992	panel.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
993	panel.Show()
994
995	def OnPageChanged(event):
996	'''Called when a tab is pressed or when a "select tab" menu button is
997	used (see RaisePage), or to refresh the current tab contents (event=None)
998	'''
999	if event: #page change event!
1000	page = event.GetSelection()
1001	else: # called directly, get current page
1002	page = G2frame.constr.GetSelection()
1003	G2frame.constr.ChangeSelection(page)
1004	text = G2frame.constr.GetPageText(page)
1005	G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_EQUIVALANCEATOMS,False)
1006	# G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_ADDRIDING,False)
1007	if text == 'Histogram/Phase':
1008	enableEditCons = [False]+4*[True]
1009	G2frame.Page = [page,'hap']
1010	UpdateConstraintPanel(HAPConstr,'HAP')
1011	elif text == 'Histogram':
1012	enableEditCons = [False]+4*[True]
1013	G2frame.Page = [page,'hst']
1014	UpdateConstraintPanel(HistConstr,'Hist')
1015	elif text == 'Phase':
1016	enableEditCons = 5*[True]
1017	G2frame.Page = [page,'phs']
1018	G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_EQUIVALANCEATOMS,True)
1019	# G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_ADDRIDING,True)
1020	if 'DELETED' in str(PhaseConstr): #seems to be no other way to do this (wx bug)
1021	if GSASIIpath.GetConfigValue('debug'):
1022	print ('DBG_wx error: PhaseConstr not cleanly deleted after Refine')
1023	return
1024	UpdateConstraintPanel(PhaseConstr,'Phase')
1025	elif text == 'Global':
1026	enableEditCons = [False]+4*[True]
1027	G2frame.Page = [page,'glb']
1028	UpdateConstraintPanel(GlobalConstr,'Global')
1029	else:
1030	enableEditCons = 5*[False]
1031	G2frame.Page = [page,'sym']
1032	UpdateConstraintPanel(SymConstr,'Sym-Generated')
1033	# remove menu items when not allowed
1034	for obj,flag in zip(G2frame.dataWindow.ConstraintEdit.GetMenuItems(),enableEditCons):
1035	obj.Enable(flag)
1036	G2frame.dataWindow.SetDataSize()
1037
1038	def RaisePage(event):
1039	'Respond to a "select tab" menu button'
1040	try:
1041	i = (G2G.wxID_CONSPHASE,
1042	G2G.wxID_CONSHAP,
1043	G2G.wxID_CONSHIST,
1044	G2G.wxID_CONSGLOBAL,
1045	G2G.wxID_CONSSYM,
1046	).index(event.GetId())
1047	G2frame.constr.SetSelection(i)
1048	wx.CallAfter(OnPageChanged,None)
1049	except ValueError:
1050	print('Unexpected event in RaisePage')
1051
1052	def SetStatusLine(text):
1053	G2frame.GetStatusBar().SetStatusText(text,1)
1054
1055	# UpdateConstraints execution starts here
1056	if not data:
1057	data.update({'Hist':[],'HAP':[],'Phase':[],'Global':[]}) #empty dict - fill it
1058	if 'Global' not in data: #patch
1059	data['Global'] = []
1060	# DEBUG code ########################################
1061	#import GSASIIconstrGUI
1062	#reload(GSASIIconstrGUI)
1063	#reload(G2obj)
1064	#reload(G2stIO)
1065	#import GSASIIstrMain
1066	#reload(GSASIIstrMain)
1067	#reload(G2mv)
1068	#reload(G2gd)
1069	###################################################
1070	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
1071	if not len(Phases) or not len(Histograms):
1072	dlg = wx.MessageDialog(G2frame,'You need both phases and histograms to see Constraints',
1073	'No phases or histograms')
1074	dlg.CenterOnParent()
1075	dlg.ShowModal()
1076	dlg.Destroy()
1077	return
1078	G2obj.IndexAllIds(Histograms,Phases)
1079	##################################################################################
1080	# patch: convert old-style (str) variables in constraints to G2VarObj objects
1081	for key,value in data.items():
1082	if key.startswith('_'): continue
1083	j = 0
1084	for cons in value:
1085	#print cons # DEBUG
1086	for i in range(len(cons[:-3])):
1087	if type(cons[i][1]) is str:
1088	cons[i][1] = G2obj.G2VarObj(cons[i][1])
1089	j += 1
1090	if j:
1091	print (str(key) + ': '+str(j)+' variable(s) as strings converted to objects')
1092	##################################################################################
1093	rigidbodyDict = G2frame.GPXtree.GetItemPyData(
1094	G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1095	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1096	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1097	badPhaseParms = ['Ax','Ay','Az','Amul','AI/A','Atype','SHorder','mV0','mV1','mV2','AwaveType','FwaveType','PwaveType','MwaveType','Vol','isMag',]
1098	globalList = list(rbDict.keys())
1099	globalList.sort()
1100	try:
1101	AtomDict = dict([Phases[phase]['pId'],Phases[phase]['Atoms']] for phase in Phases)
1102	except KeyError:
1103	G2frame.ErrorDialog('Constraint Error','Constraints cannot be set until a cycle of least squares'+
1104	' has been run.\nWe suggest you refine a scale factor.')
1105	return
1106
1107	# create a list of the phase variables
1108	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable,MFtable,maxSSwave = G2stIO.GetPhaseData(Phases,rbIds=rbIds,Print=False)
1109	phaseList = []
1110	for item in phaseDict:
1111	if item.split(':')[2] not in badPhaseParms:
1112	phaseList.append(item)
1113	phaseList.sort()
1114	phaseAtNames = {}
1115	phaseAtTypes = {}
1116	TypeList = []
1117	for item in phaseList:
1118	Split = item.split(':')
1119	if Split[2][:2] in ['AU','Af','dA','AM']:
1120	Id = int(Split[0])
1121	phaseAtNames[item] = AtomDict[Id][int(Split[3])][0]
1122	phaseAtTypes[item] = AtomDict[Id][int(Split[3])][1]
1123	if phaseAtTypes[item] not in TypeList:
1124	TypeList.append(phaseAtTypes[item])
1125	else:
1126	phaseAtNames[item] = ''
1127	phaseAtTypes[item] = ''
1128
1129	# create a list of the hist*phase variables
1130	seqList = G2frame.testSeqRefineMode()
1131	if seqList: # for sequential refinement, only process 1st histgram in list
1132	histDict = {seqList[0]:Histograms[seqList[0]]}
1133	else:
1134	histDict = Histograms
1135	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,histDict,Print=False,resetRefList=False)
1136	hapList = sorted([i for i in hapDict.keys() if i.split(':')[2] not in ('Type',)])
1137	if seqList: # convert histogram # to wildcard
1138	wildList = [] # list of variables with "*" for histogram number
1139	for i in hapList:
1140	s = i.split(':')
1141	if s[1] == "": continue
1142	s[1] = '*'
1143	sj = ':'.join(s)
1144	if sj not in wildList: wildList.append(sj)
1145	hapList = wildList
1146	histVary,histDict,controlDict = G2stIO.GetHistogramData(histDict,Print=False)
1147	histList = list(histDict.keys())
1148	histList.sort()
1149	if seqList: # convert histogram # to wildcard
1150	wildList = [] # list of variables with "*" for histogram number
1151	for i in histList:
1152	s = i.split(':')
1153	if s[1] == "": continue
1154	s[1] = '*'
1155	sj = ':'.join(s)
1156	if sj not in wildList: wildList.append(sj)
1157	histList = wildList
1158	Indx = {}
1159	G2frame.Page = [0,'phs']
1160
1161	G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.ConstraintMenu)
1162	SetStatusLine('')
1163
1164	G2frame.Bind(wx.EVT_MENU, OnAddConstraint, id=G2G.wxID_CONSTRAINTADD)
1165	G2frame.Bind(wx.EVT_MENU, OnAddFunction, id=G2G.wxID_FUNCTADD)
1166	G2frame.Bind(wx.EVT_MENU, OnAddEquivalence, id=G2G.wxID_EQUIVADD)
1167	G2frame.Bind(wx.EVT_MENU, OnAddHold, id=G2G.wxID_HOLDADD)
1168	G2frame.Bind(wx.EVT_MENU, OnAddAtomEquiv, id=G2G.wxID_EQUIVALANCEATOMS)
1169	# G2frame.Bind(wx.EVT_MENU, OnAddRiding, id=G2G.wxID_ADDRIDING)
1170	# tab commands
1171	for id in (G2G.wxID_CONSPHASE,
1172	G2G.wxID_CONSHAP,
1173	G2G.wxID_CONSHIST,
1174	G2G.wxID_CONSGLOBAL,
1175	G2G.wxID_CONSSYM,
1176	):
1177	G2frame.Bind(wx.EVT_MENU, RaisePage,id=id)
1178
1179	#G2frame.constr = G2G.GSNoteBook(parent=G2frame.dataWindow,size=G2frame.dataWindow.GetClientSize())
1180	G2frame.constr = G2G.GSNoteBook(parent=G2frame.dataWindow)
1181	G2frame.dataWindow.GetSizer().Add(G2frame.constr,1,wx.ALL\|wx.EXPAND)
1182	# note that order of pages is hard-coded in RaisePage
1183	PhaseConstr = wx.ScrolledWindow(G2frame.constr)
1184	G2frame.constr.AddPage(PhaseConstr,'Phase')
1185	HAPConstr = wx.ScrolledWindow(G2frame.constr)
1186	G2frame.constr.AddPage(HAPConstr,'Histogram/Phase')
1187	HistConstr = wx.ScrolledWindow(G2frame.constr)
1188	G2frame.constr.AddPage(HistConstr,'Histogram')
1189	GlobalConstr = wx.ScrolledWindow(G2frame.constr)
1190	G2frame.constr.AddPage(GlobalConstr,'Global')
1191	SymConstr = wx.ScrolledWindow(G2frame.constr)
1192	G2frame.constr.AddPage(SymConstr,'Sym-Generated')
1193	wx.CallAfter(OnPageChanged,None)
1194	G2frame.constr.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
1195	# validate all the constrants -- should not see any errors here normally
1196	errmsg,warnmsg = ConstraintsCheck(data)
1197	if errmsg:
1198	G2frame.ErrorDialog('Constraint Error',
1199	'Error in constraints:\n'+errmsg+'\nCheck console output for more information',
1200	parent=G2frame)
1201	print (errmsg)
1202	print (G2mv.VarRemapShow([],True))
1203	elif warnmsg:
1204	print ('Unexpected contraint warning:\n'+warnmsg)
1205
1206	################################################################################
1207	# check scale & phase fractions, create constraint if needed
1208	################################################################################
1209	def CheckAllScalePhaseFractions(G2frame):
1210	'''Check if scale factor and all phase fractions are refined without a constraint
1211	for all used histograms, if so, offer the user a chance to create a constraint
1212	on the sum of phase fractions
1213	'''
1214	histograms, phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
1215	for i,hist in enumerate(histograms):
1216	CheckScalePhaseFractions(G2frame,hist,histograms,phases)
1217
1218	def CheckScalePhaseFractions(G2frame,hist,histograms,phases):
1219	'''Check if scale factor and all phase fractions are refined without a constraint
1220	for histogram hist, if so, offer the user a chance to create a constraint
1221	on the sum of phase fractions
1222	'''
1223	if G2frame.testSeqRefineMode():
1224	histStr = '*'
1225	else:
1226	histStr = str(histograms[hist]['hId'])
1227	# Is this powder?
1228	if not hist.startswith('PWDR '): return
1229	# do this only if the scale factor is varied
1230	if not histograms[hist]['Sample Parameters']['Scale'][1]: return
1231	# are all phase fractions varied in all used histograms?
1232	phaseCount = 0
1233	for p in phases:
1234	if hist not in phases[p]['Histograms']: continue
1235	if phases[p]['Histograms'][hist]['Use'] and not phases[p]['Histograms'][hist]['Scale'][1]:
1236	return
1237	else:
1238	phaseCount += 1
1239
1240	# all phase fractions and scale factor varied, now scan through constraints
1241	sub = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
1242	Constraints = G2frame.GPXtree.GetItemPyData(sub)
1243	for c in Constraints.get('HAP',[]):
1244	if c[-1] != 'c': continue
1245	if not c[-3]: continue
1246	if len(c[:-3]) != phaseCount: continue
1247	# got a constraint equation with right number of terms, is it on phase fractions for
1248	# the correct histogram?
1249	if all([(i[1].name == 'Scale' and i[1].varname().split(':')[1] == histStr) for i in c[:-3]]):
1250	# got a constraint, this is OK
1251	return
1252	dlg = wx.MessageDialog(G2frame,'You are refining the scale factor and all phase fractions for histogram #'+
1253	histStr+'. This will produce an unstable refinement. '+
1254	'Do you want to constrain the sum of phase fractions?','Create constraint?',wx.OK\|wx.CANCEL)
1255	if dlg.ShowModal() != wx.ID_OK:
1256	dlg.Destroy()
1257	return
1258	dlg.Destroy()
1259
1260	constr = []
1261	for p in phases:
1262	if hist not in phases[p]['Histograms']: continue
1263	if not phases[p]['Histograms'][hist]['Use']: continue
1264	constr += [[1.0,G2obj.G2VarObj(':'.join((str(phases[p]['pId']),histStr,'Scale')))]]
1265	constr += [1.0,None,'c']
1266	Constraints['HAP'] += [constr]
1267
1268	################################################################################
1269	#### Make nuclear/magnetic phase transition constraints - called by OnTransform in G2phsGUI
1270	################################################################################
1271
1272	def TransConstraints(G2frame,oldPhase,newPhase,Trans,Vec,atCodes):
1273	'''Add constraints for new magnetic phase created via transformation of old
1274	nuclear one
1275	NB: A = [G11,G22,G33,2G12,2G13,2*G23]
1276	'''
1277
1278	def SetUniqAj(pId,iA,SGData):
1279	SGLaue = SGData['SGLaue']
1280	SGUniq = SGData['SGUniq']
1281	if SGLaue in ['m3','m3m']:
1282	if iA in [0,1,2]:
1283	parm = '%d::%s'%(pId,'A0')
1284	else:
1285	parm = None
1286	elif SGLaue in ['4/m','4/mmm']:
1287	if iA in [0,1]:
1288	parm = '%d::%s'%(pId,'A0')
1289	elif iA == 2:
1290	parm = '%d::%s'%(pId,'A2')
1291	else:
1292	parm = None
1293	elif SGLaue in ['6/m','6/mmm','3m1', '31m', '3']:
1294	if iA in [0,1,3]:
1295	parm = '%d::%s'%(pId,'A0')
1296	elif iA == 2:
1297	parm = '%d::%s'%(pId,'A2')
1298	else:
1299	parm = None
1300	elif SGLaue in ['3R', '3mR']:
1301	if ia in [0,1,2]:
1302	parm = '%d::%s'%(pId,'A0')
1303	else:
1304	parm = '%d::%s'%(pId,'A3')
1305	elif SGLaue in ['mmm',]:
1306	if iA in [0,1,2]:
1307	parm = '%d::A%s'%(pId,iA)
1308	else:
1309	parm = None
1310	elif SGLaue == '2/m':
1311	if iA in [0,1,2]:
1312	parm = '%d::A%s'%(pId,iA)
1313	elif iA == 3 and SGUniq == 'c':
1314	parm = '%d::A%s'%(pId,iA)
1315	elif iA == 4 and SGUniq == 'b':
1316	parm = '%d::A%s'%(pId,iA)
1317	elif iA == 5 and SGUniq == 'a':
1318	parm = '%d::A%s'%(pId,iA)
1319	else:
1320	parm = None
1321	else:
1322	parm = '%d::A%s'%(pId,iA)
1323	return parm
1324
1325	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
1326	UseList = newPhase['Histograms']
1327	detTrans = np.abs(nl.det(Trans))
1328	opId = oldPhase['pId']
1329	npId = newPhase['pId']
1330	cx,ct,cs,cia = newPhase['General']['AtomPtrs']
1331	nAtoms = newPhase['Atoms']
1332	oSGData = oldPhase['General']['SGData']
1333	nSGData = newPhase['General']['SGData']
1334	#oAcof = G2lat.cell2A(oldPhase['General']['Cell'][1:7])
1335	#nAcof = G2lat.cell2A(newPhase['General']['Cell'][1:7])
1336	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
1337	if not item:
1338	print('Error: no constraints in Data Tree')
1339	return
1340	constraints = G2frame.GPXtree.GetItemPyData(item)
1341	xnames = ['dAx','dAy','dAz']
1342	# constraints on matching atom params between phases
1343	for ia,code in enumerate(atCodes):
1344	atom = nAtoms[ia]
1345	if not ia and atom[cia] == 'A':
1346	wx.MessageDialog(G2frame,
1347	'Anisotropic thermal motion constraints are not developed at the present time',
1348	'Anisotropic thermal constraint?',style=wx.ICON_INFORMATION).ShowModal()
1349	siteSym = G2spc.SytSym(atom[cx:cx+3],nSGData)[0]
1350	CSX = G2spc.GetCSxinel(siteSym)
1351	# CSU = G2spc.GetCSuinel(siteSym)
1352	item = code.split('+')[0]
1353	iat,opr = item.split(':')
1354	Nop = abs(int(opr))%100-1
1355	if '-' in opr:
1356	Nop *= -1
1357	Opr = oldPhase['General']['SGData']['SGOps'][abs(Nop)][0]
1358	if Nop < 0: #inversion
1359	Opr *= -1
1360	XOpr = np.inner(Opr,Trans)
1361	for ix in list(set(CSX[0])):
1362	if not ix:
1363	continue
1364	name = xnames[ix-1]
1365	IndpCon = [1.0,G2obj.G2VarObj('%d::%s:%d'%(npId,name,ia))]
1366	DepCons = []
1367	for iop,opval in enumerate(XOpr[ix-1]):
1368	if opval:
1369	DepCons.append([opval,G2obj.G2VarObj('%d::%s:%s'%(opId,xnames[iop],iat))])
1370	if len(DepCons) == 1:
1371	constraints['Phase'].append([DepCons[0],IndpCon,None,None,'e'])
1372	elif len(DepCons) > 1:
1373	for Dep in DepCons:
1374	Dep[0] *= -1
1375	constraints['Phase'].append([IndpCon]+DepCons+[0.0,None,'c'])
1376	for name in ['Afrac','AUiso']:
1377	IndpCon = [1.0,G2obj.G2VarObj('%d::%s:%d'%(npId,name,ia))]
1378	DepCons = [1.0,G2obj.G2VarObj('%d::%s:%s'%(opId,name,iat))]
1379	constraints['Phase'].append([DepCons,IndpCon,None,None,'e'])
1380
1381	# unfinished Anisotropic constraint generation
1382	# Uids = [[0,0,'AU11'],[1,1,'AU22'],[2,2,'AU33'],[0,1,'AU12'],[0,2,'AU13'],[1,2,'AU23']]
1383	# DepConsDict = dict(zip(Us,[[],[],[],[],[],[]]))
1384	# for iu,Uid in enumerate(Uids):
1385	# UMT = np.zeros((3,3))
1386	# UMT[Uid[0],Uid[1]] = 1
1387	# nUMT = G2lat.prodMGMT(UMT,invTrans)
1388	# nUT = G2lat.UijtoU6(nUMT)
1389	# for iu,nU in enumerate(nUT):
1390	# if abs(nU) > 1.e-8:
1391	# parm = '%d::%s;%s'%(opId,Us[iu],iat)
1392	# DepConsDict[Uid[2]].append([abs(nU%1.),G2obj.G2VarObj(parm)])
1393	# nUcof = atom[iu:iu+6]
1394	# conStrings = []
1395	# for iU,Usi in enumerate(Us):
1396	# parm = '%d::%s;%d'%(npId,Usi,ia)
1397	# parmDict[parm] = nUcof[iU]
1398	# varyList.append(parm)
1399	# IndpCon = [1.0,G2obj.G2VarObj(parm)]
1400	# conStr = str([IndpCon,DepConsDict[Usi]])
1401	# if conStr in conStrings:
1402	# continue
1403	# conStrings.append(conStr)
1404	# if len(DepConsDict[Usi]) == 1:
1405	# if DepConsDict[Usi][0]:
1406	# constraints['Phase'].append([IndpCon,DepConsDict[Usi][0],None,None,'e'])
1407	# elif len(DepConsDict[Usi]) > 1:
1408	# for Dep in DepConsDict[Usi]:
1409	# Dep[0] *= -1
1410	# constraints['Phase'].append([IndpCon]+DepConsDict[Usi]+[0.0,None,'c'])
1411
1412	#how do I do Uij's for most Trans?
1413
1414	T = nl.inv(Trans).T
1415	conMat = [
1416	[T[0,0]2,T[0,1]2,T[0,2]*2,T[0,0]T[0,1],T[0,0]T[0,2],T[0,1]T[0,2]],
1417	[T[1,0]2,T[1,1]2,T[1,2]*2,T[1,0]T[1,1],T[1,0]T[1,2],T[1,1]T[1,2]],
1418	[T[2,0]2,T[2,1]2,T[2,2]*2,T[2,0]T[2,1],T[2,0]T[2,2],T[2,1]T[2,2]],
1419	[2.T[0,0]T[1,0],2.T[0,1]T[1,1],2.T[0,2]T[1,2],T[0,0]T[1,1]+T[0,1]T[1,0],T[0,0]T[1,2]+T[0,2]T[1,0],T[0,1]T[1,2]+T[0,2]T[1,1]],
1420	[2.T[0,0]T[2,0],2.T[0,1]T[2,1],2.T[0,2]T[2,2],T[0,0]T[2,1]+T[0,1]T[2,0],T[0,0]T[2,2]+T[0,2]T[2,0],T[0,1]T[2,2]+T[0,2]T[2,1]],
1421	[2.T[1,0]T[2,0],2.T[1,1]T[2,1],2.T[1,2]T[2,2],T[1,0]T[2,1]+T[1,1]T[2,0],T[1,0]T[2,2]+T[1,2]T[2,0],T[1,1]T[2,2]+T[1,2]T[2,1]]
1422	]
1423	# Gnew = conMat * A:
1424	# T00*2a0 T01*2a1 T02*2a2 T00T01a3 T00T02a4 T01T02a5
1425	# T10*2a0 T11*2a1 T12*2a2 T10T11a3 T10T12a4 T11T12a5
1426	# T20*2a0 T21*2a1 T22*2a2 T20T21a3 T20T22a4 T21T22a5
1427	# 2T00T10a0 2T01T11a1 2T02T12a2 (T00T11 + T01T10)a3 (T00T12 + T02T10)a4 (T01T12 + T02T11)a5
1428	# 2T00T20a0 2T01T21a1 2T02T22a2 (T00T21 + T01T20)a3 (T00T22 + T02T20)a4 (T01T22 + T02T21)a5
1429	# 2T10T20a0 2T11T21a1 2T12T22a2 (T10T21 + T11T20)a3 (T10T22 + T12T20)a4 (T11T22 + T12T21)a5
1430	# Generated as symbolic code using:
1431	# import sym
1432	# A0, A1, A2, A3, A4, A5 = sym.symbols('A0, A1, A2, A3, A4, A5')
1433	# G = sym.Matrix([ [A0, A3/2., A4/2.], [A3/2., A1, A5/2.], [A4/2., A5/2., A2]])
1434	# transformation matrix
1435	# T00, T10, T20, T01, T11, T21, T02, T12, T22 = sym.symbols('T00, T10, T20, T01, T11, T21, T02, T12, T22')
1436	# Tr = sym.Matrix([ [T00, T10, T20], [T01, T11, T21], [T02, T12, T22],])
1437	# Gnew = (Tr.TG)Tr
1438
1439	for iAnew,Asi in enumerate(['A0','A1','A2','A3','A4','A5']): # loop through A[i] for new cell
1440	Nparm = str(npId) + '::' + Asi
1441	if Nparm != SetUniqAj(npId,iAnew,nSGData): continue # skip if already constrainted
1442	multDict = {}
1443	for iAorg in range(6):
1444	cA = conMat[iAnew][iAorg] # coeff for A[i] in constraint matrix
1445	if abs(cA) < 1.e-8: continue
1446	parm = SetUniqAj(opId,iAorg,oSGData) # translate to unique A[i] in original cell
1447	if not parm: continue
1448	# sum coeff
1449	if parm in multDict:
1450	multDict[parm] += cA
1451	else:
1452	multDict[parm] = cA
1453	# any non-zero multipliers?
1454	maxMult = 0
1455	for i in multDict:
1456	maxMult = max(maxMult,abs(multDict[i]))
1457	if maxMult <= 0: continue
1458
1459	# create constraint (if needed) or equivalence
1460	if len(multDict) == 1:
1461	key = list(multDict.keys())[0]
1462	constr = [
1463	[1.0,G2obj.G2VarObj(key)],
1464	[multDict[key],G2obj.G2VarObj(Nparm)],
1465	None,None,'e']
1466	else:
1467	constr = [[-1.0,G2obj.G2VarObj(Nparm)]]
1468	for key in multDict:
1469	constr += [[multDict[key],G2obj.G2VarObj(key)]]
1470	constr += [0.0,None,'c']
1471	constraints['Phase'] += [constr]
1472
1473	# constraints on HAP Scale, etc.
1474	for hId,hist in enumerate(UseList): #HAP - seems OK
1475	ohapkey = '%d:%d:'%(opId,hId)
1476	nhapkey = '%d:%d:'%(npId,hId)
1477	IndpCon = [1.0,G2obj.G2VarObj(ohapkey+'Scale')]
1478	DepCons = [detTrans,G2obj.G2VarObj(nhapkey+'Scale')]
1479	constraints['HAP'].append([DepCons,IndpCon,None,None,'e'])
1480	for name in ['Size;i','Mustrain;i']:
1481	IndpCon = [1.0,G2obj.G2VarObj(ohapkey+name)]
1482	DepCons = [1.0,G2obj.G2VarObj(nhapkey+name)]
1483	constraints['HAP'].append([IndpCon,DepCons,None,None,'e'])
1484
1485	################################################################################
1486	#### Rigid bodies
1487	################################################################################
1488
1489	def UpdateRigidBodies(G2frame,data):
1490	'''Called when Rigid bodies tree item is selected.
1491	Displays the rigid bodies in the data window
1492	'''
1493	if not data.get('RBIds') or not data:
1494	data.update({'Vector':{'AtInfo':{}},'Residue':{'AtInfo':{}},
1495	'RBIds':{'Vector':[],'Residue':[]}}) #empty/bad dict - fill it
1496
1497	global resList,rbId
1498	Indx = {}
1499	resList = []
1500	plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':30.,'viewDir':[0,0,1],}
1501
1502	G2frame.rbBook = G2G.GSNoteBook(parent=G2frame.dataWindow)
1503	G2frame.dataWindow.GetSizer().Add(G2frame.rbBook,1,wx.ALL\|wx.EXPAND)
1504	VectorRB = wx.ScrolledWindow(G2frame.rbBook)
1505	VectorRBDisplay = wx.Panel(VectorRB)
1506	G2frame.rbBook.AddPage(VectorRB,'Vector rigid bodies')
1507	ResidueRB = wx.ScrolledWindow(G2frame.rbBook)
1508	ResidueRBDisplay = wx.Panel(ResidueRB)
1509	G2frame.rbBook.AddPage(ResidueRB,'Residue rigid bodies')
1510
1511	def OnPageChanged(event):
1512	global resList
1513	resList = []
1514	if event: #page change event!
1515	page = event.GetSelection()
1516	else:
1517	page = G2frame.rbBook.GetSelection()
1518	G2frame.rbBook.ChangeSelection(page)
1519	text = G2frame.rbBook.GetPageText(page)
1520	if text == 'Vector rigid bodies':
1521	G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.VectorBodyMenu)
1522	G2frame.Bind(wx.EVT_MENU, AddVectorRB, id=G2G.wxID_VECTORBODYADD)
1523	G2frame.Page = [page,'vrb']
1524	UpdateVectorRB()
1525	elif text == 'Residue rigid bodies':
1526	G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RigidBodyMenu)
1527	G2frame.Bind(wx.EVT_MENU, AddResidueRB, id=G2G.wxID_RIGIDBODYADD)
1528	G2frame.Bind(wx.EVT_MENU, OnImportRigidBody, id=G2G.wxID_RIGIDBODYIMPORT)
1529	G2frame.Bind(wx.EVT_MENU, OnDefineTorsSeq, id=G2G.wxID_RESIDUETORSSEQ) #enable only if residue RBs exist?
1530	G2frame.Page = [page,'rrb']
1531	UpdateResidueRB()
1532
1533	def getMacroFile(macName):
1534	defDir = os.path.join(os.path.split(__file__)[0],'GSASIImacros')
1535	dlg = wx.FileDialog(G2frame,message='Choose '+macName+' rigid body macro file',
1536	defaultDir=defDir,defaultFile="",wildcard="GSAS-II macro file (.mac)\|.mac",
1537	style=wx.FD_OPEN \| wx.FD_CHANGE_DIR)
1538	try:
1539	if dlg.ShowModal() == wx.ID_OK:
1540	macfile = dlg.GetPath()
1541	macro = open(macfile,'Ur')
1542	head = macro.readline()
1543	if macName not in head:
1544	print (head)
1545	print ('** ERROR - wrong restraint macro file selected, try again **')
1546	macro = []
1547	else: # cancel was pressed
1548	macro = []
1549	finally:
1550	dlg.Destroy()
1551	return macro #advanced past 1st line
1552
1553	def getTextFile():
1554	dlg = wx.FileDialog(G2frame,'Choose rigid body text file', '.', '',
1555	"GSAS-II text file (.txt)\|.txt\|XYZ file (.xyz)\|.xyz\|"
1556	"Sybyl mol2 file (.mol2)\|.mol2\|PDB file (.pdb;.ent)\|.pdb;.ent",
1557	wx.FD_OPEN \| wx.FD_CHANGE_DIR)
1558	try:
1559	if dlg.ShowModal() == wx.ID_OK:
1560	txtfile = dlg.GetPath()
1561	ext = os.path.splitext(txtfile)[1]
1562	text = open(txtfile,'Ur')
1563	else: # cancel was pressed
1564	ext = ''
1565	text = []
1566	finally:
1567	dlg.Destroy()
1568	if 'ent' in ext:
1569	ext = '.pdb'
1570	return text,ext.lower()
1571
1572	def OnImportRigidBody(event):
1573	page = G2frame.rbBook.GetSelection()
1574	if 'Vector' in G2frame.rbBook.GetPageText(page):
1575	pass
1576	elif 'Residue' in G2frame.rbBook.GetPageText(page):
1577	ImportResidueRB()
1578
1579	def AddVectorRB(event):
1580	AtInfo = data['Vector']['AtInfo']
1581	dlg = G2G.MultiIntegerDialog(G2frame,'New Rigid Body',['No. atoms','No. translations'],[1,1])
1582	if dlg.ShowModal() == wx.ID_OK:
1583	nAtoms,nTrans = dlg.GetValues()
1584	rbId = ran.randint(0,sys.maxsize)
1585	vecMag = [1.0 for i in range(nTrans)]
1586	vecRef = [False for i in range(nTrans)]
1587	vecVal = [np.zeros((nAtoms,3)) for j in range(nTrans)]
1588	rbTypes = ['C' for i in range(nAtoms)]
1589	Info = G2elem.GetAtomInfo('C')
1590	AtInfo['C'] = [Info['Drad'],Info['Color']]
1591	data['Vector'][rbId] = {'RBname':'UNKRB','VectMag':vecMag,'rbXYZ':np.zeros((nAtoms,3)),
1592	'rbRef':[0,1,2,False],'VectRef':vecRef,'rbTypes':rbTypes,'rbVect':vecVal,'useCount':0}
1593	data['RBIds']['Vector'].append(rbId)
1594	dlg.Destroy()
1595	UpdateVectorRB()
1596
1597	def AddResidueRB(event):
1598	AtInfo = data['Residue']['AtInfo']
1599	macro = getMacroFile('rigid body')
1600	if not macro:
1601	return
1602	macStr = macro.readline()
1603	while macStr:
1604	items = macStr.split()
1605	if 'I' == items[0]:
1606	rbId = ran.randint(0,sys.maxsize)
1607	rbName = items[1]
1608	rbTypes = []
1609	rbXYZ = []
1610	rbSeq = []
1611	atNames = []
1612	nAtms,nSeq,nOrig,mRef,nRef = [int(items[i]) for i in [2,3,4,5,6]]
1613	for iAtm in range(nAtms):
1614	macStr = macro.readline().split()
1615	atName = macStr[0]
1616	atType = macStr[1]
1617	atNames.append(atName)
1618	rbXYZ.append([float(macStr[i]) for i in [2,3,4]])
1619	rbTypes.append(atType)
1620	if atType not in AtInfo:
1621	Info = G2elem.GetAtomInfo(atType)
1622	AtInfo[atType] = [Info['Drad'],Info['Color']]
1623	rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[nOrig-1])
1624	for iSeq in range(nSeq):
1625	macStr = macro.readline().split()
1626	mSeq = int(macStr[0])
1627	for jSeq in range(mSeq):
1628	macStr = macro.readline().split()
1629	iBeg = int(macStr[0])-1
1630	iFin = int(macStr[1])-1
1631	angle = 0.0
1632	nMove = int(macStr[2])
1633	iMove = [int(macStr[i])-1 for i in range(3,nMove+3)]
1634	rbSeq.append([iBeg,iFin,angle,iMove])
1635	data['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbTypes,
1636	'atNames':atNames,'rbRef':[nOrig-1,mRef-1,nRef-1,True],'rbSeq':rbSeq,
1637	'SelSeq':[0,0],'useCount':0}
1638	data['RBIds']['Residue'].append(rbId)
1639	print ('Rigid body '+rbName+' added')
1640	macStr = macro.readline()
1641	macro.close()
1642	UpdateResidueRB()
1643
1644	def ImportResidueRB():
1645	AtInfo = data['Residue']['AtInfo']
1646	text,ext = getTextFile()
1647	if not text:
1648	return
1649	rbId = ran.randint(0,sys.maxsize)
1650	rbTypes = []
1651	rbXYZ = []
1652	atNames = []
1653	txtStr = text.readline()
1654	if 'xyz' in ext:
1655	txtStr = text.readline()
1656	txtStr = text.readline()
1657	elif 'mol2' in ext:
1658	while 'ATOM' not in txtStr:
1659	txtStr = text.readline()
1660	txtStr = text.readline()
1661	elif 'pdb' in ext:
1662	while 'ATOM' not in txtStr[:6] and 'HETATM' not in txtStr[:6]:
1663	txtStr = text.readline()
1664	#print txtStr
1665	items = txtStr.split()
1666	while len(items):
1667	if 'txt' in ext:
1668	atName = items[0]
1669	atType = items[1]
1670	rbXYZ.append([float(items[i]) for i in [2,3,4]])
1671	elif 'xyz' in ext:
1672	atType = items[0]
1673	rbXYZ.append([float(items[i]) for i in [1,2,3]])
1674	atName = atType+str(len(rbXYZ))
1675	elif 'mol2' in ext:
1676	atType = items[1]
1677	atName = items[1]+items[0]
1678	rbXYZ.append([float(items[i]) for i in [2,3,4]])
1679	elif 'pdb' in ext:
1680	atType = items[-1]
1681	atName = items[2]
1682	xyz = txtStr[30:55].split()
1683	rbXYZ.append([float(x) for x in xyz])
1684	atNames.append(atName)
1685	rbTypes.append(atType)
1686	if atType not in AtInfo:
1687	Info = G2elem.GetAtomInfo(atType)
1688	AtInfo[atType] = [Info['Drad'],Info['Color']]
1689	txtStr = text.readline()
1690	if 'mol2' in ext and 'BOND' in txtStr:
1691	break
1692	if 'pdb' in ext and ('ATOM' not in txtStr[:6] and 'HETATM' not in txtStr[:6]):
1693	break
1694	items = txtStr.split()
1695	if len(atNames) < 3:
1696	G2G.G2MessageBox(G2frame,'Not enough atoms in rigid body; must be 3 or more')
1697	else:
1698	rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[0])
1699	Xxyz = rbXYZ[1]
1700	X = Xxyz/np.sqrt(np.sum(Xxyz**2))
1701	Yxyz = rbXYZ[2]
1702	Y = Yxyz/np.sqrt(np.sum(Yxyz**2))
1703	Mat = G2mth.getRBTransMat(X,Y)
1704	rbXYZ = np.inner(Mat,rbXYZ).T
1705	data['Residue'][rbId] = {'RBname':'UNKRB','rbXYZ':rbXYZ,'rbTypes':rbTypes,
1706	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1707	data['RBIds']['Residue'].append(rbId)
1708	print ('Rigid body UNKRB added')
1709	text.close()
1710	UpdateResidueRB(rbId)
1711
1712	def FindNeighbors(Orig,XYZ,atTypes,atNames,AtInfo):
1713	Radii = []
1714	for Atype in atTypes:
1715	Radii.append(AtInfo[Atype][0])
1716	Radii = np.array(Radii)
1717	Neigh = []
1718	Dx = XYZ-XYZ[Orig]
1719	dist = np.sqrt(np.sum(Dx**2,axis=1))
1720	sumR = Radii[Orig]+Radii
1721	IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.))
1722	for j in IndB[0]:
1723	if j != Orig and atTypes[j] != 'H':
1724	Neigh.append(atNames[j])
1725	return Neigh
1726
1727	def FindAllNeighbors(XYZ,atTypes,atNames,AtInfo):
1728	NeighDict = {}
1729	for iat,xyz in enumerate(atNames):
1730	NeighDict[atNames[iat]] = FindNeighbors(iat,XYZ,atTypes,atNames,AtInfo)
1731	return NeighDict
1732
1733	def FindRiding(Orig,Pivot,NeighDict):
1734	riding = [Orig,Pivot]
1735	iAdd = 1
1736	new = True
1737	while new:
1738	newAtms = NeighDict[riding[iAdd]]
1739	for At in newAtms:
1740	new = False
1741	if At not in riding:
1742	riding.append(At)
1743	new = True
1744	iAdd += 1
1745	if iAdd < len(riding):
1746	new = True
1747	return riding[2:]
1748
1749	def OnDefineTorsSeq(event):
1750	global rbId
1751	rbData = data['Residue'][rbId]
1752	if not len(rbData):
1753	return
1754	atNames = rbData['atNames']
1755	AtInfo = data['Residue']['AtInfo']
1756	atTypes = rbData['rbTypes']
1757	XYZ = rbData['rbXYZ']
1758	neighDict = FindAllNeighbors(XYZ,atTypes,atNames,AtInfo)
1759	TargList = []
1760	dlg = wx.SingleChoiceDialog(G2frame,'Select origin atom for torsion sequence','Origin atom',rbData['atNames'])
1761	if dlg.ShowModal() == wx.ID_OK:
1762	Orig = dlg.GetSelection()
1763	TargList = neighDict[atNames[Orig]]
1764	dlg.Destroy()
1765	if not len(TargList):
1766	return
1767	dlg = wx.SingleChoiceDialog(G2frame,'Select pivot atom for torsion sequence','Pivot atom',TargList)
1768	if dlg.ShowModal() == wx.ID_OK:
1769	Piv = atNames.index(TargList[dlg.GetSelection()])
1770	riding = FindRiding(atNames[Orig],atNames[Piv],neighDict)
1771	Riding = []
1772	for atm in riding:
1773	Riding.append(atNames.index(atm))
1774	rbData['rbSeq'].append([Orig,Piv,0.0,Riding])
1775	dlg.Destroy()
1776	UpdateResidueRB(rbId)
1777
1778	def UpdateVectorRB(Scroll=0):
1779	AtInfo = data['Vector']['AtInfo']
1780	refChoice = {}
1781	if 'DELETED' in str(G2frame.GetStatusBar()): #seems to be no other way to do this (wx bug)
1782	if GSASIIpath.GetConfigValue('debug'):
1783	print ('DBG_wx error: Rigid Body/Status not cleanly deleted after Refine')
1784	return
1785	SetStatusLine(' You may use e.g. "c60" or "s60" for a vector entry')
1786	def rbNameSizer(rbId,rbData):
1787
1788	def OnRBName(event):
1789	event.Skip()
1790	Obj = event.GetEventObject()
1791	rbData['RBname'] = Obj.GetValue()
1792
1793	def OnDelRB(event):
1794	Obj = event.GetEventObject()
1795	rbId = Indx[Obj.GetId()]
1796	if rbId in data['Vector']:
1797	del data['Vector'][rbId]
1798	data['RBIds']['Vector'].remove(rbId)
1799	rbData['useCount'] -= 1
1800	wx.CallAfter(UpdateVectorRB)
1801
1802	def OnPlotRB(event):
1803	Obj = event.GetEventObject()
1804	Obj.SetValue(False)
1805	G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,rbData,plotDefaults)
1806
1807	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
1808	nameSizer.Add(wx.StaticText(VectorRBDisplay,-1,'Rigid body name: '),
1809	0,wx.ALIGN_CENTER_VERTICAL)
1810	RBname = wx.TextCtrl(VectorRBDisplay,-1,rbData['RBname'])
1811	Indx[RBname.GetId()] = rbId
1812	RBname.Bind(wx.EVT_TEXT_ENTER,OnRBName)
1813	RBname.Bind(wx.EVT_KILL_FOCUS,OnRBName)
1814	nameSizer.Add(RBname,0,wx.ALIGN_CENTER_VERTICAL)
1815	nameSizer.Add((5,0),)
1816	plotRB = wx.CheckBox(VectorRBDisplay,-1,'Plot?')
1817	Indx[plotRB.GetId()] = rbId
1818	plotRB.Bind(wx.EVT_CHECKBOX,OnPlotRB)
1819	nameSizer.Add(plotRB,0,wx.ALIGN_CENTER_VERTICAL)
1820	nameSizer.Add((5,0),)
1821	if not rbData['useCount']:
1822	delRB = wx.CheckBox(VectorRBDisplay,-1,'Delete?')
1823	Indx[delRB.GetId()] = rbId
1824	delRB.Bind(wx.EVT_CHECKBOX,OnDelRB)
1825	nameSizer.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
1826	return nameSizer
1827
1828	def rbRefAtmSizer(rbId,rbData):
1829
1830	def OnRefSel(event):
1831	Obj = event.GetEventObject()
1832	iref = Indx[Obj.GetId()]
1833	sel = Obj.GetValue()
1834	rbData['rbRef'][iref] = atNames.index(sel)
1835	FillRefChoice(rbId,rbData)
1836
1837	refAtmSizer = wx.BoxSizer(wx.HORIZONTAL)
1838	atNames = [name+str(i) for i,name in enumerate(rbData['rbTypes'])]
1839	rbRef = rbData.get('rbRef',[0,1,2,False])
1840	rbData['rbRef'] = rbRef
1841	if rbData['useCount']:
1842	refAtmSizer.Add(wx.StaticText(VectorRBDisplay,-1,
1843	'Orientation reference atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \
1844	atNames[rbRef[1]],atNames[rbRef[2]])),0)
1845	else:
1846	refAtmSizer.Add(wx.StaticText(VectorRBDisplay,-1,
1847	'Orientation reference atoms A-B-C: '),0,wx.ALIGN_CENTER_VERTICAL)
1848	for i in range(3):
1849	choices = [atNames[j] for j in refChoice[rbId][i]]
1850	refSel = wx.ComboBox(VectorRBDisplay,-1,value='',
1851	choices=choices,style=wx.CB_READONLY\|wx.CB_DROPDOWN)
1852	refSel.SetValue(atNames[rbRef[i]])
1853	refSel.Bind(wx.EVT_COMBOBOX, OnRefSel)
1854	Indx[refSel.GetId()] = i
1855	refAtmSizer.Add(refSel,0,wx.ALIGN_CENTER_VERTICAL)
1856	return refAtmSizer
1857
1858	def rbVectMag(rbId,imag,rbData):
1859
1860	def OnRBVectorMag(event):
1861	event.Skip()
1862	Obj = event.GetEventObject()
1863	rbId,imag = Indx[Obj.GetId()]
1864	try:
1865	val = float(Obj.GetValue())
1866	if val <= 0.:
1867	raise ValueError
1868	rbData['VectMag'][imag] = val
1869	except ValueError:
1870	pass
1871	Obj.SetValue('%8.4f'%(val))
1872	wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
1873	G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,data['Vector'][rbId],plotDefaults)
1874
1875	def OnRBVectorRef(event):
1876	Obj = event.GetEventObject()
1877	rbId,imag = Indx[Obj.GetId()]
1878	rbData['VectRef'][imag] = Obj.GetValue()
1879
1880	magSizer = wx.BoxSizer(wx.HORIZONTAL)
1881	magSizer.Add(wx.StaticText(VectorRBDisplay,-1,'Translation magnitude: '),
1882	0,wx.ALIGN_CENTER_VERTICAL)
1883	magValue = wx.TextCtrl(VectorRBDisplay,-1,'%8.4f'%(rbData['VectMag'][imag]))
1884	Indx[magValue.GetId()] = [rbId,imag]
1885	magValue.Bind(wx.EVT_TEXT_ENTER,OnRBVectorMag)
1886	magValue.Bind(wx.EVT_KILL_FOCUS,OnRBVectorMag)
1887	magSizer.Add(magValue,0,wx.ALIGN_CENTER_VERTICAL)
1888	magSizer.Add((5,0),)
1889	magref = wx.CheckBox(VectorRBDisplay,-1,label=' Refine?')
1890	magref.SetValue(rbData['VectRef'][imag])
1891	magref.Bind(wx.EVT_CHECKBOX,OnRBVectorRef)
1892	Indx[magref.GetId()] = [rbId,imag]
1893	magSizer.Add(magref,0,wx.ALIGN_CENTER_VERTICAL)
1894	return magSizer
1895
1896	def rbVectors(rbId,imag,mag,XYZ,rbData):
1897
1898	def TypeSelect(event):
1899	AtInfo = data['Vector']['AtInfo']
1900	r,c = event.GetRow(),event.GetCol()
1901	if vecGrid.GetColLabelValue(c) == 'Type':
1902	PE = G2elemGUI.PickElement(G2frame,oneOnly=True)
1903	if PE.ShowModal() == wx.ID_OK:
1904	if PE.Elem != 'None':
1905	El = PE.Elem.strip().lower().capitalize()
1906	if El not in AtInfo:
1907	Info = G2elem.GetAtomInfo(El)
1908	AtInfo[El] = [Info['Drad'],Info['Color']]
1909	rbData['rbTypes'][r] = El
1910	vecGrid.SetCellValue(r,c,El)
1911	PE.Destroy()
1912	wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
1913
1914	def ChangeCell(event):
1915	r,c = event.GetRow(),event.GetCol()
1916	if r >= 0 and (0 <= c < 3):
1917	try:
1918	val = float(vecGrid.GetCellValue(r,c))
1919	rbData['rbVect'][imag][r][c] = val
1920	except ValueError:
1921	pass
1922	G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,data['Vector'][rbId],plotDefaults)
1923	wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL))
1924
1925	vecSizer = wx.BoxSizer()
1926	Types = 3[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_STRING,]+3[wg.GRID_VALUE_FLOAT+':10,5',]
1927	colLabels = ['Vector x','Vector y','Vector z','Type','Cart x','Cart y','Cart z']
1928	table = []
1929	rowLabels = []
1930	for ivec,xyz in enumerate(rbData['rbVect'][imag]):
1931	table.append(list(xyz)+[rbData['rbTypes'][ivec],]+list(XYZ[ivec]))
1932	rowLabels.append(str(ivec))
1933	vecTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1934	vecGrid = G2G.GSGrid(VectorRBDisplay)
1935	vecGrid.SetTable(vecTable, True)
1936	if 'phoenix' in wx.version():
1937	vecGrid.Bind(wg.EVT_GRID_CELL_CHANGED, ChangeCell)
1938	else:
1939	vecGrid.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeCell)
1940	if not imag:
1941	vecGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, TypeSelect)
1942	attr = wx.grid.GridCellAttr()
1943	attr.SetEditor(G2G.GridFractionEditor(vecGrid))
1944	for c in range(3):
1945	vecGrid.SetColAttr(c, attr)
1946	for row in range(vecTable.GetNumberRows()):
1947	if imag:
1948	vecGrid.SetCellStyle(row,3,VERY_LIGHT_GREY,True)
1949	for col in [4,5,6]:
1950	vecGrid.SetCellStyle(row,col,VERY_LIGHT_GREY,True)
1951	# vecGrid.SetScrollRate(0,0)
1952	vecGrid.AutoSizeColumns(False)
1953	vecSizer.Add(vecGrid)
1954	return vecSizer
1955
1956	def FillRefChoice(rbId,rbData):
1957	choiceIds = [i for i in range(len(rbData['rbTypes']))]
1958
1959	rbRef = rbData.get('rbRef',[-1,-1,-1,False])
1960	for i in range(3):
1961	choiceIds.remove(rbRef[i])
1962	refChoice[rbId] = [choiceIds[:],choiceIds[:],choiceIds[:]]
1963	for i in range(3):
1964	refChoice[rbId][i].append(rbRef[i])
1965	refChoice[rbId][i].sort()
1966
1967	if VectorRB.GetSizer(): VectorRB.GetSizer().Clear(True)
1968	VectorRBSizer = wx.BoxSizer(wx.VERTICAL)
1969	for rbId in data['RBIds']['Vector']:
1970	if rbId != 'AtInfo':
1971	rbData = data['Vector'][rbId]
1972	FillRefChoice(rbId,rbData)
1973	VectorRBSizer.Add(rbNameSizer(rbId,rbData),0)
1974	VectorRBSizer.Add(rbRefAtmSizer(rbId,rbData),0)
1975	XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']])
1976	for imag,mag in enumerate(rbData['VectMag']):
1977	XYZ += mag*rbData['rbVect'][imag]
1978	VectorRBSizer.Add(rbVectMag(rbId,imag,rbData),0)
1979	VectorRBSizer.Add(rbVectors(rbId,imag,mag,XYZ,rbData),0)
1980	VectorRBSizer.Add((5,5),0)
1981	data['Vector'][rbId]['rbXYZ'] = XYZ
1982	VectorRBSizer.Layout()
1983	VectorRBDisplay.SetSizer(VectorRBSizer,True)
1984	Size = VectorRBSizer.GetMinSize()
1985	Size[0] += 40
1986	Size[1] = max(Size[1],450) + 20
1987	VectorRBDisplay.SetSize(Size)
1988	VectorRB.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
1989	VectorRB.Scroll(0,Scroll)
1990
1991	def UpdateResidueRB(rbId=0):
1992	AtInfo = data['Residue']['AtInfo']
1993	refChoice = {}
1994	RefObjs = []
1995
1996	def rbNameSizer(rbId,rbData):
1997
1998	def OnRBName(event):
1999	Obj = event.GetEventObject()
2000	rbData['RBname'] = Obj.GetValue()
2001	wx.CallAfter(UpdateResidueRB,rbId)
2002
2003	def OnDelRB(event):
2004	Obj = event.GetEventObject()
2005	rbId = Indx[Obj.GetId()]
2006	if rbId in data['Residue']:
2007	del data['Residue'][rbId]
2008	data['RBIds']['Residue'].remove(rbId)
2009	wx.CallAfter(UpdateResidueRB)
2010
2011	def OnStripH(event):
2012	Obj = event.GetEventObject()
2013	rbId = Indx[Obj.GetId()]
2014	if rbId in data['Residue']:
2015	newNames = []
2016	newTypes = []
2017	newXYZ = []
2018	for i,atype in enumerate(rbData['rbTypes']):
2019	if atype != 'H':
2020	newNames.append(rbData['atNames'][i])
2021	newTypes.append(rbData['rbTypes'][i])
2022	newXYZ.append(rbData['rbXYZ'][i])
2023	rbData['atNames'] = newNames
2024	rbData['rbTypes'] = newTypes
2025	rbData['rbXYZ'] = newXYZ
2026	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
2027	wx.CallAfter(UpdateResidueRB,rbId)
2028
2029	def OnPlotRB(event):
2030	Obj = event.GetEventObject()
2031	Obj.SetValue(False)
2032	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
2033
2034	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
2035	nameSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'Residue name: '),
2036	0,wx.ALIGN_CENTER_VERTICAL)
2037	RBname = wx.TextCtrl(ResidueRBDisplay,-1,rbData['RBname'])
2038	Indx[RBname.GetId()] = rbId
2039	RBname.Bind(wx.EVT_TEXT_ENTER,OnRBName)
2040	RBname.Bind(wx.EVT_KILL_FOCUS,OnRBName)
2041	nameSizer.Add(RBname,0,wx.ALIGN_CENTER_VERTICAL)
2042	nameSizer.Add((5,0),)
2043	plotRB = wx.CheckBox(ResidueRBDisplay,-1,'Plot?')
2044	Indx[plotRB.GetId()] = rbId
2045	plotRB.Bind(wx.EVT_CHECKBOX,OnPlotRB)
2046	nameSizer.Add(plotRB,0,wx.ALIGN_CENTER_VERTICAL)
2047	nameSizer.Add((5,0),)
2048	if not rbData['useCount']:
2049	delRB = wx.CheckBox(ResidueRBDisplay,-1,'Delete?')
2050	Indx[delRB.GetId()] = rbId
2051	delRB.Bind(wx.EVT_CHECKBOX,OnDelRB)
2052	nameSizer.Add(delRB,0,wx.ALIGN_CENTER_VERTICAL)
2053	if 'H' in rbData['rbTypes']:
2054	stripH = wx.CheckBox(ResidueRBDisplay,-1,'Strip H-atoms?')
2055	Indx[stripH.GetId()] = rbId
2056	stripH.Bind(wx.EVT_CHECKBOX,OnStripH)
2057	nameSizer.Add(stripH,0,wx.ALIGN_CENTER_VERTICAL)
2058	return nameSizer
2059
2060	def rbResidues(rbId,rbData):
2061
2062	def TypeSelect(event):
2063	AtInfo = data['Residue']['AtInfo']
2064	r,c = event.GetRow(),event.GetCol()
2065	if vecGrid.GetColLabelValue(c) == 'Type':
2066	PE = G2elemGUI.PickElement(G2frame,oneOnly=True)
2067	if PE.ShowModal() == wx.ID_OK:
2068	if PE.Elem != 'None':
2069	El = PE.Elem.strip().lower().capitalize()
2070	if El not in AtInfo:
2071	Info = G2elem.GetAtomInfo(El)
2072	AtInfo[El] = [Info['Drad']['Color']]
2073	rbData['rbTypes'][r] = El
2074	vecGrid.SetCellValue(r,c,El)
2075	PE.Destroy()
2076
2077	def ChangeCell(event):
2078	r,c = event.GetRow(),event.GetCol()
2079	if r >= 0 and (0 <= c < 3):
2080	try:
2081	val = float(vecGrid.GetCellValue(r,c))
2082	rbData['rbXYZ'][r][c] = val
2083	except ValueError:
2084	pass
2085
2086	def RowSelect(event):
2087	r,c = event.GetRow(),event.GetCol()
2088	if c < 0: #only row clicks
2089	for vecgrid in resList:
2090	vecgrid.ClearSelection()
2091	vecGrid.SelectRow(r,True)
2092
2093	def OnRefSel(event):
2094
2095	Obj = event.GetEventObject()
2096	iref,res,jref = Indx[Obj.GetId()]
2097	sel = Obj.GetValue()
2098	ind = atNames.index(sel)
2099	if rbData['rbTypes'][ind] == 'H':
2100	G2G.G2MessageBox(G2frame,'You should not select an H-atom for rigid body orientation')
2101	rbData['rbRef'][iref] = ind
2102	FillRefChoice(rbId,rbData)
2103	for i,ref in enumerate(RefObjs[jref]):
2104	ref.SetItems([atNames[j] for j in refChoice[rbId][i]])
2105	ref.SetValue(atNames[rbData['rbRef'][i]])
2106	rbXYZ = rbData['rbXYZ']
2107	if not iref: #origin change
2108	rbXYZ -= rbXYZ[ind]
2109	#TODO - transform all atom XYZ by axis choices
2110	Xxyz = rbXYZ[rbData['rbRef'][1]]
2111	X = Xxyz/np.sqrt(np.sum(Xxyz**2))
2112	Yxyz = rbXYZ[rbData['rbRef'][2]]
2113	Y = Yxyz/np.sqrt(np.sum(Yxyz**2))
2114	Mat = G2mth.getRBTransMat(X,Y)
2115	rbXYZ = np.inner(Mat,rbXYZ).T
2116	rbData['rbXYZ'] = rbXYZ
2117	res.ClearSelection()
2118	resTable = res.GetTable()
2119	for r in range(res.GetNumberRows()):
2120	row = resTable.GetRowValues(r)
2121	row[2:4] = rbXYZ[r]
2122	resTable.SetRowValues(r,row)
2123	res.ForceRefresh()
2124	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
2125
2126	Types = 2[wg.GRID_VALUE_STRING,]+3[wg.GRID_VALUE_FLOAT+':10,5',]
2127	colLabels = ['Name','Type','Cart x','Cart y','Cart z']
2128	table = []
2129	rowLabels = []
2130	for ivec,xyz in enumerate(rbData['rbXYZ']):
2131	table.append([rbData['atNames'][ivec],]+[rbData['rbTypes'][ivec],]+list(xyz))
2132	rowLabels.append(str(ivec))
2133	vecTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
2134	vecGrid = G2G.GSGrid(ResidueRBDisplay)
2135	Indx[vecGrid.GetId()] = rbId
2136	resList.append(vecGrid)
2137	vecGrid.SetTable(vecTable, True)
2138	if 'phoenix' in wx.version():
2139	vecGrid.Bind(wg.EVT_GRID_CELL_CHANGED, ChangeCell)
2140	else:
2141	vecGrid.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeCell)
2142	vecGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, TypeSelect)
2143	vecGrid.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
2144	attr = wx.grid.GridCellAttr()
2145	attr.SetEditor(G2G.GridFractionEditor(vecGrid))
2146	for c in range(3):
2147	vecGrid.SetColAttr(c, attr)
2148	for row in range(vecTable.GetNumberRows()):
2149	for col in range(5):
2150	vecGrid.SetCellStyle(row,col,VERY_LIGHT_GREY,True)
2151	vecGrid.AutoSizeColumns(False)
2152	vecSizer = wx.BoxSizer()
2153	vecSizer.Add(vecGrid)
2154
2155	refAtmSizer = wx.BoxSizer(wx.HORIZONTAL)
2156	atNames = rbData['atNames']
2157	rbRef = rbData['rbRef']
2158	if rbData['rbRef'][3] or rbData['useCount']:
2159	refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
2160	'Orientation reference non-H atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \
2161	atNames[rbRef[1]],atNames[rbRef[2]])),0)
2162	else:
2163	refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
2164	'Orientation reference non-H atoms A-B-C: '),0,wx.ALIGN_CENTER_VERTICAL)
2165	refObj = [0,0,0]
2166	for i in range(3):
2167	choices = [atNames[j] for j in refChoice[rbId][i]]
2168	refSel = wx.ComboBox(ResidueRBDisplay,-1,value='',
2169	choices=choices,style=wx.CB_READONLY\|wx.CB_DROPDOWN)
2170	refSel.SetValue(atNames[rbRef[i]])
2171	refSel.Bind(wx.EVT_COMBOBOX, OnRefSel)
2172	Indx[refSel.GetId()] = [i,vecGrid,len(RefObjs)]
2173	refObj[i] = refSel
2174	refAtmSizer.Add(refSel,0,wx.ALIGN_CENTER_VERTICAL)
2175	RefObjs.append(refObj)
2176
2177	mainSizer = wx.BoxSizer(wx.VERTICAL)
2178	mainSizer.Add(refAtmSizer)
2179	mainSizer.Add(vecSizer)
2180	return mainSizer
2181
2182	def SeqSizer(angSlide,rbId,iSeq,Seq,atNames):
2183
2184	def ChangeAngle(event):
2185	event.Skip()
2186	Obj = event.GetEventObject()
2187	rbId,Seq = Indx[Obj.GetId()][:2]
2188	val = Seq[2]
2189	try:
2190	val = float(Obj.GetValue())
2191	Seq[2] = val
2192	except ValueError:
2193	pass
2194	Obj.SetValue('%8.2f'%(val))
2195	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,data['Residue'][rbId],plotDefaults)
2196
2197	def OnRadBtn(event):
2198	Obj = event.GetEventObject()
2199	Seq,iSeq,angId = Indx[Obj.GetId()]
2200	data['Residue'][rbId]['SelSeq'] = [iSeq,angId]
2201	angSlide.SetValue(int(100*Seq[2]))
2202
2203	def OnDelBtn(event):
2204	Obj = event.GetEventObject()
2205	rbId,Seq = Indx[Obj.GetId()]
2206	data['Residue'][rbId]['rbSeq'].remove(Seq)
2207	wx.CallAfter(UpdateResidueRB,rbId)
2208
2209	seqSizer = wx.FlexGridSizer(0,5,2,2)
2210	seqSizer.AddGrowableCol(3,0)
2211	iBeg,iFin,angle,iMove = Seq
2212	ang = wx.TextCtrl(ResidueRBDisplay,-1,'%8.2f'%(angle),size=(50,20))
2213	if not iSeq:
2214	radBt = wx.RadioButton(ResidueRBDisplay,-1,'',style=wx.RB_GROUP)
2215	data['Residue'][rbId]['SelSeq'] = [iSeq,ang.GetId()]
2216	else:
2217	radBt = wx.RadioButton(ResidueRBDisplay,-1,'')
2218	radBt.Bind(wx.EVT_RADIOBUTTON,OnRadBtn)
2219	seqSizer.Add(radBt)
2220	delBt = wx.RadioButton(ResidueRBDisplay,-1,'')
2221	delBt.Bind(wx.EVT_RADIOBUTTON,OnDelBtn)
2222	seqSizer.Add(delBt)
2223	bond = wx.TextCtrl(ResidueRBDisplay,-1,'%s %s'%(atNames[iBeg],atNames[iFin]),size=(50,20))
2224	seqSizer.Add(bond,0,wx.ALIGN_CENTER_VERTICAL)
2225	Indx[radBt.GetId()] = [Seq,iSeq,ang.GetId()]
2226	Indx[delBt.GetId()] = [rbId,Seq]
2227	Indx[ang.GetId()] = [rbId,Seq,ang]
2228	ang.Bind(wx.EVT_TEXT_ENTER,ChangeAngle)
2229	ang.Bind(wx.EVT_KILL_FOCUS,ChangeAngle)
2230	seqSizer.Add(ang,0,wx.ALIGN_CENTER_VERTICAL)
2231	atms = ''
2232	for i in iMove:
2233	atms += ' %s,'%(atNames[i])
2234	moves = wx.TextCtrl(ResidueRBDisplay,-1,atms[:-1],size=(200,20))
2235	seqSizer.Add(moves,1,wx.ALIGN_CENTER_VERTICAL\|wx.EXPAND\|wx.RIGHT)
2236	return seqSizer
2237
2238	def SlideSizer():
2239
2240	def OnSlider(event):
2241	Obj = event.GetEventObject()
2242	rbData = Indx[Obj.GetId()]
2243	iSeq,angId = rbData['SelSeq']
2244	val = float(Obj.GetValue())/100.
2245	rbData['rbSeq'][iSeq][2] = val
2246	Indx[angId][2].SetValue('%8.2f'%(val))
2247	G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults)
2248
2249	slideSizer = wx.BoxSizer(wx.HORIZONTAL)
2250	slideSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'Selected torsion angle:'),0)
2251	iSeq,angId = rbData['SelSeq']
2252	angSlide = wx.Slider(ResidueRBDisplay,-1,
2253	int(100*rbData['rbSeq'][iSeq][2]),0,36000,size=(200,20),
2254	style=wx.SL_HORIZONTAL)
2255	angSlide.Bind(wx.EVT_SLIDER, OnSlider)
2256	Indx[angSlide.GetId()] = rbData
2257	slideSizer.Add(angSlide,0)
2258	return slideSizer,angSlide
2259
2260	def FillRefChoice(rbId,rbData):
2261	choiceIds = [i for i in range(len(rbData['atNames']))]
2262	for seq in rbData['rbSeq']:
2263	for i in seq[3]:
2264	try:
2265	choiceIds.remove(i)
2266	except ValueError:
2267	pass
2268	rbRef = rbData['rbRef']
2269	for i in range(3):
2270	try:
2271	choiceIds.remove(rbRef[i])
2272	except ValueError:
2273	pass
2274	refChoice[rbId] = [choiceIds[:],choiceIds[:],choiceIds[:]]
2275	for i in range(3):
2276	refChoice[rbId][i].append(rbRef[i])
2277	refChoice[rbId][i].sort()
2278
2279	def OnSelect(event):
2280	rbname = rbchoice[select.GetSelection()]
2281	rbId = RBnames[rbname]
2282	wx.CallLater(100,UpdateResidueRB,rbId)
2283
2284	GS = ResidueRBDisplay.GetSizer()
2285	if GS:
2286	try: #get around a c++ error in wx 4.0; doing is again seems to be OK
2287	GS.Clear(True)
2288	except:
2289	GS.Clear(True)
2290
2291	RBnames = {}
2292	for rbid in data['RBIds']['Residue']:
2293	RBnames.update({data['Residue'][rbid]['RBname']:rbid,})
2294	if not RBnames:
2295	return
2296	rbchoice = list(RBnames.keys())
2297	ResidueRBSizer = wx.BoxSizer(wx.VERTICAL)
2298	if len(RBnames) > 1:
2299	selSizer = wx.BoxSizer(wx.HORIZONTAL)
2300	selSizer.Add(wx.StaticText(ResidueRBDisplay,label=' Select residue to view:'),0)
2301	rbchoice.sort()
2302	select = wx.ComboBox(ResidueRBDisplay,choices=rbchoice)
2303	select.Bind(wx.EVT_COMBOBOX,OnSelect)
2304	selSizer.Add(select,0)
2305	ResidueRBSizer.Add(selSizer,0)
2306	if not rbId:
2307	rbId = RBnames[rbchoice[0]]
2308	rbData = data['Residue'][rbId]
2309	FillRefChoice(rbId,rbData)
2310	ResidueRBSizer.Add(rbNameSizer(rbId,rbData),0)
2311	ResidueRBSizer.Add(rbResidues(rbId,rbData),0)
2312	ResidueRBSizer.Add((5,5),0)
2313	if rbData['rbSeq']:
2314	slideSizer,angSlide = SlideSizer()
2315	if len(rbData['rbSeq']):
2316	ResidueRBSizer.Add(wx.StaticText(ResidueRBDisplay,-1,
2317	'Sel Del Bond Angle Riding atoms'),
2318	0,wx.ALIGN_CENTER_VERTICAL)
2319	for iSeq,Seq in enumerate(rbData['rbSeq']):
2320	ResidueRBSizer.Add(SeqSizer(angSlide,rbId,iSeq,Seq,rbData['atNames']))
2321	if rbData['rbSeq']:
2322	ResidueRBSizer.Add(slideSizer,)
2323
2324	ResidueRBSizer.Add((5,25),)
2325	ResidueRBSizer.Layout()
2326	ResidueRBDisplay.SetSizer(ResidueRBSizer,True)
2327	ResidueRBDisplay.SetAutoLayout(True)
2328	Size = ResidueRBSizer.GetMinSize()
2329	ResidueRBDisplay.SetSize(Size)
2330	ResidueRBDisplay.Show()
2331
2332	def SetStatusLine(text):
2333	G2frame.GetStatusBar().SetStatusText(text,1)
2334
2335	G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RigidBodyMenu)
2336	SetStatusLine('')
2337	UpdateVectorRB()
2338	G2frame.rbBook.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
2339	wx.CallAfter(OnPageChanged,None)

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