Source code for GSASIIphsGUI

# -*- coding: utf-8 -*-
#GSASII - phase data display routines
#========== SVN repository information ###################
# $Date: 2024-02-05 15:49:09 -0600 (Mon, 05 Feb 2024) $
# $Author: toby $
# $Revision: 5722 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIphsGUI.py $
# $Id: GSASIIphsGUI.py 5722 2024-02-05 21:49:09Z toby $
#========== SVN repository information ###################
'''
Main routine here is :func:`UpdatePhaseData`, which displays the phase information
(called from :func:`GSASIIdataGUI:SelectDataTreeItem`).

Other top-level routines are: 
:func:`GetSpGrpfromUser` (called locally only);
:func:`FindBondsDraw` and :func:`FindBondsDrawCell` (called locally and in GSASIIplot); 
:func:`SetPhaseWindow` (called locally and in GSASIIddataGUI and GSASIIrestrGUI, multiple locations)
to control scrolling.

Routines for Phase dataframes follow. 
'''
from __future__ import division, print_function
import platform
import os
import wx
import wx.grid as wg
import wx.lib.scrolledpanel as wxscroll
import matplotlib as mpl
#import math
import copy
import time
import sys
import random as ran
import subprocess as subp
import distutils.file_util as disfile
import scipy.optimize as so
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 5722 $")
import GSASIIlattice as G2lat
import GSASIIspc as G2spc
import GSASIIElem as G2elem
import GSASIIElemGUI as G2elemGUI
import GSASIIddataGUI as G2ddG
import GSASIIplot as G2plt
# if GSASIIpath.GetConfigValue('debug'):
#     print('Debug reloading',G2plt)
#     import imp
#     imp.reload(G2plt)
import GSASIIdataGUI as G2gd
import GSASIIIO as G2IO
import GSASIIstrMain as G2stMn
import GSASIIstrIO as G2stIO
import GSASIImath as G2mth
import GSASIIpwd as G2pwd
import GSASIIobj as G2obj
import GSASIIctrlGUI as G2G
import GSASIIfiles as G2fl
import GSASIIconstrGUI as G2cnstG
import numpy as np
import numpy.linalg as nl
import numpy.ma as ma
import atmdata
import ISODISTORT as ISO

try:
    wx.NewIdRef
    wx.NewId = wx.NewIdRef
except AttributeError:
    pass

try:
    VERY_LIGHT_GREY = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BTNFACE)
    WHITE = wx.SystemSettings.GetColour(wx.SYS_COLOUR_WINDOW)
    BLACK = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BTNTEXT)
    RED = wx.Colour(255,0,0)
    WACV = wx.ALIGN_CENTER_VERTICAL
except:
    pass
mapDefault = G2elem.mapDefault
TabSelectionIdDict = {}
# trig functions in degrees
sind = lambda x: np.sin(x*np.pi/180.)
tand = lambda x: np.tan(x*np.pi/180.)
cosd = lambda x: np.cos(x*np.pi/180.)
asind = lambda x: 180.*np.arcsin(x)/np.pi
acosd = lambda x: 180.*np.arccos(x)/np.pi
atan2d = lambda x,y: 180.*np.arctan2(y,x)/np.pi
is_exe = lambda fpath: os.path.isfile(fpath) and os.access(fpath, os.X_OK)
sqt2 = np.sqrt(2.)
sqt3 = np.sqrt(3.)

# previous rigid body selections
prevResId = None
prevVecId = None
prevSpnId = None

if '2' in platform.python_version_tuple()[0]:
    GkDelta = unichr(0x0394)
    Angstr = unichr(0x00c5)
else:
    GkDelta = chr(0x0394)
    Angstr = chr(0x00c5)   

RMCmisc = {}
#### phase class definitions ################################################################################
[docs] class SymOpDialog(wx.Dialog): '''Class to select a symmetry operator ''' def __init__(self,parent,SGData,New=True,ForceUnit=False): wx.Dialog.__init__(self,parent,-1,'Select symmetry operator', pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) panel = wx.Panel(self) self.SGData = SGData self.New = New self.Force = ForceUnit self.OpSelected = [0,0,0,[0,0,0],False,False] mainSizer = wx.BoxSizer(wx.VERTICAL) if ForceUnit: choice = ['No','Yes'] self.force = wx.RadioBox(panel,-1,'Force to unit cell?',choices=choice) self.force.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) mainSizer.Add(self.force,0,wx.TOP,5) # if SGData['SGInv']: choice = ['No','Yes'] self.inv = wx.RadioBox(panel,-1,'Choose inversion?',choices=choice) self.inv.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) mainSizer.Add(self.inv,0) if SGData['SGLatt'] != 'P': LattOp = G2spc.Latt2text(SGData['SGCen']).split(';') self.latt = wx.RadioBox(panel,-1,'Choose cell centering?',choices=LattOp) self.latt.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) mainSizer.Add(self.latt,0) if SGData['SGLaue'] in ['-1','2/m','mmm','4/m','4/mmm']: Ncol = 2 else: Ncol = 3 OpList = [] for Opr in SGData['SGOps']: OpList.append(G2spc.MT2text(Opr)) self.oprs = wx.RadioBox(panel,-1,'Choose space group operator?',choices=OpList, majorDimension=Ncol) self.oprs.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) mainSizer.Add(self.oprs,0,wx.BOTTOM,5) mainSizer.Add(wx.StaticText(panel,-1," Choose unit cell?"),0) cellSizer = wx.BoxSizer(wx.HORIZONTAL) cellName = ['X','Y','Z'] self.cell = [] for i in range(3): self.cell.append(wx.SpinCtrl(panel,-1,cellName[i],size=wx.Size(50,20))) self.cell[-1].SetRange(-3,3) self.cell[-1].SetValue(0) self.cell[-1].Bind(wx.EVT_SPINCTRL, self.OnOpSelect) cellSizer.Add(self.cell[-1],0) mainSizer.Add(cellSizer,0,wx.BOTTOM,5) if self.New: choice = ['No','Yes'] self.new = wx.RadioBox(panel,-1,'Generate new positions?',choices=choice) self.new.Bind(wx.EVT_RADIOBOX, self.OnOpSelect) mainSizer.Add(self.new,0) OkBtn = wx.Button(panel,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) cancelBtn = wx.Button(panel,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) panel.SetSizer(mainSizer) panel.Fit() self.Fit() def OnOpSelect(self,event): self.OpSelected[0] = self.inv.GetSelection() if self.SGData['SGLatt'] != 'P': self.OpSelected[1] = self.latt.GetSelection() self.OpSelected[2] = self.oprs.GetSelection() for i in range(3): self.OpSelected[3][i] = float(self.cell[i].GetValue()) if self.New: self.OpSelected[4] = self.new.GetSelection() if self.Force: self.OpSelected[5] = self.force.GetSelection() def GetSelection(self): return self.OpSelected def OnOk(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK) def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL)
#==============================================================================
[docs] class SphereEnclosure(wx.Dialog): ''' Add atoms within sphere of enclosure to drawing :param wx.Frame parent: reference to parent frame (or None) :param general: general data (includes drawing data) :param atoms: drawing atoms data :param indx: list of selected atoms (may be empty) ''' def __init__(self,parent,general,drawing,indx): wx.Dialog.__init__(self,parent,wx.ID_ANY,'Supply sphere info', pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw! self.General = general self.Drawing = drawing self.indx = indx self.Sphere = [3.0,] self.centers = [] self.atomTypes = [[item,False] for item in self.General['AtomTypes']] self.CenterOnParent() self.Draw() def Draw(self): def OnAtomType(event): Obj = event.GetEventObject() Id = Ind[Obj.GetId()] self.atomTypes[Id][1] = Obj.GetValue() self.panel.Destroy() self.panel = wx.Panel(self) mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(self.panel,label=' Sphere of enclosure controls:'),0) topSizer = wx.BoxSizer(wx.HORIZONTAL) atoms = [] if len(self.indx): topSizer.Add(wx.StaticText(self.panel,label=' Sphere centered at atoms: '),0,WACV) cx,ct,cs = self.Drawing['atomPtrs'][:3] for Id in self.indx: if Id < len(self.Drawing['Atoms']): atom = self.Drawing['Atoms'][Id] self.centers.append(atom[cx:cx+3]) atoms.append('%s(%s)'%(atom[ct-1],atom[cs-1])) else: self.centers.append(list(self.Drawing['viewPoint'][0])) atoms.append('View point') topSizer.Add(wx.ComboBox(self.panel,choices=atoms,value=atoms[0], style=wx.CB_READONLY|wx.CB_DROPDOWN),0,WACV) else: topSizer.Add(wx.StaticText(self.panel,label=' Sphere centered at drawing view point'),0,WACV) self.centers.append(self.Drawing['viewPoint'][0]) mainSizer.Add(topSizer,0) sphereSizer = wx.BoxSizer(wx.HORIZONTAL) sphereSizer.Add(wx.StaticText(self.panel,label=' Sphere radius: '),0,WACV) radius = G2G.ValidatedTxtCtrl(self.panel,self.Sphere,0,nDig=(10,3),size=(65,25)) sphereSizer.Add(radius,0,WACV) mainSizer.Add(sphereSizer,0) mainSizer.Add(wx.StaticText(self.panel,label=' Target selected atoms:'),0) atSizer = wx.BoxSizer(wx.HORIZONTAL) Ind = {} for i,item in enumerate(self.atomTypes): atm = wx.CheckBox(self.panel,label=item[0]) atm.SetValue(item[1]) atm.Bind(wx.EVT_CHECKBOX, OnAtomType) Ind[atm.GetId()] = i atSizer.Add(atm,0,WACV) mainSizer.Add(atSizer,0) OkBtn = wx.Button(self.panel,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) cancelBtn = wx.Button(self.panel,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) self.panel.SetSizer(mainSizer) self.panel.Fit() self.Fit() def GetSelection(self): used = [] for atm in self.atomTypes: if atm[1]: used.append(str(atm[0])) return self.centers,self.Sphere[0],used def OnOk(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK) def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL)
#==============================================================================
[docs] class TransformDialog(wx.Dialog): ''' Phase transformation X' = M*(X-U)+V :param wx.Frame parent: reference to parent frame (or None) :param phase: parent phase data #NB: commonNames & commonTrans defined in GSASIIdataGUI = G2gd ''' def __init__(self,parent,phase,Trans=np.eye(3),Uvec=np.zeros(3),Vvec=np.zeros(3),ifMag=False,BNSlatt=''): wx.Dialog.__init__(self,parent,wx.ID_ANY,'Setup phase transformation', pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw! self.Phase = copy.deepcopy(phase) #will be a new phase! # self.Super = phase['General']['Super'] # if self.Super: # self.Trans = np.eye(4) # self.Vec = np.zeros(4) # else: self.Trans = Trans self.Uvec = Uvec self.Vvec = Vvec self.oldSpGrp = copy.deepcopy(phase['General']['SGData']['SpGrp']) self.oldSGdata = copy.deepcopy(phase['General']['SGData']) self.newSpGrp = self.Phase['General']['SGData']['SpGrp'] self.SGData = G2spc.SpcGroup(self.newSpGrp)[1] self.oldCell = copy.deepcopy(phase['General']['Cell'][1:8]) self.newCell = self.Phase['General']['Cell'][1:8] self.Common = 'abc' self.ifMag = ifMag if ifMag: self.BNSlatt = BNSlatt self.ifConstr = False self.Mtrans = False self.kvec = [0.,0.,0.] self.Draw() self.CenterOnParent() def Draw(self): def OnCommon(event): Obj = event.GetEventObject() self.Common = Obj.GetValue() self.Mtrans = False if '*' in self.Common: A,B = G2lat.cell2AB(self.oldCell[:6]) self.newCell[2:5] = [A[2,2],90.,90.] a,b = G2lat.cell2AB(self.newCell[:6]) self.Trans = np.inner(a,B) #correct! self.ifConstr = False self.newSpGrp = 'P 1' SGErr,SGData = G2spc.SpcGroup(self.newSpGrp) self.Phase['General']['SGData'] = SGData else: if self.Common == G2gd.commonNames[-1]: #change setting self.Vvec = G2spc.spg2origins[self.oldSpGrp] self.newSpGrp = self.oldSpGrp else: self.Trans = G2gd.commonTrans[self.Common] if 'R' == self.Common[-1]: self.newSpGrp += ' r' SGErr,SGData = G2spc.SpcGroup(self.newSpGrp) self.Phase['General']['SGData'] = SGData SGTxt.SetLabel(self.newSpGrp) OnTest(event) def OnSpaceGroup(event): event.Skip() SpcGp = GetSpGrpfromUser(self.panel,self.newSpGrp) if SpcGp == self.newSpGrp or SpcGp is None: #didn't change it! return # try a lookup on the user-supplied name SpGrpNorm = G2spc.StandardizeSpcName(SpcGp) if SpGrpNorm: SGErr,self.SGData = G2spc.SpcGroup(SpGrpNorm) else: SGErr,self.SGData = G2spc.SpcGroup(SpcGp) if SGErr: text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous'] SGTxt.SetLabel(self.newSpGrp) msg = 'Space Group Error' Text = '\n'.join(text) wx.MessageBox(Text,caption=msg,style=wx.ICON_EXCLAMATION) else: text,table = G2spc.SGPrint(self.SGData) self.Phase['General']['SGData'] = self.SGData self.newSpGrp = SpcGp SGTxt.SetLabel(self.Phase['General']['SGData']['SpGrp']) msg = 'Space Group Information' G2G.SGMessageBox(self.panel,msg,text,table).Show() if self.ifMag: self.BNSlatt = self.SGData['SGLatt'] G2spc.SetMagnetic(self.SGData) if self.Phase['General']['Type'] == 'magnetic': Nops = len(self.SGData['SGOps'])*len(self.SGData['SGCen']) if self.SGData['SGInv']: Nops *= 2 self.SGData['SpnFlp'] = Nops*[1,] del self.oldSGdata['MAXMAGN'] wx.CallAfter(self.Draw) def OnShowOps(event): text,table = G2spc.SGPrint(self.SGData,AddInv=True) if self.ifMag: msg = 'Magnetic space group information' OprNames,SpnFlp = G2spc.GenMagOps(self.SGData) text[0] = ' Magnetic Space Group: '+self.SGData['MagSpGrp'] text[3] = ' The magnetic lattice point group is '+self.SGData['MagPtGp'] G2G.SGMagSpinBox(self.panel,msg,text,table,self.SGData['SGCen'],OprNames, self.SGData['SpnFlp'],False).Show() else: msg = 'Space group information' G2G.SGMessageBox(self.panel,msg,text,table).Show() def OnTest(event): if not self.TestMat(): return if self.Mtrans: self.newCell = G2lat.TransformCell(self.oldCell[:6],self.Trans.T) else: self.newCell = G2lat.TransformCell(self.oldCell[:6],self.Trans) wx.CallAfter(self.Draw) def OnMag(event): self.ifMag = True self.BNSlatt = self.SGData['SGLatt'] G2spc.SetMagnetic(self.SGData) wx.CallAfter(self.Draw) def OnConstr(event): self.ifConstr = constr.GetValue() def OnBNSlatt(event): Obj = event.GetEventObject() self.BNSlatt = Obj.GetValue() if self.BNSlatt == self.SGData['SGLatt']: return GenSym,GenFlg,BNSsym = G2spc.GetGenSym(self.SGData) self.SGData['BNSlattsym'] = [self.BNSlatt,BNSsym[self.BNSlatt]] self.SGData['SGSpin'] = [1,]*len(self.SGData['SGSpin']) wx.CallAfter(self.Draw) def OnMtrans(event): Obj = event.GetEventObject() self.Mtrans = Obj.GetValue() def OnSpinOp(event): Obj = event.GetEventObject() isym = Indx[Obj.GetId()]+1 spCode = {'red':-1,'black':1} self.SGData['SGSpin'][isym] = spCode[Obj.GetValue()] G2spc.CheckSpin(isym,self.SGData) G2spc.SetMagnetic(self.SGData) wx.CallAfter(self.Draw) self.panel.Destroy() self.panel = wx.Panel(self) mainSizer = wx.BoxSizer(wx.VERTICAL) if self.ifMag: if self.BNSlatt != self.SGData['SGLatt']: GenSym,GenFlg,BNSsym = G2spc.GetGenSym(self.SGData) self.SGData['BNSlattsym'] = [self.BNSlatt,BNSsym[self.BNSlatt]] else: mag = wx.Button(self.panel,label='Make new phase magnetic?') mag.Bind(wx.EVT_BUTTON,OnMag) mainSizer.Add(mag,0) MatSizer = wx.BoxSizer(wx.HORIZONTAL) transSizer = wx.BoxSizer(wx.VERTICAL) transSizer.Add((5,5),0) transSizer.Add(wx.StaticText(self.panel,label= " Cell transformation via g'=gM; g=metric tensor \n XYZ transformation via M*(X-U)+V = X'; M* = inv(M)")) # if self.Super: # Trmat = wx.FlexGridSizer(4,4,0,0) # else: commonSizer = wx.BoxSizer(wx.HORIZONTAL) commonSizer.Add(wx.StaticText(self.panel,label=' Common transformations: '),0,WACV) if self.oldSpGrp not in G2spc.spg2origins: common = wx.ComboBox(self.panel,value=self.Common,choices=G2gd.commonNames[:-1], style=wx.CB_READONLY|wx.CB_DROPDOWN) else: common = wx.ComboBox(self.panel,value=self.Common,choices=G2gd.commonNames, style=wx.CB_READONLY|wx.CB_DROPDOWN) common.Bind(wx.EVT_COMBOBOX,OnCommon) commonSizer.Add(common,0,WACV) transSizer.Add(commonSizer) transSizer.Add(G2G.XformMatrix(self.panel,self.Trans,self.Uvec,self.Vvec)) MatSizer.Add((10,0),0) MatSizer.Add(transSizer) mainSizer.Add(MatSizer) if self.ifMag: MagSizer = wx.BoxSizer(wx.HORIZONTAL) if not self.oldSGdata.get('MAXMAGN',[]): Mtrans = wx.CheckBox(self.panel,label=' Use matrix transform?') Mtrans.SetValue(self.Mtrans) Mtrans.Bind(wx.EVT_CHECKBOX,OnMtrans) MagSizer.Add(Mtrans,0,WACV) mainSizer.Add(MagSizer,0) mainSizer.Add(wx.StaticText(self.panel,label=' Old lattice parameters:'),0) mainSizer.Add(wx.StaticText(self.panel,label= ' a = %.5f b = %.5f c = %.5f'%(self.oldCell[0],self.oldCell[1],self.oldCell[2])),0) mainSizer.Add(wx.StaticText(self.panel,label=' alpha = %.3f beta = %.3f gamma = %.3f'% (self.oldCell[3],self.oldCell[4],self.oldCell[5])),0) mainSizer.Add(wx.StaticText(self.panel,label=' volume = %.3f'%(self.oldCell[6])),0) mainSizer.Add(wx.StaticText(self.panel,label=' New lattice parameters:'),0) mainSizer.Add(wx.StaticText(self.panel,label= ' a = %.5f b = %.5f c = %.5f'%(self.newCell[0],self.newCell[1],self.newCell[2])),0) mainSizer.Add(wx.StaticText(self.panel,label=' alpha = %.3f beta = %.3f gamma = %.3f'% (self.newCell[3],self.newCell[4],self.newCell[5])),0) mainSizer.Add(wx.StaticText(self.panel,label=' volume = %.3f'%(self.newCell[6])),0) sgSizer = wx.BoxSizer(wx.HORIZONTAL) sgSizer.Add(wx.StaticText(self.panel,label=' Target space group: '),0,WACV) SGTxt = wx.Button(self.panel,wx.ID_ANY,self.newSpGrp,size=(100,-1)) SGTxt.Bind(wx.EVT_BUTTON,OnSpaceGroup) sgSizer.Add(SGTxt,0,WACV) showOps = wx.Button(self.panel,label=' Show operators?') showOps.Bind(wx.EVT_BUTTON,OnShowOps) sgSizer.Add(showOps,0,WACV) mainSizer.Add(sgSizer,0) if 'magnetic' not in self.Phase['General']['Type']: if self.ifMag: Indx = {} GenSym,GenFlg,BNSsym = G2spc.GetGenSym(self.SGData) BNSizer = wx.BoxSizer(wx.HORIZONTAL) BNSizer.Add(wx.StaticText(self.panel,label=' Select BNS lattice:'),0,WACV) BNSkeys = [self.SGData['SGLatt'],]+list(BNSsym.keys()) BNSkeys.sort() try: #this is an ugly kluge - bug in wx.ComboBox if self.BNSlatt[2] in ['a','b','c']: BNSkeys.reverse() except: pass BNS = wx.ComboBox(self.panel,choices=BNSkeys,style=wx.CB_READONLY|wx.CB_DROPDOWN) BNS.SetValue(self.BNSlatt) BNS.Bind(wx.EVT_COMBOBOX,OnBNSlatt) BNSizer.Add(BNS,0,WACV) spinColor = ['black','red'] spCode = {-1:'red',1:'black'} for isym,sym in enumerate(GenSym[1:]): BNSizer.Add(wx.StaticText(self.panel,label=' %s: '%(sym.strip())),0,WACV) spinOp = wx.ComboBox(self.panel,value=spCode[self.SGData['SGSpin'][isym+1]],choices=spinColor, style=wx.CB_READONLY|wx.CB_DROPDOWN) Indx[spinOp.GetId()] = isym spinOp.Bind(wx.EVT_COMBOBOX,OnSpinOp) BNSizer.Add(spinOp,0,WACV) OprNames,SpnFlp = G2spc.GenMagOps(self.SGData) self.SGData['SpnFlp'] = SpnFlp mainSizer.Add(BNSizer,0) mainSizer.Add(wx.StaticText(self.panel,label=' Magnetic Space Group: '+self.SGData['MagSpGrp']),0) if self.ifMag: mainSizer.Add(wx.StaticText(self.panel, \ label=' NB: Nonmagnetic atoms will be deleted from new phase'),0) constr = wx.CheckBox(self.panel,label=' Make constraints between phases?') constr.SetValue(self.ifConstr) constr.Bind(wx.EVT_CHECKBOX,OnConstr) mainSizer.Add(constr,0) TestBtn = wx.Button(self.panel,-1,"Test") TestBtn.Bind(wx.EVT_BUTTON, OnTest) OkBtn = wx.Button(self.panel,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) cancelBtn = wx.Button(self.panel,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(TestBtn) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) self.panel.SetSizer(mainSizer) self.panel.Fit() self.Fit() def TestMat(self): VC = nl.det(self.Trans) if VC < 0.: wx.MessageBox('Warning - left handed transformation',caption='Transformation matrix check', style=wx.ICON_EXCLAMATION) return True try: nl.inv(self.Trans) except nl.LinAlgError: wx.MessageBox('ERROR - bad transformation matrix',caption='Transformation matrix check', style=wx.ICON_ERROR) return False return True def GetSelection(self): self.Phase['General']['SGData'] = self.SGData if self.ifMag: self.Phase['General']['Name'] += ' mag: ' else: self.Phase['General']['Name'] += ' %s'%(self.Common) if not self.TestMat(): return None if self.Mtrans: self.Phase['General']['Cell'][1:] = G2lat.TransformCell(self.oldCell[:6],self.Trans.T) return self.Phase,self.Trans.T,self.Uvec,self.Vvec,self.ifMag,self.ifConstr,self.Common else: self.Phase['General']['Cell'][1:] = G2lat.TransformCell(self.oldCell[:6],self.Trans) return self.Phase,self.Trans,self.Uvec,self.Vvec,self.ifMag,self.ifConstr,self.Common def OnOk(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK) def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL)
#==============================================================================
[docs] class UseMagAtomDialog(wx.Dialog): '''Get user selected magnetic atoms after cell transformation ''' def __init__(self,parent,Name,Atoms,atCodes,atMxyz,ifMag=True,ifOK=False,ifDelete=False): title = 'Subgroup atom list' if ifMag: title = 'Magnetic atom selection' wx.Dialog.__init__(self,parent,wx.ID_ANY,title, pos=wx.DefaultPosition,size=(450,275), style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) self.panel = wxscroll.ScrolledPanel(self) #just a dummy - gets destroyed in Draw! # self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw! self.Name = Name self.Atoms = Atoms self.atCodes = atCodes self.atMxyz = atMxyz self.ifMag = ifMag self.ifOK = ifOK self.ifDelete = ifDelete self.Use = len(self.Atoms)*[True,] self.Draw() def Draw(self): def OnUseChk(event): Obj = event.GetEventObject() iuse = Indx[Obj.GetId()] self.Use[iuse] = not self.Use[iuse] Obj.SetValue(self.Use[iuse]) self.panel.Destroy() self.panel = wxscroll.ScrolledPanel(self,style = wx.DEFAULT_DIALOG_STYLE) Indx = {} Mstr = [' Mx',' My',' Mz'] Xstr = ['X','Y','Z'] mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(self.panel,label='For: %s'%self.Name),0) if self.ifMag: mainSizer.Add(wx.StaticText(self.panel,label=' Name, x, y, z, allowed moments, mag. site sym:'),0) else: mainSizer.Add(wx.StaticText(self.panel,label=' Name, x, y, z, allowed xyz, site sym:'),0) atmSizer = wx.FlexGridSizer(0,2,5,5) for iuse,[use,atom,mxyz] in enumerate(zip(self.Use,self.Atoms,self.atMxyz)): mstr = [' ---',' ---',' ---'] for i,mx in enumerate(mxyz[1]): if mx: if self.ifMag: mstr[i] = Mstr[i] else: mstr[i] = Xstr[i] if self.ifMag: useChk = wx.CheckBox(self.panel,label='Use?') Indx[useChk.GetId()] = iuse useChk.SetValue(use) useChk.Bind(wx.EVT_CHECKBOX, OnUseChk) atmSizer.Add(useChk,0,WACV) else: atmSizer.Add((2,2),0) text = ' %5s %10.5f %10.5f %10.5f (%s,%s,%s) %s '%(atom[0],atom[3],atom[4],atom[5],mstr[0],mstr[1],mstr[2],mxyz[0]) atmSizer.Add(wx.StaticText(self.panel,label=text),0,WACV) mainSizer.Add(atmSizer) btnSizer = wx.BoxSizer(wx.HORIZONTAL) if self.ifOK: OKBtn = wx.Button(self.panel,-1,"OK") OKBtn.Bind(wx.EVT_BUTTON, self.OnNo) btnSizer.Add(OKBtn) else: YesBtn = wx.Button(self.panel,-1,"Yes") YesBtn.Bind(wx.EVT_BUTTON, self.OnYes) NoBtn = wx.Button(self.panel,-1,"No") NoBtn.Bind(wx.EVT_BUTTON, self.OnNo) btnSizer.Add((20,20),1) btnSizer.Add(YesBtn) btnSizer.Add((20,20),1) btnSizer.Add(NoBtn) if self.ifDelete: DeleteBtn = wx.Button(self.panel,-1,"Delete") DeleteBtn.Bind(wx.EVT_BUTTON, self.OnDelete) btnSizer.Add((20,20),1) btnSizer.Add(DeleteBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) self.panel.SetSizer(mainSizer) size = np.array(self.GetSize()) self.panel.SetupScrolling() self.panel.SetAutoLayout(1) size = [size[0]-5,size[1]-20] #this fiddling is needed for older wx! self.panel.SetSize(size) def GetSelection(self): useAtoms = [] useatCodes = [] for use,atom,code in zip(self.Use,self.Atoms,self.atCodes): if use: useAtoms.append(atom) useatCodes.append(code) return useAtoms,useatCodes def OnYes(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_YES) def OnNo(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_NO) def OnDelete(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_DELETE)
#==============================================================================
[docs] class RotationDialog(wx.Dialog): ''' Get Rotate & translate matrix & vector - currently not used needs rethinking - possible use to rotate a group of atoms about some vector/origin + translation ''' def __init__(self,parent): wx.Dialog.__init__(self,parent,wx.ID_ANY,'Atom group rotation/translation', pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw! self.Trans = np.eye(3) self.Vec = np.zeros(3) self.rotAngle = 0. self.rotVec = np.array([0.,0.,1.]) self.Expand = '' self.Draw() def Draw(self): def OnExpand(event): self.Expand = expand.GetValue() def OnRotAngle(event): event.Skip() self.rotAngle = float(rotangle.GetValue()) rotangle.SetValue('%5.3f'%(self.rotAngle)) Q = G2mth.AVdeg2Q(self.rotAngle,self.rotVec) self.Trans = G2mth.Q2Mat(Q) self.Draw() def OnRotVec(event): event.Skip() vals = rotvec.GetValue() vals = vals.split() self.rotVec = np.array([float(val) for val in vals]) rotvec.SetValue('%5.3f %5.3f %5.3f'%(self.rotVec[0],self.rotVec[1],self.rotVec[2])) Q = G2mth.AVdeg2Q(self.rotAngle,self.rotVec) self.Trans = G2mth.Q2Mat(Q) self.Draw() self.panel.Destroy() self.panel = wx.Panel(self) mainSizer = wx.BoxSizer(wx.VERTICAL) MatSizer = wx.BoxSizer(wx.HORIZONTAL) transSizer = wx.BoxSizer(wx.VERTICAL) transSizer.Add(wx.StaticText(self.panel,label=" XYZ Transformation matrix && vector: "+ \ "\n B*M*A*(X-V)+V = X'\n A,B: Cartesian transformation matrices")) Trmat = wx.FlexGridSizer(3,5,0,0) for iy,line in enumerate(self.Trans): for ix,val in enumerate(line): item = G2G.ValidatedTxtCtrl(self.panel,self.Trans[iy],ix,nDig=(10,3),size=(65,25)) Trmat.Add(item) Trmat.Add((25,0),0) vec = G2G.ValidatedTxtCtrl(self.panel,self.Vec,iy,nDig=(10,3),size=(65,25)) Trmat.Add(vec) transSizer.Add(Trmat) MatSizer.Add((10,0),0) MatSizer.Add(transSizer) mainSizer.Add(MatSizer) rotationBox = wx.BoxSizer(wx.HORIZONTAL) rotationBox.Add(wx.StaticText(self.panel,label=' Rotation angle: '),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) rotangle = wx.TextCtrl(self.panel,value='%5.3f'%(self.rotAngle), size=(50,25),style=wx.TE_PROCESS_ENTER) rotangle.Bind(wx.EVT_TEXT_ENTER,OnRotAngle) rotangle.Bind(wx.EVT_KILL_FOCUS,OnRotAngle) rotationBox.Add(rotangle,0,WACV) rotationBox.Add(wx.StaticText(self.panel,label=' about vector: '),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) rotvec = wx.TextCtrl(self.panel,value='%5.3f %5.3f %5.3f'%(self.rotVec[0],self.rotVec[1],self.rotVec[2]), size=(100,25),style=wx.TE_PROCESS_ENTER) rotvec.Bind(wx.EVT_TEXT_ENTER,OnRotVec) rotvec.Bind(wx.EVT_KILL_FOCUS,OnRotVec) rotationBox.Add(rotvec,0,WACV) mainSizer.Add(rotationBox,0) expandChoice = ['','xy','xz','yz','xyz'] expandBox = wx.BoxSizer(wx.HORIZONTAL) expandBox.Add(wx.StaticText(self.panel,label=' Expand -1 to +1 on: '),0,WACV) expand = wx.ComboBox(self.panel,value=self.Expand,choices=expandChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) expand.Bind(wx.EVT_COMBOBOX,OnExpand) expandBox.Add(expand,0,WACV) expandBox.Add(wx.StaticText(self.panel,label=' and find unique atoms '),0,WACV) mainSizer.Add(expandBox) OkBtn = wx.Button(self.panel,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) cancelBtn = wx.Button(self.panel,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) self.panel.SetSizer(mainSizer) self.panel.Fit() self.Fit() def GetSelection(self): return self.Trans,self.Vec,self.Expand def OnOk(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK) def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL)
#==============================================================================
[docs] class DIFFaXcontrols(wx.Dialog): ''' Solicit items needed to prepare DIFFaX control.dif file ''' def __init__(self,parent,ctrls,parms=None): wx.Dialog.__init__(self,parent,wx.ID_ANY,'DIFFaX controls', pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw! self.ctrls = ctrls self.calcType = 'powder pattern' self.plane = 'h0l' self.planeChoice = ['h0l','0kl','hhl','h-hl',] self.lmax = '2' self.lmaxChoice = [str(i+1) for i in range(6)] self.Parms = parms self.Parm = None if self.Parms != None: self.Parm = self.Parms[0] self.parmRange = [0.,1.] self.parmStep = 2 self.Inst = 'Gaussian' self.Draw() def Draw(self): def OnCalcType(event): self.calcType = calcType.GetValue() wx.CallAfter(self.Draw) def OnPlane(event): self.plane = plane.GetValue() def OnMaxL(event): self.lmax = lmax.GetValue() def OnParmSel(event): self.Parm = parmsel.GetValue() def OnNumStep(event): self.parmStep = int(numStep.GetValue()) def OnParmRange(event): event.Skip() vals = parmrange.GetValue().split() try: vals = [float(vals[0]),float(vals[1])] except ValueError: vals = self.parmRange parmrange.SetValue('%.3f %.3f'%(vals[0],vals[1])) self.parmRange = vals def OnInstSel(event): self.Inst = instsel.GetValue() self.panel.Destroy() self.panel = wx.Panel(self) mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(self.panel,label=' Controls for DIFFaX'),0) if self.Parms: mainSizer.Add(wx.StaticText(self.panel,label=' Sequential powder pattern simulation'),0) else: calcChoice = ['powder pattern','selected area'] calcSizer = wx.BoxSizer(wx.HORIZONTAL) calcSizer.Add(wx.StaticText(self.panel,label=' Select calculation type: '),0,WACV) calcType = wx.ComboBox(self.panel,value=self.calcType,choices=calcChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) calcType.Bind(wx.EVT_COMBOBOX,OnCalcType) calcSizer.Add(calcType,0,WACV) mainSizer.Add(calcSizer) if self.Parms: parmSel = wx.BoxSizer(wx.HORIZONTAL) parmSel.Add(wx.StaticText(self.panel,label=' Select parameter to vary: '),0,WACV) parmsel = wx.ComboBox(self.panel,value=self.Parm,choices=self.Parms, style=wx.CB_READONLY|wx.CB_DROPDOWN) parmsel.Bind(wx.EVT_COMBOBOX,OnParmSel) parmSel.Add(parmsel,0,WACV) mainSizer.Add(parmSel) mainSizer.Add(wx.StaticText(self.panel,label=' Enter parameter range & no. steps: ')) parmRange = wx.BoxSizer(wx.HORIZONTAL) numChoice = [str(i+1) for i in range(10)] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) parmrange = wx.TextCtrl(self.panel,value='%.3f %.3f'%(self.parmRange[0],self.parmRange[1]), style=wx.TE_PROCESS_ENTER) parmrange.Bind(wx.EVT_TEXT_ENTER,OnParmRange) parmrange.Bind(wx.EVT_KILL_FOCUS,OnParmRange) parmRange.Add(parmrange,0,WACV) numStep = wx.ComboBox(self.panel,value=str(self.parmStep),choices=numChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) numStep.Bind(wx.EVT_COMBOBOX,OnNumStep) parmRange.Add(numStep,0,WACV) mainSizer.Add(parmRange) if 'selected' in self.calcType: planeSizer = wx.BoxSizer(wx.HORIZONTAL) planeSizer.Add(wx.StaticText(self.panel,label=' Select plane: '),0,WACV) plane = wx.ComboBox(self.panel,value=self.plane,choices=self.planeChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) plane.Bind(wx.EVT_COMBOBOX,OnPlane) planeSizer.Add(plane,0,WACV) planeSizer.Add(wx.StaticText(self.panel,label=' Max. l index: '),0,WACV) lmax = wx.ComboBox(self.panel,value=self.lmax,choices=self.lmaxChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) lmax.Bind(wx.EVT_COMBOBOX,OnMaxL) planeSizer.Add(lmax,0,WACV) mainSizer.Add(planeSizer) else: instChoice = ['None','Mean Gaussian','Gaussian',] instSizer = wx.BoxSizer(wx.HORIZONTAL) instSizer.Add(wx.StaticText(self.panel,label=' Select instrument broadening: '),0,WACV) instsel = wx.ComboBox(self.panel,value=self.Inst,choices=instChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) instsel.Bind(wx.EVT_COMBOBOX,OnInstSel) instSizer.Add(instsel,0,WACV) mainSizer.Add(instSizer) OkBtn = wx.Button(self.panel,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) cancelBtn = wx.Button(self.panel,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) self.panel.SetSizer(mainSizer) self.panel.Fit() self.Fit() def GetSelection(self): if 'powder' in self.calcType: return 'PWDR',self.Inst,self.Parm,self.parmRange,self.parmStep elif 'selected' in self.calcType: return 'SADP',self.plane,self.lmax def OnOk(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK) def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL)
#==============================================================================
[docs] class AddHatomDialog(wx.Dialog): '''H atom addition dialog. After :meth:`ShowModal` returns, the results are found in dict :attr:`self.data`, which is accessed using :meth:`GetData`. :param wx.Frame parent: reference to parent frame (or None) :param dict Neigh: a dict of atom names with list of atom name, dist pairs for neighboring atoms :param dict phase: a dict containing the phase as defined by :ref:`Phase Tree Item <Phase_table>` ''' def __init__(self,parent,Neigh,phase): wx.Dialog.__init__(self,parent,wx.ID_ANY,'H atom add', pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.panel = wxscroll.ScrolledPanel(self) #just a dummy - gets destroyed in Draw! self.Neigh = Neigh self.phase = phase self.Hatoms = [] self.Draw(self.Neigh,self.phase)
[docs] def Draw(self,Neigh,phase): '''Creates the contents of the dialog. Normally called by :meth:`__init__`. ''' def OnHSelect(event): Obj = event.GetEventObject() item,i = Indx[Obj.GetId()] for obj in Indx[item]: obj.SetValue(False) Obj.SetValue(True) self.Neigh[item][2] = i def OnBond(event): Obj = event.GetEventObject() inei,ibond = Indx[Obj.GetId()] self.Neigh[inei][1][0][ibond][2] = Obj.GetValue() self.panel.Destroy() self.panel = wxscroll.ScrolledPanel(self,style = wx.DEFAULT_DIALOG_STYLE) mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(self.panel,-1,'H atom add controls for phase %s:'%(phase['General']['Name'])), 0,wx.LEFT|wx.TOP,10) mainSizer.Add(wx.StaticText(self.panel,-1,'NB: Check selections as they may not be correct'),0|wx.LEFT,10) mainSizer.Add(wx.StaticText(self.panel,-1," Atom: Add # H's Use: Neighbors, dist"),0,wx.TOP|wx.LEFT,5) nHatms = ['0','1','2','3'] dataSizer = wx.FlexGridSizer(0,3,0,0) Indx = {} for inei,neigh in enumerate(Neigh): dataSizer.Add(wx.StaticText(self.panel,-1,' %s: '%(neigh[0])),0,WACV) nH = 1 #for O atom if 'C' in neigh[0] or 'N' in neigh[0]: nH = 4-len(neigh[1][0]) checks = wx.BoxSizer(wx.HORIZONTAL) Ids = [] for i in range(nH+1): nHs = wx.CheckBox(self.panel,-1,label=nHatms[i]) if i == neigh[2]: nHs.SetValue(True) Indx[nHs.GetId()] = [inei,i] Ids.append(nHs) nHs.Bind(wx.EVT_CHECKBOX, OnHSelect) checks.Add(nHs,0,WACV) Indx[inei] = Ids dataSizer.Add(checks,0,WACV) lineSizer = wx.BoxSizer(wx.HORIZONTAL) for ib,bond in enumerate(neigh[1][0]): Bond = wx.CheckBox(self.panel,-1,label=': %s, %.3f'%(bond[0],bond[1])) Bond.SetValue(bond[2]) Indx[Bond.GetId()] = [inei,ib] Bond.Bind(wx.EVT_CHECKBOX,OnBond) lineSizer.Add(Bond,0,WACV) dataSizer.Add(lineSizer,0,WACV|wx.RIGHT,10) mainSizer.Add(dataSizer,0,wx.LEFT,5) CancelBtn = wx.Button(self.panel,-1,'Cancel') CancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) OkBtn = wx.Button(self.panel,-1,'Ok') OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(CancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.BOTTOM|wx.TOP, 10) self.panel.SetSizer(mainSizer) size = np.array(self.GetSize()) self.panel.SetupScrolling() self.panel.SetAutoLayout(1) size = [size[0]-5,size[1]-20] #this fiddling is needed for older wx! self.panel.SetSize(size)
[docs] def GetData(self): 'Returns the values from the dialog' for neigh in self.Neigh: for ibond,bond in enumerate(neigh[1][0]): if not bond[2]: neigh[1][1][1][ibond] = 0 #deselected bond neigh[1][1][1] = [a for a in neigh[1][1][1] if a] return self.Neigh #has #Hs to add for each entry
[docs] def OnOk(self,event): 'Called when the OK button is pressed' parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK)
def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL)
#### Phase editing routines ################################################################################ # def DrawAtomsReplaceByID(data,loc,atom,ID): # '''Replace all atoms in drawing array with an ID matching the specified value''' # atomData = data['Drawing']['Atoms'] # indx = G2mth.FindAtomIndexByIDs(atomData,loc,[ID,]) # for ind in indx: # atomData[ind] = MakeDrawAtom(data,atom,atomData[ind]) # def MakeDrawAtom(data,atom,oldatom=None): # 'needs a description' # AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE', # 'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK'] # AA1letter = ['A','R','N','D','C','Q','E','G','H','I', # 'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' '] # generalData = data['General'] # Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) # SGData = generalData['SGData'] # deftype = G2obj.validateAtomDrawType(GSASIIpath.GetConfigValue('DrawAtoms_default'),generalData) # if generalData['Type'] in ['nuclear','faulted',]: # if oldatom: # opr = oldatom[5] # if atom[9] == 'A': # X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17]) # atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0] # else: # X = G2spc.ApplyStringOps(opr,SGData,atom[3:6]) # atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0] # else: # atomInfo = [atom[:2]+atom[3:6]+['1',]+[deftype]+ # ['',]+[[255,255,255],]+atom[9:]+[[],[]]][0] # ct,cs = [1,8] #type & color # elif generalData['Type'] == 'magnetic': # if oldatom: # opr = oldatom[8] # mom = np.array(atom[7:10]) # if generalData['Super']: # SSGData = generalData['SSGData'] # Mom = G2spc.ApplyStringOpsMom(opr,SGData,SSGData,mom) # else: # Mom = G2spc.ApplyStringOpsMom(opr,SGData,None,mom) # if atom[12] == 'A': # X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[14:20]) # atomInfo = [atom[:2]+list(X)+list(Mom)+oldatom[8:12]+atom[12:14]+list(U)+oldatom[20:]][0] # else: # X = G2spc.ApplyStringOps(opr,SGData,atom[3:6]) # atomInfo = [atom[:2]+list(X)+list(Mom)+oldatom[8:12]+atom[12:]+oldatom[20:]][0] # else: # atomInfo = [atom[:2]+atom[3:6]+atom[7:10]+['1',]+[deftype]+ # ['',]+[[255,255,255],]+atom[12:]+[[],[]]][0] # ct,cs = [1,11] #type & color # elif generalData['Type'] == 'macromolecular': # try: # oneLetter = AA3letter.index(atom[1]) # except ValueError: # oneLetter = -1 # atomInfo = [[atom[1].strip()+atom[0],]+ # [AA1letter[oneLetter]+atom[0],]+atom[2:5]+ # atom[6:9]+['1',]+[deftype]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0] # ct,cs = [4,11] #type & color # atNum = generalData['AtomTypes'].index(atom[ct]) # atomInfo[cs] = list(generalData['Color'][atNum]) # return atomInfo
[docs] def getPawleydRange(G2frame,data): 'find d-space range in used histograms' fmtd = lambda d: '?' if d is None else '{:.5f}'.format(d) dmaxAll = dminAll = None Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() nhist = 0 for item in data['Histograms']: if 'PWDR' not in item: continue if not data['Histograms'][item]['Use']: continue nhist += 1 Inst = Histograms[item]['Instrument Parameters'][0] if 'T' in Inst['Type'][1]: dmin,dmax = [G2lat.Pos2dsp(Inst,t) for t in Histograms[item]['Limits'][1]] else: dmax,dmin = [G2lat.Pos2dsp(Inst,t) for t in Histograms[item]['Limits'][1]] if dmaxAll is None: dmaxAll = dmax else: dmaxAll = max(dmaxAll,dmax) if dminAll is None: dminAll = dmin else: dminAll = min(dminAll,dmin) # format data range lbl =" d-space range {} to {} {}-1 ({} histograms)".format( fmtd(dminAll),fmtd(dmaxAll),Angstr,nhist) if dmaxAll is None: dmaxAll = 100. if dminAll is None: dminAll = 0.25 return dminAll,dmaxAll,nhist,lbl
[docs] def getAtomSelections(AtmTbl,cn=0,action='action',includeView=False,ask=True): '''get selected atoms from table or ask user if none are selected :param list AtmTbl: atom or draw atom table :param int cn: atom name position :param str action: description for prompt, when needed :param bool includeView: if True, the viewpoint is included as an option in the selection dialog :returns: indx (list) selected atoms from indices in table. If includeView is True, indx can contain index n (where there are n atoms in table). This is indicates the viewpoint. ''' indx = AtmTbl.GetSelectedRows() indx += [row for row,col in AtmTbl.GetSelectedCells()] for top,bottom in zip([r for r,c in AtmTbl.GetSelectionBlockTopLeft()], [r for r,c in AtmTbl.GetSelectionBlockBottomRight()]): indx += list(range(top,bottom+1)) indx = list(set(indx)) if indx or not ask: return indx choices = [] for i in range(AtmTbl.GetNumberRows()): val = AtmTbl.GetCellValue(i,cn) if val in choices: val += '_' + str(i) choices.append(val) if not choices: return if includeView: choices.append('View point') dlg = G2G.G2MultiChoiceDialog(AtmTbl.GetTopLevelParent(), 'Select atoms','Select atoms for '+action,choices) if dlg.ShowModal() == wx.ID_OK: indx = dlg.GetSelections() dlg.Destroy() return indx
def SetPhaseWindow(phasePage,mainSizer=None,Scroll=0): if mainSizer is not None: phasePage.SetSizer(mainSizer) phasePage.SetAutoLayout(True) phasePage.SetScrollRate(10,10) phasePage.SendSizeEvent() phasePage.Scroll(0,Scroll) def GetSpGrpfromUser(parent,SpGrp): helptext = '''\t\t\tGSAS-II space group information Space groups are entered here as given in Volume I or Volume A of the International Tables using the short Hermann-Mauguin symbol,except that spaces are placed between axial fields (e.g. "P 4/m m m", "F D 3 M" or "p -3 1 m"). NB: the cubic "bar" in "F d -3 m" is unnecessary, and upper/lower case is not required. Where a centrosymmetric tetragonal or cubic space group has alternate origin settings, Origin choice 2 (with the center of symmetry at the origin, which gives an -x,-y,-z symmetry operator) is always used. Refer to the relevant pages in IT I or A to find the offset in atom positions between the two choices. For rhombohedral space groups, (R xxx) the hexagonal setting is assumed. Append a final R to the name (R xxx R) to indicate that a rhombohedral cell should be used (not recommended when alpha >> 120 or << 60, due to correlation.) For standard settings of space groups, space group numbers (1-230) can alternately be entered. GSAS-II will accept non-standard settings of space groups. For example, space group "P -1" can be set to include face centering, using symbol "F -1" and "P 1 1 21/a" as a nonstandard version of "P 21/c". Review the symmetry operators generated by GSAS-II to confirm that you have entered the right symbol for your structure. ''' dlg = G2G.SingleStringDialog(parent,'Get Space Group', ' Input the space group with spaces between axial fields \n (e.g. p 21/c, P 63/m m c, P 4/m m m) or enter a space\n group number between 1 and 230.', value=SpGrp,help=helptext) if not dlg.Show(): dlg.Destroy() return SpGrp else: try: # has a space group number been input? spcnum = int(dlg.GetValue()) if 1 <= spcnum <= 230: SpcGp = G2spc.spgbyNum[spcnum] else: msg = 'Space Group Error' wx.MessageBox('Invalid space group number',caption=msg,style=wx.ICON_EXCLAMATION) return except: #get rid of extra spaces between fields first Flds = dlg.GetValue().split() for fld in Flds: fld = fld.strip() SpcGp = ' '.join(Flds).capitalize() finally: dlg.Destroy() return SpcGp
[docs] def FindBondsDraw(data): '''Generally used routine where cell is from data ''' generalData = data['General'] cell = generalData['Cell'][1:7] FindBondsDrawCell(data,cell)
[docs] def getAtomRadii(data): '''Get radii for atoms, using generalData['DisAglCtls']['BondRadii'] to override generalData['BondRadii'] when present. Fix to make sure that all elements in generalData are present in DisAglCtls. ''' generalData = data['General'] if 'DisAglCtls' not in generalData: return generalData['AtomTypes'],generalData['BondRadii'] if 'BondRadii' not in generalData['DisAglCtls']: return generalData['AtomTypes'],generalData['BondRadii'] DisAglCtls = generalData['DisAglCtls'] if len(generalData['BondRadii']) != len(DisAglCtls['BondRadii']): for typ,dis in zip(generalData['AtomTypes'],generalData['BondRadii']): if typ not in DisAglCtls['AtomTypes']: DisAglCtls['AtomTypes'].append(typ) DisAglCtls['AngleRadii'].append(dis) DisAglCtls['BondRadii'].append(dis) return DisAglCtls['AtomTypes'],DisAglCtls['BondRadii']
[docs] def FindCoordinationByLabel(data): '''Map out molecular connectivity by determining the atoms bonded to each atom, by label. The atoms bonded to each atom in the asymmetric unit is determined and returned in a dict. Works best ''' generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] atomTypes,radii = getAtomRadii(data) SGData = generalData['SGData'] cellArray = G2lat.CellBlock(1) Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) neighborArray = {} error = '' for atomA in data['Atoms']: lblA = atomA[0] if lblA in neighborArray: if error: error += ', ' error += lblA else: neighborArray[lblA] = [] xyzA = np.array(atomA[cx:cx+3]) indA = atomTypes.index(atomA[ct]) for atomB in data['Atoms']: indB = atomTypes.index(atomB[ct]) sumR = data['Drawing']['radiusFactor']*(radii[indA]+radii[indB]) symAtms = [atm[0] for atm in G2spc.GenAtom(np.array(atomB[cx:cx+3]),SGData,False,6*[0],True)] symCellAtms = np.concatenate([cellArray+i for i in symAtms]) dists = np.sqrt(np.sum(np.inner(Amat,symCellAtms-xyzA)**2,axis=0)) if np.any(np.logical_and(dists < sumR, dists != 0)): if atomB[0] not in neighborArray[lblA]: neighborArray[lblA].append(atomB[0]) if error: print('Warning, duplicated atom labels:',error) return neighborArray
[docs] def FindCoordination(ind,data,neighborArray,coordsArray,cmx=0,targets=None): '''Find atoms coordinating atom ind, speed-up version. This only searches to atoms already added to the Draw Array, though we might want to search to all atoms in the asymmetric unity (which would mean searching against atomsAll, but would also require a reformat of atom entry to match difference in format between atoms and drawatoms. ''' generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) atomTypes,radii = getAtomRadii(data) atomData = data['Drawing']['Atoms'] cx,ct,cs,ci = data['Drawing']['atomPtrs'] #atomsAll = data['Atoms'] #cxa,cta,csa,cia = generalData['AtomPtrs'] SGData = generalData['SGData'] cellArray = G2lat.CellBlock(1) newAtomList = [] atomA = atomData[ind] xyzA = np.array(atomA[cx:cx+3]) lblA = atomA[0] indA = atomTypes.index(atomA[ct]) for atomB in atomData: if targets and atomB[ct] not in targets: continue if atomB[0] not in neighborArray[lblA]: continue indB = atomTypes.index(atomB[ct]) sumR = data['Drawing']['radiusFactor']*(radii[indA]+radii[indB]) xyzB = np.array(atomB[cx:cx+3]) Uij = atomB[cs+5:cs+5+6] coords = [] symMisc = [] for item in G2spc.GenAtom(xyzB,SGData,False,Uij,True): coords.append(item[0]) symMisc.append(item[1:4]) symCoords = np.array(coords) dists = np.sqrt(np.sum(np.inner(Amat, np.array([symCoords+i-xyzA for i in cellArray]) )**2,axis=0)) for icell,isym in np.argwhere(np.logical_and(dists < sumR, dists != 0.0)): xyz = symCoords[isym] + cellArray[icell] item = [None]+list(symMisc[isym]) atom = copy.deepcopy(atomB) atom[cx:cx+3] = xyz Opr = abs(item[2])%100 M = SGData['SGOps'][Opr-1][0] if cmx: opNum = G2spc.GetOpNum(item[2],SGData) mom = np.array(atom[cmx:cmx+3]) if SGData['SGGray']: atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M) else: atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SGData['SpnFlp'][opNum-1] atom[cs-1] = str(item[2])+'+' atom[cs+5:cs+5+6] = item[1] # have we already found an atom at this site? if np.any(np.all(np.isclose(xyz,coordsArray,atol=0.0002),axis=1)): continue # are we going to add it already? if True in [np.allclose(np.array(xyz),np.array(a[cx:cx+3]),atol=0.0002) for a in newAtomList]: continue C = xyz-symCoords[isym]+item[3] atom[cs-1] += str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2]))) newAtomList.append(atom) return newAtomList
[docs] def FindBondsDrawCell(data,cell): '''uses numpy & masks - very fast even for proteins! allows different cell as input from seq. refinements ''' cx,ct,cs,ci = data['Drawing']['atomPtrs'] hydro = data['Drawing']['showHydrogen'] atomData = data['Drawing']['Atoms'] generalData = data['General'] Amat,Bmat = G2lat.cell2AB(cell) atomTypes,radii = getAtomRadii(data) try: indH = atomTypes.index('H') radii[indH] = 0.5 except: pass for atom in atomData: atom[-2] = [] #clear out old bonds/polyhedra atom[-1] = [] Indx = range(len(atomData)) Atoms = [] Styles = [] Radii = [] Names = [] for atom in atomData: if 'Q' in atom[ct]: #skip spinning RB atoms continue Atoms.append(np.array(atom[cx:cx+3])) Styles.append(atom[cs]) Names.append(ord(atom[ct-1].ljust(4)[3])) try: if not hydro and atom[ct] == 'H': Radii.append(0.0) else: Radii.append(radii[atomTypes.index(atom[ct])]) except ValueError: #changed atom type! Radii.append(0.20) Atoms = np.array(Atoms) Radii = np.array(Radii) Names = np.array(Names) IASRN = zip(Indx,Atoms,Styles,Radii,Names) for atomA in IASRN: if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']: Dx = Atoms-atomA[1] dist = ma.masked_less(np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)),0.5) #gets rid of G2frame & disorder "bonds" < 0.5A if generalData['Type'] == 'macromolecular': #eliminate cross disorder residue bonds m1 = ma.getmask(dist) if atomA[4] in [ord('A'),]: m2 = ma.getmask(ma.masked_equal(Names,ord('B'))) dist = ma.array(dist,mask=ma.mask_or(m1,m2)) if atomA[4] in [ord('B'),]: m2 = ma.getmask(ma.masked_equal(Names,ord('A'))) dist = ma.array(dist,mask=ma.mask_or(m1,m2)) sumR = atomA[3]+Radii IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms i = atomA[0] for j in IndB[0]: if Styles[i] == 'polyhedra': atomData[i][-2].append(np.inner(Amat,Dx[j])) elif Styles[j] != 'polyhedra' and j > i: atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j]) atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j]) if Styles[i] == 'polyhedra': Bonds = atomData[i][-2] Faces = [] if len(Bonds) > 2: FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator for face in FaceGen: vol = nl.det(face) if abs(vol) > 1. or len(Bonds) == 3: if vol < 0.: face = [face[0],face[2],face[1]] face = np.array(face) if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any(): norm = np.cross(face[1]-face[0],face[2]-face[0]) norm /= np.sqrt(np.sum(norm**2)) Faces.append([face,norm]) atomData[i][-1] = Faces
[docs] def VoidMap(data,aMax=1,bMax=1,cMax=1,gridspacing=.25,probeRadius=.5, aMin=0,bMin=0,cMin=0): '''Compute points where there are no atoms within probeRadius A. All atoms in the Atoms list are considered, provided their occupancy is non-zero. :param dict data: Phase data array :param float aMax: Maximum along the *a* direction (fractional units). Defaults to 1. :param float bMax: Maximum along the *b* direction (fractional units). Defaults to 1. :param float cMax: Maximum along the *c* direction (fractional units). Defaults to 1. :param float gridspacing=.25: Approximate spacing of points (fractional units). Defaults to 1. :param float ,probeRadius=.5: :param float aMin: Minimum along the *a* direction (fractional units). Defaults to 0. :param float bMin: Minimum along the *b* direction (fractional units). Defaults to 0. :param float cMin: Minimum along the *c* direction (fractional units). Defaults to 0. ''' VDWdict = dict(zip(data['General']['AtomTypes'],data['General']['vdWRadii'])) cell = data['General']['Cell'][1:7] Amat,Bmat = G2lat.cell2AB(cell) # orthogonalization matrix SGData = data['General']['SGData'] surroundingCells = G2lat.CellBlock(1) xx,yy,zz = np.meshgrid( np.linspace(aMin,aMax,int(0.5+cell[0]*(aMax-aMin)/gridspacing),endpoint=False), np.linspace(bMin,bMax,int(0.5+cell[1]*(bMax-bMin)/gridspacing),endpoint=False), np.linspace(cMin,cMax,int(0.5+cell[2]*(cMax-cMin)/gridspacing),endpoint=False)) coordGrd = np.array([xyz for xyz in zip(xx.ravel(),yy.ravel(),zz.ravel())]) lgclArray = [True for i in xx.ravel()] cx,ct,cs,cia = data['General']['AtomPtrs'] nind = len(data['Atoms']) pgbar = wx.ProgressDialog('Fill unit cell for %d atoms'%nind,'Atoms done=',nind+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) for i,atom in enumerate(data['Atoms']): if atom[cx+3] <= 0: continue radius = VDWdict.get(atom[ct]) cellMin = -radius/np.array(cell[0:3]) cellMax = radius/np.array(cell[0:3]) + (aMax,bMax,cMax) if radius is None: print('Skipping atom {}, no radius'.format(atom[0])) continue radius += probeRadius result = G2spc.GenAtom(atom[cx:cx+3],SGData,Move=True) for item in result: for scell in surroundingCells: XYZ = item[0] + scell if np.any((XYZ < cellMin, XYZ > cellMax)): continue lgclArray = np.logical_and(lgclArray,np.sqrt(np.sum(np.inner(Amat,coordGrd-XYZ)**2,axis=0))>radius) GoOn = pgbar.Update(i,newmsg='Atoms done=%d'%(i)) if not GoOn[0]: break pgbar.Destroy() print('found ',len(coordGrd[lgclArray]),'points gridspacing,probeRadius=',gridspacing,probeRadius) return coordGrd[lgclArray]
[docs] def SetDrawingDefaults(drawingData): """Add required items into data['drawing'] array if not present. This does not add all the items in SetupDrawingData, but it seems that this is not a problem. Perhaps the two routines could be combined? """ defaultDrawing = {'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True, 'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5, 'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33, 'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True, 'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],'magMult':1.0, 'bondList':{},'viewDir':[1,0,0],'Plane':[[0,0,1],False,False,0.0,[255,255,0]], 'peakMoveView':True,'PeakDistRadius':0.0,'showVoids':False,'showMap':False, 'atomsExpandRadius':5.,'atomsDistRadius':2.5,'Voids':[], 'VPPeakDistRad':0.,'VPatomsExpandRad':0.,'VPatomsDistRad':0., } for key in defaultDrawing: if key not in drawingData: drawingData[key] = defaultDrawing[key]
[docs] def updateAddRBorientText(G2frame,testRBObj,Bmat): '''Update all orientation text on the Add RB panel ''' A,V = G2mth.Q2AVdeg(testRBObj['rbObj']['Orient'][0]) testRBObj['rbObj']['OrientVec'][0] = A testRBObj['rbObj']['OrientVec'][1:] = np.inner(Bmat,V) for i,val in enumerate(testRBObj['rbObj']['OrientVec']): G2frame.testRBObjSizers['OrientVecSiz'][i].SetValue(val) G2frame.testRBObjSizers['OrientVecSiz'][4].SetValue( int(10*testRBObj['rbObj']['OrientVec'][0]))
[docs] def UpdatePhaseData(G2frame,Item,data): '''Create the data display window contents when a phase is clicked on in the main (data tree) window. Called only from :meth:`GSASIIdataGUI.SelectDataTreeItem`, which in turn is called from :meth:`GSASIIdataGUI.GSASII.OnDataTreeSelChanged` when a Phase tree item is selected. This creates all tabs on the page and fills their contents. Routine OnPageChanged is called each time a tab is pressed and updates the contents of the tab's page. :param wx.frame G2frame: the main GSAS-II frame object :param wx.TreeItemId Item: the tree item that was selected :param dict data: all the information on the phase in a dictionary ''' def GetReflData(G2frame,phaseName,reflNames): ReflData = {'RefList':[],'Type':''} if '' in reflNames: return None for reflName in reflNames: if 'PWDR' in reflName: PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root, reflName) if not PatternId: #got 0 return None reflSets = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,'Reflection Lists')) reflData = reflSets[phaseName] elif 'HKLF' in reflName: PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root, reflName) if not PatternId: #got 0 return None reflData = G2frame.GPXtree.GetItemPyData(PatternId)[1] if 'Type' not in reflData: reflData['Type'] = 'SXC' if ReflData['Type'] and reflData['Type'] != ReflData['Type']: G2frame.ErrorDialog('Data type conflict', reflName+' conflicts with previous '+ReflData['Type']) return None ReflData['RefList'] += list(reflData['RefList']) ReflData['Type'] = reflData['Type'] return ReflData def SetupGeneral(): try: G2elem.SetupGeneral(data,G2frame.dirname) except ValueError as msg: wx.MessageBox(msg,caption='Element symbol error') ##### General phase routines ################################################################################ def UpdateGeneral(Scroll=0,SkipDraw=False): '''Draw the controls for the General phase data subpage ''' """ This is the default dictionary structure for phase data (taken from GSASII.py) 'General':{ 'Name':PhaseName 'Type':'nuclear' 'SGData':SGData 'Cell':[False,10.,10.,10.,90.,90.,90,1000.] 'AtomPtrs':[] 'Pawley dmin':1.0, 'Pawley neg wt':0.0} 'Atoms':[] 'Drawing':{} """ def NameSizer(): def SetDefaultSSsymbol(): if generalData['SGData']['SGLaue'] in '-1': return '(abg)' elif generalData['SGData']['SGLaue'] in ['2/m']: if generalData['SGData']['SGUniq'] == 'a': return '(a00)' elif generalData['SGData']['SGUniq'] == 'b': return '(0b0)' elif generalData['SGData']['SGUniq'] == 'c': return '(00g)' else: return '(00g)' def OnPhaseName(event): event.Skip() oldName = generalData['Name'] phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree() phaseNameList = usedHistograms.keys() # phase names in use newName = NameTxt.GetValue().strip() if newName and newName != oldName: newName = G2obj.MakeUniqueLabel(newName,list(phaseNameList)) generalData['Name'] = newName G2frame.G2plotNB.Rename(oldName,generalData['Name']) G2frame.GPXtree.SetItemText(Item,generalData['Name']) # change phase name key in Reflection Lists for each histogram for hist in data['Histograms']: ht = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist) rt = G2gd.GetGPXtreeItemId(G2frame,ht,'Reflection Lists') if not rt: continue RfList = G2frame.GPXtree.GetItemPyData(rt) if oldName not in RfList: print('Warning: '+oldName+' not in Reflection List for '+ hist) continue RfList[newName] = RfList[oldName] del RfList[oldName] NameTxt.SetValue(newName) # rename Restraints resId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints') Restraints = G2frame.GPXtree.GetItemPyData(resId) i = G2gd.GetGPXtreeItemId(G2frame,resId,oldName) if i: G2frame.GPXtree.SetItemText(i,newName) Restraints[newName] = Restraints[oldName] del Restraints[oldName] def OnPhaseType(event): if not len(generalData['AtomTypes']): #can change only if no atoms! generalData['Type'] = TypeTxt.GetValue() pages = [G2frame.phaseDisplay.GetPageText(PageNum) for PageNum in range(G2frame.phaseDisplay.GetPageCount())] if generalData['Type'] == 'faulted': G2frame.Bind(wx.EVT_MENU, OnLoadDIFFaX, id=G2G.wxID_LOADDIFFAX) G2frame.Bind(wx.EVT_MENU, OnSimulate, id=G2G.wxID_LAYERSIMULATE) G2frame.Bind(wx.EVT_MENU, OnSeqSimulate, id=G2G.wxID_SEQUENCESIMULATE) G2frame.Bind(wx.EVT_MENU, OnFitLayers, id=G2G.wxID_LAYERSFIT) if 'Wave Data' in pages: pass # G2frame.phaseDisplay.DeletePage(pages.index('Wave Data')) if 'MC/SA' in pages: pass # G2frame.phaseDisplay.DeletePage(pages.index('MC/SA')) if 'RB Models' in pages: pass # G2frame.phaseDisplay.DeletePage(pages.index('RB Models')) if 'Layers' not in pages: if 'Layers' not in data: data['Layers'] = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.], 'Width':[[1.,1.],[False,False]],'Toler':0.01,'AtInfo':{}, 'Layers':[],'Stacking':[],'Transitions':[]} G2frame.layerData = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.InsertPage(3,G2frame.layerData,'Layers') Id = wx.NewId() TabSelectionIdDict[Id] = 'Layers' wx.CallAfter(UpdateGeneral) elif generalData['Type'] == 'magnetic': generalData['AtomPtrs'] = [3,1,10,12] SGData = generalData['SGData'] Nops = len(SGData['SGOps'])*len(SGData['SGCen']) if SGData['SGInv']: Nops *= 2 SGData['SpnFlp'] = Nops*[1,] else: if 'Wave Data' in pages: G2frame.phaseDisplay.DeletePage(pages.index('Wave Data')) if 'MC/SA' not in pages: G2frame.MCSA = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.InsertPage(7,G2frame.MCSA,'MC/SA') Id = wx.NewId() TabSelectionIdDict[Id] = 'MC/SA' wx.CallAfter(UpdateGeneral) else: G2frame.ErrorDialog('Phase type change error','Can change phase type only if there are no atoms') TypeTxt.SetValue(generalData['Type']) def OnSpaceGroup(event): if generalData['SGData']['SGFixed']: msg = 'Fixed cif generated magnetic space group' text = 'space group can not be changed' wx.MessageBox(text,caption=msg,style=wx.ICON_EXCLAMATION) text,table = G2spc.SGPrint(generalData['SGData']) SGTxt.SetLabel(generalData['SGData']['SpGrp']) msg = 'cif based Space Group Information' G2G.SGMessageBox(General,msg,text,table).Show() return # try a lookup on the user-supplied name SpcGp = GetSpGrpfromUser(General,SpGrp) if SpcGp == SpGrp: text,table = G2spc.SGPrint(generalData['SGData']) SGTxt.SetLabel(generalData['SGData']['SpGrp']) msg = 'Space Group Information' G2G.SGMessageBox(General,msg,text,table).Show() return #unchanged - do nothing but show info SpGrpNorm = G2spc.StandardizeSpcName(SpcGp) if SpGrpNorm: SGErr,SGData = G2spc.SpcGroup(SpGrpNorm) else: SGErr,SGData = G2spc.SpcGroup(SpcGp) if SGErr: text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous'] SGTxt.SetLabel(generalData['SGData']['SpGrp']) msg = 'Space Group Error' Text = '\n'.join(text) wx.MessageBox(Text,caption=msg,style=wx.ICON_EXCLAMATION) else: if "1'" in SpcGp: generalData['Type'] = 'magnetic' generalData['Modulated'] = True if generalData['Type'] == 'magnetic': Nops = len(SGData['SGOps'])*len(SGData['SGCen']) if SGData['SGInv']: Nops *= 2 GenSym,GenFlg = G2spc.GetGenSym(SGData)[:2] SGData['GenSym'] = GenSym SGData['GenFlg'] = GenFlg SGData['MagSpGrp'] = G2spc.MagSGSym(SGData) G2spc.ApplyBNSlatt(SGData,SGData['BNSlattsym']) SGData['SpnFlp'] = Nops*[1,] if generalData['Modulated']: generalData['SuperSg'] = SetDefaultSSsymbol() generalData['SSGData'] = G2spc.SSpcGroup(generalData['SGData'],generalData['SuperSg'])[1] if SGData['SGGray']: SGData['SpnFlp'] += Nops*[-1,] text,table = G2spc.SGPrint(SGData) generalData['SGData'] = SGData SGTxt.SetLabel(generalData['SGData']['SpGrp']) msg = 'Space Group Information' G2G.SGMessageBox(General,msg,text,table).Show() G2spc.UpdateSytSym(data) NShkl = len(G2spc.MustrainNames(SGData)) NDij = len(G2spc.HStrainNames(SGData)) for hist in data['Histograms']: if 'HStrain' in data['Histograms'][hist]: #PWDR only data['Histograms'][hist]['Mustrain'][4:6] = [NShkl*[0.01,],NShkl*[False,]] data['Histograms'][hist]['HStrain'] = [NDij*[0.0,],NDij*[False,]] if data['Drawing']: data['Drawing']['Atoms'] = [] wx.CallAfter(UpdateGeneral) def OnModulated(event): if not len(generalData['AtomTypes']): #can change only if no atoms! pages = [G2frame.phaseDisplay.GetPageText(PageNum) for PageNum in range(G2frame.phaseDisplay.GetPageCount())] if generalData['Type'] in ['nuclear','magnetic']: generalData['Modulated'] = modulated.GetValue() if generalData['Modulated']: if 'SuperSg' not in generalData: generalData['SuperSg'] = SetDefaultSSsymbol() generalData['SSGData'] = G2spc.SSpcGroup(generalData['SGData'],generalData['SuperSg'])[1] if 'SuperVec' not in generalData: generalData['Super'] = True generalData['SuperVec'] = [[0.,0.,0.],False,4] generalData['SSGData'] = {} if '4DmapData' not in generalData: generalData['4DmapData'] = mapDefault.copy() generalData['4DmapData'].update({'MapType':'Fobs'}) if 'MC/SA' in pages: pass # G2frame.phaseDisplay.DeletePage(pages.index('MC/SA')) #this crashes!! if 'Layers' in pages: pass # G2frame.phaseDisplay.DeletePage(pages.index('Layers')) if 'Wave Data' not in pages: G2frame.waveData = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.InsertPage(3,G2frame.waveData,'Wave Data') Id = wx.NewId() TabSelectionIdDict[Id] = 'Wave Data' # deleting page now causes Mac crash, postpone until page is redrawn # else: # if 'Wave Data' in pages: # G2frame.phaseDisplay.DeletePage(pages.index('Wave Data')) wx.CallAfter(UpdateGeneral) else: if generalData['Type'] == 'magnetic': pages = [G2frame.phaseDisplay.GetPageText(PageNum) for PageNum in range(G2frame.phaseDisplay.GetPageCount())] generalData['Modulated'] = modulated.GetValue() if generalData['Modulated']: if 'SuperSg' not in generalData: generalData['SuperSg'] = SetDefaultSSsymbol() generalData['SSGData'] = G2spc.SSpcGroup(generalData['SGData'],generalData['SuperSg'])[1] if 'SuperVec' not in generalData: generalData['Super'] = 1 generalData['SuperVec'] = [[0.,0.,0.],False,4] generalData['SSGData'] = {} if '4DmapData' not in generalData: generalData['4DmapData'] = mapDefault.copy() generalData['4DmapData'].update({'MapType':'Fobs'}) if 'Wave Data' not in pages: G2frame.waveData = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.InsertPage(3,G2frame.waveData,'Wave Data') Id = wx.NewId() TabSelectionIdDict[Id] = 'Wave Data' Atoms = data['Atoms'] for atom in Atoms: atom += [{'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}] wx.CallAfter(UpdateGeneral) else: G2frame.ErrorDialog('Modulation type change error','Can change modulation only if there are no atoms') modulated.SetValue(generalData['Modulated']) nameSizer = wx.BoxSizer(wx.HORIZONTAL) nameSizer.Add(wx.StaticText(General,-1,' Phase name: '),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) NameTxt = wx.TextCtrl(General,-1,value=generalData['Name'],style=wx.TE_PROCESS_ENTER) NameTxt.Bind(wx.EVT_TEXT_ENTER,OnPhaseName) NameTxt.Bind(wx.EVT_KILL_FOCUS,OnPhaseName) nameSizer.Add(NameTxt,0,WACV) nameSizer.Add(wx.StaticText(General,-1,' Phase type: '),0,WACV) TypeTxt = wx.ComboBox(General,-1,value=generalData['Type'],choices=phaseTypes, style=wx.CB_READONLY|wx.CB_DROPDOWN) TypeTxt.Bind(wx.EVT_COMBOBOX, OnPhaseType) nameSizer.Add(TypeTxt,0,WACV) nameSizer.Add(wx.StaticText(General,-1,' Space group: '),0,WACV) SpGrp = generalData['SGData']['SpGrp'] if generalData['SGData']['SGGray']: SpGrp += " 1'" SGTxt = wx.Button(General,wx.ID_ANY,SpGrp,size=(100,-1)) SGTxt.Bind(wx.EVT_BUTTON,OnSpaceGroup) nameSizer.Add(SGTxt,0,WACV) if generalData['Type'] in ['nuclear','magnetic']: modulated = wx.CheckBox(General,label='Modulated? ') modulated.SetValue(generalData['Modulated']) modulated.Bind(wx.EVT_CHECKBOX,OnModulated) nameSizer.Add(modulated,0,WACV) # add help button to bring up help web page - at right sede of window nameSizer.Add((-1,-1),1,WACV) nameSizer.Add(G2G.HelpButton(General,helpIndex=G2frame.dataWindow.helpKey),0,WACV) return nameSizer def CellSizer(): cellGUIlist = [[['m3','m3m'],4,zip([" Unit cell: a = "," Vol = "],["%.5f","%.3f"],[True,False],[0,0])], [['3R','3mR'],6,zip([" a = "," alpha = "," Vol = "],["%.5f","%.3f","%.3f"],[True,True,False],[0,3,0])], [['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],6,zip([" a = "," c = "," Vol = "],["%.5f","%.5f","%.3f"],[True,True,False],[0,2,0])], [['mmm'],8,zip([" a = "," b = "," c = "," Vol = "],["%.5f","%.5f","%.5f","%.3f"], [True,True,True,False],[0,1,2,0])], [['2/m'+'a'],10,zip([" a = "," b = "," c = "," alpha = "," Vol = "], ["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,3,0])], [['2/m'+'b'],10,zip([" a = "," b = "," c = "," beta = "," Vol = "], ["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])], [['2/m'+'c'],10,zip([" a = "," b = "," c = "," gamma = "," Vol = "], ["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,5,0])], [['-1'],7,zip([" a = "," b = "," c = "," Vol = "," alpha = "," beta = "," gamma = "], ["%.5f","%.5f","%.5f","%.3f","%.3f","%.3f","%.3f"], [True,True,True,False,True,True,True],[0,1,2,0,3,4,5])]] def OnCellRef(event): generalData['Cell'][0] = cellRef.GetValue() def OnCellChange(invalid,value,tc): SGData = generalData['SGData'] laue = SGData['SGLaue'] if laue == '2/m': laue += SGData['SGUniq'] cell = generalData['Cell'] Obj = tc ObjId = cellList.index(Obj.GetId()) try: value = max(1.0,float(tc.GetValue())) except ValueError: if ObjId < 3: #bad cell edge - reset value = cell[ObjId+1] else: #bad angle value = 90. if laue in ['m3','m3m']: cell[1] = cell[2] = cell[3] = value cell[4] = cell[5] = cell[6] = 90.0 Obj.SetValue(cell[1]) elif laue in ['3R','3mR']: if ObjId == 0: cell[1] = cell[2] = cell[3] = value Obj.SetValue(cell[1]) else: cell[4] = cell[5] = cell[6] = value Obj.SetValue(cell[4]) elif laue in ['3','3m1','31m','6/m','6/mmm','4/m','4/mmm']: cell[4] = cell[5] = 90. cell[6] = 120. if laue in ['4/m','4/mmm']: cell[6] = 90. if ObjId == 0: cell[1] = cell[2] = value Obj.SetValue(cell[1]) else: cell[3] = value Obj.SetValue(cell[3]) elif laue in ['mmm']: cell[ObjId+1] = value cell[4] = cell[5] = cell[6] = 90. Obj.SetValue(cell[ObjId+1]) elif laue in ['2/m'+'a']: cell[5] = cell[6] = 90. if ObjId != 3: cell[ObjId+1] = value Obj.SetValue(cell[ObjId+1]) else: cell[4] = value Obj.SetValue(cell[4]) elif laue in ['2/m'+'b']: cell[4] = cell[6] = 90. if ObjId != 3: cell[ObjId+1] = value Obj.SetValue(cell[ObjId+1]) else: cell[5] = value Obj.SetValue(cell[5]) elif laue in ['2/m'+'c']: cell[4] = cell[5] = 90. if ObjId != 3: cell[ObjId+1] = value Obj.SetValue(cell[ObjId+1]) else: cell[6] = value Obj.SetValue(cell[6]) else: cell[ObjId+1] = value Obj.SetValue(cell[1+ObjId]) cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7])) volVal.SetValue("%.3f"%(cell[7])) density,mattCoeff = G2mth.getDensity(generalData) if denSizer: denSizer[1].SetValue('%.3f'%(density)) if denSizer[2]: denSizer[2].SetValue('%.3f'%(mattCoeff)) cell = generalData['Cell'] laue = generalData['SGData']['SGLaue'] if laue == '2/m': laue += generalData['SGData']['SGUniq'] for cellGUI in cellGUIlist: if laue in cellGUI[0]: useGUI = cellGUI cellSizer = wx.FlexGridSizer(0,useGUI[1]+1,5,5) if PWDR: cellRef = wx.CheckBox(General,-1,label='Refine unit cell:') cellSizer.Add(cellRef,0,WACV) cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef) cellRef.SetValue(cell[0]) cellList = [] for txt,fmt,ifEdit,Id in useGUI[2]: cellSizer.Add(wx.StaticText(General,label=txt),0,WACV) Fmt = (10,5) if '.3' in fmt: Fmt = (10,3) if ifEdit: #a,b,c,etc. cellVal = G2G.ValidatedTxtCtrl(General,generalData['Cell'],Id+1, xmin=0.1,xmax=500.,nDig=Fmt,OnLeave=OnCellChange) cellSizer.Add(cellVal,0,WACV) cellList.append(cellVal.GetId()) else: #volume volVal = G2G.ReadOnlyTextCtrl(General,value=(fmt%(cell[7]))) cellSizer.Add(volVal,0,WACV) return cellSizer def ElemSizer(): def OnIsotope(event): Obj = event.GetEventObject() item = Indx[Obj.GetId()] isotope = Obj.GetValue() nCols = len(generalData['AtomTypes'])+1 data['General']['Isotope'][item] = isotope indx = generalData['AtomTypes'].index(item) wt = generalData['Isotopes'][item][isotope]['Mass'] elemSizer.GetChildren()[indx+3*nCols+1].Window.SetValue('%.3f'%(wt)) #tricky data['General']['AtomMass'][indx] = wt density,mattCoeff = G2mth.getDensity(generalData) denSizer[1].SetValue('%.3f'%(density)) if denSizer[2]: denSizer[2].SetValue('%.3f'%(mattCoeff)) elemSizer = wx.FlexGridSizer(0,len(generalData['AtomTypes'])+1,1,1) elemSizer.Add(wx.StaticText(General,label=' Elements'),0,WACV) for elem in generalData['AtomTypes']: typTxt = G2G.ReadOnlyTextCtrl(General,value=elem) elemSizer.Add(typTxt,0,WACV) elemSizer.Add(wx.StaticText(General,label=' Isotope'),0,WACV) for elem in generalData['AtomTypes']: choices = list(generalData['Isotopes'][elem].keys()) isoSel = wx.ComboBox(General,-1,value=generalData['Isotope'][elem],choices=choices, style=wx.CB_READONLY) isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope) Indx[isoSel.GetId()] = elem elemSizer.Add(isoSel,1,wx.EXPAND) elemSizer.Add(wx.StaticText(General,label=' No. per cell'),0,WACV) for elem in generalData['AtomTypes']: numbTxt = G2G.ReadOnlyTextCtrl(General,value='%.1f'%(generalData['NoAtoms'][elem])) elemSizer.Add(numbTxt,0,WACV) elemSizer.Add(wx.StaticText(General,label=' Atom weight'),0,WACV) for wt in generalData['AtomMass']: wtTxt = G2G.ReadOnlyTextCtrl(General,value='%.3f'%(wt)) elemSizer.Add(wtTxt,0,WACV) elemSizer.Add(wx.StaticText(General,label=' Bond radii'),0,WACV) for rad in generalData['BondRadii']: bondRadii = G2G.ReadOnlyTextCtrl(General,value='%.2f'%(rad)) elemSizer.Add(bondRadii,0,WACV) elemSizer.Add(wx.StaticText(General,label=' Angle radii'),0,WACV) for rad in generalData['AngleRadii']: elemTxt = G2G.ReadOnlyTextCtrl(General,value='%.2f'%(rad)) elemSizer.Add(elemTxt,0,WACV) elemSizer.Add(wx.StaticText(General,label=' van der Waals radii'),0,WACV) for rad in generalData['vdWRadii']: elemTxt = G2G.ReadOnlyTextCtrl(General,value='%.2f'%(rad)) elemSizer.Add(elemTxt,0,WACV) elemSizer.Add(wx.StaticText(General,label=' Default color'),0,WACV) for R,G,B in generalData['Color']: colorTxt = G2G.ReadOnlyTextCtrl(General,value='') colorTxt.SetBackgroundColour(wx.Colour(R,G,B)) elemSizer.Add(colorTxt,0,WACV) if generalData['Type'] == 'magnetic': elemSizer.Add(wx.StaticText(General,label=' Lande g factor: '),0,WACV) for ig,elem in enumerate(generalData['AtomTypes']): gfac = generalData['Lande g'][ig] if gfac == None: elemSizer.Add((5,0),) else: gfacTxt = G2G.ValidatedTxtCtrl(General,generalData['Lande g'],ig, xmin=0.5,xmax=3.0,nDig=(10,2)) elemSizer.Add(gfacTxt,0,WACV) return elemSizer def DenSizer(): generalData['Mass'] = G2mth.getMass(generalData) density,mattCoeff = G2mth.getDensity(generalData) denSizer = wx.BoxSizer(wx.HORIZONTAL) denSizer.Add(wx.StaticText(General,-1,' Density: '),0,WACV) denTxt = G2G.ReadOnlyTextCtrl(General,-1,'%.3f'%(density)) denSizer.Add(denTxt,0,WACV) mattTxt = None if generalData['Type'] == 'macromolecular' and generalData['Mass'] > 0.0: denSizer.Add(wx.StaticText(General,-1,' Matthews coeff.: '), 0,WACV) mattTxt = G2G.ReadOnlyTextCtrl(General,-1,'%.3f'%(mattCoeff)) denSizer.Add(mattTxt,0,WACV) return denSizer,denTxt,mattTxt def MagSizer(): def OnSpinOp(event): if SGData['SGFixed']: msg = 'Fixed cif generated spins' text = 'Spin configuration can not be changed; it will be reset' wx.MessageBox(text,caption=msg,style=wx.ICON_EXCLAMATION) wx.CallAfter(UpdateGeneral) return Obj = event.GetEventObject() isym = Indx[Obj.GetId()]+1 spCode = {'red':-1,'black':1} SGData['SGSpin'][isym] = spCode[Obj.GetValue()] G2spc.CheckSpin(isym,SGData) wx.CallAfter(UpdateGeneral) def OnBNSlatt(event): Obj = event.GetEventObject() BNSlatt = Obj.GetValue() SGData = generalData['SGData'] SpcGrp = SGData['SpGrp'] if SGData['SGGray']: SpcGrp += " 1'" SGErr,SGData = G2spc.SpcGroup(SpcGrp) if '_' in BNSlatt: SGData['BNSlattsym'] = [BNSlatt,BNSsym[BNSlatt]] else: SGData['BNSlattsym'] = [SGData['SGLatt'],[0.,0.,0.]] SGData['SGSpin'] = [1,]*len(SGData['SGSpin']) #set to all black GenSym,GenFlg = G2spc.GetGenSym(SGData)[:2] SGData['GenSym'] = GenSym SGData['GenFlg'] = GenFlg SGData['MagSpGrp'] = G2spc.MagSGSym(SGData) G2spc.ApplyBNSlatt(SGData,SGData['BNSlattsym']) generalData['SGData'] = SGData G2spc.UpdateSytSym(data) wx.CallAfter(UpdateGeneral) def OnShowSpins(event): msg = 'Magnetic space group information' text,table = G2spc.SGPrint(SGData,AddInv=not SGData['SGFixed']) text[0] = ' Magnetic Space Group: '+SGData['MagSpGrp'] text[3] = ' The magnetic lattice point group is '+SGData['MagPtGp'] if SGData['SGGray'] and "1'" not in text[0]: text[0] += " 1'" text[3] += "1'" G2G.SGMagSpinBox(General,msg,text,table,SGData['SGCen'],OprNames, SGData['SpnFlp'],SGData['SGGray']& (not SGData['SGFixed'])).Show() SGData = generalData['SGData'] GenSym,GenFlg,BNSsym = G2spc.GetGenSym(SGData) if 'BNSlattsym' not in SGData: SGData['BNSlattsym'] = [SGData['SGLatt'],[0,0,0]] Indx = {} MagSym = SGData['MagSpGrp'] if SGData['SGGray'] and "1'" not in MagSym: MagSym += " 1'" magSizer = wx.BoxSizer(wx.VERTICAL) magSizer.Add(wx.StaticText(General,label=' Magnetic spin operator selection:'),0) spinSizer = wx.BoxSizer(wx.HORIZONTAL) if SGData['SGFixed']: SpnFlp = SGData['SpnFlp'] spinSizer.Add(wx.StaticText(General,label=' Magnetic phase from mcif file; no change in spin inversion allowed'),0,WACV) OprNames = G2spc.GenMagOps(SGData)[0] else: if not len(GenSym): # or SGData['SGGray']: spinSizer.Add(wx.StaticText(General,label=' No spin inversion allowed'),0,WACV) OprNames,SpnFlp = G2spc.GenMagOps(SGData) else: spinSizer.Add(wx.StaticText(General,label=' BNS lattice: '),0,WACV) BNSkeys = [SGData['SGLatt'],]+list(BNSsym.keys()) BNSkeys.sort() try: #this is an ugly kluge - bug in wx.ComboBox if SGData['BNSlattsym'][0][2] in ['a','b','c']: BNSkeys.reverse() except: pass BNS = wx.ComboBox(General, choices=BNSkeys,style=wx.CB_READONLY|wx.CB_DROPDOWN) BNS.SetValue(SGData['BNSlattsym'][0]) BNS.Bind(wx.EVT_COMBOBOX,OnBNSlatt) spinSizer.Add(BNS,0,WACV) spinColor = ['black','red'] spCode = {-1:'red',1:'black'} for isym,sym in enumerate(GenSym[1:]): spinSizer.Add(wx.StaticText(General,label=' %s: '%(sym.strip())),0,WACV) spinOp = wx.ComboBox(General,value=spCode[SGData['SGSpin'][isym+1]],choices=spinColor, style=wx.CB_READONLY|wx.CB_DROPDOWN) Indx[spinOp.GetId()] = isym spinOp.Bind(wx.EVT_COMBOBOX,OnSpinOp) spinSizer.Add(spinOp,0,WACV) OprNames,SpnFlp = G2spc.GenMagOps(SGData) SGData['SpnFlp'] = SpnFlp SGData['OprNames'] = OprNames magSizer.Add(spinSizer) msgSizer = wx.BoxSizer(wx.HORIZONTAL) msgSizer.Add(wx.StaticText(General,label=' Magnetic space group: %s '%(MagSym)),0,WACV) showSpins = wx.Button(General,label=' Show spins?') showSpins.Bind(wx.EVT_BUTTON,OnShowSpins) msgSizer.Add(showSpins,0,WACV) magSizer.Add(msgSizer) dminSizer = wx.BoxSizer(wx.HORIZONTAL) dminSizer.Add(wx.StaticText(General,label=' Magnetic reflection d-min: '),0,WACV) dminVal = G2G.ValidatedTxtCtrl(General,generalData,'MagDmin',nDig=(10,4),xmin=0.7) dminSizer.Add(dminVal,0,WACV) magSizer.Add(dminSizer,0) return magSizer def ModulatedSizer(name): def OnShowSOps(event): SSGData = generalData['SSGData'] text,table = G2spc.SSGPrint(generalData['SGData'],SSGData,not SGData['SGFixed']) msg = 'Superspace Group Information' G2G.SGMessageBox(General,msg,text,table,SGData.get('SpnFlp',[])).ShowModal() def OnSuperGp(event): #for HKLF needs to reject SSgps not agreeing with modVec! 'Respond to selection of a modulation group' wx.BeginBusyCursor() Choice = G2spc.SSChoice(SGData) wx.EndBusyCursor() dlg = wx.Dialog(General,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) sizer = wx.BoxSizer(wx.VERTICAL) sizer.Add(wx.StaticText(dlg,wx.ID_OK,'Select or enter a modulation group'),0,wx.ALIGN_CENTER) sizer.Add((10,10)) superGp = wx.ComboBox(dlg,value=generalData['SuperSg'],choices=Choice,style=wx.CB_DROPDOWN|wx.TE_READONLY) sizer.Add(superGp) sizer.Add((10,10)) btnsizer = wx.StdDialogButtonSizer() btn = wx.Button(dlg, wx.ID_OK) btn.SetDefault() btnsizer.AddButton(btn) btn = wx.Button(dlg, wx.ID_CANCEL) btnsizer.AddButton(btn) btnsizer.Realize() sizer.Add(btnsizer, 0, wx.EXPAND|wx.ALL, 5) dlg.SetSizer(sizer) sizer.Fit(dlg) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: try: SSymbol = superGp.GetValue().strip() except AttributeError: # not sure why needed SSymbol = superGp.GetLabel().strip() else: dlg.Destroy() return dlg.Destroy() try: E,SSGData = G2spc.SSpcGroup(generalData['SGData'],SSymbol) except: E = 'Invalid modulation group' SSGData = None if SSGData: Vec = generalData['SuperVec'][0] #(3+1) only modSymb = SSGData['modSymb'] generalData['SuperVec'][0] = G2spc.SSGModCheck(Vec,modSymb)[0] generalData['SSGData'] = SSGData generalData['SuperSg'] = SSymbol OnShowSOps(event) else: # needed in case someone manually enters an invalid SSG? Text = '\n'.join([E+'\nSuperspace Group entry ignored']) G2G.G2MessageBox(General,Text,'Superspace Group Error') wx.CallAfter(UpdateGeneral) def OnVecRef(event): generalData['SuperVec'][1] = Ref.GetValue() def OnMax(event): generalData['SuperVec'][2] = int(Max.GetValue()) Indx = {} ssSizer = wx.BoxSizer(wx.VERTICAL) modSizer = wx.BoxSizer(wx.HORIZONTAL) modSizer.Add(wx.StaticText(General,label=' '+name.capitalize()+' structure controls: '),0,WACV) SGData = generalData['SGData'] SpGrp = SGData.get('MagSpGrp',SGData['SpGrp']) if SGData['SGGray']: SpGrp += " 1'" modSizer.Add(wx.StaticText(General,label=' Superspace group: %s '%SpGrp),0,WACV) if not SGData['SGFixed']: val = generalData['SuperSg'] superGp = wx.Button(General,wx.ID_ANY,val,size=(100,-1)) superGp.Bind(wx.EVT_BUTTON,OnSuperGp) else: superGp = wx.StaticText(General,label=generalData['SuperSg']) modSizer.Add(superGp,0,WACV) modSizer.Add((5,5),0) showOps = wx.Button(General,label='Show ops.') showOps.Bind(wx.EVT_BUTTON,OnShowSOps) modSizer.Add(showOps,0,WACV) if PWDR: modSizer.Add(wx.StaticText(General,label=' Max index: '),0,WACV) indChoice = ['1','2','3','4','5','6','7'] if 'Magnetic' in name.capitalize(): #limit to one for now indChoice = ['1',] Max = wx.ComboBox(General,-1,value='%d'%(generalData['SuperVec'][2]),choices=indChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) Max.Bind(wx.EVT_COMBOBOX,OnMax) modSizer.Add(Max,0,WACV) ssSizer.Add(modSizer,0) vecSizer = wx.FlexGridSizer(1,5,5,5) vecSizer.Add(wx.StaticText(General,label=' Modulation vector: '),0,WACV) modS = G2spc.splitSSsym(generalData['SuperSg'])[0] generalData['SuperVec'][0],ifShow = G2spc.SSGModCheck(generalData['SuperVec'][0],modS) for i,[val,show] in enumerate(zip(generalData['SuperVec'][0],ifShow)): if show: modVal = G2G.ValidatedTxtCtrl(General,generalData['SuperVec'][0],i,nDig=(10,4),xmin=-1.,xmax=2.) vecSizer.Add(modVal,0,WACV) Indx[modVal.GetId()] = i else: modVal = G2G.ReadOnlyTextCtrl(General,value=('%.3f'%(val)), size=wx.Size(50,20)) vecSizer.Add(modVal,0,WACV) if PWDR: Ref = wx.CheckBox(General,label='Refine?') Ref.SetValue(generalData['SuperVec'][1]) Ref.Bind(wx.EVT_CHECKBOX, OnVecRef) vecSizer.Add(Ref,0,WACV) ssSizer.Add(vecSizer) return ssSizer def PawleySizer(): # find d-space range in used histograms dmin,dmax,nhist,lbl = getPawleydRange(G2frame,data) pawleySizer = wx.BoxSizer(wx.HORIZONTAL) pawleySizer.Add(wx.StaticText(General,label=' Pawley controls: '),0,WACV) if nhist == 0: # no data, no Pawley pawleySizer.Add(wx.StaticText(General,label=' no data'),0,WACV) generalData['doPawley'] = False return pawleySizer # force limits on dmin & dmax generalData['Pawley dmax'] = min(generalData['Pawley dmax'],dmax) generalData['Pawley dmin'] = max(generalData['Pawley dmin'],dmin) pawlRef = G2G.G2CheckBoxFrontLbl(General,' Do Pawley refinement?', generalData,'doPawley') pawleySizer.Add(pawlRef,0,WACV) pawleySizer.Add(wx.StaticText(General,label=' dmin: '),0,WACV) pawlMin = G2G.ValidatedTxtCtrl(General,generalData,'Pawley dmin',size=(75,-1), xmin=dmin,xmax=20.,nDig=(10,5)) pawleySizer.Add(pawlMin,0,WACV) pawleySizer.Add(wx.StaticText(General,label=' dmax: '),0,WACV) pawlMax = G2G.ValidatedTxtCtrl(General,generalData,'Pawley dmax',size=(75,-1), xmin=2.0,xmax=dmax,nDig=(10,5)) pawleySizer.Add(pawlMax,0,WACV) pawleySizer.Add(wx.StaticText(General,label=' Pawley neg. wt.: '),0,WACV) pawlNegWt = G2G.ValidatedTxtCtrl(General,generalData,'Pawley neg wt',size=(65,-1), xmin=0.,xmax=1.,nDig=(10,3,'g')) pawleySizer.Add(pawlNegWt,0,WACV) pawleyOuter = wx.BoxSizer(wx.VERTICAL) pawleyOuter.Add(pawleySizer) pawleyOuter.Add(wx.StaticText(General,label=lbl),0,wx.LEFT,120) return pawleyOuter def MapSizer(): def OnMapType(event): Map['MapType'] = mapType.GetValue() if 'delt-F' in Map['MapType']: data['Drawing']['contourColor'] = 'RdYlGn' else: data['Drawing']['contourColor'] = 'YlGnBu' def OnRefList(event): if not refsList: G2G.G2MessageBox(G2frame,'No reflections') return dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to use', 'Use data',refsList) try: if dlg.ShowModal() == wx.ID_OK: if not len(dlg.GetSelections()): dlg.Destroy() return Map['RefList'] = [refsList[i] for i in dlg.GetSelections()] else: dlg.Destroy() return finally: dlg.Destroy() wx.CallAfter(UpdateGeneral,General.GetScrollPos(wx.VERTICAL)) def OnDysnomia(event): data['General']['doDysnomia'] = not data['General']['doDysnomia'] pages = [G2frame.phaseDisplay.GetPageText(PageNum) for PageNum in range(G2frame.phaseDisplay.GetPageCount())] if generalData['doDysnomia']: if 'Dysnomia' not in pages: G2frame.MEMData = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.Bind(wx.EVT_MENU, OnLoadDysnomia, id=G2G.wxID_LOADDYSNOMIA) G2frame.Bind(wx.EVT_MENU, OnSaveDysnomia, id=G2G.wxID_SAVEDYSNOMIA) G2frame.Bind(wx.EVT_MENU, OnRunDysnomia, id=G2G.wxID_RUNDYSNOMIA) G2frame.phaseDisplay.InsertPage(7,G2frame.MEMData,'Dysnomia') Id = wx.NewId() TabSelectionIdDict[Id] = 'Dysnomia' if 'Dysnomia' not in data: #set defaults here data['Dysnomia'] = {'DenStart':'uniform','Optimize':'ZSPA','Lagrange':['user',0.001,0.05], 'wt pwr':0,'E_factor':1.,'Ncyc':5000,'prior':'uniform','Lam frac':[1,0,0,0,0,0,0,0], 'overlap':0.2,'MEMdmin':1.0} else: if 'Dysnomia' in pages: G2frame.phaseDisplay.DeletePage(pages.index('Dysnomia')) #patch if 'cutOff' not in Map: Map['cutOff'] = 100.0 if 'Resolution' in Map: Map['GridStep'] = Map['Resolution'] mapTypes = ['Fobs','Fcalc','delt-F','2*Fo-Fc','Omit','2Fo-Fc Omit','Patterson'] refsList = [item for item in G2gd.GetGPXtreeDataNames(G2frame,['HKLF','PWDR']) if item in data['Histograms'].keys()] if not generalData['AtomTypes']: mapTypes = ['Patterson',] Map['MapType'] = 'Patterson' mapSizer = wx.BoxSizer(wx.VERTICAL) lineSizer = wx.BoxSizer(wx.HORIZONTAL) lineSizer.Add(wx.StaticText(General,label=' Fourier map controls: Map type: '),0,WACV) mapType = wx.ComboBox(General,value=Map['MapType'],choices=mapTypes, style=wx.CB_READONLY|wx.CB_DROPDOWN) mapType.Bind(wx.EVT_COMBOBOX,OnMapType) lineSizer.Add(mapType,0,WACV) lineSizer.Add(wx.StaticText(General,label=' Reflection sets: '),0,WACV) if 'list' not in str(type(Map['RefList'])): #patch Map['RefList'] = [Map['RefList'],] lineSizer.Add(wx.ComboBox(General,value=Map['RefList'][0],choices=Map['RefList'], style=wx.CB_DROPDOWN|wx.CB_READONLY),0,WACV) refList = wx.Button(General,label='Select reflection sets') refList.Bind(wx.EVT_BUTTON,OnRefList) lineSizer.Add(refList,0,WACV) mapSizer.Add(lineSizer,0) line2Sizer = wx.BoxSizer(wx.HORIZONTAL) line2Sizer.Add(wx.StaticText(General,label=' Map grid step: '),0,WACV) mapRes = G2G.ValidatedTxtCtrl(General,Map,'GridStep',nDig=(10,2),xmin=0.1,xmax=2.) line2Sizer.Add(mapRes,0,WACV) line2Sizer.Add(wx.StaticText(General,label=' Peak cutoff %: '),0,WACV) cutOff = G2G.ValidatedTxtCtrl(General,Map,'cutOff',nDig=(10,1),xmin=1.0,xmax=100.) line2Sizer.Add(cutOff,0,WACV) if len(Map['RefList']) and not generalData['Modulated']: if all(['PWDR' in map for map in Map['RefList']]): Dysno = wx.CheckBox(General,-1,label=' Use Dysnomia?') Dysno.SetValue(generalData['doDysnomia']) Dysno.Bind(wx.EVT_CHECKBOX,OnDysnomia) line2Sizer.Add(Dysno,0,WACV) hlpText = '''Dysnomia uses the maximum entropy method to compute intensities for unobserved reflections. ''' hlp = G2G.HelpButton(General,hlpText) line2Sizer.Add(hlp,0,WACV) mapSizer.Add(line2Sizer,0) return mapSizer def FlipSizer(): #patches if 'k-Max' not in Flip: Flip['k-Max'] = 20. if 'Resolution' in Flip: Flip['GridStep'] = Flip['Resolution'] def OnRefList(event): dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to use', 'Use data',refsList) try: if dlg.ShowModal() == wx.ID_OK: if not len(dlg.GetSelections()): dlg.Destroy() return Flip['RefList'] = [refsList[i] for i in dlg.GetSelections()] else: dlg.Destroy() return finally: dlg.Destroy() wx.CallAfter(UpdateGeneral,General.GetScrollPos(wx.VERTICAL)) def OnNormElem(event): PE = G2elemGUI.PickElement(G2frame,ifNone=True) if PE.ShowModal() == wx.ID_OK: Flip['Norm element'] = PE.Elem.strip() normElem.SetLabel(Flip['Norm element']) PE.Destroy() def OnTestHKL(event): event.Skip() Obj = event.GetEventObject() name = Obj.GetName() try: vals = Obj.GetValue().split() Id = int(name.split('hkl')[1]) HKL = [int(val) for val in vals] Flip['testHKL'][Id] = HKL except ValueError: HKL = Flip['testHKL'][Id] Obj.SetValue('%3d %3d %3d'%(HKL[0],HKL[1],HKL[2])) refsList = [item for item in G2gd.GetGPXtreeDataNames(G2frame,['HKLF','PWDR']) if item in data['Histograms'].keys()] flipSizer = wx.BoxSizer(wx.VERTICAL) lineSizer = wx.BoxSizer(wx.HORIZONTAL) lineSizer.Add(wx.StaticText(General,label=' Charge flip controls: Reflection sets: '),0,WACV) if 'list' not in str(type(Flip['RefList'])): #patch Flip['RefList'] = [Flip['RefList'],] lineSizer.Add(wx.ComboBox(General,value=Flip['RefList'][0],choices=Flip['RefList'], style=wx.CB_DROPDOWN|wx.CB_READONLY),0,WACV) refList = wx.Button(General,label='Select reflection sets') refList.Bind(wx.EVT_BUTTON,OnRefList) lineSizer.Add(refList,0,WACV) lineSizer.Add(wx.StaticText(General,label=' Normalizing element: '),0,WACV) normElem = wx.Button(General,label=Flip['Norm element'],style=wx.TE_READONLY) normElem.Bind(wx.EVT_BUTTON,OnNormElem) lineSizer.Add(normElem,0,WACV) flipSizer.Add(lineSizer,0) line2Sizer = wx.BoxSizer(wx.HORIZONTAL) line2Sizer.Add(wx.StaticText(General,label=' Map grid step: '),0,WACV) flipRes = G2G.ValidatedTxtCtrl(General,Flip,'GridStep',nDig=(10,2),xmin=0.10,xmax=2.) line2Sizer.Add(flipRes,0,WACV) line2Sizer.Add(wx.StaticText(General,label=' k-Factor (0.1-1.2): '),0,WACV) kFactor = G2G.ValidatedTxtCtrl(General,Flip,'k-factor',nDig=(10,3),xmin=0.1,xmax=1.2) line2Sizer.Add(kFactor,0,WACV) line2Sizer.Add(wx.StaticText(General,label=' k-Max (>=10.0): '),0,WACV) kMax = G2G.ValidatedTxtCtrl(General,Flip,'k-Max',nDig=(10,1),xmin=10.) line2Sizer.Add(kMax,0,WACV) flipSizer.Add(line2Sizer,0) line3Sizer = wx.BoxSizer(wx.HORIZONTAL) line3Sizer.Add(wx.StaticText(General,label=' Test HKLs:'),0,WACV) if len(Flip['testHKL']) < 5: Flip['testHKL'] += [[1,1,1],[0,2,0],[1,2,3]] HKL = Flip['testHKL'] for ih,hkl in enumerate(Flip['testHKL']): # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) hkl = wx.TextCtrl(General,value='%3d %3d %3d'%(HKL[ih][0],HKL[ih][1],HKL[ih][2]), style=wx.TE_PROCESS_ENTER,name='hkl%d'%(ih)) hkl.Bind(wx.EVT_TEXT_ENTER,OnTestHKL) hkl.Bind(wx.EVT_KILL_FOCUS,OnTestHKL) line3Sizer.Add(hkl,0,WACV) flipSizer.Add(line3Sizer) return flipSizer def MCSASizer(): def OnRefList(event): MCSAdata['Data source'] = refList.GetValue() def OnCycles(event): MCSAdata['Cycles'] = int(cycles.GetValue()) def OnAlist(event): MCSAdata['Algorithm'] = Alist.GetValue() OnShowTsched() wx.CallAfter(UpdateGeneral,General.GetScrollPos(wx.VERTICAL)) def OnRanStart(event): MCSAdata['ranStart'] = ranStart.GetValue() # def OnAutoRan(event): # MCSAdata['autoRan'] = autoRan.GetValue() def OnAnneal(event): event.Skip() Obj = event.GetEventObject() ind,fmt = Indx[Obj.GetId()] if ind == 2: #No. trials try: val = int(Obj.GetValue()) if 1 <= val: MCSAdata['Annealing'][ind] = val except ValueError: Obj.SetValue(fmt%(MCSAdata['Annealing'][ind])) else: try: val = float(Obj.GetValue()) if .0 <= val: MCSAdata['Annealing'][ind] = val Obj.SetValue(fmt%(MCSAdata['Annealing'][ind])) except ValueError: MCSAdata['Annealing'][ind] = None Obj.SetValue(str(MCSAdata['Annealing'][ind])) def ShowTsched(invalid,value,tc): OnShowTsched() def OnShowTsched(): if MCSAdata['Algorithm'] in ['fast','log']: Y = G2mth.makeTsched(MCSAdata) XY = [np.arange(len(Y)),np.log10(Y)] G2plt.PlotXY(G2frame,[XY,],labelX='T-step',labelY='log(T)',newPlot=True,lines=True,Title='Annealing schedule') # OnShowTsched() refList = [] if len(data['Pawley ref']): refList = ['Pawley reflections',] refList += [item for item in G2gd.GetGPXtreeDataNames(G2frame,['HKLF','PWDR']) if item in data['Histograms'].keys()] mcsaSizer = wx.BoxSizer(wx.VERTICAL) lineSizer = wx.BoxSizer(wx.HORIZONTAL) lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,WACV) refList = wx.ComboBox(General,-1,value=MCSAdata['Data source'],choices=refList, style=wx.CB_READONLY|wx.CB_DROPDOWN) refList.Bind(wx.EVT_COMBOBOX,OnRefList) lineSizer.Add(refList,0,WACV) lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,WACV) dmin = G2G.ValidatedTxtCtrl(General,MCSAdata,'dmin',nDig=(10,3),xmin=1.,xmax=5.) lineSizer.Add(dmin,0,WACV) mcsaSizer.Add(lineSizer) mcsaSizer.Add((5,5),) line2Sizer = wx.BoxSizer(wx.HORIZONTAL) line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,WACV) Cchoice = [str(2**i) for i in range(13)] cycles = wx.ComboBox(General,-1,value=str(MCSAdata.get('Cycles',1)),choices=Cchoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) cycles.Bind(wx.EVT_COMBOBOX,OnCycles) line2Sizer.Add(cycles,0,WACV) line2Sizer.Add((5,0),) ranStart = wx.CheckBox(General,-1,label=' MC/SA Refine at ') ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart) ranStart.SetValue(MCSAdata.get('ranStart',False)) line2Sizer.Add(ranStart,0,WACV) MCSAdata['ranRange'] = MCSAdata.get('ranRange',10.) #patch for old gpx files ranRange = G2G.ValidatedTxtCtrl(General,MCSAdata,'ranRange',nDig=(10,1),xmin=1.,xmax=99.) line2Sizer.Add(ranRange,0,WACV) line2Sizer.Add(wx.StaticText(General,label='% of ranges. '),0,WACV) mcsaSizer.Add(line2Sizer) mcsaSizer.Add((5,5),) line3Sizer = wx.BoxSizer(wx.HORIZONTAL) Achoice = ['log','fast','Basin Hopping'] #these work not 'boltzmann','cauchy', line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,WACV) Alist = wx.ComboBox(General,-1,value=MCSAdata['Algorithm'],choices=Achoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) Alist.Bind(wx.EVT_COMBOBOX,OnAlist) line3Sizer.Add(Alist,0,WACV) if MCSAdata['Algorithm'] in ['fast',]: Names = [' quench: ',' c-factor: '] parms = 'fast parms' for i,name in enumerate(Names): line3Sizer.Add(wx.StaticText(General,label=name),0,WACV) Ajump = G2G.ValidatedTxtCtrl(General,MCSAdata[parms],i,nDig=(10,2),xmin=0.1,xmax=1.,OnLeave=ShowTsched) line3Sizer.Add(Ajump,0,WACV) elif 'log' in MCSAdata['Algorithm']: line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,WACV) slope = G2G.ValidatedTxtCtrl(General,MCSAdata,'log slope',nDig=(10,3),xmin=0.25,xmax=1.0,OnLeave=ShowTsched) line3Sizer.Add(slope,0,WACV) elif 'Basin Hopping' in MCSAdata['Algorithm']: pass #TODO basinhopping controls here? mcsaSizer.Add(line3Sizer) mcsaSizer.Add((5,5),) line3Sizer = wx.BoxSizer(wx.HORIZONTAL) line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,WACV) if 'Basin Hopping' in MCSAdata['Algorithm']: line3Sizer.Add(wx.StaticText(General,label=' Test temp: '),0,WACV) line3Sizer.Add(G2G.ValidatedTxtCtrl(General,MCSAdata['Annealing'],0,nDig=(10,5)),0,WACV) else: line3Sizer.Add(wx.StaticText(General,label=' Start temp: '),0,WACV) line3Sizer.Add(G2G.ValidatedTxtCtrl(General,MCSAdata['Annealing'],0,nDig=(10,5),OnLeave=ShowTsched),0,WACV) line3Sizer.Add(wx.StaticText(General,label=' Final temp: '),0,WACV) line3Sizer.Add(G2G.ValidatedTxtCtrl(General,MCSAdata['Annealing'],1,nDig=(10,5),OnLeave=ShowTsched),0,WACV) line3Sizer.Add(wx.StaticText(General,label=' No. trials: '),0,WACV) line3Sizer.Add(G2G.ValidatedTxtCtrl(General,MCSAdata['Annealing'],2),0,WACV) mcsaSizer.Add(line3Sizer) return mcsaSizer def compareSizer(): def OnOatmOsel(event): generalData['Compare']['Oatoms'] = oatmsel.GetStringSelection() def OnTatmOsel(event): generalData['Compare']['Tatoms'] = tatmsel.GetStringSelection() def OnCompPlots(event): pName = generalData['Name'] Oatoms = generalData['Compare']['Oatoms'] Tatoms = generalData['Compare']['Tatoms'] bName = '%s-%s'%(Oatoms,Tatoms) try: Bonds = generalData['Compare']['Bonds'][bName] except KeyError: print('need to do Compare first for %s polyhedra plots'%bName) return Tilts = generalData['Compare']['Tilts'][bName] Vects = generalData['Compare']['Vects'][bName] dVects = generalData['Compare']['dVects'][bName] if len(Bonds['Obonds']): print(' Octahedra:') Bonds['Obonds'] = np.array(Bonds['Obonds']) Bmean = np.mean(Bonds['Obonds']) Bstd = np.std(Bonds['Obonds']) title = '%s-%s Octahedral bond lengths'%(Oatoms,Tatoms) G2plt.PlotBarGraph(G2frame,Bonds['Obonds'],Xname=r'$Bond, \AA$',Title=title, PlotName='Oct %s Bond for %s'%(bName,pName)) Tilts['Otilts'] = np.array(Tilts['Otilts']) Tmean = np.mean(Tilts['Otilts']) Tstd = np.std(Tilts['Otilts']) G2plt.PlotBarGraph(G2frame,Tilts['Otilts'],Xname='Tilts, deg', Title='Octahedral %s tilts'%Oatoms,PlotName='Oct %s Tilts for %s'%(bName,pName)) dVects['Ovec'] = np.reshape(np.array(dVects['Ovec']),(-1,3)) for ix,aX in enumerate(['X','Y','Z']): G2plt.PlotBarGraph(G2frame,dVects['Ovec'].T[ix],Xname=r'$%s%s, \AA$'%(GkDelta,aX), Title='%s Octahedral distortion'%Oatoms,PlotName='Oct %s %s-Delta for %s'%(bName,aX,pName)) Vects['Ovec'] = np.array(Vects['Ovec']) #3D plot of tilt vectors X = Vects['Ovec'].T[0] Y = Vects['Ovec'].T[1] Z = Vects['Ovec'].T[2] R = Tilts['Otilts'] G2plt.PlotXYZvect(G2frame,X,Y,Z,R,r'X-axis',r'Y-axis',r'Z-axis', Title=r'%s Octahedral tilt vectors'%Oatoms,PlotName='Oct %s tilts for %s'%(bName,pName)) print(' %s-%s bond distance: %.3f(%d)'%(Oatoms,Tatoms,Bmean,Bstd*1000)) print(' %s tilt angle: %.2f(%d)'%(Oatoms,Tmean,Tstd*100)) if len(Bonds['Tbonds']): print('Tetrahedra:') Bonds['Tbonds'] = np.array(Bonds['Tbonds']) Bmean = np.mean(Bonds['Tbonds']) Bstd = np.std(Bonds['Tbonds']) title = '%s-%s Tetrahedral bond lengths'%(Oatoms,Tatoms) G2plt.PlotBarGraph(G2frame,Bonds['Tbonds'],Xname=r'$Bond, \AA$',Title=title, PlotName='Tet %s Bond for %s'%(bName,pName)) Tilts['Ttilts'] = np.array(Tilts['Ttilts']) Tmean = np.mean(Tilts['Ttilts']) Tstd = np.std(Tilts['Ttilts']) G2plt.PlotBarGraph(G2frame,Tilts['Ttilts'],Xname='Tilts, deg', Title='Tetrahedral %s tilts'%Oatoms,PlotName='Tet %s Tilts for %s'%(bName,pName)) dVects['Tvec'] = np.reshape(np.array(dVects['Tvec']),(-1,3)) for ix,aX in enumerate(['X','Y','Z']): G2plt.PlotBarGraph(G2frame,dVects['Tvec'].T[ix],Xname=r'$%s%s, \AA$'%(GkDelta,aX), Title='%s Tetrahedral distortion'%Oatoms,PlotName='Tet %s %s-Delta for %s'%(bName,aX,pName)) Vects['Tvec'] = np.array(Vects['Tvec']) X = Vects['Tvec'].T[0] Y = Vects['Tvec'].T[1] Z = Vects['Tvec'].T[2] R = Tilts['Ttilts'] G2plt.PlotXYZvect(G2frame,X,Y,Z,R,r'X-axis',r'Y-axis',r'Z-axis', Title=r'%s Tetrahedral tilt vectors'%Oatoms,PlotName='Tet %s tilts for %s'%(bName,pName)) print(' %s-%s bond distance: %.3f(%d)'%(Oatoms,Tatoms,Bmean,Bstd*1000)) print(' %s tilt angle: %.2f(%d)'%(Oatoms,Tmean,Tstd*100)) Oatoms = generalData['Compare']['Oatoms'] Tatoms = generalData['Compare']['Tatoms'] bName = '%s-%s'%(Oatoms,Tatoms) atTypes = generalData['AtomTypes'] compSizer = wx.BoxSizer(wx.VERTICAL) compSizer.Add(wx.StaticText(General,label=' Compare polyhedra to ideal octahedra/tetrahedra:'),0) atmselSizer = wx.BoxSizer(wx.HORIZONTAL) atmselSizer.Add(wx.StaticText(General,label=' Select origin atom type: '),0,WACV) oatmsel = wx.ComboBox(General,choices=atTypes,style=wx.CB_READONLY|wx.CB_DROPDOWN) oatmsel.SetStringSelection(generalData['Compare']['Oatoms']) oatmsel.Bind(wx.EVT_COMBOBOX,OnOatmOsel) atmselSizer.Add(oatmsel,0,WACV) atmselSizer.Add(wx.StaticText(General,label=' Select target atom type: '),0,WACV) tatmsel = wx.ComboBox(General,choices=atTypes,style=wx.CB_READONLY|wx.CB_DROPDOWN) tatmsel.SetStringSelection(generalData['Compare']['Tatoms']) tatmsel.Bind(wx.EVT_COMBOBOX,OnTatmOsel) atmselSizer.Add(tatmsel,0,WACV) atmselSizer.Add(wx.StaticText(General,label=' Sampling fraction:: '),0,WACV) atmselSizer.Add(G2G.ValidatedTxtCtrl(General,generalData['Compare'],'Sampling',nDig=(8,3),xmin=0.0,xmax=1.0,),0,WACV) try: if len(generalData['Compare']['Bonds'][bName]['Obonds']) or len(generalData['Compare']['Bonds'][bName]['Tbonds']): plotBtn = wx.Button(General,label='Show plots?') plotBtn.Bind(wx.EVT_BUTTON,OnCompPlots) atmselSizer.Add(plotBtn) except KeyError: pass compSizer.Add(atmselSizer,0) return compSizer # UpdateGeneral execution starts here phaseTypes = ['nuclear','magnetic','macromolecular','faulted'] SetupGeneral() generalData = data['General'] # remove the Wave Data tab when present and not needed if not generalData['Modulated']: pages = [G2frame.phaseDisplay.GetPageText(PageNum) for PageNum in range(G2frame.phaseDisplay.GetPageCount())] if 'Wave Data' in pages: G2frame.phaseDisplay.DeletePage(pages.index('Wave Data')) Map = generalData['Map'] Flip = generalData['Flip'] MCSAdata = generalData['MCSA controls'] PWDR = any(['PWDR' in item for item in data['Histograms'].keys()]) #patches if 'Pawley dmax' not in data['General']: data['General']['Pawley dmax'] = 100.0 if 'SGFixed' not in data['General']['SGData']: data['General']['SGData']['SGFixed'] = False if 'SGGray' not in data['General']['SGData']: data['General']['SGData']['SGGray'] = False if 'Pawley ref' not in data: data['Pawley ref'] = [] #end patches if General.GetSizer(): General.GetSizer().Clear(True) mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) mainSizer.Add(NameSizer(),0,wx.EXPAND) mainSizer.Add((5,5),0) mainSizer.Add(CellSizer(),0) mainSizer.Add((5,5),0) Indx = {} denSizer = None if len(generalData['AtomTypes']): denSizer = DenSizer() mainSizer.Add(denSizer[0]) mainSizer.Add((5,5),0) mainSizer.Add(ElemSizer()) G2G.HorizontalLine(mainSizer,General) if generalData['Type'] == 'magnetic': if not generalData['SGData']['SGFixed']: GenSym,GenFlg,BNSsym = G2spc.GetGenSym(generalData['SGData']) generalData['SGData']['GenSym'] = GenSym generalData['SGData']['GenFlg'] = GenFlg generalData['SGData']['MagSpGrp'] = G2spc.MagSGSym(generalData['SGData']) mainSizer.Add(MagSizer()) G2G.HorizontalLine(mainSizer,General) if generalData['Modulated']: G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_SINGLEMCSA,False) G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_MULTIMCSA,False) G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_4DCHARGEFLIP,True) mainSizer.Add(ModulatedSizer(generalData['Type']+' modulated')) G2G.HorizontalLine(mainSizer,General) else: G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_SINGLEMCSA,True) G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_MULTIMCSA,True) G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_4DCHARGEFLIP,False) mainSizer.Add(PawleySizer()) G2G.HorizontalLine(mainSizer,General) mainSizer.Add(MapSizer()) G2G.HorizontalLine(mainSizer,General) mainSizer.Add(FlipSizer()) if generalData['Type'] in ['nuclear','macromolecular','faulted',]: G2G.HorizontalLine(mainSizer,General) mainSizer.Add(MCSASizer()) G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_COMPARESTRUCTURE,False) if generalData['SGData']['SpGrp'] == 'P 1': G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_COMPARESTRUCTURE,True) G2G.HorizontalLine(mainSizer,General) mainSizer.Add(compareSizer()) if SkipDraw: mainSizer.Clear(True) return G2frame.GetStatusBar().SetStatusText('',1) SetPhaseWindow(General,mainSizer,Scroll=Scroll) def OnTransform(event): Trans = np.eye(3) Uvec = np.zeros(3) Vvec = np.zeros(3) ifMag = False BNSlatt = '' while True: dlg = TransformDialog(G2frame,data,Trans,Uvec,Vvec,ifMag,BNSlatt) try: if dlg.ShowModal() == wx.ID_OK: result = dlg.GetSelection() if result is None: return newPhase,Trans,Uvec,Vvec,ifMag,ifConstr,Common = result newPhase['ranId'] = ran.randint(0,sys.maxsize) SGData = newPhase['General']['SGData'] if ifMag: BNSlatt = SGData['BNSlattsym'][0] SGData['GenSym'],SGData['GenFlg'],BNSsym = G2spc.GetGenSym(SGData) if '_' in BNSlatt: SGData['BNSlattsym'] = [BNSlatt,BNSsym[BNSlatt]] G2spc.ApplyBNSlatt(SGData,SGData['BNSlattsym']) if SGData['SGGray']: if SGData['SGInv']: SGData['SpnFlp'] = np.concatenate((SGData['SpnFlp'],SGData['SpnFlp'])) SGData['SpnFlp'] = np.concatenate((SGData['SpnFlp'],-1*SGData['SpnFlp'])) SGData['MagSpGrp'] = G2spc.MagSGSym(SGData) if not '_' in BNSlatt: SGData['SGSpin'] = G2spc.GetSGSpin(SGData,SGData['MagSpGrp']) else: return finally: dlg.Destroy() if 'setting' in Common: #don't make new phase, Just move atoms! generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] SGData = generalData['SGData'] if SGData['SpGrp'] in G2spc.spg2origins: T = G2spc.spg2origins[SGData['SpGrp']] Atoms = data['Atoms'] for atom in Atoms: for i in [0,1,2]: atom[cx+i] += T[i] SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[3:6],SGData) # update symmetry & mult atom[cs:cs+2] = SytSym,Mul data['Drawing'] = [] #force redraw of page sub = G2frame.GPXtree.GetSelection() G2frame.GPXtree.SelectItem(G2frame.GPXtree.root) wx.CallAfter(G2frame.GPXtree.SelectItem,sub) return else: phaseName = newPhase['General']['Name'] newPhase,atCodes = G2lat.TransformPhase(data,newPhase,Trans,Uvec,Vvec,ifMag) detTrans = np.abs(nl.det(Trans)) generalData = newPhase['General'] SGData = generalData['SGData'] SGData['fromParent'] = [Trans,Uvec,Vvec] #save these Atoms = newPhase['Atoms'] if ifMag: atMxyz = [] for atom in Atoms: if data['General']['Super']: atom += [{'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}] SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[3:6],SGData) CSI = G2spc.GetCSpqinel(SGData['SpnFlp'],dupDir) MagSytSym = G2spc.MagSytSym(SytSym,dupDir,SGData) atMxyz.append([MagSytSym,CSI[0]]) dlg = UseMagAtomDialog(G2frame,SGData['MagSpGrp'],Atoms,atCodes,atMxyz,ifDelete=False) try: opt = dlg.ShowModal() if opt == wx.ID_YES: newPhase['Atoms'],atCodes = dlg.GetSelection() generalData['Lande g'] = len(generalData['AtomTypes'])*[2.,] break else: return finally: dlg.Destroy() else: break NShkl = len(G2spc.MustrainNames(SGData)) NDij = len(G2spc.HStrainNames(SGData)) UseList = newPhase['Histograms'] for hist in UseList: UseList[hist]['Scale'] /= detTrans #scale by 1/volume ratio if 'P' in UseList[hist]['Type']: UseList[hist]['Mustrain'][4:6] = [NShkl*[0.01,],NShkl*[False,]] UseList[hist]['HStrain'] = [NDij*[0.0,],NDij*[False,]] newPhase['General']['Map'] = mapDefault.copy() sub = G2frame.GPXtree.AppendItem(parent= G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases'),text=phaseName) G2frame.GPXtree.SetItemPyData(sub,newPhase) newPhase['Drawing'] = [] if 'RMC' in data: del newPhase['RMC'] if ifConstr: G2cnstG.TransConstraints(G2frame,data,newPhase,Trans,Vvec,atCodes) #data is old phase G2frame.GPXtree.SelectItem(sub) def OnISOSearch(event): '''Search for a higher symmetry structure consistent with the current phase using the ISOCIF web service ''' def _showWebPage(event): 'Show a web page when the user presses the "show" button' import tempfile txt = event.GetEventObject().page tmp = tempfile.NamedTemporaryFile(suffix='.html', delete=False) open(tmp.name,'w').write(txt.replace( '<HEAD>', '<head><base href="https://stokes.byu.edu/iso/">', )) fileList.append(tmp.name) G2G.ShowWebPage('file://'+tmp.name,G2frame) import tempfile import re import requests import G2export_CIF isosite="https://stokes.byu.edu/iso/" upscript='isocifuploadfile.php' isoscript='isocifform.php' isoCite = '''For use of this supergroup search, please cite H. T. Stokes, D. M. Hatch, and B. J. Campbell, ISOCIF, ISOTROPY Software Suite, iso.byu.edu.''' latTol,coordTol,occTol = 0.001, 0.01, 0.1 oacomp,occomp = G2mth.phaseContents(data) ophsnam = data['General']['Name'] fileList = [] # write a CIF as a scratch file obj = G2export_CIF.ExportPhaseCIF(G2frame) obj.InitExport(None) obj.currentExportType='phase' obj.loadTree() tmp = tempfile.NamedTemporaryFile(suffix='.cif',delete=False) try: obj.dirname,obj.filename = os.path.split(tmp.name) obj.phasenam = data['General']['Name'] obj.Writer('',data['General']['Name']) # isocif upload files = {'toProcess': open(tmp.name,'rb')} values = {'submit':'OK','input':'uploadcif'} r0 = requests.post(isosite+upscript, files=files, data=values) # get the filename out from the upload response for f in r0.text.split('INPUT')[1:]: if 'filename' in f: break else: G2G.G2MessageBox(G2frame, f'ISOCIF upload problem\nHTML output={r0.text}', 'Upload Error') return isofile = f.split('VALUE')[1].split('"')[1] finally: os.unlink(tmp.name) # CIF uploaded, now process values1 = {'submit':'OK','input':'uploadcif','filename':isofile} r1 = requests.post(isosite+isoscript, data=values1) # from processed page, pull out form try: form = re.split('</form', [i for i in re.split('<form',r1.text,flags=re.IGNORECASE) if 'Detect higher' in i][0], flags=re.IGNORECASE)[0] except IndexError: tmp1 = tempfile.NamedTemporaryFile(suffix='.html') open(tmp1.name,'w').write(r1.text.replace( '<HEAD>', '<head><base href="https://stokes.byu.edu/iso/">', )) G2G.ShowWebPage('file://'+tmp1.name,G2frame) G2G.G2MessageBox(G2frame, 'ISOCIF CIF processing problem, showing ISOCIF web page', 'ISOCIF Error') return formDict = {} for f in form.split('<'): try: name = re.split('name=',f,flags=re.IGNORECASE)[1].split('"')[1] value = re.split('value=',f,flags=re.IGNORECASE)[1].split('"')[1] formDict[name] = value except IndexError: pass repeat = True while repeat: repeat = False dlg = G2G.MultiDataDialog(G2frame,title='ISOCIF search', prompts=['lattice constants tolerance', 'coordinate tolerance', 'occupancy tolerance'], values=[latTol,coordTol,occTol], limits=3*[[0.,2.]],formats=3*['%.5g'], header=isoCite) res = dlg.ShowModal() latTol,coordTol,occTol = dlg.GetValues() dlg.Destroy() if res != wx.ID_OK: for i in fileList: os.unlink(i) # cleanup tmp web pages return formDict['acclat'], formDict['accpos'], formDict['accocc'] = latTol,coordTol,occTol r2 = requests.post(isosite+isoscript, data=formDict) # now parse out structural info from r2 and insert into current phase structure = r2.text.split('</H1>')[1].split('<p>')[2] atomList = [] change = True for l in structure.split('\n')[1:]: l = l.split('<')[0] if 'No change in actual' in l: change = False elif 'Space Group:' in l: sgnum,sglbl,shname = l.split(':')[1].split() elif 'Lattice parameters:' in l: cell = [float(i.split(',')[0].split('<')[0]) for i in l.split('=')[1:]] elif ':' in l or not l.strip(): pass else: # must be an atom record try: nam = l.split()[0] exec(l.split('),')[1].replace(',',';').strip()) xyz = [float(i) for i in eval(l.split('(')[1].split(')')[0])] atomList.append([nam,xyz]) except: if GSASIIpath.GetConfigValue('debug'): print(f'could not parse "{l}"') if change: dlg = wx.Dialog(G2frame,wx.ID_ANY,'Supergroup found', style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) mainSizer = wx.BoxSizer(wx.VERTICAL) dlg.SetSizer(mainSizer) msg = f'A supergroup structure in space group {sglbl} was found with {len(atomList)} atoms in the asymmetric unit. ' newPhase = makeIsoNewPhase(data,cell,atomList,sglbl,sgnum) nacomp,nccomp = G2mth.phaseContents(newPhase) msg += f"Unit cell {G2mth.fmtPhaseContents(nccomp)}" msg += f", vol={newPhase['General']['Cell'][7]:.2f} A^3" msg += f", density={G2mth.getDensity(newPhase['General'])[0]:.2f} g/cm^3." msg += f"\nAsymmetric unit {G2mth.fmtPhaseContents(nacomp)}." msg += f"\n\nOriginal structure is in space group {data['General']['SGData']['SpGrp']}" msg += f" and has {len(data['Atoms'])} atoms. " msg += f"Unit cell {G2mth.fmtPhaseContents(occomp)}" msg += f", vol={data['General']['Cell'][7]:.2f} A^3" msg += f", density={G2mth.getDensity(data['General'])[0]:.2f} g/cm^3." msg += f"\nAsymmetric unit {G2mth.fmtPhaseContents(oacomp)}." txt = wx.StaticText(dlg,wx.ID_ANY,msg) txt.Wrap(450) mainSizer.Add(txt) mainSizer.Add((-1,10)) showSizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_ANY,label='Show') btn.page = r2.text btn.Bind(wx.EVT_BUTTON,_showWebPage) showSizer.Add(btn) showSizer.Add(wx.StaticText(dlg,wx.ID_ANY, ' Web page with ISOCIF search results')) mainSizer.Add(showSizer) mainSizer.Add((-1,5)) G2G.HorizontalLine(mainSizer,dlg) mainSizer.Add((-1,10)) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY, 'Choose an action:')) mainSizer.Add((-1,10)) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_CANCEL, label="Quit") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_CANCEL)) btnsizer.Add(btn) btnsizer.Add((5,5)) btn = wx.Button(dlg, wx.ID_CLOSE, label="Change tolerances") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_CLOSE)) btnsizer.Add(btn) btnsizer.Add((5,5)) btn = wx.Button(dlg, wx.ID_OK, label="Create GSAS-II project\nwith this supergroup") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_OK)) btn.SetDefault() btnsizer.Add(btn) mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) mainSizer.Fit(dlg) dlg.CenterOnParent() ans = dlg.ShowModal() dlg.Destroy() #breakpoint() if ans == wx.ID_CANCEL: for i in fileList: os.unlink(i) # cleanup tmp web pages return if ans == wx.ID_CLOSE: repeat = True continue break else: dlg = wx.MessageDialog(G2frame,'A higher symmetry structure was not found, repeat search with different tolerances?', 'Repeat?',wx.YES|wx.NO) try: dlg.CenterOnParent() repeat = wx.ID_YES == dlg.ShowModal() if not repeat: for i in fileList: os.unlink(i) # cleanup tmp web pages return finally: dlg.Destroy() # now create a new .gpx file G2frame.OnFileSave(None) # save project on disk to restore to this later orgFilName = G2frame.GSASprojectfile # get restraints for later use (to clear them) resId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints') Restraints = G2frame.GPXtree.GetItemPyData(resId) resId = G2gd.GetGPXtreeItemId(G2frame,resId,ophsnam) cx,ct,cs,cia = data['General']['AtomPtrs'] if ophsnam in Restraints: Restraints[ophsnam]['Bond']['Bonds'] = [] Restraints[ophsnam]['Angle']['Angles'] = [] f = saveIsoNewPhase(G2frame,data,newPhase,orgFilName) wx.MessageBox(f"{isoCite}\n\nCreated project in space group {sglbl} as file {f}", style=wx.ICON_INFORMATION,caption='File created') for i in fileList: os.unlink(i) # cleanup tmp web pages def _GetPhase(): 'After search complete reload the project from the saved .gpx file' G2frame.OnFileOpen(None,filename=orgFilName,askSave=False) wx.CallLater(100,_ShowPhase) def _ShowPhase(): 'After search complete and project is reloaded, reopen tree to the original phase' phId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases') G2frame.GPXtree.Expand(phId) phId = G2gd.GetGPXtreeItemId(G2frame,phId,ophsnam) G2frame.GPXtree.SelectItem(phId) wx.CallLater(100,_GetPhase) def OnSuperSearch(event): '''Search for a supergroup matching the current phase using the Bilboa Pseudosymmetry search (PSEUDO) program ''' def _showWebPage(event): 'Show a web page when the user presses the "show" button' import tempfile num = event.GetEventObject().IndexNum tmp = tempfile.NamedTemporaryFile(suffix='.html', delete=False) open(tmp.name,'w').write(pagelist[num].replace( '<head>', '<head><base href="https://www.cryst.ehu.es/">', )) fileList.append(tmp.name) G2G.ShowWebPage('file://'+tmp.name,G2frame) def _selectSuperGroups(rowdict,csdict,msg,depth=0,key=0): '''Present the user with a set of supergroups and allow selection of ones to be tested. Used initially with higher symmetry cells and again later to recheck structures that have been cast into spacegroups. ''' width = 450 dlg = wx.Dialog(G2frame,wx.ID_ANY,'Supergroup Choices', style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) mainSizer = wx.BoxSizer(wx.VERTICAL) dlg.SetSizer(mainSizer) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY, SUBGROUPS.BilbaoSymSearchCite)) mainSizer.Add((-1,5)) G2G.HorizontalLine(mainSizer,dlg) txt = wx.StaticText(dlg,wx.ID_ANY, 'Searched for subgroups of model '+msg) txt.Wrap(width) mainSizer.Add(txt) if depth > 0: mainSizer.Add((-1,5)) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY, f'This is a {depth}-level supergroup of the original parent model')) showSizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_ANY,label='Show') btn.IndexNum = key btn.Bind(wx.EVT_BUTTON,_showWebPage) showSizer.Add(btn) showSizer.Add(wx.StaticText(dlg,wx.ID_ANY, ' Web page with supergroup search results')) mainSizer.Add(showSizer) mainSizer.Add((-1,5)) G2G.HorizontalLine(mainSizer,dlg) mainSizer.Add((-1,5)) txt = wx.StaticText(dlg,wx.ID_ANY, 'Select supergroups below to test with coordinate transformation.'+ ' Unselected options have been rejected due to lattice parameter'+ ' mismatch/value limits, but can be included.') txt.Wrap(width) mainSizer.Add(txt) mainSizer.Add((-1,10)) sSizer = wx.BoxSizer(wx.HORIZONTAL) sSizer.Add((20,0)) # indent results spanel = wxscroll.ScrolledPanel(dlg, wx.ID_ANY, size=(width, 200)) txtSizer = wx.FlexGridSizer(0, 3, 2, 2) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,'Use')) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,'Space group')) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,'Unit Cell')) for key in rowdict: if key not in csdict: continue txtSizer.Add(G2G.G2CheckBox(spanel,key,csdict,key)) cell = rowdict[key][5].split('\n') txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,rowdict[key][0])) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,cell[0])) sSizer.Add(txtSizer) spanel.SetSizer(sSizer) mainSizer.Add(spanel,1,wx.ALL|wx.EXPAND,1) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_CANCEL, label="Quit") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_CANCEL)) btnsizer.Add(btn) btnsizer.Add((5,5)) btn = wx.Button(dlg, wx.ID_CLOSE, label="Continue") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_OK)) btnsizer.Add(btn) mainSizer.Add((-1,10)) mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) dlg.SetSizer(mainSizer) mainSizer.Fit(dlg) spanel.SetAutoLayout(1) spanel.SetupScrolling() dlg.CenterOnParent() ans = dlg.ShowModal() return ans def _selectHiSymCell(rowdict,csdict): '''Present the user with a set of higher symmetry cells that are consistent with the starting cell. Used with monoclinic and triclinic starting cells only. ''' width = 450 dlg = wx.Dialog(G2frame,wx.ID_ANY,'Supercell Choices', style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) mainSizer = wx.BoxSizer(wx.VERTICAL) dlg.SetSizer(mainSizer) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY, SUBGROUPS.BilbaoSymSearchCite)) mainSizer.Add((-1,5)) G2G.HorizontalLine(mainSizer,dlg) showSizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_ANY,label='Show') btn.IndexNum = 0 btn.Bind(wx.EVT_BUTTON,_showWebPage) showSizer.Add(btn) showSizer.Add(wx.StaticText(dlg,wx.ID_ANY, ' Web page with cell search results')) mainSizer.Add(showSizer) mainSizer.Add((-1,10)) txt = wx.StaticText(dlg,wx.ID_ANY, 'Below select high symmetry cells to test with coordinate transformation.') txt.Wrap(width) mainSizer.Add(txt) G2G.HorizontalLine(mainSizer,dlg) mainSizer.Add((-1,10)) sSizer = wx.BoxSizer(wx.HORIZONTAL) sSizer.Add((20,0)) # indent results spanel = wxscroll.ScrolledPanel(dlg, wx.ID_ANY, size=(width, 200)) txtSizer = wx.FlexGridSizer(0, 5, 2, 20) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,'Use')) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,'Bravais\nLattice')) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,'Unit Cell\n(as calc/symmetrized)')) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,'Strain')) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,'Tolerance')) for i,row in enumerate(rowdict): txtSizer.Add(G2G.G2CheckBox(spanel,str(i),csdict,i)) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,row[1])) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,row[3]+'\n'+row[2])) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,row[5])) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY,row[6])) sSizer.Add(txtSizer) spanel.SetSizer(sSizer) mainSizer.Add(spanel,1,wx.ALL|wx.EXPAND,1) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_CANCEL, label="Quit") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_CANCEL)) btnsizer.Add(btn) btnsizer.Add((5,5)) btn = wx.Button(dlg, wx.ID_CLOSE, label="Continue") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_OK)) btnsizer.Add(btn) mainSizer.Add((-1,10)) mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) dlg.SetSizer(mainSizer) mainSizer.Fit(dlg) spanel.SetAutoLayout(1) spanel.SetupScrolling() dlg.CenterOnParent() ans = dlg.ShowModal() return ans def _GetPhase(): 'After search complete reload the project from the saved .gpx file' G2frame.OnFileOpen(None,filename=orgFilName,askSave=False) wx.CallLater(100,_ShowPhase) def _ShowPhase(): 'After search complete and project is reloaded, reopen tree to the original phase' phId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases') G2frame.GPXtree.Expand(phId) phId = G2gd.GetGPXtreeItemId(G2frame,phId,ophsnam) G2frame.GPXtree.SelectItem(phId) def _testSuperGroups(ophsnam,rowdict,csdict,valsdict,savedcookies,pagelist): 'Use the Bilbao site to test selected supergroups' print(f'*** Testing {sum(csdict.values())} transformed structures') pgbar = wx.ProgressDialog('Supergroup Search', f'Searching for supergroup(s) consistent with phase {ophsnam}', len(csdict)+2,parent=G2frame, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) try: pgbar.CenterOnParent() structDict = SUBGROUPS.BilbaoSymSearch2(valsdict,csdict,rowdict,savedcookies, pagelist=pagelist,dlg=pgbar,ophsnam=ophsnam) GoOn = pgbar.Update(len(csdict)+2,newmsg= f'Searching for supergroup(s) consistent with phase {ophsnam}'+ '\ndone') if not GoOn: return wx.GetApp().Yield() finally: pgbar.Destroy() return structDict def showSuperResults(G2frame,msgs,pagelist,fileList,ReSearch,parentpage,msg=None): '''Show a summary with info from a search of supergroups in :func:`OnSuperSearch` (in :func:`UpdatePhaseData`) ''' import SUBGROUPS def _showWebPage(event): import tempfile f = event.GetEventObject().webFile tmp = tempfile.NamedTemporaryFile(suffix='.html', delete=False) open(tmp.name,'w').write(f.replace( '<head>', '<head><base href="https://www.cryst.ehu.es/">', )) fileList.append(tmp.name) G2G.ShowWebPage('file://'+tmp.name,G2frame) width = 500 dlg = wx.Dialog(G2frame,wx.ID_ANY,'Search results', style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) mainSizer = wx.BoxSizer(wx.VERTICAL) dlg.SetSizer(mainSizer) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,SUBGROUPS.BilbaoSymSearchCite)) if msg: txt = wx.StaticText(dlg,wx.ID_ANY,'Starting from '+msg.replace('\n',' ')) txt.Wrap(width) mainSizer.Add((-1,10)) mainSizer.Add(txt) mainSizer.Add((-1,5)) showSizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_ANY,label='Show') btn.webFile = parentpage btn.Bind(wx.EVT_BUTTON,_showWebPage) showSizer.Add(btn) showSizer.Add(wx.StaticText(dlg,wx.ID_ANY,' Web page with supergroup search results')) mainSizer.Add(showSizer) mainSizer.Add((-1,10)) sSizer = wx.BoxSizer(wx.HORIZONTAL) sSizer.Add((30,0)) # indent results spanel = wxscroll.ScrolledPanel(dlg, wx.ID_ANY, size=(width, 200)) txtSizer = wx.BoxSizer(wx.VERTICAL) smsgs = sorted([i for i in pagelist if i !=0]) if len(smsgs) == 0: # prevent an empty panel txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY, '*** No higher symmetry candidate structures found ***')) txtSizer.Add((-1,10)) for num in smsgs: if num in msgs: if '@' not in num: G2G.HorizontalLine(txtSizer,spanel) txt = wx.StaticText(spanel,wx.ID_ANY,f'Case {num}: ' + msgs[num]) txt.Wrap(width-50) txtSizer.Add(txt) if pagelist[num] is None: txtSizer.Add((-1,10)) continue elif pagelist[num] is not None: txt = wx.StaticText(spanel,wx.ID_ANY, f'Processing for case {num} incomplete') txt.Wrap(width-50) txtSizer.Add(txt) elif pagelist[num] is None: txtSizer.Add((-1,5)) txtSizer.Add(wx.StaticText(spanel,wx.ID_ANY, f'Processing of case {num} failed')) txtSizer.Add((-1,10)) continue txtSizer.Add((-1,5)) showSizer = wx.BoxSizer(wx.HORIZONTAL) if '@' in num: showSizer.Add((20,-1)) btn = wx.Button(spanel, wx.ID_ANY,label='Show') btn.webFile = pagelist[num] btn.Bind(wx.EVT_BUTTON,_showWebPage) showSizer.Add(btn) showSizer.Add(wx.StaticText(spanel,wx.ID_ANY,' Web page with transform info')) txtSizer.Add(showSizer) if num in ReSearch: key = 'use_' + num if key not in ReSearch: ReSearch[key] = True reSizer = wx.BoxSizer(wx.HORIZONTAL) reSizer.Add((20,-1)) redo = G2G.G2CheckBoxFrontLbl(spanel, ' Search again for supergroups of this result?', ReSearch,key) reSizer.Add(redo) txtSizer.Add(reSizer) if num in msgs and '@' not in num: G2G.HorizontalLine(txtSizer,spanel) txtSizer.Add((-1,10)) sSizer.Add(txtSizer) spanel.SetSizer(sSizer) mainSizer.Add(spanel,1,wx.ALL|wx.EXPAND,1) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_CLOSE, label="Continue") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_CANCEL)) btnsizer.Add(btn) mainSizer.Add((-1,10)) mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) dlg.SetSizer(mainSizer) mainSizer.Fit(dlg) spanel.SetAutoLayout(1) spanel.SetupScrolling() dlg.CenterOnParent() ans = dlg.ShowModal() dlg.Destroy() return ans def _showSummary(G2frame,msgs,gpxList): '''Summarize the final results from all steps''' width = 500 dlg = wx.Dialog(G2frame,wx.ID_ANY,'Final Supergroup Search Results', style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) mainSizer = wx.BoxSizer(wx.VERTICAL) dlg.SetSizer(mainSizer) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY, SUBGROUPS.BilbaoSymSearchCite)) mainSizer.Add((-1,10)) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY, f'From the starting model, {len(gpxList)} possible supergroups were located.')) if 0 in msgs: txt = wx.StaticText(dlg,wx.ID_ANY,msgs[0] .replace('/volume:\n',' && volume:').replace('\n',' ')) txt.Wrap(width-50) mainSizer.Add(txt) spanel = wxscroll.ScrolledPanel(dlg, wx.ID_ANY, size=(width, 200)) txtSizer = wx.BoxSizer(wx.VERTICAL) G2G.HorizontalLine(mainSizer,dlg) mainSizer.Add((-1,4)) for m in gpxList: if m == 0: continue msg = 'Found ' + m.replace('\n after','. After').replace('/volume:\n',' && volume:') txt = wx.StaticText(spanel,wx.ID_ANY,msg) txt.Wrap(width-50) txtSizer.Add(txt) txtSizer.Add((-1,4)) G2G.HorizontalLine(txtSizer,spanel) spanel.SetSizer(txtSizer) mainSizer.Add(spanel,1,wx.ALL|wx.EXPAND,1) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_CLOSE, label="Continue") btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_CANCEL)) btnsizer.Add(btn) mainSizer.Add((-1,10)) mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) dlg.SetSizer(mainSizer) mainSizer.Fit(dlg) spanel.SetAutoLayout(1) spanel.SetupScrolling() dlg.CenterOnParent() ans = dlg.ShowModal() dlg.Destroy() return ans def fmtCell(cell): s = '' for i in cell[0:3]: s += f"{i:.3f}, " for i in cell[3:5]: s += f"{i:.2f}, " s += f"{cell[5]:.2f}" return s #### processing for OnSuperSearch starts here #### import SUBGROUPS fileList = [] ReSearch = {} gpxList = [] ophsnam = data['General']['Name'] pgbar = wx.ProgressDialog('Supergroup Search', f'Searching for supergroup(s) consistent with phase {ophsnam}',5, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT, parent=G2frame) pgbar.CenterOnParent() try: G2frame.OnFileSave(None) # save project on disk to restore to this later orgFilName = G2frame.GSASprojectfile # get restraints for later use (to clear them) resId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints') Restraints = G2frame.GPXtree.GetItemPyData(resId) resId = G2gd.GetGPXtreeItemId(G2frame,resId,ophsnam) cx,ct,cs,cia = data['General']['AtomPtrs'] # get starting unit cell contents oacomp,occomp = G2mth.phaseContents(data) msgs = {} msgs[0] = f"initial structure: cell = {fmtCell(data['General']['Cell'][1:7])}" msgs[0] += f", vol={data['General']['Cell'][7]:.2f} A^3" msgs[0] += f", Space group {data['General']['SGData']['SpGrp']}. " msgs[0] += f"Before any transform, unit cell {G2mth.fmtPhaseContents(occomp)}" msgs[0] += f", density={G2mth.getDensity(data['General'])[0]:.2f} g/cm^3" msgs[0] += f". Asymmetric unit {G2mth.fmtPhaseContents(oacomp)} ({len(data['Atoms'])} atoms)." startSet = msgs[0] # fix non-standard space group settings GoOn = pgbar.Update(1,newmsg= f'Searching for supergroup(s) consistent with phase {ophsnam}'+ '\nTesting structure for standard setting') if not GoOn: return wx.GetApp().Yield() # need to convert non-standard space group settings print('*** Checking space group setting') sgnum,sgsym,xmat,xoff = SUBGROUPS.GetStdSGset(data['General']['SGData']) newPhase = copy.deepcopy(data) try: if np.allclose(np.eye(3),xmat) and np.allclose(xoff,np.zeros_like(xoff)): print('*** Structure in standard setting') else: print('*** Transforming structure to standard setting') newPhase['ranId'] = ran.randint(0,sys.maxsize), newPhase['General']['SGData'] = G2spc.SpcGroup(sgsym)[1] newPhase['General']['Cell'][1:] = G2lat.TransformCell( newPhase['General']['Cell'][1:-1],xmat) uvec = np.array(xoff) vvec = np.array([0.,0.,0.]) newPhase['MagXform'] = (xmat,xoff,vvec) newPhase,atCodes = G2lat.TransformPhase( data,newPhase,xmat,uvec,vvec,False) startSet = "transformed starting structure: cell = " startSet += fmtCell(newPhase['General']['Cell'][1:7]) startSet += f". Space group {newPhase['General']['SGData']['SpGrp']}." except: G2G.G2MessageBox(G2frame, 'Standard setting check failed. Try again later.', 'Unexpected error') return # search from a standard space group setting GoOn = pgbar.Update(2,newmsg= f'Searching for supergroup(s) consistent with phase {ophsnam}'+ '\nSearching with phase') if not GoOn: return wx.GetApp().Yield() pagelist = {} valsdict,csdict,rowdict,savedcookies = SUBGROUPS.BilbaoSymSearch1( sgnum,newPhase,pagelist=pagelist) finally: pgbar.Destroy() # process initial PSEUDO results if csdict is None and len(rowdict) == 0: # this was monoclinic or triclinic # look for supergroups of the current cell pgbar = wx.ProgressDialog('Supergroup Search', f'Searching for supergroup(s) consistent with phase {ophsnam}', 1+len(rowdict), style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE, parent=G2frame) try: pgbar.CenterOnParent() wx.GetApp().Yield() valsdict,csdict,rowdict,savedcookies = SUBGROUPS.BilbaoSymSearch1( sgnum,newPhase,pagelist=pagelist,keepCell=True) finally: pgbar.Destroy() ans = _selectSuperGroups(rowdict,csdict,'from '+startSet+ '\n*** Note, no higher symmetry cells found.') if ans == wx.ID_CANCEL: return structDict = _testSuperGroups(ophsnam,rowdict,csdict,valsdict,savedcookies,pagelist) if len(structDict) != 0: ReSearch = SUBGROUPS.find2SearchAgain(pagelist,'') elif csdict is None: # this was monoclinic or triclinic structDict = {} csdict = len(rowdict)*[True] ans = _selectHiSymCell(rowdict,csdict) if ans == wx.ID_CANCEL: return pgbar = wx.ProgressDialog('Supergroup Search', f'Searching for supergroup(s) consistent with phase {ophsnam}', 1+len(rowdict), style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT, parent=G2frame) try: pgbar.CenterOnParent() wx.GetApp().Yield() for i,row in enumerate(rowdict): if not csdict[i]: continue GoOn = pgbar.Update(i,newmsg= f'Searching for supergroup(s) w/cell {str(row[2])}\nLattice {row[1]} -- starting') wx.GetApp().Yield() lbl,latticeList,vals1dict,rowList = SUBGROUPS.BilbaoLowSymSea1( valsdict,row,savedcookies,pagelist=pagelist) msgs[lbl] = (f'Using cell {str(row[2])} with lattice {row[1]}' + f'. Checking {len([i for i in rowList if i[0]])}' + f' supergroups (of {len(rowList)} found)') for row1 in rowList: if not row1[0]: continue GoOn = pgbar.Update(i,newmsg= f'Searching for supergroup(s) w/cell {str(row[2])}' + f'\nLattice {row[1]} && spacegroup {row1[2]}' ) wx.GetApp().Yield() lbl1,structure = SUBGROUPS.BilbaoLowSymSea2( row[0],vals1dict,row1,savedcookies, pagelist=pagelist) if structure is not None: structDict[lbl1] = structure else: msgs[lbl1] = f'Coordinates inconsistent with space group {row1[2]}' finally: pgbar.Destroy() if len(structDict) != 0: ReSearch = SUBGROUPS.find2SearchAgain(pagelist) else: # not monoclinic or triclinic ans = _selectSuperGroups(rowdict,csdict,'from '+startSet) if ans == wx.ID_CANCEL: return structDict = _testSuperGroups(ophsnam,rowdict,csdict,valsdict,savedcookies,pagelist) if len(structDict) != 0: ReSearch = SUBGROUPS.find2SearchAgain(pagelist,'') # searches completed. if len(structDict) != 0: # were new structures generated? # new phases will need different restraints clear them (probably # should clear constraints too) if ophsnam in Restraints: Restraints[ophsnam]['Bond']['Bonds'] = [] Restraints[ophsnam]['Angle']['Angles'] = [] # Now generate .gpx files and show results for num,s in structDict.items(): # loop over supergroup settings f = SUBGROUPS.saveNewPhase(G2frame,data,s,num,msgs,orgFilName) if f: gpxList.append(msgs[num]) ans = showSuperResults(G2frame,msgs,pagelist,fileList,ReSearch,pagelist[0],msgs[0]) for i in fileList: os.unlink(i) # cleanup tmp web pages fileList = [] # repeat search on any identified (& selected) supergroups repeatcount = 0 while ReSearch: repeatcount += 1 NextSearch = {} for key in ReSearch: #print(key,'in ReSearch') pagelist = {} if key.startswith('use_'): continue if not ReSearch.get('use_'+key,False): continue fromMsg = msgs[key] del msgs[key] # need a status bar here if GSASIIpath.GetConfigValue('debug'): print(f"processing {key}") pgbar = wx.ProgressDialog('Supergroup Search', f'Searching for supergroup(s) from case {key}', 1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE, parent=G2frame) try: pgbar.CenterOnParent() wx.GetApp().Yield() valsdict,csdict,rowdict,savedcookies = SUBGROUPS.BilbaoReSymSearch( key,ReSearch[key],pagelist=pagelist) finally: pgbar.Destroy() ans = _selectSuperGroups(rowdict,csdict, f'case {key}, {fromMsg}',repeatcount,key=key) parentpage = pagelist[key] del pagelist[key] structDict = _testSuperGroups(ophsnam,rowdict,csdict,valsdict,savedcookies,pagelist) for num,s in structDict.items(): # loop over supergroup settings f = SUBGROUPS.saveNewPhase(G2frame,data,s,num,msgs,orgFilName) if f: gpxList.append(msgs[num]) fndStruct = SUBGROUPS.find2SearchAgain(pagelist,'') if not fndStruct: continue ans = showSuperResults(G2frame,msgs,pagelist,fileList,fndStruct,parentpage,fromMsg) # rename the msg & structure entry to have a reference to the parent for k in fndStruct: if k.startswith('use_'): continue if not fndStruct.get('use_'+k,False): continue nkey = key + '_' + k NextSearch[nkey] = fndStruct[k] NextSearch['use_'+nkey] = True msgs[nkey] = msgs.pop(k) ReSearch = NextSearch for i in fileList: os.unlink(i) # cleanup tmp web pages # show final message if len(gpxList): _showSummary(G2frame, msgs, gpxList) print(f'Search done, from {msgs[0]}\n{len(gpxList)} supergroups located:\n') for i in gpxList: print(i) else: G2G.G2MessageBox(G2frame, 'No possible supergroups were found to match the starting model.', 'Search complete') print('Search done, no supergroups located') # Restore the original saved project wx.CallLater(100,_GetPhase) def OnTransform2Std(event): '''Uses the Bilbao web site to transform a space group and coordinates to a standard setting ''' import SUBGROUPS generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] sgnum,sgsym,xmat,xoff = SUBGROUPS.GetStdSGset(generalData['SGData']) if np.allclose(np.eye(3),xmat) and np.allclose(xoff,np.zeros_like(xoff)): msg = "Nothing to do. Structure is already set in the standard setting." G2G.G2MessageBox(G2frame,msg,'No change needed') return G2frame.OnFileSave(None) # save orgFilName = G2frame.GSASprojectfile ophsnam = data['General']['Name'] # get starting unit cell contents ocomp = {} for atom in data['Atoms']: if atom[ct] in ocomp: ocomp[atom[ct]] += atom[cs+1] else: ocomp[atom[ct]] = atom[cs+1] ovol = data['General']['Cell'][7] # get restraints & clear geometrical restraints resId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints') Restraints = G2frame.GPXtree.GetItemPyData(resId) resId = G2gd.GetGPXtreeItemId(G2frame,resId,ophsnam) if ophsnam in Restraints: Restraints[ophsnam]['Bond']['Bonds'] = [] Restraints[ophsnam]['Angle']['Angles'] = [] # create a new phase phaseName = f'{ophsnam}-std' newPhase = copy.deepcopy(data) newPhase['ranId'] = ran.randint(0,sys.maxsize), if 'magPhases' in data: del newPhase['magPhases'] generalData = newPhase['General'] generalData['Name'] = phaseName generalData['SGData'] = SGData = G2spc.SpcGroup(sgsym)[1] generalData['Cell'][1:] = G2lat.TransformCell(generalData['Cell'][1:-1],xmat) uvec = np.array(xoff) vvec = np.array([0.,0.,0.]) newPhase['MagXform'] = (xmat,xoff,vvec) newPhase,atCodes = G2lat.TransformPhase(data,newPhase,xmat,uvec,vvec,False) Atoms = newPhase['Atoms'] Atms = [] AtCods = [] atMxyz = [] for ia,atom in enumerate(Atoms): atom[0] += '_%d'%ia atom[2] = '' #clear away refinement flags SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[3:6],SGData) Atms.append(atom) AtCods.append(atCodes[ia]) CSI = G2spc.GetCSxinel(SytSym) atMxyz.append([SytSym,CSI[0]]) NShkl = len(G2spc.MustrainNames(SGData)) NDij = len(G2spc.HStrainNames(SGData)) UseList = newPhase['Histograms'] detTrans = np.abs(nl.det(xmat)) newPhase['Drawing'] = [] for hist in UseList: UseList[hist]['Scale'] /= detTrans #scale by 1/volume ratio # reset Dij & microstrain terms where # of terms changes if len(UseList[hist]['Mustrain'][4]) != NShkl: UseList[hist]['Mustrain'][4:6] = [NShkl*[0.01,],NShkl*[False,]] if len(UseList[hist]['HStrain'][0]) != NDij: UseList[hist]['HStrain'] = [NDij*[0.0,],NDij*[False,]] newPhase['General']['Map'] = mapDefault.copy() # phase name rename newName = generalData['Name'] = phaseName phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree() #phaseNameList = usedHistograms.keys() # phase names in use generalData['Name'] = newName G2frame.GPXtree.SetItemText(Item,generalData['Name']) # change phase name key in Reflection Lists for each histogram for hist in data['Histograms']: ht = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist) rt = G2gd.GetGPXtreeItemId(G2frame,ht,'Reflection Lists') if not rt: continue RfList = G2frame.GPXtree.GetItemPyData(rt) RfList[newName] = [] if ophsnam in RfList: del RfList[ophsnam] # copy restraints w/o the geometry-based ones if ophsnam in Restraints: Restraints[newName] = Restraints[ophsnam] del Restraints[ophsnam] if resId: G2frame.GPXtree.SetItemText(resId,newName) data.update(newPhase) # save new file G2frame.GSASprojectfile = os.path.splitext(orgFilName )[0]+'_std.gpx' #G2frame.OnFileSaveas(event) G2IO.ProjFileSave(G2frame) # get transformed contents ncomp = {} for atom in data['Atoms']: if atom[ct] in ncomp: ncomp[atom[ct]] += atom[cs+1] else: ncomp[atom[ct]] = atom[cs+1] nvol = data['General']['Cell'][7] o = ', '.join([f'{i}:{j}' for i,j in ocomp.items()]) n = ', '.join([f'{i}:{j}' for i,j in ncomp.items()]) msg = f"""New project file, {G2frame.GSASprojectfile} created. Before & after transform, unit cell contents/volume: Before {o}, {ovol:.2f} A^3 After {n}, {nvol:.2f} A^3 """ G2G.G2MessageBox(G2frame,msg,'Transform complete') # Restore the original saved project G2frame.OnFileOpen(None,filename=orgFilName,askSave=False) # reopen tree to the original phase def _ShowPhase(): phId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases') G2frame.GPXtree.Expand(phId) phId = G2gd.GetGPXtreeItemId(G2frame,phId,ophsnam) G2frame.GPXtree.SelectItem(phId) wx.CallLater(100,_ShowPhase) def OnCompareCells(event): G2G.Load2Cells(G2frame,data) def OnCompare(event): generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] atNames = [atm[ct-1] for atm in data['Atoms']] if not generalData['Compare']['Oatoms'] or not generalData['Compare']['Tatoms']: G2frame.ErrorDialog('Compare atom selection error','Select atoms for polygon comparison first') return bName = '%s-%s'%(generalData['Compare']['Oatoms'],generalData['Compare']['Tatoms']) DisAglCtls = generalData.get('DisAglCtls',{}) dlg = G2G.DisAglDialog(G2frame,DisAglCtls,generalData) if dlg.ShowModal() == wx.ID_OK: generalData['DisAglCtls'] = dlg.GetData() dlg.Destroy() Natm = len(data['Atoms']) iAtm= 0 pgbar = wx.ProgressDialog('Process polyhedron compare for %d atoms'%Natm,'Atoms done=',Natm+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) Tilts = generalData['Compare']['Tilts'] Tilts.update({bName:{'Otilts':[],'Ttilts':[]}}) Bonds = generalData['Compare']['Bonds'] Bonds.update({bName:{'Obonds':[],'Tbonds':[]}}) Vects = generalData['Compare']['Vects'] Vects.update({bName:{'Ovec':[],'Tvec':[]}}) dVects = generalData['Compare']['dVects'] dVects.update({bName:{'Ovec':[],'Tvec':[]}}) Oatoms = generalData['Compare']['Oatoms'] nOct = 0 nTet = 0 nElse = 0 for iatm,atom in enumerate(data['Atoms']): if atom[ct] == Oatoms: if ran.random() > generalData['Compare']['Sampling']: iAtm += 1 continue results = G2mth.FindAllNeighbors(data,atom[ct-1],atNames,Orig=iatm)[0] #slow step if len(results) == 4: bond,std,meanDisp,stdDisp,A,V,dVec = G2mth.FindTetrahedron(results) Bonds[bName]['Tbonds'].append(bond) Tilts[bName]['Ttilts'].append(A) Vects[bName]['Tvec'].append(V) dVects[bName]['Tvec'].append(dVec) nTet += 1 elif len(results) == 6: bond,std,meanDisp,stdDisp,A,V,dVec = G2mth.FindOctahedron(results) Bonds[bName]['Obonds'].append(bond) Tilts[bName]['Otilts'].append(A) Vects[bName]['Ovec'].append(V) dVects[bName]['Ovec'].append(dVec) nOct += 1 else: print('%s is something else with %d vertices'%(atom[ct-1],len(results))) nElse += 1 GoOn = pgbar.Update(iAtm,newmsg='Atoms done=%d'%(iAtm)) iAtm += 1 if not GoOn[0]: print(' Compare aborted') break print(' Compare finished; nOct = %d, nTet = %d, nOther = %d'%(nOct,nTet,nElse)) pgbar.Destroy() wx.CallAfter(UpdateGeneral,General.GetScrollPos(wx.VERTICAL)) def OnUseBilbao(event): '''Select and apply a transformation matrix from the Bilbao web site to create a new phase ''' PatternName = data['magPhases'] PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,PatternName) UnitCellsId = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Unit Cells List') UCdata = list(G2frame.GPXtree.GetItemPyData(UnitCellsId)) magData = UCdata[5] if len(UCdata[0]) < 17: #old version of k-SUBGROUPSMAG baseList = range(1,len(magData)+1) else: baseList = UCdata[0][16] magKeep = [] magIds = [] magchoices = [] ifMag = False itemList = [phase.get('gid',ip+1) for ip,phase in enumerate(magData)] phaseDict = dict(zip(itemList,magData)) for im,mid in enumerate(baseList): magdata = phaseDict[mid] if magdata['Keep']: if 'magAtms' in magdata: ifMag = True magdata['No.'] = im+1 trans = G2spc.Trans2Text(magdata['Trans']) vec = G2spc.Latt2text([magdata['Uvec'],]) magKeep.append(magdata) magIds.append(mid) magchoices.append('(%d) %s; (%s) + (%s)'%(im+1,magdata['Name'],trans,vec)) if not len(magKeep): G2frame.ErrorDialog('Subgroup/magnetic phase selection error','No magnetic phases found; be sure to "Keep" some') return if ifMag: dlg = wx.SingleChoiceDialog(G2frame,'Select magnetic space group','Make new magnetic phase',magchoices) else: dlg = wx.SingleChoiceDialog(G2frame,'Select subgroup','Make new subgroup phase',magchoices) opt = dlg.ShowModal() if opt == wx.ID_OK: sel = dlg.GetSelection() magchoice = magKeep[sel] magId = magIds[sel] if ifMag: phaseName = '%s-mag_%d'%(data['General']['Name'],magchoice['No.']) else: phaseName = '%s-sub_%d'%(data['General']['Name'],magchoice['No.']) newPhase = copy.deepcopy(data) newPhase['ranId'] = ran.randint(0,sys.maxsize), del newPhase['magPhases'] generalData = newPhase['General'] generalData['Name'] = phaseName generalData['SGData'] = copy.deepcopy(magchoice['SGData']) generalData['Cell'][1:] = magchoice['Cell'][:] generalData['MagDmin'] = 1.0 SGData = generalData['SGData'] vvec = np.array([0.,0.,0.]) newPhase['MagXform'] = (magchoice['Trans'],magchoice['Uvec'],vvec) newPhase,atCodes = G2lat.TransformPhase(data,newPhase,magchoice['Trans'],magchoice['Uvec'],vvec,ifMag) Atoms = newPhase['Atoms'] Atms = [] AtCods = [] atMxyz = [] for ia,atom in enumerate(Atoms): if ifMag and atom[1] == 'O': #skip "magnetic" O atoms continue if ifMag and not len(G2elem.GetMFtable([atom[1],],[2.0,])): continue atom[0] += '_%d'%ia atom[2] = '' #clear away refinement flags SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[3:6],SGData) Atms.append(atom) AtCods.append(atCodes[ia]) if ifMag: MagSytSym = G2spc.MagSytSym(SytSym,dupDir,SGData) CSI = G2spc.GetCSpqinel(SGData['SpnFlp'],dupDir) atMxyz.append([MagSytSym,CSI[0]]) else: CSI = G2spc.GetCSxinel(SytSym) atMxyz.append([SytSym,CSI[0]]) if ifMag: dlg = UseMagAtomDialog(G2frame,magchoices[sel],Atms,AtCods,atMxyz,ifMag=ifMag,ifDelete=True) try: opt = dlg.ShowModal() if opt == wx.ID_YES: G2frame.OnFileSave(event) #saves current state of Unit Cell List newPhase['Atoms'],atCodes = dlg.GetSelection() generalData['Lande g'] = len(generalData['AtomTypes'])*[2.,] elif opt == wx.ID_DELETE: magData[magId]['Keep'] = False return else: #wx.ID_NO return finally: dlg.Destroy() else: return NShkl = len(G2spc.MustrainNames(SGData)) NDij = len(G2spc.HStrainNames(SGData)) UseList = newPhase['Histograms'] detTrans = np.abs(nl.det(magchoice['Trans'])) for hist in UseList: UseList[hist]['Scale'] /= detTrans #scale by 1/volume ratio UseList[hist]['Mustrain'][4:6] = [NShkl*[0.01,],NShkl*[False,]] UseList[hist]['HStrain'] = [NDij*[0.0,],NDij*[False,]] newPhase['General']['Map'] = mapDefault.copy() sub = G2frame.GPXtree.AppendItem(parent= G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases'),text=phaseName) G2frame.GPXtree.SetItemPyData(sub,newPhase) newPhase['Drawing'] = [] if ifMag: G2cnstG.TransConstraints(G2frame,data,newPhase,magchoice['Trans'],vvec,atCodes) #data is old phase G2frame.newGPXfile = phaseName.replace('.','_')+'.gpx' #'.' in file names is a bad idea UCdata[5] = [] #clear away other mag choices from chem phase in new project G2frame.GPXtree.SetItemPyData(UnitCellsId,UCdata) G2frame.OnFileSaveas(event) G2frame.GPXtree.SelectItem(sub) def OnApplySubgroups(event): '''Select and apply a transformation matrix from the Bilbao web site to replace current phase with a subgroup ''' PatternName = data['magPhases'] PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,PatternName) UnitCellsId = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Unit Cells List') UCdata = list(G2frame.GPXtree.GetItemPyData(UnitCellsId)) if len(UCdata[0]) < 17: #old version of k-SUBGROUPSMAG baseList = range(1,len(UCdata[5])+1) else: baseList = UCdata[0][16] subKeep = [] subIds = [] subchoices = [] ifMag = False itemList = [phase.get('gid',ip+1) for ip,phase in enumerate(UCdata[5])] phaseDict = dict(zip(itemList,UCdata[5])) for im,mid in enumerate(baseList): if phaseDict[mid]['Keep']: phaseDict[mid]['No.'] = im+1 trans = G2spc.Trans2Text(phaseDict[mid]['Trans']) vec = G2spc.Latt2text([phaseDict[mid]['Uvec'],]) subKeep.append(phaseDict[mid]) subIds.append(mid) subchoices.append('(%d) %s; (%s) + (%s)'%(im+1,phaseDict[mid]['Name'],trans,vec)) if not len(subKeep): G2frame.ErrorDialog('Subgroup phase selection error','No subgroups available; be sure to "Keep" some') return dlg = G2G.G2MultiChoiceDialog(G2frame, 'Make new project using subgroups','Select subgroup(s)', subchoices) opt = dlg.ShowModal() sels = [] if opt == wx.ID_OK: sels = dlg.GetSelections() if not sels: return # G2frame.OnFileSave(None) # save orgFilName = G2frame.GSASprojectfile phsnam = data['General']['Name'] # get restraints & clear geometrical restraints resId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints') Restraints = G2frame.GPXtree.GetItemPyData(resId) resId = G2gd.GetGPXtreeItemId(G2frame,resId,phsnam) Restraints[phsnam]['Bond']['Bonds'] = [] Restraints[phsnam]['Angle']['Angles'] = [] savedRestraints = Restraints[phsnam] orgData = copy.deepcopy(data) del Restraints[phsnam] for sel in sels: data.update(copy.deepcopy(orgData)) # get rid of prev phase magchoice = subKeep[sel] spg = magchoice['SGData']['SpGrp'].replace(' ','') subId = subIds[sel] # generate the new phase newPhase = copy.deepcopy(data) generalData = newPhase['General'] generalData['SGData'] = copy.deepcopy(magchoice['SGData']) generalData['Cell'][1:] = magchoice['Cell'][:] generalData['MagDmin'] = 1.0 SGData = generalData['SGData'] vvec = np.array([0.,0.,0.]) newPhase['MagXform'] = (magchoice['Trans'],magchoice['Uvec'],vvec) newPhase,atCodes = G2lat.TransformPhase(data,newPhase,magchoice['Trans'],magchoice['Uvec'],vvec,ifMag) Atoms = newPhase['Atoms'] Atms = [] AtCods = [] atMxyz = [] for ia,atom in enumerate(Atoms): atom[0] += '_%d'%ia atom[2] = '' #clear away refinement flags SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[3:6],SGData) Atms.append(atom) AtCods.append(atCodes[ia]) CSI = G2spc.GetCSxinel(SytSym) atMxyz.append([SytSym,CSI[0]]) NShkl = len(G2spc.MustrainNames(SGData)) NDij = len(G2spc.HStrainNames(SGData)) UseList = newPhase['Histograms'] detTrans = np.abs(nl.det(magchoice['Trans'])) newPhase['Drawing'] = [] for hist in UseList: UseList[hist]['Scale'] /= detTrans #scale by 1/volume ratio # reset Dij & microstrain terms where # of terms changes if len(UseList[hist]['Mustrain'][4]) != NShkl: UseList[hist]['Mustrain'][4:6] = [NShkl*[0.01,],NShkl*[False,]] if len(UseList[hist]['HStrain'][0]) != NDij: UseList[hist]['HStrain'] = [NDij*[0.0,],NDij*[False,]] newPhase['General']['Map'] = mapDefault.copy() # phase name rename newName = generalData['Name'] = f"{phsnam}_{magchoice['No.']}_{spg}" phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree() #phaseNameList = usedHistograms.keys() # phase names in use generalData['Name'] = newName G2frame.GPXtree.SetItemText(Item,generalData['Name']) # change phase name key in Reflection Lists for each histogram for hist in data['Histograms']: ht = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist) rt = G2gd.GetGPXtreeItemId(G2frame,ht,'Reflection Lists') if not rt: continue RfList = G2frame.GPXtree.GetItemPyData(rt) RfList[newName] = [] if phsnam in RfList: del RfList[phsnam] # copy cleared restraints Restraints[generalData['Name']] = savedRestraints if resId: G2frame.GPXtree.SetItemText(resId,newName) data.update(newPhase) #clear away prev subgroup choices if 'magPhases' in data: del data['magPhases'] UCdata[5] = [] G2frame.GPXtree.SetItemPyData(UnitCellsId,UCdata) # save new file G2frame.GSASprojectfile = os.path.splitext(orgFilName )[0]+'_'+spg.replace('/','_')+'.gpx' #G2frame.OnFileSaveas(event) G2IO.ProjFileSave(G2frame) # restore the original saved project G2frame.OnFileOpen(None,filename=orgFilName,askSave=False) # reopen tree to the original phase def _ShowPhase(): phId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases') G2frame.GPXtree.Expand(phId) phId = G2gd.GetGPXtreeItemId(G2frame,phId,phsnam) G2frame.GPXtree.SelectItem(phId) wx.CallLater(100,_ShowPhase) ##### Atom routines ################################################################################ def FillAtomsGrid(Atoms): '''Display the contents of the Atoms tab ''' def RefreshAtomGrid(event): r,c = event.GetRow(),event.GetCol() if r < 0 and c < 0: for row in range(Atoms.GetNumberRows()): Atoms.SelectRow(row,True) return if r < 0: #double click on col label! Change all atoms! noSkip = True parms = '' if Atoms.GetColLabelValue(c) == 'refine': Type = generalData['Type'] if Type in ['nuclear','macromolecular','faulted',]: choice = ['F - site fraction','X - coordinates','U - thermal parameters'] elif Type in ['magnetic',]: choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment'] dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() parms = '' for x in sel: parms += choice[x][0] dlg.Destroy() elif Atoms.GetColLabelValue(c) == 'I/A': choice = ['Isotropic','Anisotropic'] dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = choice[sel][0] dlg.Destroy() elif Atoms.GetColLabelValue(c) == 'Type': choice = generalData['AtomTypes'] dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = choice[sel] noSkip = False Atoms.ClearSelection() for row in range(Atoms.GetNumberRows()): if parms == atomData[row][c]: Atoms.SelectRow(row,True) dlg.Destroy() SetupGeneral() elif Atoms.GetColLabelValue(c) == 'Name': choice = [] for r in range(Atoms.GetNumberRows()): if str(atomData[r][c]) not in choice: choice.append(str(atomData[r][c])) choice.sort() dlg = wx.SingleChoiceDialog(G2frame,'Select atom(s) by name', 'Name Selection',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = choice[sel] noSkip = False Atoms.ClearSelection() for row in range(Atoms.GetNumberRows()): if parms == atomData[row][c]: Atoms.SelectRow(row,True) dlg.Destroy() else: dlg.Destroy() return elif Atoms.GetColLabelValue(c) == 'residue': choice = [] for r in range(Atoms.GetNumberRows()): if str(atomData[r][c]) not in choice: choice.append(str(atomData[r][c])) choice.sort() dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = choice[sel] noSkip = False Atoms.ClearSelection() for row in range(Atoms.GetNumberRows()): if parms == atomData[row][c]: Atoms.SelectRow(row,True) dlg.Destroy() elif Atoms.GetColLabelValue(c) == 'res no': choice = [] for r in range(Atoms.GetNumberRows()): if str(atomData[r][c]) not in choice: choice.append(str(atomData[r][c])) dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = choice[sel] noSkip = False Atoms.ClearSelection() for row in range(Atoms.GetNumberRows()): if int(parms) == atomData[row][c]: Atoms.SelectRow(row,True) dlg.Destroy() elif Atoms.GetColLabelValue(c) == 'chain': choice = [] for r in range(Atoms.GetNumberRows()): if atomData[r][c] not in choice: choice.append(atomData[r][c]) dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = choice[sel] noSkip = False Atoms.ClearSelection() for row in range(Atoms.GetNumberRows()): if parms == atomData[row][c]: Atoms.SelectRow(row,True) dlg.Destroy() elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value return #& then change all 'I' atoms; now do nothing else: return if noSkip: ui = colLabels.index('U11') us = colLabels.index('Uiso') ss = colLabels.index('site sym') for r in range(Atoms.GetNumberRows()): ID = atomData[r][ui+6] if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A': if parms == 'A': #'I' --> 'A' Uiso = float(Atoms.GetCellValue(r,us)) sytsym = atomData[r][ss] CSI = G2spc.GetCSuinel(sytsym) atomData[r][ui:ui+6] = Uiso*np.array(CSI[3]) atomData[r][us] = 0.0 Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True) for i in range(6): ci = ui+i Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True) if CSI[2][i]: Atoms.SetCellStyle(r,ci,WHITE,False) else: #'A' --> 'I' Uij = atomData[r][ui:ui+6] Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0 atomData[r][us] = Uiso Atoms.SetCellStyle(r,us,WHITE,False) for i in range(6): ci = ui+i atomData[r][ci] = 0.0 Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True) if not Atoms.IsReadOnly(r,c): if Atoms.GetColLabelValue(c) == 'refine': rbExcl = rbAtmDict.get(atomData[r][ui+6],'') if rbExcl: for excl in rbExcl: atomData[r][c] = parms.replace(excl,'') else: atomData[r][c] = parms else: atomData[r][c] = parms if 'Atoms' in data['Drawing']: G2mth.DrawAtomsReplaceByID(data,ui+6,atomData[r],ID) wx.CallAfter(Paint) def ChangeAtomCell(event): def chkUij(Uij,CSI): #needs to do something!!! return Uij SGData = generalData['SGData'] r,c = event.GetRow(),event.GetCol() replot = True if r >= 0 and c >= 0: ci = colLabels.index('I/A') ID = atomData[r][ci+8] if Atoms.GetColLabelValue(c) in ['x','y','z']: ci = colLabels.index('x') XYZ = atomData[r][ci:ci+3] if None in XYZ: XYZ = [0,0,0] SScol = colLabels.index('site sym') Mulcol = colLabels.index('mult') Sytsym,Mult = G2spc.SytSym(XYZ,SGData)[:2] atomData[r][SScol] = Sytsym atomData[r][Mulcol] = Mult if atomData[r][colLabels.index('I/A')] == 'A': ui = colLabels.index('U11') CSI = G2spc.GetCSuinel(Sytsym) atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym) for i in range(6): ci = i+ui Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True) if CSI[2][i]: Atoms.SetCellStyle(r,ci,WHITE,False) SetupGeneral() elif Atoms.GetColLabelValue(c) == 'Type': AtomTypeSelect(event) elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish! if atomData[r][c] == 'I': Uij = atomData[r][c+2:c+8] atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0 Atoms.SetCellStyle(r,c+1,WHITE,False) Atoms.SetCellTextColour(r,c+1,BLACK) for i in range(6): ci = i+colLabels.index('U11') Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True) Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY) atomData[r][ci] = 0.0 else: value = atomData[r][c+1] CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')]) Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True) Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY) for i in range(6): ci = i+colLabels.index('U11') atomData[r][ci] = value*CSI[3][i] Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True) Atoms.SetCellTextColour(r,ci,BLACK) if CSI[2][i]: Atoms.SetCellStyle(r,ci,WHITE,False) atomData[r][c+1] = 0.0 elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']: value = atomData[r][c] CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')]) iUij = CSI[0][c-colLabels.index('U11')] for i in range(6): if iUij == CSI[0][i]: atomData[r][i+colLabels.index('U11')] = value*CSI[1][i] elif Atoms.GetColLabelValue(c) == 'refine': ci = colLabels.index('I/A') atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][ci+8],''),'') replot = False elif Atoms.GetColLabelValue(c) in ['Mx','My','Mz']: value = atomData[r][c] cx = colLabels.index('x') SpnFlp = generalData['SGData']['SpnFlp'] SytSym,Mul,Nop,dupDir = G2spc.SytSym(atomData[r][cx:cx+3],SGData) CSI = G2spc.GetCSpqinel(SpnFlp,dupDir) iM = CSI[0][c-colLabels.index('Mx')] for i in range(3): if iM == CSI[0][i]: atomData[r][i+colLabels.index('Mx')] = value*CSI[1][i] if 'Atoms' in data['Drawing'] and replot: ci = colLabels.index('I/A') G2mth.DrawAtomsReplaceByID(data,ci+8,atomData[r],ID) G2plt.PlotStructure(G2frame,data) if SGData['SpGrp'] != 'P 1': #no need to update P 1 structures! wx.CallAfter(Paint) def AtomTypeSelect(event): r,c = event.GetRow(),event.GetCol() if Atoms.GetColLabelValue(c) == 'Type': PE = G2elemGUI.PickElement(G2frame,ifMag=ifMag) if PE.ShowModal() == wx.ID_OK: if PE.Elem != 'None': atomData[r][c] = PE.Elem.strip() name = atomData[r][c] if len(name) in [2,4]: atomData[r][c-1] = name[:2]+'%d'%(r+1) else: atomData[r][c-1] = name[:1]+'%d'%(r+1) PE.Destroy() SetupGeneral() wx.CallAfter(Paint) value = Atoms.GetCellValue(r,c) atomData[r][c] = value ci = colLabels.index('I/A') ID = atomData[r][ci+8] if 'Atoms' in data['Drawing']: G2mth.DrawAtomsReplaceByID(data,ci+8,atomData[r],ID) G2plt.PlotStructure(G2frame,data) SetupGeneral() else: event.Skip() def RowSelect(event): r,c = event.GetRow(),event.GetCol() if not (event.AltDown() or (event.ShiftDown() and event.ControlDown())): Atoms.frm = -1 if r < 0 and c < 0: if Atoms.IsSelection(): Atoms.ClearSelection() elif c < 0: #only row clicks ci = colLabels.index('I/A') if event.ControlDown() and not event.ShiftDown(): if r in Atoms.GetSelectedRows(): Atoms.DeselectRow(r) else: Atoms.SelectRow(r,True) elif event.ShiftDown() and not event.ControlDown(): indxs = Atoms.GetSelectedRows() Atoms.ClearSelection() ibeg = 0 if indxs: ibeg = indxs[-1] for row in range(ibeg,r+1): Atoms.SelectRow(row,True) elif event.AltDown() or (event.ShiftDown() and event.ControlDown()): if atomData[r][ci+8] in rbAtmDict: G2frame.ErrorDialog('Atom move error','Atoms in rigid bodies can not be moved') Atoms.frm = -1 Atoms.ClearSelection() else: if Atoms.frm < 0: #pick atom to be moved Atoms.frm = r Atoms.SelectRow(r,True) n = colLabels.index('Name') G2frame.GetStatusBar().SetStatusText('Atom '+atomData[r][n]+' is to be moved',1) else: #move it item = atomData.pop(Atoms.frm) atomData.insert(r,item) Atoms.frm = -1 G2frame.GetStatusBar().SetStatusText('',1) data['Drawing']['Atoms'] = [] #clear & rebuild Draw atoms table UpdateDrawAtoms() wx.CallAfter(Paint) else: G2frame.GetStatusBar().SetStatusText('Use right mouse click to brng up Atom editing options',1) Atoms.ClearSelection() Atoms.SelectRow(r,True) G2plt.PlotStructure(G2frame,data) def ChangeSelection(event): r,c = event.GetRow(),event.GetCol() if r < 0 and c < 0: Atoms.ClearSelection() if c < 0: if r in Atoms.GetSelectedRows(): Atoms.DeselectRow(r) else: Atoms.SelectRow(r,True) if r < 0: if c in Atoms.GetSelectedCols(): Atoms.DeselectCol(c) else: Atoms.SelectCol(c,True) def Paint(Scroll=0): 'Place atom info into the table' table = [] rowLabels = [] for i,atom in enumerate(atomData): table.append(atom) rowLabels.append(str(i)) atomTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) try: Atoms.SetTable(atomTable, True, useFracEdit=False) # Paint may be called after the Grid has been deleted except: return Atoms.frm = -1 colType = colLabels.index('Type') colR = colLabels.index('refine') colSS = colLabels.index('site sym') colF = colLabels.index('frac') colX = colLabels.index('x') colIA = colLabels.index('I/A') colU11 = colLabels.index('U11') colUiso = colLabels.index('Uiso') colM = 0 if 'Mx' in colLabels: colM = colLabels.index('Mx') # loop over all cols in table, set cell editor for numerical items for c,t in enumerate(Types): if not t.startswith(wg.GRID_VALUE_FLOAT): continue attr = wx.grid.GridCellAttr() attr.IncRef() #fix from Jim Hester attr.SetEditor(G2G.GridFractionEditor(Atoms)) if c in range(colU11-1,colU11+6): Atoms.SetColSize(c,50) attr.SetBackgroundColour(VERY_LIGHT_GREY) # make invisible attr.SetTextColour(VERY_LIGHT_GREY) attr.SetReadOnly(True) Atoms.SetColAttr(c, attr) for row in range(Atoms.GetNumberRows()): #this is slow for large numbers of atoms atId = atomData[row][colIA+8] rbExcl = rbAtmDict.get(atId,'') if Atoms.GetCellValue(row,colIA) == 'A': try: #patch for sytsym name changes CSI = G2spc.GetCSuinel(atomData[row][colSS]) except KeyError: Sytsym,Mult = G2spc.SytSym(atomData[row][colX:colX+3],SGData)[:2] atomData[row][colSS] = Sytsym atomData[row][colSS+1] = Mult CSI = G2spc.GetCSuinel(Sytsym) Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True) Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY) for i in range(6): cj = colU11+i Atoms.SetCellTextColour(row,cj,BLACK) if G2lat.Uij2Ueqv(atomData[row][colU11:colU11+6],GS,Amat)[1]: Atoms.SetCellTextColour(row,cj,RED) Atoms.SetCellStyle(row,cj,VERY_LIGHT_GREY,True) if CSI[2][i] and 'U' not in rbExcl: Atoms.SetCellStyle(row,cj,WHITE,False) else: Atoms.SetCellStyle(row,colUiso,WHITE,False) Atoms.SetCellTextColour(row,colUiso,BLACK) if atomData[row][colUiso] < 0.: Atoms.SetCellTextColour(row,colUiso,RED) if 'U' in rbExcl: Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True) if colM: SytSym,Mul,Nop,dupDir = G2spc.SytSym(atomData[row][colX:colX+3],SGData) MagSytSym = G2spc.MagSytSym(SytSym,dupDir,SGData) Atoms.SetCellValue(row,colSS,MagSytSym) CSI = [] if not SGData['SGGray']: CSI = G2spc.GetCSpqinel(SpnFlp,dupDir) saveCSI = 0 for i in range(3): ci = i+colM Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True) Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY) if CSI and CSI[1][i]: # and AtInfo and AtInfo[atomData[row][colType]]: if saveCSI != CSI[0][i]: Atoms.SetCellStyle(row,ci,WHITE,False) saveCSI = CSI[0][i] Atoms.SetCellTextColour(row,ci,BLACK) if 'F' in rbExcl: Atoms.SetCellStyle(row,colF,VERY_LIGHT_GREY,True) if 'X' in rbExcl: for c in range(0,colX+3): if c != colR: Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True) Atoms.SetReadOnly(row,colType,True) Atoms.SetReadOnly(row,colSS,True) #site sym Atoms.SetReadOnly(row,colSS+1,True) #Mult oldSizer = AtomList.GetSizer() if oldSizer: # 2nd+ use, clear out old entries for i in oldSizer.GetChildren(): # look for grids in sizer if type(i.GetWindow()) is G2G.GSGrid: oldSizer.Detach(i.GetWindow()) # don't delete them oldSizer.Clear(True) Atoms.AutoSizeColumns(False) mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(AtomList,label='Atom parameters list for %s:'%generalData['Name']),0,WACV) topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(AtomList,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(topSizer,0,wx.EXPAND) mainSizer.Add(Atoms) SetPhaseWindow(AtomList,mainSizer,Scroll=Atoms.GetScrollPos(wx.VERTICAL)) #### FillAtomsGrid main code if not data['Drawing']: #if new drawing - no drawing data! SetupDrawingData() generalData = data['General'] cell = generalData['Cell'][1:7] Amat = G2lat.cell2AB(cell)[0] GS = G2lat.cell2GS(cell) SpnFlp = generalData['SGData'].get('SpnFlp',[]) atomData = data['Atoms'] resRBData = data['RBModels'].get('Residue',[]) vecRBData = data['RBModels'].get('Vector',[]) global rbAtmDict rbAtmDict = {} for rbObj in resRBData+vecRBData: exclList = ['FX' for i in range(len(rbObj['Ids']))] rbAtmDict.update(dict(zip(rbObj['Ids'],exclList))) if rbObj['ThermalMotion'][0] != 'None': for id in rbObj['Ids']: rbAtmDict[id] += 'U' # exclList will be 'fx' or 'fxu' if TLS used in RB Items = [G2G.wxID_ATOMSEDITINSERT,G2G.wxID_ATOMSEDITDELETE, G2G.wxID_ATOMSMODIFY,G2G.wxID_ATOMSTRANSFORM,G2G.wxID_MAKEMOLECULE, G2G.wxID_ATOMVIEWINSERT,G2G.wxID_ATOMMOVE,G2G.wxID_ADDHATOM] if atomData: for item in Items: G2frame.dataWindow.AtomsMenu.Enable(item,True) else: for item in Items: G2frame.dataWindow.AtomsMenu.Enable(item,False) Items = [G2G.wxID_ATOMVIEWINSERT, G2G.wxID_ATOMSVIEWADD,G2G.wxID_ATOMMOVE] if 'showABC' in data['Drawing']: for item in Items: G2frame.dataWindow.AtomsMenu.Enable(item,True) else: for item in Items: G2frame.dataWindow.AtomsMenu.Enable(item,False) parmChoice = ': ,X,XU,U,F,FX,FXU,FU' if generalData['Type'] == 'magnetic': parmChoice += ',M,MX,MXU,MU,MF,MFX,MFXU,MFU' AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK" Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+parmChoice,]+ \ 3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",] Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',] colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23'] ifMag = False if generalData['Type'] == 'macromolecular': colLabels = ['res no','residue','chain'] + colLabels Types = [wg.GRID_VALUE_STRING, wg.GRID_VALUE_CHOICE+AAchoice, wg.GRID_VALUE_STRING] + Types elif generalData['Type'] == 'magnetic': ifMag = True colLabels = colLabels[:7]+['Mx','My','Mz']+colLabels[7:] Types = Types[:7]+3*[wg.GRID_VALUE_FLOAT+':10,4',]+Types[7:] SGData = data['General']['SGData'] G2frame.GetStatusBar().SetStatusText('',1) if SGData['SpGrp'] in G2spc.spg2origins: G2frame.GetStatusBar().SetStatusText('Warning: Atom positions must correspond to 2nd setting for the space group '+SGData['SpGrp'],1) if SGData['SGPolax']: G2frame.GetStatusBar().SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'],1) if 'phoenix' in wx.version(): Atoms.Unbind(wg.EVT_GRID_CELL_CHANGED) Atoms.Bind(wg.EVT_GRID_CELL_CHANGED, ChangeAtomCell) else: Atoms.Unbind(wg.EVT_GRID_CELL_CHANGE) Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell) Atoms.Unbind(wg.EVT_GRID_CELL_LEFT_DCLICK) Atoms.Unbind(wg.EVT_GRID_LABEL_LEFT_DCLICK) Atoms.Unbind(wg.EVT_GRID_LABEL_LEFT_CLICK) Atoms.Unbind(wg.EVT_GRID_LABEL_RIGHT_CLICK) Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect) Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid) Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect) Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection) lblList = ('Set refine flags','Modify selected parameters', 'Insert new before selected','Transform selected', 'Set selected xyz to view point','Select all', 'Select from list','Set view point from selected', 'Delete') callList = (AtomRefine,AtomModify,OnAtomInsert,AtomTransform, OnAtomMove,OnSetAll,OnSetbyList,SetAtomsViewPoint, AtomDelete) onRightClick = Atoms.setupPopup(lblList,callList) Atoms.Bind(wg.EVT_GRID_CELL_RIGHT_CLICK, onRightClick) Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, onRightClick) Atoms.SetMargins(0,0) Paint() def OnAtomAdd(event): Elem = 'H' if data['General']['Type'] == 'magnetic': Elem = 'Fe' AtomAdd(0.,0.,0.,El=Elem) FillAtomsGrid(Atoms) event.StopPropagation() if data['Drawing']: G2plt.PlotStructure(G2frame,data) def OnAtomViewAdd(event): Elem = 'H' if data['General']['Type'] == 'magnetic': Elem = 'Fe' try: drawData = data['Drawing'] x,y,z = drawData['viewPoint'][0] AtomAdd(x,y,z,El=Elem) except: AtomAdd(0.,0.,0.,El=Elem) FillAtomsGrid(Atoms) event.StopPropagation() data['Drawing']['Atoms'] = [] UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) def AtomAdd(x,y,z,El='H',Name='UNK',update=True): atomData = data['Atoms'] generalData = data['General'] atId = ran.randint(0,sys.maxsize) if 'Q' in El: #dummy fill spin rb pointer generalData['SpnIds'][atId] = -1 SGData = generalData['SGData'] Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)[:2] if generalData['Type'] == 'macromolecular': atomData.append([0,Name,'',Name,El,'',x,y,z,1.,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId]) elif generalData['Type'] in ['nuclear','faulted',]: if generalData['Modulated']: atomData.append([Name,El,'',x,y,z,1.,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId,[],[], {'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}]) else: atomData.append([Name,El,'',x,y,z,1.,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId]) elif generalData['Type'] == 'magnetic': if generalData['Modulated']: atomData.append([Name,El,'',x,y,z,1.,0.,0.,0.,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId,[],[], {'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}]) else: atomData.append([Name,El,'',x,y,z,1.,0.,0.,0.,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId]) SetupGeneral() # might be better to add new atom to Draw Atoms data['Drawing']['Atoms'] = [] # if 'Atoms' in data['Drawing']: # DrawAtomAdd(data['Drawing'],atomData[-1]) if update: UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) def OnAtomInsert(event): '''Inserts a new atom into list immediately before every selected atom ''' cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) for a in reversed(sorted(indx)): AtomInsert(a,0.,0.,0.) event.StopPropagation() FillAtomsGrid(Atoms) data['Drawing']['Atoms'] = [] UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) def OnAtomViewInsert(event): if 'Drawing' in data: drawData = data['Drawing'] x,y,z = drawData['viewPoint'][0] AtomAdd(x,y,z) FillAtomsGrid(Atoms) event.StopPropagation() def OnHydAtomAdd(event): '''Adds H atoms to fill out coordination sphere for selected atoms ''' cx,ct,cs,cia = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) if not indx: return DisAglCtls = {} generalData = data['General'] if 'DisAglCtls' in generalData: DisAglCtls = generalData['DisAglCtls'] dlg = G2G.DisAglDialog(G2frame,DisAglCtls,generalData,Reset=False) if dlg.ShowModal() == wx.ID_OK: DisAglCtls = dlg.GetData() if 'H' not in DisAglCtls['AtomTypes']: DisAglCtls['AtomTypes'].append('H') DisAglCtls['AngleRadii'].append(0.5) DisAglCtls['BondRadii'].append(0.5) else: dlg.Destroy() return dlg.Destroy() generalData['DisAglCtls'] = DisAglCtls atomData = data['Atoms'] AtNames = [atom[ct-1] for atom in atomData] AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8) Neigh = [] AddHydIds = [] for ind in indx: atom = atomData[ind] if atom[ct] not in ['C','N','O']: continue neigh = [atom[ct-1],G2mth.FindNeighbors(data,atom[ct-1],AtNames),0] if len(neigh[1][0]) > 3 or (atom[ct] == 'O' and len(neigh[1][0]) > 1): continue nH = 1 #for O atom if atom[ct] in ['C','N']: nH = 4-len(neigh[1][0]) bonds = {item[0]:item[1:] for item in neigh[1][0]} nextName = '' if len(bonds) == 1: nextName = list(bonds.keys())[0] for bond in bonds: if 'C' in atom[ct]: if 'C' in bond and bonds[bond][0] < 1.42: nH -= 1 break elif 'O' in bond and bonds[bond][0] < 1.3: nH -= 1 break elif 'O' in atom[ct] and 'C' in bonds and bonds[bond][0] < 1.3: nH -= 1 break nextneigh = [] if nextName: nextneigh = G2mth.FindNeighbors(data,nextName,AtNames,notName=neigh[0]) if nextneigh[0]: neigh[1][1].append(nextneigh[1][1][0]) neigh[2] = max(0,nH) #set expected no. H's needed if len(neigh[1][0]): AddHydIds.append(neigh[1][1]) Neigh.append(neigh) if Neigh: letters = ['A','B','C'] HydIds = {} mapError = False dlg = AddHatomDialog(G2frame,Neigh,data) if dlg.ShowModal() == wx.ID_OK: Nat = len(atomData) Neigh = dlg.GetData() mapData = generalData['Map'] for ineigh,neigh in enumerate(Neigh): AddHydIds[ineigh].append(neigh[2]) loc = AtLookUp[AddHydIds[ineigh][0]]+1 if 'O' in neigh[0] and (not len(mapData['rho']) or not 'delt-F' in mapData['MapType']): mapError = True continue Hxyz,HU = G2mth.AddHydrogens(AtLookUp,generalData,atomData,AddHydIds[ineigh]) for iX,X in enumerate(Hxyz): AtomInsert(loc+iX,X[0],X[1],X[2],'H','H%s'%(neigh[0][1:]+letters[iX])) data['Atoms'][loc+iX][cia+1] = HU[iX] Id = data['Atoms'][loc+iX][cia+8] HydIds[Id] = [iX,AddHydIds[ineigh]] Nat += 1 AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8) if mapError: G2frame.ErrorDialog('Add H atom error','Adding O-H atoms requires delt-F map') SetupGeneral() data['General']['HydIds'].update(HydIds) G2frame.dataWindow.AtomEdit.Enable(G2G.wxID_UPDATEHATOM,True) data['Drawing']['Atoms'] = [] UpdateDrawAtoms() FillAtomsGrid(Atoms) dlg.Destroy() G2plt.PlotStructure(G2frame,data) else: wx.MessageBox('No candidates found',caption='Add H atom Error',style=wx.ICON_EXCLAMATION) def OnHydAtomUpdate(event): generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] atomData = data['Atoms'] AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8) HydIds = data['General']['HydIds'] delList = [] for HId in HydIds: hydIds = HydIds[HId] num = hydIds[0] Hxyz,HU = G2mth.AddHydrogens(AtLookUp,generalData,atomData,hydIds[1]) try: if data['Atoms'][AtLookUp[HId]][ct] != 'H': raise KeyError data['Atoms'][AtLookUp[HId]][cx:cx+3] = Hxyz[num] data['Atoms'][AtLookUp[HId]][cia+1] = HU[num] except KeyError: delList.append(HId) continue for HId in delList: #clear out deleted H-atom pointers del HydIds[HId] if not len(HydIds): G2frame.dataWindow.AtomEdit.Enable(G2G.wxID_UPDATEHATOM,False) data['Drawing']['Atoms'] = [] UpdateDrawAtoms() FillAtomsGrid(Atoms) G2plt.PlotStructure(G2frame,data) def OnAtomMove(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) drawData = data['Drawing'] atomData = data['Atoms'] x,y,z = drawData['viewPoint'][0] colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] cx = colLabels.index('x') ci = colLabels.index('I/A') if len(indx) != 1: G2frame.ErrorDialog('Atom move error','Only one atom can be moved') elif atomData[indx[0]][ci+8] in rbAtmDict: G2frame.ErrorDialog('Atom move error','Atoms in rigid bodies can not be moved') else: atomData[indx[0]][cx:cx+3] = [x,y,z] SetupGeneral() FillAtomsGrid(Atoms) ID = atomData[indx[0]][ci+8] G2mth.DrawAtomsReplaceByID(data,ci+8,atomData[indx[0]],ID) G2plt.PlotStructure(G2frame,data) event.StopPropagation() def AtomInsert(indx,x,y,z,El='H',Name='UNK'): atomData = data['Atoms'] generalData = data['General'] SGData = generalData['SGData'] Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)[:2] atId = ran.randint(0,sys.maxsize) if generalData['Type'] == 'macromolecular': atomData.insert(indx,[0,Name,'',Name,El,'',x,y,z,1.,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId]) elif generalData['Type'] in ['nuclear','faulted',]: if generalData['Modulated']: atomData.insert(indx,[Name,El,'',x,y,z,1,Sytsym,Mult,0.,'I',0.01,0,0,0,0,0,0,atId,[],[], {'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}]) else: atomData.insert(indx,[Name,El,'',x,y,z,1.,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId]) SetupGeneral() elif generalData['Type'] == 'magnetic': if generalData['Modulated']: atomData.insert(indx,[Name,El,'',x,y,z,1.,0.,0.,0.,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,atId,[],[], {'SS1':{'waveType':'Fourier','Sfrac':[],'Spos':[],'Sadp':[],'Smag':[]}}]) else: atomData.insert(indx,[Name,El,'',x,y,z,1.,0.,0.,0.,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId]) data['Drawing']['Atoms'] = [] UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) def AtomDelete(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms) colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] delList = '' for i in indx: if delList: delList += ', ' delList += data['Atoms'][i][0] dlg = wx.MessageDialog(G2frame,'Do you want to delete atom(s): {}?'.format(delList), 'Confirm delete',wx.YES|wx.NO) try: dlg.CenterOnParent() result = dlg.ShowModal() finally: dlg.Destroy() if result != wx.ID_YES: return HydIds = data['General']['HydIds'] ci = colLabels.index('I/A') IDs = [] if not indx: return atomData = data['Atoms'] indx.sort() indx.reverse() msg = '' for ind in indx: atom = atomData[ind] if atom[ci+8] in rbAtmDict: if msg: msg += ', ' msg += atom[0] else: if atom[ci+8] in HydIds: #remove Hs from Hatom update dict del HydIds[atom[ci+8]] IDs.append(atom[ci+8]) del atomData[ind] if msg: G2frame.ErrorDialog('Atom delete error', 'ERROR - atom(s) in a rigid body were not deleted: '+msg) if 'Atoms' in data['Drawing']: Atoms.ClearSelection() DrawAtomsDeleteByIDs(IDs) data['Drawing']['Atoms'] = [] UpdateDrawAtoms() wx.CallAfter(FillAtomsGrid,Atoms) G2plt.PlotStructure(G2frame,data) SetupGeneral() if not len(HydIds): G2frame.dataWindow.AtomEdit.Enable(G2G.wxID_UPDATEHATOM,False) event.StopPropagation() def AtomRefine(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) if not indx: return colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] c = colLabels.index('refine') atomData = data['Atoms'] generalData = data['General'] Type = generalData['Type'] if Type in ['nuclear','macromolecular','faulted',]: choice = ['F - site fraction','X - coordinates','U - thermal parameters'] elif Type in ['magnetic',]: choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment'] dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() parms = '' for x in sel: parms += choice[x][0] for r in indx: if not Atoms.IsReadOnly(r,c): atomData[r][c] = parms Atoms.ForceRefresh() dlg.Destroy() def AtomModify(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) if not indx: return atomData = data['Atoms'] generalData = data['General'] ifMag = False colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] ci = colLabels.index('I/A') choices = ['Type','Name','x','y','z','frac','I/A','Uiso','Uij'] if generalData['Type'] == 'magnetic': choices += ['Mx','My','Mz',] ifMag = True dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices) parm = '' if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parm = choices[sel] cid = -1 if parm != 'Uij': cid = colLabels.index(parm) dlg.Destroy() if parm in ['Type']: dlg = G2elemGUI.PickElement(G2frame,ifMag=ifMag) if dlg.ShowModal() == wx.ID_OK: if dlg.Elem not in ['None']: El = dlg.Elem.strip() for r in indx: if not Atoms.IsReadOnly(r,0): #not if in RB! atomData[r][cid] = El if len(El) in [2,4]: atomData[r][cid-1] = El[:2]+'%d'%(r+1) else: atomData[r][cid-1] = El[:1]+'%d'%(r+1) SetupGeneral() if 'Atoms' in data['Drawing']: for r in indx: ID = atomData[r][ci+8] G2mth.DrawAtomsReplaceByID(data,ci+8,atomData[r],ID) FillAtomsGrid(Atoms) dlg.Destroy() elif parm in ['Name',]: dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename', wx.YES_NO | wx.ICON_QUESTION) try: result = dlg.ShowModal() if result == wx.ID_YES: for r in indx: if not Atoms.IsReadOnly(r,0): #not if in RB! El = atomData[r][cid+1] if len(El) in [2,4]: atomData[r][cid] = El[:2]+'%d'%(r+1) else: atomData[r][cid] = El[:1]+'%d'%(r+1) FillAtomsGrid(Atoms) finally: dlg.Destroy() elif parm in ['I/A']: choices = ['Isotropic','Anisotropic'] dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parm = choices[sel][0] for r in indx: if Atoms.IsReadOnly(r,0): #not if in RB! continue atomData[r][cid] = parm if parm == 'A' and not any(atomData[r][cid+2:cid+8]): sytsym = atomData[r][cs] CSI = G2spc.GetCSuinel(sytsym) atomData[r][ci+2:ci+8] = atomData[r][ci+1]*np.array(CSI[3]) FillAtomsGrid(Atoms) dlg.Destroy() elif parm in ['frac','Uiso']: limits = [-1.,1.] val = 1.0 if parm in ['Uiso']: limits = [-0.25,0.25] val = 0.01 dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits) if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in indx: if not Atoms.IsReadOnly(r,0): #not if in RB! atomData[r][cid] = parm SetupGeneral() FillAtomsGrid(Atoms) dlg.Destroy() elif parm == 'Uij': limits = [0.,0.25] val = 0.01 dlg = G2G.SingleFloatDialog(G2frame,'Convert Uiso to Uij','Enter default for Uiso'+parm,val,limits) if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in indx: if not Atoms.IsReadOnly(r,0): #not if in RB! atomData[r][ci] = 'A' sytsym = atomData[r][cs] CSI = G2spc.GetCSuinel(sytsym) if atomData[r][ci+1] > 0.: atomData[r][ci+2:ci+8] = atomData[r][ci+1]*np.array(CSI[3]) else: atomData[r][ci+2:ci+8] = parm*np.array(CSI[3]) SetupGeneral() FillAtomsGrid(Atoms) dlg.Destroy() elif parm in ['x','y','z']: limits = [-1.,1.] val = 0. dlg = G2G.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits) if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in indx: if not Atoms.IsReadOnly(r,0): #not if in RB! atomData[r][cid] += parm SetupGeneral() FillAtomsGrid(Atoms) dlg.Destroy() elif parm in ['Mx','My','Mz',]: limits = [-10.,10.] val = 0. dlg = G2G.SingleFloatDialog(G2frame,'Atom moment','Enter new value for '+parm,val,limits) if dlg.ShowModal() == wx.ID_OK: parm = dlg.GetValue() for r in indx: if not Atoms.IsReadOnly(r,0): #not if in RB! atomData[r][cid] = parm SetupGeneral() FillAtomsGrid(Atoms) dlg.Destroy() data['Drawing']['Atoms'] = [] UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) def AtomTransform(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) if not indx: return generalData = data['General'] SpnFlp = generalData['SGData'].get('SpnFlp',[]) colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] cx = colLabels.index('x') cuia = colLabels.index('I/A') cuij = colLabels.index('U11') css = colLabels.index('site sym') cmx = 0 if 'Mx' in colLabels: cmx = colLabels.index('Mx') atomData = data['Atoms'] SGData = generalData['SGData'] dlg = SymOpDialog(G2frame,SGData,True,True) New = False try: if dlg.ShowModal() == wx.ID_OK: Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection() Cell = np.array(Cell) cent = SGData['SGCen'][Cent] M,T = SGData['SGOps'][Opr] for ind in indx: XYZ = np.array(atomData[ind][cx:cx+3]) XYZ = np.inner(M,XYZ)+T if Inv and not SGData['SGFixed']: XYZ = -XYZ XYZ = XYZ+cent+Cell if Force: XYZ,cell = G2spc.MoveToUnitCell(XYZ) Cell += cell if New: atom = copy.copy(atomData[ind]) else: atom = atomData[ind] atom[cx:cx+3] = XYZ atom[css:css+2] = G2spc.SytSym(XYZ,SGData)[:2] OprNum = ((Opr+1)+100*Cent)*(1-2*Inv) if atom[cuia] == 'A': Uij = atom[cuij:cuij+6] U = G2spc.Uij2U(Uij) U = np.inner(np.inner(M,U),M) Uij = G2spc.U2Uij(U) atom[cuij:cuij+6] = Uij if cmx: opNum = G2spc.GetOpNum(OprNum,SGData) mom = np.array(atom[cmx:cmx+3]) atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum-1] if New: atomData.append(atom) finally: dlg.Destroy() Atoms.ClearSelection() if New: FillAtomsGrid(Atoms) else: Atoms.ForceRefresh() data['Drawing']['Atoms'] = [] UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) # def AtomRotate(event): # '''Currently not used - Bind commented out below # ''' # Units = {'':np.zeros(3), # 'xy':np.array([[i,j,0] for i in range(3) for j in range(3)])-np.array([1,1,0]), # 'xz':np.array([[i,0,j] for i in range(3) for j in range(3)])-np.array([1,1,0]), # 'yz':np.array([[0,i,j] for i in range(3) for j in range(3)])-np.array([1,1,0]), # 'xyz':np.array([[i,j,k] for i in range(3) for j in range(3) for k in range(3)])-np.array([1,1,1])} # cx,ct,cs,ci = G2mth.getAtomPtrs(data) # indx = getAtomSelections(Atoms,ct-1) # if indx: # generalData = data['General'] # A,B = G2lat.cell2AB(generalData['Cell'][1:7]) # colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] # cx = colLabels.index('x') # cuia = colLabels.index('I/A') #need to not do aniso atoms - stop with error? or force isotropic? # css = colLabels.index('site sym') # atomData = data['Atoms'] # SGData = generalData['SGData'] # dlg = G2gd.RotationDialog(G2frame) # try: # if dlg.ShowModal() == wx.ID_OK: # M,T,Expand = dlg.GetSelection() # Unit = Units[Expand] # for ind in indx: # XYZ = np.array(atomData[ind][cx:cx+3]) # XYZS = XYZ+Unit # XYZS -= T # XYZS = np.inner(A,XYZS).T #to Cartesian # XYZS = np.inner(M,XYZS).T #rotate # XYZS = np.inner(B,XYZS).T+T #back to crystal & translate # GSASIIpath.IPyBreak() # atomData[ind][cx:cx+3] = XYZ # for unit in Unit: # XYZ = np.copy(np.array(atomData[ind][cx:cx+3])) # XYZ += unit # XYZ -= T # XYZ = np.inner(A,XYZ) #to Cartesian # XYZ = np.inner(M,XYZ) #rotate # XYZ = np.inner(B,XYZ)+T #back to crystal & translate # if np.all(XYZ>=0.) and np.all(XYZ<1.0): # atomData[ind][cx:cx+3] = XYZ ## atom[css:css+2] = G2spc.SytSym(XYZ,SGData)[:2] # break # finally: # dlg.Destroy() # Atoms.ClearSelection() # Atoms.ForceRefresh() # else: # print "select one or more rows of atoms" # G2frame.ErrorDialog('Select atom',"select one or more atoms then redo") def CollectAtoms(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data) Ind = getAtomSelections(Atoms,ct-1) if Ind: choice = ['x=0','y=0','z=0','origin','center'] dlg = wx.SingleChoiceDialog(G2frame,'Atoms closest to:','Select',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection()+1 dlg.Destroy() else: dlg.Destroy() return wx.BeginBusyCursor() data['Atoms'] = G2mth.AtomsCollect(data,Ind,sel) wx.EndBusyCursor() Atoms.ClearSelection() data['Drawing']['Atoms'] = [] OnReloadDrawAtoms(event) FillAtomsGrid(Atoms) def MakeMolecule(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) DisAglCtls = {} if indx is not None and len(indx) == 1: generalData = data['General'] if 'DisAglCtls' in generalData: DisAglCtls = generalData['DisAglCtls'] dlg = G2G.DisAglDialog(G2frame,DisAglCtls,generalData) if dlg.ShowModal() == wx.ID_OK: DisAglCtls = dlg.GetData() else: dlg.Destroy() return dlg.Destroy() generalData['DisAglCtls'] = DisAglCtls atomData = copy.deepcopy(data['Atoms']) result = G2mth.FindMolecule(indx[0],generalData,atomData) if 'str' in str(type(result)): G2frame.ErrorDialog('Assemble molecule',result) else: data['Atoms'] = result Atoms.ClearSelection() data['Drawing']['Atoms'] = [] OnReloadDrawAtoms(event) FillAtomsGrid(Atoms) # G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types') else: print ("select one atom") G2frame.ErrorDialog('Select one atom',"select one atom to begin molecule build then redo") def OnDensity(event): 'show the density for the current phase' density,mattCoeff = G2mth.getDensity(data['General']) msg = 'Density of phase {:s} = {:.3f} g/cc'.format(data['General']['Name'],density) print(msg) G2G.G2MessageBox(G2frame,msg,'Density') def OnSetAll(event): 'set all atoms in table as selected' for row in range(Atoms.GetNumberRows()): Atoms.SelectRow(row,True) G2plt.PlotStructure(G2frame,data) def OnSetbyList(event): 'select atoms using a filtered listbox' choices = [atm[0] for atm in data['Atoms']] dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select atoms','Choose atoms to select',choices) indx = [] if dlg.ShowModal() == wx.ID_OK: indx = dlg.GetSelections() dlg.Destroy() if len(indx) == 0: return Atoms.ClearSelection() for row in indx: Atoms.SelectRow(row,True) G2plt.PlotStructure(G2frame,data) def SetAtomsViewPoint(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) if not indx: return pos = np.zeros(3) for i in indx: pos += data['Atoms'][i][cx:cx+3] data['Drawing']['viewPoint'] = [list(pos/len(indx)),[indx[0],0]] G2plt.PlotStructure(G2frame,data) def OnDistAnglePrt(event): 'save distances and angles to a file' fp = open(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile)[0]+'.disagl'),'w') OnDistAngle(event,fp=fp) fp.close() def OnDistAngleHist(event): OnDistAngle(event,hist=True) def OnDistAngle(event,fp=None,hist=False): 'Compute distances and angles' cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) Oxyz = [] xyz = [] DisAglData = {} DisAglCtls = {} if indx: generalData = data['General'] DisAglData['OrigIndx'] = indx if 'DisAglCtls' in generalData: DisAglCtls = generalData['DisAglCtls'] dlg = G2G.DisAglDialog(G2frame,DisAglCtls,generalData) if dlg.ShowModal() == wx.ID_OK: DisAglCtls = dlg.GetData() else: dlg.Destroy() return dlg.Destroy() generalData['DisAglCtls'] = DisAglCtls atomData = data['Atoms'] colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())] cx = colLabels.index('x') cn = colLabels.index('Name') ct = colLabels.index('Type') Atypes = [] for i,atom in enumerate(atomData): xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3]) if i in indx: Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3]) Atypes.append(atom[ct]) Atypes = set(Atypes) Atypes = ', '.join(Atypes) DisAglData['OrigAtoms'] = Oxyz DisAglData['TargAtoms'] = xyz generalData = data['General'] DisAglData['SGData'] = generalData['SGData'] DisAglData['Cell'] = generalData['Cell'][1:] #+ volume if 'pId' in data: DisAglData['pId'] = data['pId'] DisAglData['covData'] = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Covariance')) try: if hist: pgbar = wx.ProgressDialog('Distance Angle calculation','Atoms done=',len(Oxyz)+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE) AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(DisAglCtls,DisAglData,pgbar) pgbar.Destroy() Bonds = [] for dists in DistArray: Bonds += [item[3] for item in DistArray[dists]] G2plt.PlotBarGraph(G2frame,Bonds,Xname=r'$\mathsf{Bonds,\AA}$', Title='Bond distances for %s'%Atypes,PlotName='%s Bonds'%Atypes) print('Total number of bonds to %s is %d'%(Atypes,len(Bonds))) Angles = [] for angles in AngArray: Angles += [item[2][0] for item in AngArray[angles]] G2plt.PlotBarGraph(G2frame,Angles,Xname=r'$\mathsf{Angles,{^o}}$', Title='Bond angles about %s'%Atypes,PlotName='%s Angles'%Atypes) print('Total number of angles about %s is %d'%(Atypes,len(Angles))) elif fp: G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp) else: G2stMn.PrintDistAngle(DisAglCtls,DisAglData) except KeyError: # inside DistAngle for missing atom types in DisAglCtls G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types') else: print ("select one or more rows of atoms") G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo") def OnFracSplit(event): 'Split atom frac accordintg to atom type & refined site fraction' cx,ct,cs,ci = G2mth.getAtomPtrs(data) indx = getAtomSelections(Atoms,ct-1) if indx: atomData = data['Atoms'] PE = G2elemGUI.PickElement(G2frame,oneOnly=True) if PE.ShowModal() == wx.ID_OK: Atype2 = PE.Elem.strip() AtomInfo2 = G2elem.GetAtomInfo(Atype2) Z2 = AtomInfo2['Z'] B2 = AtomInfo2['Isotopes']['Nat. Abund.']['SL'][0] PE.Destroy() for ind in indx: Aname1 = atomData[ind][ct-1] Atype1 = G2elem.FixValence(atomData[ind][ct]) Afrac = atomData[ind][cx+3] Amult = float(atomData[ind][cx+5]) AtomInfo1 = G2elem.GetAtomInfo(Atype1) if Atype1 == Atype2: print('ERROR - 2nd atom type must be different from selected atom') continue Z1 = AtomInfo1['Z'] B1 = AtomInfo1['Isotopes']['Nat. Abund.']['SL'][0] frac1 = (Z1*Afrac-Z2)/(Z1-Z2) bfrac1 = (B1*Afrac-B2)/(B1-B2) print(' For %s: X-ray based site fractions %s = %.3f, %.3f/cell; %s = %.3f, %.3f/cell' \ %(Aname1,Atype1,frac1,frac1*Amult,Atype2,(1.-frac1),(1.-frac1)*Amult)) print(' neutron based site fractions %s = %.3f, %.3f/cell; %s = %.3f, %.3f/cell\n' \ %(Atype1,bfrac1,bfrac1*Amult,Atype2,(1.-bfrac1),(1.-bfrac1)*Amult)) def OnValidProtein(event): def pickHandler(resName): drawData = data['Drawing'] resid = resIDs[resName] drawData['viewPoint'][0] = atomData[AtLookUp[resid]][cx:cx+3] UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) atomData = data['Atoms'] cx,ct,cs,cia = data['General']['AtomPtrs'] AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8) resNames,Probs1,resIDs = G2mth.validProtein(data,True) #old version resNames,Probs2,resIDs = G2mth.validProtein(data,False) #new version print ('Plot 1 is Protein validation based on errat.f') print ('Ref: Colovos, C. & Yeates, T.O. Protein Science 2, 1511-1519 (1991).') print ('Residue error scores >6 for 5% & >8 for 1% likelihood of being correct') print ('NB: this calc. matches errat.f result') print ('Plot 2 is Protein validation based on erratv2.cpp; by D. Obukhov & T. Yeates (2002)') print ('Residue error scores >11.5 for 5% & >17.2 for 1% likelihood of being correct') print ('NB: this calc. gives a close approximate to original erratv2 result') G2plt.PlotAAProb(G2frame,resNames,Probs1,Probs2,Title='Error score for %s'%(data['General']['Name']), thresh=[[8.0,6.0],[17.191,11.527]],pickHandler=pickHandler) def OnShowIsoDistortCalc(event): Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() G2cnstG.ShowIsoDistortCalc(G2frame,data['General']['Name']) def OnShowIsoModes(event): Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() #import imp #imp.reload(G2cnstG) G2cnstG.ShowIsoModes(G2frame,data['General']['Name']) def OnReImport(event): generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] reqrdr = G2frame.dataWindow.ReImportMenuId.get(event.GetId()) rdlist = G2frame.OnImportGeneric(reqrdr, G2frame.ImportPhaseReaderlist,'phase') if len(rdlist) == 0: return # rdlist is only expected to have one element rd = rdlist[0] Strict = True if 'rmc6f' in rd.readfilename: Strict = False idx = -1 G2frame.OnFileSave(event) # rd contains all info for a phase PhaseName = rd.Phase['General']['Name'] print ('Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)) atomData = data['Atoms'] atomNames = [] All = False for atom in atomData: atomNames.append(''.join(atom[:ct+1]).capitalize()) #eliminate spurious differences for atom in rd.Phase['Atoms']: try: if Strict: idx = atomNames.index(''.join(atom[:ct+1]).capitalize()) #eliminate spurious differences else: idx += 1 atId = atomData[idx][cia+8] #save old Id atomData[idx][:cia+8] = atom[:cia+8]+[atId,] except ValueError: if All: atomData.append(atom) else: dlg = wx.MessageDialog(G2frame,'Some atoms not in List; do you want to append them all', \ 'Unknown atom '+atom[0],wx.YES_NO|wx.ICON_QUESTION) try: result = dlg.ShowModal() if result in [wx.ID_YES,]: All = True atomData.append(atom) else: print (atom[:ct+1]+ 'not in Atom array; not updated') finally: dlg.Destroy() SetupGeneral() OnReloadDrawAtoms(event) wx.CallAfter(FillAtomsGrid,Atoms) #### Dysnomia (MEM) Data page ############################################################################## def UpdateDysnomia(): ''' Present the controls for running Dysnomia ''' def OnOptMeth(event): DysData['Optimize'] = OptMeth.GetValue() wx.CallAfter(UpdateDysnomia) def OnZmult(event): DysData['Lagrange'][0] = Zmult.GetValue() wx.CallAfter(UpdateDysnomia) def OnStart(event): DysData['DenStart'] = Start.GetValue() def OnPrior(event): DysData['prior'] = Prior.GetValue() if DysData['prior'] == 'last run': if os.path.isfile(pName+'_prior.pgrid'): os.remove(pName+'_prior.pgrid') os.rename(pName+'.pgrid',pName+'_prior.pgrid') def OnFileCheck(event): DysData['clear'] = fileCheck.GetValue() cite = ''' For use of Dysnomia, please cite: Dysnomia, a computer program for maximum-entropy method (MEM) analysis and its performance in the MEM-based pattern fitting, K. Moma, T. Ikeda, A.A. Belik & F. Izumi, Powder Diffr. 2013, 28, 184-193. doi: https://doi.org/10.1017/S088571561300002X ''' generalData = data['General'] pName = generalData['Name'].replace(' ','_') Map = generalData['Map'] UseList = Map['RefList'] pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,UseList[0]) #only use 1st histogram if not pId: wx.MessageBox('You must prepare a fourier map before running Dysnomia','Dysnomia Error', style=wx.ICON_ERROR) return reflSets = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,'Reflection Lists')) reflData = reflSets[generalData['Name']]['RefList'] refDmin = reflData[-1][4] mulMin = np.argmin(reflData[:][3]) if reflData[mulMin][3] < 0: refDmin = reflData[mulMin-1][4] MEMData = G2frame.MEMData if MEMData.GetSizer(): MEMData.GetSizer().Clear(True) DysData = data['Dysnomia'] if 'overlap' not in DysData: DysData['overlap'] = 1.0 if 'MEMdmin' not in DysData: DysData['MEMdmin'] = refDmin if 'clear' not in DysData: DysData['clear'] = True mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(MEMData,label=' Maximum Entropy Method (Dysnomia) controls:')) topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(MEMData,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(topSizer,0,wx.EXPAND) mainSizer.Add(wx.StaticText(MEMData,label=cite)) lineSizer = wx.BoxSizer(wx.HORIZONTAL) lineSizer.Add(wx.StaticText(MEMData,label=' MEM Optimization method: '),0,WACV) OptMeth = wx.ComboBox(MEMData,-1,value=DysData['Optimize'],choices=['ZSPA','L-BFGS'], style=wx.CB_READONLY|wx.CB_DROPDOWN) OptMeth.Bind(wx.EVT_COMBOBOX,OnOptMeth) lineSizer.Add(OptMeth,0,WACV) lineSizer.Add(wx.StaticText(MEMData,label=' Peak overlap factor'),0,WACV) overlap = G2G.ValidatedTxtCtrl(MEMData,DysData,'overlap',nDig=(10,4),xmin=0.1,xmax=1.) lineSizer.Add(overlap,0,WACV) mainSizer.Add(lineSizer) if DysData['Optimize'] == 'ZSPA': Zsizer = wx.BoxSizer(wx.HORIZONTAL) Zsizer.Add(wx.StaticText(MEMData,label=' Initial Lagrangian multiplier: from '),0,WACV) Zmult = wx.ComboBox(MEMData,value=DysData['Lagrange'][0],choices=['user','Dysnomia'], style=wx.CB_READONLY|wx.CB_DROPDOWN) Zmult.Bind(wx.EVT_COMBOBOX,OnZmult) Zsizer.Add(Zmult,0,WACV) if DysData['Lagrange'][0] == 'user': Zsizer.Add(wx.StaticText(MEMData,label=' value: '),0,WACV) lamb = G2G.ValidatedTxtCtrl(MEMData,DysData['Lagrange'],1,nDig=(10,4),xmin=0.0001,xmax=1.) Zsizer.Add(lamb,0,WACV) Zsizer.Add(wx.StaticText(MEMData,label=' Adjust by: '),0,WACV) dlamb = G2G.ValidatedTxtCtrl(MEMData,DysData['Lagrange'],2,nDig=(8,2),xmin=0.05,xmax=0.1) Zsizer.Add(dlamb,0,WACV) mainSizer.Add(Zsizer) Esizer = wx.BoxSizer(wx.HORIZONTAL) Esizer.Add(wx.StaticText(MEMData,label=' Weight by d-spacing**'),0,WACV) Efact = G2G.ValidatedTxtCtrl(MEMData,DysData,'wt pwr',xmin=0,xmax=4,size=(50,20)) Esizer.Add(Efact,0,WACV) Dmin = G2G.ValidatedTxtCtrl(MEMData,DysData,'MEMdmin',xmin=0.5,xmax=refDmin,size=(50,20)) Esizer.Add(wx.StaticText(MEMData,label=' Minimum d-spacing for generated reflections: '),0,WACV) Esizer.Add(Dmin,0,WACV) mainSizer.Add(Esizer) if os.path.isfile(pName+'.pgrid'): PriorSizer = wx.BoxSizer(wx.HORIZONTAL) PriorSizer.Add(wx.StaticText(MEMData,label=' Start from densities: '),0,WACV) Start = wx.ComboBox(MEMData,-1,value=DysData['DenStart'],choices=['uniform','last run'], style=wx.CB_READONLY|wx.CB_DROPDOWN) Start.Bind(wx.EVT_COMBOBOX,OnStart) PriorSizer.Add(Start,0,WACV) PriorSizer.Add(wx.StaticText(MEMData,label=' Use as prior: '),0,WACV) Prior = wx.ComboBox(MEMData,-1,value=DysData['prior'],choices=['uniform','last run'], style=wx.CB_READONLY|wx.CB_DROPDOWN) Prior.Bind(wx.EVT_COMBOBOX,OnPrior) PriorSizer.Add(Prior,0,WACV) mainSizer.Add(PriorSizer) else: DysData['DenStart'] = 'uniform' DysData['prior'] = 'uniform' Csizer = wx.BoxSizer(wx.HORIZONTAL) Csizer.Add(wx.StaticText(MEMData,label=' Maximum number of cycles: '),0,WACV) Cyc = G2G.ValidatedTxtCtrl(MEMData,DysData,'Ncyc',xmin=0,xmax=10000,size=(50,20)) Csizer.Add(Cyc,0,WACV) fileCheck = wx.CheckBox(MEMData,label='Clear Dynsomia files? ') fileCheck.SetValue(DysData['clear']) fileCheck.Bind(wx.EVT_CHECKBOX,OnFileCheck) Csizer.Add(fileCheck,0,WACV) mainSizer.Add(Csizer) SetPhaseWindow(G2frame.MEMData,mainSizer) def OnLoadDysnomia(event): print('Load MEM - might not be implemented') def OnSaveDysnomia(event): print('Save MEM - might not be implemented') def OnRunDysnomia(event): path2GSAS2 = os.path.dirname(os.path.abspath(os.path.expanduser(__file__))) DYSNOMIA = os.path.join(path2GSAS2,'Dysnomia','Dysnomia64.exe') DysData = data['Dysnomia'] if not os.path.exists(DYSNOMIA): wx.MessageBox(''' Dysnomia is not installed. Please download it from https://jp-minerals.org/dysnomia/en/ and install it at.'''+DYSNOMIA, caption='Dysnomia not installed',style=wx.ICON_ERROR) return generalData = data['General'] Map = generalData['Map'] UseList = Map['RefList'] pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,UseList[0]) #only use 1st histogram if not pId: wx.MessageBox('You must prepare a Fourier map before running Dysnomia','Dysnomia Error', style=wx.ICON_ERROR) return reflSets = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,'Reflection Lists')) reflData = reflSets[generalData['Name']]['RefList'] if 'Type' not in Map: wx.MessageBox('You must prepare a Fourier map before running Dysnomia','Dysnomia Error', style=wx.ICON_ERROR) return Type = Map['Type'] MEMtype = 0 if 'N' in Type: for el in generalData['Isotope']: isotope = generalData['Isotope'][el] if el not in generalData['Isotopes']: continue if generalData['Isotopes'][el][isotope]['SL'][0] < 0.: MEMtype = 1 prfName = str(G2pwd.makePRFfile(data,MEMtype)) if not G2pwd.makeMEMfile(data,reflData,MEMtype,DYSNOMIA): SpGrp = generalData['SGData']['SpGrp'] wx.MessageBox('Non standard space group '+SpGrp+' not permitted in Dysnomia','Dysnomia Error', style=wx.ICON_ERROR) return cite = ''' For use of Dysnomia, please cite: Dysnomia, a computer program for maximum-entropy method (MEM) analysis and its performance in the MEM-based pattern fitting, K. Moma, T. Ikeda, A.A. Belik & F. Izumi, Powder Diffr. 2013, 28, 184-193. doi: https://doi.org/10.1017/S088571561300002X''' wx.MessageBox(cite,caption='Dysnomia (MEM)',style=wx.ICON_INFORMATION) print('Run '+DYSNOMIA) subp.call([DYSNOMIA,prfName]) DysData['DenStart'] = 'uniform' DysData['prior'] = 'uniform' wx.CallAfter(UpdateDysnomia) goon,reflData = G2pwd.MEMupdateReflData(prfName,data,reflData) if goon: reflSets[generalData['Name']]['RefList'] = reflData G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,'Reflection Lists'),reflSets) OnFourierMaps(event) #auto run Fourier if DysData['clear']: os.remove(os.path.splitext(prfName)[0]+'.fba') os.remove(os.path.splitext(prfName)[0]+'.mem') os.remove(os.path.splitext(prfName)[0]+'.out') os.remove(os.path.splitext(prfName)[0]+'.prf') os.remove(os.path.splitext(prfName)[0]+'_eps.raw') else: wx.MessageBox('Dysnomia failed to make new structure factors','Dysnomia Error', style=wx.ICON_ERROR) #### RMC Data page ################################################################################ # fullrmc stuff TODO: # 1) need to implement swapping in scripts # 2) fullrmc tutorials def UpdateRMC(event=None): ''' Present the controls for running fullrmc, RMCProfile or PDFfit ''' global runFile def OnRMCselect(event): G2frame.RMCchoice = RMCsel.GetStringSelection() wx.CallAfter(UpdateRMC) def GetAtmChoice(pnl,RMCPdict): Indx = {} def OnAtSel(event): Obj = event.GetEventObject() itype = Indx[Obj.GetId()] tid = RMCPdict['atSeq'].index(Obj.GetStringSelection()) if itype < nTypes: if itype == tid: tid += 1 RMCPdict['atSeq'] = G2lat.SwapItems(RMCPdict['atSeq'],itype,tid) Pairs= [] atSeq = RMCPdict['atSeq'] lenA = len(atSeq) for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA)] for i in range(lenA)]: # for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA) if 'Va' not in atSeq[j]] for i in range(lenA) if 'Va' not in atSeq[i]]: Pairs += pair RMCPdict['Pairs'] = {pairs:[0.0,0.0,0.0] for pairs in Pairs} if RMCPdict['useBVS']: BVSpairs = [] for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i+1,lenA)] for i in range(lenA)]: BVSpairs += pair RMCPdict['BVS'] = {pairs:[0.0,0.0,0.0,0.0] for pairs in BVSpairs} wx.CallAfter(UpdateRMC) def OnValSel(event): Obj = event.GetEventObject() itype = Indx[Obj.GetId()] RMCPdict['Oxid'][itype][0] = Obj.GetStringSelection() wx.CallAfter(UpdateRMC) nTypes = len(RMCPdict['aTypes']) atmChoice = wx.FlexGridSizer(nTypes+1,5,5) atmChoice.Add(wx.StaticText(pnl,label='atom ordering: '),0,WACV) for iType in range(nTypes): atChoice = RMCPdict['atSeq'][iType:] atmSel = wx.ComboBox(pnl,choices=atChoice,style=wx.CB_DROPDOWN|wx.TE_READONLY) atmSel.SetStringSelection(RMCPdict['atSeq'][iType]) atmSel.Bind(wx.EVT_COMBOBOX,OnAtSel) Indx[atmSel.GetId()] = iType atmChoice.Add(atmSel,0,WACV) if RMCPdict['useBVS']: atmChoice.Add(wx.StaticText(pnl,label='Valence: '),0,WACV) for itype in range(nTypes): valChoice = atmdata.BVSoxid[RMCPdict['atSeq'][itype]] valSel = wx.ComboBox(pnl,choices=valChoice,style=wx.CB_DROPDOWN|wx.TE_READONLY) try: valSel.SetStringSelection(RMCPdict['Oxid'][itype][0]) except IndexError: RMCPdict['Oxid'].append([RMCPdict['atSeq'][itype],0.0]) valSel.Bind(wx.EVT_COMBOBOX,OnValSel) Indx[valSel.GetId()] = itype atmChoice.Add(valSel,0,WACV) atmChoice.Add(wx.StaticText(pnl,label='BVS weight: '),0,WACV) for itype in range(nTypes): atmChoice.Add(G2G.ValidatedTxtCtrl(pnl,RMCPdict['Oxid'][itype],1,xmin=0.),0,WACV) if G2frame.RMCchoice == 'RMCProfile': atmChoice.Add(wx.StaticText(pnl,label='max shift: '),0,WACV) for iType in range(nTypes): atId = RMCPdict['atSeq'][iType] atmChoice.Add(G2G.ValidatedTxtCtrl(pnl,RMCPdict['aTypes'],atId,xmin=0.,xmax=1.),0,WACV) atmChoice.Add(wx.StaticText(pnl,label='Isotope: '),0,WACV) for iType in range(nTypes): atId = RMCPdict['atSeq'][iType] try: lbl = RMCPdict['Isotope'][atId] except: lbl = '?' atmChoice.Add(wx.StaticText(pnl,label=lbl),0,WACV) return atmChoice def GetSwapSizer(RMCPdict): def OnDelSwap(event): Obj = event.GetEventObject() swap = Indx[Obj.GetId()] del RMCPdict['Swaps'][swap] wx.CallAfter(UpdateRMC) Indx = {} atChoice = RMCPdict['atSeq'] # if G2frame.RMCchoice == 'fullrmc': # atChoice = atNames swapSizer = wx.FlexGridSizer(6,5,5) swapLabels = [' ','Atom-A','Atom-B',' Swap prob.',' ','delete'] for lab in swapLabels: swapSizer.Add(wx.StaticText(G2frame.FRMC,label=lab),0,WACV) for ifx,swap in enumerate(RMCPdict['Swaps']): swapSizer.Add((20,-1)) for i in [0,1]: if swap[i] not in atChoice: swap[i] = atChoice[0] atmSel = G2G.EnumSelector(G2frame.FRMC,swap,i,atChoice) swapSizer.Add(atmSel,0,WACV) swapSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,swap,2,xmin=0.01,xmax=0.5,size=(50,25)),0,WACV) swapSizer.Add((20,-1)) delBtn = wx.Button(G2frame.FRMC,label='Del',style=wx.BU_EXACTFIT) delBtn.Bind(wx.EVT_BUTTON,OnDelSwap) Indx[delBtn.GetId()] = ifx swapSizer.Add(delBtn,0,WACV) return swapSizer def GetPairSizer(pnl,RMCPdict): pairSizer = wx.FlexGridSizer(len(RMCPdict['Pairs'])+1,5,5) pairSizer.Add((5,5),0) for pair in RMCPdict['Pairs']: pairSizer.Add(wx.StaticText(pnl,label=pair),0,WACV) if G2frame.RMCchoice == 'RMCProfile': pairSizer.Add(wx.StaticText(pnl,label='%14s'%' Hard min: '),0,WACV) for pair in RMCPdict['Pairs']: pairSizer.Add(G2G.ValidatedTxtCtrl(pnl,RMCPdict['Pairs'][pair],0,xmin=0.,xmax=10.,size=(50,25)),0,WACV) pairSizer.Add(wx.StaticText(pnl,label='%14s'%' Search from: '),0,WACV) elif G2frame.RMCchoice == 'fullrmc': pairSizer.Add(wx.StaticText(pnl,label='%14s'%' Distance min: '),0,WACV) for pair in RMCPdict['Pairs']: pairSizer.Add(G2G.ValidatedTxtCtrl(pnl,RMCPdict['Pairs'][pair], 1,xmin=0.,xmax=10.,size=(50,25)),0,WACV) pairSizer.Add(wx.StaticText(pnl,label='%14s'%'to: '),0,WACV) for pair in RMCPdict['Pairs']: pairSizer.Add(G2G.ValidatedTxtCtrl(pnl,RMCPdict['Pairs'][pair],2,xmin=0.,xmax=10.,size=(50,25)),0,WACV) return pairSizer def GetMetaSizer(RMCPdict,metalist): metaSizer = wx.FlexGridSizer(0,2,5,5) for item in metalist: metaSizer.Add(wx.StaticText(G2frame.FRMC,label=' Metadata item: '+item+' '),0,WACV) metaSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['metadata'],item),0,WACV) return metaSizer def SetRestart(invalid,value,tc): RMCPdict['ReStart'] = [True,True] def GetSuperSizer(RMCPdict,Xmax): superSizer = wx.BoxSizer(wx.HORIZONTAL) axes = ['X','Y','Z'] for i,ax in enumerate(axes): superSizer.Add(wx.StaticText(G2frame.FRMC,label=' %s-axis: '%ax),0,WACV) superSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['SuperCell'], i,xmin=1,xmax=Xmax,size=(50,25),OnLeave=SetRestart),0,WACV) return superSizer def FileSizer(RMCPdict): def OnFileSel(event): Obj = event.GetEventObject() fil = Indx[Obj.GetId()] G2frame.OnFileSave(event) dlg = wx.FileDialog(G2frame.FRMC, 'Choose '+fil,G2G.GetImportPath(G2frame), style=wx.FD_OPEN ,wildcard=fil+'(*.*)|*.*') if dlg.ShowModal() == wx.ID_OK: fpath,fName = os.path.split(dlg.GetPath()) if os.path.exists(fName): # is there a file by this name in the current directory? RMCPdict['files'][fil][0] = fName else: # nope, copy it disfile.copy_file(dlg.GetPath(),os.path.join(G2frame.LastGPXdir,fName)) if not os.path.exists(fName): # sanity check print(f'Error: file {fName} not found in .gpx directory ({G2frame.LastGPXdir})') return G2frame.LastImportDir = fpath #set so next file is found in same place dlg.Destroy() RMCPdict['ReStart'][0] = True if G2frame.RMCchoice == 'PDFfit': start = 0 XY = np.empty((1,2)) while XY.shape[0] == 1: try: XY = np.loadtxt(fName,skiprows=start) except ValueError: start += 1 name = 'Ndata' if 'X' in fil: name = 'Xdata' RMCPdict[name]['Datarange'][0] = np.min(XY.T[0]) RMCPdict[name]['Datarange'][1] = np.max(XY.T[0]) RMCPdict[name]['Fitrange'][1] = np.max(XY.T[0]) else: dlg.Destroy() wx.CallAfter(UpdateRMC) def OnFileFormat(event): Obj = event.GetEventObject() fil = Indx[Obj.GetId()] RMCPdict['files'][fil][3] = Obj.GetStringSelection() def OnPlotBtn(event): Obj = event.GetEventObject() fil = Indx[Obj.GetId()] fileItem = RMCPdict['files'][fil] start = 0 XY = np.empty((1,2)) while XY.shape[0] == 1: try: XY = np.loadtxt(fileItem[0],skiprows=start) except ValueError: start += 1 if start > 500: #absurd number of header lines! wx.MessageBox('WARNING: %s has bad data at end;\n RMCProfile may fail to read it'%fileItem[0], style=wx.ICON_ERROR) break Xlab = 'Q' if 'G(R)' in fileItem[2].upper(): Xlab = 'R' G2plt.PlotXY(G2frame,[XY.T[:2],],labelX=Xlab, labelY=fileItem[2],newPlot=True,Title=fileItem[0], lines=True) def OnCorrChk(event): Obj = event.GetEventObject() fil = Indx[Obj.GetId()] RMCPdict['files'][fil][3] = not RMCPdict['files'][fil][3] def OnDelBtn(event): Obj = event.GetEventObject() fil = Indx[Obj.GetId()] RMCPdict['files'][fil][0] = 'Select' RMCPdict['ReStart'][0] = True wx.CallAfter(UpdateRMC) def OnRef(event): Obj = event.GetEventObject() name,item = Indx[Obj.GetId()] RMCPdict[name][item][1] = not RMCPdict[name][item][1] def OnRefSel(event): RMCPdict['refinement'] = reftype.GetStringSelection() wx.CallLater(100,UpdateRMC) def OnDataSel(event): RMCPdict['SeqDataType'] = dataType.GetStringSelection() def OnSeqCopy(event): RMCPdict['SeqCopy'] = not RMCPdict['SeqCopy'] def OnSeqReverse(event): RMCPdict['SeqReverse'] = not RMCPdict['SeqReverse'] # --- FileSizer starts here Indx = {} mainSizer = wx.BoxSizer(wx.VERTICAL) if G2frame.RMCchoice == 'PDFfit': topSizer = wx.BoxSizer(wx.HORIZONTAL) reftype = wx.RadioBox(G2frame.FRMC,label='PDFfit refinement type:',choices=['normal','sequential']) reftype.SetStringSelection(RMCPdict.get('refinement','normal')) reftype.Bind(wx.EVT_RADIOBOX,OnRefSel) topSizer.Add(reftype) if 'seq' in RMCPdict.get('refinement','normal'): dataType = wx.RadioBox(G2frame.FRMC,label='Seq data type:',choices=['X','N']) dataType.SetStringSelection(RMCPdict.get('SeqDataType','X')) dataType.Bind(wx.EVT_RADIOBOX,OnDataSel) topSizer.Add(dataType) endSizer = wx.BoxSizer(wx.VERTICAL) seqcopy = wx.CheckBox(G2frame.FRMC,label=' Copy to next') seqcopy.SetValue(RMCPdict['SeqCopy']) seqcopy.Bind(wx.EVT_CHECKBOX,OnSeqCopy) endSizer.Add(seqcopy) seqreverse = wx.CheckBox(G2frame.FRMC,label=' Reverse processing') seqreverse.SetValue(RMCPdict['SeqReverse']) seqreverse.Bind(wx.EVT_CHECKBOX,OnSeqReverse) endSizer.Add(seqreverse) topSizer.Add(endSizer,0,WACV) mainSizer.Add(topSizer) elif G2frame.RMCchoice == 'fullrmc': topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(G2frame.FRMC,label=' Select data for processing (files must be 2 columns w/headers preceeded by "#"; edit if needed)')) mainSizer.Add(topSizer) Heads = ['Name','File','type','Plot','Delete'] fileSizer = wx.FlexGridSizer(5,5,5) Formats = ['RMC','GUDRUN','STOG'] for head in Heads: fileSizer.Add(wx.StaticText(G2frame.FRMC,label=head),0,WACV) for fil in RMCPdict['files']: fileSizer.Add(wx.StaticText(G2frame.FRMC,label=fil),0,WACV) Rfile = RMCPdict['files'][fil][0] filSel = wx.Button(G2frame.FRMC,label=Rfile) filSel.Bind(wx.EVT_BUTTON,OnFileSel) Indx[filSel.GetId()] = fil fileSizer.Add(filSel,0,WACV) if Rfile and os.path.exists(Rfile): # in case .gpx file is moved away from G(R), F(Q), etc. files #fileSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['files'][fil],1,size=(50,25)),0,WACV) #patch if len(RMCPdict['files'][fil]) < 4: RMCPdict['files'][fil].append(0) if len(RMCPdict['files'][fil]) < 5: RMCPdict['files'][fil].append(True) #end patch if 'G(r)' in fil: choices = 'G(r)-RMCProfile','G(r)-PDFFIT','g(r)' if type(RMCPdict['files'][fil][3]) is bool: RMCPdict['files'][fil][3] = 0 fmtTyp = G2G.G2ChoiceButton(G2frame.FRMC,choices,RMCPdict['files'][fil],3) elif '(Q)' in fil: choices = 'F(Q)-RMCProfile','S(Q)-PDFFIT' if type(RMCPdict['files'][fil][3]) is bool: RMCPdict['files'][fil][3] = 0 fmtTyp = G2G.G2ChoiceButton(G2frame.FRMC,choices,RMCPdict['files'][fil],3) else: fmtTyp = (-1,-1) fileSizer.Add(fmtTyp,0,WACV) plotBtn = wx.Button(G2frame.FRMC,label='Plot',style=wx.BU_EXACTFIT) plotBtn.Bind(wx.EVT_BUTTON,OnPlotBtn) Indx[plotBtn.GetId()] = fil fileSizer.Add(plotBtn,0,WACV) delBtn = wx.Button(G2frame.FRMC,label='Del',style=wx.BU_EXACTFIT) delBtn.Bind(wx.EVT_BUTTON,OnDelBtn) Indx[delBtn.GetId()] = fil fileSizer.Add(delBtn,0,WACV) if '(Q)' in fil: fileSizer.Add((-1,-1),0) corrChk = wx.CheckBox(G2frame.FRMC,label='Apply sinc convolution? ') corrChk.SetValue(RMCPdict['files'][fil][4]) Indx[corrChk.GetId()] = fil corrChk.Bind(wx.EVT_CHECKBOX,OnCorrChk) fileSizer.Add(corrChk,0,WACV) #fileSizer.Add((-1,-1),0) fileSizer.Add((-1,-1),0) fileSizer.Add((-1,-1),0) fileSizer.Add((-1,-1),0) elif 'Select' not in Rfile: # file specified, but must not exist RMCPdict['files'][fil][0] = 'Select' # set filSel? fileSizer.Add(wx.StaticText(G2frame.FRMC, label='Warning: file not found.\nWill be removed'),0) fileSizer.Add((-1,-1),0) fileSizer.Add((-1,-1),0) else: RMCPdict['files'][fil][0] = 'Select' # set filSel? #fileSizer.Add((-1,-1),0) fileSizer.Add((-1,-1),0) fileSizer.Add((-1,-1),0) fileSizer.Add((-1,-1),0) mainSizer.Add(fileSizer,0) return mainSizer if G2frame.RMCchoice == 'PDFfit' and RMCPdict['refinement'] == 'sequential': def OnAddPDF(event): ''' Add PDF G(r)s while maintanining original sequence ''' usedList = RMCPdict['seqfiles'] PDFlist = [item[1:][0] for item in G2frame.GetFileList('PDF')] PDFdict = dict([item[1:] for item in G2frame.GetFileList('PDF')]) PDFnames = [item for item in PDFdict if item not in [itm[0] for itm in usedList]] dlg = G2G.G2MultiChoiceDialog(G2frame.FRMC,'Add PDF dataset', 'Select G(r) data to use in seq. PDFfit',PDFnames) if dlg.ShowModal() == wx.ID_OK: PDFuse = dlg.GetSelections() for item in PDFuse: pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,PDFnames[item]) data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,'PDF Controls')) try: insrt = PDFlist.index(PDFnames[item])-1 RMCPdict['seqfiles'].insert(insrt+1,[PDFnames[item],data]) except ValueError: RMCPdict['seqfiles'].append([PDFnames[item],data]) dlg.Destroy() wx.CallAfter(UpdateRMC) def OnDelPDF(event): usedList = [item[0] for item in RMCPdict['seqfiles']] dlg = G2G.G2MultiChoiceDialog(G2frame.FRMC,'Delete PDF dataset', 'Select G(r) data to delete frpm seq. PDFfit',usedList) if dlg.ShowModal() == wx.ID_OK: PDFdel = dlg.GetSelections() PDFdel.reverse() for item in PDFdel: del RMCPdict['seqfiles'][item] dlg.Destroy() wx.CallAfter(UpdateRMC) def OnSetColVal(event): parms = {'Rmin':[0.01,5.0],'Rmax':[5.,30.],'dscale':[0.5,2.0], 'qdamp':[0.0,0.5],'qbroad':[0.0,0.1],'Temp':300} c = event.GetCol() if c >= 0: if c in [3,5,7]: seqGrid.ClearSelection() seqGrid.SelectCol(c,True) if seqGrid.GetColLabelValue(c) != 'refine': return choice = ['Y - vary all','N - vary none',] dlg = wx.SingleChoiceDialog(G2frame,'Select refinement option for '+seqGrid.GetColLabelValue(c-1), 'Refinement controls',choice) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() varib = colLabels[c-1] if sel == 0: for row in range(seqGrid.GetNumberRows()): RMCPdict['seqfiles'][row][1][varib][1]=True else: for row in range(seqGrid.GetNumberRows()): RMCPdict['seqfiles'][row][1][varib][1]=False elif c in [0,1,2,4,6,8]: seqGrid.ClearSelection() seqGrid.SelectCol(c,True) parm = colLabels[c] dlg = G2G.SingleFloatDialog(G2frame,'New value','Enter value for '+parm,0.0,parms[parm]) if dlg.ShowModal() == wx.ID_OK: value = dlg.GetValue() if c in [2,4,6]: for row in range(seqGrid.GetNumberRows()): RMCPdict['seqfiles'][row][1][parm][0] = value elif c == 8: for row in range(seqGrid.GetNumberRows()): RMCPdict['seqfiles'][row][1][parm] = value else: for row in range(seqGrid.GetNumberRows()): RMCPdict['seqfiles'][row][1]['Fitrange'][c] = value wx.CallAfter(UpdateRMC) def OnSetVal(event): r,c= event.GetRow(),event.GetCol() if c >= 0: if c in [3,5,7]: varib = colLabels[c-1] RMCPdict['seqfiles'][r][1][varib][1] = bool(seqGrid.GetCellValue(r,c)) elif c in [0,1,2,4,6,8]: parm = colLabels[c] if c in [2,4,6]: RMCPdict['seqfiles'][r][1][parm][0] = float(seqGrid.GetCellValue(r,c)) elif c == 8: RMCPdict['seqfiles'][r][1][parm] = float(seqGrid.GetCellValue(r,c)) else: RMCPdict['seqfiles'][r][1]['Fitrange'][c] = float(seqGrid.GetCellValue(r,c)) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(G2frame.FRMC,label=' Select data for processing: ')) mainSizer.Add(topSizer) G2frame.GetStatusBar().SetStatusText('NB: All PDFs used in sequential PDFfit must be the same type ("X" or "N") - there is no check',1) if 'seqfiles' not in RMCPdict: RMCPdict['seqfiles'] = [] topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(G2frame.FRMC,label=' Sequential data list for PDFfit: '),0,WACV) addPDF = wx.Button(G2frame.FRMC,label='Add PDF G(r) data sets') addPDF.Bind(wx.EVT_BUTTON,OnAddPDF) topSizer.Add(addPDF,0,WACV) delPDF = wx.Button(G2frame.FRMC,label='Delete PDF G(r) data sets') delPDF.Bind(wx.EVT_BUTTON,OnDelPDF) topSizer.Add(delPDF,0,WACV) mainSizer.Add(topSizer) table = [[item[1]['Fitrange'][0],item[1]['Fitrange'][1], item[1]['dscale'][0],item[1]['dscale'][1],item[1]['qdamp'][0],item[1]['qdamp'][1], item[1]['qbroad'][0],item[1]['qbroad'][1],item[1].get('Temp',300.)] for item in RMCPdict['seqfiles']] colLabels = ['Rmin','Rmax','dscale','refine','qdamp','refine','qbroad','refine','Temp'] rowLabels = [item[0] for item in RMCPdict['seqfiles']] Types = [wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_FLOAT+':10,2', wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL, wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL, wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL,wg.GRID_VALUE_FLOAT+':10,2'] seqTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) seqGrid = G2G.GSGrid(G2frame.FRMC) seqGrid.SetTable(seqTable, True) seqGrid.AutoSizeColumns(True) seqGrid.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, OnSetColVal) seqGrid.Bind(wg.EVT_GRID_CELL_CHANGED, OnSetVal) mainSizer.Add(seqGrid) return mainSizer # begin FileSizer topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(G2frame.FRMC,label=' Select data for processing: ')) mainSizer.Add(topSizer) # RMCProfile & PDFfit (Normal) Heads = ['Name','File','Format','Weight','Plot','Delete'] fileSizer = wx.FlexGridSizer(6,5,5) Formats = ['RMC','GUDRUN','STOG'] for head in Heads: fileSizer.Add(wx.StaticText(G2frame.FRMC,label=head),0,WACV) for fil in RMCPdict['files']: for head in Heads: fileSizer.Add(wx.StaticText(G2frame.FRMC,label=20*'-'),0,WACV) fileSizer.Add(wx.StaticText(G2frame.FRMC,label=fil),0,WACV) Rfile = RMCPdict['files'][fil][0] filSel = wx.Button(G2frame.FRMC,label=Rfile) filSel.Bind(wx.EVT_BUTTON,OnFileSel) Indx[filSel.GetId()] = fil fileSizer.Add(filSel,0,WACV) nform = 3 Name = 'Ndata' if 'Xray' in fil: nform = 1 Name = 'Xdata' if Rfile and os.path.exists(Rfile): #incase .gpx file is moved away from G(R), F(Q), etc. files fileFormat = wx.ComboBox(G2frame.FRMC,choices=Formats[:nform],style=wx.CB_DROPDOWN|wx.TE_READONLY) fileFormat.SetStringSelection(RMCPdict['files'][fil][3]) Indx[fileFormat.GetId()] = fil fileFormat.Bind(wx.EVT_COMBOBOX,OnFileFormat) fileSizer.Add(fileFormat,0,WACV) fileSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['files'][fil],1),0,WACV) plotBtn = wx.Button(G2frame.FRMC,label='Plot?',style=wx.BU_EXACTFIT) plotBtn.Bind(wx.EVT_BUTTON,OnPlotBtn) Indx[plotBtn.GetId()] = fil fileSizer.Add(plotBtn,0,WACV) delBtn = wx.Button(G2frame.FRMC,label='Del',style=wx.BU_EXACTFIT) delBtn.Bind(wx.EVT_BUTTON,OnDelBtn) Indx[delBtn.GetId()] = fil fileSizer.Add(delBtn,0,WACV) else: RMCPdict['files'][fil][0] = 'Select' fileSizer.Add((5,5),0) fileSizer.Add((5,5),0) fileSizer.Add((5,5),0) fileSizer.Add((5,5),0) if 'Select' not in Rfile and 'PDFfit' in G2frame.RMCchoice: fileSizer.Add(wx.StaticText(G2frame.FRMC,label=' R-range (from/to)'),0,WACV) fileSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict[Name]['Fitrange'],0,xmin=RMCPdict[Name]['Datarange'][0],xmax=3.0),0,WACV) fileSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict[Name]['Fitrange'],1,xmin=10.0,xmax=RMCPdict[Name]['Datarange'][1]),0,WACV) fileSizer.Add(wx.StaticText(G2frame.FRMC,label=' Scale factor: '),0,WACV) fileSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict[Name]['dscale'],0,xmin=0.001,xmax=20.0),0,WACV) scaleref = wx.CheckBox(G2frame.FRMC,label='refine') scaleref.SetValue(RMCPdict[Name]['dscale'][1]) Indx[scaleref.GetId()] = [Name,'dscale'] scaleref.Bind(wx.EVT_CHECKBOX,OnRef) fileSizer.Add(scaleref,0,WACV) fileSizer.Add(wx.StaticText(G2frame.FRMC,label=' Qdamp '),0,WACV) fileSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict[Name]['qdamp'],0,xmin=0.0,xmax=1.0),0,WACV) qdampref = wx.CheckBox(G2frame.FRMC,label='refine') qdampref.SetValue(RMCPdict[Name]['qdamp'][1]) Indx[qdampref.GetId()] = [Name,'qdamp'] qdampref.Bind(wx.EVT_CHECKBOX,OnRef) fileSizer.Add(qdampref,0,WACV) fileSizer.Add(wx.StaticText(G2frame.FRMC,label=' Qbroad '),0,WACV) fileSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict[Name]['qbroad'],0,xmin=0.0,xmax=1.0),0,WACV) qbroadref = wx.CheckBox(G2frame.FRMC,label='refine') qbroadref.SetValue(RMCPdict[Name]['qbroad'][1]) Indx[qbroadref.GetId()] = [Name,'qbroad'] qbroadref.Bind(wx.EVT_CHECKBOX,OnRef) fileSizer.Add(qbroadref,0,WACV) mainSizer.Add(fileSizer,0) return mainSizer def fullrmcSizer(RMCPdict): mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(G2frame.FRMC,label= '''* "Atomic Stochastic Modeling & Optimization with fullrmc", B. Aoun, J. Appl. Cryst. 2022, 55(6) 1664-1676, DOI: 10.1107/S1600576722008536; * "Fullrmc, a Rigid Body Reverse Monte Carlo Modeling Package Enabled with Machine Learning and Artificial Intelligence", B. Aoun, Jour. Comp. Chem. (2016), 37, 1102-1111. DOI: 10.1002/jcc.24304; * www.fullrmc.com ''')) # if G2pwd.findfullrmc() is None: # mainSizer.Add(wx.StaticText(G2frame.FRMC, # label="\nsorry, fullrmc not installed or was not located")) # return mainSizer G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_SETUPRMC,True) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,True) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_VIEWRMC,True) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_ATOMSRMC,True) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_SUPERRMC,True) #mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' fullrmc big box starting pdb file preparation:'),0) # initialize fullrmc dictionary if needed RMCPdict = data['RMC']['fullrmc'] = data['RMC'].get('fullrmc',{}) # update, if atoms list has been updated Atypes = [atype.split('+')[0].split('-')[0] for atype in data['General']['AtomTypes']] aTypes = dict(zip(Atypes,len(Atypes)*[0.10,])) if len(data['RMC']['fullrmc'].get('aTypes',{})) != len(aTypes): #print('atypes has changed') atSeq = list(aTypes.keys()) lenA = len(atSeq) Pairs= [] for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA) if 'Va' not in atSeq[j]] for i in range(lenA) if 'Va' not in atSeq[i]]: Pairs += pair Pairs = {pairs:[0.0,0.0,0.0] for pairs in Pairs} RMCPdict.update({'aTypes':aTypes,'atSeq':atSeq,'Pairs':Pairs}) RMCPdict['files'] = RMCPdict.get('files', {'Neutron real space data; G(r): ':['Select',1.,'G(r)',0,True], 'Neutron reciprocal space data; S(Q)-1: ':['Select',1.,'F(Q)',0,True], 'Xray real space data; G(r): ':['Select',1.,'G(r)',0,True], 'Xray reciprocal space data; S(Q)-1: ':['Select',1.,'F(Q)',0,True]}) if 'moleculePdb' not in RMCPdict: RMCPdict.update({'moleculePdb':'Select','targetDensity':1.0,'maxRecursion':10000}) if 'Angles' not in RMCPdict: RMCPdict.update({'Angles':[],'Angle Weight':1.e-5,'Bond Weight':1.e-5,'Torsions':[],'Torsion Weight':1.e-5}) for key,val in {'SuperCell':[1,1,1],'Box':[10.,10.,10.],'ReStart':[False,False],'Cycles':1, 'Swaps':[],'useBVS':False,'FitScale':False,'AveCN':[],'FxCN':[], 'min Contact':1.5,'periodicBound':True}.items(): RMCPdict[key] = RMCPdict.get(key,val) def GetSuperSizer(): def ShowRmax(*args,**kwargs): cell = data['General']['Cell'][1:7] bigcell = np.array(cell)*np.array(RMCPdict['SuperCell']+[1,1,1]) bigG = G2lat.cell2Gmat(bigcell)[0] rmax = min([0.5/np.sqrt(G2lat.calc_rDsq2(H,bigG)) for H in np.eye(3)]) rmaxlbl.SetLabel(' Rmax = {:.1f}'.format(rmax)) superSizer = wx.BoxSizer(wx.HORIZONTAL) axes = ['X','Y','Z'] for i,ax in enumerate(axes): superSizer.Add(wx.StaticText(G2frame.FRMC,label=' %s-axis: '%ax),0,WACV) superSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['SuperCell'], i,xmin=1,xmax=20,size=(50,25),OnLeave=ShowRmax),0,WACV) rmaxlbl = wx.StaticText(G2frame.FRMC,label=' Rmax=?') superSizer.Add(rmaxlbl,0,WACV) ShowRmax() return superSizer def GetBoxSizer(): boxSizer = wx.BoxSizer(wx.HORIZONTAL) axes = ['X','Y','Z'] for i,ax in enumerate(axes): boxSizer.Add(wx.StaticText(G2frame.FRMC,label=' %s-axis: '%ax),0,WACV) boxSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['Box'], i,xmin=10.,xmax=50.,size=(50,25)),0,WACV) return boxSizer def OnReStart(event): RMCPdict['ReStart'][0] = not RMCPdict['ReStart'][0] def OnAddSwap(event): RMCPdict['Swaps'].append(['','',0.0,]) wx.CallAfter(UpdateRMC) def OnPdbButton(event): dlg = wx.FileDialog(G2frame.FRMC, 'Choose molecule pdb file',G2frame.LastGPXdir, style=wx.FD_OPEN ,wildcard='PDB file(*.pdb)|*.pdb') if dlg.ShowModal() == wx.ID_OK: fpath,fName = os.path.split(dlg.GetPath()) RMCPdict['moleculePdb'] = fName pdbButton.SetLabel(fName) def OnAddAngle(event): RMCPdict['Angles'].append(['','','',0.,0.,0.,0.]) wx.CallAfter(UpdateRMC) # def OnAddTorsion(event): # RMCPdict['Torsions'].append(['','','','',0.,0.,0.,0.,0.,0.]) # wx.CallAfter(UpdateRMC) def GetAngleSizer(): def OnDelAngle(event): Obj = event.GetEventObject() angle = Indx[Obj.GetId()] del RMCPdict['Angles'][angle] wx.CallAfter(UpdateRMC) # def OnAngleAtSel(event): # Obj = event.GetEventObject() # angle,i = Indx[Obj.GetId()] # RMCPdict['Angles'][angle][i] = Obj.GetStringSelection() def SetRestart1(invalid,value,tc): RMCPdict['ReStart'][1] = True Indx = {} atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm] angleSizer = wx.GridBagSizer(0,5) fxcnLabels1 = [' ',' ','Central','',None,'angle restraint values (deg)',None,'search distance (A)'] fxcnLabels2 = [' ','Atom-A','Atom','Atom-C','min','max','from','to'] for i in range(8): if fxcnLabels1[i]: cspan=1 coloff = 0 if fxcnLabels1[i-1] is None: cspan=2 coloff = 1 angleSizer.Add(wx.StaticText(G2frame.FRMC,label=fxcnLabels1[i]), (0,i-coloff),(1,cspan)) if fxcnLabels2[i]: angleSizer.Add(wx.StaticText(G2frame.FRMC,wx.ID_ANY, label=fxcnLabels2[i],style=wx.CENTER),(1,i)) row = 1 for ifx,angle in enumerate(RMCPdict['Angles']): row += 1 angleSizer.Add((30,-1),(row,0)) for i in range(3): if angle[i] not in atChoice: angle[i] = atChoice[0] atmSel = G2G.EnumSelector(G2frame.FRMC,angle,i,atChoice) angleSizer.Add(atmSel,(row,1+i)) for i in range(4): if i == 0: xmin,xmax=0.,180. elif i == 2: xmin,xmax=0.1,6. angleSizer.Add( G2G.ValidatedTxtCtrl(G2frame.FRMC,angle,3+i,xmin=xmin,xmax=xmax, OnLeave=SetRestart1,size=(50,25)),(row,4+i)) delBtn = wx.Button(G2frame.FRMC,label='Del',style=wx.BU_EXACTFIT) delBtn.Bind(wx.EVT_BUTTON,OnDelAngle) Indx[delBtn.GetId()] = ifx angleSizer.Add(delBtn,(row,9)) return angleSizer # def GetTorsionSizer(): # def OnDelTorsion(event): # Obj = event.GetEventObject() # angle = Indx[Obj.GetId()] # del RMCPdict['Torsions'][angle] # wx.CallAfter(UpdateRMC) # def OnTorsionAtSel(event): # Obj = event.GetEventObject() # torsion,i = Indx[Obj.GetId()] # RMCPdict['Torsions'][torsion][i] = Obj.GetStringSelection() # def SetRestart1(invalid,value,tc): # RMCPdict['ReStart'][1] = True # Indx = {} # atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm] # torsionSizer = wx.FlexGridSizer(11,5,5) # fxcnLabels = [' ','Atom-A','Atom-B','Atom-C','Atom-D',' min angle1',' max angle1',' min angle2',' max angle2',' min angle3',' max angle3'] # for lab in fxcnLabels: # torsionSizer.Add(wx.StaticText(G2frame.FRMC,label=lab),0,WACV) # for ifx,torsion in enumerate(RMCPdict['Torsions']): # delBtn = wx.Button(G2frame.FRMC,label='Delete') # delBtn.Bind(wx.EVT_BUTTON,OnDelTorsion) # Indx[delBtn.GetId()] = ifx # torsionSizer.Add(delBtn,0,WACV) # for i in [0,1,2,3]: # atmSel = wx.ComboBox(G2frame.FRMC,choices=atChoice,style=wx.CB_DROPDOWN|wx.TE_READONLY) # atmSel.SetStringSelection(torsion[i]) # atmSel.Bind(wx.EVT_COMBOBOX,OnTorsionAtSel) # Indx[atmSel.GetId()] = [ifx,i] # torsionSizer.Add(atmSel,0,WACV) # for i in [4,5,6,7,8,9]: # torsionSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,torsion,i,xmin=0.,xmax=360.,OnLeave=SetRestart1,size=(50,25)),0,WACV) # return torsionSizer generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] #atomData = data['Atoms'] # atNames = [atom[ct-1] for atom in atomData] # ifP1 = False # if generalData['SGData']['SpGrp'] == 'P 1': # ifP1 = True ifBox = False if 'macromolecular' in generalData['Type']: ifBox = True lineSizer = wx.BoxSizer(wx.HORIZONTAL) if ifBox: lineSizer.Add(wx.StaticText(G2frame.FRMC,label=' Big box dimensions, %s:'%Angstr),0,WACV) lineSizer.Add(GetBoxSizer(),0,WACV) # elif ifP1: lineSizer.Add(wx.StaticText(G2frame.FRMC,label=' Lattice multipliers:'),0,WACV) lineSizer.Add(GetSuperSizer(),0,WACV) lineSizer.Add((5,-1)) # Bachir suggests that w/o periodic boundaries, users are likely to use fullrmc wrong #lineSizer.Add(G2G.G2CheckBox(G2frame.FRMC,'Impose periodic boundaries',RMCPdict,'periodicBound'), # 0,WACV) mainSizer.Add(lineSizer,0) if ifBox: molecSizer = wx.BoxSizer(wx.HORIZONTAL) molecSizer.Add(wx.StaticText(G2frame.FRMC,label=' Source molecule file '),0,WACV) pdbButton = wx.Button(G2frame.FRMC,label=RMCPdict['moleculePdb']) pdbButton.Bind(wx.EVT_BUTTON,OnPdbButton) molecSizer.Add(pdbButton,0,WACV) molecSizer.Add(wx.StaticText(G2frame.FRMC,label=' target density, gm/cc '),0,WACV) molecSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'targetDensity',xmin=0.1,size=[60,25]),0,WACV) molecSizer.Add(wx.StaticText(G2frame.FRMC,label=' max tries '),0,WACV) molecSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'maxRecursion',xmin=1000,xmax=1000000,size=[60,25]),0,WACV) mainSizer.Add(molecSizer,0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' fullrmc run file preparation:')) resLine = wx.BoxSizer(wx.HORIZONTAL) resLine.Add(wx.StaticText(G2frame.FRMC,label=' Run '),0,WACV) resLine.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Cycles',xmin=1,size=[60,25])) resLine.Add(wx.StaticText(G2frame.FRMC, label=' computation cycles of '),0,WACV) RMCPdict['Steps/cycle'] = RMCPdict.get('Steps/cycle',5000) resLine.Add(G2G.EnumSelector(G2frame.FRMC,RMCPdict,'Steps/cycle', ['1K','5K','10K','50K'],[1000,5000,10000,50000]),0,WACV) resLine.Add(wx.StaticText(G2frame.FRMC, label=' steps per cycle'),0,WACV) mainSizer.Add(resLine,0) resLine = wx.BoxSizer(wx.HORIZONTAL) resLine.Add(wx.StaticText(G2frame.FRMC, label=' Restart fullrmc Engine? '),0,WACV) restart = wx.CheckBox(G2frame.FRMC,label='(will clear old result!) ') resLine.Add(restart,0,WACV) restart.SetValue(RMCPdict['ReStart'][0]) restart.Bind(wx.EVT_CHECKBOX,OnReStart) mainSizer.Add(resLine,0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(GetAtmChoice(G2frame.FRMC,RMCPdict),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) swapBox = wx.BoxSizer(wx.HORIZONTAL) swapBox.Add(wx.StaticText(G2frame.FRMC,label='Atom swap probabiities: '),0,WACV) swapAdd = wx.Button(G2frame.FRMC,label='Add',style=wx.BU_EXACTFIT) swapAdd.Bind(wx.EVT_BUTTON,OnAddSwap) swapBox.Add(swapAdd,0,WACV) mainSizer.Add(swapBox,0) if len(RMCPdict['Swaps']): mainSizer.Add(GetSwapSizer(RMCPdict),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(wx.StaticText(G2frame.FRMC,label='Geometry constraints && restraints'),0) distBox = wx.BoxSizer(wx.HORIZONTAL) distBox.Add(wx.StaticText(G2frame.FRMC,label='Distance constraints'),0,WACV) # weights removed for now #distBox.Add(wx.StaticText(G2frame.FRMC,label=', distance weight:'),0,WACV) #distBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Bond Weight',xmin=0.,xmax=100.,size=(50,25)),0,WACV) distBox.Add(wx.StaticText(G2frame.FRMC,label=' min contact dist: '),0,WACV) distBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'min Contact',xmin=0.,xmax=4.,size=(50,25)),0,WACV) RMCPdict['useBondConstraints'] = RMCPdict.get('useBondConstraints',True) distBox.Add(wx.StaticText(G2frame.FRMC,label=' Use bond constraints? '),0,WACV) distBox.Add(G2G.G2CheckBox(G2frame.FRMC,'',RMCPdict,'useBondConstraints',OnChange=UpdateRMC), 0,WACV) mainSizer.Add(distBox,0) if RMCPdict['useBondConstraints']: mainSizer.Add(GetPairSizer(G2frame.FRMC,RMCPdict),0) mainSizer.Add((-1,10)) angBox = wx.BoxSizer(wx.HORIZONTAL) angBox.Add(wx.StaticText(G2frame.FRMC,label='A-B-C angle restraints'),0,WACV) # weights removed for now #angBox.Add(wx.StaticText(G2frame.FRMC,label=', angle weight:'),0,WACV) #angBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Angle Weight',xmin=0.,xmax=100.,size=(50,25)),0,WACV) angBox.Add((20,-1)) angAdd = wx.Button(G2frame.FRMC,label='Add',style=wx.BU_EXACTFIT) angAdd.Bind(wx.EVT_BUTTON,OnAddAngle) angBox.Add(angAdd,0,WACV) mainSizer.Add(angBox,0) if len(RMCPdict['Angles']): mainSizer.Add(GetAngleSizer(),0) RMCPdict['Groups'] = RMCPdict.get('Groups',[]) def OnAddGroup(event): index = len(RMCPdict['Groups']) RMCPdict['Groups'].append([]) GroupEditor(index) def OnDelGroup(event): index = event.EventObject.index del RMCPdict['Groups'][index] wx.CallAfter(UpdateRMC) def OnEdtGroup(event): index = event.EventObject.index GroupEditor(index) def GroupEditor(index): cx,ct,cs,cia = data['General']['AtomPtrs'] atomlbs = [a[ct-1] for a in data['Atoms']] dlg = G2G.G2MultiChoiceDialog(G2frame.FRMC,'Atom Selector', 'Select atoms to include in group',atomlbs,selected=RMCPdict['Groups'][index]) if dlg.ShowModal() == wx.ID_OK: RMCPdict['Groups'][index] = dlg.GetSelections() dlg.Destroy() if len(RMCPdict['Groups'][index]) == 0: del RMCPdict['Groups'][index] wx.CallAfter(UpdateRMC) if len(RMCPdict['Groups']) == 0: grpAdd = wx.Button(G2frame.FRMC,label='Define atom group',style=wx.BU_EXACTFIT) grpAdd.Bind(wx.EVT_BUTTON,OnAddGroup) mainSizer.Add(grpAdd,0) else: grpBox = wx.BoxSizer(wx.HORIZONTAL) grpBox.Add(wx.StaticText(G2frame.FRMC,label='Atom Groups: '),0,WACV) grpAdd = wx.Button(G2frame.FRMC,label='Add group',style=wx.BU_EXACTFIT) grpAdd.Bind(wx.EVT_BUTTON,OnAddGroup) RMCPdict['GroupMode'] = RMCPdict.get('GroupMode',0) grpBox.Add(grpAdd,0,WACV) grpBox.Add(wx.StaticText(G2frame.FRMC, label=' Group refinement mode: '),0,WACV) grpBox.Add(G2G.EnumSelector(G2frame.FRMC,RMCPdict,'GroupMode', ('Rotate & Translate','Rotate only','Translate only'), [0,1,2]),0,WACV) mainSizer.Add(grpBox,0) for i,g in enumerate(RMCPdict['Groups']): grpBox = wx.BoxSizer(wx.HORIZONTAL) grpBox.Add((20,-1)) grpBox.Add(wx.StaticText(G2frame.FRMC,label='Group #'+str(i+1)),0,WACV) grpBox.Add((4,-1)) grpdel = wx.Button(G2frame.FRMC,label='Del',style=wx.BU_EXACTFIT) grpdel.Bind(wx.EVT_BUTTON,OnDelGroup) grpdel.index = i grpBox.Add(grpdel,0,WACV) grpadd = wx.Button(G2frame.FRMC,label='Edit',style=wx.BU_EXACTFIT) grpadd.Bind(wx.EVT_BUTTON,OnEdtGroup) grpadd.index = i grpBox.Add(grpadd,0,WACV) msg = ' Contains atoms: ' for i,n in enumerate(g): if i+1 == len(g): msg += ' && ' elif i > 0: msg += ', ' msg += str(i) grpBox.Add(wx.StaticText(G2frame.FRMC,label=msg),0,WACV) mainSizer.Add(grpBox,0) RMCPdict['addThermalBroadening'] = RMCPdict.get('addThermalBroadening',False) mainSizer.Add((-1,5)) distBox = wx.BoxSizer(wx.HORIZONTAL) distBox.Add(wx.StaticText(G2frame.FRMC,label=' Add thermal broadening? '),0,WACV) distBox.Add(G2G.G2CheckBox(G2frame.FRMC,'',RMCPdict,'addThermalBroadening',OnChange=UpdateRMC), 0,WACV) if RMCPdict['addThermalBroadening']: distBox.Add((15,-1)) distBox.Add(wx.StaticText(G2frame.FRMC,label='Uiso equiv.'),0,WACV) RMCPdict['ThermalU'] = RMCPdict.get('ThermalU',{}) for atm in RMCPdict['aTypes']: RMCPdict['ThermalU'][atm] = RMCPdict['ThermalU'].get(atm,0.005) distBox.Add(wx.StaticText(G2frame.FRMC,label=' '+atm+':'),0,WACV) distBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['ThermalU'],atm, xmin=0.0001,xmax=0.25,size=(50,25)),0,WACV) mainSizer.Add(distBox,0) if RMCPdict['addThermalBroadening']: mainSizer.Add((-1,5)) # Torsions are difficult to implement. Need to be internal to a unit cell & named with fullrmc # atom labels. Leave this out, at least for now. # torBox = wx.BoxSizer(wx.HORIZONTAL) # torAdd = wx.Button(G2frame.FRMC,label='Add') # torAdd.Bind(wx.EVT_BUTTON,OnAddTorsion) # torBox.Add(torAdd,0,WACV) # torBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B-C-D torsion angle restraints (intracell only), weight: '),0,WACV) # torBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,'Torsion Weight',xmin=0.,xmax=100.,size=(50,25)),0,WACV) # mainSizer.Add(torBox,0) # if len(RMCPdict['Torsions']): # mainSizer.Add(GetTorsionSizer(),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(FileSizer(RMCPdict)) return mainSizer def RMCProfileSizer(RMCPdict): def CheckAtms(Atypes): newAtm = False for atm in Atypes: if atm not in data['RMC']['RMCProfile'].get('aTypes',{}): newAtm = True break for atm in data['RMC']['RMCProfile'].get('aTypes',{}): if atm not in Atypes: newAtm = True break return newAtm mainSizer = wx.BoxSizer(wx.VERTICAL) subSizer = wx.BoxSizer(wx.HORIZONTAL) subSizer.Add((-1,-1),1,wx.EXPAND) subSizer.Add(wx.StaticText(G2frame.FRMC,label='RMCProfile setup'),0,WACV) subSizer.Add((-1,-1),1,wx.EXPAND) mainSizer.Add(subSizer) mainSizer.Add((5,5)) mainSizer.Add(wx.StaticText(G2frame.FRMC,label= '''"RMCProfile: Reverse Monte Carlo for polycrystalline materials", M.G. Tucker, D.A. Keen, M.T. Dove, A.L. Goodwin and Q. Hui, Jour. Phys.: Cond. Matter (2007), 19, 335218. doi: https://doi.org/10.1088/0953-8984/19/33/335218''')) mainSizer.Add((5,5)) Atypes = [atype.split('+')[0].split('-')[0] for atype in data['General']['AtomTypes']] aTypes = dict(zip(Atypes,len(Atypes)*[0.10,])) atSeq = list(aTypes.keys()) lenA = len(atSeq) atOxid = [[atmdata.BVSoxid[atm][0],0.001] for atm in atSeq] if CheckAtms(Atypes): oldPairs = data['RMC']['RMCProfile'].get('Pairs',{}) Pairs = {} # for pairs in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA) if 'Va' not in atSeq[j]] for i in range(lenA) if 'Va' not in atSeq[i]]: for pairs in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA)] for i in range(lenA)]: for pair in pairs: if pair in oldPairs: Pairs[pair] = oldPairs[pair] else: Pairs[pair] = [0.0,0.0,0.0] data['RMC']['RMCProfile'].update({'aTypes':aTypes,'atSeq':atSeq,'Pairs':Pairs,'Oxid':atOxid,}) if not data['RMC']['RMCProfile'] or 'metadata' not in RMCPdict: Pairs = {} # for pairs in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA) if 'Va' not in atSeq[j]] for i in range(lenA) if 'Va' not in atSeq[i]]: for pairs in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA)] for i in range(lenA)]: for pair in pairs: Pairs[pair] = [0.0,0.0,0.0] BVSpairs = [] if lenA > 1: # for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA) if 'Va' not in atSeq[j]] for i in range(lenA) if 'Va' not in atSeq[i]]: for pair in [[' %s-%s'%(atSeq[i],atSeq[j]) for j in range(i,lenA)] for i in range(lenA)]: BVSpairs += pair BVS = {pairs:[0.0,0.0,0.0,0.0] for pairs in BVSpairs} files = {'Neutron real space data; G(r): ':['Select',0.05,'G(r)','RMC',], 'Neutron reciprocal space data; F(Q): ':['Select',0.05,'F(Q)','RMC',], 'Neutron reciprocal space data; S(Q): ':['Select',0.05,'S(Q)','RMC',], # 'Xray real space data; G(r): ':['Select',0.01,'G(r)','RMC',], 'Xray reciprocal space data; F(Q): ':['Select',0.01,'F(Q)','RMC',],} runTimes = [10.,1.] metadata = {'title':'none','owner':'no one','date':str(time.ctime()),'temperature':'300K', 'material':'nothing','phase':'vacuum','comment':'none ','source':'nowhere'} data['RMC']['RMCProfile'].update({'SuperCell':[1,1,1],'UseSampBrd':[True,True],'aTypes':aTypes, 'histogram':['',1.0],'files':files,'metadata':metadata,'FitScale':False,'atSeq':atSeq, 'runTimes':runTimes,'ReStart':[False,False],'BVS':BVS,'Oxid':atOxid,'useBVS':False,'Swaps':[], 'AveCN':[],'FxCN':[],'Potentials':{'Angles':[],'Angle search':10.,'Stretch':[],'Pairs':Pairs, 'Stretch search':10.,'Pot. Temp.':300.,'useGPU':False,}}) # data['RMC']['RMCProfile']['aTypes'] = {aTypes[atype] for atype in aTypes if atype in Atypes} data['RMC']['RMCProfile']['Isotope'] = copy.copy(data['General']['Isotope']) data['RMC']['RMCProfile']['Isotopes'] = copy.deepcopy(data['General']['Isotopes']) data['RMC']['RMCProfile']['NoAtoms'] = copy.copy(data['General']['NoAtoms']) RMCPdict = data['RMC']['RMCProfile'] #patches if 'FitScale' not in RMCPdict: RMCPdict['FitScale'] = False if 'useGPU' not in RMCPdict: RMCPdict['useGPU'] = False #end patches def OnHisto(event): RMCPdict['histogram'][0] = histo.GetStringSelection() def OnSize(event): RMCPdict['UseSampBrd'][0] = samSize.GetValue() def OnStrain(event): RMCPdict['UseSampBrd'][1] = strain.GetValue() def OnFitScale(event): RMCPdict['FitScale'] = not RMCPdict['FitScale'] def SetRestart(invalid,value,tc): RMCPdict['ReStart'] = [True,True] def OnUseBVS(event): RMCPdict['useBVS'] = not RMCPdict['useBVS'] wx.CallAfter(UpdateRMC) def OnAddSwap(event): RMCPdict['Swaps'].append(['','',0.0,]) wx.CallAfter(UpdateRMC) def OnAddFxCN(event): RMCPdict['FxCN'].append(['','',0.5,2.0,6,1.0,0.00001]) wx.CallAfter(UpdateRMC) def OnAddAveCN(event): RMCPdict['AveCN'].append(['','',0.5,2.0,6.,0.00001]) wx.CallAfter(UpdateRMC) def OnAddAnglePot(event): RMCPdict['Potentials']['Angles'].append(['','','',0.,0.,0.,0.]) wx.CallAfter(UpdateRMC) def OnAddBondPot(event): RMCPdict['Potentials']['Stretch'].append(['','',0.,0.]) wx.CallAfter(UpdateRMC) def GetTimeSizer(): def OnUseGPU(event): RMCPdict['useGPU'] = not RMCPdict['useGPU'] timeSizer = wx.BoxSizer(wx.HORIZONTAL) timeSizer.Add(wx.StaticText(G2frame.FRMC,label=' Total running time (min): '),0,WACV) timeSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['runTimes'],0,xmin=0.,size=(70,25)),0,WACV) timeSizer.Add(wx.StaticText(G2frame.FRMC,label=' Save interval time (min): '),0,WACV) timeSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['runTimes'],1,xmin=0.1,xmax=20.,size=(50,25)),0,WACV) usegpu = wx.CheckBox(G2frame.FRMC,label=' use GPU?') usegpu.SetValue(RMCPdict['useGPU']) usegpu.Bind(wx.EVT_CHECKBOX,OnUseGPU) timeSizer.Add(usegpu,0,WACV) return timeSizer # def GetSuperSizer(Xmax): # superSizer = wx.BoxSizer(wx.HORIZONTAL) # axes = ['X','Y','Z'] # for i,ax in enumerate(axes): # superSizer.Add(wx.StaticText(G2frame.FRMC,label=' %s-axis: '%ax),0,WACV) # superSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['SuperCell'], # i,xmin=1,xmax=xamx,size=(50,25),OnLeave=SetRestart),0,WACV) # return superSizer def GetBvsSizer(pnl): def OnResetBVS(event): Obj = event.GetEventObject() pair = Indx[Obj.GetId()] pId = [key for key in RMCPdict['BVS']].index(pair)+1 nId = len(RMCPdict['BVS'])+1 dist = G2elem.GetBVS(pair,RMCPdict['atSeq'],RMCPdict['Oxid']) if dist: RMCPdict['BVS'][pair] = [dist,0.37,3.0] bvsCh = bvsSizer.GetChildren() addr = 2*nId+pId bvsCh[addr].Window.SetValue('%6.3f'%dist) bvsCh[addr+nId].Window.SetValue('0.37') bvsCh[addr+2*nId].Window.SetValue('3.00') bvsSizer = wx.FlexGridSizer(len(RMCPdict['BVS'])+1,5,5) bvsSizer.Add((5,5),0) for pair in RMCPdict['BVS']: bvsSizer.Add(wx.StaticText(pnl,label=pair),0,WACV) bvsSizer.Add(wx.StaticText(pnl,label=' Reset:'),0,WACV) for pair in RMCPdict['BVS']: reset = wx.Button(pnl,label='Yes') bvsSizer.Add(reset,0,WACV) reset.Bind(wx.EVT_BUTTON,OnResetBVS) Indx[reset.GetId()] = pair bvsSizer.Add(wx.StaticText(pnl,label=' Bond length:'),0,WACV) for pair in RMCPdict['BVS']: bvsSizer.Add(G2G.ValidatedTxtCtrl(pnl,RMCPdict['BVS'][pair],0,xmin=0.,xmax=10.,size=(50,25)),0,WACV) bvsSizer.Add(wx.StaticText(pnl,label=' B constant (0.37): '),0,WACV) for pair in RMCPdict['BVS']: bvsSizer.Add(G2G.ValidatedTxtCtrl(pnl,RMCPdict['BVS'][pair],1,xmin=0.,xmax=10.,size=(50,25)),0,WACV) bvsSizer.Add(wx.StaticText(pnl,label=' Cut off: '),0,WACV) for pair in RMCPdict['BVS']: bvsSizer.Add(G2G.ValidatedTxtCtrl(pnl,RMCPdict['BVS'][pair],2,xmin=0.,xmax=10.,size=(50,25)),0,WACV) return bvsSizer def GetFxcnSizer(): def OnDelFxCN(event): Obj = event.GetEventObject() fxCN = Indx[Obj.GetId()] del RMCPdict['FxCN'][fxCN] wx.CallAfter(UpdateRMC) def OnFxcnAtSel(event): Obj = event.GetEventObject() ifxCN,i = Indx[Obj.GetId()] RMCPdict['FxCN'][ifxCN][i] = Obj.GetStringSelection() fxcnSizer = wx.FlexGridSizer(8,5,5) atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm] fxcnLabels = [' ','Atom-1','Atom-2','min dist','max dist','CN','fraction','weight'] for lab in fxcnLabels: fxcnSizer.Add(wx.StaticText(G2frame.FRMC,label=lab),0,WACV) for ifx,fxCN in enumerate(RMCPdict['FxCN']): delBtn = wx.Button(G2frame.FRMC,label='Delete') delBtn.Bind(wx.EVT_BUTTON,OnDelFxCN) Indx[delBtn.GetId()] = ifx fxcnSizer.Add(delBtn,0,WACV) for i in [0,1]: atmSel = wx.ComboBox(G2frame.FRMC,choices=atChoice,style=wx.CB_DROPDOWN|wx.TE_READONLY) atmSel.SetStringSelection(fxCN[i]) atmSel.Bind(wx.EVT_COMBOBOX,OnFxcnAtSel) Indx[atmSel.GetId()] = [ifx,i] fxcnSizer.Add(atmSel,0,WACV) fxcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,2,xmin=0.,xmax=5.,size=(50,25)),0,WACV) fxcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,3,xmin=0.,xmax=5.,size=(50,25)),0,WACV) fxcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,4,xmin=1,xmax=12,size=(50,25)),0,WACV) fxcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,5,xmin=0.,xmax=1.,size=(50,25)),0,WACV) fxcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,6,xmin=0.,size=(50,25)),0,WACV) return fxcnSizer def GetAvcnSizer(): def OnDelAvCN(event): Obj = event.GetEventObject() fxCN = Indx[Obj.GetId()] del RMCPdict['AveCN'][fxCN] wx.CallAfter(UpdateRMC) def OnAvcnAtSel(event): Obj = event.GetEventObject() ifxCN,i = Indx[Obj.GetId()] RMCPdict['AveCN'][ifxCN][i] = Obj.GetStringSelection() avcnSizer = wx.FlexGridSizer(7,5,5) atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm] fxcnLabels = [' ','Atom-1','Atom-2','min dist','max dist','CN','weight'] for lab in fxcnLabels: avcnSizer.Add(wx.StaticText(G2frame.FRMC,label=lab),0,WACV) for ifx,fxCN in enumerate(RMCPdict['AveCN']): delBtn = wx.Button(G2frame.FRMC,label='Delete') delBtn.Bind(wx.EVT_BUTTON,OnDelAvCN) Indx[delBtn.GetId()] = ifx avcnSizer.Add(delBtn,0,WACV) for i in [0,1]: atmSel = wx.ComboBox(G2frame.FRMC,choices=atChoice,style=wx.CB_DROPDOWN|wx.TE_READONLY) atmSel.SetStringSelection(fxCN[i]) atmSel.Bind(wx.EVT_COMBOBOX,OnAvcnAtSel) Indx[atmSel.GetId()] = [ifx,i] avcnSizer.Add(atmSel,0,WACV) avcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,2,xmin=0.,xmax=5.,size=(50,25)),0,WACV) avcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,3,xmin=0.,xmax=5.,size=(50,25)),0,WACV) avcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,4,xmin=1.,xmax=12.,size=(50,25)),0,WACV) avcnSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,fxCN,5,xmin=0.,size=(50,25)),0,WACV) return avcnSizer def GetAngleSizer(): def OnDelAngle(event): Obj = event.GetEventObject() angle = Indx[Obj.GetId()] del RMCPdict['Potentials']['Angles'][angle] wx.CallAfter(UpdateRMC) def OnAngleAtSel(event): Obj = event.GetEventObject() angle,i = Indx[Obj.GetId()] RMCPdict['Potentials']['Angles'][angle][i] = Obj.GetStringSelection() def SetRestart1(invalid,value,tc): RMCPdict['ReStart'][1] = True atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm] angleSizer = wx.FlexGridSizer(8,5,5) fxcnLabels = [' ','Atom-A','Atom-B','Atom-C',' ABC angle','AB dist','BC dist','potential'] for lab in fxcnLabels: angleSizer.Add(wx.StaticText(G2frame.FRMC,label=lab),0,WACV) for ifx,angle in enumerate(RMCPdict['Potentials']['Angles']): delBtn = wx.Button(G2frame.FRMC,label='Delete') delBtn.Bind(wx.EVT_BUTTON,OnDelAngle) Indx[delBtn.GetId()] = ifx angleSizer.Add(delBtn,0,WACV) for i in [0,1,2]: atmSel = wx.ComboBox(G2frame.FRMC,choices=atChoice,style=wx.CB_DROPDOWN|wx.TE_READONLY) atmSel.SetStringSelection(angle[i]) atmSel.Bind(wx.EVT_COMBOBOX,OnAngleAtSel) Indx[atmSel.GetId()] = [ifx,i] angleSizer.Add(atmSel,0,WACV) angleSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,angle,3,xmin=0.,xmax=180.,OnLeave=SetRestart1,size=(50,25)),0,WACV) angleSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,angle,4,xmin=0.5,xmax=5.,OnLeave=SetRestart1,size=(50,25)),0,WACV) angleSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,angle,5,xmin=0.5,xmax=5.,OnLeave=SetRestart1,size=(50,25)),0,WACV) angleSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,angle,6,xmin=0.,OnLeave=SetRestart1,size=(50,25)),0,WACV) return angleSizer def GetBondSizer(): def OnDelBond(event): Obj = event.GetEventObject() bond = Indx[Obj.GetId()] del RMCPdict['Potentials']['Stretch'][bond] wx.CallAfter(UpdateRMC) def OnBondAtSel(event): Obj = event.GetEventObject() bond,i = Indx[Obj.GetId()] RMCPdict['Potentials']['Stretch'][bond][i] = Obj.GetStringSelection() def SetRestart1(invalid,value,tc): RMCPdict['ReStart'][1] = True atChoice = [atm for atm in RMCPdict['atSeq'] if 'Va' not in atm] bondSizer = wx.FlexGridSizer(5,5,5) fxcnLabels = [' ','Atom-A','Atom-B',' AB dist','potential'] for lab in fxcnLabels: bondSizer.Add(wx.StaticText(G2frame.FRMC,label=lab),0,WACV) for ifx,bond in enumerate(RMCPdict['Potentials']['Stretch']): delBtn = wx.Button(G2frame.FRMC,label='Delete') delBtn.Bind(wx.EVT_BUTTON,OnDelBond) Indx[delBtn.GetId()] = ifx bondSizer.Add(delBtn,0,WACV) for i in [0,1]: atmSel = wx.ComboBox(G2frame.FRMC,choices=atChoice,style=wx.CB_DROPDOWN|wx.TE_READONLY) atmSel.SetStringSelection(bond[i]) atmSel.Bind(wx.EVT_COMBOBOX,OnBondAtSel) Indx[atmSel.GetId()] = [ifx,i] bondSizer.Add(atmSel,0,WACV) bondSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,bond,2,xmin=0.,xmax=5.,OnLeave=SetRestart1,size=(50,25)),0,WACV) bondSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,bond,3,xmin=0.,size=(50,25)),0,WACV) return bondSizer Indx = {} mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' Enter metadata items:'),0) mainSizer.Add(GetMetaSizer(RMCPdict,['title','owner','material','phase','comment','source',]),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(GetTimeSizer(),0) mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' Lattice multipliers; if changed will force reset of atom positions:'),0) mainSizer.Add(GetSuperSizer(RMCPdict,20),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mSizer = wx.BoxSizer(wx.VERTICAL) mSizer.Add(wx.StaticText(G2frame.FRMC,label='Enter atom settings'),0) mSizer.Add(GetAtmChoice(G2frame.FRMC,RMCPdict),0) mSizer.Add(wx.StaticText(G2frame.FRMC,label=' N.B.: be sure to set cations first && anions last in atom ordering')) mainSizer.Add(mSizer) G2G.HorizontalLine(mainSizer,G2frame.FRMC) swapBox = wx.BoxSizer(wx.HORIZONTAL) swapAdd = wx.Button(G2frame.FRMC,label='Add') swapAdd.Bind(wx.EVT_BUTTON,OnAddSwap) swapBox.Add(swapAdd,0,WACV) swapBox.Add(wx.StaticText(G2frame.FRMC,label=' Atom swap probabilities: '),0,WACV) mainSizer.Add(swapBox,0) if len(RMCPdict['Swaps']): mainSizer.Add(GetSwapSizer(RMCPdict),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mSizer = wx.BoxSizer(wx.VERTICAL) mSizer.Add(wx.StaticText(G2frame.FRMC,label='Enter constraints && restraints via minimum && maximum distances for atom pairs:'),0) mSizer.Add(GetPairSizer(G2frame.FRMC,RMCPdict),0) mainSizer.Add(mSizer) G2G.HorizontalLine(mainSizer,G2frame.FRMC) useBVS = wx.CheckBox(G2frame.FRMC,label=' Use bond valence sum restraints for (set to 0 for non-bonded ones):') useBVS.SetValue(RMCPdict.get('useBVS',False)) useBVS.Bind(wx.EVT_CHECKBOX,OnUseBVS) mainSizer.Add(useBVS,0) if RMCPdict.get('useBVS',False): mSizer = wx.BoxSizer(wx.VERTICAL) mSizer.Add(GetBvsSizer(G2frame.FRMC),0) mainSizer.Add(mSizer) G2G.HorizontalLine(mainSizer,G2frame.FRMC) fxcnBox = wx.BoxSizer(wx.HORIZONTAL) fxcnAdd = wx.Button(G2frame.FRMC,label='Add') fxcnAdd.Bind(wx.EVT_BUTTON,OnAddFxCN) fxcnBox.Add(fxcnAdd,0,WACV) fxcnBox.Add(wx.StaticText(G2frame.FRMC,label=' Fixed coordination number restraint: '),0,WACV) mainSizer.Add(fxcnBox,0) if len(RMCPdict['FxCN']): mainSizer.Add(GetFxcnSizer(),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) avcnBox = wx.BoxSizer(wx.HORIZONTAL) avcnAdd = wx.Button(G2frame.FRMC,label='Add') avcnAdd.Bind(wx.EVT_BUTTON,OnAddAveCN) avcnBox.Add(avcnAdd,0,WACV) avcnBox.Add(wx.StaticText(G2frame.FRMC,label=' Average coordination number restraint: '),0,WACV) mainSizer.Add(avcnBox,0) if len(RMCPdict['AveCN']): mainSizer.Add(GetAvcnSizer(),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) pottempBox = wx.BoxSizer(wx.HORIZONTAL) pottempBox.Add(wx.StaticText(G2frame.FRMC,label=' Potential temperature (K): '),0,WACV) pottempBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['Potentials'],'Pot. Temp.',xmin=0.,xmax=1000.,size=(50,25)),0,WACV) mainSizer.Add(pottempBox,0) bondpotBox = wx.BoxSizer(wx.HORIZONTAL) bondpotAdd = wx.Button(G2frame.FRMC,label='Add') bondpotAdd.Bind(wx.EVT_BUTTON,OnAddBondPot) bondpotBox.Add(bondpotAdd,0,WACV) bondpotBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B stretch potential restraints, search range (%): '),0,WACV) bondpotBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['Potentials'],'Stretch search',xmin=0.,xmax=100.,size=(50,25)),0,WACV) mainSizer.Add(bondpotBox,0) if len(RMCPdict['Potentials']['Stretch']): mainSizer.Add(GetBondSizer(),0) angpotBox = wx.BoxSizer(wx.HORIZONTAL) angpotAdd = wx.Button(G2frame.FRMC,label='Add') angpotAdd.Bind(wx.EVT_BUTTON,OnAddAnglePot) angpotBox.Add(angpotAdd,0,WACV) angpotBox.Add(wx.StaticText(G2frame.FRMC,label=' A-B-C angle potential restraints, search range (%): '),0,WACV) angpotBox.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['Potentials'],'Angle search',xmin=0.,xmax=100.,size=(50,25)),0,WACV) mainSizer.Add(angpotBox,0) if len(RMCPdict['Potentials']['Angles']): mainSizer.Add(GetAngleSizer(),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' Select data:'),0) histograms = data['Histograms'] histNames = list(histograms.keys()) mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' Select one histogram for Bragg processing:'),0) histoSizer = wx.BoxSizer(wx.HORIZONTAL) histo = wx.ComboBox(G2frame.FRMC,choices=histNames,style=wx.CB_DROPDOWN|wx.TE_READONLY) if RMCPdict['histogram'][0] == '': RMCPdict['histogram'][0] = histo.GetStringSelection() histo.SetStringSelection(RMCPdict['histogram'][0]) histo.Bind(wx.EVT_COMBOBOX,OnHisto) histoSizer.Add(histo,0,WACV) histoSizer.Add(wx.StaticText(G2frame.FRMC,label=' Weight '),0,WACV) histoSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['histogram'],1,xmin=0.,xmax=10000.,size=(50,25)),0,WACV) mainSizer.Add(histoSizer,0) samSizer = wx.BoxSizer(wx.HORIZONTAL) samSize = wx.CheckBox(G2frame.FRMC,label=' Use size broadening?') samSize.SetValue(RMCPdict['UseSampBrd'][0]) samSize.Bind(wx.EVT_CHECKBOX,OnSize) strain = wx.CheckBox(G2frame.FRMC,label=' Use mustrain broadening?') strain.SetValue(RMCPdict['UseSampBrd'][1]) strain.Bind(wx.EVT_CHECKBOX,OnStrain) samSizer.Add(samSize,0,WACV) samSizer.Add(strain,0,WACV) fitscale = wx.CheckBox(G2frame.FRMC,label=' Fit scale factors?') fitscale.SetValue(RMCPdict['FitScale']) fitscale.Bind(wx.EVT_CHECKBOX,OnFitScale) samSizer.Add(fitscale,0,WACV) mainSizer.Add(samSizer,0) mainSizer.Add(FileSizer(RMCPdict)) return mainSizer def PDFfitSizer(data): mainSizer = wx.BoxSizer(wx.VERTICAL) Indx = {} def PDFParmSizer(): def OnShape(event): RMCPdict['shape'] = shape.GetValue() wx.CallAfter(UpdateRMC) parmSizer = wx.FlexGridSizer(3,6,5,5) Names = ['delta1','delta2','sratio','rcut','spdiameter'] Names2 = ['stepcut',] for name in Names: def OnRefine(event): Obj = event.GetEventObject() name = Indx[Obj.GetId()] RMCPdict[name][1] = not RMCPdict[name][1] if name == 'spdiameter' and RMCPdict.get('shape','sphere') != 'sphere': pass else: parmSizer.Add(wx.StaticText(G2frame.FRMC,label=name),0,WACV) if name == 'rcut': parmSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,name,xmin=0.,size=(70,25)),0,WACV) parmSizer.Add((5,5)) continue parmSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict[name],0,xmin=0.,size=(70,25)),0,WACV) refine = wx.CheckBox(G2frame.FRMC,label='Refine') refine.SetValue(RMCPdict[name][1]) refine.Bind(wx.EVT_CHECKBOX,OnRefine) Indx[refine.GetId()] = name parmSizer.Add(refine,0,WACV) parmSizer.Add(wx.StaticText(G2frame.FRMC,label=' Shape'),0,WACV) shape = wx.ComboBox(G2frame.FRMC,choices=['sphere','stepcut'],style=wx.CB_DROPDOWN|wx.TE_READONLY) shape.SetStringSelection(RMCPdict.get('shape','sphere')) shape.Bind(wx.EVT_COMBOBOX,OnShape) parmSizer.Add(shape,0,WACV) if RMCPdict.get('shape','sphere') == 'stepcut': for name in Names2: parmSizer.Add(wx.StaticText(G2frame.FRMC,label=name),0,WACV) parmSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict,name,xmin=0.,size=(70,25)),0,WACV) return parmSizer def OnSpaceGroup(event): # try a lookup on the user-supplied name SpcGp = GetSpGrpfromUser(G2frame.FRMC,SpGrp) SGErr,SGData = G2spc.SpcGroup(SpcGp) if SGErr: text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous'] SGTxt.SetLabel(RMCPdict.get('Target SpGrp','P 1')) msg = 'Space Group Error' Text = '\n'.join(text) wx.MessageBox(Text,caption=msg,style=wx.ICON_EXCLAMATION) else: text,table = G2spc.SGPrint(SGData) RMCPdict['SGData'] = SGData SGTxt.SetLabel(RMCPdict['SGData']['SpGrp']) msg = 'Target Space Group Information' G2G.SGMessageBox(G2frame.FRMC,msg,text,table).Show() G2spc.UpdateSytSym(data) def OnCellRef(event): RMCPdict['cellref'] = not RMCPdict['cellref'] def AtomSizer(): def OnSetVal(event): r,c = event.GetRow(),event.GetCol() if c > 0: strval = atmGrid.GetCellValue(r,c).strip() try: # if strval == '' or ('@' in strval and int(strval.split('@')[-1]) >= 20): if strval == '' or '@' in strval: RMCPdict['AtomConstr'][r][c+1] = strval else: raise ValueError except ValueError: atmGrid.SetCellValue(r,c,RMCPdict['AtomConstr'][r][c+1]) wx.MessageBox('ERROR - atom constraints must be blank or have "@n" with n >= 20', style=wx.ICON_ERROR) wx.CallAfter(UpdateRMC) def OnUisoRefine(event): RMCPdict['UisoRefine'] = uiso.GetValue() nextP = 80 oType = '' oName = '' for atom in RMCPdict['AtomConstr']: if RMCPdict['UisoRefine'] == 'No': atom[6] = '' elif 'same' in RMCPdict['UisoRefine']: atom[6] = '@81' RMCPdict['AtomVar']['@81'] = 0.005 elif 'type' in RMCPdict['UisoRefine']: if atom[1] != oType: oType = atom[1] nextP += 1 atom[6] = '@%d'%nextP RMCPdict['AtomVar']['@%d'%nextP] = 0.005 elif 'parent' in RMCPdict['UisoRefine']: if atom[0] != oName: oName = atom[0] nextP += 1 atom[6] = '@%d'%nextP RMCPdict['AtomVar']['@%d'%nextP] = 0.005 wx.CallAfter(UpdateRMC) atmSizer = wx.BoxSizer(wx.VERTICAL) atmSizer.Add(wx.StaticText(G2frame.FRMC,label=' Atom Constraints; enter as e.g. "@n" or "0.5-@n"; n>=20 && "@n" should be at end')) uisoSizer = wx.BoxSizer(wx.HORIZONTAL) uisoSizer.Add(wx.StaticText(G2frame.FRMC,label=' Refine Uiso? '),0,WACV) uiso = wx.ComboBox(G2frame.FRMC,choices=['No','by type','by parent name','all same'],style=wx.CB_DROPDOWN|wx.TE_READONLY) uiso.SetValue(RMCPdict['UisoRefine']) uiso.Bind(wx.EVT_COMBOBOX,OnUisoRefine) uisoSizer.Add(uiso,0,WACV) atmSizer.Add(uisoSizer) table = [item[1:] for item in RMCPdict['AtomConstr']] addCol = False if len(RMCPdict['AtomConstr'][0]) > 6: addCol = True colLabels = ['Type','x constraint','y constraint','z constraint','frac constr','Uiso constr'] rowLabels = [item[0] for item in RMCPdict['AtomConstr']] Types = 6*[wg.GRID_VALUE_STRING,] if addCol: colLabels += ['sym opr',] Types = 7*[wg.GRID_VALUE_STRING,] atmTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) atmGrid = G2G.GSGrid(G2frame.FRMC) atmGrid.SetTable(atmTable, True,useFracEdit=False) atmGrid.AutoSizeColumns(True) atmGrid.Bind(wg.EVT_GRID_CELL_CHANGED, OnSetVal) atmSizer.Add(atmGrid) return atmSizer def AtomVarSizer(): atomVarSizer = wx.FlexGridSizer(0,8,5,5) for item in RMCPdict['AtomVar']: atomVarSizer.Add(wx.StaticText(G2frame.FRMC,label=item),0,WACV) atomVarSizer.Add(G2G.ValidatedTxtCtrl(G2frame.FRMC,RMCPdict['AtomVar'], item,xmin=-3.,xmax=3.,size=(70,25)),0,WACV) return atomVarSizer subSizer = wx.BoxSizer(wx.HORIZONTAL) subSizer.Add((-1,-1),1,wx.EXPAND) subSizer.Add(wx.StaticText(G2frame.FRMC,label='For use of PDFfit, please cite:'),0,WACV) subSizer.Add((-1,-1),1,wx.EXPAND) mainSizer.Add(subSizer) mainSizer.Add((5,5)) mainSizer.Add(wx.StaticText(G2frame.FRMC,label= '''"PDFfit2 and PDFgui: computer programs for studying nanostructures in crystals", C.L. Farrow, P.Juhas, J.W. Liu, D. Bryndin, E.S. Bozin, J. Bloch, Th. Proffen && S.J.L. Billinge, J. Phys, Condens. Matter 19, 335219 (2007)., Jour. Phys.: Cond. Matter (2007), 19, 335218. doi: https://doi.org/10.1088/0953-8984/19/33/335219''')) mainSizer.Add((5,5)) if 'PDFfit' not in data['RMC'] or not data['RMC']['PDFfit'] or 'delta1' not in data['RMC']['PDFfit']: if 'PDFfit' not in data['RMC']: data['RMC']['PDFfit'] = {} metadata = {'title':'none','date':str(time.ctime()),'temperature':'300K','doping':0} files = {'Neutron real space data; G(r): ':['Select',0.05,'G(r)','RMC',], 'Xray real space data; G(r): ':['Select',0.01,'G(r)','RMC',],} data['RMC']['PDFfit'].update({'files':files,'ReStart':[False,False],'metadata':metadata, 'delta1':[0.,False],'delta2':[0.,False],'spdiameter':[0.,False],'refinement':'normal', 'sratio':[1.,False],'rcut':0.0,'stepcut':0.0,'shape':'sphere','cellref':False, 'SeqDataType':'X','SeqCopy':True,'SeqReverse':False, 'Xdata':{'dscale':[1.0,False],'Datarange':[0.,30.],'Fitrange':[0.,30.],'qdamp':[0.03,False],'qbroad':[0.,False]}, 'Ndata':{'dscale':[1.0,False],'Datarange':[0.,30.],'Fitrange':[0.,30.],'qdamp':[0.03,False],'qbroad':[0.,False]},}) RMCPdict = data['RMC']['PDFfit'] #patch if 'AtomConstr' not in RMCPdict: #keep this one RMCPdict['AtomConstr'] = [] if 'AtomVar' not in RMCPdict: RMCPdict['AtomVar'] = {} if 'SGData' not in RMCPdict: RMCPdict['SGData'] = G2spc.SpcGroup('P 1')[1] if 'refinement' not in RMCPdict: RMCPdict['refinement'] = 'normal' if 'cellref' not in RMCPdict: RMCPdict['cellref'] = False if 'metadata' not in RMCPdict: RMCPdict['metadata'] = {'title':'none','date':str(time.ctime()),'temperature':'300K','doping':0} if 'SeqDataType' not in RMCPdict: RMCPdict['SeqDataType'] = 'X' if 'SeqCopy' not in RMCPdict: RMCPdict['SeqCopy'] = False RMCPdict['SeqReverse'] = False if 'UisoRefine' not in RMCPdict: RMCPdict['UisoRefine'] = 'No' #end patch Atoms = data['Atoms'] cx,ct,cs,ci = G2mth.getAtomPtrs(data) if not RMCPdict['AtomConstr']: for atom in Atoms: RMCPdict['AtomConstr'].append([atom[ct-1],atom[ct],'','','','','']) else: #update name/type changes for iatm,atom in enumerate(Atoms): RMCPdict['AtomConstr'][iatm][:2] = atom[ct-1:ct+1] mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' Enter metadata items:'),0) mainSizer.Add(GetMetaSizer(RMCPdict,['title','date','temperature','doping']),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) SgSizer = wx.BoxSizer(wx.HORIZONTAL) SgSizer.Add(wx.StaticText(G2frame.FRMC,label=' Target space group: '),0,WACV) mainSizer.Add(wx.StaticText(G2frame.FRMC,label='PDFfit phase structure parameters:')) SpGrp = RMCPdict['SGData']['SpGrp'] SGTxt = wx.Button(G2frame.FRMC,wx.ID_ANY,SpGrp,size=(100,-1)) SGTxt.Bind(wx.EVT_BUTTON,OnSpaceGroup) SgSizer.Add(SGTxt,0,WACV) mainSizer.Add(SgSizer) cellref = wx.CheckBox(G2frame.FRMC,label=' Refine unit cell?') cellref.SetValue(RMCPdict['cellref']) cellref.Bind(wx.EVT_CHECKBOX,OnCellRef) mainSizer.Add(cellref) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(wx.StaticText(G2frame.FRMC,label='PDFfit atom parameters:')) mainSizer.Add(AtomSizer()) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(wx.StaticText(G2frame.FRMC,label='PDFfit starting atom variables:')) G2pwd.GetPDFfitAtomVar(data,RMCPdict) mainSizer.Add(AtomVarSizer()) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(wx.StaticText(G2frame.FRMC,label=' PDFfit phase profile coefficients:')) mainSizer.Add(PDFParmSizer(),0) G2G.HorizontalLine(mainSizer,G2frame.FRMC) mainSizer.Add(FileSizer(RMCPdict)) return mainSizer ####start of UpdateRMC G2frame.GetStatusBar().SetStatusText('',1) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_ATOMSRMC,False) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_SUPERRMC,False) if G2frame.RMCchoice == 'RMCProfile': G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_SETUPRMC,True) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,True) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_VIEWRMC,True) #G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_STOPRMC,False) elif G2frame.RMCchoice == 'fullrmc': G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_SETUPRMC,False) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,False) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_VIEWRMC,False) #G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_STOPRMC,False) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_ATOMSRMC,True) G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_SUPERRMC,True) try: if G2frame.FRMC.GetSizer(): G2frame.FRMC.GetSizer().Clear(True) except: #wxAssertionError from C++ pass bigSizer = wx.BoxSizer(wx.HORIZONTAL) mainSizer = wx.BoxSizer(wx.VERTICAL) if not len(data['Atoms']): mainSizer.Add(wx.StaticText(G2frame.FRMC,label='No atoms found - RMC not available for display')) return mainSizer runFile = ' ' choice = ['RMCProfile','fullrmc','PDFfit'] topSizer = wx.BoxSizer(wx.HORIZONTAL) RMCsel = wx.RadioBox(G2frame.FRMC,-1,' Select RMC method:',choices=choice) RMCsel.SetStringSelection(G2frame.RMCchoice) RMCsel.Bind(wx.EVT_RADIOBOX, OnRMCselect) topSizer.Add(RMCsel,0) topSizer.Add((20,0)) txt = wx.StaticText(G2frame.FRMC, label=' NB: if you change any of the entries below, you must redo the Operations/Setup RMC step above to apply them before doing Operations/Execute') txt.Wrap(400) topSizer.Add(txt,0) mainSizer.Add(topSizer,0) RMCmisc['RMCnote'] = wx.StaticText(G2frame.FRMC) mainSizer.Add(RMCmisc['RMCnote']) G2G.HorizontalLine(mainSizer,G2frame.FRMC) if G2frame.RMCchoice == 'fullrmc': RMCPdict = data['RMC']['fullrmc'] mainSizer.Add(fullrmcSizer(RMCPdict)) elif G2frame.RMCchoice == 'RMCProfile': RMCPdict = data['RMC']['RMCProfile'] mainSizer.Add(RMCProfileSizer(RMCPdict)) else: #PDFfit mainSizer.Add(PDFfitSizer(data)) bigSizer.Add(mainSizer,1,wx.EXPAND) bigSizer.Add(G2G.HelpButton(G2frame.FRMC,helpIndex=G2frame.dataWindow.helpKey)) SetPhaseWindow(G2frame.FRMC,bigSizer) if G2frame.RMCchoice == 'PDFfit' and not checkPDFfit(G2frame): RMCmisc['RMCnote'].SetLabel('PDFfit may not be installed or operational') elif G2frame.RMCchoice == 'fullrmc' and G2pwd.findfullrmc() is None: msg = ('The fullrmc Python image is not found.'+ ' Do you want it installed for you from '+ 'https://github.com/bachiraoun/fullrmc/tree/master/standalones?'+ '\n\n40-50 Mb (download times vary)') dlg = wx.MessageDialog(G2frame,msg,'Install fullrmc',wx.YES|wx.NO) try: dlg.CenterOnParent() result = dlg.ShowModal() finally: dlg.Destroy() if result == wx.ID_YES: wx.BeginBusyCursor() G2pwd.fullrmcDownload() wx.EndBusyCursor() else: RMCmisc['RMCnote'].SetLabel('Note that fullrmc is not installed or was not located') return mainSizer def OnSetupRMC(event): generalData = data['General'] if not G2frame.GSASprojectfile: #force a project save G2frame.OnFileSaveas(event) dName = G2frame.LastGPXdir os.chdir(dName) if G2frame.RMCchoice == 'fullrmc': RMCPdict = data['RMC']['fullrmc'] pName = G2frame.GSASprojectfile.split('.')[0] + '-' + generalData['Name'] pName = pName.replace(' ','_') G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,True) if RMCPdict['Swaps']: wx.MessageDialog(G2frame, G2G.StripIndents( '''GSAS-II does not yet fully support use of swapping in fullrmc. Edit the script by hand before using.''',True), 'No swaps yet',wx.OK).ShowModal() #--------- debug stuff # if GSASIIpath.GetConfigValue('debug'): # print('reloading',G2pwd) # import imp # imp.reload(G2pwd) #--------- end debug stuff rname = G2pwd.MakefullrmcRun(pName,data,RMCPdict) print('build of fullrmc file {} completed'.format(rname)) elif G2frame.RMCchoice == 'RMCProfile': if ' ' in generalData['Name']: wx.MessageDialog(G2frame,'ERROR: Phase name has space; change phase name','Bad phase name',wx.ICON_ERROR).ShowModal() G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,False) return dName = G2frame.LastGPXdir pName = generalData['Name'] G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,True) RMCPdict = data['RMC']['RMCProfile'] PWId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,RMCPdict['histogram'][0]) if PWId: PWDdata = G2frame.GetPWDRdatafromTree(PWId) histoName = G2frame.GPXtree.GetItemPyData(PWId)[2] Size = data['Histograms'][histoName]['Size'] Mustrain = data['Histograms'][histoName]['Mustrain'] reset = False print(G2pwd.MakeInst(PWDdata,pName,Size,Mustrain,RMCPdict['UseSampBrd'])+ ' written') backfile = G2pwd.MakeBack(PWDdata,pName) if backfile is None: print(' Chebyschev-1 background not used; no .back file written') wx.MessageDialog(G2frame,' Chebyschev-1 background not used; '+ \ 'no .back file written & RMCProfile will not run','Wrong background function',wx.OK).ShowModal() G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,False) return else: print(backfile+ ' written') print(G2pwd.MakeBragg(PWDdata,pName,data)+ ' written') if RMCPdict['ReStart'][0]: if os.path.isfile(pName+'.his6f'): os.remove(pName+'.his6f') RMC6f,reset = G2pwd.MakeRMC6f(PWDdata,pName,data,RMCPdict) print(RMC6f+ ' written') fname = G2pwd.MakeRMCPdat(PWDdata,pName,data,RMCPdict) if 'Error' in fname: print(fname) wx.MessageDialog(G2frame,fname,'Missing reflection list',wx.OK).ShowModal() G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,False) return print(fname+ ' written') print('RMCProfile file build completed') RMCPdict['ReStart'] = [False,False] if reset: wx.MessageDialog(G2frame,' Vacancies found & "Va" atoms added to list. '+ \ 'You may need to revise RMCProfile setup parameters.','Repeat Setup RMC',wx.OK).ShowModal() wx.CallAfter(UpdateRMC) else: print('RMCProfile file build failed - no histogram selected') G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,False) elif G2frame.RMCchoice == 'PDFfit': if ' ' in generalData['Name']: wx.MessageDialog(G2frame,'ERROR: Phase name has space; change phase name','Bad phase name',wx.ICON_ERROR).ShowModal() G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,False) return G2frame.dataWindow.FRMCDataEdit.Enable(G2G.wxID_RUNRMC,True) RMCPdict = data['RMC']['PDFfit'] msg = G2pwd.MakePDFfitAtomsFile(data,RMCPdict) if msg: G2G.G2MessageBox(G2frame,'ERROR: '+msg,'PDFfit setup failure') return fname = G2pwd.MakePDFfitRunFile(data,RMCPdict) if fname is None: wx.MessageDialog(G2frame,'ERROR: failure to setup PDFfit; check console','PDFfit setup failure',wx.ICON_ERROR).ShowModal() else: print(fname+ ' written') print('PDFfit file build completed') def RunPDFfit(event): generalData = data['General'] ISOdict = data['ISODISTORT'] PDFfit_exec,_ = G2pwd.findPDFfit() #returns location of python with PDFfit installed and path(s) for pdffit if not PDFfit_exec: wx.MessageBox(''' PDFfit2 is not currently installed for this platform. Please contact us for assistance''',caption='No PDFfit2',style=wx.ICON_INFORMATION) return RMCPdict = data['RMC']['PDFfit'] pName = generalData['Name'].replace(' ','_') if 'sequential' in RMCPdict['refinement']: rname = 'Seq_PDFfit.py' else: rname = pName+'-PDFfit.py' if not os.path.exists(rname): wx.MessageBox(f'File {rname} does not exist. Has the Operations/"Setup RMC" menu command been run?', caption='Run setup',style=wx.ICON_WARNING) return wx.MessageBox(''' For use of PDFfit2, please cite: PDFfit2 and PDFgui: computer progerama for studying nanostructures in crystals, C.L. Farrow, P.Juhas, J.W. Liu, D. Bryndin, E.S. Bozin, J. Bloch, Th. Proffen & S.J.L. Billinge, J. Phys, Condens. Matter 19, 335219 (2007)., Jour. Phys.: Cond. Matter (2007), 19, 335218. doi: https://doi.org/10.1088/0953-8984/19/33/335219''', caption='PDFfit2',style=wx.ICON_INFORMATION) G2frame.OnFileSave(event) print (' GSAS-II project saved') if sys.platform.lower().startswith('win'): batch = open('pdffit2.bat','w') # Include an activate command here p = os.path.split(PDFfit_exec)[0] while p: if os.path.exists(os.path.join(p,'Scripts','activate')): batch.write('call '+os.path.join(p,'Scripts','activate')+'\n') break prevp = p p = os.path.split(p)[0] if prevp == p: print('Note, no activate command found') break batch.write(PDFfit_exec+' '+rname+'\n') # batch.write('pause') if 'normal' in RMCPdict['refinement']: batch.write('pause') batch.close() else: batch = open('pdffit2.sh','w') batch.write('#!/bin/bash\n') # include an activate command here p = os.path.split(PDFfit_exec)[0] while p: if os.path.exists(os.path.join(p,'bin','activate')): batch.write('source '+os.path.join(p,'Scripts','activate')+'\n') break prevp = p p = os.path.split(p)[0] if prevp == p: print('Note, no activate command found') break batch.write('cd ' + os.path.split(os.path.abspath(rname))[0] + '\n') batch.write(PDFfit_exec + ' ' + os.path.abspath(rname) + '\n') batch.close() if 'sequential' in RMCPdict['refinement']: Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential PDFfit2 results') # if Id: # saveSeqResult = G2frame.GPXtree.GetItemPyData(Id) # else: if not Id: SeqResult = {} Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Sequential PDFfit2 results') G2Names = [item.name for item in ISOdict['G2ModeList']] SeqResult = {'SeqPseudoVars':{},'SeqParFitEqList':[]} SeqResult['histNames'] = [] #this clears the previous seq. result! SeqNames = [] for itm in range(len(RMCPdict['seqfiles'])): SeqNames.append([itm,RMCPdict['seqfiles'][itm][0]]) if RMCPdict['SeqReverse']: SeqNames.reverse() nPDF = len(SeqNames) pgbar = wx.ProgressDialog('Sequential PDFfit','PDF G(R) done = 0',nPDF+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) newParms = {} for itm,Item in enumerate(SeqNames): PDFfile = RMCPdict['seqfiles'][Item[0]] pfdata = PDFfile[1]['G(R)'][1].T # pfname = PDFfile[0].replace(' ','_') pfname = 'Seq_PDF.gr' pfile = open(pfname,'w') for dp in pfdata: pfile.write('%12.5f%12.5f\n'%(dp[0],dp[1])) pfile.close() rfile = open('Seq_PDFfit_template.py','r') lines = rfile.readlines() #template lines rfile.close() newlines = [] parms = {} Np = 0 for line in lines: if '#sequential' in line: newlines += "pf.read_data('%s', '%s', 30.0, %.4f)\n"%(pfname,PDFfile[1]['Type'][0],PDFfile[1]['qdamp'][0]) newlines += 'pf.setdata(1)\n' newlines += 'pf.pdfrange(1, %6.2f, %6.2f)\n'%(PDFfile[1]['Fitrange'][0],PDFfile[1]['Fitrange'][1]) for item in ['dscale','qdamp','qbroad']: if PDFfile[1][item][1]: Np += 1 newlines += 'pf.constrain(pf.%s(),"@%d")\n'%(item,Np) parms[item] = '%d'%Np if itm and RMCPdict['SeqCopy']: newParms[parms[item]] = RMCPdict['Parms'][parms[item]] else: if not itm and 'result' not in PDFfile[1]: newParms[parms[item]] = PDFfile[1][item][0] else: newParms[parms[item]] = PDFfile[1]['result'][parms[item]][0] elif '#parameters' in line: startParms = RMCPdict['Parms'] if newParms or RMCPdict['SeqCopy']: if newParms: startParms = newParms for iprm in startParms: if int(iprm) > 9: break newlines += 'pf.setpar(%s,%.6f)\n'%(iprm,startParms[iprm]) print('Begin dscale: %d %.4f'%(itm,startParms['1'])) for iprm in RMCPdict['Parms']: if isinstance(RMCPdict['Parms'][iprm],float): newlines += 'pf.setpar(%s,%.6f)\n'%(iprm,RMCPdict['Parms'][iprm]) else: newlines += 'pf.setpar(%s,%.6f)\n'%(iprm,RMCPdict['Parms'][iprm][0]) elif not RMCPdict['SeqCopy']: startParms = PDFfile[1]['result'] for iprm in startParms: newlines += 'pf.setpar(%s,%.6f)\n'%(iprm,startParms[iprm][0]) print('Begin dscale: %d %.4f'%(itm,startParms['1'])) else: newlines += line rfile= open('Seq_PDFfit.py','w') rfile.writelines(newlines) rfile.close() fName = 'Sequential_PDFfit' #clean out old PDFfit output files if os.path.isfile(fName+'.res'): os.remove(fName+'.res') if os.path.isfile(fName+'.rstr'): os.remove(fName+'.rstr') if os.path.isfile(fName+'.fgr'): os.remove(fName+'.fgr') if sys.platform.lower().startswith('win'): Proc = subp.Popen('pdffit2.bat',creationflags=subp.CREATE_NEW_CONSOLE) Proc.wait() #for it to finish before continuing on else: if sys.platform == "darwin": GSASIIpath.MacRunScript(os.path.abspath('pdffit2.sh')) else: Proc = subp.Popen(['/bin/bash','pdffit2.sh']) Proc.wait() newParms,Rwp = G2pwd.UpdatePDFfit(data,RMCPdict) if isinstance(newParms,str): wx.MessageBox('Singular matrix in PDFfit',caption='PDFfit2 failed',style=wx.ICON_INFORMATION) break for item in ['dscale','qdamp','qbroad']: if PDFfile[1][item][1]: PDFfile[1][item][0] = newParms[parms[item]][0] PDFfile[1]['result'] = copy.deepcopy(newParms) parmDict = copy.deepcopy(newParms) parmDict.update({'Temperature':PDFfile[1]['Temp']}) tempList = ['%s-%s'%(parms[item],item) for item in parms] #these come first parmkeys = [int(item) for item in RMCPdict['ParmNames']] parmkeys.sort() tempList += ['%s-%s'%(item,RMCPdict['ParmNames'][item]) for item in parmkeys] print('result dscale: ',parmDict['1'],' Rw: ',Rwp) atParms = [str(i+21) for i in range(len(G2Names))] varyList = [] for item in tempList: pid = item.split('-')[0] if pid in atParms: item = '%s-%s'%(pid,G2Names[int(pid)-21]) varyList.append(item) result = np.array(list(newParms.values())).T SeqResult[PDFfile[0]] = {'variables':result[0],'varyList':varyList,'sig':result[1],'Rvals':{'Rwp':Rwp,}, 'covMatrix':[],'title':PDFfile[0],'parmDict':parmDict} pfile = open('Sequential_PDFfit.fgr') XYcalc = np.loadtxt(pfile).T[:2] pfile.close() pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,PDFfile[0]) PDFctrl = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,'PDF Controls')) XYobs = PDFctrl['G(R)'][1] if XYobs.shape[0] < 4: XYobs = np.concatenate((XYobs,np.zeros_like(XYobs)),axis=0) ibeg = np.searchsorted( XYobs[0],XYcalc[0][0]) ifin = ibeg+XYcalc.shape[1] XYobs[2][ibeg:ifin] = XYcalc[1] XYobs[3] = XYobs[1]-XYobs[2] PDFctrl['G(R)'][1] = XYobs SeqResult['histNames'].append(Item[1]) GoOn = pgbar.Update(itm,newmsg='PDF G(R) done = %d'%(itm)) if not GoOn[0]: print(' Sequential PDFfit aborted') break pgbar.Destroy() G2frame.GPXtree.SetItemPyData(Id,SeqResult) G2frame.G2plotNB.Delete('Sequential refinement') #clear away probably invalid plot G2frame.GPXtree.SelectItem(Id) else: #normal #remove any old PDFfit output files fName = generalData['Name'].replace(' ','_')+'-PDFfit' if os.path.isfile(fName+'.res'): os.remove(fName+'.res') if os.path.isfile(fName+'.rstr'): os.remove(fName+'.rstr') if os.path.isfile(fName+'N.fgr'): os.remove(fName+'N.fgr') if os.path.isfile(fName+'X.fgr'): os.remove(fName+'X.fgr') if sys.platform.lower().startswith('win'): Proc = subp.Popen('pdffit2.bat',creationflags=subp.CREATE_NEW_CONSOLE) Proc.wait() #for it to finish before continuing on else: if sys.platform == "darwin": GSASIIpath.MacRunScript(os.path.abspath('pdffit2.sh')) else: Proc = subp.Popen(['/bin/bash','pdffit2.sh']) Proc.wait() #for it to finish before continuing on #update choice? here? dlg = wx.MessageDialog(G2frame,'Check PDFfit console for results; do you want to update?', 'PDFfit run finished',wx.YES|wx.NO) try: dlg.CenterOnParent() result = dlg.ShowModal() finally: dlg.Destroy() if result == wx.ID_YES: Error = G2pwd.UpdatePDFfit(data,RMCPdict) if Error: wx.MessageBox('PDFfit failed',caption='%s not found'%Error[0],style=wx.ICON_EXCLAMATION) UpdateRMC() def Runfullrmc(event): fullrmc_exec = G2pwd.findfullrmc() if fullrmc_exec is None: G2G.G2MessageBox(G2frame,'fullrmc Python not found. How did we get here?') return generalData = data['General'] pName = G2frame.GSASprojectfile.split('.')[0] + '-' + generalData['Name'] pName = pName.replace(' ','_') rname = pName+'-fullrmc.py' if not os.path.exists(rname): G2G.G2MessageBox(G2frame,'The fullrmc script has not been created. Running setup.', 'Not setup') OnSetupRMC(event) RMCPdict = data['RMC']['fullrmc'] rmcname = pName+'-fullrmc.rmc' if os.path.isdir(rmcname) and RMCPdict['ReStart'][0]: msg = '''You have asked to start a new fullrmc run rather than continue the existing {} run. %%Press "Yes" to continue, deleting this previous run or "No" to change the restart checkbox to continue from the previous results.'''.format(rmcname) dlg = wx.MessageDialog(G2frame,G2G.StripIndents(msg,True), 'Restart or continue',wx.YES|wx.NO) try: dlg.CenterOnParent() result = dlg.ShowModal() finally: dlg.Destroy() if result == wx.ID_YES: import shutil shutil.rmtree(rmcname) else: return G2G.G2MessageBox(G2frame, '''For use of fullrmc, please cite: "Atomic Stochastic Modeling & Optimization with fullrmc", B. Aoun, J. Appl. Cryst. 2022, 55(6) 1664-1676, DOI: 10.1107/S1600576722008536. "Fullrmc, a Rigid Body Reverse Monte Carlo Modeling Package Enabled with Machine Learning and Artificial Intelligence", B. Aoun, Jour. Comp. Chem. 2016, 37, 1102-1111. DOI: 10.1002/jcc.24304 Note: A more advanced version of fullrmc can be found at www.fullrmc.com''', 'Please cite fullrmc') ilog = 0 while True: logname = '%s_%d.log'%(pName,ilog) if os.path.isfile(logname): if GSASIIpath.GetConfigValue('debug'): print('removing',logname) os.remove(logname) else: break ilog += 1 if sys.platform.lower().startswith('win'): batch = open('fullrmc.bat','w') #batch.write('CALL '+sys.exec_prefix+'\\Scripts\\activate\n') batch.write(fullrmc_exec+' '+rname+'\n') batch.write('pause') batch.close() Proc = subp.Popen('fullrmc.bat',creationflags=subp.CREATE_NEW_CONSOLE) Proc.wait() #for it to finish before continuing on else: batch = open('fullrmc.sh','w') batch.write('#!/bin/bash\n') #activate = os.path.split(os.environ.get('CONDA_EXE',''))[0] +'/activate' batch.write('cd ' + os.path.split(os.path.abspath(rname))[0] + '\n') #if os.path.exists(activate): # batch.write('source ' + activate + ' ' + # os.environ['CONDA_DEFAULT_ENV'] +'\n') # batch.write('python ' + rname + '\n') #else: # batch.write(sys.exec_prefix+'/python ' + rname + '\n') batch.write(fullrmc_exec + ' ' + os.path.abspath(rname) + '\n') batch.close() if sys.platform == "darwin": GSASIIpath.MacRunScript(os.path.abspath('fullrmc.sh')) else: Proc = subp.Popen(['/bin/bash','fullrmc.sh']) # Proc.wait() #for it to finish before continuing on UpdateRMC() def RunRMCProfile(event): generalData = data['General'] pName = generalData['Name'].replace(' ','_') rmcfile = G2fl.find('rmcprofile.exe',GSASIIpath.path2GSAS2) if rmcfile is None: wx.MessageBox(''' RMCProfile is not correctly installed for use in GSAS-II Obtain the zip file distribution from www.rmcprofile.org, unzip it and place the RMCProfile main directory in the main GSAS-II directory ''', caption='RMCProfile',style=wx.ICON_INFORMATION) return rmcexe = os.path.split(rmcfile)[0] print(rmcexe) wx.MessageBox(''' For use of RMCProfile, please cite: RMCProfile: Reverse Monte Carlo for polycrystalline materials, M.G. Tucker, D.A. Keen, M.T. Dove, A.L. Goodwin and Q. Hui, Jour. Phys.: Cond. Matter 2007, 19, 335218. doi: https://doi.org/10.1088/0953-8984/19/33/335218''', caption='RMCProfile',style=wx.ICON_INFORMATION) if os.path.isfile(pName+'.his6f'): os.remove(pName+'.his6f') if os.path.isfile(pName+'.xray'): os.remove(pName+'.xray') if os.path.isfile(pName+'.neigh'): os.remove(pName+'.neigh') if os.path.isfile(pName+'.bonds'): os.remove(pName+'.bonds') if os.path.isfile(pName+'.triplets'): os.remove(pName+'.triplets') i = 1 while True: if os.path.isfile(pName+'.bondodf_%d'%i): os.remove(pName+'.bondodf_%d'%i) os.remove(pName+'_bondplot_%d.ppm'%i) i += 1 else: break i = 1 while True: if os.path.isfile(pName+'_anglehist_%d.csv'%i): os.remove(pName+'_anglehist_%d.csv'%i) i += 1 else: break G2frame.OnFileSave(event) print (' GSAS-II project saved') pName = generalData['Name'].replace(' ','_') exstr = rmcexe+'\\rmcprofile.exe '+pName batch = open('runrmc.bat','w') batch.write('Title RMCProfile\n') batch.write(exstr+'\n') batch.write('pause\n') batch.close() Proc = subp.Popen('runrmc.bat',creationflags=subp.CREATE_NEW_CONSOLE) # Proc.wait() #for it to finish before continuing on UpdateRMC() def OnRunRMC(event): '''Run a previously created RMCProfile/fullrmc/PDFfit2 script ''' if G2frame.RMCchoice == 'fullrmc': Runfullrmc(event) elif G2frame.RMCchoice == 'RMCProfile': RunRMCProfile(event) elif G2frame.RMCchoice == 'PDFfit': RunPDFfit(event) # def OnStopRMC(event): # if G2frame.RMCchoice == 'fullrmc': # generalData = data['General'] # pName = G2frame.GSASprojectfile.split('.')[0] + '-' + generalData['Name'] # pName = pName.replace(' ','_') # engineFilePath = pName+'.rmc' # if not os.path.exists(engineFilePath): # print('fullrmc repository {} not found'.format(engineFilePath)) # return # try: # from fullrmc import InterceptHook # hook = InterceptHook(path=engineFilePath) # hook.stop_engine() # print('hook.stop_engine() sent to {}'.format(engineFilePath)) # except Exception as msg: # print('failed, msg=',msg) def OnLoadRMC(event): '''Used to load the output from fullrmc with all atoms placed in the original cell ''' fullrmcLoadPhase(super=False) def OnLoadRMCsuper(event): '''Used to load the output from fullrmc with atoms in the simulation supercell cell ''' fullrmcLoadPhase(super=True) def fullrmcLoadPhase(super): '''Used to load the output from fullrmc. Creates a new phase, reads all atoms & converts coordinates to fractional. If super is False all atoms placed in the original cell. Called from :func:`OnLoadRMC` or :func:`OnLoadRMCsuper` from the RMC tab Operations menu commands 'Superimpose into cell' and 'Load Supercell'. ''' if G2frame.RMCchoice != 'fullrmc': print('fullrmcLoadPhase: How did this happen?') return # create a new phase phId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases') phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree() phaseNameList = list(usedHistograms.keys()) # phase names in use PhaseName = G2obj.MakeUniqueLabel(data['General']['Name']+'_fullrmc',phaseNameList) psub = G2frame.GPXtree.AppendItem(parent=phId,text=PhaseName) E,SGData = G2spc.SpcGroup('P 1') G2frame.GPXtree.SetItemPyData(psub,G2obj.SetNewPhase(Name=PhaseName,SGData=SGData)) newPhase = G2frame.GPXtree.GetItemPyData(psub) # read in info from file pName = (G2frame.GSASprojectfile.split('.')[0] + '-' + data['General']['Name']) pName = pName.replace(' ','_') try: with open(pName+'-fullrmc.atoms','r') as fp: cell = [float(i) for i in fp.readline().split(':')[1].split()] supercell = [int(i) for i in fp.readline().split(':')[1].split()] if super: for i in range(3): cell[i] *= supercell[i] # set cell & volume newPhase['General']['Cell'][1:7] = cell newPhase['General']['Cell'][7] = G2lat.calc_V(G2lat.cell2A(cell)) A,B = G2lat.cell2AB(cell) # add atoms for line in fp: Name,El,ox,oy,oz = line.split() oxyz = [float(i) for i in (ox,oy,oz)] if super: (x,y,z) = np.inner(B,oxyz) else: (x,y,z),disp = G2spc.MoveToUnitCell(np.inner(B,oxyz)) atId = ran.randint(0,sys.maxsize) newPhase['Atoms'].append([Name,El,'',x,y,z,1.,'1',1,'I',0.01,0,0,0,0,0,0,atId]) except: G2G.G2MessageBox(G2frame, 'Unable to open or read file '+pName+'-fullrmc.atoms. ' 'Was a fullrmc run from the current .gpx file ' 'and for the current phase?', 'Error on read') G2frame.GPXtree.Delete(psub) return # add a restraint tree entry for new phase subr = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints') G2frame.GPXtree.GetItemPyData(subr).update({PhaseName:{}}) SetupGeneral() # index elements #wx.CallAfter(G2frame.GPXtree.SelectItem,psub) # should call SelectDataT def OnViewRMC(event): if G2frame.RMCchoice == 'fullrmc': RMCPdict = data['RMC']['fullrmc'] generalData = data['General'] pName = G2frame.GSASprojectfile.split('.')[0] + '-' + generalData['Name'] pName = pName.replace(' ','_') engineFilePath = pName+'-fullrmc.rmc' if not os.path.exists(engineFilePath): dlg = wx.FileDialog(G2frame, 'Open fullrmc directory', defaultFile='*.rmc',wildcard='*.rmc') try: if dlg.ShowModal() == wx.ID_OK: engineFilePath = dlg.GetPath() else: return finally: dlg.Destroy() engineFilePath = os.path.splitext(engineFilePath)[0] + '.rmc' if not os.path.exists(engineFilePath): return choices = [] statFilePath = os.path.splitext(engineFilePath)[0] + '.stats' plotFilePath = os.path.splitext(engineFilePath)[0] + '.plots' imgDict = {} if os.path.exists(statFilePath): fp = open(statFilePath,'r') vals = [] for i,line in enumerate(fp): v = line.strip().split(',')[:-1] # ends with comma, remove last empty element if i == 0: lbls = [i.strip() for i in v[1:]] continue try: vals.append([float(i) for i in v]) except: print('Error reading line ',i,'in',statFilePath) fp.close() steps = np.array(vals)[:,0] yvals = np.array(vals)[:,1:].T choices = ['Constraints vs. Steps'] if os.path.exists(plotFilePath): import pickle fp = open(plotFilePath,'rb') while True: try: title = pickle.load(fp) imgDict[title] = fp.tell() im = pickle.load(fp) choices += [title] except: break fp.close() if not choices: G2G.G2MessageBox(G2frame, 'Nothing to plot. '+ 'No results in '+statFilePath+' or '+plotFilePath, 'Nothing to plot') return dlg = G2G.G2MultiChoiceDialog(G2frame,'Select plots to see displayed.', 'Select plots',choices) try: result = dlg.ShowModal() if result == wx.ID_OK: selectedPlots = [choices[i] for i in dlg.GetSelections()] else: return finally: dlg.Destroy() for plt in selectedPlots: if plt in imgDict: fp = open(plotFilePath,'rb') fp.seek(imgDict[plt]) try: im = pickle.load(fp) G2plt.PlotRawImage(G2frame,im,plt) except: pass fp.close() else: plotLbls = [] plotVals = [] for lbl,row in zip(lbls,yvals): # deal with <=0 costs if sum(row**2) == 0: continue # drop if all zeros if min(row) <= 0: row = np.where(row>0,row,min(row[np.where(row>0)])/10.) plotLbls.append(lbl) plotVals.append([steps,np.log10(row)]) title = 'fullrmc residuals for '+pName G2plt.PlotXY(G2frame,plotVals, labelX='generated steps', labelY=r'$log_{10}$ ($\mathsf{\chi^2})$', newPlot=True,Title=title, lines=True,names=plotLbls) return elif G2frame.RMCchoice == 'RMCProfile': generalData = data['General'] RMCPdict = data['RMC']['RMCProfile'] pName = generalData['Name'].replace(' ','_') dlg = wx.FileDialog(G2frame, "Choose any RMCProfile csv results file for "+pName+":", defaultDir=G2frame.LastGPXdir,style=wx.FD_CHANGE_DIR,wildcard='RMCProfile result csv files|'+pName+'*.csv') if dlg.ShowModal() == wx.ID_OK: path = os.path.split(dlg.GetPath())[0] dlg.Destroy() else: dlg.Destroy() return ifXray = False ifNeut = False try: datFile = open(os.path.join(path,pName+'.dat'),'r') datLines = datFile.readlines() datFile.close() for line in datLines: if 'xray' in line: ifXray = True except: pass files = {'_PDF1.csv':[],'_PDF2.csv':[],'_PDFpartials.csv':[],'_SQ1.csv':[],'_SQ2.csv':[],'_XFQ1.csv':[], '_SQ1partials.csv':[],'_SQ2partials.csv':[],'_FQ1.csv':[],'_FT_XFQ1.csv':[], '_FQ1partials.csv':[],'_bragg.csv':[],'.chi2':[]} for item in files: if os.path.exists(os.path.join(path,pName+item)): OutFile = open(pName+item,'r') files[item] = OutFile.readlines() OutFile.close() print('RMCProfile file %s read'%(pName+item)) # else: # print('RMCProfile file %s not found'%(pName+item)) #total result plots Labels = {'_PDF1.csv':[r'$\mathsf{R,\AA}$','G(R)','RMCP G(R) for '], '_PDF2.csv':[r'$\mathsf{R,\AA}$','G(R)','RMCP G(R)-2 for '], '_SQ1.csv':[r'$\mathsf{Q,\AA^{-1}}$','S(Q)','RMCP S(Q) for '], '_SQ2.csv':[r'$\mathsf{Q,\AA^{-1}}$','S(Q)','RMCP S(Q)-2 for '], '_FQ1.csv':[r'$\mathsf{Q,\AA^{-1}}$','S(Q)','RMCP x-ray S(Q) for '], '_FT_XFQ1.csv':[r'$\mathsf{R,\AA}$','g(R)','RMCP x-ray g(R) for '], '_bragg.csv':[r'$\mathsf{TOF,\mu s}$','Normalized Intensity','RMCP bragg for ']} Ysave = [] for label in Labels: X = [] Yobs = [] Ycalc = [] if len(files[label]): if 'PDF1' in label: ifNeut = True Names = files[label][0][:-1].split(',') Xmax = 100. if 'XFQ' in label: Xmax = RMCPdict.get('Rmax',100.) for line in files[label][1:]: items = line.split(',') if 'XFQ' in label and float(items[0]) > Xmax: break X.append(float(items[0])) Yobs.append(float(items[2])) Ycalc.append(float(items[1])) Yobs = np.array([X,Yobs]) Ycalc = np.array([X,Ycalc]) if '(R)' in Labels[label][1]: Ysave.append(Ycalc) Ymin = Ysave[0][1][0] if 'bragg' in label: Ydiff = np.array([X,(Yobs-Ycalc)[1]]) Yoff = np.max(Ydiff[1])-np.min(Yobs[1]) Ydiff[1] -= Yoff if ifXray: Labels[label][0] = r'$\mathsf{2\theta ,deg}$' Labels[label][1] = 'Intensity' G2plt.PlotXY(G2frame,[Yobs,Ycalc],XY2=[Ydiff,],labelX=Labels[label][0], labelY=Labels[label][1],newPlot=True,Title=Labels[label][2]+pName, lines=True,names=Names[1:]) else: G2plt.PlotXY(G2frame,[Ycalc,Yobs],labelX=Labels[label][0], labelY=Labels[label][1],newPlot=True,Title=Labels[label][2]+pName, lines=True,names=Names[1:]) RMCPdict[pName+label] = np.sum(Ycalc[1])/np.sum(Yobs[1]) print(' %s scale Ycalc/Yobs: %.4f'%(label,RMCPdict[pName+label])) #partials plots Labels = {'_PDFpartials.csv':[r'$\mathsf{R,\AA}$','G(R)','RMCP G(R) partials for '], '_SQ1partials.csv':[r'$\mathsf{Q,\AA^{-1}}$','S(Q)','RMCP S(Q) partials for '], '_SQ2partials.csv':[r'$\mathsf{Q,\AA^{-1}}$','S(Q)-2','RMCP S(Q) partials for '], '_FQ1partials.csv':[r'$\mathsf{Q,\AA^{-1}}$','F(Q)','RMCP F(Q) partials for ']} for label in Labels: X = [] Partials = [] if len(files[label]): Names = files[label][0][:-1].split(',') for line in files[label][1:]: items = line.split(',')[:-1] X.append(float(items[0])) Partials.append([float(item) for item in items[1:]]) X = np.array(X) DX = X[1]-X[0] #should be 0.02 Partials = np.array(Partials).T if 'Q' in label: continue #skip these partials XY = [[X.T,Y.T] for iy,Y in enumerate(Partials) if 'Va' not in Names[iy+1]] else: if ifNeut: XY = [[X.T,(DX*Y.T)] for iy,Y in enumerate(Partials) if 'Va' not in Names[iy+1]] else: XY = [[X.T,(DX*Y.T)*X.T] for iy,Y in enumerate(Partials) if 'Va' not in Names[iy+1]] Names = [name for name in Names if 'Va' not in name] ylabel = Labels[label][1] if 'G(R)' in Labels[label][1]: if ifNeut: title = 'Neutron '+Labels[label][2]+pName else: continue #skip for now - x-ray partials are missing header record title = 'X-ray '+Labels[label][2].replace('G','g')+pName ylabel = 'g(R)' sumAtm = 0 BLtables = G2elem.GetBLtable(generalData) AtNum = generalData['NoAtoms'] if ifNeut: for atm in AtNum: sumAtm += AtNum[atm] else: for atm in AtNum: sumAtm += AtNum[atm]*G2elem.GetFFtable([atm,])[atm]['Z'] bfac = {} bcorr = [] for atm in AtNum: if ifNeut: if 'SL' in BLtables[atm][1]: bfac[atm] = 10.*BLtables[atm][1]['SL'][0]*AtNum[atm]/sumAtm #scale to pm else: #resonant scatters (unlikely!) bfac[atm] = AtNum[atm]/sumAtm else: bfac[atm] = 10.*G2elem.GetFFtable([atm,])[atm]['Z']*AtNum[atm]/sumAtm for name in Names: if '-' in name: at1,at2 = name.strip().split('-') if 'Va' in name: bcorr.append(0.) else: bcorr.append(bfac[at1]*bfac[at2]) if at1 == at2: bcorr[-1] /= 2. #no double counting for ixy,xy in enumerate(XY): xy[1] *= bcorr[ixy] xy[1] += Ymin Xmax = np.searchsorted(Ysave[0][0],XY[0][0][-1]) G2plt.PlotXY(G2frame,XY2=XY,XY=[Ysave[0][:,0:Xmax],],labelX=Labels[label][0], labelY=ylabel,newPlot=True,Title=title, lines=False,names=[r' $G(R)_{calc}$',]+Names[1:]) else: G2plt.PlotXY(G2frame,XY,labelX=Labels[label][0], labelY=ylabel,newPlot=True,Title=Labels[label][2]+pName, lines=True,names=Names[1:]) #chi**2 plot X = [] Chi = [] if len(files['.chi2']) > 2: Names = files['.chi2'][0][:-1].split() for line in files['.chi2'][1:]: items = line[:-1].split() X.append(float(items[1])) Chi.append([float(item) for item in items[3:]]) X = np.array(X) Chi = np.array(Chi).T XY = [[X.T,np.log10(Y.T)] for Y in Chi] G2plt.PlotXY(G2frame,XY,labelX='no. generated', labelY=r'$log_{10}$ (reduced $\mathsf{\chi^2})$',newPlot=True,Title='RMCP Chi^2 for '+pName, lines=True,names=Names[3:]) #get atoms from rmc6f file rmc6fName = pName+'.rmc6f' rmc6f = open(rmc6fName,'r') rmc6fAtoms = [] while True: line = rmc6f.readline() if 'Number of atoms:' in line: Natm = int(line.split(':')[1]) if 'Atoms:' in line: break for iAtm in range(Natm): line = rmc6f.readline().split() rmc6fAtoms.append([line[1],float(line[3]),float(line[4]),float(line[5])]) rmc6f.close() #alt bond histograms - from rmc6 & bond files bondName = pName+'.bonds' if os.path.exists(os.path.join(path,bondName)): nBond = len(RMCPdict['Potentials']['Stretch']) bondList = [] bonds = open(bondName,'r') while True: line = bonds.readline() if '............' in line: break #positions at start of 1st bond list for iBond in range(nBond): bondList.append([]) Bonds = RMCPdict['Potentials']['Stretch'][iBond] for iAtm in range(Natm): #same as in rmc6f above line = bonds.readline().split('::') if Bonds[0] in line[0]: items = line[1].replace(';','').split()[:-1:2] items = np.array([int(item) for item in items]) bondList[iBond].append([iAtm,items]) bonds.close() for iBond in range(nBond): Bonds = RMCPdict['Potentials']['Stretch'][iBond] title = '%s-%s'%(Bonds[0],Bonds[1]) bondDist = G2pwd.GetRMCBonds(generalData,RMCPdict,rmc6fAtoms,bondList[iBond]) print('%s mean %.3f(%d)'%(title,np.mean(bondDist),int(1000*np.std(bondDist)))) G2plt.PlotBarGraph(G2frame,bondDist,Xname=r'$Bond, \AA$',Title=title+' from Potential Energy Restraint', PlotName='%s Bond for %s'%(title,pName)) print(' %d %s bonds found'%(len(bondDist),title)) #alt angle histograms - from rmc6 & triplets files tripName = pName+'.triplets' if os.path.exists(os.path.join(path,tripName)): nAng = len(RMCPdict['Potentials']['Angles']) tripList = [] triples = open(tripName,'r') while True: line = triples.readline() if '............' in line: break #positions at start of 1st triple list for iAng in range(nAng): tripList.append([]) Angles = RMCPdict['Potentials']['Angles'][iAng] for iAtm in range(Natm): #same as in rmc6f above line = triples.readline().split('::') if Angles[1] in line[0]: items = line[1].replace(';','').split()[:-1:2] items = np.array([int(item) for item in items]).reshape((-1,2)) tripList[iAng].append([iAtm,items]) line = triples.readline() #to skip a line triples.close() for iAng in range(nAng): Angles = RMCPdict['Potentials']['Angles'][iAng] angles = G2pwd.GetRMCAngles(generalData,RMCPdict,rmc6fAtoms,tripList[iAng]) title = '%s-%s-%s'%(Angles[0],Angles[1],Angles[2]) print('%s mean %.2f(%d)'%(title,np.mean(angles),int(100*np.std(angles)))) G2plt.PlotBarGraph(G2frame,angles,Xname=r'$Angle, \AA$',Title=title+' from Potential Energy Restraint', PlotName='%s Angle for %s'%(title,pName)) print(' %d %s angles found'%(len(angles),title)) #bond odf plots nPot = len(RMCPdict['Potentials']['Stretch']) for iPot in range(nPot): fname = pName+'.bondodf_%d'%(iPot+1) bond = RMCPdict['Potentials']['Stretch'][iPot] if os.path.exists(os.path.join(path,fname)): OutFile = open(fname,'r') odfFile = OutFile.readlines() if len(odfFile) > 1: OutFile.seek(0) odfData = np.fromfile(OutFile,sep=' ') numx,numy = odfData[:2] G2plt.Plot3dXYZ(G2frame,int(numx),int(numy),odfData[2:], newPlot=False,Title='Number of %s-%s Bonds'%(bond[0],bond[1]),Centro=True) OutFile.close() elif G2frame.RMCchoice == 'PDFfit': generalData = data['General'] RMCPdict = data['RMC']['PDFfit'] pName = generalData['Name'].replace(' ','_') Labels = [r'$\mathsf{R,\AA}$','G(R)','PDFfit2 G(R) for '] files = RMCPdict['files'] for file in files: if 'Select' not in files[file][0]: XY = np.empty((1,2)) start = 0 while XY.shape[0] == 1: try: XY = np.loadtxt(files[file][0],skiprows=start) except ValueError: start += 1 if 'Neutron' in file: cname = pName+'-PDFfitN.fgr' else: cname = pName+'-PDFfitX.fgr' XYobs = XY.T[:2] XY = np.empty((1,2)) start = 0 while XY.shape[0] == 1: try: XY = np.loadtxt(cname,skiprows=start) except ValueError: start += 1 XYcalc = XY.T[:2] XYdiff = np.zeros_like(XYcalc) XYdiff[0] = XYcalc[0] ibeg = np.searchsorted(XYobs[0],XYdiff[0][0]) ifin = ibeg+XYcalc.shape[1] XYdiff[1] = XYobs[1][ibeg:ifin]-XYcalc[1] offset = 1.1*(np.max(XYdiff[1])-np.min(XYcalc[1])) XYdiff[1] -= offset G2plt.PlotXY(G2frame,[XYobs,],XY2=[XYcalc,XYdiff],labelX=Labels[0], labelY=Labels[1],newPlot=True,Title=Labels[2]+files[file][0], lines=False,names=['G(R) obs','G(R) calc','diff',]) #### ISODISTORT tab ############################################################################### def UpdateISODISTORT(Scroll=0): ''' Setup ISODISTORT and present the results. Allow selection of a distortion model for PDFfit or GSAS-II structure refinement as a cif file produced by ISODISTORT. Allows manipulation of distortion mode displacements selection their refinement for this new phase. ''' def displaySetup(): def OnParentCif(event): dlg = wx.FileDialog(ISODIST, 'Select parent cif file',G2frame.LastGPXdir, style=wx.FD_OPEN ,wildcard='cif file(*.cif)|*.cif') if dlg.ShowModal() == wx.ID_OK: fName = dlg.GetFilename() fDir = dlg.GetDirectory() ISOdata['ParentCIF'] = os.path.join(fDir,fName) dlg.Destroy() else: dlg.Destroy() UpdateISODISTORT() def OnUsePhase(event): ISOdata['ParentCIF'] = 'Use this phase' UpdateISODISTORT() def OnMethodSel(event): method = methodSel.GetSelection()+1 if method in [1,4]: ISOdata['ISOmethod'] = method UpdateISODISTORT() def OnChildCif(event): dlg = wx.FileDialog(ISODIST, 'Select child cif file',G2frame.LastGPXdir, style=wx.FD_OPEN ,wildcard='cif file(*.cif)|*.cif') if dlg.ShowModal() == wx.ID_OK: fName = dlg.GetFilename() fDir = dlg.GetDirectory() ISOdata['ChildCIF'] = os.path.join(fDir,fName) dlg.Destroy() else: dlg.Destroy() UpdateISODISTORT() def OnUsePhase2(event): ISOdata['ChildCIF'] = 'Use this phase' UpdateISODISTORT() topSizer = wx.BoxSizer(wx.VERTICAL) topSizer.Add(wx.StaticText(ISODIST,label=' ISODISTORT setup controls:')) parentSizer = wx.BoxSizer(wx.HORIZONTAL) parentSizer.Add(wx.StaticText(ISODIST,label=' Parent cif file:'),0,WACV) parentCif = wx.Button(ISODIST,label=ISOdata['ParentCIF'],size=(300,24)) parentCif.Bind(wx.EVT_BUTTON,OnParentCif) parentSizer.Add(parentCif,0,WACV) if 'Use this phase' not in ISOdata['ChildCIF'] and 'Use this phase' not in ISOdata['ParentCIF']: usePhase = wx.Button(ISODIST,label=' Use this phase? ') usePhase.Bind(wx.EVT_BUTTON,OnUsePhase) parentSizer.Add(usePhase,0,WACV) topSizer.Add(parentSizer) #patch if 'ISOmethod' not in ISOdata: ISOdata['ISOmethod'] = 1 #end patch choice = ['Method 1: Search over all special k points - yields only single Irrep models', 'Method 2: not implemented in GSAS-II', 'Method 3: not implemented in GSAS-II', 'Method 4: Mode decomposition of known child structure'] methodSel = wx.RadioBox(ISODIST,label='Select ISODISTORT method:',choices=choice, majorDimension=1,style=wx.RA_SPECIFY_COLS) methodSel.SetSelection(ISOdata['ISOmethod']-1) methodSel.Bind(wx.EVT_RADIOBOX,OnMethodSel) topSizer.Add(methodSel) if ISOdata['ISOmethod'] == 4: childSizer = wx.BoxSizer(wx.HORIZONTAL) childSizer.Add(wx.StaticText(ISODIST,label=' Child cif file:'),0,WACV) childCif = wx.Button(ISODIST,label=ISOdata['ChildCIF'],size=(300,24)) childCif.Bind(wx.EVT_BUTTON,OnChildCif) childSizer.Add(childCif,0,WACV) if 'Use this phase' not in ISOdata['ChildCIF'] and 'Use this phase' not in ISOdata['ParentCIF']: usePhase2 = wx.Button(ISODIST,label=' Use this phase? ') usePhase2.Bind(wx.EVT_BUTTON,OnUsePhase2) childSizer.Add(usePhase2,0,WACV) topSizer.Add(childSizer) return topSizer def displaySubset(): def OnLaue(event): Obj = event.GetEventObject() name = Indx[Obj.GetId()] ISOdata['SGselect'][name[:4]] = not ISOdata['SGselect'][name[:4]] ISOdata['selection'] = None UpdateISODISTORT() def OnAllBtn(event): for item in ISOdata['SGselect']: ISOdata['SGselect'][item] = not ISOdata['SGselect'][item] ISOdata['selection'] = None UpdateISODISTORT() topSizer = wx.BoxSizer(wx.VERTICAL) G2G.HorizontalLine(topSizer,ISODIST) topSizer.Add(wx.StaticText(ISODIST,label='ISODISTORT Method 1 distortion search results:')) topSizer.Add(wx.StaticText(ISODIST,label=' Subset selection if desired:')) laueName = ['Cubic','Hexagonal','Trigonal','Tetragonal','Orthorhombic','Monoclinic','Triclinic'] littleSizer = wx.FlexGridSizer(0,8,5,5) Indx = {} for name in laueName: laueCk = wx.CheckBox(ISODIST,label=name) Indx[laueCk.GetId()] = name laueCk.SetValue(ISOdata['SGselect'][name[:4]]) laueCk.Bind(wx.EVT_CHECKBOX,OnLaue) littleSizer.Add(laueCk,0,WACV) allBtn = wx.Button(ISODIST,label='Toggle all') allBtn.Bind(wx.EVT_BUTTON,OnAllBtn) littleSizer.Add(allBtn) topSizer.Add(littleSizer) return topSizer def displayRadio(): def CheckItem(item): SGnum = int(item.split()[1].split('*')[0]) for SGtype in ISOdata['SGselect']: if ISOdata['SGselect'][SGtype] and SGnum in SGrange[SGtype]: return True return False def OnSelect(event): r,c = event.GetRow(),event.GetCol() if c == 0: ISOdata['selection'] = [r,isoTable.GetValue(r,1)] for row in range(isoGrid.GetNumberRows()): isoTable.SetValue(row,c,False) isoTable.SetValue(r,c,True) isoGrid.ForceRefresh() SGrange = {'Cubi':np.arange(195,231),'Hexa':np.arange(168,195),'Trig':np.arange(143,168),'Tetr':np.arange(75,143), 'Orth':np.arange(16,75),'Mono':np.arange(3,16),'Tric':np.arange(1,3)} bottomSizer = wx.BoxSizer(wx.VERTICAL) colLabels = ['select',' ISODISTORT order parameter direction description'] colTypes = [wg.GRID_VALUE_BOOL,wg.GRID_VALUE_STRING,] Radio = ISOdata['radio'] rowLabels = [] table = [] for i,item in enumerate(Radio): if CheckItem(Radio[item]): if ISOdata['selection'] and ISOdata['selection'][0] == i: table.append([True,Radio[item]]) else: table.append([False,Radio[item]]) rowLabels.append(str(i)) isoTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=colTypes) isoGrid = G2G.GSGrid(ISODIST) isoGrid.SetTable(isoTable,True,useFracEdit=False) isoGrid.AutoSizeColumns(True) isoGrid.SetColLabelAlignment(wx.ALIGN_LEFT,wx.ALIGN_CENTRE) bottomSizer.Add(isoGrid) attr = wg.GridCellAttr() attr.SetReadOnly(True) attr.SetBackgroundColour(VERY_LIGHT_GREY) isoGrid.SetColAttr(1,attr) isoGrid.Bind(wg.EVT_GRID_CELL_LEFT_CLICK, OnSelect) return bottomSizer def displayModes(): def OnDispl(event): '''Respond to movement of distortion mode slider''' Obj = event.GetEventObject() idsp,dispVal = Indx[Obj.GetId()] modeDisp[idsp] = Obj.GetValue()/1000. dispVal.SetValue(modeDisp[idsp]) err = G2mth.ApplyModeDisp(data) if err: G2G.G2MessageBox(G2frame,'Do Draw atoms first') FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) def OnDispVal(invalid,value,tc): '''Respond to entry of a value into a distortion mode entry widget''' idsp,displ = Indx[tc.GetId()] displ.SetValue(int(value*1000)) err = G2mth.ApplyModeDisp(data) if err: G2G.G2MessageBox(G2frame,'Do Draw atoms first') FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) def OnRefDispl(event): Obj = event.GetEventObject() idsp,item = Indx[Obj.GetId()] item[-2] = not item[-2] def OnReset(event): '''Reset all distortion mode values to initial values''' ISOdata['modeDispl'] = copy.deepcopy(ISOdata['ISOmodeDispl']) err = G2mth.ApplyModeDisp(data) if err: G2G.G2MessageBox(G2frame,'Do Draw atoms first') FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) UpdateISODISTORT() def OnSetZero(event): '''Reset all distortion mode values to 0''' ISOdata['modeDispl'] = [0.0 for i in ISOdata['ISOmodeDispl']] err = G2mth.ApplyModeDisp(data) if err: G2G.G2MessageBox(G2frame,'Do Draw atoms first') FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) UpdateISODISTORT() def OnSaveModes(event): '''Set saved distortion mode values to displayed values''' dlg = wx.MessageDialog(G2frame,'Are you sure you want to replace the saved mode values?', 'Confirm replace',wx.YES|wx.NO) try: dlg.CenterOnParent() result = dlg.ShowModal() finally: dlg.Destroy() if result != wx.ID_YES: return ISOdata['ISOmodeDispl'] = copy.deepcopy(ISOdata['modeDispl']) G2plt.PlotStructure(G2frame,data) UpdateISODISTORT() #### displayModes code starts here ConstrData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Constraints')) pId = data['ranId'] mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(ISODIST,label=' ISODISTORT distortion modes for phase %s'%data['General']['Name']),0,wx.BOTTOM,5) topSizer.Add((-1,-1),1,wx.EXPAND,1) topSizer.Add(G2G.HelpButton(ISODIST,helpIndex=G2frame.dataWindow.helpKey),0,wx.ALIGN_TOP) mainSizer.Add(topSizer,0,wx.EXPAND) if SGLaue not in ['mmm','2/m','-1']: mainSizer.Add(wx.StaticText(ISODIST,label=' NB: ISODISTORT distortion mode symmetry is too high to be used in PDFfit')) mainSizer.Add(wx.StaticText(ISODIST,label=ISOcite)) mainSizer.Add(wx.StaticText(ISODIST,label= u''' The 2nd column below shows the last saved mode values. The 3rd && 4th columns will set the display mode values. The positions in the Atoms and Draw Atoms tabs, as well as the atom positions shown in the Plot Window are changed to reflect the display mode values. The range of the slider corresponds to making a maximum atomic displacement between -2 && +2 \u212B.''')) mainSizer.Add((-1,10)) slideSizer = wx.FlexGridSizer(0,5,0,0) modeDisp = ISOdata['modeDispl'] idsp = 0 slideSizer.Add(wx.StaticText(ISODIST,label='Name'),0,wx.ALIGN_CENTER) slideSizer.Add(wx.StaticText(ISODIST,label='Save value')) slideSizer.Add(wx.StaticText(ISODIST,label='Value'),0,wx.ALIGN_CENTER) slideSizer.Add(wx.StaticText(ISODIST,label='Refine?'),0,wx.ALIGN_CENTER) slideSizer.Add(wx.StaticText(ISODIST,label='Atom displacements'),0,wx.EXPAND|wx.LEFT,15) isoDict = {i.name:j for (i,j) in zip(data['ISODISTORT']['G2ModeList'],data['ISODISTORT']['IsoModeList'])} for item in ConstrData['Phase']: if item[-1] != 'f': continue # only want new vars if item[-3] is None: continue # unnamed new var is not ISO try: if pId != item[-3].phase: continue # at present only ISO modes are associated with a phase except AttributeError: continue if item[-3].name not in isoDict: continue isoName = item[-3].varname().split('::')[1] slideSizer.Add(wx.StaticText(ISODIST,label=isoName),0,WACV) slideSizer.Add(wx.StaticText(ISODIST,label=' %.5g '%ISOdata['ISOmodeDispl'][idsp], style=wx.ALIGN_CENTER_HORIZONTAL),0,WACV|wx.EXPAND) lineSizer = wx.BoxSizer(wx.HORIZONTAL) dispVal = G2G.ValidatedTxtCtrl(ISODIST,modeDisp,idsp,xmin=-2.,xmax=2.,size=(75,20),OnLeave=OnDispVal) lineSizer.Add(dispVal,0,WACV) displ = G2G.G2Slider(ISODIST,style=wx.SL_HORIZONTAL,minValue=-2000,maxValue=2000, value=int(modeDisp[idsp]*1000),size=(250,20)) displ.Bind(wx.EVT_SLIDER, OnDispl) Indx[displ.GetId()] = [idsp,dispVal] Indx[dispVal.GetId()] = [idsp,displ] lineSizer.Add(displ) slideSizer.Add(lineSizer) refDispl = wx.CheckBox(ISODIST) refDispl.SetValue(item[-2]) refDispl.Bind(wx.EVT_CHECKBOX,OnRefDispl) Indx[refDispl.GetId()] = [idsp,item] slideSizer.Add(refDispl,0,WACV|wx.EXPAND|wx.LEFT,15) slideSizer.Add(wx.StaticText(ISODIST,label=', '.join(ModeDispList[idsp])),0,wx.EXPAND|wx.LEFT,15) idsp += 1 slideSizer.SetMinSize(wx.Size(650,10)) mainSizer.Add(slideSizer) lineSizer = wx.BoxSizer(wx.HORIZONTAL) reset = wx.Button(ISODIST,label='Reset modes to save values') reset.Bind(wx.EVT_BUTTON,OnReset) lineSizer.Add(reset,0,WACV) reset = wx.Button(ISODIST,label='Set all modes to zero') reset.Bind(wx.EVT_BUTTON,OnSetZero) lineSizer.Add(reset,0,wx.ALL,10) reset = wx.Button(ISODIST,label='Save mode values') reset.Bind(wx.EVT_BUTTON,OnSaveModes) lineSizer.Add(reset,0,WACV) mainSizer.Add(lineSizer,0,wx.TOP,5) mainSizer.Layout() SetPhaseWindow(ISODIST,mainSizer,Scroll=Scroll) #### UpdateISODISTORT code starts here Indx = {} ISOdata = data['ISODISTORT'] SGLaue = data['General']['SGData']['SGLaue'] G2frame.dataWindow.ISODDataEdit.Enable(G2G.wxID_ISODNEWPHASE,'rundata' in ISOdata) G2frame.dataWindow.ISODDataEdit.Enable(G2G.wxID_ISOPDFFIT,(('G2VarList' in ISOdata) and (SGLaue in ['mmm','2/m','-1']))) G2frame.dataWindow.ISODDataEdit.Enable(G2G.wxID_SHOWISO1,('G2VarList' in ISOdata) or ('G2OccVarList' in ISOdata)) G2frame.dataWindow.ISODDataEdit.Enable(G2G.wxID_SHOWISOMODES,('G2VarList' in ISOdata)) ISOcite = ''' For use of ISODISTORT, please cite: H. T. Stokes, D. M. Hatch, and B. J. Campbell, ISODISTORT, ISOTROPY Software Suite, iso.byu.edu. B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions." J. Appl. Cryst. 39, 607-614 (2006). ''' if ISODIST.GetSizer(): ISODIST.GetSizer().Clear(True) if 'G2ModeList' in ISOdata: #invoked only if phase is from a ISODISTORT cif file & thus contains distortion mode constraints # #patch # if 'modeDispl' not in ISOdata: # ISOdata['modeDispl'] = np.zeros(len(ISOdata['G2ModeList'])) # #end patch ModeDispList = G2pwd.GetAtmDispList(ISOdata) displayModes() return #initialization if 'ParentCIF' not in ISOdata: ISOdata.update({'ParentCIF':'Select','ChildCIF':'Select','ISOmethod':4, 'ChildMatrix':np.eye(3),'ChildSprGp':'P 1','ChildCell':'abc',}) #these last 3 currently unused #end initialization mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(ISODIST,label=ISOcite)) mainSizer.Add(displaySetup()) if 'radio' in ISOdata: mainSizer.Add(displaySubset()) mainSizer.Add(displayRadio()) SetPhaseWindow(ISODIST,mainSizer,Scroll=Scroll) def OnRunISODISTORT(event): ''' this needs to setup for method #3 or #4 in ISODISTORT after providing parent cif: #3 asks for transformation matrix & space group of child structure #4 asks for cif file of child structure ''' if not G2frame.GSASprojectfile: #force a project save to establish location of output cif file G2frame.OnFileSaveas(event) radio,rundata = ISO.GetISODISTORT(data) if radio: data['ISODISTORT']['radio'] = radio data['ISODISTORT']['rundata'] = rundata data['ISODISTORT']['SGselect'] = {'Tric':True,'Mono':True,'Orth':True,'Tetr':True,'Trig':True,'Hexa':True,'Cubi':True} data['ISODISTORT']['selection'] = None print('ISODISTORT run complete') wx.CallAfter(UpdateISODISTORT) elif data['ISODISTORT']['ISOmethod'] != 4 or radio is None: G2G.G2MessageBox(G2frame,'ISODISTORT run failed - see page opened in web browser') else: G2G.G2MessageBox(G2frame,'ISODISTORT run complete; new cif file %s created.\n To use, import it as a new phase.'%rundata) print(' ISODISTORT run complete; new cif file %s created. To use, import it as a new phase.'%rundata) def OnNewISOPhase(event): ''' Make CIF file with ISODISTORT ''' if 'rundata' in data['ISODISTORT'] and data['ISODISTORT']['selection'] is not None: CIFfile = ISO.GetISODISTORTcif(data) G2G.G2MessageBox(G2frame,'ISODISTORT generated cif file %s has been created.'%CIFfile) elif 'rundata' in data['ISODISTORT']: G2G.G2MessageBox(G2frame,'Need to select an ISODISTORTdistortion model first before creating a CIF') else: G2G.G2MessageBox(G2frame,'ERROR - need to run ISODISTORT first - see General/Compute menu') def OnNewPDFfitPhase(event): ''' Make new phase for PDFfit using ISODISTORT mode definitions as constraints ''' newPhase = G2pwd.ISO2PDFfit(data) phaseName = newPhase['General']['Name'] sub = G2frame.GPXtree.AppendItem(G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases'),text=phaseName) G2frame.GPXtree.SetItemPyData(sub,newPhase) G2frame.GPXtree.SelectItem(sub) #### DIFFax Layer Data page ################################################################################ def UpdateLayerData(Scroll=0): '''Present the contents of the Phase/Layers tab for stacking fault simulation ''' laueChoice = ['-1','2/m(ab)','2/m(c)','mmm','-3','-3m','4/m','4/mmm', '6/m','6/mmm','unknown'] colLabels = ['Name','Type','x','y','z','frac','Uiso'] transLabels = ['Prob','Dx','Dy','Dz','refine','plot'] colTypes = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+ \ 3*[wg.GRID_VALUE_FLOAT+':10,5',]+2*[wg.GRID_VALUE_FLOAT+':10,4',] #x,y,z,frac,Uiso transTypes = [wg.GRID_VALUE_FLOAT+':10,3',]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \ [wg.GRID_VALUE_CHOICE+": ,P,Dx,Dy,Dz,Dxy,Dxz,Dyz,Dxyz",wg.GRID_VALUE_BOOL,] plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':30.,'viewDir':[0,0,1], 'viewPoint':[[0.,0.,0.],[]],} Indx = {} def OnLaue(event): Obj = event.GetEventObject() data['Layers']['Laue'] = Obj.GetValue() wx.CallAfter(UpdateLayerData) def OnSadpPlot(event): sadpPlot.SetValue(False) labels = Layers['Sadp']['Plane'] lmax = float(Layers['Sadp']['Lmax']) XY = 2*lmax*np.mgrid[0:256:256j,0:256:256j]/256.-lmax G2frame.Cmax = 1.0 G2plt.PlotXYZ(G2frame,XY,Layers['Sadp']['Img'].T,labelX=labels[:-1], labelY=labels[-1],newPlot=False,Title=Layers['Sadp']['Plane']) def OnSeqPlot(event): seqPlot.SetValue(False) resultXY,resultXY2,seqNames = Layers['seqResults'] pName = Layers['seqCodes'][0] G2plt.PlotXY(G2frame,resultXY,XY2=resultXY2,labelX=r'$\mathsf{2\theta}$', labelY='Intensity',newPlot=True,Title='Sequential simulations on '+pName, lines=True,names=seqNames) def CellSizer(): cellGUIlist = [ [['-3','-3m','6/m','6/mmm','4/m','4/mmm'],6,zip([" a = "," c = "],["%.5f","%.5f",],[True,True],[0,2])], [['mmm'],8,zip([" a = "," b = "," c = "],["%.5f","%.5f","%.5f"],[True,True,True],[0,1,2,])], [['2/m(ab)','2/m(c)','-1','axial','unknown'],10,zip([" a = "," b = "," c = "," gamma = "], ["%.5f","%.5f","%.5f","%.3f"],[True,True,True,True],[0,1,2,5])]] def OnCellRef(event): data['Layers']['Cell'][0] = cellRef.GetValue() def OnCellChange(event): event.Skip() laue = data['Layers']['Laue'] cell = data['Layers']['Cell'] Obj = event.GetEventObject() ObjId = cellList.index(Obj.GetId()) try: value = max(1.0,float(Obj.GetValue())) except ValueError: if ObjId < 3: #bad cell edge - reset value = cell[ObjId+1] else: #bad angle value = 90. if laue in ['-3','-3m','6/m','6/mmm','4/m','4/mmm']: cell[4] = cell[5] = 90. cell[6] = 120. if laue in ['4/m','4/mmm']: cell[6] = 90. if ObjId == 0: cell[1] = cell[2] = value Obj.SetValue("%.5f"%(cell[1])) else: cell[3] = value Obj.SetValue("%.5f"%(cell[3])) elif laue in ['mmm']: cell[ObjId+1] = value cell[4] = cell[5] = cell[6] = 90. Obj.SetValue("%.5f"%(cell[ObjId+1])) elif laue in ['2/m','-1']: cell[4] = cell[5] = 90. if ObjId != 3: cell[ObjId+1] = value Obj.SetValue("%.5f"%(cell[ObjId+1])) else: cell[6] = value Obj.SetValue("%.3f"%(cell[6])) cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7])) volVal.SetLabel(' Vol = %.3f'%(cell[7])) cell = data['Layers']['Cell'] laue = data['Layers']['Laue'] for cellGUI in cellGUIlist: if laue in cellGUI[0]: useGUI = cellGUI cellSizer = wx.FlexGridSizer(0,useGUI[1]+1,5,5) cellRef = wx.CheckBox(layerData,-1,label='Refine unit cell:') cellSizer.Add(cellRef,0,WACV) cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef) cellRef.SetValue(cell[0]) cellList = [] for txt,fmt,ifEdit,Id in useGUI[2]: cellSizer.Add(wx.StaticText(layerData,label=txt),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) cellVal = wx.TextCtrl(layerData,value=(fmt%(cell[Id+1])), style=wx.TE_PROCESS_ENTER) cellVal.Bind(wx.EVT_TEXT_ENTER,OnCellChange) cellVal.Bind(wx.EVT_KILL_FOCUS,OnCellChange) cellSizer.Add(cellVal,0,WACV) cellList.append(cellVal.GetId()) volVal = wx.StaticText(layerData,label=' Vol = %.3f'%(cell[7])) cellSizer.Add(volVal,0,WACV) return cellSizer def WidthSizer(): def OnRefWidth(event): Id = Indx[event.GetEventObject()] Layers['Width'][1][Id] = not Layers['Width'][1][Id] Labels = ['a','b'] flags = Layers['Width'][1] widthSizer = wx.BoxSizer(wx.HORIZONTAL) for i in range(2): widthSizer.Add(wx.StaticText(layerData,label=u' layer width(%s) (<= 1\xb5m): '%(Labels[i])),0,WACV) widthVal = G2G.ValidatedTxtCtrl(layerData,Layers['Width'][0],i,nDig=(10,3),xmin=0.005,xmax=1.0) widthSizer.Add(widthVal,0,WACV) widthRef = wx.CheckBox(layerData,label='Refine?') widthRef.SetValue(flags[i]) Indx[widthRef] = i widthRef.Bind(wx.EVT_CHECKBOX, OnRefWidth) widthSizer.Add(widthRef,0,WACV) return widthSizer def OnNewLayer(event): data['Layers']['Layers'].append({'Name':'Unk','SameAs':'','Symm':'None','Atoms':[]}) Trans = data['Layers']['Transitions'] if len(Trans): Trans.append([[0.,0.,0.,0.,'',False] for trans in Trans]) for trans in Trans: trans.append([0.,0.,0.,0.,'',False]) else: Trans = [[[1.,0.,0.,0.,'',False],],] data['Layers']['Transitions'] = Trans wx.CallLater(100,UpdateLayerData) def OnDeleteLast(event): del(data['Layers']['Layers'][-1]) del(data['Layers']['Transitions'][-1]) for trans in data['Layers']['Transitions']: del trans[-1] wx.CallAfter(UpdateLayerData) def OnImportLayer(event): dlg = wx.FileDialog(G2frame, 'Choose GSAS-II project file', G2G.GetImportPath(G2frame), wildcard='GSAS-II project file (*.gpx)|*.gpx',style=wx.FD_OPEN| wx.FD_CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: GPXFile = dlg.GetPath() phaseNames = G2stIO.GetPhaseNames(GPXFile) else: return finally: dlg.Destroy() dlg = wx.SingleChoiceDialog(G2frame,'Phase to use for layer','Select',phaseNames) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() PhaseName = phaseNames[sel] else: return Phase = G2stIO.GetAllPhaseData(GPXFile,PhaseName) #need cell compatibility check here Layer = {'Name':Phase['General']['Name'],'SameAs':'','Symm':'None'} cx,ct,cs,cia = Phase['General']['AtomPtrs'] atoms = Phase['Atoms'] Atoms = [] for atom in atoms: x,y,z,f = atom[cx:cx+4] u = atom[cia+1] if not u: u = 0.01 Atoms.append([atom[ct-1],atom[ct],x,y,z,f,u]) if atom[ct] not in data['Layers']['AtInfo']: data['Layers']['AtInfo'][atom[ct]] = G2elem.GetAtomInfo(atom[ct]) Layer['Atoms'] = Atoms data['Layers']['Layers'].append(Layer) Trans = data['Layers']['Transitions'] if len(Trans): Trans.append([[0.,0.,0.,0.,'',False] for trans in Trans]) for trans in Trans: trans.append([0.,0.,0.,0.,'',False]) else: Trans = [[[1.,0.,0.,0.,'',False],],] data['Layers']['Transitions'] = Trans wx.CallAfter(UpdateLayerData) def LayerSizer(il,Layer): def OnNameChange(event): event.Skip() Layer['Name'] = layerName.GetValue() wx.CallLater(100,UpdateLayerData) def OnAddAtom(event): Layer['Atoms'].append(['Unk','Unk',0.,0.,0.,1.,0.01]) wx.CallAfter(UpdateLayerData) def OnSymm(event): Layer['Symm'] = symm.GetValue() def AtomTypeSelect(event): r,c = event.GetRow(),event.GetCol() if atomGrid.GetColLabelValue(c) == 'Type': PE = G2elemGUI.PickElement(G2frame) if PE.ShowModal() == wx.ID_OK: if PE.Elem != 'None': atType = PE.Elem.strip() Layer['Atoms'][r][c] = atType name = Layer['Atoms'][r][c] if len(name) in [2,4]: Layer['Atoms'][r][c-1] = name[:2]+'%d'%(r+1) else: Layer['Atoms'][r][c-1] = name[:1]+'%d'%(r+1) if atType not in data['Layers']['AtInfo']: data['Layers']['AtInfo'][atType] = G2elem.GetAtomInfo(atType) PE.Destroy() wx.CallAfter(UpdateLayerData) else: event.Skip() def OnDrawLayer(event): drawLayer.SetValue(False) G2plt.PlotLayers(G2frame,Layers,[il,],plotDefaults) def OnSameAs(event): Layer['SameAs'] = sameas.GetValue() wx.CallLater(100,UpdateLayerData) layerSizer = wx.BoxSizer(wx.VERTICAL) nameSizer = wx.BoxSizer(wx.HORIZONTAL) nameSizer.Add(wx.StaticText(layerData,label=' Layer name: '),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) layerName = wx.TextCtrl(layerData,value=Layer['Name'],style=wx.TE_PROCESS_ENTER) layerName.Bind(wx.EVT_TEXT_ENTER,OnNameChange) layerName.Bind(wx.EVT_KILL_FOCUS,OnNameChange) layerName.Bind(wx.EVT_LEAVE_WINDOW,OnNameChange) nameSizer.Add(layerName,0,WACV) if il: nameSizer.Add(wx.StaticText(layerData,label=' Same as: '),0,WACV) sameas = wx.ComboBox(layerData,value=Layer['SameAs'],choices=['',]+layerNames[:-1], style=wx.CB_READONLY|wx.CB_DROPDOWN) sameas.Bind(wx.EVT_COMBOBOX, OnSameAs) nameSizer.Add(sameas,0,WACV) if Layer['SameAs']: indx = layerNames.index(Layer['SameAs']) if indx < il: #previously used : same layer layerSizer.Add(nameSizer) return layerSizer nameSizer.Add(wx.StaticText(layerData,label=' Layer symmetry: '),0,WACV) symmChoice = ['-1','None'] symm = wx.ComboBox(layerData,value=Layer['Symm'],choices=symmChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) symm.Bind(wx.EVT_COMBOBOX,OnSymm) nameSizer.Add(symm,0,WACV) addAtom = wx.CheckBox(layerData,label=' Add atom? ') addAtom.Bind(wx.EVT_CHECKBOX, OnAddAtom) nameSizer.Add(addAtom,0,WACV) drawLayer = wx.CheckBox(layerData,label=' Draw layer? ') drawLayer.Bind(wx.EVT_CHECKBOX, OnDrawLayer) nameSizer.Add(drawLayer,0,WACV) layerSizer.Add(nameSizer) table = [] rowLabels = [] for i,atom in enumerate(Layer['Atoms']): table.append(atom) rowLabels.append(str(i)) atomTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=colTypes) atomGrid = G2G.GSGrid(layerData) atomGrid.SetTable(atomTable,True,useFracEdit=False) # atomGrid.SetScrollRate(0,0) #get rid of automatic scroll bars # loop over all cols in table, set cell editor for numerical items for c,t in enumerate(colTypes): if not t.startswith(wg.GRID_VALUE_FLOAT): continue attr = wx.grid.GridCellAttr() attr.IncRef() #fix from Jim Hester attr.SetEditor(G2G.GridFractionEditor(atomGrid)) atomGrid.SetColAttr(c, attr) for row,atom in enumerate(Layer['Atoms']): atomGrid.SetReadOnly(row,1,True) atomGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect) atomGrid.AutoSizeColumns(True) layerSizer.Add(atomGrid) return layerSizer def TransSizer(): def PlotSelect(event): Obj = event.GetEventObject() Yi = Indx[Obj.GetId()] Xi,c = event.GetRow(),event.GetCol() if Xi >= 0 and c == 5: #plot column G2plt.PlotLayers(G2frame,Layers,[Yi,Xi,],plotDefaults) else: Psum = 0. for Xi in range(len(transArray)): Psum += transArray[Xi][Xi][0] Psum /= len(transArray) totalFault.SetLabel(' Total fault density = %.3f'%(1.-Psum)) event.Skip() def OnNormProb(event): for Yi,Yname in enumerate(Names): Psum = 0. for Xi,Xname in enumerate(Names): Psum += transArray[Yi][Xi][0] if not Psum: transArray[Yi][0][0] = 1.0 Psum = 1.0 for Xi,Xname in enumerate(Names): transArray[Yi][Xi][0] /= Psum wx.CallAfter(UpdateLayerData) def OnSymProb(event): if symprob.GetValue(): Nx = len(Names)-1 Layers['SymTrans'] = True for Yi,Yname in enumerate(Names): for Xi,Xname in enumerate(Names): if transArray[Nx-Yi][Nx-Xi][0] != transArray[Yi][Xi][0]: Layers['SymTrans'] = False symprob.SetValue(False) wx.MessageBox('%s-%s not equal %s-%s'%(Yname,Xname,Xname,Yname), caption='Probability symmetry error',style=wx.ICON_EXCLAMATION) break else: Layers['SymTrans'] = False transSizer = wx.BoxSizer(wx.VERTICAL) transSizer.Add(wx.StaticText(layerData,label=' Layer-Layer transition probabilities: '),0) topSizer = wx.BoxSizer(wx.HORIZONTAL) normprob = wx.CheckBox(layerData,label=' Normalize probabilities?') normprob.Bind(wx.EVT_CHECKBOX,OnNormProb) topSizer.Add(normprob,0,WACV) symprob = wx.CheckBox(layerData,label=' Symmetric probabilities?') symprob.SetValue(Layers.get('SymTrans',False)) symprob.Bind(wx.EVT_CHECKBOX,OnSymProb) topSizer.Add(symprob,0,WACV) transSizer.Add(topSizer,0) Names = [layer['Name'] for layer in Layers['Layers']] transArray = Layers['Transitions'] layerData.transGrids = [] if not Names or not transArray: return transSizer diagSum = 0. for Yi,Yname in enumerate(Names): transSizer.Add(wx.StaticText(layerData,label=' From %s to:'%(Yname)),0) table = [] rowLabels = [] diagSum += transArray[Yi][Yi][0] for Xi,Xname in enumerate(Names): table.append(transArray[Yi][Xi]) rowLabels.append(Xname) if transArray[Yi][Xi][0] > 0.: Layers['allowedTrans'].append([str(Yi+1),str(Xi+1)]) transTable = G2G.Table(table,rowLabels=rowLabels,colLabels=transLabels,types=transTypes) transGrid = G2G.GSGrid(layerData) transGrid.SetTable(transTable,True,useFracEdit=False) # transGrid.SetScrollRate(0,0) #get rid of automatic scroll bars Indx[transGrid.GetId()] = Yi for c,t in enumerate(transTypes): if not t.startswith(wg.GRID_VALUE_FLOAT): continue attr = wx.grid.GridCellAttr() attr.IncRef() #fix from Jim Hester attr.SetEditor(G2G.GridFractionEditor(transGrid)) transGrid.SetColAttr(c, attr) transGrid.Bind(wg.EVT_GRID_CELL_LEFT_CLICK, PlotSelect) transGrid.AutoSizeColumns(True) transSizer.Add(transGrid) layerData.transGrids.append(transGrid) if len(transArray): diagSum /= len(transArray) totalFault = wx.StaticText(layerData, label=' Total fault density = %.3f'%(1.-diagSum)) transSizer.Add(totalFault,0) return transSizer def PlotSizer(): def OnPlotSeq(event): event.Skip() vals = plotSeq.GetValue().split() try: vals = [int(val)-1 for val in vals] if not all([0 <= val < len(Names) for val in vals]): raise ValueError except ValueError: plotSeq.SetValue('Error in string '+plotSeq.GetValue()) return G2plt.PlotLayers(G2frame,Layers,vals,plotDefaults) Names = [' %s: %d,'%(layer['Name'],iL+1) for iL,layer in enumerate(Layers['Layers'])] plotSizer = wx.BoxSizer(wx.VERTICAL) Str = ' Using sequence nos. from:' for name in Names: Str += name plotSizer.Add(wx.StaticText(layerData,label=Str[:-1]),0) lineSizer = wx.BoxSizer(wx.HORIZONTAL) lineSizer.Add(wx.StaticText(layerData,label=' Enter sequence of layers to plot:'),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) plotSeq = wx.TextCtrl(layerData,value = '',style=wx.TE_PROCESS_ENTER) plotSeq.Bind(wx.EVT_TEXT_ENTER,OnPlotSeq) plotSeq.Bind(wx.EVT_KILL_FOCUS,OnPlotSeq) lineSizer.Add(plotSeq,0,WACV) plotSizer.Add(lineSizer,0) return plotSizer def StackSizer(): stackChoice = ['recursive','explicit',] seqChoice = ['random','list',] def OnStackType(event): newType = stackType.GetValue() if newType == data['Layers']['Stacking'][0]: return data['Layers']['Stacking'][0] = newType if newType == 'recursive': data['Layers']['Stacking'][1] = 'infinite' else: #explicit data['Layers']['Stacking'][1] = 'random' data['Layers']['Stacking'][2] = '250' wx.CallAfter(UpdateLayerData) def OnSeqType(event): newType = seqType.GetValue() if newType == data['Layers']['Stacking'][1]: return data['Layers']['Stacking'][1] = newType if newType == 'random': data['Layers']['Stacking'][2] = '250' else: #List data['Layers']['Stacking'][2] = '' wx.CallAfter(UpdateLayerData) def OnNumLayers(event): event.Skip() val = numLayers.GetValue() if val == 'infinite': data['Layers']['Stacking'][1] = val else: try: if 0 < int(val) < 1023: data['Layers']['Stacking'][1] = val else: data['Layers']['Stacking'][1] = 'infinite' except ValueError: pass numLayers.SetValue(data['Layers']['Stacking'][1]) def OnNumRan(event): event.Skip() val = numRan.GetValue() try: if 0 > int(val) > 1022: raise ValueError else: data['Layers']['Stacking'][2] = val except ValueError: val = data['Layers']['Stacking'][2] numRan.SetValue(val) def OnStackList(event): event.Skip() stack = stackList.GetValue() stack = stack.replace('\n',' ').strip().strip('\n') nstar = stack.count('*') if nstar: try: newstack = '' Istar = 0 for star in range(nstar): Istar = stack.index('*',Istar+1) iB = stack[:Istar].rfind(' ') if iB == -1: mult = int(stack[:Istar]) else: mult = int(stack[iB:Istar]) pattern = stack[Istar+2:stack.index(')',Istar)]+' ' newstack += mult*pattern stack = newstack except ValueError: stack += ' Error in string' Slist = stack.split() if len(Slist) < 2: stack = 'Error in sequence - too short!' OKlist = [Slist[i:i+2] in Layers['allowedTrans'] for i in range(len(Slist[:-1]))] if all(OKlist): data['Layers']['Stacking'][2] = stack else: stack = 'Improbable sequence or bad string' stackList.SetValue(stack) stackSizer = wx.BoxSizer(wx.VERTICAL) stackSizer.Add(wx.StaticText(layerData,label=' Layer stacking parameters:'),0) if not Layers['Stacking']: Layers['Stacking'] = ['recursive','infinite',''] topLine = wx.BoxSizer(wx.HORIZONTAL) topLine.Add(wx.StaticText(layerData,label=' Stacking type: '),0,WACV) stackType = wx.ComboBox(layerData,value=Layers['Stacking'][0],choices=stackChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) stackType.Bind(wx.EVT_COMBOBOX,OnStackType) topLine.Add(stackType,0,WACV) if Layers['Stacking'][0] == 'recursive': topLine.Add(wx.StaticText(layerData,label=' number of layers (<1022 or "infinite"): '),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) numLayers = wx.TextCtrl(layerData,value=data['Layers']['Stacking'][1],style=wx.TE_PROCESS_ENTER) numLayers.Bind(wx.EVT_TEXT_ENTER,OnNumLayers) numLayers.Bind(wx.EVT_KILL_FOCUS,OnNumLayers) topLine.Add(numLayers,0,WACV) stackSizer.Add(topLine) elif Layers['Stacking'][0] == 'explicit': topLine.Add(wx.StaticText(layerData,label=' layer sequence: '),0,WACV) seqType = wx.ComboBox(layerData,value=data['Layers']['Stacking'][1],choices=seqChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) seqType.Bind(wx.EVT_COMBOBOX,OnSeqType) topLine.Add(seqType,0,WACV) if Layers['Stacking'][1] == 'list': stackSizer.Add(topLine,0) Names = [' %s: %d,'%(layer['Name'],iL+1) for iL,layer in enumerate(Layers['Layers'])] stackSizer.Add(wx.StaticText(layerData,label=' Explicit layer sequence; enter space delimited list of numbers:'),0) Str = ' Use sequence nos. from:' for name in Names: Str += name stackSizer.Add(wx.StaticText(layerData,label=Str[:-1]+' Repeat sequences can be used: e.g. 6*(1 2) '),0) stackSizer.Add(wx.StaticText(layerData,label=' Zero probability sequences not allowed'),0) stackList = wx.TextCtrl(layerData,value=Layers['Stacking'][2],size=(600,-1), style=wx.TE_MULTILINE|wx.TE_PROCESS_ENTER) stackList.Bind(wx.EVT_TEXT_ENTER,OnStackList) stackList.Bind(wx.EVT_KILL_FOCUS,OnStackList) stackSizer.Add(stackList,0,wx.ALL|wx.EXPAND,8) else: #random topLine.Add(wx.StaticText(layerData,label=' Length of random sequence: '),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) numRan = wx.TextCtrl(layerData,value=Layers['Stacking'][2],style=wx.TE_PROCESS_ENTER) numRan.Bind(wx.EVT_TEXT_ENTER,OnNumRan) numRan.Bind(wx.EVT_KILL_FOCUS,OnNumRan) topLine.Add(numRan,0,WACV) stackSizer.Add(topLine,0) return stackSizer Layers = data['Layers'] layerNames = [] Layers['allowedTrans'] = [] if len(Layers['Layers']): layerNames = [layer['Name'] for layer in Layers['Layers']] G2frame.GetStatusBar().SetStatusText('',1) layerData = G2frame.layerData try: if layerData.GetSizer(): layerData.GetSizer().Clear(True) except: pass mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.VERTICAL) bottomSizer = wx.BoxSizer(wx.VERTICAL) headSizer = wx.BoxSizer(wx.HORIZONTAL) headSizer.Add(wx.StaticText(layerData,label=' Global layer description: '),0,WACV) if 'Sadp' in Layers: sadpPlot = wx.CheckBox(layerData,label=' Plot selected area diffraction?') sadpPlot.Bind(wx.EVT_CHECKBOX,OnSadpPlot) headSizer.Add(sadpPlot,0,WACV) if 'seqResults' in Layers: seqPlot = wx.CheckBox(layerData,label=' Plot sequential result?') seqPlot.Bind(wx.EVT_CHECKBOX,OnSeqPlot) headSizer.Add(seqPlot,0,WACV) topSizer.Add(headSizer) laueSizer = wx.BoxSizer(wx.HORIZONTAL) laueSizer.Add(wx.StaticText(layerData,label=' Diffraction Laue symmetry:'),0,WACV) laue = wx.ComboBox(layerData,value=Layers['Laue'],choices=laueChoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) laue.Bind(wx.EVT_COMBOBOX,OnLaue) laueSizer.Add(laue,0,WACV) if Layers['Laue'] == 'unknown': laueSizer.Add(wx.StaticText(layerData,label=' Diffraction symmetry tolerance: '),0,WACV) toler = G2G.ValidatedTxtCtrl(layerData,Layers,'Toler',nDig=(10,3)) laueSizer.Add(toler,0,WACV) topSizer.Add(laueSizer,0) topSizer.Add(wx.StaticText(layerData,label=' Reference unit cell for all layers:'),0) topSizer.Add(CellSizer(),0) topSizer.Add(WidthSizer()) topSizer.Add(wx.StaticText(layerData,label=' NB: stacking fault refinement currently not available'),0) G2G.HorizontalLine(topSizer,layerData) titleSizer = wx.BoxSizer(wx.HORIZONTAL) titleSizer.Add(wx.StaticText(layerData,label=' Layer descriptions: '),0,WACV) newLayer = wx.Button(layerData,label='Add new layer') newLayer.Bind(wx.EVT_BUTTON, OnNewLayer) titleSizer.Add(newLayer,0,WACV) importLayer = wx.Button(layerData,label=' Import new layer') importLayer.Bind(wx.EVT_BUTTON, OnImportLayer) titleSizer.Add(importLayer,0,WACV) deleteLast = wx.Button(layerData,label='Delete last layer') deleteLast.Bind(wx.EVT_BUTTON, OnDeleteLast) titleSizer.Add(deleteLast,0,WACV) topSizer.Add(titleSizer,0) for il,layer in enumerate(Layers['Layers']): topSizer.Add(LayerSizer(il,layer)) G2G.HorizontalLine(topSizer,layerData) mainSizer.Add(topSizer) bottomSizer.Add(TransSizer()) G2G.HorizontalLine(bottomSizer,layerData) bottomSizer.Add(PlotSizer(),0) G2G.HorizontalLine(bottomSizer,layerData) bottomSizer.Add(StackSizer()) mainSizer.Add(bottomSizer) SetPhaseWindow(G2frame.layerData,mainSizer,Scroll=Scroll) def OnCopyPhase(event): dlg = wx.FileDialog(G2frame, 'Choose GSAS-II project file', G2G.GetImportPath(G2frame), wildcard='GSAS-II project file (*.gpx)|*.gpx',style=wx.FD_OPEN| wx.FD_CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: GPXFile = dlg.GetPath() phaseNames = G2stIO.GetPhaseNames(GPXFile) else: return finally: dlg.Destroy() dlg = wx.SingleChoiceDialog(G2frame,'Phase to use for cell data','Select',phaseNames) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() PhaseName = phaseNames[sel] else: return General = G2stIO.GetAllPhaseData(GPXFile,PhaseName)['General'] data['Layers']['Cell'] = General['Cell'] wx.CallAfter(UpdateLayerData) def OnLoadDIFFaX(event): if len(data['Layers']['Layers']): dlg = wx.MessageDialog(G2frame,'Do you really want to replace the Layer data?','Load DIFFaX file', wx.YES_NO | wx.ICON_QUESTION) try: result = dlg.ShowModal() if result == wx.ID_NO: return finally: dlg.Destroy() dlg = wx.FileDialog(G2frame, 'Choose DIFFaX file name to read', G2G.GetImportPath(G2frame), '', 'DIFFaX file (*.*)|*.*',style=wx.FD_OPEN | wx.FD_CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: DIFFaXfile = dlg.GetPath() data['Layers'] = G2IO.ReadDIFFaX(DIFFaXfile) finally: dlg.Destroy() wx.CallAfter(UpdateLayerData) def OnSimulate(event): debug = False #set True to run DIFFax to compare/debug (must be in bin) idebug = 0 if debug: idebug = 1 wx.MessageBox(''' For use of DIFFaX, please cite: A general recursion method for calculating diffracted intensities from crystals containing planar faults, M.M.J. Treacy, J.M. Newsam & M.W. Deem, Proc. Roy. Soc. Lond. A 433, 499-520 (1991) doi: https://doi.org/10.1098/rspa.1991.0062 ''',caption='DIFFaX',style=wx.ICON_INFORMATION) ctrls = '' dlg = DIFFaXcontrols(G2frame,ctrls) if dlg.ShowModal() == wx.ID_OK: simCodes = dlg.GetSelection() else: return if 'PWDR' in simCodes[0]: #powder pattern data['Layers']['selInst'] = simCodes[1] UseList = [] for item in data['Histograms']: if 'PWDR' in item: UseList.append(item) if not UseList: wx.MessageBox('No PWDR data for this phase to simulate',caption='Data error',style=wx.ICON_EXCLAMATION) return dlg = wx.SingleChoiceDialog(G2frame,'Data to simulate','Select',UseList) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() HistName = UseList[sel] else: return dlg.Destroy() G2frame.PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,HistName) sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,G2frame.PatternId, 'Sample Parameters')) scale = sample['Scale'][0] background = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,G2frame.PatternId, 'Background')) limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,G2frame.PatternId, 'Limits'))[1] inst = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[0] if 'T' in inst['Type'][0]: wx.MessageBox("Can't simulate neutron TOF patterns yet",caption='Data error',style=wx.ICON_EXCLAMATION) return profile = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[1] G2pwd.CalcStackingPWDR(data['Layers'],scale,background,limits,inst,profile,debug) if debug: ctrls = '0\n%d\n3\n'%(idebug) G2pwd.StackSim(data['Layers'],ctrls,scale,background,limits,inst,profile) test1 = np.copy(profile[3]) test1 = np.where(test1,test1,1.0) G2pwd.CalcStackingPWDR(data['Layers'],scale,background,limits,inst,profile,debug) test2 = np.copy(profile[3]) rat = test1-test2 XY = np.vstack((profile[0],rat)) G2plt.PlotXY(G2frame,[XY,],XY2=[],labelX=r'$\mathsf{2\theta}$', labelY='difference',newPlot=True,Title='DIFFaX vs GSASII',lines=True) G2plt.PlotPatterns(G2frame,plotType='PWDR',newPlot=True) else: #selected area data['Layers']['Sadp'] = {} data['Layers']['Sadp']['Plane'] = simCodes[1] data['Layers']['Sadp']['Lmax'] = simCodes[2] if debug: planeChoice = ['h0l','0kl','hhl','h-hl',] lmaxChoice = [str(i+1) for i in range(6)] ctrls = '0\n%d\n4\n1\n%d\n%d\n16\n1\n1\n0\nend\n'% \ (idebug,planeChoice.index(simCodes[1])+1,lmaxChoice.index(simCodes[2])+1) G2pwd.StackSim(data['Layers'],ctrls) G2pwd.CalcStackingSADP(data['Layers'],debug) wx.MessageBox('Simulation finished',caption='Stacking fault simulation',style=wx.ICON_EXCLAMATION) wx.CallAfter(UpdateLayerData) def OnFitLayers(event): print (' fit stacking fault model TBD') # import scipy.optimize as opt wx.BeginBusyCursor() # see pwd.SetupPDFEval() and pwd.OptimizePDF() for an example minimization wx.EndBusyCursor() wx.CallAfter(UpdateLayerData) G2plt.PlotPatterns(G2frame,plotType='PWDR') def OnSeqSimulate(event): cellSel = ['cellA','cellB','cellC','cellG'] transSel = ['TransP','TransX','TransY','TransZ'] ctrls = '' cell = data['Layers']['Cell'] data['Layers']['seqResults'] = [] data['Layers']['seqCodes'] = [] Parms = G2pwd.GetStackParms(data['Layers']) dlg = DIFFaXcontrols(G2frame,ctrls,Parms) if dlg.ShowModal() == wx.ID_OK: simCodes = dlg.GetSelection() else: return UseList = [] for item in data['Histograms']: if 'PWDR' in item: UseList.append(item) if not UseList: wx.MessageBox('No PWDR data for this phase to simulate',caption='Data error',style=wx.ICON_EXCLAMATION) return dlg = wx.SingleChoiceDialog(G2frame,'Data to simulate','Select',UseList) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() HistName = UseList[sel] else: return dlg.Destroy() G2frame.PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,HistName) sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,G2frame.PatternId, 'Sample Parameters')) scale = sample['Scale'][0] background = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,G2frame.PatternId, 'Background')) limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,G2frame.PatternId, 'Limits'))[1] inst = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[0] if 'T' in inst['Type'][0]: wx.MessageBox("Can't simulate neutron TOF patterns yet",caption='Data error',style=wx.ICON_EXCLAMATION) return profile = np.copy(G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[1]) resultXY2 = [] resultXY = [np.vstack((profile[0],profile[1])),] #observed data data['Layers']['selInst'] = simCodes[1] data['Layers']['seqCodes'] = simCodes[2:] Layers = copy.deepcopy(data['Layers']) pName = simCodes[2] BegFin = simCodes[3] nSteps = simCodes[4] laue = Layers['Laue'] vals = np.linspace(BegFin[0],BegFin[1],nSteps+1,True) simNames = [] for val in vals: print (' Stacking simulation step for %s = %.5f'%(pName,val)) simNames.append('%.3f'%(val)) if 'cell' in pName: cellId = cellSel.index(pName) cell = Layers['Cell'] cell[cellId+1] = val if laue in ['-3','-3m','6/m','6/mmm','4/m','4/mmm']: cell[2] = cell[1] cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7])) Layers['Cell'] = cell elif 'Trans' in pName: names = pName.split(';') transId = transSel.index(names[0]) iY = int(names[1]) iX = int(names[2]) Trans = Layers['Transitions'][iY] Nx = len(Trans)-1 if not transId: #i.e. probability osum = 1.-Trans[iX][0] nsum = 1.-val for i in range(Nx+1): if i != iX: Trans[i][0] *= (nsum/osum) Trans[iX][0] = val if Layers.get('SymTrans',False): Layers['Transitions'][Nx-iX][Nx-iY][0] = val for i in range(Nx+1): Layers['Transitions'][Nx-iY][Nx-i][0] = Layers['Transitions'][iY][i][0] print (' Transition matrix:') for trans in Layers['Transitions']: line = str([' %.3f'%(item[0]) for item in trans]) print (line[1:-2].replace("'",'')) else: Trans[iX][transId] = val G2pwd.CalcStackingPWDR(Layers,scale,background,limits,inst,profile,False) resultXY2.append([np.vstack((profile[0],profile[3])),][0]) data['Layers']['seqResults'] = [resultXY,resultXY2,simNames] wx.MessageBox('Sequential simulation finished',caption='Stacking fault simulation',style=wx.ICON_EXCLAMATION) wx.CallAfter(UpdateLayerData) #### Wave Data page ################################################################################ def UpdateWavesData(Scroll=0): generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] typeNames = {'Sfrac':' Site fraction','Spos':' Position','Sadp':' Thermal motion','Smag':' Magnetic moment'} numVals = {'Sfrac':2,'Spos':6,'Sadp':12,'Smag':6,'ZigZag':5,'Block':5,'Crenel':2} posNames = ['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'] adpNames = ['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin', 'U11cos','U22cos','U33cos','U12cos','U13cos','U23cos'] magNames = ['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos'] fracNames = ['Fsin','Fcos','Fzero','Fwid'] waveTypes = {'Sfrac':['Fourier','Crenel'],'Spos':['Fourier','ZigZag','Block',],'Sadp':['Fourier',],'Smag':['Fourier',]} Labels = {'Spos':posNames,'Sfrac':fracNames,'Sadp':adpNames,'Smag':magNames} Indx = {} waveData = G2frame.waveData G2frame.GetStatusBar().SetStatusText('',1) generalData = data['General'] SGData = generalData['SGData'] SSGData = generalData['SSGData'] cx,ct,cs,cia = generalData['AtomPtrs'] atomData = data['Atoms'] D4Map = generalData.get('4DmapData',{'rho':[]}) if waveData.GetSizer(): waveData.GetSizer().Clear(True) mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(waveData,label=' Incommensurate propagation wave data: Select atom to edit: '),0,WACV) atNames = [] for atm in atomData: atNames.append(atm[ct-1]) if not atNames: return if G2frame.atmSel not in atNames: G2frame.atmSel = atNames[0] def OnAtmSel(event): Obj = event.GetEventObject() G2frame.atmSel = Obj.GetValue() RepaintAtomInfo() def RepaintAtomInfo(Scroll=0): G2frame.bottomSizer.Clear(True) G2frame.bottomSizer = ShowAtomInfo() mainSizer.Add(G2frame.bottomSizer) mainSizer.Layout() G2frame.dataWindow.Refresh() waveData.SetVirtualSize(mainSizer.GetMinSize()) waveData.Scroll(0,Scroll) G2frame.dataWindow.SendSizeEvent() def ShowAtomInfo(): global mapSel #so it can be seen below in OnWavePlot def AtomSizer(atom): global mapSel def OnShowWave(event): Obj = event.GetEventObject() atom = Indx[Obj.GetId()] Ax = Obj.GetValue() G2plt.ModulationPlot(G2frame,data,atom,Ax) atomSizer = wx.BoxSizer(wx.HORIZONTAL) atomSizer.Add(wx.StaticText(waveData,label= ' Modulation data for atom: %s Site sym: %s'%(atom[0],atom[cs].strip())),0,WACV) axchoice = ['x','y','z'] if len(D4Map['rho']): atomSizer.Add(wx.StaticText(waveData,label=' Show contour map for axis: '),0,WACV) mapSel = wx.ComboBox(waveData,value=' ',choices=axchoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) mapSel.Bind(wx.EVT_COMBOBOX,OnShowWave) Indx[mapSel.GetId()] = atom atomSizer.Add(mapSel,0,WACV) return atomSizer def WaveSizer(iatm,wavedata,Stype,typeName,Names): def OnWaveType(event): Obj = event.GetEventObject() item = Indx[Obj.GetId()] if len(atm[-1]['SS1'][item]) <= 1: atm[-1]['SS1'][item] = [0,] atm[-1]['SS1'][item][0] = waveType.GetValue() wx.CallAfter(RepaintAtomInfo,G2frame.waveData.GetScrollPos(wx.VERTICAL)) else: if len(waveTypes[Stype]) > 1: waveType.SetValue(atm[-1]['SS1'][Stype][0]) G2G.G2MessageBox(G2frame,'Warning: can only change wave type if no waves','Not changed') def OnAddWave(event): Obj = event.GetEventObject() item = Indx[Obj.GetId()] nt = numVals[Stype] if not len(atm[-1]['SS1'][item]): if waveTyp in ['ZigZag','Block','Crenel']: nt = numVals[waveTyp] atm[-1]['SS1'][item] = [0,] atm[-1]['SS1'][item][0] = waveType.GetValue() atm[-1]['SS1'][item].append([[0.0 for i in range(nt)],False]) wx.CallAfter(RepaintAtomInfo,G2frame.waveData.GetScrollPos(wx.VERTICAL)) def OnRefWave(event): Obj = event.GetEventObject() item,iwave = Indx[Obj.GetId()] atm[-1]['SS1'][item][iwave+1][1] = not atm[-1]['SS1'][item][iwave+1][1] def OnDelWave(event): Obj = event.GetEventObject() item,iwave = Indx[Obj.GetId()] del atm[-1]['SS1'][item][iwave+1] if len(atm[-1]['SS1'][item]) == 1: atm[-1]['SS1'][item][0] = 'Fourier' wx.CallAfter(RepaintAtomInfo,G2frame.waveData.GetScrollPos(wx.VERTICAL)) def OnWavePlot(invalid,value,tc): if len(D4Map['rho']): Ax = mapSel.GetValue() if Ax: G2plt.ModulationPlot(G2frame,data,atm,Ax) waveTyp,waveBlk = 'Fourier',[] if len(wavedata): waveTyp = wavedata[0] waveBlk = wavedata[1:] waveSizer = wx.BoxSizer(wx.VERTICAL) waveHead = wx.BoxSizer(wx.HORIZONTAL) waveHead.Add(wx.StaticText(waveData,label=typeName+' modulation parameters: '),0,WACV) if Stype == 'Smag' and len(waveBlk): #only allow one magnetic wave - keeps it simple for now pass else: waveAdd = wx.Button(waveData,label='Add wave?') waveAdd.Bind(wx.EVT_BUTTON, OnAddWave) Indx[waveAdd.GetId()] = Stype waveHead.Add(waveAdd,0,WACV) waveHead.Add(wx.StaticText(waveData,label=' WaveType: '),0,WACV) waveType = wx.ComboBox(waveData,value=waveTyp,choices=waveTypes[Stype], style=wx.CB_READONLY|wx.CB_DROPDOWN) Indx[waveType.GetId()] = Stype waveType.Bind(wx.EVT_COMBOBOX,OnWaveType) waveHead.Add(waveType,0,WACV) waveSizer.Add(waveHead) if len(waveBlk): nx = 0 for iwave,wave in enumerate(waveBlk): if not iwave: if waveTyp in ['ZigZag','Block','Crenel']: nx = 1 CSI = G2spc.GetSSfxuinel(waveTyp,Stype,1,xyz,SGData,SSGData)[0] else: CSI = G2spc.GetSSfxuinel('Fourier',Stype,iwave+1-nx,xyz,SGData,SSGData)[0] waveName = 'Fourier' if Stype == 'Sfrac': nterm = 2 if 'Crenel' in waveTyp and not iwave: waveName = 'Crenel' names = Names[2:] else: names = Names[:2] Waves = wx.FlexGridSizer(0,4,5,5) elif Stype == 'Spos': nterm = 6 if waveTyp in ['ZigZag','Block'] and not iwave: nterm = 5 names = Names[6:] Waves = wx.FlexGridSizer(0,7,5,5) waveName = waveTyp else: names = Names[:6] Waves = wx.FlexGridSizer(0,8,5,5) elif Stype == 'Sadp': nterm = 12 names = Names Waves = wx.FlexGridSizer(0,8,5,5) elif Stype == 'Smag': nterm = 6 names = Names Waves = wx.FlexGridSizer(0,8,5,5) waveSizer.Add(wx.StaticText(waveData,label=' %s parameters: %s'%(waveName,str(names).rstrip(']').lstrip('[').replace("'",''))),0) for ival in range(nterm): val = wave[0][ival] if np.any(CSI[0][ival]): minmax = [-0.2,0.2] if Stype == 'Smag': minmax = [-20.,20.] if waveTyp in ['ZigZag','Block','Crenel'] and not iwave and ival < 2: if not ival: minmax = [0.,2.] else: minmax = [wave[0][0],1.0+wave[0][0]] waveVal = G2G.ValidatedTxtCtrl(waveData,wave[0],ival,nDig=(10,5),xmin=minmax[0],xmax=minmax[1],OnLeave=OnWavePlot) else: waveVal = G2G.ReadOnlyTextCtrl(waveData,value='%.5f'%(val)) Waves.Add(waveVal,0,WACV) if len(wave[0]) > 6 and ival == 5: Waves.Add((5,5),0) Waves.Add((5,5),0) waveRef = wx.CheckBox(waveData,label='Refine?') waveRef.SetValue(wave[1]) Indx[waveRef.GetId()] = [Stype,iwave] waveRef.Bind(wx.EVT_CHECKBOX, OnRefWave) Waves.Add(waveRef,0,WACV) if iwave < len(waveBlk)-1: Waves.Add((5,5),0) else: waveDel = wx.Button(waveData,wx.ID_ANY,'Delete',style=wx.BU_EXACTFIT) Indx[waveDel.GetId()] = [Stype,iwave] waveDel.Bind(wx.EVT_BUTTON,OnDelWave) Waves.Add(waveDel,0,WACV) waveSizer.Add(Waves) return waveSizer iatm = atNames.index(G2frame.atmSel) atm = atomData[iatm] xyz = atm[cx:cx+3] atomSizer = wx.BoxSizer(wx.VERTICAL) G2G.HorizontalLine(atomSizer,waveData) atomSizer.Add(AtomSizer(atm)) for Stype in ['Sfrac','Spos','Sadp','Smag']: if atm[cia] != 'A' and Stype == 'Sadp': #Uiso can't have modulations! (why not?) continue if generalData['Type'] != 'magnetic' and Stype == 'Smag': break atomSizer.Add(WaveSizer(iatm,atm[-1]['SS1'][Stype],Stype,typeNames[Stype],Labels[Stype])) return atomSizer atms = wx.ComboBox(waveData,value=G2frame.atmSel,choices=atNames, style=wx.CB_READONLY|wx.CB_DROPDOWN) atms.Bind(wx.EVT_COMBOBOX,OnAtmSel) topSizer.Add(atms,0) mainSizer.Add(topSizer,0) G2frame.bottomSizer = ShowAtomInfo() mainSizer.Add(G2frame.bottomSizer) SetPhaseWindow(G2frame.waveData,mainSizer,Scroll=Scroll) def OnWaveVary(event): generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] atomData = data['Atoms'] atNames = [] names = ['Sfrac','Spos','Sadp','Smag'] flags = dict(zip(names,[[],[],[],[]])) for atom in atomData: atNames.append(atom[ct-1]) waves = atom[-1]['SS1'] for name in names: if waves[name]: flags[name].append(True) else: flags[name].append(False) dlg = G2G.FlagSetDialog(G2frame,'Wave refinement flags',['Atom',]+names,atNames,flags) try: if dlg.ShowModal() == wx.ID_OK: flags = dlg.GetSelection() for ia,atom in enumerate(atomData): for name in names: for wave in atom[-1]['SS1'][name][1:]: wave[1] = flags[name][ia] finally: dlg.Destroy() UpdateWavesData() #### Structure drawing GUI stuff ################################################################################ def SetupDrawingData(): generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) atomData = data['Atoms'] defaultDrawing = {'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True, 'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5, 'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33, 'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,'contourMax':1.0, 'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],'magMult':1.0,'SymFade':False, 'bondList':{},'viewDir':[1,0,0],'Plane':[[0,0,1],False,False,0.0,[255,255,0]]} V0 = np.array([0,0,1]) V = np.inner(Amat,V0) V /= np.sqrt(np.sum(V**2)) A = np.arccos(np.sum(V*V0)) defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0]) try: drawingData = data['Drawing'] except KeyError: data['Drawing'] = {} drawingData = data['Drawing'] if not drawingData: #fill with defaults if empty drawingData = defaultDrawing.copy() if 'Zstep' not in drawingData: drawingData['Zstep'] = 0.5 if 'contourLevel' not in drawingData: drawingData['contourLevel'] = 1. if 'contourMax' not in drawingData: drawingData['contourMax'] = 1. if 'viewDir' not in drawingData: drawingData['viewDir'] = [0,0,1] if 'Quaternion' not in drawingData: drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1])) if 'showRigidBodies' not in drawingData: drawingData['showRigidBodies'] = True if 'showSlice' not in drawingData: drawingData['showSlice'] = 0 if 'contourColor' not in drawingData: drawingData['contourColor'] = 'RdYlGn' if 'Plane' not in drawingData: drawingData['Plane'] = [[0,0,1],False,False,0.0,[255,255,0]] if 'magMult' not in drawingData: drawingData['magMult'] = 1.0 if 'SymFade' not in drawingData: drawingData['SymFade'] = False if 'Voids' not in drawingData: drawingData['Voids'] = [] drawingData['showVoids'] = False drawingData['showMap'] = False cx,ct,cs,ci = [0,0,0,0] if generalData['Type'] in ['nuclear','faulted',]: cx,ct,cs,ci = [2,1,6,17] #x, type, style & index elif generalData['Type'] == 'macromolecular': cx,ct,cs,ci = [5,4,9,20] #x, type, style & index elif generalData['Type'] == 'magnetic': cx,ct,cs,ci = [2,1,9,20] #x, type, style & index drawingData['vdwScale'] = 0.20 drawingData['atomPtrs'] = [cx,ct,cs,ci] if not drawingData.get('Atoms'): for atom in atomData: DrawAtomAdd(drawingData,atom) data['Drawing'] = drawingData if len(drawingData['Plane']) < 5: drawingData['Plane'].append([255,255,0]) def DrawAtomAdd(drawingData,atom): drawingData['Atoms'].append(G2mth.MakeDrawAtom(data,atom)) def OnRestraint(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) indx = getAtomSelections(drawAtoms,ct-1) if not indx: return indx = drawAtoms.GetSelectedRows() restData = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints')) drawingData = data['Drawing'] generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) atomData = drawingData['Atoms'] atXYZ = [] atSymOp = [] atIndx = [] for item in indx: atXYZ.append(np.array(atomData[item][cx:cx+3])) atSymOp.append(atomData[item][cs-1]) atIndx.append(atomData[item][ci]) if event.GetId() == G2G.wxID_DRAWRESTRBOND and len(indx) == 2: try: bondData = restData[PhaseName]['Bond'] except KeyError: bondData = {'wtFactor':1.0,'Bonds':[],'Use':True} restData[PhaseName] = {} restData[PhaseName]['Bond'] = bondData bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01]) elif event.GetId() == G2G.wxID_DRAWRESTRANGLE and len(indx) == 3: try: angleData = restData[PhaseName]['Angle'] except KeyError: angleData = {'wtFactor':1.0,'Angles':[],'Use':True} restData[PhaseName] = {} restData[PhaseName]['Angle'] = angleData angleData['Angles'].append([atIndx,atSymOp,109.5,1.0]) elif event.GetId() == G2G.wxID_DRAWRESTRPLANE and len(indx) > 3: try: planeData = restData[PhaseName]['Plane'] except KeyError: planeData = {'wtFactor':1.0,'Planes':[],'Use':True} restData[PhaseName] = {} restData[PhaseName]['Plane'] = planeData planeData['Planes'].append([atIndx,atSymOp,0.0,0.01]) elif event.GetId() == G2G.wxID_DRAWRESTRCHIRAL and len(indx) == 4: try: chiralData = restData[PhaseName]['Chiral'] except KeyError: chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True} restData[PhaseName] = {} restData[PhaseName]['Chiral'] = chiralData chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1]) else: print ('**** ERROR wrong number of atoms selected for this restraint') return G2frame.GPXtree.SetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints'),restData) def OnDefineRB(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) indx = getAtomSelections(drawAtoms,ct-1) if not indx: return indx.sort() RBData = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies')) drawingData = data['Drawing'] generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) atomData = drawingData['Atoms'] rbXYZ = [] rbType = [] atNames = [] AtInfo = RBData['Residue']['AtInfo'] for i,item in enumerate(indx): rbtype = atomData[item][ct] atNames.append(rbtype+str(i)) rbType.append(rbtype) if rbtype not in AtInfo: Info = G2elem.GetAtomInfo(rbtype) AtInfo[rbtype] = [Info['Drad'],Info['Color']] rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat)) rbXYZ = np.array(rbXYZ) rbXYZ -= rbXYZ[0] rbId = ran.randint(0,sys.maxsize) rbName = 'UNKRB' dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body', 'Edit rigid body name',rbName ,style=wx.OK) if dlg.ShowModal() == wx.ID_OK: rbName = dlg.GetValue() dlg.Destroy() RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType, 'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0} RBData['RBIds']['Residue'].append(rbId) G2frame.GetStatusBar().SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies',1) ##### Draw Atom routines ################################################################################ def UpdateDrawAtoms(atomStyle=''): def RefreshDrawAtomGrid(event): def SetChoice(name,c,n=0): choice = [] for r in range(len(atomData)): if n: srchStr = str(atomData[r][c][:n]) else: srchStr = str(atomData[r][c]) if srchStr not in choice: if n: choice.append(str(atomData[r][c][:n])) else: choice.append(str(atomData[r][c])) choice.sort() dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() parms = [] for x in sel: parms.append(choice[x]) drawAtoms.ClearSelection() drawingData['selectedAtoms'] = [] for row in range(len(atomData)): test = atomData[row][c] if n: test = test[:n] if test in parms: drawAtoms.SelectRow(row,True) drawingData['selectedAtoms'].append(row) G2plt.PlotStructure(G2frame,data) dlg.Destroy() r,c = event.GetRow(),event.GetCol() if r < 0 and c < 0: for row in range(drawAtoms.GetNumberRows()): drawingData['selectedAtoms'].append(row) drawAtoms.SelectRow(row,True) elif r < 0: #dclick on col label sel = -1 if drawAtoms.GetColLabelValue(c) == 'Style': dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = styleChoice[sel] for r in range(len(atomData)): atomData[r][c] = parms drawAtoms.SetCellValue(r,c,parms) FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) dlg.Destroy() elif drawAtoms.GetColLabelValue(c) == 'Label': dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = labelChoice[sel] for r in range(len(atomData)): atomData[r][c] = parms drawAtoms.SetCellValue(r,c,parms) dlg.Destroy() elif drawAtoms.GetColLabelValue(c) == 'Color': colors = wx.ColourData() colors.SetChooseFull(True) dlg = wx.ColourDialog(G2frame.GetParent(),colors) if dlg.ShowModal() == wx.ID_OK: color = dlg.GetColourData().GetColour()[:3] attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop! attr.SetReadOnly(True) attr.SetBackgroundColour(color) for r in range(len(atomData)): atomData[r][c] = color drawingData['Atoms'][r][c] = color drawAtoms.SetAttr(r,c,attr) UpdateDrawAtoms() dlg.Destroy() elif drawAtoms.GetColLabelValue(c) == 'Residue': SetChoice('Residue',c,3) elif drawAtoms.GetColLabelValue(c) == '1-letter': SetChoice('1-letter',c,1) elif drawAtoms.GetColLabelValue(c) == 'Chain': SetChoice('Chain',c) elif drawAtoms.GetColLabelValue(c) == 'Name': SetChoice('Name',c) elif drawAtoms.GetColLabelValue(c) == 'Sym Op': SetChoice('Name',c) elif drawAtoms.GetColLabelValue(c) == 'Type': SetChoice('Type',c) elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']: drawAtoms.ClearSelection() else: if drawAtoms.GetColLabelValue(c) in ['Style','Label']: atomData[r][c] = drawAtoms.GetCellValue(r,c) FindBondsDraw(data) elif drawAtoms.GetColLabelValue(c) == 'Color': colors = wx.ColourData() colors.SetChooseFull(True) dlg = wx.ColourDialog(G2frame.GetParent(),colors) if dlg.ShowModal() == wx.ID_OK: color = dlg.GetColourData().GetColour()[:3] attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop! attr.SetReadOnly(True) attr.SetBackgroundColour(color) atomData[r][c] = color drawingData['Atoms'][r][c] = color drawAtoms.SetAttr(i,cs+2,attr) dlg.Destroy() UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) def NextAtom(event): 'respond to a tab by cycling through the atoms' next = 0 for r in drawAtoms.GetSelectedRows(): next = r + 1 break if next >= drawAtoms.GetNumberRows(): next = 0 drawAtoms.ClearSelection() drawAtoms.SelectRow(next,True) drawAtoms.MakeCellVisible(next,0) drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows() G2plt.PlotStructure(G2frame,data) G2frame.Raise() def RowSelect(event): r,c = event.GetRow(),event.GetCol() if r < 0 and c < 0: if drawAtoms.IsSelection(): drawAtoms.ClearSelection() elif c < 0: #only row clicks if event.ControlDown(): if r in drawAtoms.GetSelectedRows(): drawAtoms.DeselectRow(r) else: drawAtoms.SelectRow(r,True) elif event.ShiftDown(): indxs = drawAtoms.GetSelectedRows() drawAtoms.ClearSelection() ibeg = 0 if indxs: ibeg = indxs[-1] for row in range(ibeg,r+1): drawAtoms.SelectRow(row,True) else: G2frame.GetStatusBar().SetStatusText('Use right mouse click to brng up Draw Atom editing options',1) drawAtoms.ClearSelection() drawAtoms.SelectRow(r,True) drawingData['selectedAtoms'] = [] drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows() G2plt.PlotStructure(G2frame,data) #### UpdateDrawAtoms executable code starts here G2frame.GetStatusBar().SetStatusText('',1) oldSizer = drawAtomsList.GetSizer() if oldSizer: # 2nd+ use, clear out old entries for i in oldSizer.GetChildren(): # look for grids in sizer if type(i.GetWindow()) is G2G.GSGrid: oldSizer.Detach(i.GetWindow()) # don't delete them oldSizer.Clear(True) generalData = data['General'] SetupDrawingData() drawingData = data['Drawing'] SetDrawingDefaults(drawingData) cx,ct,cs,ci = drawingData['atomPtrs'] atomData = drawingData['Atoms'] if atomStyle: for atom in atomData: atom[cs] = atomStyle Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \ [wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra", wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,] styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra'] labelChoice = [' ','type','name','number'] colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A'] if generalData['Type'] == 'macromolecular': colLabels = ['Residue','1-letter','Chain'] + colLabels Types = 3*[wg.GRID_VALUE_STRING,]+Types Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic" styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic'] labelChoice = [' ','type','name','number','residue','1-letter','chain'] Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain" elif generalData['Type'] == 'magnetic': colLabels = colLabels[:5]+['Mx','My','Mz']+colLabels[5:] Types = Types[:5]+3*[wg.GRID_VALUE_FLOAT+':10,4',]+Types[5:] table = [] rowLabels = [] for i,atom in enumerate(drawingData['Atoms']): table.append(atom[:colLabels.index('I/A')+1]) rowLabels.append(str(i)) G2frame.atomTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) drawAtoms.SetTable(G2frame.atomTable, True) drawAtoms.SetMargins(0,0) drawAtoms.AutoSizeColumns(True) drawAtoms.SetColSize(colLabels.index('Style'),80) drawAtoms.SetColSize(colLabels.index('Color'),50) if 'phoenix' in wx.version(): drawAtoms.Unbind(wg.EVT_GRID_CELL_CHANGED) drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGED, RefreshDrawAtomGrid) else: drawAtoms.Unbind(wg.EVT_GRID_CELL_CHANGE) drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshDrawAtomGrid) drawAtoms.Unbind(wg.EVT_GRID_LABEL_LEFT_DCLICK) drawAtoms.Unbind(wg.EVT_GRID_CELL_LEFT_DCLICK) drawAtoms.Unbind(wg.EVT_GRID_LABEL_LEFT_CLICK) drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshDrawAtomGrid) drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshDrawAtomGrid) drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect) lblList = ('Delete','Set atom style','Set atom label', 'Set atom color','Set view point','Generate copy', 'Generate surrounding sphere','Transform atoms', 'Generate bonded','Select from list') callList = (DrawAtomsDelete,DrawAtomStyle, DrawAtomLabel, DrawAtomColor,SetViewPoint,AddSymEquiv, AddSphere,TransformSymEquiv, FillCoordSphere,SelDrawList) onRightClick = drawAtoms.setupPopup(lblList,callList) drawAtoms.Bind(wg.EVT_GRID_CELL_RIGHT_CLICK, onRightClick) drawAtoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, onRightClick) try: drawAtoms.Bind(wg.EVT_GRID_TABBING, NextAtom) except: # patch: for pre-2.9.5 wx pass for i,atom in enumerate(drawingData['Atoms']): attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop! attr.SetReadOnly(True) attr.SetBackgroundColour(atom[cs+2]) drawAtoms.SetAttr(i,cs+2,attr) drawAtoms.SetCellValue(i,cs+2,'') indx = drawingData['selectedAtoms'] if indx: for r in range(len(atomData)): if r in indx: drawAtoms.SelectRow(r) for c in range(len(colLabels)): attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop! attr.SetReadOnly(True) attr.SetBackgroundColour(VERY_LIGHT_GREY) if colLabels[c] not in ['Style','Label','Color']: drawAtoms.SetColAttr(c,attr) mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(drawAtomsList,label='Draw Atom list for %s:'%generalData['Name']),0,WACV) topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(drawAtomsList,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(topSizer,0,wx.EXPAND) mainSizer.Add(drawAtoms) SetPhaseWindow(drawAtomsList,mainSizer) FindBondsDraw(data) drawAtoms.ClearSelection() def DrawAtomStyle(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) indx = getAtomSelections(drawAtoms,ct-1) if not indx: return generalData = data['General'] atomData = data['Drawing']['Atoms'] styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra'] if generalData['Type'] == 'macromolecular': styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids', 'backbone','ribbons','schematic'] dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = styleChoice[sel] for r in indx: atomData[r][cs] = parms drawAtoms.SetCellValue(r,cs,parms) dlg.Destroy() FindBondsDraw(data) drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def DrawAtomLabel(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) indx = getAtomSelections(drawAtoms,ct-1) if not indx: return generalData = data['General'] atomData = data['Drawing']['Atoms'] styleChoice = [' ','type','name','number'] if generalData['Type'] == 'macromolecular': styleChoice = [' ','type','name','number','residue','1-letter','chain'] dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parms = styleChoice[sel] for r in indx: atomData[r][cs+1] = parms drawAtoms.SetCellValue(r,cs+1,parms) dlg.Destroy() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def DrawAtomColor(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) indx = getAtomSelections(drawAtoms,ct-1) if not indx: return if len(indx) > 1: G2frame.GetStatusBar().SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK',1) else: G2frame.GetStatusBar().SetStatusText('Change color, Add to Custom Colors, then OK',1) atomData = data['Drawing']['Atoms'] atmColors = [] atmTypes = [] for r in indx: if atomData[r][cs+2] not in atmColors: atmColors.append(atomData[r][cs+2]) atmTypes.append(atomData[r][ct]) if len(atmColors) > 16: break colors = wx.ColourData() colors.SetChooseFull(True) dlg = wx.ColourDialog(None,colors) if dlg.ShowModal() == wx.ID_OK: for i in range(len(atmColors)): atmColors[i] = dlg.GetColourData().GetColour()[:3] colorDict = dict(zip(atmTypes,atmColors)) for r in indx: color = colorDict[atomData[r][ct]] atomData[r][cs+2] = color attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop! attr.SetBackgroundColour(color) drawAtoms.SetAttr(r,cs+2,attr) data['Drawing']['Atoms'][r][cs+2] = color drawAtoms.ClearSelection() dlg.Destroy() G2frame.GetStatusBar().SetStatusText('',1) G2plt.PlotStructure(G2frame,data) def ResetAtomColors(event): generalData = data['General'] atomData = data['Drawing']['Atoms'] cx,ct,cs,ci = data['Drawing']['atomPtrs'] for atom in atomData: atNum = generalData['AtomTypes'].index(atom[ct]) atom[cs+2] = list(generalData['Color'][atNum]) UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def OnEditAtomRadii(event): DisAglCtls = {} generalData = data['General'] if 'DisAglCtls' in generalData: DisAglCtls = generalData['DisAglCtls'] dlg = G2G.DisAglDialog(G2frame,DisAglCtls,generalData,Angle=False) if dlg.ShowModal() == wx.ID_OK: DisAglCtls = dlg.GetData() dlg.Destroy() generalData['DisAglCtls'] = DisAglCtls FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) def SetViewPoint(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) indx = getAtomSelections(drawAtoms,ct-1) if not indx: return atomData = data['Drawing']['Atoms'] pos = np.zeros(3) for i in indx: pos += atomData[i][cx:cx+3] data['Drawing']['viewPoint'] = [list(pos/len(indx)),[indx[0],0]] G2plt.PlotStructure(G2frame,data) def noDuplicate(xyz,atomData): #be careful where this is used - it's slow cx = data['Drawing']['atomPtrs'][0] if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]: return False else: return True def AddSymEquiv(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) indx = getAtomSelections(drawAtoms,ct-1) if not indx: return indx.sort() colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] cuij = ci+2 cmx = 0 if 'Mx' in colLabels: cmx = colLabels.index('Mx') atomData = data['Drawing']['Atoms'] generalData = data['General'] SGData = generalData['SGData'] SpnFlp = SGData.get('SpnFlp',[]) dlg = SymOpDialog(G2frame,SGData,False,True) try: if dlg.ShowModal() == wx.ID_OK: Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection() Cell = np.array(Cell) cent = SGData['SGCen'][Cent] M,T = SGData['SGOps'][Opr] for ind in indx: XYZ = np.array(atomData[ind][cx:cx+3]) XYZ = np.inner(M,XYZ)+T if Inv and not SGData['SGFixed']: XYZ = -XYZ XYZ = XYZ+cent+Cell if Force: XYZ %= 1. #G2spc.MoveToUnitCell(XYZ) if noDuplicate(XYZ,atomData): atom = copy.copy(atomData[ind]) atom[cx:cx+3] = XYZ atomOp = atom[cs-1] OprNum = ((Opr+1)+100*Cent)*(1-2*Inv) newOp = str(OprNum)+'+'+ \ str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2])) atom[cs-1] = G2spc.StringOpsProd(atomOp,newOp,SGData) if cmx: #magnetic moment opNum = G2spc.GetOpNum(OprNum,SGData) mom = np.array(atom[cmx:cmx+3]) if SGData['SGGray']: atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M) else: atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum-1] if atom[cuij] == 'A': Uij = atom[cuij:cuij+6] Uij = G2spc.U2Uij(np.inner(np.inner(M,G2spc.Uij2U(Uij)),M)) atom[cuij:cuij+6] = Uij atomData.append(atom[:cuij+9]) #not SS stuff finally: dlg.Destroy() UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def AddSphere(event): cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) indx = getAtomSelections(drawAtoms,ct-1,'as center of sphere addition', includeView=True) if not indx: return generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) atomData = data['Drawing']['Atoms'] numAtoms = len(atomData) cuij = cs+5 colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] cmx = 0 if 'Mx' in colLabels: cmx = colLabels.index('Mx') SGData = generalData['SGData'] SpnFlp = SGData.get('SpnFlp',[]) cellArray = G2lat.CellBlock(1) indx.sort() dlg = SphereEnclosure(G2frame,data['General'],data['Drawing'],indx) try: if dlg.ShowModal() == wx.ID_OK: centers,radius,targets = dlg.GetSelection() ncent = len(centers) pgbar = wx.ProgressDialog('Sphere of enclosure for %d atoms'%ncent,'Centers done=',ncent+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) for ic,orig in enumerate(centers): xyzA = np.array(orig) for atomB in atomData[:numAtoms]: if atomB[ct] not in targets: continue xyzB = np.array(atomB[cx:cx+3]) Uij = atomB[cuij:cuij+6] result = G2spc.GenAtom(xyzB,SGData,False,Uij,True) for item in result: atom = copy.copy(atomB) atom[cx:cx+3] = item[0] Opr = abs(item[2])%100 M = SGData['SGOps'][Opr-1][0] if cmx: opNum = G2spc.GetOpNum(item[2],SGData) mom = np.array(atom[cmx:cmx+3]) if SGData['SGGray']: atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M) else: atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum-1] atom[cs-1] = str(item[2])+'+' atom[cuij:cuij+6] = item[1] for xyz in cellArray+np.array(atom[cx:cx+3]): dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2)) if 0 < dist <= radius: if noDuplicate(xyz,atomData): C = xyz-atom[cx:cx+3]+item[3] newAtom = atom[:] newAtom[cx:cx+3] = xyz newAtom[cs-1] += str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2]))) atomData.append(newAtom) GoOn = pgbar.Update(ic,newmsg='Centers done=%d'%(ic)) if not GoOn[0]: break pgbar.Destroy() finally: dlg.Destroy() UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def TransformSymEquiv(event): indx = getAtomSelections(drawAtoms) if not indx: return indx.sort() atomData = data['Drawing']['Atoms'] colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] cx,ct,cs,ci = data['Drawing']['atomPtrs'] cuij = ci+2 cmx = 0 if 'Mx' in colLabels: cmx = colLabels.index('Mx') atomData = data['Drawing']['Atoms'] generalData = data['General'] SGData = generalData['SGData'] SpnFlp = SGData.get('SpnFlp',[]) dlg = SymOpDialog(G2frame,SGData,False,True) try: if dlg.ShowModal() == wx.ID_OK: Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection() Cell = np.array(Cell) cent = SGData['SGCen'][Cent] M,T = SGData['SGOps'][Opr] for ind in indx: XYZ = np.array(atomData[ind][cx:cx+3]) XYZ = np.inner(M,XYZ)+T if Inv and not SGData['SGFixed']: XYZ = -XYZ XYZ = XYZ+cent+Cell if Force: XYZ,cell = G2spc.MoveToUnitCell(XYZ) Cell += cell atom = atomData[ind] atom[cx:cx+3] = XYZ OprNum = ((Opr+1)+100*Cent)*(1-2*Inv) if cmx: opNum = G2spc.GetOpNum(OprNum,SGData) mom = np.array(atom[cmx:cmx+3]) atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum-1] atomOp = atom[cs-1] newOp = str(((Opr+1)+100*Cent)*(1-2*Inv))+'+'+ \ str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2])) atom[cs-1] = G2spc.StringOpsProd(atomOp,newOp,SGData) if atom[ci] == 'A': Uij = atom[cuij:cuij+6] U = G2spc.Uij2U(Uij) U = np.inner(np.inner(M,U),M) Uij = G2spc.U2Uij(U) atom[cuij:cuij+6] = Uij data['Drawing']['Atoms'] = atomData finally: dlg.Destroy() UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def FillMolecule(event): '''This is called by the Complete Molecule command. It adds a layer of bonded atoms of the selected types for all selected atoms in the Draw Atoms table. If the number of repetitions is greater than one, the added atoms (other than H atoms, which are assumed to only have one bond) are then searched for the next surrounding layer of bonded atoms. ''' indx = getAtomSelections(drawAtoms) if not indx: return generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) atomTypes,radii = getAtomRadii(data) dlg = wx.Dialog(G2frame,wx.ID_ANY,'Addition criteria', pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) dlg.CenterOnParent() mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,'Molecular completion parameters'),0) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,'Pause after: '),0) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add((45,-1)) choices = [1,2,5,10,50] params = {'maxrep':10, 'maxatm':1000} topSizer.Add(G2G.EnumSelector(dlg,params,'maxrep', [str(i) for i in choices],choices)) topSizer.Add(wx.StaticText(dlg,wx.ID_ANY,' repetitions'),0,WACV) mainSizer.Add(topSizer,0) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add((45,-1)) choices = [100,500,1000,5000,10000] topSizer.Add(G2G.EnumSelector(dlg,params,'maxatm', [str(i) for i in choices],choices)) topSizer.Add(wx.StaticText(dlg,wx.ID_ANY,' added atoms'),0,WACV) mainSizer.Add(topSizer,0) mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,'Atom types to add:'),0) atSizer = wx.BoxSizer(wx.HORIZONTAL) for i,item in enumerate(atomTypes): params[item] = True atm = G2G.G2CheckBox(dlg,item,params,item) atSizer.Add(atm,0,WACV) mainSizer.Add(atSizer,0) OkBtn = wx.Button(dlg,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_OK)) cancelBtn = wx.Button(dlg,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_CANCEL)) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) dlg.SetSizer(mainSizer) dlg.Fit() if dlg.ShowModal() != wx.ID_OK: dlg.Destroy() return dlg.Destroy() try: indH = atomTypes.index('H') radii[indH] = 0.5 except: pass colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] cmx = 0 if 'Mx' in colLabels: cmx = colLabels.index('Mx') neighborArray = FindCoordinationByLabel(data) time1 = time.time() added = 0 targets = [item for item in atomTypes if params[item]] cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True) rep = 0 allrep = 0 while True: if rep == 0: pgbar = wx.ProgressDialog('Fill molecular coordination', 'Passes done=0 %0',params['maxrep']+1, parent=G2frame, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) pgbar.Raise() wx.Yield() startlen = len(data['Drawing']['Atoms']) coordsArray = np.array([a[cx:cx+3] for a in data['Drawing']['Atoms']]) addedAtoms = [] for Ind,ind in enumerate(indx): addedAtoms += FindCoordination(ind,data,neighborArray,coordsArray,cmx,targets) GoOn = pgbar.Update(rep+1, newmsg='Passes done={} atom #{} of {}' .format(rep+1,Ind+1,len(indx))) if not GoOn[0]: break if not GoOn[0]: break print('pass {} processed {} atoms adding {}; Search time: {:.2f}s'.format( allrep+1,len(indx),len(addedAtoms),time.time()-time1)) time1 = time.time() rep += 1 allrep += 1 if len(addedAtoms) == 0: break added += len(addedAtoms) data['Drawing']['Atoms'] += addedAtoms # atoms to search over (omit H) indx = [i+startlen for i in range(len(addedAtoms)) if addedAtoms[i][ct] != 'H'] if len(indx) == 0: break if added > params['maxatm']: msg = "Exceeded number added atoms. Continue?" dlg = wx.MessageDialog(G2frame,msg,caption='Continue?',style=wx.YES_NO) if dlg.ShowModal() != wx.ID_YES: dlg.Destroy() break dlg.Destroy() rep = 0 added = 1 pgbar.Destroy() if rep >= params['maxrep']: msg = "Exceeded number of repetitions. Continue?" dlg = wx.MessageDialog(G2frame,msg,caption='Continue?',style=wx.YES_NO) if dlg.ShowModal() != wx.ID_YES: dlg.Destroy() break dlg.Destroy() rep = 0 added = 1 pgbar.Destroy() UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) pgbar.Destroy() UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def FillCoordSphere(event): time0 = time.time() generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) radii = generalData['BondRadii'] atomTypes = generalData['AtomTypes'] try: indH = atomTypes.index('H') radii[indH] = 0.5 except: pass indx = drawAtoms.GetSelectedRows() if indx: indx.sort() atomData = data['Drawing']['Atoms'] numAtoms = len(atomData) cx,ct,cs,ci = data['Drawing']['atomPtrs'] cij = ci+2 SGData = generalData['SGData'] cellArray = G2lat.CellBlock(1) nind = len(indx) pgbar = wx.ProgressDialog('Fill CN sphere for %d atoms'%nind,'Atoms done=',nind+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) for Ind,ind in enumerate(indx): atomA = atomData[ind] xyzA = np.array(atomA[cx:cx+3]) indA = atomTypes.index(atomA[ct]) for atomB in atomData[:numAtoms]: indB = atomTypes.index(atomB[ct]) sumR = radii[indA]+radii[indB] xyzB = np.array(atomB[cx:cx+3]) for xyz in cellArray+xyzB: dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2)) if 0 < dist <= data['Drawing']['radiusFactor']*sumR: if noDuplicate(xyz,atomData): oprB = atomB[cs-1] C = xyz-xyzB newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2]))) newAtom = atomB[:] newAtom[cx:cx+3] = xyz newAtom[cs-1] = G2spc.StringOpsProd(oprB,newOp,SGData) atomData.append(newAtom[:cij+9]) #not SS stuff GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind)) if not GoOn[0]: break pgbar.Destroy() data['Drawing']['Atoms'] = atomData print('search time: %.3f'%(time.time()-time0)) UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) else: G2G.G2MessageBox(G2frame,'Select atoms first') def FillCoordSphereNew(event): time0 = time.time() indx = getAtomSelections(drawAtoms) if not indx: return generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) atomTypes,radii = getAtomRadii(data) try: indH = atomTypes.index('H') radii[indH] = 0.5 except: pass indx.sort() atomData = data['Drawing']['Atoms'] cx,ct,cs,ci = data['Drawing']['atomPtrs'] colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] neighborArray = FindCoordinationByLabel(data) coordsArray = np.array([a[cx:cx+3] for a in data['Drawing']['Atoms']]) cmx = 0 if 'Mx' in colLabels: cmx = colLabels.index('Mx') nind = len(indx) pgbar = wx.ProgressDialog('Fill CN sphere for %d atoms'%nind,'Atoms done=',nind+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) for Ind,ind in enumerate(indx): atomData += FindCoordination(ind,data,neighborArray,coordsArray,cmx,atomTypes) GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind)) if not GoOn[0]: break pgbar.Destroy() data['Drawing']['Atoms'] = atomData print('search time: %.3f'%(time.time()-time0)) UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def FillUnitCell(event): indx = getAtomSelections(drawAtoms) if not indx: return indx.sort() atomData = data['Drawing']['Atoms'] colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] cx,ct,cs,ci = data['Drawing']['atomPtrs'] cmx = 0 if 'Mx' in colLabels: cmx = colLabels.index('Mx') cuij = cs+5 generalData = data['General'] SGData = generalData['SGData'] SpnFlp = SGData.get('SpnFlp',[]) nind = len(indx) pgbar = wx.ProgressDialog('Fill unit cell for %d atoms'%nind,'Atoms done=',nind+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) for Ind,ind in enumerate(indx): atom = atomData[ind] XYZ = np.array(atom[cx:cx+3]) Uij = atom[cuij:cuij+6] result = G2spc.GenAtom(XYZ,SGData,False,Uij,True) for item in result: atom = copy.copy(atomData[ind]) atom[cx:cx+3] = item[0] if cmx: Opr = abs(item[2])%100 M = SGData['SGOps'][Opr-1][0] opNum = G2spc.GetOpNum(item[2],SGData) mom = np.array(atom[cmx:cmx+3]) if SGData['SGGray']: atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M) else: atom[cmx:cmx+3] = np.inner(mom,M)*nl.det(M)*SpnFlp[opNum-1] atom[cs-1] = str(item[2])+'+' \ +str(item[3][0])+','+str(item[3][1])+','+str(item[3][2]) atom[cuij:cuij+6] = item[1] Opp = G2spc.Opposite(item[0]) for key in Opp: if noDuplicate(Opp[key],atomData) or atom[ct] == 'Q': unit = item[3]+np.array(eval(key))*1. cell = '%d+%d,%d,%d'%(item[2],unit[0],unit[1],unit[2]) atom[cx:cx+3] = Opp[key] atom[cs-1] = cell atomData.append(atom[:cuij+7]+atom[-2:]) #not SS stuff data['Drawing']['Atoms'] = atomData GoOn = pgbar.Update(Ind,newmsg='Atoms done=%d'%(Ind)) if not GoOn[0]: break pgbar.Destroy() UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def DrawAtomsDelete(event): indx = getAtomSelections(drawAtoms) if not indx: return indx.sort() atomData = data['Drawing']['Atoms'] indx.reverse() for ind in indx: del atomData[ind] UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) event.StopPropagation() def SelDrawList(event): 'select atoms using a filtered listbox' choices = [] for i in range(drawAtoms.GetNumberRows()): val = drawAtoms.GetCellValue(i,0) if val in choices: val += '_' + str(i) choices.append(val) if not choices: return dlg = G2G.G2MultiChoiceDialog(G2frame,'Select atoms','Choose atoms to select',choices) indx = [] if dlg.ShowModal() == wx.ID_OK: indx = dlg.GetSelections() dlg.Destroy() if len(indx) == 0: return drawAtoms.ClearSelection() for row in indx: drawAtoms.SelectRow(row,True) G2plt.PlotStructure(G2frame,data) event.StopPropagation() def DrawLoadSel(event): '''Copy selected atoms from the atoms list into the draw atoms list, making sure not to duplicate any. ''' choices = [atm[0] for atm in data['Atoms']] dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select atoms','Choose atoms to select',choices) indx = [] if dlg.ShowModal() == wx.ID_OK: indx = dlg.GetSelections() dlg.Destroy() if len(indx) == 0: return drawingData = data['Drawing'] cxD,ctD,_,_ = data['Drawing']['atomPtrs'] cx,ct,cs,cia = data['General']['AtomPtrs'] atmsXYZ = [np.array(a[cx:cx+3]) for a in data['Atoms']] for i in indx: found = False for dA in drawingData['Atoms']: if (dA[ctD] == data['Atoms'][i][ct] and dA[ctD-1] == data['Atoms'][i][ct-1] and dA[cxD+3] == '1' and np.sum((atmsXYZ[i]-dA[cxD:cxD+3])**2) < 0.001): found = True break if not found: DrawAtomAdd(drawingData,data['Atoms'][i]) UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) event.StopPropagation() def OnReloadDrawAtoms(event=None): atomData = data['Atoms'] cx,ct,cs,ci = data['General']['AtomPtrs'] for atom in atomData: ID = atom[ci+8] G2mth.DrawAtomsReplaceByID(data,ci+8,atom,ID) UpdateDrawAtoms() drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) if event: event.StopPropagation() def DrawAtomsDeleteByIDs(IDs): atomData = data['Drawing']['Atoms'] cx,ct,cs,ci = data['General']['AtomPtrs'] loc = ci+8 indx = G2mth.FindAtomIndexByIDs(atomData,loc,IDs) indx.reverse() for ind in indx: del atomData[ind] def ChangeDrawAtomsByIDs(colName,IDs,value): atomData = data['Drawing']['Atoms'] cx,ct,cs,ci = data['Drawing']['atomPtrs'] if colName == 'Name': col = ct-1 elif colName == 'Type': col = ct elif colName == 'I/A': col = cs indx = G2mth.FindAtomIndexByIDs(atomData,ci+8,IDs) for ind in indx: atomData[ind][col] = value def OnDrawPlane(event): indx = getAtomSelections(drawAtoms) if len(indx) < 4: G2G.G2MessageBox(G2frame,'Select four or more atoms first') print ('**** ERROR - need 4+ atoms for plane calculation') return PlaneData = {} drawingData = data['Drawing'] atomData = drawingData['Atoms'] colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] cx = colLabels.index('x') cn = colLabels.index('Name') xyz = [] for i,atom in enumerate(atomData): if i in indx: xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3]) generalData = data['General'] PlaneData['Name'] = generalData['Name'] PlaneData['Atoms'] = xyz PlaneData['Cell'] = generalData['Cell'][1:] #+ volume G2stMn.BestPlane(PlaneData) def OnDrawDistVP(event): # distance to view point indx = getAtomSelections(drawAtoms,action='distance calc') if not indx: return generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) drawingData = data['Drawing'] viewPt = np.array(drawingData['viewPoint'][0]) print (' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])) atomDData = drawingData['Atoms'] colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] cx = colLabels.index('x') cn = colLabels.index('Name') cs = colLabels.index('Sym Op') for i in indx: atom = atomDData[i] Dx = np.array(atom[cx:cx+3])-viewPt dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)) print ('Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cs],dist)) def OnDrawDAT(event): #compute distance, angle, or torsion depending on number of selections indx = getAtomSelections(drawAtoms) if len(indx) not in [2,3,4]: G2G.G2MessageBox(G2frame,'Select 2, 3 or 4 atoms first') print ('**** ERROR - wrong number of atoms for distance, angle or torsion calculation') return DATData = {} ocx,oct,ocs,cia = data['General']['AtomPtrs'] drawingData = data['Drawing'] atomData = data['Atoms'] atomDData = drawingData['Atoms'] colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())] cx = colLabels.index('x') cn = colLabels.index('Name') cid = colLabels.index('I/A')+8 xyz = [] Oxyz = [] DATData['Natoms'] = len(indx) for i in indx: atom = atomDData[i] xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op Id = G2mth.FindAtomIndexByIDs(atomData,cid,[atom[cid],],False)[0] Oxyz.append([Id,]+atomData[Id][cx+1:cx+4]) DATData['Datoms'] = xyz DATData['Oatoms'] = Oxyz generalData = data['General'] DATData['Name'] = generalData['Name'] DATData['SGData'] = generalData['SGData'] DATData['Cell'] = generalData['Cell'][1:] #+ volume if 'pId' in data: DATData['pId'] = data['pId'] DATData['covData'] = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Covariance')) G2stMn.DisAglTor(DATData) def MapVoid(event): generalData = data['General'] rMax = max(data['General']['vdWRadii']) cell = data['General']['Cell'][1:7] drawingData = data['Drawing'] voidDlg = wx.Dialog(G2frame,wx.ID_ANY,'Void computation parameters',style=wx.DEFAULT_DIALOG_STYLE) mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(voidDlg,wx.ID_ANY, 'Set parameters for void computation for phase '+generalData.get('Name','?'))) # get cell ranges xmax = 2. - rMax/cell[0] voidPar = {'a':1., 'b':1., 'c':1., 'grid':.25, 'probe':0.5} for i in ('a', 'b', 'c'): mainSizer.Add(G2G.G2SliderWidget(voidDlg,voidPar,i,'Max '+i+' value: ',0.,xmax,100)) hSizer = wx.BoxSizer(wx.HORIZONTAL) hSizer.Add(wx.StaticText(voidDlg,wx.ID_ANY,'Grid spacing (A)')) hSizer.Add(G2G.ValidatedTxtCtrl(voidDlg,voidPar,'grid',nDig=(5,2), xmin=0.1, xmax=2., typeHint=float)) mainSizer.Add(hSizer) hSizer = wx.BoxSizer(wx.HORIZONTAL) hSizer.Add(wx.StaticText(voidDlg,wx.ID_ANY,'Probe radius (A)')) hSizer.Add(G2G.ValidatedTxtCtrl(voidDlg,voidPar,'probe',nDig=(5,2), xmin=0.1, xmax=2., typeHint=float)) mainSizer.Add(hSizer) def OnOK(event): voidDlg.EndModal(wx.ID_OK) mainSizer.Add([5,5]) btnsizer = wx.StdDialogButtonSizer() btn = wx.Button(voidDlg, wx.ID_OK) btn.Bind(wx.EVT_BUTTON, OnOK) btn.SetDefault() btnsizer.AddButton(btn) btn = wx.Button(voidDlg, wx.ID_CANCEL) btnsizer.AddButton(btn) btnsizer.Realize() mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) voidDlg.SetSizer(mainSizer) mainSizer.Fit(voidDlg) voidDlg.CenterOnParent() res = voidDlg.ShowModal() voidDlg.Destroy() if res != wx.ID_OK: return drawingData['Voids'] = VoidMap(data, voidPar['a'], voidPar['b'], voidPar['c'], voidPar['grid'],voidPar['probe']) drawingData['showVoids'] = True G2plt.PlotStructure(G2frame,data) #### Draw Options page ################################################################################ def UpdateDrawOptions(): def SlopSizer(): def OnCameraPos(): #old code # drawingData['cameraPos'] = cameraPos.GetValue() # cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos'])) # Zclip.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.)) #new code # drawingData['Zclip'] = min(drawingData['Zclip'],0.95*drawingData['cameraPos']) Zclip.SetScaledValue(drawingData['Zclip']) Zval.SetValue(drawingData['Zclip']) xmin=1.0 #.01*drawingData['Zclip']*drawingData['cameraPos']/100. xmax=2.*drawingData['cameraPos'] Zclip.SetScaledRange(xmin,xmax) Zclip.SetMax(xmax) Zval.Validator.xmin = xmin Zval.Validator.xmax = xmax #end new code G2plt.PlotStructure(G2frame,data) def OnMoveZ(event): #old code # drawingData['Zclip'] = Zclip.GetValue() # Zclip.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.)) #new code move = MoveZ.GetValue()*drawingData['Zstep'] MoveZ.SetValue(0) VP = np.inner(Amat,np.array(drawingData['viewPoint'][0])) VD = np.inner(Amat,np.array(drawingData['viewDir'])) VD /= np.sqrt(np.sum(VD**2)) VP += move*VD VP = np.inner(Bmat,VP) drawingData['viewPoint'][0] = VP panel = drawOptions.GetChildren() names = [child.GetName() for child in panel] panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2])) #end new code G2plt.PlotStructure(G2frame,data) def OnRadFactor(invalid,value,tc): FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) slopSizer = wx.BoxSizer(wx.HORIZONTAL) slideSizer = wx.FlexGridSizer(0,3,0,0) slideSizer.AddGrowableCol(2,1) valSize = (50,20) cameraPosTxt,cameraPos = G2G.G2SliderWidget( drawOptions,drawingData,'cameraPos', sizer=slideSizer, nDig=(10,1),xmin=5.,xmax=500.,size=valSize, label=' Camera Distance, '+Angstr+': ',iscale=5., onChange=OnCameraPos) G2frame.phaseDisplay.cameraPosTxt = cameraPosTxt G2frame.phaseDisplay.cameraSlider = cameraPos Zval,Zclip = G2G.G2SliderWidget( drawOptions,drawingData,'Zclip', sizer=slideSizer,size=valSize, xmin=1.0, #.01*drawingData['Zclip']*drawingData['cameraPos']/100., xmax=2.*drawingData['cameraPos'], nDig=(10,2), label=' Z clipping, '+Angstr+': ',iscale=50., onChange=G2plt.PlotStructure,onChangeArgs=[G2frame,data]) G2frame.phaseDisplay.Zval = Zval G2frame.phaseDisplay.Zclip = Zclip OnCameraPos() slideSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,' Z step, '+Angstr+': '),0,WACV) Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0,size=valSize) slideSizer.Add(Zstep,0,WACV) MoveSizer = wx.BoxSizer(wx.HORIZONTAL) MoveSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,' Press to step:'),0,WACV) MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=valSize) MoveZ.SetValue(0) MoveZ.SetRange(-1,1) MoveZ.Bind(wx.EVT_SPIN, OnMoveZ) MoveSizer.Add(MoveZ) slideSizer.Add(MoveSizer,1,wx.EXPAND|wx.RIGHT) G2G.G2SliderWidget( drawOptions,drawingData,'vdwScale', sizer=slideSizer,size=valSize, xmin=0.01, xmax=1.0, nDig=(10,3),iscale=50., label=' van der Waals scale: ', onChange=G2plt.PlotStructure,onChangeArgs=[G2frame,data]) G2G.G2SliderWidget( drawOptions,drawingData,'ellipseProb', sizer=slideSizer,size=valSize, xmin=1, xmax=99, nDig=(10,2),iscale=2., label=' Ellipsoid probability, %: ', onChange=G2plt.PlotStructure,onChangeArgs=[G2frame,data]) G2G.G2SliderWidget( drawOptions,drawingData,'ballScale', sizer=slideSizer,size=valSize, xmin=0.01, xmax=0.99, nDig=(10,3),iscale=100., label=' Ball scale: ', onChange=G2plt.PlotStructure,onChangeArgs=[G2frame,data]) G2G.G2SliderWidget( drawOptions,drawingData,'bondRadius', sizer=slideSizer,size=valSize, xmin=0.01, xmax=0.25, nDig=(10,2),iscale=500., label=' Bond radius, '+Angstr+': ', onChange=G2plt.PlotStructure,onChangeArgs=[G2frame,data]) if generalData['Type'] == 'magnetic': G2G.G2SliderWidget( drawOptions,drawingData,'magMult', sizer=slideSizer,size=valSize, xmin=0.1, xmax=1.2, nDig=(10,2),iscale=100., label=' Mag. mom. mult.: ', onChange=G2plt.PlotStructure,onChangeArgs=[G2frame,data]) slideSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,' Bond search factor: '),0,WACV) slideSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,drawingData,'radiusFactor', nDig=(10,2),xmin=0.1,xmax=1.2,size=valSize,OnLeave=OnRadFactor),0,WACV) slideSizer.Add((-1,-1)) slopSizer.Add(slideSizer,1,wx.EXPAND|wx.RIGHT) slopSizer.Add((10,5),0) slopSizer.SetMinSize(wx.Size(350,10)) return slopSizer def ShowSizer(): def OnShowABC(event): drawingData['showABC'] = showABC.GetValue() G2plt.PlotStructure(G2frame,data) def OnShowUnitCell(event): drawingData['unitCellBox'] = unitCellBox.GetValue() G2plt.PlotStructure(G2frame,data) G2frame.GPXtree.UpdateSelection() # wx.CallAfter(UpdateDrawOptions) def OnShowHyd(event): drawingData['showHydrogen'] = showHydrogen.GetValue() FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) def OnShowRB(event): drawingData['showRigidBodies'] = showRB.GetValue() FindBondsDraw(data) G2plt.PlotStructure(G2frame,data) def OnSymFade(event): drawingData['SymFade'] = symFade.GetValue() G2plt.PlotStructure(G2frame,data) def OnShowVoids(event): drawingData['showVoids'] = showVoids.GetValue() G2plt.PlotStructure(G2frame,data) def OnShowSlice(event): drawingData['showSlice'] = G2frame.phaseDisplay.showCS.GetSelection() G2frame.phaseDisplay.showCS.SetValue(slices[drawingData['showSlice']]) G2plt.PlotStructure(G2frame,data) def OnContourMax(event): drawingData['contourMax'] = contourMax.GetValue()/100. contourMaxTxt.SetLabel(' Max.: '+'%.2f'%(drawingData['contourMax']*generalData['Map']['rhoMax'])) G2plt.PlotStructure(G2frame,data) def OnViewPoint(event): event.Skip() Obj = event.GetEventObject() viewPt = Obj.GetValue().split() try: VP = [float(viewPt[i]) for i in range(3)] except (ValueError,IndexError): VP = drawingData['viewPoint'][0] Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2])) drawingData['viewPoint'][0] = VP G2plt.PlotStructure(G2frame,data) def OnViewDir(event): event.Skip() Obj = event.GetEventObject() viewDir = Obj.GetValue().split() try: Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) #reset view to stndard drawingData['viewDir'] = [0,0,1] drawingData['oldxy'] = [] V0 = np.array([0,0,1]) V = np.inner(Amat,V0) V /= np.sqrt(np.sum(V**2)) A = np.arccos(np.sum(V*V0)) Q = G2mth.AV2Q(A,[0,1,0]) drawingData['Quaternion'] = Q #new view made here VD = np.array([float(viewDir[i]) for i in range(3)]) VC = np.inner(Amat,VD) VC /= np.sqrt(np.sum(VC**2)) V = np.array(drawingData['viewDir']) VB = np.inner(Amat,V) VB /= np.sqrt(np.sum(VB**2)) VX = np.cross(VC,VB) A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.)) if A == 0.0 and len(viewDir) == 3: raise ValueError #avoid a no op # print('\nnew view =',viewDir) # print('A=%.3f, V='%A,VX) QV = G2mth.AVdeg2Q(A,VX) if len(viewDir) > 3: Model = drawingData['modelView'][:3,:3] invModel = nl.inv(Model) rt2 = np.sqrt(2.)/2. VX0 = np.array([-1.,0.,0.]) VY0 = np.array([0.,-1.,0.]) if 'H' == viewDir[3].upper(): QV = G2mth.prodQQ(np.array([rt2,0.,rt2,0.]),QV) #rotate 90deg about +ve Y VD = np.inner(invModel.T,VX0) elif 'V' == viewDir[3].upper(): QV = G2mth.prodQQ(np.array([rt2,-rt2,0.,0.]),QV) #rotate 90deg about -ve X VD = np.inner(invModel.T,VY0) # NAV = G2mth.Q2AVdeg(QV) # print('dir = %s, A= %.3f, V = '%(viewDir[3],NAV[0]),NAV[1:]) VD /= np.sqrt(np.sum(VD**2)) # print('new view dir = ',VD) Q = drawingData['Quaternion'] QN = G2mth.prodQQ(Q,QV) drawingData['Quaternion'] = QN except (ValueError,IndexError): VD = drawingData['viewDir'] Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2])) drawingData['viewDir'] = VD G2plt.PlotStructure(G2frame,data) showSizer = wx.BoxSizer(wx.VERTICAL) lineSizer = wx.BoxSizer(wx.HORIZONTAL) lineSizer.Add(wx.StaticText(drawOptions,label=' Background color:'),0,WACV) backColor = G2G.setColorButton(drawOptions,drawingData, 'backColor', G2plt.PlotStructure,[G2frame,data]) lineSizer.Add(backColor,0,WACV) lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,WACV) VD = drawingData['viewDir'] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]), style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir') viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir) # viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir) G2frame.phaseDisplay.viewDir = viewDir lineSizer.Add(viewDir,0,WACV) showSizer.Add(lineSizer) showSizer.Add((0,5),0) lineSizer = wx.BoxSizer(wx.HORIZONTAL) showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?') showABC.Bind(wx.EVT_CHECKBOX, OnShowABC) showABC.SetValue(drawingData['showABC']) lineSizer.Add(showABC,0,WACV) lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,WACV) VP = drawingData['viewPoint'][0] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]), style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint') G2frame.phaseDisplay.viewPoint = viewPoint viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint) viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint) lineSizer.Add(viewPoint,0,WACV) showSizer.Add(lineSizer) mapSizer = DistanceSettingSizer(drawingData, 'VPPeakDistRad','VPatomsExpandRad','VPatomsDistRad') showSizer.Add(mapSizer,0,wx.LEFT,20) showSizer.Add((0,5),0) line2Sizer = wx.BoxSizer(wx.HORIZONTAL) unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?') unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell) unitCellBox.SetValue(drawingData['unitCellBox']) line2Sizer.Add(unitCellBox,0,WACV) showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?') showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd) showHydrogen.SetValue(drawingData['showHydrogen']) line2Sizer.Add(showHydrogen,0,WACV) showRB = wx.CheckBox(drawOptions,-1,label=' Show Rigid Bodies?') showRB.Bind(wx.EVT_CHECKBOX, OnShowRB) showRB.SetValue(drawingData['showRigidBodies']) line2Sizer.Add(showRB,0,WACV) showSizer.Add(line2Sizer) line3Sizer = wx.BoxSizer(wx.HORIZONTAL) symFade = wx.CheckBox(drawOptions,-1,label=' Fade sym equivs?') symFade.Bind(wx.EVT_CHECKBOX, OnSymFade) symFade.SetValue(drawingData['SymFade']) line3Sizer.Add(symFade,0,WACV) showVoids = wx.CheckBox(drawOptions,-1,label=' Show void map?') showVoids.Bind(wx.EVT_CHECKBOX, OnShowVoids) showVoids.SetValue(drawingData['showVoids']) line3Sizer.Add(showVoids,0,WACV) showSizer.Add(line3Sizer) if generalData['Map']['rhoMax']: line3Sizer = wx.BoxSizer(wx.HORIZONTAL) slices = ['','lines','colors','lines+colors'] line3Sizer.Add(wx.StaticText(drawOptions,label=' Show map slice as '),0,WACV) G2frame.phaseDisplay.showCS = wx.ComboBox(drawOptions,value=slices[drawingData['showSlice']], choices=slices,style=wx.CB_READONLY|wx.CB_DROPDOWN) G2frame.phaseDisplay.showCS.Bind(wx.EVT_COMBOBOX, OnShowSlice) G2frame.phaseDisplay.showCS.SetValue(slices[drawingData['showSlice']]) line3Sizer.Add(G2frame.phaseDisplay.showCS,0,WACV) contourMaxTxt = wx.StaticText(drawOptions,label=' Max.: '+'%.2f'%(drawingData['contourMax']*generalData['Map']['rhoMax'])) line3Sizer.Add(contourMaxTxt,0,WACV) contourMax = G2G.G2Slider(drawOptions,style=wx.SL_HORIZONTAL,size=(150,25), value=int(100*drawingData['contourMax']),minValue=1,maxValue=100) contourMax.Bind(wx.EVT_SLIDER, OnContourMax) line3Sizer.Add(contourMax,1,wx.EXPAND|wx.RIGHT) showSizer.Add(line3Sizer) return showSizer def MapSizer(): def OnShowMap(event): drawingData['showMap'] = showMap.GetValue() G2plt.PlotStructure(G2frame,data) valSize = (50,20) mapSizer = wx.BoxSizer(wx.VERTICAL) showMap = wx.CheckBox(drawOptions,label=' Show density map?') showMap.Bind(wx.EVT_CHECKBOX, OnShowMap) showMap.SetValue(drawingData['showMap']) mapSizer.Add(showMap,0) sliders = wx.FlexGridSizer(0,3,5,5) G2G.G2SliderWidget(drawOptions,drawingData,'contourLevel', 'Fraction of rho max ({:.2f}): '.format(generalData['Map']['rhoMax']),0.01,1.0,100., sizer=sliders,size=valSize,onChange=G2plt.PlotStructure,onChangeArgs=(G2frame,data)) G2G.G2SliderWidget(drawOptions,drawingData,'mapSize', 'Visible map radius: ',0.1,10.,10.,sizer=sliders,size=valSize, onChange=G2plt.PlotStructure,onChangeArgs=(G2frame,data)) mapSizer.Add(sliders) lineSizer = wx.BoxSizer(wx.HORIZONTAL) lineSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'On map peak selection: '),0,WACV) lineSizer.Add(G2G.G2CheckBox(drawOptions,'Move view point',drawingData,'peakMoveView')) mapSizer.Add(lineSizer,0) mapSizer.Add(DistanceSettingSizer(drawingData, 'PeakDistRadius','atomsExpandRadius','atomsDistRadius'),0,wx.LEFT,20) return mapSizer def PlaneSizer(): def OnPlane(event): event.Skip() vals = plane.GetValue().split() try: hkl = [float(vals[i]) for i in range(3)] if not any(hkl): #can't be all zeros! raise ValueError except (ValueError,IndexError): hkl = drawingData['Plane'][0] drawingData['Plane'][0] = hkl plane.SetValue('%5.3f %5.3f %5.3f'%(hkl[0],hkl[1],hkl[2])) G2plt.PlotStructure(G2frame,data) def OnShowPlane(event): drawingData['Plane'][1] = showPlane.GetValue() G2plt.PlotStructure(G2frame,data) def OnShowStack(event): drawingData['Plane'][2] = showStack.GetValue() G2plt.PlotStructure(G2frame,data) def OnPhase(invalid,value,tc): G2plt.PlotStructure(G2frame,data) planeSizer = wx.BoxSizer(wx.VERTICAL) planeSizer1 = wx.BoxSizer(wx.HORIZONTAL) planeSizer1.Add(wx.StaticText(drawOptions,label=' Plane: '),0,WACV) H = drawingData['Plane'][0] plane = wx.TextCtrl(drawOptions,value='%5.3f %5.3f %5.3f'%(H[0],H[1],H[2]), style=wx.TE_PROCESS_ENTER,size=(140,20)) plane.Bind(wx.EVT_TEXT_ENTER,OnPlane) plane.Bind(wx.EVT_KILL_FOCUS,OnPlane) planeSizer1.Add(plane,0,WACV) showPlane = wx.CheckBox(drawOptions,label=' Show plane?') showPlane.SetValue(drawingData['Plane'][1]) showPlane.Bind(wx.EVT_CHECKBOX, OnShowPlane) planeSizer1.Add(showPlane,0,WACV) showStack = wx.CheckBox(drawOptions,label=' As a stack?') showStack.SetValue(drawingData['Plane'][2]) showStack.Bind(wx.EVT_CHECKBOX, OnShowStack) planeSizer1.Add(showStack,0,WACV) planeSizer2 = wx.BoxSizer(wx.HORIZONTAL) planeSizer2.Add(wx.StaticText(drawOptions,label=' Phase shift (deg): '),0,WACV) phase = G2G.ValidatedTxtCtrl(drawOptions,drawingData['Plane'],3,nDig=(10,2),OnLeave=OnPhase) planeSizer2.Add(phase,0,WACV) planeSizer2.Add(wx.StaticText(drawOptions,-1,' Plane color: '),0,WACV) planeColor = G2G.setColorButton(drawOptions,drawingData['Plane'], 4, G2plt.PlotStructure,[G2frame,data]) planeSizer2.Add(planeColor,0,WACV) planeSizer.Add(planeSizer1) planeSizer.Add(planeSizer2) return planeSizer def DistanceSettingSizer(var,key1,key2,key3): '''Sizer to get distances to show''' def onLeave(*args,**kwargs): G2plt.PlotStructure(G2frame,data) for key in key1,key2,key3: if key not in var: var[key] = 0 mapSizer = wx.FlexGridSizer(0,3,5,5) mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Show Map points within:'),0,WACV) mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,var,key1, xmin=0.0,xmax=5.0,nDig=(10,1),size=(50,-1), OnLeave=onLeave)) mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV) mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Show atoms within:'),0,WACV) mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,var,key2, xmin=0.0,xmax=15.0,nDig=(10,1),size=(50,-1), OnLeave=onLeave)) mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV) mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,'Label distance to atoms within:'),0,WACV) mapSizer.Add(G2G.ValidatedTxtCtrl(drawOptions,var,key3, xmin=0.0,xmax=15.0,nDig=(10,1),size=(50,-1), OnLeave=onLeave)) mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,u"\u212B"),0,WACV) return mapSizer # UpdateDrawOptions exectable code starts here generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) SetupDrawingData() drawingData = data['Drawing'] SetDrawingDefaults(drawingData) G2frame.GetStatusBar().SetStatusText('Add h or v to View Dir to set vector horizontal or vertical',1) if drawOptions.GetSizer(): drawOptions.GetSizer().Clear(True) mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(drawOptions,label=' Drawing controls:'),0,WACV) # add help button to bring up help web page - at right side of window topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(drawOptions,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(topSizer,0,wx.EXPAND) mainSizer.Add(SlopSizer(),0) G2G.HorizontalLine(mainSizer,drawOptions) mainSizer.Add(ShowSizer(),0,) if generalData['Map']['rhoMax'] and not generalData.get('4DmapData',{}): G2G.HorizontalLine(mainSizer,drawOptions) mainSizer.Add(MapSizer()) G2G.HorizontalLine(mainSizer,drawOptions) mainSizer.Add(PlaneSizer(),0,) SetPhaseWindow(drawOptions,mainSizer) #### Deformation form factor routines ################################################################ def SetDefDist(event): generalData = data['General'] DisAglCtls = {} if 'DisAglCtls' in generalData: DisAglCtls = generalData['DisAglCtls'] dlg = G2G.DisAglDialog(G2frame,DisAglCtls,generalData,Angle=False) if dlg.ShowModal() == wx.ID_OK: generalData['DisAglCtls'] = dlg.GetData() UpdateDeformation(None) event.StopPropagation() def SelDeformAtom(event): 'select deformation atom using a filtered listbox' generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] choices = [] types = [] Ids = [] for atom in data['Atoms']: if atom[ct] in atmdata.OrbFF and atom[cia+8] not in data['Deformations']: choices.append(atom[ct-1]) types.append(atom[ct]) Ids.append(atom[cia+8]) if not choices: return #no atoms in phase! dlg = G2G.G2MultiChoiceDialog(G2frame,'Select atom','Choose atom to select',choices) indxes = [] if dlg.ShowModal() == wx.ID_OK: indxes = dlg.GetSelections() for indx in indxes: orbs = atmdata.OrbFF[types[indx]] data['Deformations'][Ids[indx]] = [] data['Deformations'][-Ids[indx]] = {'U':'X','V':'Z','UVmat':np.eye(3)} newj0 = True newjn = True for orb in orbs: if 'core' in orb: continue #skip core - has no parameters else: if 'j0' in orb: if newj0: data['Deformations'][Ids[indx]].append([orb,{'Ne':[float(orbs[orb]['Ne']),False],'kappa':[1.0,False]}]) #no sp. harm for j0 terms newj0 = False else: data['Deformations'][Ids[indx]].append([orb,{'Ne':[float(orbs[orb]['Ne']),False]}]) #no sp. harm for j0 terms; one kappa only elif 'j' in orb: if newjn: orbDict = {'kappa':[1.0,False],} newjn = False else: orbDict = {} Order = int(orb.split('>')[0][-1]) cofNames,cofSgns = G2lat.GenRBCoeff('1','1',Order) cofNames = [name.replace('C','D') for name in cofNames] cofTerms = {name:[0.0,False] for name in cofNames if str(Order) in name} for name in cofNames: if str(Order) in name and '0' not in name: negname = name.replace(',',',-') cofTerms.update({negname:[0.0,False]}) orbDict.update(cofTerms) data['Deformations'][Ids[indx]].append([orb,orbDict]) dlg.Destroy() if not len(indxes): return drawAtoms.ClearSelection() drawAtoms.SelectRow(indx,True) G2plt.PlotStructure(G2frame,data) UpdateDeformation(None) event.StopPropagation() def UpdateDeformation(AtdId): def OnDeformRef(event): Obj = event.GetEventObject() dId,oId,dkey = Indx[Obj.GetId()] deformationData[dId][oId][1][dkey][1] = not deformationData[dId][oId][1][dkey][1] def OnPlotAtm(event): Obj = event.GetEventObject() dId = Indx[Obj.GetId()] atom = atomData[AtLookUp[dId]] neigh = G2mth.FindAllNeighbors(data,atom[ct-1],AtNames) deform = deformationData[dId] UVmat = deformationData[-dId]['UVmat'] G2plt.PlotDeform(G2frame,generalData,atom[ct-1],atom[ct],deform,UVmat,neigh) def OnDelAtm(event): Obj = event.GetEventObject() dId = Indx[Obj.GetId()] del deformationData[dId] wx.CallAfter(UpdateDeformation,None) def OnMatSel(event): "Cartesian axes: A: X'=U, Y'=(UxV)xU & Z'=UxV,B: X'=U, Y'=UxV & Z'=Ux(UxV)" Obj = event.GetEventObject() dId = Indx[Obj.GetId()] deformationData[-dId]['MUV'] = Obj.GetValue() wx.CallAfter(UpdateDeformation,dId) def OnUvec(event): "Cartesian axes: A: X'=U, Y'=(UxV)xU & Z'=UxV,B: X'=U, Y'=UxV & Z'=Ux(UxV)" Obj = event.GetEventObject() dId = Indx[Obj.GetId()] if Obj.GetValue() == deformationData[-dId]['V']: Obj.SetValue(deformationData[-dId]['U']) else: MX = UVvec[dId][Obj.GetSelection()] if 'A' in deformationData[-dId]['MUV']: MY = UVvec[dId][UVchoice[dId].index(deformationData[-dId]['V'])] MZ = np.cross(MX,MY) MZ /= nl.norm(MZ) MY = np.cross(MZ,MX) MY /= nl.norm(MY) else: MZ = UVvec[dId][UVchoice[dId].index(deformationData[-dId]['V'])] MY = np.cross(MZ,MX) MY /= nl.norm(MY) MZ = np.cross(MX,MY) MZ /= nl.norm(MZ) UVmat = np.array([MX,MY,MZ]) if np.any(np.isnan(UVmat)): Obj.SetValue(deformationData[-dId]['U']) G2G.G2MessageBox(G2frame,'ERROR: Z: U-vector zero or parallel to V','Invalid vector choice') return if nl.det(UVmat) < 0.: #ensure right hand UVmat *= -1. deformationData[-dId]['U'] = Obj.GetValue() data['Deformations'][-dId]['UVmat'] = UVmat def OnVvec(event): "Cartesian axes: A: X'=U, Y'=(UxV)xU & Z'=UxV,B: X'=U, Y'=UxV & Z'=Ux(UxV)" Obj = event.GetEventObject() dId = Indx[Obj.GetId()] if Obj.GetValue() == deformationData[-dId]['U']: Obj.SetValue(deformationData[-dId]['V']) else: MX = UVvec[dId][UVchoice[dId].index(deformationData[-dId]['U'])] if 'A' in deformationData[-dId]['MUV']: MY = UVvec[dId][Obj.GetSelection()] MZ = np.cross(MX,MY) MZ /= nl.norm(MZ) MY = np.cross(MZ,MX) MY /= nl.norm(MY) else: MZ = UVvec[dId][Obj.GetSelection()] MY = np.cross(MZ,MX) MY /= nl.norm(MY) MZ = np.cross(MX,MY) MZ /= nl.norm(MZ) UVmat = np.array([MX,MY,MZ]) if np.any(np.isnan(UVmat)): Obj.SetValue(deformationData[-dId]['V']) G2G.G2MessageBox(G2frame,'ERROR: V-vector zero or parallel to U','Invalid vector choice') return if nl.det(UVmat) < 0.: #ensure right hand UVmat *= -1. deformationData[-dId]['V'] = Obj.GetValue() data['Deformations'][-dId]['UVmat'] = UVmat def OnAtSel(event): dId = atomList[atSel.GetValue()] wx.CallAfter(UpdateDeformation,dId) # UpdateDeformation exectable code starts here alpha = ['A','B','C','D','E','F','G','H',] generalData = data['General'] cx,ct,cs,cia = generalData['AtomPtrs'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) atomData = data['Atoms'] AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8) AtNames = [atom[ct-1] for atom in atomData] deformationData = data['Deformations'] dId = AtdId if deformation.GetSizer(): deformation.GetSizer().Clear(True) atomList = {} for item in deformationData: if item in AtLookUp: atom = atomData[AtLookUp[item]] atomList.update({atom[ct-1]:item}) AtChoice = ' ' if dId is not None: AtChoice = atomData[AtLookUp[dId]][ct-1] elif len(atomList): AtChoice = list(atomList.keys())[0] dId = atomList[AtChoice] mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(deformation,label=' Atomic deformation data: Select atom '),0,WACV) atSel = wx.ComboBox(deformation,value=AtChoice,choices=list(atomList.keys()),style=wx.CB_READONLY|wx.CB_DROPDOWN) atSel.Bind(wx.EVT_COMBOBOX,OnAtSel) topSizer.Add(atSel,0,WACV) # add help button to bring up help web page - at right side of window topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(deformation,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(topSizer,0,wx.EXPAND) if dId is not None: Indx = {} UVchoice = {} UVvec = {} #patch if 'UVmat' not in deformationData[-dId] or 'MUV' not in deformationData[-dId]: deformationData[-dId] = {'U':'X','V':'Y','UVmat':np.eye(3),'MUV':"A: X'=U, Y'=(UxV)xU & Z'=UxV"} #end patch atom = atomData[AtLookUp[dId]] neigh = G2mth.FindAllNeighbors(data,atom[ct-1],AtNames)[0] lineSizer = wx.BoxSizer(wx.HORIZONTAL) lineSizer.Add(wx.StaticText(deformation,label=' For atom %s, site sym %s:'%(atom[ct-1],atom[cs])),0,WACV) names = [] if not len(neigh): lineSizer.Add(wx.StaticText(deformation,label=' No neighbors found; Do Set bond parms to expand search'),0,WACV) elif len(neigh) < 9: names = ['%s=%s'%(alpha[i],item[0].replace(' ','')) for i,item in enumerate(neigh)] lineSizer.Add(wx.StaticText(deformation,label=' Neighbors: '+str(names)),0,WACV) else: names = 'Too many neighbors - change atom radii to fix' Nneigh = len(neigh) if Nneigh > 2: Nneigh += 1 Nneigh = min(4,Nneigh) UVchoice[dId] = ['X','Y','Z','X+Y','X+Y+Z','A','B','A+B','A+B+C'] UVvec[dId] = [[1.,0.,0.],[0.,1.,0.],[0.,0.,1.],[1.,1.,0.]/sqt2,[1.,1.,1.]/sqt3,] if Nneigh >= 1: UVvec[dId] += [neigh[0][3]/neigh[0][2],] #A if Nneigh >= 2: UVvec[dId] += [neigh[1][3]/neigh[1][2],(neigh[0][3]+neigh[1][3])/np.sqrt(neigh[0][2]**2+neigh[1][2]**2),] #B, A+B if Nneigh == 4: UVvec[dId] += [(neigh[0][3]+neigh[1][3]+neigh[2][3])/np.sqrt(neigh[0][2]**2+neigh[1][2]**2+neigh[2][2]**2),] #A+B+C plotAtm = wx.Button(deformation,label='Plot') plotAtm.Bind(wx.EVT_BUTTON,OnPlotAtm) Indx[plotAtm.GetId()] = dId lineSizer.Add(plotAtm,0,WACV) delAtm = wx.Button(deformation,label='Delete') delAtm.Bind(wx.EVT_BUTTON,OnDelAtm) Indx[delAtm.GetId()] = dId lineSizer.Add(delAtm,0,WACV) mainSizer.Add(lineSizer) matSizer = wx.BoxSizer(wx.HORIZONTAL) Mchoice = ["A: X'=U, Y'=(UxV)xU & Z'=UxV","B: X'=U, Y'=UxV & Z'=Ux(UxV)"] matSizer.Add(wx.StaticText(deformation,label=' Orbital Cartesian axes:'),0,WACV) matSel = wx.ComboBox(deformation,choices=Mchoice,value=deformationData[-dId]['MUV'],style=wx.CB_READONLY|wx.CB_DROPDOWN) matSel.Bind(wx.EVT_COMBOBOX,OnMatSel) Indx[matSel.GetId()] = dId matSizer.Add(matSel,0,WACV) mainSizer.Add(matSizer) oriSizer = wx.BoxSizer(wx.HORIZONTAL) oriSizer.Add(wx.StaticText(deformation,label=' Select orbital U vector: '),0,WACV) Uvec = wx.ComboBox(deformation,value=deformationData[-dId]['U'],choices=UVchoice[dId][:Nneigh+5],style=wx.CB_READONLY|wx.CB_DROPDOWN) Uvec.Bind(wx.EVT_COMBOBOX,OnUvec) Indx[Uvec.GetId()] = dId oriSizer.Add(Uvec,0,WACV) oriSizer.Add(wx.StaticText(deformation,label=' Select orbital V vector: '),0,WACV) Vvec = wx.ComboBox(deformation,value=deformationData[-dId]['V'],choices=UVchoice[dId][:Nneigh+5],style=wx.CB_READONLY|wx.CB_DROPDOWN) Vvec.Bind(wx.EVT_COMBOBOX,OnVvec) Indx[Vvec.GetId()] = dId oriSizer.Add(Vvec,0,WACV) mainSizer.Add(oriSizer) orbSizer = wx.FlexGridSizer(0,9,2,2) for iorb,orb in enumerate(deformationData[dId]): if 'kappa' in orb[1]: name = ' kappa: ' if '<j0>' not in orb[0]: for i in range(3): orbSizer.Add((5,5),0) name = " kappa': " orbSizer.Add(wx.StaticText(deformation,label=orb[0]+name)) orbSizer.Add(G2G.ValidatedTxtCtrl(deformation,orb[1]['kappa'],0,nDig=(8,3),xmin=0.5,xmax=1.5)) Tcheck = wx.CheckBox(deformation,-1,'Refine?') Tcheck.SetValue(orb[1]['kappa'][1]) Tcheck.Bind(wx.EVT_CHECKBOX,OnDeformRef) Indx[Tcheck.GetId()] = [dId,iorb,'kappa'] orbSizer.Add(Tcheck) if '<j0>' in orb[0]: if 'kappa' not in orb[1]: orbSizer.Add(wx.StaticText(deformation,label=orb[0]+' Ne:')) else: orbSizer.Add(wx.StaticText(deformation,label=' Ne:')) orbSizer.Add(G2G.ValidatedTxtCtrl(deformation,orb[1]['Ne'],0,nDig=(8,3),xmin=0.,xmax=10.)) Tcheck = wx.CheckBox(deformation,-1,'Refine?') Tcheck.SetValue(orb[1]['Ne'][1]) Tcheck.Bind(wx.EVT_CHECKBOX,OnDeformRef) Indx[Tcheck.GetId()] = [dId,iorb,'Ne'] orbSizer.Add(Tcheck) for i in range(3): orbSizer.Add((5,5),0) continue nItem = 0 if 'kappa' not in orb[1]: for i in range(3): orbSizer.Add((5,5),0) for item in orb[1]: if 'D' in item: nItem += 1 orbSizer.Add(wx.StaticText(deformation,label=item+':')) orbSizer.Add(G2G.ValidatedTxtCtrl(deformation,orb[1][item],0,nDig=(8,3),xmin=-2.,xmax=2.)) Tcheck = wx.CheckBox(deformation,-1,'Refine?') Tcheck.SetValue(orb[1][item][1]) Tcheck.Bind(wx.EVT_CHECKBOX,OnDeformRef) Indx[Tcheck.GetId()] = [dId,iorb,item] orbSizer.Add(Tcheck) if nItem in [2,4,6,8,10]: for i in range(3): orbSizer.Add((5,5),0) for i in range(3): orbSizer.Add((5,5),0) mainSizer.Add(orbSizer) SetPhaseWindow(deformation,mainSizer) #### Texture routines ################################################################################ def UpdateTexture(): def SetSHCoef(): cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order']) newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames)))) SHCoeff = textureData['SH Coeff'][1] for cofName in SHCoeff: if cofName in cofNames: newSHCoef[cofName] = SHCoeff[cofName] return newSHCoef def OnShOrder(event): Obj = event.GetEventObject() # the Kaduk test: is Texture appropriate? Look for a 2nd histogram # of any type with differing setting angles from the 1st. instArray = {} if int(Obj.GetValue()) > 0: for h in data['Histograms']: PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,h) if not PatternId: #skip bogus histograms continue Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,'Instrument Parameters'))[0] Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,'Sample Parameters')) if Inst['Type'][1] in instArray: if instArray[Inst['Type'][1]] != [Sample['Chi'],Sample['Phi'],Sample['Omega']]: textureData['Order'] = int(Obj.GetValue()) break else: instArray[Inst['Type'][1]] = [Sample['Chi'],Sample['Phi'],Sample['Omega']] else: if textureData['Model'] != 'cylindrical': textureData['Order'] = 0 wx.MessageBox('Incorrect use of Texture. Use preferred orientation (on data tab) unless you have multiple histograms taken with different orientations', caption='Texture Error',style=wx.ICON_EXCLAMATION) else: textureData['Order'] = int(Obj.GetValue()) else: textureData['Order'] = 0 textureData['SH Coeff'][1] = SetSHCoef() G2frame.GPXtree.UpdateSelection() # wx.CallLater(100,UpdateTexture) wx.CallAfter(G2plt.PlotTexture,G2frame,data) def OnShModel(event): Obj = event.GetEventObject() textureData['Model'] = Obj.GetValue() textureData['SH Coeff'][1] = SetSHCoef() G2frame.GPXtree.UpdateSelection() # wx.CallLater(100,UpdateTexture) wx.CallAfter(G2plt.PlotTexture,G2frame,data) def OnSHRefine(event): Obj = event.GetEventObject() textureData['SH Coeff'][0] = Obj.GetValue() def OnSHShow(event): Obj = event.GetEventObject() textureData['SHShow'] = Obj.GetValue() G2frame.GPXtree.UpdateSelection() # wx.CallLater(100,UpdateTexture) def OnProjSel(event): Obj = event.GetEventObject() G2frame.Projection = Obj.GetValue() wx.CallAfter(G2plt.PlotTexture,G2frame,data) def OnShoDet(event): Obj = event.GetEventObject() textureData['ShoDet'] = Obj.GetValue() wx.CallAfter(G2plt.PlotTexture,G2frame,data) def OnColorSel(event): Obj = event.GetEventObject() G2frame.ContourColor = Obj.GetValue() wx.CallAfter(G2plt.PlotTexture,G2frame,data) def OnAngRef(event): Obj = event.GetEventObject() textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue() def OnODFValue(invalid,value,tc): wx.CallAfter(G2plt.PlotTexture,G2frame,data) def OnPfType(event): Obj = event.GetEventObject() textureData['PlotType'] = Obj.GetValue() G2frame.GPXtree.UpdateSelection() # wx.CallLater(100,UpdateTexture) wx.CallAfter(G2plt.PlotTexture,G2frame,data) def OnPFValue(event): event.Skip() Obj = event.GetEventObject() Saxis = Obj.GetValue().split() if textureData['PlotType'] in ['Pole figure','Axial pole distribution','3D pole distribution']: try: hkl = [int(Saxis[i]) for i in range(3)] except (ValueError,IndexError): hkl = textureData['PFhkl'] if not np.any(np.array(hkl)): #can't be all zeros! hkl = textureData['PFhkl'] Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2])) textureData['PFhkl'] = hkl else: try: xyz = [float(Saxis[i]) for i in range(3)] except (ValueError,IndexError): xyz = textureData['PFxyz'] if not np.any(np.array(xyz)): #can't be all zeros! xyz = textureData['PFxyz'] Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2])) textureData['PFxyz'] = xyz wx.CallAfter(G2plt.PlotTexture,G2frame,data) def OnpopLA(event): pfName = PhaseName cell = generalData['Cell'][1:7] PH = np.array(textureData['PFhkl']) phi,beta = G2lat.CrsAng(PH,cell,SGData) SHCoef = textureData['SH Coeff'][1] ODFln = G2lat.Flnh(SHCoef,phi,beta,SGData) pfName = PhaseName+'%d%d%d.gpf'%(PH[0],PH[1],PH[2]) pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose popLA pole figure file name', pth, pfName, 'popLA file (*.gpf)|*.gpf',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: pfFile = dlg.GetPath() finally: dlg.Destroy() print ('popLA save '+pfFile) if pfFile: pf = open(pfFile,'w') pf.write(PhaseName+'\n') str = ' %d%d%d 5.0 90.0 5.0360.0 1 1 2 1 3 100 1'%(PH[0],PH[1],PH[2]) pf.write(str+'\n') Psi,Gam = np.mgrid[0:19,0:72] Psi = Psi.flatten()*5. Gam = Gam.flatten()*5. Z = np.array(G2lat.polfcal(ODFln,SamSym[textureData['Model']],Psi,Gam)*100.,dtype='int') Z = np.where(Z>0,Z,0) Z = np.where(Z<9999,Z,9999) for i in range(76): iBeg = i*18 iFin = iBeg+18 np.savetxt(pf,Z[iBeg:iFin],fmt='%4d',newline='') pf.write('\n') pf.close() print (' popLA %d %d %d pole figure saved to %s'%(PH[0],PH[1],PH[2],pfFile)) def OnCSV(event): pfName = PhaseName pfFile = '' cell = generalData['Cell'][1:7] if 'Inverse' in textureData['PlotType']: SHCoef = textureData['SH Coeff'][1] PX = np.array(textureData['PFxyz']) gam = atan2d(PX[0],PX[1]) xy = np.sqrt(PX[0]**2+PX[1]**2) xyz = np.sqrt(PX[0]**2+PX[1]**2+PX[2]**2) psi = asind(xy/xyz) IODFln = G2lat.Glnh(SHCoef,psi,gam,SamSym[textureData['Model']]) pfName = PhaseName+'%d%d%dIPF.csv'%(int(PX[0]),int(PX[1]),int(PX[2])) pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose CSV inverse pole figure file name', pth, pfName, 'CSV file (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) else: PH = np.array(textureData['PFhkl']) phi,beta = G2lat.CrsAng(PH,cell,SGData) SHCoef = textureData['SH Coeff'][1] ODFln = G2lat.Flnh(SHCoef,phi,beta,SGData) pfName = PhaseName+'%d%d%dPF.csv'%(PH[0],PH[1],PH[2]) pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose CSV pole figure file name', pth, pfName, 'CSV file (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: pfFile = dlg.GetPath() print ('CSV save '+pfFile) finally: dlg.Destroy() if pfFile: pf = open(pfFile,'w') pf.write('"%s"\n'%(PhaseName)) if 'Inverse' in textureData['PlotType']: pf.write('" %s %d %d %d inverse pole figure"\n'%(PhaseName,int(PX[0]),int(PX[1]),int(PX[2]))) P,R = np.mgrid[0:19,0:72] pf.write('"phi/beta",') np.savetxt(pf,np.linspace(0.,90.,19,True),fmt='%10.4f,',newline='') pf.write('\n') P = P.flatten()*5. R = R.flatten()*5. Z = G2lat.invpolfcal(IODFln,SGData,P,R) Z = np.reshape(Z,(19,72)).T for i,row in enumerate(Z): pf.write('%8d, '%(i*5)) np.savetxt(pf,row,fmt='%10.4f,',newline='') pf.write('\n') pf.close() print (' %s %d %d %d inverse pole figure saved to %s'%(PhaseName,int(PX[0]),int(PX[1]),int(PX[2]),pfFile)) else: pf.write('" %s %d %d %d pole figure"\n'%(PhaseName,PH[0],PH[1],PH[2])) Psi,Gam = np.mgrid[0:19,0:72] pf.write('"psi/gam",') np.savetxt(pf,np.linspace(0.,90.,19,True),fmt='%10.4f,',newline='') pf.write('\n') Psi = Psi.flatten()*5. Gam = Gam.flatten()*5. Z = np.array(G2lat.polfcal(ODFln,SamSym[textureData['Model']],Psi,Gam)) Z = np.reshape(Z,(19,72)).T for i,row in enumerate(Z): pf.write('%8d, '%(i*5)) np.savetxt(pf,row,fmt='%10.4f,',newline='') pf.write('\n') pf.close() print (' %s %d %d %d pole figure saved to %s'%(PhaseName,PH[0],PH[1],PH[2],pfFile)) def SHPenalty(Penalty): def OnHKLList(event): event.Skip() dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select penalty hkls', 'Penalty hkls',hkls,filterBox=False) try: if dlg.ShowModal() == wx.ID_OK: Penalty[0] = [hkls[i] for i in dlg.GetSelections()] if not Penalty[0]: Penalty[0] = ['',] else: return finally: dlg.Destroy() G2frame.GPXtree.UpdateSelection() # wx.CallLater(100,UpdateTexture) A = G2lat.cell2A(generalData['Cell'][1:7]) hkls = G2lat.GenPfHKLs(10,SGData,A) shPenalty = wx.BoxSizer(wx.HORIZONTAL) shPenalty.Add(wx.StaticText(Texture,wx.ID_ANY,' Negative MRD penalty list: '),0,WACV) shPenalty.Add(wx.ComboBox(Texture,value=Penalty[0][0],choices=Penalty[0], style=wx.CB_DROPDOWN|wx.CB_READONLY),0,WACV) hklList = wx.Button(Texture,label='Select penalty hkls') hklList.Bind(wx.EVT_BUTTON,OnHKLList) shPenalty.Add(hklList,0,WACV) shPenalty.Add(wx.StaticText(Texture,wx.ID_ANY,' Zero MRD tolerance: '),0,WACV) shToler = G2G.ValidatedTxtCtrl(Texture,Penalty,1,nDig=(10,2),xmin=0.001) shPenalty.Add(shToler,0,WACV) return shPenalty def OnProj(event): Obj = event.GetEventObject() generalData['3Dproj'] = Obj.GetValue() wx.CallAfter(G2plt.PlotTexture,G2frame,data) # UpdateTexture executable starts here generalData = data['General'] SGData = generalData['SGData'] try: textureData = generalData['SH Texture'] except KeyError: #fix old files! textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical', 'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0], 'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],'ShoDet':False, 'PFxyz':[0,0,1.],'PlotType':'Pole figure'} if 'SHShow' not in textureData: textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'}) if 'PlotType' not in textureData: textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'}) if 'Penalty' not in textureData: textureData['Penalty'] = [['',],0.1,False,1.0] if 'ShoDet' not in textureData: textureData['ShoDet'] = False shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) keyList = G2frame.GetHistogramNames(['PWDR',]) UseList = data['Histograms'] HistsInPhase = [name for name in keyList if name in UseList] textureData['det Angles'] = [] for hist in HistsInPhase: pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist) #only use 1st histogram Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,'Sample Parameters')) Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,'Instrument Parameters'))[0] if 'NT' in Inst['Type'][0]: Tth = Inst['2-theta'][1]/2. Gangls = [Sample['Phi'],Sample['Chi'],Sample['Omega'],Sample['Azimuth']] Sangls = [textureData['Sample omega'][1],textureData['Sample chi'][1],textureData['Sample phi'][1]] phi,gam,x,x = G2lat.SamAng(Tth,Gangls,Sangls,False) if phi > 90.: phi = 180.-phi gam += 180. gam %= 360. textureData['det Angles'].append([hist,phi,gam]) G2frame.GetStatusBar().SetStatusText('',1) if Texture.GetSizer(): Texture.GetSizer().Clear(True) mainSizer = wx.BoxSizer(wx.VERTICAL) # sanity check: should this project be fitting texture? mainSizer.Add(wx.StaticText(Texture,label= ' NB: Normally texture model fitting generally requires multiple datasets with differing sample orientations/detector values')) msg = '' if G2frame.testSeqRefineMode() and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential results'): mainSizer.Add(wx.StaticText(Texture,label= " Sequential result found. Use Texture/Refine texture above. See Method B in texture tutorial.")) h,pd = G2frame.GetUsedHistogramsAndPhasesfromTree() if len(h) < 3: mainSizer.Add(wx.StaticText(Texture,label=' Insufficient number of patterns for usual texture analysis')) mainSizer.Add(wx.StaticText(Texture,label= ' For structural fits that need preferred orientation corrections, use terms in the Data tab instead.')) else: unique = [] for i in h: setting = [h[i]['Sample Parameters'][key] for key in ('Omega', 'Chi', 'Phi', 'Azimuth')] if setting not in unique: unique.append(setting) if len(unique) == 1: mainSizer.Add(wx.StaticText(Texture,label= " All your histograms have the same values for Omega, Chi, Phi and Azimuth.\n Texture fitting requires differing values.")) elif len(unique) == 2: mainSizer.Add(wx.StaticText(Texture,label= " You have only two unique settings for Omega, Chi, Phi and Azimuth.\n Texture fitting requires more differing values.")) if textureData['Order'] or textureData['SH Coeff'][0]: mainSizer.Add(wx.StaticText(Texture,wx.ID_ANY, '\n *** To remove this texture: Turn off refinement and set Harmonic order to zero below.\n')) G2G.HorizontalLine(mainSizer,Texture) titleSizer = wx.BoxSizer(wx.HORIZONTAL) titleSizer.Add(wx.StaticText(Texture,label=' Spherical harmonics texture data for '+PhaseName+':'),0,WACV) titleSizer.Add(wx.StaticText(Texture,label=' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),0,WACV) # add help button to bring up help web page - at right side of window titleSizer.Add((-1,-1),1,wx.EXPAND) titleSizer.Add(G2G.HelpButton(Texture,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(titleSizer,0,wx.EXPAND) mainSizer.Add((0,5),0) shSizer = wx.FlexGridSizer(0,6,5,5) shSizer.Add(wx.StaticText(Texture,-1,' Texture model: '),0,WACV) shModel = wx.ComboBox(Texture,value=textureData['Model'],choices=shModels, style=wx.CB_READONLY|wx.CB_DROPDOWN) shModel.Bind(wx.EVT_COMBOBOX,OnShModel) shSizer.Add(shModel,0,WACV) shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,WACV) shOrder = wx.ComboBox(Texture,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)], style=wx.CB_READONLY|wx.CB_DROPDOWN) shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder) shSizer.Add(shOrder,0,WACV) shRef = wx.CheckBox(Texture,label=' Refine texture?') shRef.SetValue(textureData['SH Coeff'][0]) shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine) shSizer.Add(shRef,0,WACV) shShow = wx.CheckBox(Texture,label=' Show coeff.?') shShow.SetValue(textureData['SHShow']) shShow.Bind(wx.EVT_CHECKBOX, OnSHShow) shSizer.Add(shShow,0,WACV) mainSizer.Add(shSizer,0,0) mainSizer.Add((0,5),0) PTSizer = wx.FlexGridSizer(0,5,5,5) PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,WACV) choices = ['Axial pole distribution','Pole figure','Inverse pole figure','3D pole distribution'] pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices, style=wx.CB_READONLY|wx.CB_DROPDOWN) pfType.Bind(wx.EVT_COMBOBOX,OnPfType) PTSizer.Add(pfType,0,WACV) if 'Axial' not in textureData['PlotType'] and '3D' not in textureData['PlotType']: PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,WACV) projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic'], style=wx.CB_READONLY|wx.CB_DROPDOWN) projSel.Bind(wx.EVT_COMBOBOX,OnProjSel) PTSizer.Add(projSel,0,WACV) if textureData['PlotType'] == 'Pole figure' and len(textureData['det Angles']): shoDet = wx.CheckBox(Texture,-1,label=' Show detectors?') shoDet.SetValue(textureData['ShoDet']) shoDet.Bind(wx.EVT_CHECKBOX, OnShoDet) PTSizer.Add(shoDet,0,WACV) else: PTSizer.Add((0,5),0) elif '3D' in textureData['PlotType']: PTSizer.Add(wx.StaticText(Texture,-1,' Show projections for: '),0,WACV) proj = ['','x','y','z','xy','xz','yz','xyz'] projType = wx.ComboBox(Texture,wx.ID_ANY,value=generalData['3Dproj'],choices=proj, style=wx.CB_READONLY|wx.CB_DROPDOWN) projType.Bind(wx.EVT_COMBOBOX, OnProj) PTSizer.Add(projType,0,WACV) PTSizer.Add((0,5),0) if textureData['PlotType'] in ['Pole figure','Axial pole distribution','3D pole distribution']: PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,WACV) PH = textureData['PFhkl'] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER) else: PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,WACV) PX = textureData['PFxyz'] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER) pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue) pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue) PTSizer.Add(pfVal,0,WACV) if 'Axial' not in textureData['PlotType'] and '3D' not in textureData['PlotType']: PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,WACV) choice = [m for m in mpl.cm.datad.keys()]+['GSPaired','GSPaired_r',] #if not m.endswith("_r") choice.sort() colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice, style=wx.CB_READONLY|wx.CB_DROPDOWN) colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel) PTSizer.Add(colorSel,0,WACV) if 'figure' in textureData['PlotType']: popLA = wx.Button(Texture,-1,"Make CSV file") popLA.Bind(wx.EVT_BUTTON, OnCSV) PTSizer.Add(popLA,0,WACV) mainSizer.Add(PTSizer,0) mainSizer.Add((0,5),0) if textureData['SHShow']: mainSizer.Add(wx.StaticText(Texture,-1,' Spherical harmonic coefficients: ')) mainSizer.Add((0,5),0) ODFSizer = wx.FlexGridSizer(0,8,2,2) ODFkeys = list(textureData['SH Coeff'][1].keys()) ODFkeys.sort() for item in ODFkeys: ODFSizer.Add(wx.StaticText(Texture,-1,item),0,WACV) ODFval = G2G.ValidatedTxtCtrl(Texture,textureData['SH Coeff'][1],item,nDig=(8,3),OnLeave=OnODFValue) ODFSizer.Add(ODFval,0,WACV) mainSizer.Add(ODFSizer,0) mainSizer.Add((0,5),0) mainSizer.Add((0,5),0) mainSizer.Add(wx.StaticText(Texture,-1,' Sample orientation angle zeros: '),0) mainSizer.Add((0,5),0) angSizer = wx.BoxSizer(wx.HORIZONTAL) angIndx = {} for item in ['Sample omega','Sample chi','Sample phi']: angRef = wx.CheckBox(Texture,-1,label=item+': ') angRef.SetValue(textureData[item][0]) angIndx[angRef.GetId()] = item angRef.Bind(wx.EVT_CHECKBOX, OnAngRef) angSizer.Add(angRef,0,WACV) angVal = G2G.ValidatedTxtCtrl(Texture,textureData[item],1,nDig=(8,2)) angSizer.Add(angVal,0,WACV|wx.LEFT,5) mainSizer.Add(angSizer,0,wx.LEFT,5) # mainSizer.Add(SHPenalty(textureData['Penalty']),0,wx.LEFT,5) for future SetPhaseWindow(Texture,mainSizer) ##### DData routines - GUI stuff in GSASIIddataGUI.py. Used for Phase/data "Edit Phase" menu def OnHklfAdd(event): keyList = list(data['Histograms'].keys()) TextList = [] if not G2frame.GPXtree.GetCount(): return item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while item: name = G2frame.GPXtree.GetItemText(item) if name not in keyList and 'HKLF' in name: TextList.append(name) item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) if not TextList: G2G.G2MessageBox(G2frame,'No reflections') return dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to use', 'Use data',TextList) try: if dlg.ShowModal() == wx.ID_OK: result = dlg.GetSelections() else: return finally: dlg.Destroy() # get the histograms used in other phases phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree() usedHKLFhists = [] # used single-crystal histograms for p in usedHistograms: for h in usedHistograms[p]: if h.startswith('HKLF ') and h not in usedHKLFhists: usedHKLFhists.append(h) # check that selected single crystal histograms are not already in use! for i in result: used = [TextList[i] for i in result if TextList[i] in usedHKLFhists] if used: msg = 'The following single crystal histogram(s) are already in use' for i in used: msg += '\n '+str(i) msg += '\nAre you sure you want to add them to this phase? ' msg += 'Associating a single crystal dataset to >1 histogram is usually an error, ' msg += 'so No is suggested here.' if G2frame.ErrorDialog('Likely error',msg,G2frame,wtype=wx.YES_NO) != wx.ID_YES: return wx.BeginBusyCursor() for i in result: histoName = TextList[i] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,histoName) refDict,reflData = G2frame.GPXtree.GetItemPyData(Id) data['Histograms'][histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True], 'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}, 'Extinction':['Lorentzian','None', {'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-7,False],'Es':[1.e-7,False],'Ep':[1.e-7,False]},], 'Flack':[0.0,False],'Twins':[[np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,0]],]} if 'TwMax' in reflData: #nonmerohedral twins present data['Histograms'][histoName]['Twins'] = [] for iT in range(reflData['TwMax'][0]+1): if iT in reflData['TwMax'][1]: data['Histograms'][histoName]['Twins'].append([False,0.0]) else: data['Histograms'][histoName]['Twins'].append([np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,reflData['TwMax'][0]]]) else: #no nonmerohedral twins data['Histograms'][histoName]['Twins'] = [[np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,0]],] UpdateHKLFdata(histoName) wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data) wx.EndBusyCursor() def OnDataUse(event): # hist = G2frame.hist if data['Histograms']: dlg = G2G.G2MultiChoiceDialog(G2frame, 'Use histograms', 'Use which histograms?',G2frame.dataWindow.HistsInPhase) try: if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() for Id,item in enumerate(G2frame.dataWindow.HistsInPhase): if Id in sel: data['Histograms'][item]['Use'] = True else: data['Histograms'][item]['Use'] = False finally: dlg.Destroy() wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data) # Note: function replaced by one with identical name, below # def UpdateHKLFdata(histoName): # generalData = data['General'] # Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,histoName) # refDict,reflData = G2frame.GPXtree.GetItemPyData(Id) # SGData = generalData['SGData'] # Cell = generalData['Cell'][1:7] # G,g = G2lat.cell2Gmat(Cell)) # try: # if dlg.ShowModal() == wx.ID_OK: # sel = dlg.GetSelections() # for id,item in enumerate(keyList): # <<<<< something is likely wrong here # if id in sel: # data['Histograms'][item]['Use'] = True # else: # data['Histograms'][item]['Use'] = False # finally: # dlg.Destroy() # wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data) def UpdateHKLFdata(histoName): generalData = data['General'] Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,histoName) refDict,reflData = G2frame.GPXtree.GetItemPyData(Id) SGData = generalData['SGData'] Cell = generalData['Cell'][1:7] G,g = G2lat.cell2Gmat(Cell) for iref,ref in enumerate(reflData['RefList']): H = list(ref[:3]) ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G)) iabsnt,ref[3],Uniq,phi = G2spc.GenHKLf(H,SGData) if iabsnt: ref[3] = 0 def OnDataCopy(event): hist = G2frame.hist keyList = G2frame.dataWindow.HistsInPhase[:] if hist in keyList: keyList.remove(hist) if not keyList: G2G.G2MessageBox(G2frame,'No histograms to copy to') return sourceDict = copy.deepcopy(data['Histograms'][hist]) if 'HKLF' in sourceDict['Histogram']: copyNames = ['Extinction','Babinet','Flack','Twins'] else: #PWDR copyNames = ['Pref.Ori.','Size','Mustrain','HStrain','Extinction','Babinet','LeBail','newLeBail','Layer Disp'] copyNames += ['Scale','Fix FXU','FixedSeqVars'] copyDict = {} for name in copyNames: if name not in sourceDict: continue copyDict[name] = copy.deepcopy(sourceDict[name]) #force copy dlg = G2G.G2MultiChoiceDialog(G2frame,u'Copy phase/histogram parameters\nfrom '+hist[5:][:35], 'Copy phase/hist parameters', keyList) try: if dlg.ShowModal() == wx.ID_OK: for sel in dlg.GetSelections(): data['Histograms'][keyList[sel]].update(copy.deepcopy(copyDict)) finally: dlg.Destroy() def OnDataCopyFlags(event): hist = G2frame.hist sourceDict = copy.deepcopy(data['Histograms'][hist]) copyDict = {} if 'HKLF' in sourceDict['Histogram']: copyNames = ['Extinction','Babinet','Flack','Twins'] else: #PWDR copyNames = ['Pref.Ori.','Size','Mustrain','HStrain','Extinction','Babinet','Layer Disp'] copyNames += ['Scale','Fix FXU','FixedSeqVars'] babNames = ['BabA','BabU'] for name in copyNames: if name not in sourceDict: continue if name in ['Scale','Extinction','HStrain','Flack','Twins','Layer Disp']: if name == 'Extinction' and 'HKLF' in sourceDict['Histogram']: copyDict[name] = {name:[sourceDict[name][:2]]} for item in ['Eg','Es','Ep']: copyDict[name][item] = sourceDict[name][2][item][1] elif name == 'Twins': copyDict[name] = sourceDict[name][0][1][1] else: copyDict[name] = sourceDict[name][1] elif name in ['Size','Mustrain']: copyDict[name] = [sourceDict[name][0],sourceDict[name][2],sourceDict[name][5]] elif name == 'Pref.Ori.': copyDict[name] = [sourceDict[name][0],sourceDict[name][2]] if sourceDict[name][0] == 'SH': SHterms = sourceDict[name][5] SHflags = {} for item in SHterms: SHflags[item] = SHterms[item] copyDict[name].append(SHflags) elif name == 'Babinet': copyDict[name] = {} for bab in babNames: copyDict[name][bab] = sourceDict[name][bab][1] elif name == 'Fix FXU' or name == 'FixedSeqVars': copyDict[name] = copy.deepcopy(sourceDict[name]) keyList = G2frame.dataWindow.HistsInPhase[:] if hist in keyList: keyList.remove(hist) if not keyList: G2G.G2MessageBox(G2frame,'No histograms to copy to') return dlg = G2G.G2MultiChoiceDialog(G2frame,u'Copy phase/histogram flags\nfrom '+hist[5:][:35], 'Copy phase/hist flags', keyList) try: if dlg.ShowModal() == wx.ID_OK: for sel in dlg.GetSelections(): item = keyList[sel] for name in copyNames: if name not in sourceDict: continue if name in ['Scale','Extinction','HStrain','Flack','Twins','Layer Disp']: if name == 'Extinction' and 'HKLF' in sourceDict['Histogram']: data['Histograms'][item][name][:2] = copy.deepcopy(sourceDict[name][:2]) for itm in ['Eg','Es','Ep']: data['Histograms'][item][name][2][itm][1] = copy.deepcopy(copyDict[name][itm]) elif name == 'Twins': data['Histograms'][item]['Twins'][0][1][1] = copy.deepcopy(copyDict['Twins']) else: try: data['Histograms'][item][name][1] = copy.deepcopy(copyDict[name]) except KeyError: continue elif name in ['Size','Mustrain']: data['Histograms'][item][name][0] = copy.deepcopy(copyDict[name][0]) data['Histograms'][item][name][2] = copy.deepcopy(copyDict[name][1]) data['Histograms'][item][name][5] = copy.deepcopy(copyDict[name][2]) elif name == 'Pref.Ori.': data['Histograms'][item][name][0] = copy.deepcopy(copyDict[name][0]) data['Histograms'][item][name][2] = copy.deepcopy(copyDict[name][1]) if sourceDict[name][0] == 'SH': SHflags = copy.deepcopy(copyDict[name][2]) SHterms = copy.deepcopy(sourceDict[name][5]) data['Histograms'][item][name][6] = copy.deepcopy(sourceDict[name][6]) data['Histograms'][item][name][7] = copy.deepcopy(sourceDict[name][7]) elif name == 'Babinet': for bab in babNames: data['Histograms'][item][name][bab][1] = copy.deepcopy(copyDict[name][bab]) elif name == 'Fix FXU' or name == 'FixedSeqVars': data['Histograms'][item][name] = copy.deepcopy(sourceDict[name]) finally: dlg.Destroy() def OnSelDataCopy(event): '''Select HAP items to copy from one Phase/Hist to other(s) ''' hist = G2frame.hist sourceDict = data['Histograms'][hist] keyList = G2frame.dataWindow.HistsInPhase[:] if hist in keyList: keyList.remove(hist) if not keyList: G2G.G2MessageBox(G2frame,'No histograms to copy to') return if 'HKLF' in sourceDict['Histogram']: copyNames = ['Extinction','Babinet','Flack','Twins'] else: #PWDR copyNames = ['Pref.Ori.','Size','Mustrain','HStrain','Extinction','Babinet','LeBail','newLeBail','Layer Disp'] copyNames += ['Scale','Fix FXU','FixedSeqVars'] dlg = G2G.G2MultiChoiceDialog(G2frame,'Select which parameters to copy', 'Select phase data parameters', copyNames) selectedItems = [] try: if dlg.ShowModal() == wx.ID_OK: selectedItems = [copyNames[i] for i in dlg.GetSelections()] finally: dlg.Destroy() if not selectedItems: return # nothing to copy copyDict = {} for parm in selectedItems: if parm not in sourceDict: continue copyDict[parm] = copy.deepcopy(sourceDict[parm]) dlg = G2G.G2MultiChoiceDialog(G2frame,u'Copy selected phase/histogram parameters\nfrom '+hist[5:][:35], 'Copy selected phase/hist parameters', keyList) try: if dlg.ShowModal() == wx.ID_OK: for sel in dlg.GetSelections(): data['Histograms'][keyList[sel]].update(copy.deepcopy(copyDict)) finally: dlg.Destroy() def OnSelDataRead(event): '''Select HAP items to copy from another GPX file to current phase & hist ''' sourceDict = data['Histograms'][G2frame.hist] try: dlg = G2G.gpxFileSelector(parent=G2frame) if wx.ID_OK == dlg.ShowModal(): filename = dlg.Selection else: return finally: dlg.Destroy() import pickle phases = None phasenames = [] try: fp = open(filename,'rb') while True: try: d = pickle.load(fp) except EOFError: break if d[0][0] == 'Phases': phases = d phasenames = [phases[i][0] for i in range(1,len(phases))] except: return finally: fp.close() if not phasenames: return if len(phasenames) == 1: phNum = 1 else: dlg = wx.SingleChoiceDialog(G2frame,'Select Phase to use', 'Select',phasenames) if dlg.ShowModal() == wx.ID_OK: phNum = dlg.GetSelection()+1 else: return histograms = list(phases[phNum][1]['Histograms'].keys()) if len(histograms) == 0: return elif len(histograms) == 1: histNam = histograms[0] else: dlg = wx.SingleChoiceDialog(G2frame,'Select histogram to use', 'Select',histograms) if dlg.ShowModal() == wx.ID_OK: histNam = histograms[dlg.GetSelection()] else: return if 'HKLF' in histNam: copyNames = ['Extinction','Babinet','Flack','Twins'] else: #PWDR copyNames = ['Pref.Ori.','Size','Mustrain','HStrain','Extinction','Babinet','LeBail','newLeBail','Layer Disp'] copyNames += ['Scale','Fix FXU','FixedSeqVars'] dlg = G2G.G2MultiChoiceDialog(G2frame,'Select which parameters to copy', 'Select phase data parameters', copyNames) selectedItems = [] try: if dlg.ShowModal() == wx.ID_OK: selectedItems = [copyNames[i] for i in dlg.GetSelections()] finally: dlg.Destroy() if not selectedItems: return # nothing to copy for i in selectedItems: sourceDict[i] = phases[phNum][1]['Histograms'][histNam][i] wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data) def OnPwdrAdd(event): generalData = data['General'] SGData = generalData['SGData'] newList = [] NShkl = len(G2spc.MustrainNames(SGData)) NDij = len(G2spc.HStrainNames(SGData)) keyList = data['Histograms'].keys() TextList = [] if G2frame.GPXtree.GetCount(): item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) while item: name = G2frame.GPXtree.GetItemText(item) if name not in keyList and 'PWDR' in name: TextList.append(name) item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) if not TextList: G2G.G2MessageBox(G2frame,'No histograms') return dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select powder histograms to use', 'Use data',TextList) try: if dlg.ShowModal() == wx.ID_OK: result = dlg.GetSelections() for i in result: newList.append(TextList[i]) if 'All PWDR' in newList: newList = TextList[1:] for histoName in newList: Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,histoName) Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Instrument Parameters'))[0] data['Histograms'][histoName] = {'Histogram':histoName,'Show':False,'LeBail':False,'newLeBail':True, 'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{},['',],0.1],'Type':Inst['Type'][0], 'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1], [1.,1.,1.,0.,0.,0.],6*[False,]], 'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1], NShkl*[0.01,],NShkl*[False,]], 'HStrain':[NDij*[0.0,],NDij*[False,]], 'Layer Disp':[0.0,False], 'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},'Fix FXU':' ','FixedSeqVars':[]} refList = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Reflection Lists')) refList[generalData['Name']] = {} wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data) finally: dlg.Destroy() def OnDataDelete(event): if G2frame.dataWindow.HistsInPhase: DelList = [] extraOpts= {'label_0':'Remove from all phases','value_0':False} h,pd = G2frame.GetUsedHistogramsAndPhasesfromTree() if len(pd) > 1: opts = extraOpts else: opts = {} dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select histogram(s) to remove \nfrom this phase:', 'Remove histograms', G2frame.dataWindow.HistsInPhase, extraOpts=opts) try: if dlg.ShowModal() == wx.ID_OK: DelList = [G2frame.dataWindow.HistsInPhase[i] for i in dlg.GetSelections()] finally: dlg.Destroy() if extraOpts['value_0']: for p in pd: for i in DelList: if i in pd[p]['Histograms']: del pd[p]['Histograms'][i] else: for i in DelList: del data['Histograms'][i] #wx.CallLater(100,G2ddG.UpdateDData,G2frame,DData,data) # produces error G2frame.GPXtree.UpdateSelection() # TId = G2frame.GPXtree.GetFocusedItem() # G2frame.GPXtree.SelectItem(G2frame.root) # G2frame.GPXtree.SelectItem(TId) # UpdatePhaseData(G2frame,Item,data) def OnDataApplyStrain(event): SGData = data['General']['SGData'] DijVals = data['Histograms'][G2frame.hist]['HStrain'][0][:] # apply the Dij values to the reciprocal cell newA = [] Dijdict = dict(zip(G2spc.HStrainNames(SGData),DijVals)) for Aij,lbl in zip(G2lat.cell2A(data['General']['Cell'][1:7]),['D11','D22','D33','D12','D13','D23']): newA.append(Aij + Dijdict.get(lbl,0.0)) # convert back to direct cell data['General']['Cell'][1:7] = G2lat.A2cell(newA) data['General']['Cell'][7] = G2lat.calc_V(newA) # subtract the selected histograms Dij values from all for this phase for hist in data['Histograms']: for i,val in enumerate(DijVals): data['Histograms'][hist]['HStrain'][0][i] -= val # for hist in sorted(data['Histograms']): # list effective lattice constants applying Dij values # DijVals = data['Histograms'][hist]['HStrain'][0] # newA = [] # Dijdict = dict(zip(G2spc.HStrainNames(SGData),DijVals)) # for Aij,lbl in zip(G2lat.cell2A(data['General']['Cell'][1:7]), # ['D11','D22','D33','D12','D13','D23']): # newA.append(Aij + Dijdict.get(lbl,0.0)) # print(hist, G2lat.A2cell(newA)[:3], G2lat.calc_V(newA)) wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data) #### Rigid bodies ################################################################################ def FillRigidBodyGrid(refresh=True,vecId=None,resId=None,spnId=None): '''Fill the Rigid Body Phase information tab page. Note that the page is a ScrolledWindow, not a Grid ''' resVarLookup = [] def OnThermSel(event): Obj = event.GetEventObject() RBObj = Indx[Obj.GetId()] val = Obj.GetValue() Ttype = 'A' if val == 'Uiso': Ttype = 'I' RBObj['ThermalMotion'][0] = 'Uiso' elif val == 'T': RBObj['ThermalMotion'][0] = 'T' elif val == 'TL': RBObj['ThermalMotion'][0] = 'TL' elif val == 'TLS': RBObj['ThermalMotion'][0] = 'TLS' elif val == 'None': RBObj['ThermalMotion'][0] = 'None' if val != 'None': cia = data['General']['AtomPtrs'][3] for i,Id in enumerate(RBObj['Ids']): data['Atoms'][AtLookUp[Id]][cia] = Ttype resId,vecId = None,None #,spnId,None if resSelect is not None: resId = resSelect.GetSelection() if vecSelect is not None: vecId = vecSelect.GetSelection() # if spnSelect: # spnId = spnSelect.GetSelection() wx.CallAfter(FillRigidBodyGrid,True,vecId=vecId,resId=resId) ##,spnId=spnId G2plt.PlotStructure(G2frame,data) def ThermDataSizer(RBObj,rbType): def OnThermval(invalid,value,tc): Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1] Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj) cia = data['General']['AtomPtrs'][3] for i,Id in enumerate(RBObj['Ids']): if Uout[i][0] == 'I': data['Atoms'][AtLookUp[Id]][cia+1] = Uout[i][1] else: data['Atoms'][AtLookUp[Id]][cia+2:cia+8] = Uout[i][2:8] G2plt.PlotStructure(G2frame,data) def OnTLSRef(event): Obj = event.GetEventObject() item = Indx[Obj.GetId()] RBObj['ThermalMotion'][2][item] = Obj.GetValue() thermSizer = wx.FlexGridSizer(0,9,5,5) model = RBObj['ThermalMotion'] if model[0] == 'Uiso': names = ['Uiso',] elif 'T' in model[0]: names = ['T11','T22','T33','T12','T13','T23'] if 'L' in model[0]: names += ['L11','L22','L33','L12','L13','L23'] if 'S' in model[0]: names += ['S12','S13','S21','S23','S31','S32','SAA','SBB'] for i,name in enumerate(names): thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,WACV) thermVal = G2G.ValidatedTxtCtrl(RigidBodies,model[1],i,nDig=(8,4),OnLeave=OnThermval) thermSizer.Add(thermVal) Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?') Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef) Tcheck.SetValue(model[2][i]) Indx[Tcheck.GetId()] = i thermSizer.Add(Tcheck,0,WACV) return thermSizer def LocationSizer(RBObj,rbType): def OnOrigRef(event): RBObj['Orig'][1] = Ocheck.GetValue() def OnOrienRef(event): RBObj['Orient'][1] = Qcheck.GetValue() def OnOrigX(invalid,value,tc): '''Called when the position info is changed (vector or azimuth) ''' newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0] Sytsym,Mult = G2spc.SytSym(RBObj['Orig'][0],SGData)[:2] sytsymtxt.SetLabel('Origin site symmetry: %s, multiplicity: %d '%(Sytsym,Mult)) maxFrac = 0.0 for Id in RBObj['Ids']: maxFrac = max(maxFrac,data['Atoms'][AtLookUp[Id]][cx+3]) for i,Id in enumerate(RBObj['Ids']): data['Atoms'][AtLookUp[Id]][cx:cx+3] = newXYZ[i] data['Atoms'][AtLookUp[Id]][cx+3] = maxFrac data['Atoms'] = G2lat.RBsymCheck(data['Atoms'],ct,cx,cs,AtLookUp,Amat,RBObj['Ids'],SGData) data['Drawing']['Atoms'] = [] UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) def OnOrien(*args, **kwargs): '''Called when the orientation info is changed (vector or azimuth) ''' try: orient = [float(Indx['Orien'][i].GetValue()) for i in range(4)] A = orient[0] V = np.inner(Amat,orient[1:]) # normalized in AVdeg2Q Q = G2mth.AVdeg2Q(A,V) if not any(Q): raise ValueError RBObj['Orient'][0] = Q if rbType != 'Spin': newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0] maxFrac = 0.0 for Id in RBObj['Ids']: maxFrac = max(maxFrac,data['Atoms'][AtLookUp[Id]][cx+3]) for i,Id in enumerate(RBObj['Ids']): data['Atoms'][AtLookUp[Id]][cx:cx+3] = newXYZ[i] data['Atoms'][AtLookUp[Id]][cx+3] = maxFrac data['Atoms'] = G2lat.RBsymCheck(data['Atoms'],ct,cx,cs,AtLookUp,Amat,RBObj['Ids'],SGData) data['Drawing']['Atoms'] = [] UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) except ValueError: pass SGData = data['General']['SGData'] rbSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.FlexGridSizer(0,6,5,5) if rbType != 'Spin': if type(RBObj['Orig'][0]) is tuple: # patch because somehow adding RB origin is becoming a tuple if GSASIIpath.GetConfigValue('debug'): print('patching origin!') RBObj['Orig'][0] = list(RBObj['Orig'][0]) Sytsym,Mult = G2spc.SytSym(RBObj['Orig'][0],SGData)[:2] topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z (frac)'),0,WACV) topSizer.Add((-1,-1)) for ix in range(3): origX = G2G.ValidatedTxtCtrl(RigidBodies,RBObj['Orig'][0],ix,nDig=(8,5), typeHint=float,OnLeave=OnOrigX,xmin=-1,xmax=1.,size=(70,-1)) topSizer.Add(origX,0,WACV) Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?') Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef) Ocheck.SetValue(RBObj['Orig'][1]) # TODO: does spin RB need orientation vector? Does need angle & fix vector = [0,0,1]? topSizer.Add(Ocheck,0,WACV) Name = 'Origin' else: if 'Orig' in RBObj: #cleanout - not using Orig for spinning RBs! del RBObj['Orig'] atId = RBObj['Ids'][0] Atom = data['Atoms'][AtLookUp[atId]] atXYZ = Atom[cx:cx+3] Sytsym,Mult = G2spc.SytSym(atXYZ,SGData)[:2] Name = Atom[ct-1] topSizer.Add(wx.StaticText(RigidBodies,-1, 'Rotation angle (deg)\n&& Orient. vector (frac)'),0,WACV) Indx['Orien'] = {} Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0]) Orien = [Orien,] Orien.extend(np.inner(Bmat,OrienV)) # fractional coords dp,xmin,xmax = 2,-180.,360. for ix,x in enumerate(Orien): orien = G2G.ValidatedTxtCtrl(RigidBodies,Orien,ix,nDig=(8,dp), typeHint=float,OnLeave=OnOrien,xmin=xmin,xmax=xmax,size=(70,-1)) dp, xmin,xmax = 4,-1.,1. Indx['Orien'][ix] = orien topSizer.Add(orien,0,WACV) Qchoice = [' ','A','AV','V'] Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=Qchoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef) Qcheck.SetValue(RBObj['Orient'][1]) topSizer.Add(Qcheck,0,WACV) RBObj['SytSym'] = Sytsym #Only needed for spinning RBs sytsymtxt = wx.StaticText(RigidBodies,label='%s site symmetry: %s, multiplicity: %d '%(Name,Sytsym,Mult)) rbSizer.Add(topSizer) rbSizer.Add(sytsymtxt) return rbSizer def SpnrbSizer(RBObj,spnIndx): '''Displays details for selected spinning rigid body''' def OnDelSpnRB(event): Obj = event.GetEventObject() RBId = Indx[Obj.GetId()] RBData['Spin'][RBId[0]]['useCount'] -= 1 cia = data['General']['AtomPtrs'][3] atomData = data['Atoms'] atomId = data['RBModels']['Spin'][spnIndx]['Ids'][0] for ia,atom in enumerate(atomData): if atomId == atom[cia+8]: #by definition only one del atomData[ia] break del data['RBModels']['Spin'][spnIndx] del data['General']['SpnIds'][atomId] data['Drawing']['Atoms'] = [] G2plt.PlotStructure(G2frame,data) wx.CallAfter(FillRigidBodyGrid,True) def OnSymRadioSet(event): '''Set the polar axis for the sp. harm. as RBdata['Spin'][RBId]['symAxis']. This may never be set, so use RBdata['Spin'][RBId].get('symAxis') to access this so the default value is [0,0,1]. ''' Obj = event.GetEventObject() axis = ([1,0,0],[0,1,0],[0,0,1],[1,1,0],[1,1,1])[Obj.GetSelection()] RBObj['symAxis'] = axis G2plt.PlotStructure(G2frame,data) def OnAddShell(event): rbNames = [] rbIds = {} for rbId in RBData['Spin']: name = RBData['Spin'][rbId]['RBname'] rbNames.append(name) rbIds[name] = rbId if len(rbNames) == 1: selection = rbNames[0] else: choices = sorted(rbNames) dlg = G2G.G2SingleChoiceDialog( G2frame,'Select rigid body to\nadd to structure', 'Select rigid body',choices) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: selection = choices[dlg.GetSelection()] else: return finally: dlg.Destroy() rbData = RBData['Spin'][rbIds[selection]] RBObj['RBId'].append(rbIds[selection]) RBObj['SHC'].append({}) for name in ['atColor','atType','Natoms','nSH','RBname','RBsym','Radius']: RBObj[name].append(rbData[name]) RBObj['hide'].append(False) RBData['Spin'][rbIds[selection]]['useCount'] += 1 G2plt.PlotStructure(G2frame,data) wx.CallAfter(FillRigidBodyGrid,True,spnId=rbId) def SHsizer(): def OnSHOrder(event): Obj = event.GetEventObject() iSh = Indx[Obj.GetId()] RBObj['nSH'][iSh] = int(Obj.GetValue()) RBObj['SHC'][iSh] = SetSHCoef(iSh,RBObj['nSH'][iSh]) G2plt.PlotStructure(G2frame,data) wx.CallAfter(FillRigidBodyGrid,True,spnId=rbId) def SetSHCoef(iSh,Order): Sytsym = RBObj['SytSym'] cofNames,cofSgns = G2lat.GenRBCoeff(Sytsym,RBObj['RBsym'][iSh],Order) cofTerms = [[0.0,val,False] for val in cofSgns] newSHcoef = dict(zip(cofNames,cofTerms)) SHcoef = RBObj['SHC'][iSh] for cofName in SHcoef: #transfer old values to new set if cofName in newSHcoef: newSHcoef[cofName] = SHcoef[cofName] return newSHcoef def OnSchRef(event): Obj = event.GetEventObject() iSh,name = Indx[Obj.GetId()] RBObj['SHC'][iSh][name][2] = not RBObj['SHC'][iSh][name][2] def OnRadRef(event): Obj = event.GetEventObject() iSh = Indx[Obj.GetId()] RBObj['Radius'][iSh][1] = not RBObj['Radius'][iSh][1] def NewSHC(invalid,value,tc): G2plt.PlotStructure(G2frame,data) def OnDelShell(event): Obj = event.GetEventObject() iSh = Indx[Obj.GetId()] rbId = RBObj['RBId'][iSh] RBData['Spin'][rbId]['useCount'] -= 1 RBData['Spin'][rbId]['useCount'] = max(0,RBData['Spin'][rbId]['useCount']) for name in ['atColor','atType','Natoms','nSH','RBId','RBname','RBsym','SHC','Radius']: del RBObj[name][iSh] G2plt.PlotStructure(G2frame,data) wx.CallAfter(FillRigidBodyGrid,True,spnId=rbId) shSizer = wx.BoxSizer(wx.VERTICAL) for iSh,nSh in enumerate(RBObj['nSH']): #patch if 'Radius' not in RBObj: RBObj['Radius'] = [[1.0,False] for i in range(len(RBObj['nSH']))] #end patch rbId = RBObj['RBId'][iSh] RBObj['atType'][iSh] = RBData['Spin'][rbId]['atType'] RBObj['atColor'][iSh] = G2elem.GetAtomInfo(RBObj['atType'][iSh])['Color'] #correct atom color for shell if iSh: subLine = wx.BoxSizer(wx.HORIZONTAL) subLine.Add(wx.StaticText(RigidBodies,label='Shell %d: Name: %s Atom type: %s RB sym: %s ' \ %(iSh,RBObj['RBname'][iSh],RBObj['atType'][iSh],RBObj['RBsym'][iSh])),0,WACV) delShell = wx.Button(RigidBodies,label='Delete shell',style=wx.BU_EXACTFIT) Indx[delShell.GetId()] = iSh delShell.Bind(wx.EVT_BUTTON,OnDelShell) subLine.Add(delShell,0,WACV) hidesh = wx.CheckBox(RigidBodies,label='Hide shell?') hidesh.SetValue(RBObj['hide'][iSh]) hidesh.Bind(wx.EVT_CHECKBOX,OnHideSh) Indx[hidesh.GetId()] = iSh subLine.Add(hidesh,0,WACV) shSizer.Add(subLine) shoSizer = wx.BoxSizer(wx.HORIZONTAL) shoSizer.Add(wx.StaticText(RigidBodies,label=' Bessel/Harmonic order: '),0,WACV) shOrder = wx.ComboBox(RigidBodies,value=str(RBObj['nSH'][iSh]),choices=[str(i) for i in range(19)], style=wx.CB_READONLY|wx.CB_DROPDOWN) Indx[shOrder.GetId()] = iSh shOrder.Bind(wx.EVT_COMBOBOX,OnSHOrder) shoSizer.Add(shOrder,0,WACV) if RBObj['nSH'][iSh]>0: shoSizer.Add(wx.StaticText(RigidBodies,label=" 'c' for cubic harmonic term. "),0,WACV) shoSizer.Add(wx.StaticText(RigidBodies,label=' Radius: '),0,WACV) shoSizer.Add(G2G.ValidatedTxtCtrl(RigidBodies,RBObj['Radius'][iSh],0,nDig=(8,5),xmin=0.0,xmax=5.0, typeHint=float,size=(70,-1),OnLeave=NewSHC),0,WACV) if 'Q' in RBObj['atType'][iSh]: radref = wx.StaticText(RigidBodies,label=' For drawing only') else: radref = wx.CheckBox(RigidBodies,label=' refine? ') radref.SetValue(RBObj['Radius'][iSh][1]) radref.Bind(wx.EVT_CHECKBOX,OnRadRef) Indx[radref.GetId()] = iSh shoSizer.Add(radref,0,WACV) shSizer.Add(shoSizer) if not RBObj['nSH'][iSh]: shSizer.Add(wx.StaticText(RigidBodies, label=' Select harmonic order or try different equivalent position')) elif len(RBObj['SHC'][iSh]) > 12: shSizer.Add(wx.StaticText(RigidBodies, label=' WARNING: More than 12 terms found; use lower harmonic order')) else: shcSizer = wx.FlexGridSizer(0,9,5,5) for item in RBObj['SHC'][iSh]: shcSizer.Add(wx.StaticText(RigidBodies,label='%s'%item.strip('+').strip('-'))) shcSizer.Add(G2G.ValidatedTxtCtrl(RigidBodies,RBObj['SHC'][iSh][item],0,nDig=(8,5), typeHint=float,size=(70,-1),OnLeave=NewSHC)) schref = wx.CheckBox(RigidBodies,label=' refine? ') schref.SetValue(RBObj['SHC'][iSh][item][2]) schref.Bind(wx.EVT_CHECKBOX,OnSchRef) Indx[schref.GetId()] = iSh,item shcSizer.Add(schref) shSizer.Add(shcSizer) return shSizer def OnHideSh(event): Obj = event.GetEventObject() iSh = Indx[Obj.GetId()] RBObj['hide'][iSh] = not RBObj['hide'][iSh] G2plt.PlotStructure(G2frame,data) RBObj['hide'] = RBObj.get('hide',[False for i in range(len(RBObj['atType']))]) rbId = RBObj['RBId'][0] atId = RBObj['Ids'][0] atName = data['Atoms'][AtLookUp[atId]][ct-1] RBObj['atType'][0] = RBData['Spin'][rbId]['atType'] sprbSizer = wx.BoxSizer(wx.VERTICAL) sprbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-')) topLine = wx.BoxSizer(wx.HORIZONTAL) topLine.Add(wx.StaticText(RigidBodies,label='Shell 0: Name: %s Atom name: %s Atom type: %s RB sym: %s '% (RBObj['RBname'][0],atName,RBObj['atType'][0],RBObj['RBsym'][0])),0,WACV) rbId = RBObj['RBId'] if len(RBObj['nSH']) == 1: delRB = wx.Button(RigidBodies,wx.ID_ANY,'Delete',style=wx.BU_EXACTFIT) delRB.Bind(wx.EVT_BUTTON,OnDelSpnRB) Indx[delRB.GetId()] = rbId topLine.Add(delRB,0,WACV) addShell = wx.Button(RigidBodies,wx.ID_ANY,'Add new shell',style=wx.BU_EXACTFIT) addShell.Bind(wx.EVT_BUTTON,OnAddShell) Indx[addShell.GetId()] = rbId topLine.Add(addShell,0,WACV) hidesh = wx.CheckBox(RigidBodies,label='Hide shell?') hidesh.SetValue(RBObj['hide'][0]) hidesh.Bind(wx.EVT_CHECKBOX,OnHideSh) Indx[hidesh.GetId()] = 0 topLine.Add(hidesh,0,WACV) sprbSizer.Add(topLine) sprbSizer.Add(LocationSizer(RBObj,'Spin')) choices = [' x ',' y ',' z ','x+y','x+y+z'] RBObj['symAxis'] = RBObj.get('symAxis',[0,0,1]) #set default as 'z' symax = dict(zip([str(x) for x in [[1,0,0],[0,1,0],[0,0,1],[1,1,0],[1,1,1]]],choices))[str(RBObj['symAxis'])] symRadioSet = wx.RadioBox(RigidBodies,choices=choices,label='Sp harm polar axis is aligned along:') symRadioSet.SetStringSelection(symax) symRadioSet.Bind(wx.EVT_RADIOBOX, OnSymRadioSet) Indx[symRadioSet.GetId()] = rbId sprbSizer.Add(symRadioSet) sprbSizer.Add(SHsizer()) return sprbSizer def ResrbSizer(RBObj,resIndx): '''Displays details for selected residue rigid body''' def OnTorsionRef(event): Obj = event.GetEventObject() item = Indx[Obj.GetId()] RBObj['Torsions'][item][1] = Obj.GetValue() def OnTorsion(invalid,value,tc): newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0] for i,Id in enumerate(RBObj['Ids']): data['Atoms'][AtLookUp[Id]][cx:cx+3] = newXYZ[i] data['Drawing']['Atoms'] = [] UpdateDrawAtoms(atomStyle) drawAtoms.ClearSelection() G2plt.PlotStructure(G2frame,data) def OnFrac(invalid,value,tc): for i,Id in enumerate(RBObj['Ids']): if data['Atoms'][AtLookUp[Id]][cx+3]: data['Atoms'][AtLookUp[Id]][cx+3] = value def OnRefFrac(event): RBObj['AtomFrac'][1] = not RBObj['AtomFrac'][1] def OnDelResRB(event): Obj = event.GetEventObject() RBId = Indx[Obj.GetId()] RBData['Residue'][RBId]['useCount'] -= 1 del data['RBModels']['Residue'][resIndx] G2plt.PlotStructure(G2frame,data) wx.CallAfter(FillRigidBodyGrid,True,resId=resIndx) resrbSizer = wx.BoxSizer(wx.VERTICAL) resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-')) topLine = wx.BoxSizer(wx.HORIZONTAL) topLine.Add(wx.StaticText(RigidBodies,-1,'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,WACV) rbId = RBObj['RBId'] delRB = wx.Button(RigidBodies,wx.ID_ANY,'Delete',style=wx.BU_EXACTFIT) delRB.Bind(wx.EVT_BUTTON,OnDelResRB) Indx[delRB.GetId()] = rbId topLine.Add(delRB,0,WACV) symAxis = RBObj.get('symAxis') if np.any(symAxis): if np.all(symAxis): lbl = 'x+y+z' elif np.all(symAxis[:2]): lbl = 'x+y' elif symAxis[0]: lbl = 'x' elif symAxis[1]: lbl = 'y' else: lbl = 'z' topLine.Add(wx.StaticText(RigidBodies,-1, ' Rigid body {} axis is aligned along oriention vector'.format(lbl)),0,WACV) try: varname = str(data['pId'])+'::RBRxxx:'+resVarLookup[resIndx] except: # happens when phase has no histograms varname = '?::RBRxxx:'+resVarLookup[resIndx] topLine.Add(wx.StaticText(RigidBodies,-1, ' (variables '+varname+')'),0,WACV) resrbSizer.Add(topLine) resrbSizer.Add(LocationSizer(RBObj,'Residue')) if len(RBObj['Torsions']): resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0) torSizer = wx.FlexGridSizer(0,6,5,5) for itors,tors in enumerate(RBObj['Torsions']): torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,WACV) torsTxt = G2G.ValidatedTxtCtrl(RigidBodies,RBObj['Torsions'][itors],0,nDig=(10,3),OnLeave=OnTorsion) torSizer.Add(torsTxt) torCheck = wx.CheckBox(RigidBodies,-1,'Refine?') torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef) torCheck.SetValue(tors[1]) Indx[torCheck.GetId()] = itors torSizer.Add(torCheck,0,WACV) resrbSizer.Add(torSizer) members = 'Rigid body members: ' for nId,Id in enumerate(RBObj['Ids']): if nId and not nId%10: members += ('\n'+30*' ') members += data['Atoms'][AtLookUp[Id]][ct-1].strip()+', ' resrbSizer.Add(wx.StaticText(RigidBodies,label=members[:-2]),0) fracSizer = wx.BoxSizer(wx.HORIZONTAL) fracSizer.Add(wx.StaticText(RigidBodies,label='Rigid Body atom site fraction: ')) fracTxt = G2G.ValidatedTxtCtrl(RigidBodies,RBObj['AtomFrac'],0,nDig=(10,3),OnLeave=OnFrac) fracSizer.Add(fracTxt,0,WACV) fracRef = wx.CheckBox(RigidBodies,label='Refine?') fracRef.SetValue(RBObj['AtomFrac'][1]) fracRef.Bind(wx.EVT_CHECKBOX,OnRefFrac) fracSizer.Add(fracRef,0,WACV) resrbSizer.Add(fracSizer) tchoice = ['None','Uiso','T','TL','TLS'] thermSizer = wx.BoxSizer(wx.HORIZONTAL) thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,WACV) thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) Indx[thermSel.GetId()] = RBObj thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel) thermSizer.Add(thermSel,0,WACV) thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,WACV) resrbSizer.Add(thermSizer) if RBObj['ThermalMotion'][0] != 'None': resrbSizer.Add(ThermDataSizer(RBObj,'Residue')) return resrbSizer def VecrbSizer(RBObj,resIndx): '''Displays details for selected vector rigid body''' def OnFrac(invalid,value,tc): for Id in RBObj['Ids']: if data['Atoms'][AtLookUp[Id]][cx+3]: data['Atoms'][AtLookUp[Id]][cx+3] = value def OnRefFrac(event): RBObj['AtomFrac'][1] = not RBObj['AtomFrac'][1] def OnDelVecRB(event): Obj = event.GetEventObject() RBId = Indx[Obj.GetId()] RBData['Vector'][RBId]['useCount'] -= 1 del data['RBModels']['Vector'][resIndx] G2plt.PlotStructure(G2frame,data) wx.CallAfter(FillRigidBodyGrid,True,vecId=resIndx) vecrbSizer = wx.BoxSizer(wx.VERTICAL) vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-')) topLine = wx.BoxSizer(wx.HORIZONTAL) topLine.Add(wx.StaticText(RigidBodies,-1, 'Name: '+RBObj['RBname']+' '),0,WACV) rbId = RBObj['RBId'] delRB = wx.Button(RigidBodies,wx.ID_ANY,'Delete',style=wx.BU_EXACTFIT) delRB.Bind(wx.EVT_BUTTON,OnDelVecRB) Indx[delRB.GetId()] = rbId topLine.Add(delRB,0,WACV) vecrbSizer.Add(topLine) vecrbSizer.Add(LocationSizer(RBObj,'Vector')) members = 'Rigid body members: ' for Id in RBObj['Ids']: members += data['Atoms'][AtLookUp[Id]][ct-1].strip()+', ' vecrbSizer.Add(wx.StaticText(RigidBodies,label=members[:-2])) fracSizer = wx.BoxSizer(wx.HORIZONTAL) fracSizer.Add(wx.StaticText(RigidBodies,label='Rigid Body atom site fraction: ')) fracTxt = G2G.ValidatedTxtCtrl(RigidBodies,RBObj['AtomFrac'],0,nDig=(10,3),OnLeave=OnFrac) fracSizer.Add(fracTxt,0,WACV) fracRef = wx.CheckBox(RigidBodies,label='Refine?') fracRef.SetValue(RBObj['AtomFrac'][1]) fracRef.Bind(wx.EVT_CHECKBOX,OnRefFrac) fracSizer.Add(fracRef,0,WACV) vecrbSizer.Add(fracSizer) tchoice = ['None','Uiso','T','TL','TLS'] thermSizer = wx.BoxSizer(wx.HORIZONTAL) thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,WACV) thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice, style=wx.CB_READONLY|wx.CB_DROPDOWN) Indx[thermSel.GetId()] = RBObj thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel) thermSizer.Add(thermSel,0,WACV) thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,WACV) vecrbSizer.Add(thermSizer) if RBObj['ThermalMotion'][0] != 'None': vecrbSizer.Add(ThermDataSizer(RBObj,'Vector')) return vecrbSizer def OnVecSelect(event): global prevVecId prevVecId = vecSelect.GetSelection() try: resSelect.Deselect(resSelect.GetSelection()) except: pass try: spnSelect.Deselect(spnSelect.GetSelection()) except: pass wx.CallLater(100,RepaintRBInfo,'Vector',prevVecId) def OnResSelect(event): global prevResId prevResId = resSelect.GetSelection() try: vecSelect.Deselect(vecSelect.GetSelection()) except: pass try: spnSelect.Deselect(spnSelect.GetSelection()) except: pass wx.CallLater(100,RepaintRBInfo,'Residue',prevResId) def OnSpnSelect(event): global prevSpnId prevSpnId = spnSelect.GetSelection() try: resSelect.Deselect(resSelect.GetSelection()) except: pass try: vecSelect.Deselect(vecSelect.GetSelection()) except: pass wx.CallLater(100,RepaintRBInfo,'Spin',prevSpnId) def RepaintRBInfo(rbType,rbIndx,Scroll=0): oldFocus = wx.Window.FindFocus() try: if 'phoenix' in wx.version(): G2frame.bottomSizer.Clear(True) else: G2frame.bottomSizer.DeleteWindows() except: return Indx.clear() rbObj = data['RBModels'][rbType][rbIndx] data['Drawing']['viewPoint'][0] = data['Atoms'][AtLookUp[rbObj['Ids'][0]]][cx:cx+3] Quad = rbObj['Orient'][0] data['Drawing']['Quaternion'] = G2mth.invQ(Quad) if rbType == 'Residue': G2frame.bottomSizer = ResrbSizer(rbObj,rbIndx) elif rbType == 'Spin': G2frame.bottomSizer = SpnrbSizer(rbObj,rbIndx) else: #Vector G2frame.bottomSizer = VecrbSizer(rbObj,rbIndx) mainSizer.Add(G2frame.bottomSizer) mainSizer.Layout() G2frame.dataWindow.Refresh() RigidBodies.SetVirtualSize(mainSizer.GetMinSize()) RigidBodies.Scroll(0,Scroll) G2frame.dataWindow.SendSizeEvent() G2plt.PlotStructure(G2frame,data) wx.CallAfter(oldFocus.SetFocus) # FillRigidBodyGrid executable code starts here if refresh: if RigidBodies.GetSizer(): RigidBodies.GetSizer().Clear(True) if 'testRBObj' in data: del data['testRBObj'] general = data['General'] cx,ct,cs,cia = general['AtomPtrs'] AtLookUp = G2mth.FillAtomLookUp(data['Atoms'],cia+8) Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7]) Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies') if not Id: G2frame.CheckNotebook() Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies') if not Id: print('Strange! Why no Rigid Bodies tree entry?') return RBData = G2frame.GPXtree.GetItemPyData(Id) Indx = {} atomStyle = 'balls & sticks' if 'macro' in general['Type']: atomStyle = 'sticks' G2frame.GetStatusBar().SetStatusText('',1) mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(RigidBodies,label='Select rigid body to view:'),0,WACV) topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(RigidBodies,helpIndex=G2frame.dataWindow.helpKey),0,WACV) mainSizer.Add(topSizer) nobody = True resSelect = None vecSelect = None spnSelect = None rbSizer = wx.BoxSizer(wx.HORIZONTAL) if 'Residue' in data['RBModels'] and len(data['RBModels']['Residue']): nobody = False resSizer = wx.BoxSizer(wx.VERTICAL) resSizer.Add(wx.StaticText(RigidBodies,label='Residue RBs:')) RBnames = [] resVarLookup = [] for irb,RBObj in enumerate(data['RBModels']['Residue']): # patch if 'AtomFrac' not in RBObj: RBObj['AtomFrac'] = [1.0,False] #end patch name = RBObj['RBname']+RBObj['numChain'] RBnames.append(name) jrb = RBData['RBIds']['Residue'].index(RBObj['RBId']) resVarLookup.append(str(irb)+':'+str(jrb)) # var name suffix following G2strMath.ApplyRBModels() if prevResId is not None: resId = prevResId try: rbName = RBnames[resId] except: resId = 0 rbName = RBnames[resId] rbObj = data['RBModels']['Residue'][resId] data['Drawing']['viewPoint'][0] = rbObj['Orig'][0] data['Drawing']['Quaternion'] = rbObj['Orient'][0] resSelect = wx.ListBox(RigidBodies,choices=RBnames,style=wx.LB_SINGLE,size=(-1,120)) if resId: resSelect.SetSelection(resId) OnResSelect(None) resSelect.Bind(wx.EVT_LISTBOX,OnResSelect) resSizer.Add(resSelect) rbSizer.Add(resSizer) if 'Vector' in data['RBModels'] and len(data['RBModels']['Vector']): vecSizer = wx.BoxSizer(wx.VERTICAL) vecSizer.Add(wx.StaticText(RigidBodies,label='Vector RBs:')) nobody = False RBnames = [] for RBObj in data['RBModels']['Vector']: # patch if 'AtomFrac' not in RBObj: RBObj['AtomFrac'] = [1.0,False] #end patch RBnames.append(RBObj['RBname']) vecId = -1 if prevVecId is not None: vecId = prevVecId try: rbName = RBnames[vecId] except: vecId = 0 rbName = RBnames[vecId] rbObj = data['RBModels']['Vector'][vecId] data['Drawing']['viewPoint'][0] = rbObj['Orig'][0] data['Drawing']['Quaternion'] = rbObj['Orient'][0] vecSelect = wx.ListBox(RigidBodies,choices=RBnames,style=wx.LB_SINGLE,size=(-1,120)) if vecId is not None: vecSelect.SetSelection(vecId) OnVecSelect(None) vecSelect.Bind(wx.EVT_LISTBOX,OnVecSelect) vecSizer.Add(vecSelect) rbSizer.Add(vecSizer) if 'Spin' in data['RBModels'] and len(data['RBModels']['Spin']): spnSizer = wx.BoxSizer(wx.VERTICAL) spnSizer.Add(wx.StaticText(RigidBodies,label='Spinning RBs:')) nobody = False RBnames = [] for RBObj in data['RBModels']['Spin']: RBnames.append(RBObj['RBname'][0]) spnId = -1 if prevSpnId is not None: spnId = prevSpnId try: rbName = RBnames[spnId] except: spnId = 0 rbName = RBnames[spnId] rbObj = data['RBModels']['Spin'][spnId] data['Drawing']['viewPoint'][0] = data['Atoms'][AtLookUp[RBObj['Ids'][0]]][cx:cx+3] data['Drawing']['Quaternion'] = rbObj['Orient'][0] spnSelect = wx.ListBox(RigidBodies,choices=RBnames,style=wx.LB_SINGLE,size=(-1,120)) if spnId != -1: spnSelect.SetSelection(spnId) OnSpnSelect(None) spnSelect.Bind(wx.EVT_LISTBOX,OnSpnSelect) spnSizer.Add(spnSelect,0) rbSizer.Add(spnSizer) mainSizer.Add(rbSizer,0,wx.EXPAND) G2frame.bottomSizer = wx.BoxSizer(wx.VERTICAL) G2frame.bottomSizer.Add(wx.StaticText(RigidBodies,label=' ')) mainSizer.Add(G2frame.bottomSizer) G2plt.PlotStructure(G2frame,data) G2plt.PlotStructure(G2frame,data) # draw twice initially for mac if nobody: msg = 'Define a rigid body with the "Rigid Bodies" tree entry before adding it to the phase here' if RBData.get('RBIds') is None: pass elif len(RBData['RBIds'].get('Vector',[])) + len(RBData['RBIds'].get('Residue',[])) == 0: pass else: msg = 'No rigid bodies defined in phase. Use "Edit Body"/"Locate & Insert..."\ncommand to add them.' mainSizer.Add(wx.StaticText(RigidBodies,label=msg),0) SetPhaseWindow(RigidBodies,mainSizer) def OnRBCopyParms(event): RBObjs = [] for rbType in ['Vector','Residue']: RBObjs += data['RBModels'].get(rbType,[]) if not len(RBObjs): print ('**** ERROR - no rigid bodies defined ****') return if len(RBObjs) == 1: print ('**** INFO - only one rigid body defined; nothing to copy to ****') return Source = [] sourceRB = {} for RBObj in RBObjs: Source.append(RBObj['RBname']) dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() for item in ['Orig','Orient','ThermalMotion','AtomFract']: sourceRB.update({item:RBObjs[sel][item],}) dlg.Destroy() if not sourceRB: return dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() for x in sel: RBObjs[x].update(copy.copy(sourceRB)) G2plt.PlotStructure(G2frame,data) wx.CallAfter(FillRigidBodyGrid,True) def assignAtoms(RBData,selDict={},unmatchedRBatoms=None): '''Find the closest RB atoms to atoms in the structure If selDict is specified, it overrides the assignments to specify atoms that should be matched. ''' general = data['General'] cx,ct = general['AtomPtrs'][:2] Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7]) rbType = data['testRBObj']['rbType'] rbObj = data['testRBObj']['rbObj'] rbId = rbObj['RBId'] matchTable = [] if rbType == 'Spin': rbData = RBData['Spin'][rbId] rbData['Orig'] = [0.,0.,0.] matchTable.append([rbData['RBname'],rbData['rbType']]+list(rbData['Orig'])) return matchTable rbAtmTypes = RBData[rbType][rbId]['rbTypes'] atomData = data['Atoms'] if 'atNames' in RBData[rbType][rbId]: rbAtmLbs = RBData[rbType][rbId]['atNames'] else: rbAtmLbs = None newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0] rbUsedIds = [] # Ids of atoms in current phase used inside RBs for i in data['RBModels']: for j in data['RBModels'][i]: rbUsedIds += j['Ids'] # categorize atoms by type, omitting any that are already assigned # in a rigid body atmTypes = [None if atomData[i][-1] in rbUsedIds else atomData[i][ct] for i in range(len(atomData))] # remove assigned atoms from search groups for i in selDict: if selDict[i] is None: continue atmTypes[selDict[i]] = None atmXYZ = G2mth.getAtomXYZ(atomData,cx) # separate structure's atoms by type (w/o assigned atoms) oXYZbyT = {} atmNumByT = {} for t in set(atmTypes): if t is None: continue oXYZbyT[t] = np.array([atmXYZ[i] for i in range(len(atmXYZ)) if atmTypes[i] == t]) atmNumByT[t] = [i for i in range(len(atmXYZ)) if atmTypes[i] == t] Ids = [] # create table of fixed and found assignments unmatched = [] for i,xyz in enumerate(newXYZ): t = rbAtmTypes[i] if rbAtmLbs: lbl = rbAtmLbs[i] else: lbl = '' if i in selDict and selDict[i] is None: matchTable.append([t , lbl] + list(xyz)) continue elif i in selDict: searchXYZ = [atmXYZ[selDict[i]]] #assigned numLookup = [selDict[i]] else: if t not in oXYZbyT: unmatched.append(i) matchTable.append([t , lbl] + list(xyz)) continue searchXYZ = oXYZbyT[t] numLookup = atmNumByT[t] dist = G2mth.GetXYZDist(xyz,searchXYZ,Amat) while True: pidIndx = np.argmin(dist) d = dist[pidIndx] pid = numLookup[pidIndx] if atomData[pid][-1] in Ids: #duplicate - 2 atoms on same site; invalidate & look again dist[pidIndx] = 100. if min(dist) == 100: pid = None break else: break if pid is not None: Ids.append(atomData[pid][-1]) matchTable.append([t , lbl] + list(xyz) + [pid, atomData[pid][0]] + atomData[pid][cx:cx+3] + [d, Ids[-1]]) else: unmatched.append(i) matchTable.append([t , lbl] + list(xyz)) if unmatched and unmatchedRBatoms is not None: unmatchedRBatoms[:] = unmatched return matchTable def OnRBAssign(event): '''Assign RB to atoms in a phase with tools to locate the RB in the structure ''' def Draw(): '''Create the window for assigning RB to atoms''' def OnAddRB(event): 'respond to RB Add button, sets RB info in phase' dataGeneral = data['General'] dataGeneral['SpnIds'] = dataGeneral.get('SpnIds',{}) cx,ct,cs,cia = dataGeneral['AtomPtrs'] rbType = data['testRBObj']['rbType'] atomData = data['Atoms'] if RigidBodies.atomsGrid: matchTable = UpdateTable() else: matchTable = assignAtoms(RBData) dmax = 0. for line in matchTable: if len(line) >= 11: dmax = max(dmax,line[10]) if dmax > 1.0: msg = "Atoms may not be properly located. Are you sure you want to do this?" dlg = wx.MessageDialog(G2frame,msg,caption='Continue?',style=wx.YES_NO|wx.ICON_EXCLAMATION) if dlg.ShowModal() != wx.ID_YES: dlg.Destroy() return dlg.Destroy() Ids = [] updateNeeded = False for line in matchTable: if len(line) < 11: if rbType == 'Spin': elem = line[1] x,y,z = rbObj['Orig'][0] else: elem = line[0] x,y,z = line[2:5] nextNum = len(data['Atoms']) lbl = 'Rb' + elem + str(nextNum) AtomAdd(x,y,z,El=elem,Name=lbl,update=False) if rbType == 'Spin': dataGeneral['SpnIds'][atomData[nextNum][-1]] = rbObj['RBId'] Ids.append(atomData[nextNum][-1]) updateNeeded = True else: atomData[line[5]][cx:cx+3] = line[2:5] Ids.append(line[11]) if len(Ids): AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8) G2lat.RBsymCheck(atomData,ct,cx,cs,AtLookUp,Amat,Ids,SGData) if updateNeeded: SetupGeneral() UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) rbNames = [[]] for item in data['RBModels'].get(rbType,[]): if rbType == 'Spin': rbNames.append(item['RBname'][0]) else: rbNames.append(item['RBname']) rbObj['Ids'] = Ids #atomids rbId = rbObj['RBId'] #RB obj id rbObj['AtomFract'] = [1.0,False] if rbType == 'Spin': del data['testRBObj']['rbData']['Spin'][rbId]['Orig'] rbObj.update(data['testRBObj']['rbData']['Spin'][rbId]) del rbObj['rbPos'] else: rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags i = 0 while True: #find unique name rbName = '%s:%d'%(rbObj['RBname'],i) if rbName in rbNames: i += 1 else: break rbObj['RBname'] = rbName if not rbType in data['RBModels']: data['RBModels'][rbType] = [] if rbType == 'Spin': #convert items to lists of shells for name in ['atColor','atType','Natoms','nSH','Radius','RBId','RBname','RBsym']: #patch if name == 'Radius' and name not in rbObj: item = rbObj['radius'] else: item = rbObj[name] rbObj[name] = [item,] data['RBModels'][rbType].append(copy.deepcopy(rbObj)) RBData[rbType][rbId]['useCount'] += 1 del data['testRBObj'] # Update the draw atoms array & recompute bonds for atom in atomData: ID = atom[cia+8] G2mth.DrawAtomsReplaceByID(data,cia+8,atom,ID) FindBondsDraw(data) G2plt.PlotStructure(G2frame,data,False) FillRigidBodyGrid(True) def OnCancel(event): del data['testRBObj'] FillRigidBodyGrid(True) def OnTorAngle(invalid,value,tc): '''respond to a number entered into the torsion editor. Update the slider (number is already saved) recompute atom distances ''' [tor,torSlide] = Indx[tc.GetId()] torSlide.SetValue(int(value*10)) UpdateTablePlot() def OnTorSlide(event): '''respond to the slider moving. Put value into editor & save recompute atom distances ''' Obj = event.GetEventObject() tor,ang = Indx[Obj.GetId()] Tors = data['testRBObj']['rbObj']['Torsions'][tor] val = float(Obj.GetValue())/10. Tors[0] = val ang.SetValue(val) UpdateTablePlot() def UpdateTable(event=None): '''get fixed atom assignments, find closest mappings & update displayed table ''' if not RigidBodies.atomsGrid: return [] RigidBodies.atomsGrid.completeEdits() # add new atoms and reassign added = False selDict = getSelectedAtoms() if selDict is None: return for i,l in enumerate(RigidBodies.atomsTable.data): if l[4] == 'Create new': l[1:4] = -1,'?',-1 rbAssignments[i] = None selDict[i] = None matchTable = assignAtoms(RBData,selDict) for i,l in enumerate(matchTable): if len(l) < 11: continue RigidBodies.atomsTable.data[i][1:4] = l[5],l[6],l[10] if RigidBodies.atomsGrid: RigidBodies.atomsGrid.ForceRefresh() if added: wx.CallLater(100,Draw) return matchTable def OnAzSlide(event): '''respond to the azimuth slider moving. Save & put value into azimuth edit widget; show Q & update the plot and table ''' Obj = event.GetEventObject() rbObj['OrientVec'][0] = float(Obj.GetValue())/10. for i in range(4): val = rbObj['OrientVec'][i] G2frame.testRBObjSizers['OrientVecSiz'][i].SetValue(val) Q = G2mth.AVdeg2Q(rbObj['OrientVec'][0], np.inner(Amat,rbObj['OrientVec'][1:])) rbObj['Orient'][0] = Q A,V = G2mth.Q2AVdeg(Q) rbObj['OrientVec'][1:] = np.inner(Bmat,V) G2plt.PlotStructure(G2frame,data,False,UpdateTable) UpdateTable() def UpdateOrientation(*args,**kwargs): '''Respond to a change in the azimuth or vector via the edit widget; update Q display & azimuth slider ''' Q = G2mth.AVdeg2Q(rbObj['OrientVec'][0], np.inner(Amat,rbObj['OrientVec'][1:])) rbObj['Orient'][0] = Q G2frame.testRBObjSizers['OrientVecSiz'][4].SetValue( int(10*rbObj['OrientVec'][0])) G2plt.PlotStructure(G2frame,data,False,UpdateTable) UpdateTable() def UpdateTablePlot(*args,**kwargs): '''update displayed table and plot ''' G2plt.PlotStructure(G2frame,data,False,UpdateTable) UpdateTable() def UpdateSytSym(*args,**kwargs): Sytsym,Mult = G2spc.SytSym(rbObj['Orig'][0],data['General']['SGData'])[:2] sytsymtxt.SetLabel('Origin site symmetry: %s, multiplicity: %d '%(Sytsym,Mult)) UpdateTablePlot(args,kwargs) def getSelectedAtoms(): 'Find the FB atoms that have been assigned to specific atoms in structure' if not RigidBodies.atomsGrid: return RigidBodies.atomsGrid.completeEdits() tbl = RigidBodies.atomsGrid.GetTable() selDict = {} dups = [] assigned = [] atomsLabels = [a[0] for a in data['Atoms']] for r in range(tbl.GetRowsCount()): sel = tbl.GetValue(r,4).strip() if sel == 'Create new': continue # ignore positions of new atoms if sel not in atomsLabels: continue atmNum = atomsLabels.index(sel) if atmNum < 0: continue if atmNum in assigned: if sel not in dups: dups.append(sel) else: assigned.append(atmNum) selDict[r] = atmNum if dups: msg = 'Error: The following atom(s) are assigned multiple times: ' for i in dups: msg += i msg += ', ' wx.MessageBox(msg[:-2],caption='Duplicated Fixed Atoms', style=wx.ICON_EXCLAMATION) return return selDict def getDeltaXYZ(selDict,data,rbObj): '''Evaluate the RB position & return the difference between the coordinates and RB coordinates with origin and orientation from data['testRBObj'] ''' Amat,Bmat = G2lat.cell2AB(data['General']['Cell'][1:7]) rbXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,data['testRBObj']['rbData'],data['testRBObj']['rbType'])[0] phaseXYZ = G2mth.getAtomXYZ(atomData,cx) deltaList = [] for i in selDict: if selDict[i] is None: continue deltaList.append(phaseXYZ[selDict[i]]-rbXYZ[i]) return np.array(deltaList) def objectiveDeltaPos(vals,selDict,data,rbObj_in): '''Objective function for minimization. Returns a list of distances between atom positions and located rigid body positions :param list vals: a 4 or 7 element array with 4 quaterian values or 4 quaterian values followed by 3 origin (x,y,z) values :returns: the 3*n distances between the n selected atoms ''' rbObj = copy.deepcopy(rbObj_in) rbObj['Orient'][0][:] = G2mth.normQ(vals[:4]) if len(vals) == 7: rbObj['Orig'][0][:] = vals[4:] #print(np.sqrt(sum(getDeltaXYZ(selDict,data,rbObj).flatten()**2))) return getDeltaXYZ(selDict,data,rbObj).flatten() def onSetOrigin(event): 'Set Origin to best fit selected atoms' if rbObj['fixOrig']: wx.MessageBox('Not possible with origin locked',caption='Οrigin Locked', style=wx.ICON_EXCLAMATION) return selDict = getSelectedAtoms() if len(selDict) < 1: wx.MessageBox('No existing atoms were selected',caption='Select Atom(s)', style=wx.ICON_EXCLAMATION) return deltaList = getDeltaXYZ(selDict,data,rbObj) data['testRBObj']['rbObj']['Orig'][0] += deltaList.sum(axis=0)/len(deltaList) for i,item in enumerate(Xsizers): item.SetValue(data['testRBObj']['rbObj']['Orig'][0][i]) UpdateTablePlot() def onFitOrientation(event): 'Set Orientation to best fit selected atoms' selDict = getSelectedAtoms() if len(selDict) < 2: wx.MessageBox('At least two existing atoms must be selected',caption='Select Atoms', style=wx.ICON_EXCLAMATION) return vals = rbObj['Orient'][0][:] #+ rbObj['Orig'][0][:] out = so.leastsq(objectiveDeltaPos,vals,(selDict,data,rbObj)) data['testRBObj']['rbObj']['Orient'][0][:] = G2mth.normQ(out[0]) updateAddRBorientText(G2frame,data['testRBObj'],Bmat) UpdateTablePlot() def onFitBoth(event): 'Set Orientation and origin to best fit selected atoms' if rbObj['fixOrig']: wx.MessageBox('Not possible with origin locked',caption='Οrigin Locked', style=wx.ICON_EXCLAMATION) return selDict = getSelectedAtoms() if len(selDict) < 3: wx.MessageBox('At least three existing atoms must be selected',caption='Select Atoms', style=wx.ICON_EXCLAMATION) return vals = np.concatenate((rbObj['Orient'][0], rbObj['Orig'][0])) out = so.leastsq(objectiveDeltaPos,vals,(selDict,data,rbObj)) data['testRBObj']['rbObj']['Orig'][0][:] = out[0][4:] data['testRBObj']['rbObj']['Orient'][0][:] = G2mth.normQ(out[0][:4]) for i,item in enumerate(Xsizers): item.SetValue(data['testRBObj']['rbObj']['Orig'][0][i]) updateAddRBorientText(G2frame,data['testRBObj'],Bmat) UpdateTablePlot() def BallnSticks(event): '''Set all draw atoms in crystal structure to balls & stick ''' for a in data['Drawing']['Atoms']: a[6] = "balls & sticks" FindBondsDraw(data) G2plt.PlotStructure(G2frame,data,False,UpdateTable) RigidBodies.SetFocus() # make sure tab presses go to panel def Sticks(event): '''Set all draw atoms in crystal structure to stick ''' for a in data['Drawing']['Atoms']: a[6] = "sticks" FindBondsDraw(data) G2plt.PlotStructure(G2frame,data,False,UpdateTable) RigidBodies.SetFocus() # make sure tab presses go to panel def OnRowSelect(event): '''Respond to the selection of a rigid body atom. Highlight the atom in the body and the paired atom in the crystal ''' event.Skip() cryatom = event.GetEventObject().Table.GetValue(event.GetRow(),4) if not cryatom: cryatom = event.GetEventObject().Table.GetValue(event.GetRow(),2) data['testRBObj']['RBhighLight'] = event.GetRow() data['testRBObj']['CRYhighLight'] = [ i for i,a in enumerate(data['Atoms']) if a[0] == cryatom] G2plt.PlotStructure(G2frame,data,False,UpdateTable) misc['showSelect'].setByString(cryatom) G2frame.Raise() #RigidBodies.atomsGrid.SetFocus() def OnSymRadioSet(event): '''Set the symmetry axis for the body as data['testRBObj']['rbObj']['symAxis']. This may never be set, so use data['testRBObj']['rbObj'].get('symAxis') to access this so the default value is None. ''' axis = (None,[1,0,0],[0,1,0],[0,0,1],[1,1,0],[1,1,1] )[event.GetEventObject().GetSelection()] if axis: axis = np.array(axis)/nl.norm(axis) data['testRBObj']['rbObj']['symAxis'] = axis UpdateTablePlot() def OnOrigSet(event): data['testRBObj']['rbObj']['Orig'][0] = data['Drawing']['viewPoint'][0] for i,item in enumerate(Xsizers): item.SetValue(data['testRBObj']['rbObj']['Orig'][0][i]) UpdateSytSym() UpdateTablePlot() showAtom = [None] def showCryAtom(*args,**kwargs): '''Respond to selection of a crystal atom ''' data['testRBObj']['CRYhighLight'] = [ i for i,a in enumerate(data['Atoms']) if a[0] == showAtom[0]] G2plt.PlotStructure(G2frame,data,False,UpdateTable) # Start of Draw() RBdirlbl = [' x ',' y ',' z ','x+y','x+y+z'] if not data['testRBObj']: return if RigidBodies.GetSizer(): RigidBodies.GetSizer().Clear(True) unmatchedRBatoms = [] matchTable = assignAtoms(RBData,unmatchedRBatoms=unmatchedRBatoms) if unmatchedRBatoms: # msg = 'There are {} atoms that will need to be added to atoms list.'.format(len(unmatchedRBatoms)) # G2G.G2MessageBox(G2frame,msg,title='Please note') for i in unmatchedRBatoms: rbAssignments[i] = None mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) rbObj = data['testRBObj']['rbObj'] data['RBModels']['SpnIds'] = data['RBModels'].get('SpnIds',{}) rbType = data['testRBObj']['rbType'] rbName = rbObj['RBname'] rbId = rbObj['RBId'] Torsions = rbObj['Torsions'] atNames = data['testRBObj']['atNames'] topSizer = wx.BoxSizer(wx.HORIZONTAL) helpText = ''' This window is used to insert a rigid body into a unit cell, determining the initial settings for the position and orientation of the body, as well as any internal torsion angles. The origin determines where the origin of the rigid body will be placed in the unit cell (expressed in fractional coordinates). The orientation is determined by a quaternion that is expressed here as vector (in fraction coordinates) and an azimuthal rotation (in degrees) around that quaternion vector. For systems where the rigid body is placed on a crystallographic symmetry element, the "Rigid body symmetry axis" ("x", "y", "z", "x+y" or "x+y+z") specifies the rotation axis that aligns with an allowed rotation for this symmetry element (NB: could be perpendicular to a mirror). This places the selected Cartesian axis along the quaternion vector. The quaternion vector may be set by the user to force the rotation to be about a particular crystallographic direction (e.g. along a rotation axis or perpendicular to a mirror). The rotation action can be tested via the slider. %%If there are atoms in the unit cell that are of the appropriate type and are not already assigned to rigid bodies, a table shows each atom in the rigid body and the closest crystallographic atom, and the distance between them. Set this pairing by using the pulldown menu in the "Assign as atom" column by selecting a particular atom. If the selection is changed, "Update Assignments" recomputes distance between paired atoms. If one atom is paired manually using "Assign as", the "Set Origin" button can be used to place the rigid body origin to best fit the paired atom(s). Likewise, with two or more atoms assigned, the "Set Orientation" button will determine the quaternion azimuth and vector. Three or more pairs are assignments allow use of the "Set both" button, which sets the orientation and origin to best give the smallest distances between the assigned atoms. NB: if apparently stuck with a poor fit, try shifting the Orientation azimuth slider and try Set both again. Note that when a row in the table is selected, the corresponding atoms are highlighted in green. The tab key or the "Crystal Highlight" pulldown can be used to highlight differing unit cell atoms. Alt-Tab highlights different RB atoms. %%If there are no unassigned atoms of the right type (existing RBs will have orange sticks for bonds), then the table will show "Create new" in the "Assign as atom" column. The proposed RB can be positioned via Alt mouse operations and/or by entering appropriate values in the Orientation azimuth and vector x,y,z boxes. Symmetry element issues should be attended to by proper selections as noted above. "Add" will then add the rigid body atoms to the Atom list. %%The GSAS-II graphics window shows the unit cell contents (use the "Ball & Sticks" or "Sticks" buttons to change the display of this) and the rigid body is shown with small balls and green sticks. At the origin of the RB the axes are indicated with red, green and blue lines (for x, y, & z). A white line indicates the quaternion vector direction. The mouse can also be used to position the rigid body in the plot by holding the Alt key down while dragging with the mouse: Alt+left button to rotates the RB in the screen x & y; Alt+middle mouse to rotate the RB around the viewing direction; Alt+right mouse translates the RB in the screen x-y plane. Note that dragging the mouse without the Alt button changes the view of the crystal structure. %%Once the rigid body has been placed in the desired position, press the "Add" button. ''' topSizer.Add(G2G.HelpButton(RigidBodies,helpText,wrap=700),0,wx.RIGHT,5) topSizer.Add(wx.StaticText(RigidBodies,label='Locating rigid body: '+rbName), 0, WACV) topSizer.Add((10,-1),0) topSizer.Add(wx.StaticText(RigidBodies,label='Display crystal structure as:'), 0, WACV) btn = wx.Button(RigidBodies,label="Ball && Sticks") btn.Bind(wx.EVT_BUTTON, BallnSticks) topSizer.Add(btn) btn = wx.Button(RigidBodies,label="Sticks") btn.Bind(wx.EVT_BUTTON, Sticks) topSizer.Add(btn) mainSizer.Add(topSizer) mainSizer.Add((-1,5),0) OriSizer = wx.BoxSizer(wx.HORIZONTAL) OriSizer.Add(wx.StaticText(RigidBodies,label='Origin: '),0,WACV) Xsizers = [] for ix in range(3): OriSizer.Add(wx.StaticText(RigidBodies,label=RBdirlbl[ix]),0,WACV,4) origX = G2G.ValidatedTxtCtrl(RigidBodies,rbObj['Orig'][0],ix,nDig=(10,5), xmin=-1.5,xmax=1.5,typeHint=float,OnLeave=UpdateSytSym) OriSizer.Add(origX,0,WACV) Xsizers.append(origX) try: rbObj['fixOrig'] except: rbObj['fixOrig'] = False if rbType != 'Spin': fixOrig = G2G.G2CheckBox(RigidBodies,'Lock',rbObj,'fixOrig') OriSizer.Add(fixOrig,0,WACV,10) if not rbObj['fixOrig']: origSet = wx.Button(RigidBodies,label='Set to view point') origSet.Bind(wx.EVT_BUTTON,OnOrigSet) OriSizer.Add(origSet,0,WACV) mainSizer.Add(OriSizer) Sytsym,Mult = G2spc.SytSym(rbObj['Orig'][0],data['General']['SGData'])[:2] sytsymtxt = wx.StaticText(RigidBodies,label='Origin site symmetry: %s, multiplicity: %d '%(Sytsym,Mult)) mainSizer.Add(sytsymtxt) if rbType != 'Spin': OriSizer1 = wx.FlexGridSizer(0,5,5,5) if len(atomData): choice = list(atNames[0].keys()) choice.sort() G2frame.testRBObjSizers.update({'Xsizers':Xsizers}) mainSizer.Add(OriSizer1) mainSizer.Add((5,5),0) OriSizer2 = wx.BoxSizer(wx.HORIZONTAL) if 'OrientVec' not in rbObj: rbObj['OrientVec'] = [0.,0.,0.,0.] rbObj['OrientVec'][0],V = G2mth.Q2AVdeg(rbObj['Orient'][0]) rbObj['OrientVec'][1:] = np.inner(Bmat,V) OriSizer2.Add(wx.StaticText(RigidBodies,label='Orientation azimuth: '),0,WACV) OrientVecSiz = [] OrientVecSiz.append(G2G.ValidatedTxtCtrl(RigidBodies,rbObj['OrientVec'],0,nDig=(10,2), xmin=0.,xmax=360.,typeHint=float,OnLeave=UpdateOrientation)) OriSizer2.Add(OrientVecSiz[-1],0,WACV) azSlide = G2G.G2Slider(RigidBodies,style=wx.SL_HORIZONTAL,size=(200,25), minValue=0,maxValue=3600,value=int(10*rbObj['OrientVec'][0])) azSlide.Bind(wx.EVT_SLIDER, OnAzSlide) OriSizer2.Add(azSlide,0,WACV) mainSizer.Add(OriSizer2) OriSizer3 = wx.BoxSizer(wx.HORIZONTAL) OriSizer3.Add(wx.StaticText(RigidBodies,label='Orientation vector'),0,WACV) for ix,lbl in enumerate('xyz'): OriSizer3.Add(wx.StaticText(RigidBodies,label=' '+lbl+': '),0,WACV) OrientVecSiz.append(G2G.ValidatedTxtCtrl(RigidBodies,rbObj['OrientVec'],ix+1,nDig=(10,4), xmin=-1.,xmax=1.,typeHint=float,OnLeave=UpdateOrientation)) OriSizer3.Add(OrientVecSiz[-1],0,WACV) OrientVecSiz.append(azSlide) OriSizer3.Add(wx.StaticText(RigidBodies,label=' (frac coords)'),0,WACV) G2frame.testRBObjSizers.update({'OrientVecSiz':OrientVecSiz}) mainSizer.Add(OriSizer3) mainSizer.Add((5,5),0) OriSizer4 = wx.BoxSizer(wx.HORIZONTAL) OriSizer4.Add(wx.StaticText(RigidBodies,label='Rigid body symmetry axis: '),0, WACV) choices = ['None']+RBdirlbl symRadioSet = wx.RadioBox(RigidBodies,choices=choices) symRadioSet.Bind(wx.EVT_RADIOBOX, OnSymRadioSet) OriSizer4.Add(symRadioSet) mainSizer.Add(OriSizer4) mainSizer.Add((5,5),0) RefSizer = wx.FlexGridSizer(0,7,5,5) mainSizer.Add(RefSizer) mainSizer.Add((5,5),0) if Torsions: rbSeq = RBData['Residue'][rbId]['rbSeq'] TorSizer = wx.FlexGridSizer(0,4,5,5) TorSizer.AddGrowableCol(1,1) for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)): torName = '' for item in [seq[0],seq[1],seq[3][0]]: if data['testRBObj']['NameLookup'][item]: torName += data['testRBObj']['NameLookup'][item]+' ' else: torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' ' TorSizer.Add(wx.StaticText(RigidBodies,label='Side chain torsion for rb seq: '+torName),0,WACV) torSlide = G2G.G2Slider(RigidBodies,style=wx.SL_HORIZONTAL,minValue=0,maxValue=3600,value=int(torsion[0]*10.)) torSlide.Bind(wx.EVT_SLIDER, OnTorSlide) TorSizer.Add(torSlide,1,wx.EXPAND|wx.RIGHT) TorSizer.Add(wx.StaticText(RigidBodies,label=' Angle: '),0,WACV) ang = G2G.ValidatedTxtCtrl(RigidBodies,torsion,0,nDig=(8,3),typeHint=float,OnLeave=OnTorAngle) Indx[torSlide.GetId()] = [t,ang] Indx[ang.GetId()] = [t,torSlide] TorSizer.Add(ang,0,WACV) mainSizer.Add(TorSizer,0,wx.EXPAND|wx.RIGHT) else: mainSizer.Add(wx.StaticText(RigidBodies,label='No side chain torsions'),0) OkBtn = wx.Button(RigidBodies,label="Add") OkBtn.Bind(wx.EVT_BUTTON, OnAddRB) CancelBtn = wx.Button(RigidBodies,label='Cancel') CancelBtn.Bind(wx.EVT_BUTTON, OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) if OkBtn: btnSizer.Add(OkBtn) btnSizer.Add(CancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.BOTTOM|wx.TOP, 20) SetPhaseWindow(RigidBodies,mainSizer) data['testRBObj']['RBhighLight'] = None data['testRBObj']['CRYhighLight'] = [] assignable = [a[0] for a in data['Atoms'] if a[-1] not in rbUsedIds] data['testRBObj']['availAtoms'] = [' '] + assignable if len(assignable) == 0 and rbType != 'Spin': mainSizer.Add(wx.StaticText(RigidBodies,label= 'No matching atoms between rigid body and crystal.'+ ' All rigid body atoms will be added to structure.'),0) misc['UpdateTable'] = None mainSizer.Layout() # G2plt.PlotStructure(G2frame,data,True) RigidBodies.atomsGrid = None return G2plt.PlotStructure(G2frame,data,True,UpdateTable) if rbType != 'Spin': mainSizer.Add(wx.StaticText(RigidBodies,label=' Spinning rigid body:'),0) else: mainSizer.Add(wx.StaticText(RigidBodies,label= 'Match between atoms in rigid body and crystal. Use assignments to align bodies.'),0) mainSizer.Add((5,5)) gridSizer = wx.BoxSizer(wx.HORIZONTAL) colLabels = ['RB\ntype','Atom\n#','Atom\nlabel','delta, A','Assign as atom'] rowLabels = [l[1] for l in matchTable] displayTable = [] Actions = True for i,l in enumerate(matchTable): lbl = '' if i in rbAssignments: if rbAssignments[i] is None: displayTable.append([l[0],-1,'?',-1,'Create new']) # Actions = False else: lbl = rbAssignments[i] displayTable.append([l[0],l[5],l[6],l[10],lbl]) # TODO: think about this else: if rbType == 'Spin': displayTable.append([l[1],-1,l[1]+str(i),-1,'Create new']) # Actions = False else: displayTable.append([l[0],l[5],l[6],l[10],lbl]) Types = [wg.GRID_VALUE_STRING, wg.GRID_VALUE_NUMBER, wg.GRID_VALUE_STRING, wg.GRID_VALUE_FLOAT+':8,3',wg.GRID_VALUE_STRING] RigidBodies.atomsTable = G2G.Table(displayTable,rowLabels=rowLabels,colLabels=colLabels,types=Types) RigidBodies.atomsGrid = G2G.GSGrid(RigidBodies) RigidBodies.atomsGrid.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK,OnRowSelect) choiceeditor = wg.GridCellChoiceEditor(data['testRBObj']['availAtoms']+['Create new'], False) RigidBodies.atomsGrid.SetTable(RigidBodies.atomsTable,True) # make all grid entries read only attr = wg.GridCellAttr() attr.SetReadOnly(True) for i in range(len(colLabels)-1): attr.IncRef() RigidBodies.atomsGrid.SetColAttr(i, attr) attr = wg.GridCellAttr() attr.SetAlignment(wx.ALIGN_RIGHT,wx.ALIGN_CENTRE) RigidBodies.atomsGrid.SetColAttr(1, attr) attr = wg.GridCellAttr() attr.SetEditor(choiceeditor) RigidBodies.atomsGrid.SetColAttr(4, attr) RigidBodies.atomsGrid.AutoSizeColumns(True) RigidBodies.atomsGrid.SetMargins(0,0) gridSizer.Add(RigidBodies.atomsGrid)#,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) gridSizer.Add((5,5)) if Actions: btnSizer = wx.BoxSizer(wx.VERTICAL) hSizer = wx.BoxSizer(wx.HORIZONTAL) hSizer.Add(wx.StaticText(RigidBodies,label='Crystal Highlight: ')) misc['showSelect'] = G2G.G2ChoiceButton(RigidBodies, data['testRBObj']['availAtoms'],None,None,showAtom,0,showCryAtom,size=(75,-1)) hSizer.Add(misc['showSelect']) btnSizer.Add(hSizer) btnSizer.Add((-1,20)) btnSizer.Add(wx.StaticText(RigidBodies,label='Actions with assigned\natom(s)...'),0,wx.ALL) btnSizer.Add((-1,10)) btn = wx.Button(RigidBodies,label='Update Assignments') btn.Bind(wx.EVT_BUTTON,UpdateTable) btnSizer.Add(btn,0,wx.ALIGN_CENTER) btnSizer.Add((-1,10)) btn = wx.Button(RigidBodies,label='Set Origin') btn.Bind(wx.EVT_BUTTON,onSetOrigin) btnSizer.Add(btn,0,wx.ALIGN_CENTER) btnSizer.Add((-1,5)) btn = wx.Button(RigidBodies,label='Set Orientation') btn.Bind(wx.EVT_BUTTON,onFitOrientation) btnSizer.Add(btn,0,wx.ALIGN_CENTER) btnSizer.Add((-1,5)) btn = wx.Button(RigidBodies,label='Set both') btn.Bind(wx.EVT_BUTTON,onFitBoth) btnSizer.Add(btn,0,wx.ALIGN_CENTER) gridSizer.Add(btnSizer) mainSizer.Add(gridSizer) mainSizer.Layout() RigidBodies.SetScrollRate(10,10) RigidBodies.SendSizeEvent() RigidBodies.Scroll(0,0) RigidBodies.SetFocus() # make sure tab presses go to panel misc['UpdateTable'] = UpdateTable # start of OnRBAssign(event) rbAssignments = {} rbUsedIds = [] # Ids of atoms in current phase used inside RBs for i in data['RBModels']: if i == 'SpnIds': continue for j in data['RBModels'][i]: rbUsedIds += j['Ids'] G2frame.GetStatusBar().SetStatusText('',1) RBData = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies')) rbNames = {} dups = [] for rbVec in RBData['Vector']: if rbVec == 'AtInfo': continue key = RBData['Vector'][rbVec]['RBname'] if key in rbNames: dups.append(key) else: rbNames[key] = ['Vector',rbVec] for rbRes in RBData['Residue']: if rbRes == 'AtInfo': continue key = RBData['Residue'][rbRes]['RBname'] if key in rbNames: dups.append(key) else: rbNames[key] = ['Residue',rbRes] if data['General']['Type'] == 'nuclear': #exclude other phase types for rbSpn in RBData.get('Spin',{}): #patch get for old files key = RBData['Spin'][rbSpn]['RBname'] if key in rbNames: dups.append(key) else: rbNames[key] = ['Spin',rbSpn] if dups: msg = 'Two or more rigid bodies have the same name. This must be corrected before bodies can be added.' msg += '\n\n Duplicated name(s): ' for d in dups: msg += d msg += ' ' G2G.G2MessageBox(G2frame,msg,'Duplicate Rigid Body Names') return if not rbNames: print ('**** ERROR - no rigid bodies defined ****') G2G.G2MessageBox(G2frame, 'You must define bodies in the Rigid Bodies tree item before trying to add them to a phase', 'No Rigid Bodies') return general = data['General'] SGData = general['SGData'] Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7]) cx,ct,cs,cia = general['AtomPtrs'] atomData = data['Atoms'] #AtLookUp = G2mth.FillAtomLookUp(atomData,cia+8) Indx = {} data['testRBObj'] = {} if len(rbNames) == 1: selection = list(rbNames.keys())[0] else: choices = sorted(list(rbNames.keys())) dlg = G2G.G2SingleChoiceDialog( G2frame,'Select rigid body to\nadd to structure', 'Select rigid body',choices) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: selection = choices[dlg.GetSelection()] else: return finally: dlg.Destroy() if selection not in rbNames: print('Invalid RB selection',selection,'How did this happen?') return rbType,rbId = rbNames[selection] if rbType == 'Spin': data['testRBObj']['rbAtTypes'] = [RBData[rbType][rbId]['rbType'],] data['testRBObj']['AtInfo'] = {RBData[rbType][rbId]['rbType']:[1.0,(128, 128, 255)],} data['testRBObj']['rbType'] = rbType data['testRBObj']['rbData'] = RBData data['testRBObj']['Sizers'] = {} rbRef = RBData[rbType][rbId].get('rbRef',[]) #get only for spinning RBs data['testRBObj']['rbRef'] = rbRef else: data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes'] data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo'] data['testRBObj']['NameLookup'] = RBData[rbType][rbId].get('atNames',[]) #only for residues data['testRBObj']['rbType'] = rbType data['testRBObj']['rbData'] = RBData data['testRBObj']['Sizers'] = {} rbRef = RBData[rbType][rbId]['rbRef'] data['testRBObj']['rbRef'] = rbRef refType = [] #refName = [] for ref in rbRef[:3]: reftype = data['testRBObj']['rbAtTypes'][ref] refType.append(reftype) #refName.append(reftype+' '+str(rbRef[0])) atNames = [{},{},{}] AtNames = {} for iatm,atom in enumerate(atomData): AtNames[atom[ct-1]] = iatm for i,reftype in enumerate(refType): if atom[ct] == reftype: atNames[i][atom[ct-1]] = iatm data['testRBObj']['atNames'] = atNames data['testRBObj']['AtNames'] = AtNames data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False], 'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[], 'numChain':'','RBname':RBData[rbType][rbId]['RBname']} # if rbType == 'Spin': # data['testRBObj']['rbObj']['Radius'] = [1.0,False] data['testRBObj']['torAtms'] = [] for item in RBData[rbType][rbId].get('rbSeq',[]): data['testRBObj']['rbObj']['Torsions'].append([item[2],False]) data['testRBObj']['torAtms'].append([-1,-1,-1]) wx.CallAfter(Draw) def OnAutoFindResRB(event): RBData = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies')) rbKeys = list(RBData['Residue'].keys()) rbKeys.remove('AtInfo') if not len(rbKeys): print ('**** ERROR - no residue rigid bodies are defined ****') return RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys] RBIds = dict(zip(RBNames,rbKeys)) general = data['General'] cx,ct,cs,cia = general['AtomPtrs'] Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7]) Atoms = data['Atoms'] AtLookUp = G2mth.FillAtomLookUp(Atoms,cia+8) if 'macro' not in general['Type']: print ('**** ERROR - this phase is not a macromolecule ****') return if not len(Atoms): print ('**** ERROR - this phase has no atoms ****') return RBObjs = [] cx,ct = general['AtomPtrs'][:2] iatm = 0 wx.BeginBusyCursor() try: isave = 0 while iatm < len(Atoms): atom = Atoms[iatm] res = atom[1].strip() numChain = ' %s %s'%(atom[0],atom[2]) if res not in RBIds or atom[ct-1] == 'OXT': iatm += 1 continue #skip for OXT, water molecules, etc. rbRes = RBData['Residue'][RBIds[res]] rbRef = rbRes['rbRef'] VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]] VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]] incr = 1 isave = 0 if 'N A' in atom[3]: #disordered residue - read every other atom isave = iatm+1 incr = 2 if 'N B' in atom[3]: incr = 2 rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain} rbAtoms = [] rbIds = [] for iratm in range(len(rbRes['atNames'])): if res != Atoms[iatm][1]: print('Short %s residue at atom %d is skipped'%(Atoms[iatm][1],iatm)) break rbAtoms.append(np.array(Atoms[iatm][cx:cx+3])) rbIds.append(Atoms[iatm][20]) iatm += incr #puts this at beginning of next residue? else: if 'N B' in atom[3]: #end of disorder - reset next atom position iatm -= 1 incr = 1 Orig = rbAtoms[rbRef[0]] rbObj['RBId'] = RBIds[res] rbObj['Ids'] = rbIds rbObj['Orig'] = [Orig,False] # print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \ # ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2]) VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig) VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig) VCC = np.cross(VAR,VAC) QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0] VAR = G2mth.prodQVQ(QuatA,VAR) VBR = G2mth.prodQVQ(QuatA,VBR) QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0] QuatC = G2mth.prodQQ(QuatB,QuatA) rbObj['Orient'] = [QuatC,' '] rbObj['AtomFract'] = [1.0,False] rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags SXYZ = [] TXYZ = [] rbObj['Torsions'] = [] for i,xyz in enumerate(rbRes['rbXYZ']): SXYZ.append(G2mth.prodQVQ(QuatC,xyz)) TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig)) for Oatm,Patm,x,Riders in rbRes['rbSeq']: VBR = SXYZ[Oatm]-SXYZ[Patm] VAR = SXYZ[Riders[0]]-SXYZ[Patm] VAC = TXYZ[Riders[0]]-TXYZ[Patm] QuatA,D = G2mth.makeQuat(VAR,VAC,VBR) ang = 180.*D/np.pi rbObj['Torsions'].append([ang,False]) for ride in Riders: SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm] rbRes['useCount'] += 1 RBObjs.append(rbObj) if isave: iatm = isave data['RBModels']['Residue'] = RBObjs for RBObj in RBObjs: newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0] for i,Id in enumerate(RBObj['Ids']): data['Atoms'][AtLookUp[Id]][cx:cx+3] = newXYZ[i] finally: wx.EndBusyCursor() wx.CallAfter(FillRigidBodyGrid,True) def OnRBRemoveAll(event): data['RBModels']['Residue'] = [] data['RBModels']['Vector'] = [] data['RBModels']['Spin'] = [] RBData = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies')) for RBType in ['Vector','Residue','Spin']: for rbId in RBData[RBType]: RBData[RBType][rbId]['useCount'] = 0 FillRigidBodyGrid(True) def OnGlobalResRBTherm(event): RBObjs = data['RBModels']['Residue'] names = ['None','Uiso','T','TL','TLS'] cia = data['General']['AtomPtrs'][3] AtLookUp = G2mth.FillAtomLookUp(data['Atoms'],cia+8) dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() parm = names[sel] Ttype = 'A' if parm == 'Uiso': Ttype = 'I' for rbObj in RBObjs: rbObj['ThermalMotion'][0] = parm if parm != 'None': for i,Id in enumerate(rbObj['Ids']): data['Atoms'][AtLookUp[Id]][cia] = Ttype dlg.Destroy() wx.CallAfter(FillRigidBodyGrid,True) def OnGlobalResRBRef(event): RBObjs = data['RBModels']['Residue'] names = ['Origin','Orient. angle','Full Orient.'] nTor = 0 for rbObj in RBObjs: nTor = max(nTor,len(rbObj['Torsions'])) names += ['Torsion '+str(i) for i in range(nTor)] if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]): names += ['Uiso',] if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]): names += ['Tii','Tij','Lii','Lij','Sij'] elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]): names += ['Tii','Tij','Lii','Lij'] elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]): names += ['Tii','Tij'] dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelections() parms = [] for x in sel: parms.append(names[x]) wx.BeginBusyCursor() try: for rbObj in RBObjs: if 'Origin' in parms: rbObj['Orig'][1] = True else: rbObj['Orig'][1] = False if 'Full Orient.' in parms: rbObj['Orient'][1] = 'AV' elif 'Orient. angle' in parms: rbObj['Orient'][1] = 'A' else: rbObj['Orient'][1] = ' ' for i in range(len(rbObj['Torsions'])): if 'Torsion '+str(i) in parms: rbObj['Torsions'][i][1] = True else: rbObj['Torsions'][i][1] = False if rbObj['ThermalMotion'][0] == 'Uiso': if 'Uiso' in parms: rbObj['ThermalMotion'][2][0] = True else: rbObj['ThermalMotion'][2][0] = False if 'T' in rbObj['ThermalMotion'][0]: if 'Tii' in parms: rbObj['ThermalMotion'][2][0:2] = [True,True,True] else: rbObj['ThermalMotion'][2][0:2] = [False,False,False] if 'Tij' in parms: rbObj['ThermalMotion'][2][3:6] = [True,True,True] else: rbObj['ThermalMotion'][2][3:6] = [False,False,False] if 'L' in rbObj['ThermalMotion'][0]: if 'Lii' in parms: rbObj['ThermalMotion'][2][6:9] = [True,True,True] else: rbObj['ThermalMotion'][2][6:9] = [False,False,False] if 'Lij' in parms: rbObj['ThermalMotion'][2][9:12] = [True,True,True] else: rbObj['ThermalMotion'][2][9:12] = [False,False,False] if 'S' in rbObj['ThermalMotion'][0]: if 'Sij' in parms: rbObj['ThermalMotion'][2][12:20] = [True,True,True,True,True,True,True,True] else: rbObj['ThermalMotion'][2][12:20] = [False,False,False,False,False,False,False,False] finally: wx.EndBusyCursor() FillRigidBodyGrid() #### MC/SA routines ################################################################################ def UpdateMCSA(Scroll=0): Indx = {} def OnPosRef(event): Obj = event.GetEventObject() model,item,ix = Indx[Obj.GetId()] model[item][1][ix] = Obj.GetValue() def OnPosVal(invalid,value,tc): G2plt.PlotStructure(G2frame,data) def OnPosRange(event): event.Skip() Obj = event.GetEventObject() model,item,ix = Indx[Obj.GetId()] Range = Obj.GetValue().split() try: rmin,rmax = [float(Range[i]) for i in range(2)] if rmin >= rmax: raise ValueError except (ValueError,IndexError): rmin,rmax = model[item][2][ix] model[item][2][ix] = [rmin,rmax] Obj.SetValue('%.3f %.3f'%(rmin,rmax)) def atomSizer(model): atomsizer = wx.FlexGridSizer(0,7,5,5) atomsizer.Add(wx.StaticText(G2frame.MCSA,-1,' Atom: '+model['name']+': '),0,WACV) for ix,item in enumerate(['x','y','z']): posRef = wx.CheckBox(G2frame.MCSA,-1,label=item+': ') posRef.SetValue(model['Pos'][1][ix]) posRef.Bind(wx.EVT_CHECKBOX,OnPosRef) Indx[posRef.GetId()] = [model,'Pos',ix] atomsizer.Add(posRef,0,WACV) posVal = G2G.ValidatedTxtCtrl(G2frame.MCSA,model['Pos'][0],ix,nDig=(10,4),OnLeave=OnPosVal) atomsizer.Add(posVal,0,WACV) atomsizer.Add((5,5),0) for ix,item in enumerate(['x','y','z']): atomsizer.Add(wx.StaticText(G2frame.MCSA,-1,' Range: '),0,WACV) rmin,rmax = model['Pos'][2][ix] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) posRange = wx.TextCtrl(G2frame.MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER) Indx[posRange.GetId()] = [model,'Pos',ix] posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange) posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange) atomsizer.Add(posRange,0,WACV) return atomsizer def rbSizer(model): def OnOrVar(event): Obj = event.GetEventObject() model = Indx[Obj.GetId()] model['Ovar'] = Obj.GetValue() def OnOriVal(event): event.Skip() Obj = event.GetEventObject() model,ix,ObjA,ObjV = Indx[Obj.GetId()] A = model['Ori'][0][0] V = model['Ori'][0][1:] if ix: Anew = A Vec = ObjV.GetValue().split() try: Vnew = [float(Vec[i]) for i in range(3)] except ValueError: Vnew = V else: Vnew = V try: Anew = float(ObjA.GetValue()) if not Anew: #==0.0! Anew = 360. except ValueError: Anew = A Q = G2mth.AVdeg2Q(Anew,Vnew) A,V = G2mth.Q2AVdeg(Q) model['Ori'][0][0] = A model['Ori'][0][1:] = V if ix: ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2])) else: ObjA.SetValue('%.5f'%(A)) ObjV.SetValue('%.3f %.3f %.3f'%(V[0],V[1],V[2])) G2plt.PlotStructure(G2frame,data) def OnMolCent(event): Obj = event.GetEventObject() model = Indx[Obj.GetId()] model['MolCent'][1] = Obj.GetValue() if model['MolCent'][1]: G2mth.SetMolCent(model,RBData) G2plt.PlotStructure(G2frame,data) rbsizer = wx.BoxSizer(wx.VERTICAL) rbsizer1 = wx.FlexGridSizer(0,7,5,5) rbsizer1.Add(wx.StaticText(G2frame.MCSA,-1,model['Type']+': '+model['name']+': '),0) for ix,item in enumerate(['x','y','z']): posRef = wx.CheckBox(G2frame.MCSA,-1,label=item+': ') posRef.SetValue(model['Pos'][1][ix]) posRef.Bind(wx.EVT_CHECKBOX,OnPosRef) Indx[posRef.GetId()] = [model,'Pos',ix] rbsizer1.Add(posRef,0,WACV) posVal = G2G.ValidatedTxtCtrl(G2frame.MCSA,model['Pos'][0],ix,nDig=(10,4),OnLeave=OnPosVal) rbsizer1.Add(posVal,0,WACV) molcent = wx.CheckBox(G2frame.MCSA,-1,label=' Use mol. center? ') molcent.SetValue(model['MolCent'][1]) molcent.Bind(wx.EVT_CHECKBOX,OnMolCent) Indx[molcent.GetId()] = model rbsizer1.Add(molcent,0,WACV) for ix,item in enumerate(['x','y','z']): rbsizer1.Add(wx.StaticText(G2frame.MCSA,-1,' Range: '),0,WACV) rmin,rmax = model['Pos'][2][ix] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) posRange = wx.TextCtrl(G2frame.MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER) Indx[posRange.GetId()] = [model,'Pos',ix] posRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange) posRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange) rbsizer1.Add(posRange,0,WACV) rbsizer2 = wx.FlexGridSizer(0,6,5,5) Ori = model['Ori'][0] rbsizer2.Add(wx.StaticText(G2frame.MCSA,-1,'Oa: '),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) angVal = wx.TextCtrl(G2frame.MCSA,-1,'%.5f'%(Ori[0]),style=wx.TE_PROCESS_ENTER) angVal.Bind(wx.EVT_TEXT_ENTER,OnOriVal) angVal.Bind(wx.EVT_KILL_FOCUS,OnOriVal) rbsizer2.Add(angVal,0,WACV) rbsizer2.Add(wx.StaticText(G2frame.MCSA,-1,'Oi,Oj,Ok: '),0,WACV) # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) vecVal = wx.TextCtrl(G2frame.MCSA,-1,'%.3f %.3f %.3f'%(Ori[1],Ori[2],Ori[3]),style=wx.TE_PROCESS_ENTER) vecVal.Bind(wx.EVT_TEXT_ENTER,OnOriVal) vecVal.Bind(wx.EVT_KILL_FOCUS,OnOriVal) Indx[angVal.GetId()] = [model,0,angVal,vecVal] Indx[vecVal.GetId()] = [model,1,angVal,vecVal] rbsizer2.Add(vecVal,0,WACV) rbsizer2.Add(wx.StaticText(G2frame.MCSA,-1,' Vary? '),0,WACV) choice = [' ','A','AV'] orvar = wx.ComboBox(G2frame.MCSA,-1,value=model['Ovar'],choices=choice, style=wx.CB_READONLY|wx.CB_DROPDOWN) orvar.Bind(wx.EVT_COMBOBOX, OnOrVar) Indx[orvar.GetId()] = model rbsizer2.Add(orvar,0,WACV) rbsizer2.Add(wx.StaticText(G2frame.MCSA,-1,' Range: Oa: '),0,WACV) Rge = model['Ori'][2] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) angRange = wx.TextCtrl(G2frame.MCSA,-1,'%.3f %.3f'%(Rge[0][0],Rge[0][1]),style=wx.TE_PROCESS_ENTER) Indx[angRange.GetId()] = [model,'Ori',0] angRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange) angRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange) rbsizer2.Add(angRange,0,WACV) rbsizer2.Add(wx.StaticText(G2frame.MCSA,-1,'Oi,Oj,Ok: '),0,WACV) for io,item in enumerate(['Oi','Oj','Ok']): rmin,rmax = Rge[io+1] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) vecRange = wx.TextCtrl(G2frame.MCSA,-1,'%.3f %.3f '%(rmin,rmax),style=wx.TE_PROCESS_ENTER) Indx[vecRange.GetId()] = [model,'Ori',io+1] vecRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange) vecRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange) rbsizer2.Add(vecRange,0,WACV) rbsizer.Add(rbsizer1) rbsizer.Add(rbsizer2) if model['Type'] == 'Residue': try: atNames = RBData['Residue'][model['RBId']]['atNames'] rbsizer.Add(wx.StaticText(G2frame.MCSA,-1,'Torsions:'),0) rbsizer3 = wx.FlexGridSizer(0,8,5,5) for it,tor in enumerate(model['Tor'][0]): iBeg,iFin = RBData['Residue'][model['RBId']]['rbSeq'][it][:2] name = atNames[iBeg]+'-'+atNames[iFin] torRef = wx.CheckBox(G2frame.MCSA,label=' %s: '%(name)) torRef.SetValue(model['Tor'][1][it]) torRef.Bind(wx.EVT_CHECKBOX,OnPosRef) Indx[torRef.GetId()] = [model,'Tor',it] rbsizer3.Add(torRef,0,WACV) torVal = G2G.ValidatedTxtCtrl(G2frame.MCSA,model['Tor'][0],it,nDig=(10,4),OnLeave=OnPosVal) rbsizer3.Add(torVal,0,WACV) rbsizer3.Add(wx.StaticText(G2frame.MCSA,-1,' Range: '),0,WACV) rmin,rmax = model['Tor'][2][it] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) torRange = wx.TextCtrl(G2frame.MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER) Indx[torRange.GetId()] = [model,'Tor',it] torRange.Bind(wx.EVT_TEXT_ENTER,OnPosRange) torRange.Bind(wx.EVT_KILL_FOCUS,OnPosRange) rbsizer3.Add(torRange,0,WACV) rbsizer.Add(rbsizer3) except KeyError: #Missing RB - clear all away! data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}} wx.CallAfter(UpdateMCSA) return rbsizer def MDSizer(POData): def OnPORef(event): POData['Coef'][1] = poRef.GetValue() def OnPORange(event): event.Skip() Range = poRange.GetValue().split() try: rmin,rmax = [float(Range[i]) for i in range(2)] if 0. < rmin < rmax: pass else: raise ValueError except (ValueError,IndexError): rmin,rmax = POData['Coef'][2] POData['Coef'][2] = [rmin,rmax] poRange.SetValue('%.3f %.3f'%(rmin,rmax)) def OnPOAxis(event): event.Skip() Saxis = poAxis.GetValue().split() try: hkl = [int(Saxis[i]) for i in range(3)] except (ValueError,IndexError): hkl = POData['axis'] if not np.any(np.array(hkl)): hkl = POData['axis'] POData['axis'] = hkl h,k,l = hkl poAxis.SetValue('%3d %3d %3d'%(h,k,l)) poSizer = wx.BoxSizer(wx.HORIZONTAL) poRef = wx.CheckBox(G2frame.MCSA,-1,label=' March-Dollase ratio: ') poRef.SetValue(POData['Coef'][1]) poRef.Bind(wx.EVT_CHECKBOX,OnPORef) poSizer.Add(poRef,0,WACV) poVal = G2G.ValidatedTxtCtrl(G2frame.MCSA,POData['Coef'],0,nDig=(10,3),xmin=0.) poSizer.Add(poVal,0,WACV) poSizer.Add(wx.StaticText(G2frame.MCSA,-1,' Range: '),0,WACV) rmin,rmax = POData['Coef'][2] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) poRange = wx.TextCtrl(G2frame.MCSA,-1,'%.3f %.3f'%(rmin,rmax),style=wx.TE_PROCESS_ENTER) poRange.Bind(wx.EVT_TEXT_ENTER,OnPORange) poRange.Bind(wx.EVT_KILL_FOCUS,OnPORange) poSizer.Add(poRange,0,WACV) poSizer.Add(wx.StaticText(G2frame.MCSA,-1,' Unique axis, H K L: '),0,WACV) h,k,l = POData['axis'] # Zstep = G2G.ValidatedTxtCtrl(drawOptions,drawingData,'Zstep',nDig=(10,2),xmin=0.01,xmax=4.0) poAxis = wx.TextCtrl(G2frame.MCSA,-1,'%3d %3d %3d'%(h,k,l),style=wx.TE_PROCESS_ENTER) poAxis.Bind(wx.EVT_TEXT_ENTER,OnPOAxis) poAxis.Bind(wx.EVT_KILL_FOCUS,OnPOAxis) poSizer.Add(poAxis,0,WACV) return poSizer def ResultsSizer(Results): def OnCellChange(event): r,c = event.GetRow(),event.GetCol() if c == 0: for row in range(resultsGrid.GetNumberRows()): resultsTable.SetValue(row,c,False) Results[row][0] = False result = Results[r] Models = data['MCSA']['Models'] SetSolution(result,Models) Results[r][0] = True resultsTable.SetValue(r,0,True) # resultsGrid.ForceRefresh() G2plt.PlotStructure(G2frame,data) wx.CallAfter(UpdateMCSA,G2frame.MCSA.GetScrollPos(wx.VERTICAL)) elif c == 1: if Results[r][1]: Results[r][1] = False else: Results[r][1] = True resultsTable.SetValue(r,c,Results[r][1]) resultsGrid.ForceRefresh() resultsSizer = wx.BoxSizer(wx.VERTICAL) maxVary = 0 resultVals = [] for result in Results: maxVary = max(maxVary,len(result[-1])) resultVals.append(result[:-1]) rowLabels = [] for i in range(len(Results)): rowLabels.append(str(i)) colLabels = ['Select','Keep','Residual','Tmin',] for item in result[-1]: colLabels.append(item) #from last result from for loop above Types = [wg.GRID_VALUE_BOOL,wg.GRID_VALUE_BOOL,wg.GRID_VALUE_FLOAT+':10,4', wg.GRID_VALUE_FLOAT+':10,4',]+maxVary*[wg.GRID_VALUE_FLOAT+':10,5',] resultsTable = G2G.Table(resultVals,rowLabels=rowLabels,colLabels=colLabels,types=Types) resultsGrid = G2G.GSGrid(G2frame.MCSA) resultsGrid.SetTable(resultsTable, True) resultsGrid.Bind(wg.EVT_GRID_CELL_LEFT_CLICK, OnCellChange) resultsGrid.AutoSizeColumns(True) resultsGrid.SetMargins(0,0) for r in range(resultsGrid.GetNumberRows()): for c in range(resultsGrid.GetNumberCols()): if c in [0,1]: resultsGrid.SetReadOnly(r,c,isReadOnly=False) else: resultsGrid.SetCellStyle(r,c,VERY_LIGHT_GREY,True) # resultsGrid.SetScrollRate(0,0) resultsSizer.Add(resultsGrid,0,wx.EXPAND) return resultsSizer def OnSelect(event): rbId = rbids[select.GetSelection()] wx.CallLater(100,RepaintRBInfo,rbId) def RepaintRBInfo(rbId,Scroll=0): oldFocus = wx.Window.FindFocus() if 'phoenix' in wx.version(): G2frame.bottomSizer.Clear(True) else: G2frame.bottomSizer.DeleteWindows() Indx.clear() rbObj = data['MCSA']['Models'][rbId] G2frame.bottomSizer.Insert(0,rbSizer(rbObj)) mainSizer.Layout() G2frame.dataWindow.Refresh() G2frame.dataWindow.SendSizeEvent() wx.CallAfter(oldFocus.SetFocus) def OnShoLabels(event): data['MCSA']['showLabels'] = not data['MCSA']['showLabels'] G2plt.PlotStructure(G2frame,data) # UpdateMCSA executable code starts here if G2frame.MCSA.GetSizer(): G2frame.MCSA.GetSizer().Clear(True) #patch data['MCSA']['showLabels'] = data['MCSA'].get('showLabels',False) #end patch if not data['Drawing']: #if new drawing - no drawing data! SetupDrawingData() general = data['General'] Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7]) Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies') if not Id: return RBData = G2frame.GPXtree.GetItemPyData(Id) Indx = {} # atomStyle = 'balls & sticks' # if 'macro' in general['Type']: # atomStyle = 'sticks' G2frame.GetStatusBar().SetStatusText('',1) mainSizer = wx.BoxSizer(wx.VERTICAL) if not data['MCSA']['Models']: mainSizer.Add((5,5),0) mainSizer.Add(wx.StaticText(G2frame.MCSA,-1,'No MC/SA models:'),0) mainSizer.Add((5,5),0) else: mainSizer.Add((5,5),0) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(G2frame.MCSA,label='MC/SA models:'),0,WACV) # add help button to bring up help web page - at right sede of window topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(G2frame.MCSA,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(topSizer,0,wx.EXPAND) mainSizer.Add((5,5),0) rbNames = [] rbids = [] for im,model in enumerate(data['MCSA']['Models']): if model['Type'] == 'MD': mainSizer.Add(MDSizer(model)) elif model['Type'] == 'Atom': Asizer = atomSizer(model) mainSizer.Add(Asizer) else: rbNames.append(model['name']) rbids.append(im) G2G.HorizontalLine(mainSizer,G2frame.MCSA) if len(rbNames): rbName = rbNames[0] select = wx.ListBox(G2frame.MCSA,choices=rbNames,style=wx.LB_SINGLE,size=(-1,65)) select.SetSelection(rbNames.index(rbName)) select.SetFirstItem(rbNames.index(rbName)) select.Bind(wx.EVT_LISTBOX,OnSelect) mainSizer.Add(select,0) G2frame.bottomSizer = wx.BoxSizer(wx.VERTICAL) G2frame.bottomSizer.Add(rbSizer(data['MCSA']['Models'][rbids[0]])) mainSizer.Add(G2frame.bottomSizer) mainSizer.Add((5,5),0) bottomSizer = wx.BoxSizer(wx.HORIZONTAL) resStr = 'MC/SA results: ' if not data['MCSA']['Results']: resStr = 'No'+resStr bottomSizer.Add(wx.StaticText(G2frame.MCSA,-1,resStr),0,WACV) shoLabels = wx.CheckBox(G2frame.MCSA,label=' Show atom labels? ') shoLabels.SetValue(data['MCSA']['showLabels']) shoLabels.Bind(wx.EVT_CHECKBOX,OnShoLabels) bottomSizer.Add(shoLabels,0,WACV) mainSizer.Add(bottomSizer) mainSizer.Add((5,5),0) if data['MCSA']['Results']: Results = data['MCSA']['Results'] mainSizer.Add(ResultsSizer(Results),0,wx.EXPAND) SetPhaseWindow(G2frame.MCSA,mainSizer) def SetSolution(result,Models): for key,val in zip(result[-1],result[4:-1]): vals = key.split(':') nObj,name = int(vals[0]),vals[1] if 'A' in name: ind = ['Ax','Ay','Az'].index(name) Models[nObj]['Pos'][0][ind] = val elif 'Q' in name: ind = ['Qa','Qi','Qj','Qk'].index(name) Models[nObj]['Ori'][0][ind] = val elif 'P' in name: ind = ['Px','Py','Pz'].index(name) Models[nObj]['Pos'][0][ind] = val elif 'T' in name: tnum = int(name.split('Tor')[1]) Models[nObj]['Tor'][0][tnum] = val else: #March Dollase Models[0]['Coef'][0] = val def OnRunMultiMCSA(event): RunMCSA('multi') def OnRunSingleMCSA(event): RunMCSA('single') def RunMCSA(process): generalData = data['General'] mcsaControls = generalData['MCSA controls'] reflName = mcsaControls['Data source'] phaseName = generalData['Name'] MCSAdata = data['MCSA'] saveResult = [] for result in MCSAdata['Results']: if result[1]: #keep? saveResult.append(result) MCSAdata['Results'] = saveResult covData = {} if 'PWDR' in reflName: PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root, reflName) reflSets = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,'Reflection Lists')) try: #patch for old reflection data reflData = reflSets[phaseName]['RefList'] except TypeError: reflData = reflSets[phaseName] reflType = 'PWDR' elif 'HKLF' in reflName: PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root, reflName) try: reflData = G2frame.GPXtree.GetItemPyData(PatternId)[1]['RefList'] except TypeError: reflData = G2frame.GPXtree.GetItemPyData(PatternId)[1] reflType = 'HKLF' elif reflName == 'Pawley reflections': reflData = data['Pawley ref'] covData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Covariance')) reflType = 'Pawley' else: print ('**** ERROR - No data defined for MC/SA run') return print ('MC/SA run:') print ('Reflection type:'+reflType+' Total No. reflections: %d'%len(reflData)) RBdata = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies')) MCSAmodels = MCSAdata['Models'] if not len(MCSAmodels): print ('**** ERROR - no models defined for MC/SA run****') return time1 = time.time() nprocs = GSASIIpath.GetConfigValue('Multiprocessing_cores',0) if process == 'single' or not nprocs: pgbar = wx.ProgressDialog('MC/SA','Residual Rcf =',101, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) else: pgbar = None try: tsf = 0. nCyc = mcsaControls['Cycles'] if process == 'single' or not nprocs: for i in range(nCyc): pgbar.SetTitle('MC/SA run '+str(i+1)+' of '+str(nCyc)) Result,tsum,nsum,rcov = G2mth.mcsaSearch(data,RBdata,reflType,reflData,covData,pgbar) MCSAdata['Results'].append(Result) print(' MC/SA run completed: %d residual: %.3f%% SFcalc time: %.2fs Nsfcalc: %d'%(i,100*Result[2],tsum,nsum)) tsf += tsum print (' Total SF time: %.2fs'%(tsf)) XY = np.mgrid[0:rcov.shape[0],0:rcov.shape[1]] G2plt.PlotXYZ(G2frame,XY,rcov,labelX='ref No.',labelY='ref No.',newPlot=False, Title='Reflection covariance matrix',zrange=[-1.,1.],color='RdYlGn') else: Results,sftime,numsf = G2mth.MPmcsaSearch(nCyc,data,RBdata,reflType,reflData,covData,nprocs) MCSAdata['Results'] += Results #+= to any saved ones print (' Total SF time: %.2fs MC/SA run time: %.2fs Nsfcalc: %d'%(sftime,time.time()-time1,numsf)) finally: if process == 'single' or not nprocs: pgbar.Destroy() MCSAdata['Results'] = G2mth.sortArray(MCSAdata['Results'],2,reverse=False) MCSAdata['Results'][0][0] = True SetSolution(MCSAdata['Results'][0],data['MCSA']['Models']) G2frame.phaseDisplay.SetFocus() Page = G2frame.phaseDisplay.FindPage('MC/SA') G2frame.phaseDisplay.SetSelection(Page) G2plt.PlotStructure(G2frame,data) wx.CallAfter(UpdateMCSA) def OnMCSAaddAtom(event): dlg = G2elemGUI.PickElement(G2frame) if dlg.ShowModal() == wx.ID_OK: El = dlg.Elem.strip() Info = G2elem.GetAtomInfo(El) dlg.Destroy() atom = {'Type':'Atom','atType':El,'Pos':[[0.,0.,0.], [False,False,False],[[0.,1.],[0.,1.],[0.,1.]]], 'name':El+'('+str(len(data['MCSA']['Models']))+')'} data['MCSA']['Models'].append(atom) data['MCSA']['AtInfo'][El] = [Info['Drad'],Info['Color']] G2plt.PlotStructure(G2frame,data) UpdateMCSA() def OnMCSAaddRB(event): rbData = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies')) rbNames = {} for rbVec in rbData['Vector']: if rbVec != 'AtInfo': rbNames[rbData['Vector'][rbVec]['RBname']] = ['Vector',rbVec] for rbRes in rbData['Residue']: if rbRes != 'AtInfo': rbNames[rbData['Residue'][rbRes]['RBname']] = ['Residue',rbRes] if not rbNames: print ('**** ERROR - no rigid bodies defined ****') return dlg = wx.SingleChoiceDialog(G2frame,'Select','Rigid body',list(rbNames.keys())) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() rbname = list(rbNames.keys())[sel] rbType,rbId = rbNames[rbname] RB = rbData[rbType][rbId] body = {'name':RB['RBname']+'('+str(len(data['MCSA']['Models']))+')','RBId':rbId,'Type':rbType, 'Pos':[[0.,0.,0.],[False,False,False],[[0.,1.],[0.,1.],[0.,1.]]],'Ovar':'','MolCent':[[0.,0.,0.],False], 'Ori':[[180.,0.,0.,1.],[False,False,False,False],[[0.,360.],[-1.,1.],[-1.,1.],[-1.,1.]]]} if rbType == 'Residue': body['Tor'] = [[],[],[]] for i,tor in enumerate(RB['rbSeq']): body['Tor'][0].append(0.0) body['Tor'][1].append(False) body['Tor'][2].append([0.,360.]) data['MCSA']['Models'].append(body) data['MCSA']['rbData'] = rbData data['MCSA']['AtInfo'].update(rbData[rbType]['AtInfo']) UpdateMCSA() wx.CallAfter(G2plt.PlotStructure,G2frame,data) def OnMCSAclear(event): data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}} G2plt.PlotStructure(G2frame,data) UpdateMCSA() def OnMCSAmove(event): general = data['General'] Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7]) xyz,aTypes = G2mth.UpdateMCSAxyz(Bmat,data['MCSA']) for iat,atype in enumerate(aTypes): x,y,z = xyz[iat] AtomAdd(x,y,z,atype,Name=atype+'(%d)'%(iat+1)) G2plt.PlotStructure(G2frame,data) def OnClearResults(event): data['MCSA']['Results'] = [] UpdateMCSA() ##### Pawley routines ################################################################################ def FillPawleyReflectionsGrid(): def onRefineDClick(event): '''Called after a double-click on a cell label''' c = event.GetCol() if c == 5: #refine column label: just select it (& redisplay) G2frame.PawleyRefl.ClearSelection() G2frame.PawleyRefl.SelectCol(c,True) choice = ['Y - vary all','N - vary none',] dlg = wx.SingleChoiceDialog(G2frame,'Select refinement option', 'Refinement controls',choice) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() if sel == 0: for row in range(G2frame.PawleyRefl.GetNumberRows()): PawleyPeaks[row][c]=True else: for row in range(G2frame.PawleyRefl.GetNumberRows()): PawleyPeaks[row][c]=False FillPawleyReflectionsGrid() def KeyEditPawleyGrid(event): colList = G2frame.PawleyRefl.GetSelectedCols() rowList = G2frame.PawleyRefl.GetSelectedRows() PawleyPeaks = data['Pawley ref'] if event.GetKeyCode() == wx.WXK_RETURN: event.Skip(True) elif event.GetKeyCode() == wx.WXK_CONTROL: event.Skip(True) elif event.GetKeyCode() == wx.WXK_SHIFT: event.Skip(True) elif colList: G2frame.PawleyRefl.ClearSelection() key = event.GetKeyCode() for col in colList: if PawleyTable.GetTypeName(0,col) == wg.GRID_VALUE_BOOL: if key == 89: #'Y' for row in range(PawleyTable.GetNumberRows()): PawleyPeaks[row][col]=True elif key == 78: #'N' for row in range(PawleyTable.GetNumberRows()): PawleyPeaks[row][col]=False FillPawleyReflectionsGrid() elif rowList: if event.GetKeyCode() == wx.WXK_DELETE: rowList.reverse() for row in rowList: del(PawleyPeaks[row]) FillPawleyReflectionsGrid() # FillPawleyReflectionsGrid executable starts here G2frame.GetStatusBar().SetStatusText('To delete a Pawley reflection: select row & press Delete',1) if G2frame.PawleyRefl in G2frame.phaseDisplay.gridList: G2frame.phaseDisplay.gridList.remove(G2frame.PawleyRefl) oldSizer = PawleyRefList.GetSizer() if oldSizer: oldSizer.Clear(True) generalData = data['General'] PawleyPeaks = data['Pawley ref'] mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) if len(PawleyPeaks) and generalData['doPawley']: topSizer.Add(wx.StaticText(PawleyRefList,label='Pawley reflections for %s:'%generalData['Name']),0,WACV) else: topSizer.Add(wx.StaticText(PawleyRefList,label='There are no Pawley reflections for %s:'%generalData['Name']),0,WACV) topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(PawleyRefList,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(topSizer,0,wx.EXPAND) rowLabels = [] if len(PawleyPeaks) and generalData['doPawley']: for i in range(len(PawleyPeaks)): rowLabels.append(str(i)) if generalData['Modulated']: colLabels = ['h','k','l','m','mul','d','refine','Fsq(hkl)','sig(Fsq)'] Types = 5*[wg.GRID_VALUE_LONG,]+[wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL,]+ \ 2*[wg.GRID_VALUE_FLOAT+':10,2',] pos = [6,7] else: colLabels = ['h','k','l','mul','d','refine','Fsq(hkl)','sig(Fsq)'] Types = 4*[wg.GRID_VALUE_LONG,]+[wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_BOOL,]+ \ 2*[wg.GRID_VALUE_FLOAT+':10,2',] pos = [5,6] PawleyTable = G2G.Table(PawleyPeaks,rowLabels=rowLabels,colLabels=colLabels,types=Types) G2frame.PawleyRefl = G2G.GSGrid(PawleyRefList) G2frame.PawleyRefl.SetTable(PawleyTable, True) G2frame.PawleyRefl.Unbind(wx.EVT_KEY_DOWN) G2frame.PawleyRefl.Bind(wx.EVT_KEY_DOWN, KeyEditPawleyGrid) G2frame.PawleyRefl.Unbind(wg.EVT_GRID_LABEL_LEFT_DCLICK) G2frame.PawleyRefl.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, onRefineDClick) for r in range(G2frame.PawleyRefl.GetNumberRows()): for c in range(G2frame.PawleyRefl.GetNumberCols()): if c in pos: G2frame.PawleyRefl.SetReadOnly(r,c,isReadOnly=False) else: G2frame.PawleyRefl.SetCellStyle(r,c,VERY_LIGHT_GREY,True) G2frame.PawleyRefl.SetMargins(0,0) G2frame.PawleyRefl.AutoSizeColumns(False) mainSizer.Add(G2frame.PawleyRefl) for r in range(G2frame.PawleyRefl.GetNumberRows()): try: if float(G2frame.PawleyRefl.GetCellValue(r,6)) < 0: G2frame.PawleyRefl.SetCellBackgroundColour(r,6,wx.RED) except: pass else: msg = ('\tPawley refinement has not yet been set up. Use the Operations->"Pawley setup"'+ ' menu command to change this.\n\t'+ '(If Pawley settings have already been set on the General tab, use Operations->"Pawley create").') mainSizer.Add(wx.StaticText(PawleyRefList,label=msg)) SetPhaseWindow(PawleyRefList,mainSizer) def OnPawleySet(event): '''Set Pawley parameters and optionally recompute ''' def DisablePawleyOpts(*args): for c in controlsList: c.Enable(generalData['doPawley']) controlsList = [] dmin,dmax,nhist,lbl = getPawleydRange(G2frame,data) generalData = data['General'] prevPawleySetting = generalData['doPawley'] generalData['doPawley'] = True # make Pawley extraction the default if window is opened if nhist == 0: # no data, no Pawley (probably can't happen here) generalData['doPawley'] = False else: # force limits on dmin & dmax generalData['Pawley dmax'] = min(generalData['Pawley dmax'],dmax) generalData['Pawley dmin'] = max(generalData['Pawley dmin'],dmin) startDmin = generalData['Pawley dmin'] genDlg = wx.Dialog(G2frame,title='Set Pawley Parameters', style=wx.DEFAULT_DIALOG_STYLE) mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(wx.StaticText(genDlg,label='Set Pawley Extraction Parameters for phase '+generalData['Name'])) mainSizer.Add([5,10]) pawlRef = G2G.G2CheckBoxFrontLbl(genDlg,' Do Pawley refinement?: ',generalData,'doPawley',DisablePawleyOpts) mainSizer.Add(pawlRef) mainSizer.Add(wx.StaticText(genDlg,label=lbl),0,wx.BOTTOM,10) pawleySizer = wx.BoxSizer(wx.HORIZONTAL) pawleySizer.Add(wx.StaticText(genDlg,label=' Pawley dmin: '),0,WACV) #def d2Q(*a,**kw): # temp['Qmax'] = 2 * math.pi / generalData['Pawley dmin'] # pawlQVal.SetValue(temp['Qmax']) pawlVal = G2G.ValidatedTxtCtrl(genDlg,generalData,'Pawley dmin', xmin=dmin,xmax=20.,nDig=(10,5),typeHint=float) # xmin=dmin,xmax=20.,nDig=(10,5),typeHint=float,OnLeave=d2Q) controlsList.append(pawlVal) pawleySizer.Add(pawlVal,0,WACV) #pawleySizer.Add(wx.StaticText(genDlg,label=' Qmax: '),0,WACV) #temp = {'Qmax':2 * math.pi / generalData['Pawley dmin']} #def Q2D(*args,**kw): # generalData['Pawley dmin'] = 2 * math.pi / temp['Qmax'] # pawlVal.SetValue(generalData['Pawley dmin']) #pawlQVal = G2G.ValidatedTxtCtrl(genDlg,temp,'Qmax', # xmin=0.314,xmax=25.,nDig=(10,5),typeHint=float,OnLeave=Q2D) #controlsList.append(pawlQVal) #pawleySizer.Add(pawlQVal,0,WACV) mainSizer.Add(pawleySizer) pawleySizer = wx.BoxSizer(wx.HORIZONTAL) pawleySizer.Add(wx.StaticText(genDlg,label=' Pawley dmax: '),0,WACV) pawlVal = G2G.ValidatedTxtCtrl(genDlg,generalData,'Pawley dmax', xmin=2.,xmax=dmax,nDig=(10,5),typeHint=float) controlsList.append(pawlVal) pawleySizer.Add(pawlVal,0,WACV) mainSizer.Add(pawleySizer) pawleySizer = wx.BoxSizer(wx.HORIZONTAL) pawleySizer.Add(wx.StaticText(genDlg,label=' Pawley neg. wt.: '),0,WACV) pawlNegWt = G2G.ValidatedTxtCtrl(genDlg,generalData,'Pawley neg wt', xmin=0.,xmax=1.,nDig=(10,4),typeHint=float) pawleySizer.Add(pawlNegWt,0,WACV) controlsList.append(pawlNegWt) mainSizer.Add(pawleySizer) # make OK button def OnOK(event): genDlg.EndModal(wx.ID_OK) mainSizer.Add([5,5]) btnsizer = wx.StdDialogButtonSizer() btn = wx.Button(genDlg, wx.ID_OK) btn.Bind(wx.EVT_BUTTON, OnOK) btn.SetDefault() btnsizer.AddButton(btn) btn = wx.Button(genDlg, wx.ID_CANCEL) btnsizer.AddButton(btn) btnsizer.Realize() mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) genDlg.SetSizer(mainSizer) mainSizer.Fit(genDlg) genDlg.CenterOnParent() res = genDlg.ShowModal() genDlg.Destroy() if res == wx.ID_NO: return # ask to generate the reflections if the extraction setting or dmin has changed if generalData['doPawley'] and res == wx.ID_OK and ( not prevPawleySetting or startDmin != generalData['Pawley dmin']): dlg = wx.MessageDialog(G2frame,'Do you want to generate the Pawley reflections with these settings? ("Pawley create" command)','Initialize Pawley?', wx.YES_NO | wx.ICON_QUESTION) try: result = dlg.ShowModal() if result == wx.ID_NO: wx.CallAfter(FillPawleyReflectionsGrid) return finally: dlg.Destroy() wx.CallAfter(OnPawleyLoad,event) else: wx.CallAfter(FillPawleyReflectionsGrid) def OnPawleyLoad(event): generalData = data['General'] histograms = data['Histograms'].keys() cell = generalData['Cell'][1:7] A = G2lat.cell2A(cell) SGData = generalData['SGData'] dmin = generalData['Pawley dmin'] dmax = generalData['Pawley dmax'] for hist in histograms: if 'PWDR' in hist[:4]: Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist) inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId( G2frame,Id, 'Instrument Parameters'))[0] limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Limits')) Tmin = G2lat.Dsp2pos(inst,dmin) if 'T' in inst['Type'][0]: limits[1][0] = max(limits[0][0],Tmin) else: limits[1][1] = min(limits[0][1],Tmin) PawleyPeaks = [] HKLd = np.array(G2lat.GenHLaue(dmin,SGData,A)) if generalData['Modulated']: Vec,x,maxH = generalData['SuperVec'] SSGData = G2spc.SSpcGroup(SGData,generalData['SuperSg'])[1] wx.BeginBusyCursor() try: HKLd = G2lat.GenSSHLaue(dmin,SGData,SSGData,Vec,maxH,A) for h,k,l,m,d in HKLd: if d > dmax: continue ext,mul = G2spc.GenHKLf([h,k,l],SGData)[:2] if m or not ext: mul *= 2 #for powder multiplicity PawleyPeaks.append([h,k,l,m,mul,d,False,100.0,1.0]) PawleyPeaks = G2mth.sortArray(PawleyPeaks,5,reverse=True) finally: wx.EndBusyCursor() else: wx.BeginBusyCursor() try: for h,k,l,d in HKLd: if d > dmax: continue ext,mul = G2spc.GenHKLf([h,k,l],SGData)[:2] if not ext: mul *= 2 #for powder multiplicity PawleyPeaks.append([h,k,l,mul,d,False,100.0,1.0]) PawleyPeaks = G2mth.sortArray(PawleyPeaks,4,reverse=True) finally: wx.EndBusyCursor() data['Pawley ref'] = PawleyPeaks dlg = wx.MessageDialog(G2frame,'Do you want to initialize Pawley reflection intensities? ("Pawley estimate" command)','Initialize Pawley?', wx.YES_NO | wx.ICON_QUESTION) try: result = dlg.ShowModal() if result == wx.ID_NO: wx.CallAfter(FillPawleyReflectionsGrid) return finally: dlg.Destroy() wx.CallAfter(OnPawleyEstimate,event) def OnPawleyEstimate(event): #Algorithm thanks to James Hester try: Refs = data['Pawley ref'] Histograms = data['Histograms'] except KeyError: G2frame.ErrorDialog('Pawley estimate','No histograms defined for this phase') return Vst = 1.0/data['General']['Cell'][7] #Get volume generalData = data['General'] im = 0 if generalData['Modulated']: im = 1 HistoNames = list(filter(lambda a:Histograms[a]['Use']==True,list(Histograms.keys()))) if not len(HistoNames): G2frame.ErrorDialog('Pawley estimate','No histograms defined for this phase') return PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,HistoNames[0]) #only use 1st histogram xdata = G2frame.GPXtree.GetItemPyData(PatternId)[1] Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,'Instrument Parameters'))[0] Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,'Sample Parameters')) const = 9.e-2/(np.pi*Sample['Gonio. radius']) #shifts in microns gconst = 2.35482 # sqrt(8 ln 2) dx = (xdata[0][1]-xdata[0][0])*20. #this ian approximation - not correct, but CW seems to be needed cw = np.diff(xdata[0]) cw = np.append(cw,cw[-1]) gconst *= dx wx.BeginBusyCursor() try: for ref in Refs: pos = G2lat.Dsp2pos(Inst,ref[4+im]) if 'Bragg' in Sample['Type']: pos -= const*(4.*Sample['Shift'][0]*cosd(pos/2.0)+ \ Sample['Transparency'][0]*sind(pos)*100.0) #trans(=1/mueff) in cm elif 'E' not in Inst['Type'][0]: #Debye-Scherrer - simple but maybe not right - +Layer Disp from DData? pos -= const*(Sample['DisplaceX'][0]*cosd(pos)+Sample['DisplaceY'][0]*sind(pos)) indx = np.searchsorted(xdata[0],pos) try: FWHM = max(0.001,G2pwd.getFWHM(pos,Inst)) # We want to estimate Pawley F^2 as a drop-in replacement for F^2 calculated by the structural # routines, which use Icorr * F^2 * peak profile, where peak profile has an area of 1. So # we multiply the observed peak height by sqrt(8 ln 2)/(FWHM*sqrt(pi)) to determine the value of Icorr*F^2 # then divide by Icorr to get F^2. ref[6+im] = (xdata[1][indx]-xdata[4][indx])*FWHM*np.sqrt(np.pi) #Area of Gaussian is height * FWHM * sqrt(pi) if 'E' not in Inst['Type'][0]: if 'C' in Inst['Type'][0]: Lorenz = 1./(2.*sind(xdata[0][indx]/2.)**2*cosd(xdata[0][indx]/2.)) #Lorentz correction else: Lorenz = ref[4+im]**4 pola = 1.0 if 'X' in Inst['Type']: pola,dIdPola = G2pwd.Polarization(Inst['Polariz.'][1],xdata[0][indx],Inst['Azimuth'][1]) else: pola = 1.0 # Include histo scale and volume in calculation ref[6+im] /= (Sample['Scale'][0] * Vst * Lorenz * pola * ref[3+im]) else: ref[6+im] /= (Sample['Scale'][0] * ref[3+im]*cw[indx]) except IndexError: ref[6+im] = 0.0 finally: wx.EndBusyCursor() FillPawleyReflectionsGrid() def OnPawleyUpdate(event): '''This is the place for any reflection modification trick Patterson squared, etc. ''' try: Refs = data['Pawley ref'] Histograms = data['Histograms'] except KeyError: G2frame.ErrorDialog('Pawley update','No histograms defined for this phase') return HistoNames = list(Histograms.keys()) PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,HistoNames[0]) refData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, \ PatternId,'Reflection Lists'))[PhaseName]['RefList'] im = 0 if data['General']['Modulated']: im = 1 Inv = data['General']['SGData']['SGInv'] mult = 0.5 if Inv: mult = 0.3 wx.BeginBusyCursor() try: for iref,ref in enumerate(Refs): try: if ref[6+im] < 0.: ref[6+im] *= -mult refData[iref][8+im] *= -mult refData[iref][9+im] *= -mult ref[5+im] = False ref[7+im] = 1.0 except IndexError: print ('skipped',ref) pass finally: wx.EndBusyCursor() wx.CallAfter(FillPawleyReflectionsGrid) def OnPawleySelAll(event): refcol = [G2frame.PawleyRefl.GetColLabelValue(c) for c in range(G2frame.PawleyRefl.GetNumberCols())].index('refine') for r in range(G2frame.PawleyRefl.GetNumberRows()): G2frame.PawleyRefl.GetTable().SetValue(r,refcol,True) G2frame.PawleyRefl.ForceRefresh() def OnPawleySelNone(event): refcol = [G2frame.PawleyRefl.GetColLabelValue(c) for c in range(G2frame.PawleyRefl.GetNumberCols())].index('refine') for r in range(G2frame.PawleyRefl.GetNumberRows()): G2frame.PawleyRefl.GetTable().SetValue(r,refcol,False) G2frame.PawleyRefl.ForceRefresh() def OnPawleyToggle(event): refcol = [G2frame.PawleyRefl.GetColLabelValue(c) for c in range(G2frame.PawleyRefl.GetNumberCols())].index('refine') for r in range(G2frame.PawleyRefl.GetNumberRows()): G2frame.PawleyRefl.GetTable().SetValue( r,refcol, not G2frame.PawleyRefl.GetTable().GetValueAsBool(r,refcol)) G2frame.PawleyRefl.ForceRefresh() ##### Fourier routines ################################################################################ def FillMapPeaksGrid(): def RowSelect(event): r,c = event.GetRow(),event.GetCol() if r < 0 and c < 0: if MapPeaks.IsSelection(): MapPeaks.ClearSelection() else: for row in range(MapPeaks.GetNumberRows()): MapPeaks.SelectRow(row,True) elif c < 0: #only row clicks if event.ControlDown(): if r in getAtomSelections(MapPeaks): MapPeaks.DeselectRow(r) else: MapPeaks.SelectRow(r,True) elif event.ShiftDown(): indxs = getAtomSelections(MapPeaks) MapPeaks.ClearSelection() ibeg = 0 if indxs: ibeg = indxs[-1] for row in range(ibeg,r+1): MapPeaks.SelectRow(row,True) else: MapPeaks.ClearSelection() MapPeaks.SelectRow(r,True) elif r < 0: #a column pick mapPeaks = data['Map Peaks'] c = event.GetCol() if colLabels[c] == 'mag': #big to small order mapPeaks = G2mth.sortArray(mapPeaks,c,reverse=True) elif colLabels[c] in ['x','y','z','dzero','dcent']: #small to big mapPeaks = G2mth.sortArray(mapPeaks,c) else: return data['Map Peaks'] = mapPeaks wx.CallAfter(FillMapPeaksGrid) G2plt.PlotStructure(G2frame,data) # beginning of FillMapPeaksGrid() G2frame.GetStatusBar().SetStatusText('',1) oldSizer = MapPeakList.GetSizer() if oldSizer: # 2nd+ use, clear out old entries for i in oldSizer.GetChildren(): # look for grids in sizer if type(i.GetWindow()) is G2G.GSGrid: oldSizer.Detach(i.GetWindow()) # don't delete them oldSizer.Clear(True) mainSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(MapPeakList,label='Fourier map peak positions for %s:'%data['General']['Name']),0,WACV) topSizer.Add((-1,-1),1,wx.EXPAND) topSizer.Add(G2G.HelpButton(MapPeakList,helpIndex=G2frame.dataWindow.helpKey)) mainSizer.Add(topSizer,0,wx.EXPAND) if 'Map Peaks' in data: G2frame.GetStatusBar().SetStatusText('Double click any column heading to sort',1) mapPeaks = data['Map Peaks'] rowLabels = [] for i in range(len(mapPeaks)): rowLabels.append(str(i)) colLabels = ['mag','x','y','z','dzero','dcent'] Types = 6*[wg.GRID_VALUE_FLOAT+':10,4',] G2frame.MapPeaksTable = G2G.Table(mapPeaks,rowLabels=rowLabels,colLabels=colLabels,types=Types) MapPeaks.SetTable(G2frame.MapPeaksTable, True) MapPeaks.Unbind(wg.EVT_GRID_LABEL_LEFT_CLICK) MapPeaks.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect) for r in range(MapPeaks.GetNumberRows()): for c in range(MapPeaks.GetNumberCols()): MapPeaks.SetCellStyle(r,c,VERY_LIGHT_GREY,True) MapPeaks.SetMargins(0,0) MapPeaks.AutoSizeColumns(False) mainSizer.Add(MapPeaks) else: mainSizer.Add(wx.StaticText(MapPeakList,label=' Map peak list is empty')) SetPhaseWindow(MapPeakList,mainSizer) def OnPeaksMove(event): if 'Map Peaks' in data: mapPeaks = np.array(data['Map Peaks']) peakMax = np.amax(mapPeaks.T[0]) Ind = getAtomSelections(MapPeaks) pgbar = wx.ProgressDialog('Move peaks','Map peak no. 0 processed',len(Ind)+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE) for i,ind in enumerate(Ind): mag,x,y,z = mapPeaks[ind][:4] AtomAdd(x,y,z,'H',Name='M '+'%d'%(int(100*mag/peakMax))) pgbar.Update(i+1,'Map peak no. %d processed'%ind) pgbar.Destroy() G2plt.PlotStructure(G2frame,data) def OnPeaksClear(event): data['Map Peaks'] = [] FillMapPeaksGrid() G2plt.PlotStructure(G2frame,data) def OnPeaksSave(event): if 'Map Peaks' in data: mapPeaks = data['Map Peaks'] pfName = PhaseName+'_peaks.csv' pfFile = '' pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose map peaks file name', pth, pfName, 'csv (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: pfFile = dlg.GetPath() finally: dlg.Destroy() if pfFile: pf = open(pfFile,'w') pf.write('"%s"\n'%(PhaseName)) pf.write(' mag, x, y, z, dzero, dcent \n') for peak in mapPeaks: pf.write(' %.4f, %.4f, %.4f, %.4f, %.4f, %.4f \n'%(peak[0],peak[1],peak[2],peak[3],peak[4],peak[5])) pf.close() def OnPeaksDelete(event): if 'Map Peaks' in data: mapPeaks = data['Map Peaks'] Ind = getAtomSelections(MapPeaks) Ind.sort() Ind.reverse() for ind in Ind: mapPeaks = np.delete(mapPeaks,ind,0) data['Map Peaks'] = mapPeaks FillMapPeaksGrid() G2plt.PlotStructure(G2frame,data) def OnPeaksInvert(event): if 'Map Peaks' in data: generalData = data['General'] mapData = generalData['Map'] try: mapData['rho'] = np.flip(mapData['rho'],(0,1,2)) except TypeError: mapData['rho'] = np.flip(mapData['rho'],0) mapData['rho'] = np.flip(mapData['rho'],1) mapData['rho'] = np.flip(mapData['rho'],2) mapData['rho'] = np.roll(np.roll(np.roll(mapData['rho'],1,axis=0),1,axis=1),1,axis=2) OnSearchMaps(event) FillMapPeaksGrid() G2plt.PlotStructure(G2frame,data) def OnRollMap(event): if 'Map Peaks' in data: half = np.array([.5,.5,.5]) mapPeaks = data['Map Peaks'] generalData = data['General'] mapData = generalData['Map'] if mapData['Flip'] != True: wx.MessageBox('Only valid for charge flip maps',caption='Roll map error',style=wx.ICON_EXCLAMATION) return Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) dims = mapData['rho'].shape dlg = G2G.MultiDataDialog(G2frame,title='Roll map shifts', prompts=['delt-X (-1. to 1.)','delt-Y (-1. to 1.)', 'delt-Z (-1. to 1.)'],values=[0.,0.,0.,], limits=[[-1.,1.],[-1.,1.],[-1.,1.]],formats=['%.6f','%.6f','%.6f']) if dlg.ShowModal() == wx.ID_OK: rollsteps = dlg.GetValues() dxy = np.array([float(R) for R in rollsteps]) rollsteps = np.array([round(float(R)*dims[iR]) for iR,R in enumerate(rollsteps)]) mapData['rho'] = np.roll(np.roll(np.roll(mapData['rho'],rollsteps[0],axis=0),rollsteps[1],axis=1),rollsteps[2],axis=2) for peak in mapPeaks: peak[1:4] += dxy peak[1:4] %= 1. peak[4] = np.sqrt(np.sum(np.inner(Amat,peak[1:4])**2)) if len(peak)>4: peak[5] = np.sqrt(np.sum(np.inner(Amat,(peak[1:4]-half)%1.)**2)) FillMapPeaksGrid() G2plt.PlotStructure(G2frame,data) dlg.Destroy() def OnPeaksEquiv(event): if 'Map Peaks' in data: Ind = getAtomSelections(MapPeaks) if Ind: wx.BeginBusyCursor() try: Ind = G2mth.PeaksEquiv(data,Ind) for r in range(MapPeaks.GetNumberRows()): if r in Ind: MapPeaks.SelectRow(r,addToSelected=True) else: MapPeaks.DeselectRow(r) finally: wx.EndBusyCursor() G2plt.PlotStructure(G2frame,data) def OnShowBonds(event): generalData = data['General'] if generalData['Map'].get('Show bonds',False): generalData['Map']['Show bonds'] = False G2frame.dataWindow.MapPeaksEdit.SetLabel(G2G.wxID_SHOWBONDS,'Show bonds') else: generalData['Map']['Show bonds'] = True G2frame.dataWindow.MapPeaksEdit.SetLabel(G2G.wxID_SHOWBONDS,'Hide bonds') FillMapPeaksGrid() G2plt.PlotStructure(G2frame,data) def OnPeaksUnique(event): if 'Map Peaks' in data: mapPeaks = data['Map Peaks'] Ind = getAtomSelections(MapPeaks) if Ind: choice = ['x=0','y=0','z=0','origin','center'] dlg = wx.SingleChoiceDialog(G2frame,'Peaks closest to:','Select',choice) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection()+1 dlg.Destroy() else: dlg.Destroy() return pgbar = wx.ProgressDialog('Unique peaks','Map peak no. 0 processed',len(Ind)+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE) Ind = G2mth.PeaksUnique(data,Ind,sel,pgbar) print (' No. unique peaks: %d Unique peak fraction: %.3f'%(len(Ind),float(len(Ind))/len(mapPeaks))) tbl = MapPeaks.GetTable().data tbl[:] = [t for i,t in enumerate(tbl) if i in Ind] + [ t for i,t in enumerate(tbl) if i not in Ind] for r in range(MapPeaks.GetNumberRows()): if r < len(Ind): MapPeaks.SelectRow(r,addToSelected=True) else: MapPeaks.DeselectRow(r) MapPeaks.ForceRefresh() G2plt.PlotStructure(G2frame,data) def OnPeaksViewPoint(event): # set view point indx = getAtomSelections(MapPeaks) if not indx: G2frame.ErrorDialog('Set viewpoint','No peaks selected') return mapPeaks = data['Map Peaks'] drawingData = data['Drawing'] drawingData['viewPoint'][0] = mapPeaks[indx[0]][1:4] G2plt.PlotStructure(G2frame,data) def OnPeaksDistVP(event): # distance to view point indx = getAtomSelections(MapPeaks) if not indx: G2frame.ErrorDialog('Peak distance','No peaks selected') return generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) mapPeaks = data['Map Peaks'] drawingData = data['Drawing'] viewPt = np.array(drawingData['viewPoint'][0]) print (' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])) colLabels = [MapPeaks.GetColLabelValue(c) for c in range(MapPeaks.GetNumberCols())] cx = colLabels.index('x') cm = colLabels.index('mag') for i in indx: peak = mapPeaks[i] Dx = np.array(peak[cx:cx+3])-viewPt dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)) print ('Peak: %5d mag= %8.2f distance = %.3f'%(i,peak[cm],dist)) def OnPeaksDA(event): #distance, angle indx = getAtomSelections(MapPeaks) if len(indx) not in [2,3]: G2frame.ErrorDialog('Peak distance/angle','Wrong number of atoms for distance or angle calculation') return generalData = data['General'] Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7]) mapPeaks = data['Map Peaks'] xyz = [] for i in indx: xyz.append(mapPeaks[i][1:4]) if len(indx) == 2: print (' distance for atoms %s = %.3f'%(str(indx),G2mth.getRestDist(xyz,Amat))) else: print (' angle for atoms %s = %.2f'%(str(indx),G2mth.getRestAngle(xyz,Amat))) def OnFourierMaps(event): generalData = data['General'] mapData = generalData['Map'] reflNames = mapData['RefList'] if not generalData['Map']['MapType']: G2frame.ErrorDialog('Fourier map error','Fourier map type not defined') return if not reflNames[0]: G2frame.ErrorDialog('Fourier map error','No reflections defined for Fourier map') return phaseName = generalData['Name'] ReflData = GetReflData(G2frame,phaseName,reflNames) if ReflData == None: G2frame.ErrorDialog('Fourier map error','No reflections defined for Fourier map') return if 'Omit' in mapData['MapType']: dim = '3D ' pgbar = wx.ProgressDialog('Omit map','Blocks done',65, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE) mapData.update(G2mth.OmitMap(data,ReflData,pgbar)) pgbar.Destroy() else: if generalData['Modulated']: dim = '4D ' G2mth.Fourier4DMap(data,ReflData) else: dim = '3D ' G2mth.FourierMap(data,ReflData) mapData['Flip'] = False mapSig = np.std(mapData['rho']) if not data['Drawing']: #if new drawing - no drawing data! SetupDrawingData() data['Drawing']['contourLevel'] = 1. data['Drawing']['mapSize'] = 10. data['Drawing']['showMap'] = True ftext = dim+mapData['MapType']+' computed: rhomax = %.3f rhomin = %.3f sigma = %.3f'%(np.max(mapData['rho']),np.min(mapData['rho']),mapSig) print (ftext) G2frame.AddToNotebook('Fourier '+ftext) UpdateDrawAtoms() G2plt.PlotStructure(G2frame,data) def OnFourClear(event): generalData = data['General'] generalData['Map'] = mapDefault.copy() data['Drawing']['showMap'] = False G2plt.PlotStructure(G2frame,data) # map printing for testing purposes def printRho(SGLaue,rho,rhoMax): dim = len(rho.shape) if dim == 2: ix,jy = rho.shape for j in range(jy): line = '' if SGLaue in ['3','3m1','31m','6/m','6/mmm']: line += (jy-j)*' ' for i in range(ix): r = int(100*rho[i,j]/rhoMax) line += '%4d'%(r) print (line+'\n') else: ix,jy,kz = rho.shape for k in range(kz): print ('k = %d'%k) for j in range(jy): line = '' if SGLaue in ['3','3m1','31m','6/m','6/mmm']: line += (jy-j)*' ' for i in range(ix): r = int(100*rho[i,j,k]/rhoMax) line += '%4d'%(r) print (line+'\n') ## keep this def OnSearchMaps(event): print (' Begin fourier map search - can take some time') time0 = time.time() generalData = data['General'] drawingData = data['Drawing'] mapData = generalData['Map'] if len(mapData['rho']): wx.BeginBusyCursor() try: peaks,mags,dzeros,dcents = G2mth.SearchMap(generalData,drawingData) if mapData['MapType'] in ['delt-F',] or 'N' in mapData['Type']: npeaks,nmags,ndzeros,ndcents = G2mth.SearchMap(generalData,drawingData,Neg=True) peaks = np.concatenate((peaks,npeaks)) mags = np.concatenate((mags,nmags)) dzeros = np.concatenate((dzeros,ndzeros)) dcents = np.concatenate((dcents,ndcents)) finally: wx.EndBusyCursor() if len(peaks): mapPeaks = np.concatenate((mags,peaks,dzeros,dcents),axis=1) data['Map Peaks'] = G2mth.sortArray(mapPeaks,0,reverse=True) print (' Map search finished, time = %.2fs'%(time.time()-time0)) print (' No.peaks found: %d'%len(peaks)) Page = G2frame.phaseDisplay.FindPage('Map peaks') G2frame.phaseDisplay.SetSelection(Page) wx.CallAfter(FillMapPeaksGrid) UpdateDrawAtoms() else: print ('No map available') def On4DChargeFlip(event): generalData = data['General'] mapData = generalData['Map'] map4DData = generalData['4DmapData'] flipData = generalData['Flip'] reflNames = flipData['RefList'] if not reflNames[0]: G2frame.ErrorDialog('Charge flip error','No reflections defined for charge flipping') return phaseName = generalData['Name'] ReflData = GetReflData(G2frame,phaseName,reflNames) if ReflData == None: G2frame.ErrorDialog('Charge flip error','No reflections defined for charge flipping') return pgbar = wx.ProgressDialog('Charge flipping','Residual Rcf =',101, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) try: result = G2mth.SSChargeFlip(data,ReflData,pgbar) finally: pgbar.Destroy() G2frame.AddToNotebook('4D Charge flip: '+result[2]) G2frame.AddToNotebook('4D Charge flip: '+result[3]) mapData.update(result[0]) map4DData.update(result[1]) mapData['Flip'] = True mapSig = np.std(mapData['rho']) if not data['Drawing']: #if new drawing - no drawing data! SetupDrawingData() data['Drawing']['contourLevel'] = 1. data['Drawing']['mapSize'] = 10. print (' 4D Charge flip map computed: rhomax = %.3f rhomin = %.3f sigma = %.3f'%(np.max(mapData['rho']),np.min(mapData['rho']),mapSig)) if mapData['Rcf'] < 99.: OnSearchMaps(event) #does a plot structure at end else: print ('Bad charge flip map - no peak search done') def OnChargeFlip(event): generalData = data['General'] mapData = generalData['Map'] flipData = generalData['Flip'] reflNames = flipData['RefList'] if not reflNames[0]: G2frame.ErrorDialog('Charge flip error','No reflections defined for charge flipping') return phaseName = generalData['Name'] ReflData = GetReflData(G2frame,phaseName,reflNames) if ReflData == None: G2frame.ErrorDialog('Charge flip error','No reflections defined for charge flipping') return pgbar = wx.ProgressDialog('Charge flipping','Residual Rcf =',101, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT) screenSize = wx.ClientDisplayRect() Size = pgbar.GetSize() testNames = ['%3d%3d%3d'%(h,k,l) for h,k,l in flipData['testHKL']] if 50 < Size[0] < 500: # sanity check on size, since this fails w/Win & wx3.0 pgbar.SetSize((int(Size[0]*1.2),Size[1])) # increase size a bit along x pgbar.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5)) try: result = G2mth.ChargeFlip(data,ReflData,pgbar) G2frame.AddToNotebook('Charge flip: '+result[2]) G2frame.AddToNotebook('Charge flip: '+result[3]) mapData.update(result[0]) X = range(len(result[1])) Y = 180.*np.array(result[1]).T/np.pi XY = [[X,y] for y in Y] XY = np.array(XY).reshape((5,2,-1)) G2plt.PlotXY(G2frame,XY,labelX='charge flip cycle',labelY='phase, deg',newPlot=True, Title='Test HKL phases',lines=True,names=testNames) finally: pgbar.Destroy() mapData['Flip'] = True mapSig = np.std(mapData['rho']) if not data['Drawing']: #if new drawing - no drawing data! SetupDrawingData() data['Drawing']['contourLevel'] = 1. data['Drawing']['mapSize'] = 10. data['Drawing']['showMap'] = True print (' Charge flip map computed: rhomax = %.3f rhomin = %.3f sigma = %.3f'%(np.max(mapData['rho']),np.min(mapData['rho']),mapSig)) if mapData['Rcf'] < 99.: OnSearchMaps(event) #does a plot structure at end else: print ('Bad charge flip map - no peak search done') def OnTextureRefine(event): General = data['General'] phaseName = General['Name'] keyList = G2frame.GetHistogramNames('PWDR') histNames = [] refData = {} Gangls = {} for name in keyList: if 'PWDR' in name: im = 0 it = 0 histNames.append(name) Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name) Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Instrument Parameters')) Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Sample Parameters')) Gangls[name] = copy.copy([Sample[item] for item in['Phi','Chi','Omega','Azimuth']]) RefDict = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Reflection Lists'))[phaseName] Refs = RefDict['RefList'].T #np.array! if RefDict['Super']: im = 1 #(3+1) offset for m if 'T' in RefDict['Type']: it = 3 #TOF offset for alp, bet, wave tth = np.ones_like(Refs[0])*Inst[0]['2-theta'][0] refData[name] = np.column_stack((Refs[0],Refs[1],Refs[2],tth,Refs[8+im],Refs[12+im+it],np.zeros_like(Refs[0]))) else: # xray - typical caked 2D image data refData[name] = np.column_stack((Refs[0],Refs[1],Refs[2],Refs[5+im],Refs[8+im],Refs[12+im+it],np.zeros_like(Refs[0]))) pgbar = wx.ProgressDialog('Texture fit','Residual = %5.2f'%(101.0),101, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE) Error = G2mth.FitTexture(General,Gangls,refData,keyList,pgbar) pgbar.Destroy() if Error: wx.MessageBox(Error,caption='Fit Texture Error',style=wx.ICON_EXCLAMATION) XY = [] for hist in keyList: x = refData[hist].T[5].T y = refData[hist].T[6].T xy = [x,y] XY.append(np.array(xy)) G2plt.PlotXY(G2frame,XY,XY2=[],labelX='POobs',labelY='POcalc',newPlot=False,Title='Texture fit error') UpdateTexture() G2plt.PlotTexture(G2frame,data,Start=False) def OnTextureClear(event): print ('clear texture? - does nothing') ##### Phase page routines ############################################################################### def FillSelectPageMenu(TabSelectionIdDict, menuBar): '''Fill "Select tab" menu with menu items for each tab and assign bindings to the menu item to switch between phase tabs ''' def OnSelectPage(event): 'Called when an item is selected from the Select page menu' # lookup the menu item that called us and get its text tabname = TabSelectionIdDict.get(event.GetId()) if not tabname: print ('Warning: menu item not in dict! id=%d'%event.GetId()) return # find the matching tab for PageNum in range(G2frame.phaseDisplay.GetPageCount()): if tabname == G2frame.phaseDisplay.GetPageText(PageNum): G2frame.phaseDisplay.SetSelection(PageNum) return else: print ("Warning: tab "+tabname+" was not found") mid = menuBar.FindMenu('Select tab') menu = menuBar.GetMenu(mid) for ipage,page in enumerate(Pages): if menu.FindItem(page) == wx.NOT_FOUND: # is tab already in menu? Id = wx.NewId() TabSelectionIdDict[Id] = page menu.Append(Id,page,'') G2frame.Bind(wx.EVT_MENU, OnSelectPage, id=Id) def OnPageChanged(event): '''This is called every time that a Notebook tab button is pressed on a Phase data item window ''' page = event.GetSelection() G2frame.phaseDisplay.SetSize(G2frame.dataWindow.GetClientSize()) #TODO -almost right ChangePage(page) def ChangePage(page): newlist = [] # force edits in open grids to complete for p in G2frame.phaseDisplay.gridList: if not p: continue # skip deleted grids try: p.ClearGrid() newlist.append(p) except: pass G2frame.phaseDisplay.gridList = newlist # remove deleted grids from list text = G2frame.phaseDisplay.GetPageText(page) G2frame.lastSelectedPhaseTab = text G2frame.dataWindow.helpKey = 'Phase-'+text # use name of Phase tab for help lookup if text == 'General': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DataGeneral) UpdateGeneral() elif text == 'Data': # only when conf 'SeparateHistPhaseTreeItem' is False G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DataMenu) G2plt.PlotSizeStrainPO(G2frame,data,hist='') G2ddG.UpdateDData(G2frame,DData,data) elif text == 'Atoms': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.AtomsMenu) FillAtomsGrid(Atoms) elif text == 'Layers': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.LayerData) UpdateLayerData() elif text == 'Wave Data' and data['General']['Modulated']: G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.WavesData) G2plt.PlotStructure(G2frame,data,firstCall=True) UpdateWavesData() elif text == 'Dysnomia': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.MEMMenu) UpdateDysnomia() elif text == 'RMC': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.FRMCMenu) UpdateRMC() elif text == 'ISODISTORT': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.ISODData) UpdateISODISTORT() elif text == 'Draw Options': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DataDrawOptions) G2plt.PlotStructure(G2frame,data,firstCall=True) UpdateDrawOptions() elif text == 'Draw Atoms': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DrawAtomsMenu) G2plt.PlotStructure(G2frame,data,firstCall=True) UpdateDrawAtoms() elif text == 'Deformation': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DeformationMenu) G2plt.PlotStructure(G2frame,data,firstCall=True) UpdateDeformation(None) elif text == 'RB Models': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RigidBodiesMenu) FillRigidBodyGrid() elif text == 'Map peaks': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.MapPeaksMenu) G2plt.PlotStructure(G2frame,data,firstCall=True) FillMapPeaksGrid() elif text == 'MC/SA': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.MCSAMenu) G2plt.PlotStructure(G2frame,data,firstCall=True) UpdateMCSA() elif text == 'Texture': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.TextureMenu) G2plt.PlotTexture(G2frame,data,Start=True) UpdateTexture() elif text == 'Pawley reflections': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PawleyMenu) FillPawleyReflectionsGrid() else: G2gd.SetDataMenuBar(G2frame) def FillMenus(): '''Create the Select tab menus and bind to all menu items ''' # General FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.DataGeneral) G2frame.Bind(wx.EVT_MENU, OnFourierMaps, id=G2G.wxID_FOURCALC) G2frame.Bind(wx.EVT_MENU, OnSearchMaps, id=G2G.wxID_FOURSEARCH) G2frame.Bind(wx.EVT_MENU, OnChargeFlip, id=G2G.wxID_CHARGEFLIP) G2frame.Bind(wx.EVT_MENU, On4DChargeFlip, id=G2G.wxID_4DCHARGEFLIP) G2frame.Bind(wx.EVT_MENU, OnFourClear, id=G2G.wxID_FOURCLEAR) G2frame.Bind(wx.EVT_MENU, OnRunSingleMCSA, id=G2G.wxID_SINGLEMCSA) G2frame.Bind(wx.EVT_MENU, OnRunMultiMCSA, id=G2G.wxID_MULTIMCSA) G2frame.Bind(wx.EVT_MENU, OnTransform, id=G2G.wxID_TRANSFORMSTRUCTURE) G2frame.Bind(wx.EVT_MENU, OnTransform2Std, id=G2G.wxID_TRANSFORMSTD) G2frame.Bind(wx.EVT_MENU, OnSuperSearch, id=G2G.wxID_SUPERSRCH) G2frame.Bind(wx.EVT_MENU, OnISOSearch, id=G2G.wxID_ISOSRCH) G2frame.Bind(wx.EVT_MENU, OnCompare, id=G2G.wxID_COMPARESTRUCTURE) G2frame.Bind(wx.EVT_MENU, OnCompareCells, id=G2G.wxID_COMPARECELLS) G2frame.Bind(wx.EVT_MENU, OnUseBilbao, id=G2G.wxID_USEBILBAOMAG) G2frame.Bind(wx.EVT_MENU, OnApplySubgroups, id=G2G.wxID_USEBILBAOSUB) G2frame.Bind(wx.EVT_MENU, OnValidProtein, id=G2G.wxID_VALIDPROTEIN) # Data (unless Hist/Phase tree entry shown) if not GSASIIpath.GetConfigValue('SeparateHistPhaseTreeItem',False): FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.DataMenu) G2frame.Bind(wx.EVT_MENU, OnDataUse, id=G2G.wxID_DATAUSE) G2frame.Bind(wx.EVT_MENU, OnDataCopy, id=G2G.wxID_DATACOPY) G2frame.Bind(wx.EVT_MENU, OnDataCopyFlags, id=G2G.wxID_DATACOPYFLAGS) G2frame.Bind(wx.EVT_MENU, OnSelDataCopy, id=G2G.wxID_DATASELCOPY) G2frame.Bind(wx.EVT_MENU, OnSelDataRead, id=G2G.wxID_DATASELREAD) G2frame.Bind(wx.EVT_MENU, OnPwdrAdd, id=G2G.wxID_PWDRADD) G2frame.Bind(wx.EVT_MENU, OnHklfAdd, id=G2G.wxID_HKLFADD) G2frame.Bind(wx.EVT_MENU, OnDataDelete, id=G2G.wxID_DATADELETE) G2frame.Bind(wx.EVT_MENU, OnDataApplyStrain, id=G2G.wxID_DATADIJ) # Atoms FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.AtomsMenu) G2frame.Bind(wx.EVT_MENU, OnSetAll, id=G2G.wxID_ATOMSSETALL) G2frame.Bind(wx.EVT_MENU, OnSetbyList, id=G2G.wxID_ATOMSSETLST) G2frame.Bind(wx.EVT_MENU, AtomRefine, id=G2G.wxID_ATOMSSETSEL) G2frame.Bind(wx.EVT_MENU, AtomModify, id=G2G.wxID_ATOMSMODIFY) G2frame.Bind(wx.EVT_MENU, OnAtomInsert, id=G2G.wxID_ATOMSEDITINSERT) G2frame.Bind(wx.EVT_MENU, OnHydAtomAdd, id=G2G.wxID_ADDHATOM) G2frame.Bind(wx.EVT_MENU, AtomDelete, id=G2G.wxID_ATOMSEDITDELETE) G2frame.Bind(wx.EVT_MENU, AtomTransform, id=G2G.wxID_ATOMSTRANSFORM) # G2frame.Bind(wx.EVT_MENU, AtomRotate, id=G2G.wxID_ATOMSROTATE) G2frame.Bind(wx.EVT_MENU, SetAtomsViewPoint, id=G2G.wxID_ATOMSSETVP) G2frame.Bind(wx.EVT_MENU, OnAtomAdd, id=G2G.wxID_ATOMSEDITADD) G2frame.Bind(wx.EVT_MENU, OnAtomViewAdd, id=G2G.wxID_ATOMSVIEWADD) G2frame.Bind(wx.EVT_MENU, OnAtomViewInsert, id=G2G.wxID_ATOMVIEWINSERT) G2frame.Bind(wx.EVT_MENU, OnHydAtomUpdate, id=G2G.wxID_UPDATEHATOM) G2frame.Bind(wx.EVT_MENU, OnAtomMove, id=G2G.wxID_ATOMMOVE) G2frame.Bind(wx.EVT_MENU, MakeMolecule, id=G2G.wxID_MAKEMOLECULE) G2frame.Bind(wx.EVT_MENU, CollectAtoms, id=G2G.wxID_COLLECTATOMS) G2frame.Bind(wx.EVT_MENU, OnReloadDrawAtoms, id=G2G.wxID_RELOADDRAWATOMS) G2frame.Bind(wx.EVT_MENU, OnDistAngle, id=G2G.wxID_ATOMSDISAGL) G2frame.Bind(wx.EVT_MENU, OnDistAnglePrt, id=G2G.wxID_ATOMSPDISAGL) G2frame.Bind(wx.EVT_MENU, OnDistAngleHist, id=G2G.wxID_ATOMSBNDANGLHIST) G2frame.Bind(wx.EVT_MENU, OnFracSplit, id=G2G.wxID_ATOMFRACSPLIT) G2frame.Bind(wx.EVT_MENU, OnDensity, id=G2G.wxID_ATOMSDENSITY) G2frame.Bind(wx.EVT_MENU, OnShowIsoDistortCalc, id=G2G.wxID_ISODISP) if 'HydIds' in data['General']: G2frame.dataWindow.AtomEdit.Enable(G2G.wxID_UPDATEHATOM,True) else: G2frame.dataWindow.AtomEdit.Enable(G2G.wxID_UPDATEHATOM,False) for Id in G2frame.dataWindow.ReImportMenuId: #loop over submenu items G2frame.Bind(wx.EVT_MENU, OnReImport, id=Id) # Wave Data if data['General']['Modulated']: FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.WavesData) G2frame.Bind(wx.EVT_MENU, OnWaveVary, id=G2G.wxID_WAVEVARY) # Dysnomia (MEM) if data['General']['doDysnomia']: FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.MEMMenu) G2frame.Bind(wx.EVT_MENU, OnLoadDysnomia, id=G2G.wxID_LOADDYSNOMIA) G2frame.Bind(wx.EVT_MENU, OnSaveDysnomia, id=G2G.wxID_SAVEDYSNOMIA) G2frame.Bind(wx.EVT_MENU, OnRunDysnomia, id=G2G.wxID_RUNDYSNOMIA) # Stacking faults FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.LayerData) G2frame.Bind(wx.EVT_MENU, OnCopyPhase, id=G2G.wxID_COPYPHASE) G2frame.Bind(wx.EVT_MENU, OnLoadDIFFaX, id=G2G.wxID_LOADDIFFAX) G2frame.Bind(wx.EVT_MENU, OnSimulate, id=G2G.wxID_LAYERSIMULATE) G2frame.Bind(wx.EVT_MENU, OnFitLayers, id=G2G.wxID_LAYERSFIT) G2frame.Bind(wx.EVT_MENU, OnSeqSimulate, id=G2G.wxID_SEQUENCESIMULATE) # Draw Options FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.DataDrawOptions) # Draw Atoms FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.DrawAtomsMenu) G2frame.Bind(wx.EVT_MENU, DrawAtomStyle, id=G2G.wxID_DRAWATOMSTYLE) G2frame.Bind(wx.EVT_MENU, DrawAtomLabel, id=G2G.wxID_DRAWATOMLABEL) G2frame.Bind(wx.EVT_MENU, DrawAtomColor, id=G2G.wxID_DRAWATOMCOLOR) G2frame.Bind(wx.EVT_MENU, ResetAtomColors, id=G2G.wxID_DRAWATOMRESETCOLOR) G2frame.Bind(wx.EVT_MENU, OnEditAtomRadii, id=G2G.wxID_DRWAEDITRADII) G2frame.Bind(wx.EVT_MENU, SetViewPoint, id=G2G.wxID_DRAWVIEWPOINT) G2frame.Bind(wx.EVT_MENU, AddSymEquiv, id=G2G.wxID_DRAWADDEQUIV) G2frame.Bind(wx.EVT_MENU, AddSphere, id=G2G.wxID_DRAWADDSPHERE) G2frame.Bind(wx.EVT_MENU, TransformSymEquiv, id=G2G.wxID_DRAWTRANSFORM) G2frame.Bind(wx.EVT_MENU, FillCoordSphere, id=G2G.wxID_DRAWFILLCOORD) G2frame.Bind(wx.EVT_MENU, FillUnitCell, id=G2G.wxID_DRAWFILLCELL) G2frame.Bind(wx.EVT_MENU, DrawAtomsDelete, id=G2G.wxID_DRAWDELETE) G2frame.Bind(wx.EVT_MENU, OnReloadDrawAtoms, id=G2G.wxID_RELOADATOMS) G2frame.Bind(wx.EVT_MENU, OnDrawDistVP, id=G2G.wxID_DRAWDISTVP) G2frame.Bind(wx.EVT_MENU, OnDrawDAT, id=G2G.wxID_DRAWDISAGLTOR) G2frame.Bind(wx.EVT_MENU, OnDrawPlane, id=G2G.wxID_DRAWPLANE) G2frame.Bind(wx.EVT_MENU, OnRestraint, id=G2G.wxID_DRAWRESTRBOND) G2frame.Bind(wx.EVT_MENU, OnRestraint, id=G2G.wxID_DRAWRESTRANGLE) G2frame.Bind(wx.EVT_MENU, OnRestraint, id=G2G.wxID_DRAWRESTRPLANE) G2frame.Bind(wx.EVT_MENU, OnRestraint, id=G2G.wxID_DRAWRESTRCHIRAL) G2frame.Bind(wx.EVT_MENU, OnDefineRB, id=G2G.wxID_DRAWDEFINERB) G2frame.Bind(wx.EVT_MENU, FillMolecule, id=G2G.wxID_DRAWADDMOLECULE) G2frame.Bind(wx.EVT_MENU, MapVoid, id=G2G.wxID_DRAWVOIDMAP) G2frame.Bind(wx.EVT_MENU, SelDrawList, id=G2G.wxID_DRAWSETSEL) G2frame.Bind(wx.EVT_MENU, DrawLoadSel, id=G2G.wxID_DRAWLOADSEL) # Deformation form factors FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.DeformationMenu) G2frame.Bind(wx.EVT_MENU, SelDeformAtom, id=G2G.wxID_DEFORMSETSEL) G2frame.Bind(wx.EVT_MENU, SetDefDist, id=G2G.wxID_DEFORMDISTSET) # RB Models FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.RigidBodiesMenu) G2frame.Bind(wx.EVT_MENU, OnAutoFindResRB, id=G2G.wxID_AUTOFINDRESRB) G2frame.Bind(wx.EVT_MENU, OnRBAssign, id=G2G.wxID_ASSIGNATMS2RB) G2frame.Bind(wx.EVT_MENU, OnRBCopyParms, id=G2G.wxID_COPYRBPARMS) G2frame.Bind(wx.EVT_MENU, OnGlobalResRBTherm, id=G2G.wxID_GLOBALTHERM) G2frame.Bind(wx.EVT_MENU, OnGlobalResRBRef, id=G2G.wxID_GLOBALRESREFINE) G2frame.Bind(wx.EVT_MENU, OnRBRemoveAll, id=G2G.wxID_RBREMOVEALL) # Map peaks FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.MapPeaksMenu) G2frame.Bind(wx.EVT_MENU, OnPeaksMove, id=G2G.wxID_PEAKSMOVE) G2frame.Bind(wx.EVT_MENU, OnPeaksViewPoint, id=G2G.wxID_PEAKSVIEWPT) G2frame.Bind(wx.EVT_MENU, OnPeaksDistVP, id=G2G.wxID_PEAKSDISTVP) G2frame.Bind(wx.EVT_MENU, OnPeaksDA, id=G2G.wxID_PEAKSDA) G2frame.Bind(wx.EVT_MENU, OnShowBonds, id=G2G.wxID_SHOWBONDS) G2frame.Bind(wx.EVT_MENU, OnPeaksEquiv, id=G2G.wxID_FINDEQVPEAKS) G2frame.Bind(wx.EVT_MENU, OnPeaksInvert, id=G2G.wxID_INVERTPEAKS) G2frame.Bind(wx.EVT_MENU, OnRollMap, id=G2G.wxID_ROLLMAP) G2frame.Bind(wx.EVT_MENU, OnPeaksUnique, id=G2G.wxID_PEAKSUNIQUE) G2frame.Bind(wx.EVT_MENU, OnPeaksSave, id=G2G.wxID_PEAKSSAVE) G2frame.Bind(wx.EVT_MENU, OnPeaksDelete, id=G2G.wxID_PEAKSDELETE) G2frame.Bind(wx.EVT_MENU, OnPeaksClear, id=G2G.wxID_PEAKSCLEAR) # RMCProfile/fullrmc/PDFfit FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.FRMCMenu) G2frame.Bind(wx.EVT_MENU, OnSetupRMC, id=G2G.wxID_SETUPRMC) G2frame.Bind(wx.EVT_MENU, OnRunRMC, id=G2G.wxID_RUNRMC) G2frame.Bind(wx.EVT_MENU, OnViewRMC, id=G2G.wxID_VIEWRMC) #G2frame.Bind(wx.EVT_MENU, OnStopRMC, id=G2G.wxID_STOPRMC) G2frame.Bind(wx.EVT_MENU, OnLoadRMC, id=G2G.wxID_ATOMSRMC) G2frame.Bind(wx.EVT_MENU, OnLoadRMCsuper, id=G2G.wxID_SUPERRMC) # ISODISTORT FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.ISODData) G2frame.Bind(wx.EVT_MENU, OnRunISODISTORT, id=G2G.wxID_ISODISTORT) G2frame.Bind(wx.EVT_MENU, OnNewISOPhase, id=G2G.wxID_ISODNEWPHASE) G2frame.Bind(wx.EVT_MENU, OnNewPDFfitPhase, id=G2G.wxID_ISOPDFFIT) G2frame.Bind(wx.EVT_MENU, OnShowIsoDistortCalc, id=G2G.wxID_SHOWISO1) G2frame.Bind(wx.EVT_MENU, OnShowIsoModes, id=G2G.wxID_SHOWISOMODES) # MC/SA FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.MCSAMenu) G2frame.Bind(wx.EVT_MENU, OnMCSAaddAtom, id=G2G.wxID_ADDMCSAATOM) G2frame.Bind(wx.EVT_MENU, OnMCSAaddRB, id=G2G.wxID_ADDMCSARB) G2frame.Bind(wx.EVT_MENU, OnMCSAclear, id=G2G.wxID_CLEARMCSARB) G2frame.Bind(wx.EVT_MENU, OnMCSAmove, id=G2G.wxID_MOVEMCSA) G2frame.Bind(wx.EVT_MENU, OnClearResults, id=G2G.wxID_MCSACLEARRESULTS) # Texture FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.TextureMenu) G2frame.Bind(wx.EVT_MENU, OnTextureRefine, id=G2G.wxID_REFINETEXTURE) # G2frame.Bind(wx.EVT_MENU, OnTextureClear, id=G2G.wxID_CLEARTEXTURE) # Pawley reflections FillSelectPageMenu(TabSelectionIdDict, G2frame.dataWindow.PawleyMenu) G2frame.Bind(wx.EVT_MENU, OnPawleySet, id=G2G.wxID_PAWLEYSET) G2frame.Bind(wx.EVT_MENU, OnPawleyLoad, id=G2G.wxID_PAWLEYLOAD) G2frame.Bind(wx.EVT_MENU, OnPawleyEstimate, id=G2G.wxID_PAWLEYESTIMATE) G2frame.Bind(wx.EVT_MENU, OnPawleyUpdate, id=G2G.wxID_PAWLEYUPDATE) G2frame.Bind(wx.EVT_MENU, OnPawleySelAll, id=G2G.wxID_PAWLEYSELALL) G2frame.Bind(wx.EVT_MENU, OnPawleySelNone, id=G2G.wxID_PAWLEYSELNONE) G2frame.Bind(wx.EVT_MENU, OnPawleyToggle, id=G2G.wxID_PAWLEYSELTOGGLE) def rbKeyPress(event): '''Respond to a Tab to highlight the next RB or crystal atom TODO: this is not getting called in Windows. Is a bind needed elsewhere? ''' if 'testRBObj' not in data: return if not RigidBodies.atomsGrid: return alt = event.GetModifiers() & wx.MOD_ALT event.Skip() try: # IsKeyInCategory not in wx 2.9 if not event.IsKeyInCategory(wx.WXK_CATEGORY_TAB): return except: return if alt: # advance RB selection #GSASIIpath.IPyBreak() rows = RigidBodies.atomsGrid.GetSelectedRows() if len(rows) == 0: rows = [0] else: rows[0] += 1 if rows[0] > RigidBodies.atomsGrid.GetNumberRows()-1: rows = [0] elif rows[0] < 0: rows[0] = RigidBodies.atomsGrid.GetNumberRows()-1 RigidBodies.atomsGrid.SelectRow(rows[0]) RigidBodies.atomsGrid.MakeCellVisible(rows[0],0) data['testRBObj']['RBhighLight'] = rows[0] else: Ind = data['testRBObj'].get('CRYhighLight',[]) if len(Ind) == 0: I = -1 else: I = Ind[0] wrap = False while True: I += 1 if I >= len(data['Atoms']) and wrap: print('How did this happen?',Ind,I, len(data['testRBObj']['availAtoms']),len(data['Atoms'])) return elif I >= len(data['Atoms']): wrap = True I = 0 if data['Atoms'][I][0] in data['testRBObj']['availAtoms']: data['testRBObj']['CRYhighLight'] = [I] misc['showSelect'].setByString(data['Atoms'][I][0]) break G2plt.PlotStructure(G2frame,data,False,misc['UpdateTable']) G2frame.Raise() return #### UpdatePhaseData execution starts here #patch if 'RBModels' not in data: data['RBModels'] = {} if 'MCSA' not in data: data['MCSA'] = {'Models':[{'Type':'MD','Coef':[1.0,False,[.8,1.2],],'axis':[0,0,1]}],'Results':[],'AtInfo':{}} #if isinstance(data['MCSA']['Results'],dict): if 'dict' in str(type(data['MCSA']['Results'])): data['MCSA']['Results'] = [] if 'Modulated' not in data['General']: data['General']['Modulated'] = False if 'doDysnomia' not in data['General']: data['General']['doDysnomia'] = False if 'modulated' in data['General']['Type']: data['General']['Modulated'] = True data['General']['Type'] = 'nuclear' if 'RMC' not in data: data['RMC'] = {'RMCProfile':{},'fullrmc':{},'PDFfit':{}} if 'ISODISTORT' not in data: data['ISODISTORT'] = {} if 'Deformations' not in data: data['Deformations'] = {} #end patch global rbAtmDict rbAtmDict = {} misc = {} PhaseName = G2frame.GPXtree.GetItemText(Item) G2gd.SetDataMenuBar(G2frame) G2frame.phaseDisplay = G2G.GSNoteBook(parent=G2frame.dataWindow) G2frame.dataWindow.GetSizer().Add(G2frame.phaseDisplay,1,wx.ALL|wx.EXPAND,1) G2frame.phaseDisplay.gridList = [] # list of all grids in notebook Pages = [] General = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(General,'General') Pages.append('General') if not GSASIIpath.GetConfigValue('SeparateHistPhaseTreeItem',False): DData = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(DData,'Data') Pages.append('Data') AtomList = wx.ScrolledWindow(G2frame.phaseDisplay) Atoms = G2G.GSGrid(AtomList) G2frame.phaseDisplay.gridList.append(Atoms) G2frame.phaseDisplay.AddPage(AtomList,'Atoms') Pages.append('Atoms') if data['General']['Modulated']: G2frame.waveData = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(G2frame.waveData,'Wave Data') Pages.append('Wave Data') if data['General']['Type'] == 'faulted': G2frame.layerData = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(G2frame.layerData,'Layers') Pages.append('Layers') drawOptions = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(drawOptions,'Draw Options') Pages.append('Draw Options') drawAtomsList = wx.ScrolledWindow(G2frame.phaseDisplay) drawAtoms = G2G.GSGrid(drawAtomsList) G2frame.phaseDisplay.gridList.append(drawAtoms) G2frame.phaseDisplay.AddPage(drawAtomsList,'Draw Atoms') Pages.append('Draw Atoms') if any('X' in item for item in G2frame.GetHistogramTypes()): deformation = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(deformation,'Deformation') Pages.append('Deformation') if data['General']['Type'] not in ['faulted',] and not data['General']['Modulated']: RigidBodies = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(RigidBodies,'RB Models') # note the bind is here so that it is only done once, but # TODO: might need to be on a different widget for Windows RigidBodies.Bind(wx.EVT_CHAR,rbKeyPress) Pages.append('RB Models') MapPeakList = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(MapPeakList,'Map peaks') # create the grid once; N.B. need to reference at this scope MapPeaks = G2G.GSGrid(MapPeakList) G2frame.phaseDisplay.gridList.append(MapPeaks) if data['General']['doDysnomia']: G2frame.MEMData = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(G2frame.MEMData,'Dysnomia') Pages.append('Dysnomia') Pages.append('Map peaks') if data['General']['Type'] not in ['faulted',] and not data['General']['Modulated']: G2frame.MCSA = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(G2frame.MCSA,'MC/SA') Pages.append('MC/SA') G2frame.FRMC = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(G2frame.FRMC,'RMC') Pages.append('RMC') if data['General']['Type'] == 'nuclear': ISODIST = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(ISODIST,'ISODISTORT') Pages.append('ISODISTORT') Texture = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.phaseDisplay.AddPage(Texture,'Texture') Pages.append('Texture') PawleyRefList = wx.ScrolledWindow(G2frame.phaseDisplay) G2frame.PawleyRefl = None # grid now created when needed # G2frame.PawleyRefl = G2G.GSGrid(PawleyRefList) # G2frame.PawleyRefl.SetScrollRate(0,0) # G2frame.phaseDisplay.gridList.append(G2frame.PawleyRefl) G2frame.phaseDisplay.AddPage(PawleyRefList,'Pawley reflections') Pages.append('Pawley reflections') G2frame.dataWindow.AtomCompute.Enable(G2G.wxID_ISODISP,'ISODISTORT' in data) G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_VALIDPROTEIN,'macro' in data['General']['Type']) G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_USEBILBAOMAG,'magPhases' in data) flag = False if 'magPhases' in data: PatternName = data['magPhases'] PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,PatternName) if (PatternId): UnitCellsId = G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Unit Cells List') UCdata = list(G2frame.GPXtree.GetItemPyData(UnitCellsId)) flag = not any(['magAtms' in i for i in UCdata[5]]) else: del data['magPhases'] G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_USEBILBAOSUB,flag) G2frame.phaseDisplay.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged) FillMenus() if G2frame.lastSelectedPhaseTab in Pages: ind = Pages.index(G2frame.lastSelectedPhaseTab) if ind: UpdateGeneral(SkipDraw=ind) G2frame.phaseDisplay.SetSelection(ind) return ChangePage(0)
[docs] def checkPDFfit(G2frame): '''Checks to see if PDFfit2 is available and can be imported. PDFfit2 can be installed in a separate Python interpreter (saved in the pdffit2_exec config variable). If this is defined, no attempt is made to check that it actually runs. Otherwise, if diffpy.PDFfit has been installed with conda/pip, it is checked if the install command. The fallback is to check if a .so/.pyd file has been supplied with GSAS-II. This requires that GSL (GNU Scientific Library) be installed. If the current Python is being run from conda, this will be loaded. :returns: False if PDFfit2 cannot be run/accessed. True if it appears it can be run. ''' # if a separate Python interpreter has been specified, just use it, no checking if GSASIIpath.GetConfigValue('pdffit2_exec') is not None and is_exe( GSASIIpath.GetConfigValue('pdffit2_exec')): return True # see if diffpy has been installed directly try: from diffpy.pdffit2 import PdfFit return True except: pass # See if if we can import the GSAS-II supplied PDFfit pdffitloc = os.path.join(GSASIIpath.path2GSAS2,'PDFfit2') print(pdffitloc,'\n',GSASIIpath.binaryPath) if pdffitloc not in sys.path: sys.path.append(pdffitloc) try: from diffpy.pdffit2 import PdfFit #pf = PdfFit() return True except Exception as err: pass #print('Failed to import PDFfit2 with error:\n'+str(err)) if not os.path.exists(pdffitloc): print('PDFfit2 not found in GSAS-II \n\t(expected in '+pdffitloc+')') return False import glob # see if we can fix things so the GSAS-II version can be used if not GSASIIpath.condaTest() and glob.glob(os.path.join(GSASIIpath.binaryPath,'pdffit*')): msg = ('GSAS-II supplies a version of PDFfit2 that should be compatible with '+ 'this Python installation. Since Python was not installed under conda you need '+ 'to correct this for yourself. You likely need to '+ 'install GSL (GNU Software Library).') G2G.G2MessageBox(G2frame,msg,'PDFfit2 will not load; No conda') return False elif not GSASIIpath.condaTest(): msg = ('GSAS-II does not supply a version of PDFfit2 compatible with '+ 'this Python installation. Since Python was not installed under conda you need '+ 'to correct this for yourself. You likely need to '+ 'install the GSL (GNU Software Library) and use "pip install diffpy.pdffit2".'+ ' This is best done in a separate Python installation/virtual environment.') G2G.G2MessageBox(G2frame,msg,'PDFfit2 not provided; No conda') return False try: # have conda. Can we access it programmatically? import conda.cli.python_api except: if not glob.glob(os.path.join(GSASIIpath.binaryPath,'pdffit*')): msg = 'GSAS-II does not supply PDFfit2 for the version of Python that you are using' else: msg = 'GSAS-II supplies PDFfit2 that should be compatible with the version of Python that you are using. The problem is likely that the GSL package needs to be installed.' msg += ('\n\nYou do not have the conda package installed in this '+ 'environment. This is needed for GSAS-II to install software.'+ '\n\nDo you want to have conda installed for you?') dlg = wx.MessageDialog(G2frame,msg,caption='Install?', style=wx.YES_NO|wx.ICON_QUESTION) if dlg.ShowModal() != wx.ID_YES: dlg.Destroy() return False dlg.Destroy() try: wx.BeginBusyCursor() print('Preparing to install conda. This may take a few minutes...') GSASIIpath.addCondaPkg() finally: wx.EndBusyCursor() try: # have conda. Can we access it programmatically? import conda.cli.python_api except: print('command line conda install did not provide package. Unexpected!') return False if ('gsl' not in conda.cli.python_api.run_command( conda.cli.python_api.Commands.LIST,'gsl')[0].lower() and glob.glob(os.path.join(GSASIIpath.binaryPath,'pdffit*'))): msg = ('The gsl (GNU Software Library), needed by PDFfit2, '+ ' is not installed in this Python. Do you want to have this installed?') dlg = wx.MessageDialog(G2frame,msg,caption='Install?', style=wx.YES_NO|wx.ICON_QUESTION) if dlg.ShowModal() != wx.ID_YES: dlg.Destroy() return False dlg.Destroy() try: wx.BeginBusyCursor() print('Preparing to install gsl. This may take a few minutes...') res = GSASIIpath.condaInstall(['gsl','-c','conda-forge']) finally: wx.EndBusyCursor() if res: msg = 'Installation of the GSL package failed with error:\n' + str(res) G2G.G2MessageBox(G2frame,msg,'Install GSL Error') # GSAS-II supplied version for PDFfit now runs? if pdffitloc not in sys.path: sys.path.append(pdffitloc) try: from diffpy.pdffit2 import PdfFit #pf = PdfFit() return True except Exception as err: msg = 'Failed to import PDFfit2 with error:\n'+str(err) print(msg) if glob.glob(os.path.join(GSASIIpath.binaryPath,'pdffit*')): G2G.G2MessageBox(G2frame,msg,'PDFfit2 import error') # Last effort: With conda we should be able to create a separate Python in a separate # environment msg = ('Do you want to try using conda to install PDFfit2 into a separate environment? '+ '\n\nIf successful, the pdffit2_exec configuration option will be set to the '+ 'this new Python environment.') dlg = wx.MessageDialog(G2frame,msg,caption='Install?', style=wx.YES_NO|wx.ICON_QUESTION) if dlg.ShowModal() != wx.ID_YES: return False try: wx.BeginBusyCursor() print('Preparing to create a conda environment. This may take a few minutes...') # for now use the older diffpy version of pdffit: # conda create -n pdffit2 python=3.7 conda gsl diffpy.pdffit2=1.2 -c conda-forge -c diffpy res,PDFpython = GSASIIpath.condaEnvCreate('pdffit2', ['python=3.7', 'conda', 'gsl', 'diffpy.pdffit2=1.2', '-c', 'conda-forge', '-c', 'diffpy']) # someday perhaps this will work: # conda create -n pdffit2 python conda gsl diffpy.pdffit2 -c conda-forge finally: wx.EndBusyCursor() if os.path.exists(PDFpython): vars = G2G.GetConfigValsDocs() vars['pdffit2_exec'][1] = PDFpython GSASIIpath.SetConfigValue(vars) G2G.SaveConfigVars(vars) print('pdffit2_exec config set with ',GSASIIpath.GetConfigValue('pdffit2_exec')) return True else: msg = 'Failed to install PDFfit2 with error:\n'+str(PDFpython) print(msg) G2G.G2MessageBox(G2frame, 'Install failed. See console for error message\n\n'+ 'All attempts to install PDFfit2 have failed. '+ 'Do you have write access to where GSAS-II is installed?', 'PDFfit2 install error') return False
[docs] def makeIsoNewPhase(phData,cell,atomList,sglbl,sgnum): '''create a new phase from a supergroup structure generated by ISOCIF ''' if len(atomList) == 0: print(sglbl,'empty structure') return # create a new phase try: sgnum = int(sgnum) sgsym = G2spc.spgbyNum[sgnum] sgname = sgsym.replace(" ","") except: print(f'Problem with processing space group name {sglbl} and number {sgnum}') return newPhase = copy.deepcopy(phData) newPhase['ranId'] = ran.randint(0,sys.maxsize), if 'magPhases' in phData: del newPhase['magPhases'] generalData = newPhase['General'] generalData['SGData'] = SGData = G2spc.SpcGroup(sgsym)[1] generalData['Cell'][1:7] = cell generalData['Cell'][7] = G2lat.calc_V(G2lat.cell2A(generalData['Cell'][1:7])) cx,ct,cs,cia = generalData['AtomPtrs'] Atoms = newPhase['Atoms'] = [] for nam,(x,y,z) in atomList: try: atom = [] atom.append(nam) if nam[1].isdigit(): atom.append(nam[0:1]) else: atom.append(nam[0:2]) atom.append('') for i in x,y,z: atom.append(float(i)) atom.append(1.0) SytSym,Mult = G2spc.SytSym(np.array(atom[3:6]),SGData)[:2] atom.append(SytSym) atom.append(Mult) atom.append('I') atom += [0.02,0.,0.,0.,0.,0.,0.,] atom.append(ran.randint(0,sys.maxsize)) Atoms.append(atom) except Exception as msg: print(f'{msg} error in atom {nam}') G2elem.SetupGeneral(newPhase,generalData['Mydir']) # fixup composition info return newPhase
[docs] def saveIsoNewPhase(G2frame,phData,newPhase,orgFilName): '''save the new phase generated by ISOCIF created in :func:`makeIsoNewPhase` into a GSAS-II project (.gpx) file ''' import re phData.update(newPhase) # save new file sgname = newPhase['General']['SGData']['SpGrp'].replace(' ','') G2frame.GSASprojectfile = os.path.splitext(orgFilName )[0]+'_super_'+sgname.replace('/','$')+'.gpx' while os.path.exists(G2frame.GSASprojectfile): s = re.split(r'_([\d]+)\.gpx',G2frame.GSASprojectfile) if len(s) == 1: G2frame.GSASprojectfile = os.path.splitext(G2frame.GSASprojectfile)[0] + '_1.gpx' else: num = 10 try: num = int(s[1]) + 1 except: pass G2frame.GSASprojectfile = f'{s[0]}_{num}.gpx' G2IO.ProjFileSave(G2frame) return G2frame.GSASprojectfile