# -*- coding: utf-8 -*-
#GSASII - phase data display routines
'''
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 math
import copy
import time
import sys
import random as ran
import subprocess as subp
#import platform
import shutil
import numpy as np
import numpy.linalg as nl
import numpy.ma as ma
import scipy.optimize as so
from . import GSASIIpath
from . import GSASIIlattice as G2lat
from . import GSASIIspc as G2spc
from . import GSASIIElem as G2elem
from . import GSASIIElemGUI as G2elemGUI
from . import GSASIIddataGUI as G2ddG
from . import GSASIIplot as G2plt
from . import GSASIIpwdplot as G2pwpl
from . import GSASIIphsGUI2 as G2phsG2
from . import GSASIIrmcGUI as G2rmcG
# if GSASIIpath.GetConfigValue('debug'):
# print('Debug reloading',G2plt)
# import imp
# imp.reload(G2plt)
from . import GSASIIdataGUI as G2gd
from . import GSASIImiscGUI as G2IO
from . import GSASIIstrMain as G2stMn
from . import GSASIIstrIO as G2stIO
from . import GSASIImath as G2mth
from . import GSASIIpwd as G2pwd
from . import GSASIIobj as G2obj
from . import GSASIIctrlGUI as G2G
from . import GSASIIconstrGUI as G2cnstG
from . import atmdata
from . import ISODISTORT as ISO
from . import SUBGROUPS
from pathlib import Path
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
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
GkDelta = chr(0x0394)
Angstr = chr(0x00c5)
RMCmisc = {}
ranDrwDict = {}
ranDrwDict['atomList'] = []
DrawStyleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
#### 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 self.indx is None:
pass
elif 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 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 ################################################################################
[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
chist = 0
for item in data['Histograms']:
if 'HKLF' in item: #count single crystal histograms
chist += 1
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,chist
[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
[docs]
def SetPhaseWindow(phasePage,mainSizer=None,Scroll=0):
'''Finish off processing for all items going into a phase notebook page
This connects the sizer to the Panel/ScrolledWindow that is assigned
as the notebook's page for a tab.
Note that a wx.ScrolledWindow is used for most tab pages, with the
exception of Atoms, drawAtoms, G2frame.MapPeaks and G2frame.PawleyRefl,
where a wx.Panel is used with a single Grid inside. This allows the grid
to handle scrolling.
When a wx.ScrolledWindows is used, scrolling is turned on here. The
optional Scroll parameter is used to restore the scroll position to
the previous position so that the window can be redrawn without
disruption.
'''
if mainSizer is not None:
phasePage.SetSizer(mainSizer)
if isinstance(phasePage,wx.ScrolledWindow):
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:
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
return
[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]],
'Line':[[0,0,1.],False,False,1.0,[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,ifSlide=True):
'''Update all origin/orientation text on the Add RB panel or
on main RB Models page in response to Alt+mouse movement
'''
A,V = G2mth.Q2AVdeg(testRBObj['rbObj']['Orient'][0])
testRBObj['rbObj']['OrientVec'][0] = A
testRBObj['rbObj']['OrientVec'][1:] = np.inner(Bmat,V)
for i in range(4):
val = testRBObj['rbObj']['OrientVec'][i]
if not i: #in that BoxSizer from G2SpinWidget
BSI = G2frame.testRBObjSizers['OrientVecSiz'][i].GetChildren()[-2].GetWindow()
else:
BSI = G2frame.testRBObjSizers['OrientVecSiz'][i]
BSI.ChangeValue(val)
# for i,val in enumerate(testRBObj['rbObj']['OrientVec']):
# if not ifSlide: #skip spin button
# G2frame.testRBObjSizers['OrientVecSiz'][i+1].ChangeValue(val)
# else:
# G2frame.testRBObjSizers['OrientVecSiz'][i].ChangeValue(val)
if ifSlide: #from the addRB GUI
G2frame.testRBObjSizers['OrientVecSiz'][4].SetValue(
int(10*testRBObj['rbObj']['OrientVec'][0]))
for i,sizer in enumerate(G2frame.testRBObjSizers.get('Xsizers',[])):
sizer.ChangeValue(testRBObj['rbObj']['Orig'][0][i])
# redraw asymmetric unit when called on an existing body
# if G2frame.testRBObjSizers.get('OnOrien') is None: return
# G2frame.testRBObjSizers['OnOrien'](mode=testRBObj['rbObj'].get('drawMode',DrawStyleChoice[4]))
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
[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 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):
'called when the phase name is changed in "General"'
event.Skip()
newName = NameTxt.GetValue().strip()
renamePhaseName(G2frame,data,Item,generalData,newName)
NameTxt.SetValue(newName)
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'] = G2elem.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'] = G2elem.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)
# removed this because modulation info is now added to atoms
# 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)
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.ChangeValue(cell[1])
elif laue in ['3R','3mR']:
if ObjId == 0:
cell[1] = cell[2] = cell[3] = value
Obj.ChangeValue(cell[1])
else:
cell[4] = cell[5] = cell[6] = value
Obj.ChangeValue(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.ChangeValue(cell[1])
else:
cell[3] = value
Obj.ChangeValue(cell[3])
elif laue in ['mmm']:
cell[ObjId+1] = value
cell[4] = cell[5] = cell[6] = 90.
Obj.ChangeValue(cell[ObjId+1])
elif laue in ['2/m'+'a']:
cell[5] = cell[6] = 90.
if ObjId != 3:
cell[ObjId+1] = value
Obj.ChangeValue(cell[ObjId+1])
else:
cell[4] = value
Obj.ChangeValue(cell[4])
elif laue in ['2/m'+'b']:
cell[4] = cell[6] = 90.
if ObjId != 3:
cell[ObjId+1] = value
Obj.ChangeValue(cell[ObjId+1])
else:
cell[5] = value
Obj.ChangeValue(cell[5])
elif laue in ['2/m'+'c']:
cell[4] = cell[5] = 90.
if ObjId != 3:
cell[ObjId+1] = value
Obj.ChangeValue(cell[ObjId+1])
else:
cell[6] = value
Obj.ChangeValue(cell[6])
else:
cell[ObjId+1] = value
Obj.ChangeValue(cell[1+ObjId])
cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
volVal.ChangeValue("%.3f"%(cell[7]))
density,mattCoeff = G2mth.getDensity(generalData)
if denSizer:
denSizer[1].ChangeValue('%.3f'%(density))
if denSizer[2]:
denSizer[2].ChangeValue('%.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.ChangeValue('%.3f'%(wt)) #tricky
data['General']['AtomMass'][indx] = wt
density,mattCoeff = G2mth.getDensity(generalData)
denSizer[1].ChangeValue('%.3f'%(density))
if denSizer[2]:
denSizer[2].ChangeValue('%.3f'%(mattCoeff))
def onDefColor(event):
'''Called when a color bar in elements table is clicked on.
Changes default color for element in all phases
N.B. Change is not saved; will go back to original color when
GSAS-II is restarted.
Changes colors of matching atoms in Draw Atoms table for
current phase -- only.
'''
if not hasattr(event.GetEventObject(),'atomNum'): return
anum = event.GetEventObject().atomNum
(R,G,B) = generalData['Color'][anum]
dlg = wx.ColourDialog(event.GetEventObject().GetTopLevelParent())
dlg.GetColourData().SetChooseFull(False)
dlg.GetColourData().SetColour(wx.Colour(R,G,B))
if dlg.ShowModal() == wx.ID_OK:
El = generalData['AtomTypes'][anum]
RGB = dlg.GetColourData().GetColour()[0:3]
G2elem.SetAtomColor(El, RGB)
cx,ct,cs,ci = data['Drawing']['atomPtrs']
for atom in data['Drawing']['Atoms']:
if atom[ct] != El: continue
atom[cs+2] = RGB
wx.CallAfter(UpdateGeneral)
dlg.Destroy()
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 i,(R,G,B) in enumerate(generalData['Color']):
colorTxt = G2G.ReadOnlyTextCtrl(General,value='')
colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
colorTxt.atomNum = i
colorTxt.Bind(wx.EVT_SET_FOCUS,onDefColor)
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']
if not SSGData: # SS sym defined?
G2G.G2MessageBox(General,'Select a modulation group first','Superspace Group Error')
return
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
def enablePawley(*args):
for c in PawleyCtrlsList:
c.Enable(generalData['doPawley'])
# If Pawley is on, turn off Le Bail settings (since they will
# be hidden)
if generalData['doPawley']:
Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.GPXtree.root, 'Controls'))
Controls['newLeBail'] = False
for h in data['Histograms']:
data['Histograms'][h]['LeBail'] = False
G2G.G2MessageBox(G2frame,title='Note:',
msg='Use Pawley Create in Operations menu of Pawley'+
' Reflections tab to complete the Pawley setup')
dmin,dmax,nhist,lbl,chist = 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)
PawleyCtrlsList = []
pawlRef = G2G.G2CheckBoxFrontLbl(General,' Do Pawley refinement?',
generalData,'doPawley',enablePawley)
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))
PawleyCtrlsList.append(pawlMin)
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))
PawleyCtrlsList.append(pawlMax)
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'))
PawleyCtrlsList.append(pawlNegWt)
pawleySizer.Add(pawlNegWt,0,WACV)
pawleyOuter = wx.BoxSizer(wx.VERTICAL)
pawleyOuter.Add(pawleySizer)
pawleyOuter.Add(wx.StaticText(General,label=lbl),0,wx.LEFT,120)
for c in PawleyCtrlsList:
c.Enable(generalData['doPawley'])
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, lambda event:G2phsG2.OnLoadDysnomia(event,G2frame,data), id=G2G.wxID_LOADDYSNOMIA)
# G2frame.Bind(wx.EVT_MENU, lambda event:G2phsG2.OnSaveDysnomia(event,G2frame,data), id=G2G.wxID_SAVEDYSNOMIA)
# G2frame.Bind(wx.EVT_MENU, lambda event:G2phsG2.OnRunDysnomia(event,G2frame,data), id=G2G.wxID_RUNDYSNOMIA)
# 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
Flip['k-Max'] = Flip.get('k-Max',20.)
Flip['MScorr'] = Flip.get('Mscorr',0.0)
Flip['d-max'] = Flip.get('d-max',100.)
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.ChangeValue('%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'],]
refName = Flip['RefList'][0]
refType = ''
if refName and refName in data['Histograms']:
refType = data['Histograms'][refName].get('Type','')
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)
lineSizer.Add(wx.StaticText(General,label=' d-max (3.-100.): '),0,WACV)
lineSizer.Add(G2G.ValidatedTxtCtrl(General,Flip,'d-max',nDig=(10,2),xmin=3.,xmax=100.),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 (0.01-1.2): '),0,WACV)
kFactor = G2G.ValidatedTxtCtrl(General,Flip,'k-factor',nDig=(10,3),xmin=0.01,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)
if refType == 'SEC':
line2Sizer.Add(wx.StaticText(General,label=' MScorr (0-0.1): '),0,WACV)
line2Sizer.Add(G2G.ValidatedTxtCtrl(General,Flip,'MScorr',nDig=(10,4),xmin=0.,xmax=0.10),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))
def OnSaveDist(event):
pName = generalData['Name']
fName = os.path.abspath(os.path.splitext(G2frame.GSASprojectfile)[0]+'_TOdist.csv')
fp = open(fName,'w')
fp.write('Phase name: %s,'%pName)
Oatoms = generalData['Compare']['Oatoms']
Tatoms = generalData['Compare']['Tatoms']
bName = '%s-%s'%(Oatoms,Tatoms)
Bonds = generalData['Compare']['Bonds'][bName]
# Vects = generalData['Compare']['Vects'][bName]
# dVects = generalData['Compare']['dVects'][bName]
if len(Bonds['Obonds']):
fp.write('\n%s-%s Octahedral bond lengths,\n'%(Oatoms,Tatoms))
for ib,bond in enumerate(Bonds['Obonds']):
fp.write('%7.4f,'%bond)
if not (ib+1)%10: fp.write('\n')
if len(Bonds['Tbonds']):
fp.write('\n%s-%s Tetrahedral bond lengths,\n'%(Oatoms,Tatoms))
for ib,bond in enumerate(Bonds['Tbonds']):
fp.write('%7.4f,'%bond)
if not (ib+1)%10: fp.write('\n')
fp.close()
print(' %s written'%fName)
Oatoms = generalData['Compare']['Oatoms']
Tatoms = generalData['Compare']['Tatoms']
bName = '%s-%s'%(Oatoms,Tatoms)
atTypes = generalData['AtomTypes']
compSizer = wx.BoxSizer(wx.VERTICAL)
topSizer = wx.BoxSizer(wx.HORIZONTAL)
topSizer.Add(wx.StaticText(General,label=' Compare polyhedra to ideal octahedra/tetrahedra:'),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)
topSizer.Add(plotBtn,0,WACV)
saveBtn = wx.Button(General,label='Save distributions?')
saveBtn.Bind(wx.EVT_BUTTON,OnSaveDist)
topSizer.Add(saveBtn,0,WACV)
except KeyError:
pass
compSizer.Add(topSizer)
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)
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)
topSizer = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
lbl= f"Overall params for {generalData['Name']!r} (type={data['General']['Type']})"[:60]
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
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)
dmin,dmax,nhist,lbl,chist = getPawleydRange(G2frame,data)
if nhist > 0:
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 = ''
ifRB = False
RBModels = data['RBModels']
for item in RBModels:
if RBModels[item]:
ifRB = True
if ifRB:
msg = 'Rigid Bodies present'
text = 'Rigid bodies must be deleted before transform can be done'
wx.MessageBox(text,caption=msg,style=wx.ICON_EXCLAMATION)
return
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]])
# TODO: might want to select atoms by element 1st
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'] = G2elem.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)
with open(tmp.name,'w') as fp:
fp.write(txt.replace(
'<HEAD>',
'<head><base href="https://iso.byu.edu/">',
))
fileList.append(tmp.name)
G2G.ShowWebPage('file://'+tmp.name,G2frame)
import tempfile
import re
import requests
from GSASII.exports import G2export_CIF
isosite="https://iso.byu.edu/"
upscript='isocifuploadfile.php'
isoscript='isocifform.php'
isoSubCite = ('For use of this supergroup search, please cite:\n'+
G2G.GetCite('ISOTROPY, ISODISTORT, ISOCIF...',wrap=60,indent=5))
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')
with open(tmp1.name,'w') as fp:
fp.write(r1.text.replace(
'<HEAD>',
'<head><base href="https://iso.byu.edu/">',
))
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=isoSubCite)
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()
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"{isoSubCite}\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 OnNISTLatSym(event):
# '''Run NIST*LATTICE cell search
# This is a quick copy of the capability in GSASIIpwdGUI, but uses
# the cell from the current phase. It would be better if this
# would actually transform the unit cell and coordinates using any
# new cell found here. Someday. (TODO)
# '''
# #pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
# #controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
# nistInput=[0.2,1.,2,3]
# msg = G2G.NISTlatUse(True)
# dlg = wx.Dialog(G2frame,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER)
# sizer = wx.BoxSizer(wx.VERTICAL)
# sizer.Add(wx.StaticText(dlg,label='NIST*LATTICE Cell Symmetry Search Settings'),
# 0,wx.ALIGN_CENTER_HORIZONTAL,0)
# sizer.Add((-1,15))
# sizer.Add(wx.StaticText(dlg,label=msg))
# sizer.Add((-1,15))
# sizer.Add(wx.StaticText(dlg,label=(
# ('Starting cell: '+3*'{:.3f}, '+3*'{:.2f}, ').format(
# *data['General']['Cell'][1:7]))))
# sizer.Add((-1,15))
# tableSizer = wx.FlexGridSizer(0,2,0,0)
# tableSizer.Add(wx.StaticText(dlg,label='Cell length tolerance (A) '),
# 0,WACV|wx.ALIGN_LEFT)
# w = G2G.ValidatedTxtCtrl(dlg,nistInput,0,nDig=(6,2))
# tableSizer.Add(w)
# tableSizer.Add(wx.StaticText(dlg,label='Cell angle tolerance (deg) '),
# 0,WACV|wx.ALIGN_LEFT)
# w = G2G.ValidatedTxtCtrl(dlg,nistInput,1,nDig=(6,1))
# tableSizer.Add(w)
# #
# # next option makes it too easy to create a really
# # long-running (infinite?) computation. Removed for now.
# #
# #tableSizer.Add(wx.StaticText(dlg,label='Cell volume range (ratio) '),
# # 0,WACV|wx.ALIGN_LEFT)
# #w = G2G.ValidatedTxtCtrl(dlg,nistInput,2)
# #tableSizer.Add(w)
# tableSizer.Add(wx.StaticText(dlg,label='Search mode: Generate '),
# 0,WACV|wx.ALIGN_LEFT)
# tableSizer.Add(G2G.EnumSelector(dlg,nistInput,3,
# ['supercells', 'subcells', 'sub- and supercells'],[1,2,3]))
# sizer.Add(tableSizer,1,wx.EXPAND)
# btnsizer = wx.StdDialogButtonSizer()
# btn = wx.Button(dlg, wx.ID_OK)
# btn.SetDefault()
# btn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_OK))
# btnsizer.AddButton(btn)
# btn = wx.Button(dlg, wx.ID_CANCEL)
# btn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(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:
# dlg.Destroy()
# else:
# dlg.Destroy()
# return
# tol = 3*[nistInput[0]]+3*[nistInput[1]]
# cell = data['General']['Cell'][1:7]
# center = data['General']['SGData']['SGLatt']
# delta = nistInput[2]
# mode = nistInput[3]
# wx.BeginBusyCursor()
# import nistlat
# out = nistlat.CellSymSearch(cell, center, tolerance=tol, mode=mode,deltaV=delta)
# wx.EndBusyCursor()
# if not out: return
# cells.clear()
# for o in out:
# cells.append([])
# c = o[2][0]
# # assign a Laue class
# laue = 16 # P1
# if c[0] == c[1] == c[2] and c[3] == c[4] == c[5] == 90:
# if o[2][1] == 'F':
# laue = 0 # Fm3m
# elif o[2][1] == 'I':
# laue = 1 # Im3m
# else:
# laue = 2 # Pm3m
# elif o[2][1] == 'R':
# laue = 3 # R3
# elif c[0] == c[1] and c[5] == 120:
# laue = 4 # P6/mmm
# elif c[0] == c[1] and c[3] == c[4] == c[5] == 90 and o[2][1] == 'I':
# laue = 5 # I4/mmm
# elif c[0] == c[1] and c[3] == c[4] == c[5] == 90 and o[2][1] == 'P':
# laue = 6 # P4/mmm
# elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'F':
# laue = 7 # 'Fmmm'
# elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'I':
# laue = 8 # 'Immm'
# elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'A':
# laue = 9 # 'Ammm'
# elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'B':
# laue = 10 # 'Bmmm'
# elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'C':
# laue = 11 # 'Cmmm'
# elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'P':
# laue = 12 # 'Pmmm'
# elif c[3] == c[5] == 90 and o[2][1] == 'C':
# laue = 13 # 'C2/m'
# elif c[3] == c[5] == 90 and o[2][1] == 'P':
# laue = 14 # 'P2/m'
# elif o[2][1] == 'C':
# laue = 15 # 'C1'
# cells[-1] += [o[4],0,laue]
# cells[-1] += c
# cells[-1] += [G2lat.calc_V(G2lat.cell2A(c)),False,False]
# G2frame.GPXtree.SetItemPyData(pUCid,data)
# G2frame.OnFileSave(event)
# wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnSuperSearch(event):
'''Search for a supergroup matching the current phase using the
Bilbao 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)
with open(tmp.name,'w') as fp:
fp.write(pagelist[num].replace(
'<head>',
f'<head><base href="{SUBGROUPS.bilbaoURL}/">',
))
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,
f'''Using the Bilbao Crystallographic Server Pseudosymmetry search (PSEUDO)
program; Please cite:
{G2G.GetCite('Bilbao: PSEUDO',wrap=70,indent=5)}'''))
mainSizer.Add((-1,5))
G2G.HorizontalLine(mainSizer,dlg)
txt = wx.StaticText(dlg,wx.ID_ANY,
'Searched for supergroups 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 level {depth} 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,
f'''Using the Bilbao Crystallographic Server Pseudosymmetry search (PSEUDO)
program; Please cite:
{G2G.GetCite('Bilbao: PSEUDO',wrap=70,indent=5)}'''))
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 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`)
'''
def _showWebPage(event):
import tempfile
f = event.GetEventObject().webFile
tmp = tempfile.NamedTemporaryFile(suffix='.html',
delete=False)
with open(tmp.name,'w') as fp:
fp.write(f.replace(
'<head>',
f'<head><base href="{SUBGROUPS.bilbaoURL}/">',
))
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,
f'''Using the Bilbao Crystallographic Server Pseudosymmetry search (PSEUDO)
program; Please cite:
{G2G.GetCite('Bilbao: PSEUDO',wrap=70,indent=5)}'''))
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 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 ####
fileList = [] # contains a list of displayed web pages
ophsnam = data['General']['Name']
pgbar = wx.ProgressDialog('Supergroup Search',
f'Searching for supergroup(s) consistent with phase {ophsnam}',11,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT,
parent=G2frame)
if SUBGROUPS.RegisterProgressDialog(pgbar):
pgbar.Destroy()
return
pgNum = 0
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)."
# fix non-standard space group settings
pgNum = 1 + pgNum % 10
GoOn = pgbar.Update(pgNum,newmsg=
f'Testing for standard setting for phase {ophsnam}')
if not GoOn[0]: return
pgbar.Raise()
wx.GetApp().Yield()
print('*** Checking space group setting')
sgnum,sgsym,xmat,xoff = SUBGROUPS.GetStdSGset(data['General']['SGData'])
if sgnum is None:
G2G.G2MessageBox(G2frame,
'Standard setting check failed. Check console output.',
'Bilbao error')
return
newPhase = copy.deepcopy(data)
try:
pgNum = 1 + pgNum % 10
if np.allclose(np.eye(3),xmat) and np.allclose(xoff,np.zeros_like(xoff)):
print('*** Structure in standard setting')
GoOn = pgbar.Update(pgNum,newmsg=
'Searching for supergroups with original setting')
else:
GoOn = pgbar.Update(pgNum,newmsg=
'Revised to standard setting; Now searching for supergroups')
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)
msgs[0] += " Transformed starting structure: new cell = "
msgs[0] += fmtCell(newPhase['General']['Cell'][1:7])
msgs[0] += f". Space group {newPhase['General']['SGData']['SpGrp']}."
except:
G2G.G2MessageBox(G2frame,
'Standard setting check failed. Try again later.',
'Unexpected error')
return
if not GoOn[0]: return
pgbar.Raise()
wx.GetApp().Yield()
# search from a standard space group setting
pagelist = {}
keepCell = False
if sgnum <= 16: # warn on unimplemented search capability
msg = '''
Code to search for higher symmetry
cells with the Bilboa web site is
not fully implemented. You are
suggested to do this with NIST*LATTICE
using the Unit Cells List "Cell
Symmetry Search" command, or by
using "No" here, but either way
you will need to manually transform
the structure into any higher
symmetry cells.
Skip search for higher symmetry cell?'''
dlg = wx.MessageDialog(G2frame,msg,'Skip cell search for mono/triclinic?',
wx.YES_NO | wx.ICON_QUESTION)
try:
result = dlg.ShowModal()
if result == wx.ID_YES:
keepCell = True
finally:
dlg.Destroy()
formDict,csdict,rowdict,stru = SUBGROUPS.BilbaoSymSearch1(sgnum,newPhase,pagelist=pagelist,
keepCell=keepCell)
# process initial PSEUDO results
if csdict is None and len(rowdict) == 0: # this was monoclinic or triclinic,
# but no new cell. Repeat search looking for supergroups of the current cell
# BHT TODO: needs testing
pgNum = 1 + pgNum % 10
GoOn = pgbar.Update(pgNum,newmsg=
'Mono/Triclinic: No improved cell, repeating supergroup search')
if not GoOn[0]: return
pgbar.Raise()
wx.GetApp().Yield()
formDict,csdict,rowdict,stru = SUBGROUPS.BilbaoSymSearch1(sgnum,newPhase,
pagelist=pagelist,keepCell=True)
ans = _selectSuperGroups(rowdict,csdict,'from '+msgs[0]+
'\n*** Note, no higher symmetry cells found.')
if ans == wx.ID_CANCEL: return
structDict,pgNum = SUBGROUPS.BilbaoGetStructure(csdict,rowdict,stru,
pagelist=pagelist,dlg=pgbar,dlgNum=pgNum)
if structDict is None: return
if len(structDict) != 0: NextSearch = SUBGROUPS.find2SearchAgain(pagelist,'')
elif csdict is None: # this was monoclinic or triclinic, but >0 new cells found
# BHT TODO: needs testing
structDict = {}
csdict = len(rowdict)*[True]
ans = _selectHiSymCell(rowdict,csdict)
G2G.G2MessageBox(G2frame,'Sorry the GSAS-II code is not yet able to convert Triclinic/Monoclinic cells','Sorry')
return
if ans == wx.ID_CANCEL: return
for i,row in enumerate(rowdict): # only expecting one cell?
if not csdict[i]: continue
pgNum = 1 + pgNum % 10
GoOn = pgbar.Update(pgNum,newmsg=
'Starting search for supergroup(s) w/cell'+
f' {str(row[2])}\nLattice {row[1]}')
pgbar.Raise()
if not GoOn[0]: return
wx.GetApp().Yield()
### WRONG? ******************************************************
lbl,latticeList,vals1dict,rowList = SUBGROUPS.BilbaoLowSymSea1(
formDict,row,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
pgNum = 1 + pgNum % 10
GoOn = pgbar.Update(pgNum,newmsg=
f'Searching for supergroup(s) w/cell {str(row[2])}'
+ f'\nLattice {row[1]} && spacegroup {row1[2]}'
)
if not GoOn[0]: return
pgbar.Raise()
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]}'
if len(structDict) != 0: NextSearch = SUBGROUPS.find2SearchAgain(pagelist)
else: # not monoclinic or triclinic
ans = _selectSuperGroups(rowdict,csdict,'from '+msgs[0])
if ans == wx.ID_CANCEL: return
if any(csdict.values()):
pgNum = 1 + pgNum % 10
GoOn = pgbar.Update(pgNum,newmsg=
f'Getting coordinates for {sum(csdict.values())} selected supergroup(s)')
if not GoOn[0]: return
pgbar.Raise()
wx.GetApp().Yield()
structDict,pgNum = SUBGROUPS.BilbaoGetStructure(csdict,rowdict,stru,
pagelist=pagelist,dlg=pgbar,dlgNum=pgNum)
if structDict is None: return
if len(structDict) != 0: NextSearch = SUBGROUPS.find2SearchAgain(pagelist,'')
else:
structDict = {}
NextSearch = {}
# searches completed.
if len(structDict) != 0: # were new structures generated?
# new phases will need different restraints clear them (probably
# should clear constraints too)
try:
Restraints[ophsnam]['Bond']['Bonds'] = []
Restraints[ophsnam]['Angle']['Angles'] = []
except:
pass
# Now generate .gpx files and show results
for num,s in structDict.items(): # loop over supergroup settings
G2IO.saveNewPhase(G2frame,data,s,num,msgs,orgFilName)
ans = showSuperResults(G2frame,msgs,pagelist,fileList,NextSearch,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
# pull out entries to be used again
ReSearch = {}
for key in NextSearch:
if key.startswith('use_'): continue
if NextSearch.get('use_'+key,False):
ReSearch[key] = NextSearch[key]
while ReSearch:
NextSearch = {}
repeatcount += 1
for key in ReSearch:
newpages = {}
sgnum = ReSearch[key]['stru'].split('\n')[0]
if GSASIIpath.GetConfigValue('debug'): print(f"processing {key} sg# {sgnum}")
pgNum = 1 + pgNum % 10
GoOn = pgbar.Update(pgNum,newmsg=
f'Searching for supergroup(s) from case {key} sg# {sgnum}')
if not GoOn[0]:
NextSearch = ReSearch = {}
break
pgbar.Raise()
wx.GetApp().Yield()
formDict,csdict,rowdict = SUBGROUPS.BilbaoReSymSearch(
key,ReSearch[key],pagelist=pagelist)
ans = _selectSuperGroups(rowdict,csdict,
f'case {key}, {msgs[key]}',repeatcount,key=key)
if ans == wx.ID_CANCEL:
continue
if not any(csdict.values()): continue
pgNum = 1 + pgNum % 10
GoOn = pgbar.Update(pgNum,newmsg=
'Getting coordinates for selected supergroup(s)')
if not GoOn[0]:
NextSearch = ReSearch = {}
break
pgbar.Raise()
wx.GetApp().Yield()
stru = ReSearch[key]['stru']
structDict,pgNum = SUBGROUPS.BilbaoGetStructure(csdict,rowdict,stru,
pagelist=newpages,dlg=pgbar,dlgNum=pgNum,prefix=key+'-')
if structDict is None:
NextSearch = ReSearch = {}
break
for num,s in structDict.items(): # loop over supergroup settings
G2IO.saveNewPhase(G2frame,data,s,num,msgs,orgFilName)
NextSearch.update(SUBGROUPS.find2SearchAgain(newpages,''))
ans = showSuperResults(G2frame,msgs,newpages,fileList,NextSearch,
pagelist[key],msgs[key])
pagelist.update(newpages)
ReSearch = {}
for key in NextSearch:
if key.startswith('use_'): continue
if NextSearch.get('use_'+key,False):
ReSearch[key] = NextSearch[key]
finally:
pgbar.Destroy()
SUBGROUPS.RegisterProgressDialog()
for i in fileList: os.unlink(i) # cleanup tmp web pages
ans = showFinalResults(G2frame,msgs,pagelist,fileList) # show final summary
wx.CallLater(100,_GetPhase) # Restore the original saved project
def OnSubSearch(event):
'''Search for a lower symmetry structure consistent with the
current phase using the Bilbao SUBGROUPS web service
Based on GSASIIpwdGUI.OnRunSubs
'''
generalData = data['General']
Kx = [' ','0','1/2','-1/2','1/3','-1/3','2/3','1']
Ky = [' ','0','1/2','1/3','2/3','1']
Kz = [' ','0','1/2','3/2','1/3','2/3','1']
kvec = [['0','0','0'],[' ',' ',' '],[' ',' ',' ',' ']]
dlg = G2G.MultiDataDialog(G2frame,title='SUBGROUPS options',
prompts=[' k-vector 1', \
' Use whole star',' Filter by','preserve axes','max unique'],
values=kvec[0:1]+[False,'',True,100],
limits=[[Kx[1:],Ky[1:],Kz[1:]],[True,False],['',' Landau transition',' Only maximal subgroups',],
[True,False],[1,100]],
formats=[['choice','choice','choice'],'bool','choice',
'bool','%d',])
dlg.CenterOnParent()
if dlg.ShowModal() != wx.ID_OK: return
subcells = []
newVals = dlg.GetValues()
kvec = newVals[0]+7*[' ']
star = newVals[1]
filterby = newVals[2]
keepaxes = newVals[3]
maxequiv = newVals[4]
nkvec = kvec.index(' ')
if 'maximal' in filterby:
maximal = True
Landau = False
elif 'Landau' in filterby:
maximal = False
Landau = True
else:
maximal = False
Landau = False
if nkvec not in [0,3,6,9]:
wx.MessageBox('Error: check your propagation vector(s)',
caption='Bilbao SUBGROUPS setup error',style=wx.ICON_EXCLAMATION)
return
if nkvec in [6,9] and Landau:
wx.MessageBox('Error, multi k-vectors & Landau not compatible',
caption='Bilbao SUBGROUPS setup error',style=wx.ICON_EXCLAMATION)
return
dlg = wx.ProgressDialog('SUBGROUPS results','Getting SubGroups',11,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
if SUBGROUPS.RegisterProgressDialog(dlg):
dlg.Destroy()
return
wx.MessageBox(' For use of SUBGROUPS, please cite:\n\n'+
G2G.GetCite('Bilbao: k-SUBGROUPSMAG'),
caption='Bilbao SUBGROUPS',
style=wx.ICON_INFORMATION)
try:
SGData = generalData['SGData']
from . import SUBGROUPS as kSUB
SubGroups,baseList = kSUB.GetNonStdSubgroups(SGData,kvec[:9],star,Landau)
if SubGroups is None:
wx.MessageBox('Internet connection problem? Check console output.',
caption='Bilbao SUBGROUPS error',
style=wx.ICON_EXCLAMATION)
return
if not SubGroups:
if Landau:
wx.MessageBox('No results from SUBGROUPS, multi k-vectors & Landau not compatible',
caption='Bilbao SUBGROUPS error',style=wx.ICON_EXCLAMATION)
else:
wx.MessageBox('No results from SUBGROUPS, check your propagation vector(s)',
caption='Bilbao SUBGROUPS error',style=wx.ICON_EXCLAMATION)
return
# emulate indexing controls
controls = 16*[None]
controls[6:12] = generalData['Cell'][1:7] # cell
cx,ct,cs,cia = data['General']['AtomPtrs']
controls[15] = [atom[:cx+3] for atom in data['Atoms']]
import GSASII.GSASIIpwdGUI
for ir,result in enumerate(SubGroups):
dlg.Update(ir%10,newmsg=f'Processing {result[0]}')
dlg.Raise()
wx.GetApp().Yield()
Trans = np.array(eval(result[1][0]))
Uvec = np.array(eval(result[1][1]))
phase = G2lat.makeBilbaoPhase(result,Uvec,Trans)
phase['gid'] = result[2]
phase['altList'] = result[3]
phase['supList'] = eval(result[4])
RVT = None
if keepaxes:
RVT = G2lat.FindNonstandard(controls,phase)
if RVT is not None:
result,Uvec,Trans = RVT
phase.update(G2lat.makeBilbaoPhase(result,Uvec,Trans))
phase['Cell'] = G2lat.TransformCell(controls[6:12],Trans)
phase['maxequiv'] = maxequiv
phase['nAtoms'] = len(GSASII.GSASIIpwdGUI.TestAtoms(phase,controls[15],SGData,Uvec,Trans,maxequiv,maximal))
subcells.append(phase)
finally:
dlg.Destroy()
SUBGROUPS.RegisterProgressDialog()
data['SUBGROUPS'] = (subcells,baseList)
msg = f'''{len(subcells)} subgroup entries were generated. Use menu commands
"Select magnetic/subgroup phase" or "Make subgroup project file(s)"
to use these entries'''
G2G.G2MessageBox(G2frame,msg,'Sugbroups stored')
wx.CallAfter(UpdatePhaseData,G2frame,Item,data)
def OnTransform2Std(event):
'''Uses the Bilbao web site to transform a space group and coordinates
to a standard setting
'''
generalData = data['General']
cx,ct,cs,cia = generalData['AtomPtrs']
sgnum,sgsym,xmat,xoff = SUBGROUPS.GetStdSGset(generalData['SGData'])
if sgnum is None:
G2G.G2MessageBox(G2frame,
'Standard setting check failed. Check console output.',
'Bilbao error')
return
if xmat is None:
G2G.G2MessageBox(G2frame,"Unable to reach web site.",'No connection')
return
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'] = G2elem.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
'''
if 'SUBGROUPS' in data:
magData,baseList = data['SUBGROUPS']
else:
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)
# remove subgroup info on parent from new phase
if 'magPhases' in newPhase: del newPhase['magPhases']
if 'SUBGROUPS' in newPhase: del newPhase['SUBGROUPS']
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'] = G2elem.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
'''
if 'SUBGROUPS' in data:
subPhases,baseList = data['SUBGROUPS']
UnitCellsId = None
else:
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]
subPhases = UCdata[5]
subKeep = []
subIds = []
subchoices = []
ifMag = False
itemList = [phase.get('gid',ip+1) for ip,phase in enumerate(subPhases)]
phaseDict = dict(zip(itemList,subPhases))
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)
savedRestraints = None
if phsnam in Restraints:
Restraints[phsnam]['Bond']['Bonds'] = []
Restraints[phsnam]['Angle']['Angles'] = []
savedRestraints = Restraints[phsnam]
del Restraints[phsnam]
orgData = copy.deepcopy(data)
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'] = G2elem.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]
if savedRestraints: # restore 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']
if 'SUBGROUPS' in data: del data['SUBGROUPS']
if UnitCellsId:
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)
G2frame.GetStatusBar().SetStatusText('Structure changed: Do "Edit Atoms/Update draw atoms" to refresh structure drawing',1)
# 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)
G2frame.GetStatusBar().SetStatusText('Structure changed: Do "Edit Atoms/Update draw atoms" to refresh structure drawing',1)
# 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(G2frame,data)
wx.CallAfter(Paint)
else:
G2frame.GetStatusBar().SetStatusText('Use right mouse click to brng up Atom editing options',1)
Atoms.ClearSelection()
Atoms.SelectRow(r,True)
G2frame.GetStatusBar().SetStatusText('Structure changed: Do "Edit Atoms/Update draw atoms" to refresh structure drawing',1)
# 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)
mainSizer.Add(Atoms,1,wx.EXPAND)
Atoms.SetScrollRate(10,10) # allow grid to scroll
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']
topSizer = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
lbl= f"Atom parameters list for {generalData['Name']}"[:60]
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
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 = {}
# exclList will be 'fxu' for non spin RBs
for rbObj in resRBData+vecRBData:
exclList = ['FXU' for i in range(len(rbObj['Ids']))]
rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
Items = [G2G.wxID_ATOMSEDITINSERT,G2G.wxID_ATOMSEDITDELETE,
G2G.wxID_ATOMSMODIFY,G2G.wxID_ATOMSTRANSFORM,G2G.wxID_MAKEMOLECULE,
G2G.wxID_ATOMMOVE,G2G.wxID_ADDHATOM] # G2G.wxID_ATOMVIEWINSERT,
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_ATOMSVIEWADD,G2G.wxID_ATOMMOVE] # G2G.wxID_ATOMVIEWINSERT,
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)
Atoms.SetRowLabelSize(45)
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(G2frame,data)
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 pointerat
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(G2frame,data)
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(G2frame,data)
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(G2frame,data)
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(G2frame,data)
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(G2frame,data)
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(G2frame,data)
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(G2frame,data)
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(G2frame,data)
G2plt.PlotStructure(G2frame,data)
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 = f"Density of phase {data['General']['Name']!r} = {density:.3f} g/cc"
msg += '\n\nCell contents:'
for typ,num in data['General']['NoAtoms'].items():
msg += f'\n {typ}: {num}'
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 OnSaveDAHist(event):
Bonds = data.get('Bonds',{})
Angles = data.get('Angles',{})
if not len(Bonds) and not len(Angles):
print('No bond or angle histograms to save!')
return
generalData = data['General']
pName = generalData['Name']
fName = os.path.abspath(os.path.splitext(G2frame.GSASprojectfile)[0]+'_BAdist.csv')
fp = open(fName,'w')
fp.write('Phase name: %s,'%pName)
for Atypes in Bonds:
fp.write('\nBond distances for %s, \n'%Atypes)
for ib,bond in enumerate(Bonds[Atypes]):
fp.write('%7.4f,'%bond)
if not (ib+1)%10: fp.write('\n')
for Atypes in Angles:
fp.write('\nBond angles about %s, \n'%Atypes)
for ib,angle in enumerate(Angles[Atypes]):
fp.write('%7.2f,'%angle)
if not (ib+1)%10: fp.write('\n')
fp.close()
print(' %s written'%fName)
def OnClearDAHist(event):
data['Bonds'] = {}
data['Angles'] = {}
print('Bond & Angle histograms now empty')
def OnDistAngle(event,fp=None,hist=False):
'''Compute distances and angles in response to a menu command
or may be called by :func:`OnDistAnglePrt` or :func:`OnDistAngleHist`.
This calls :func:`GSASIIstrMain.PrintDistAngle` to compute
bond distances & angles (computed in
:func:`GSASIIstrMain.RetDistAngle`) and
then format the results in a convenient way or plot them
using G2plt.PlotBarGraph.
'''
cx,ct,cs,ci = G2mth.getAtomPtrs(data)
indx = getAtomSelections(Atoms,ct-1)
if not indx:
print ("select one or more rows of atoms")
G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
return
Oxyz = []
xyz = []
DisAglData = {}
DisAglCtls = {}
# add RB stuff to DisAglData
DisAglData['RBlist'] = [] # list of atom numbers used in the RB
for d in data['RBModels'].get('Residue',{}):
for rId in d['Ids']:
num = int(G2obj.LookupAtomId(ranId=rId,pId=data['pId']))
DisAglData['RBlist'].append(num)
DisAglData['rigidbodyDict'] = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies'))
_,DisAglData['Phases'] = G2frame.GetUsedHistogramsAndPhasesfromTree()
DisAglData['parmDict'] = G2IO.mkParmDictfromTree(G2frame)
# other setup prep
generalData = data['General']
DisAglData['OrigIndx'] = indx
if 'DisAglCtls' in generalData:
DisAglCtls = generalData['DisAglCtls']
# get atomic radii
dlg = G2G.DisAglDialog(G2frame,DisAglCtls,generalData)
if dlg.ShowModal() == wx.ID_OK:
DisAglCtls = dlg.GetData()
dlg.Destroy()
else:
dlg.Destroy()
return
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 = []
DisAglData['TargIndx'] = list(range(len(atomData)))
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:
Bonds = data['Bonds'] = data.get('Bonds',{})
Angles = data['Angles'] = data.get('Angles',{})
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)))
Bonds[Atypes] = bonds
angles = []
for Item in AngArray:
angles += [item[2][0] for item in AngArray[Item]]
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)))
Angles[Atypes] = 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')
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:
B2 = {}
atomData = data['Atoms']
PE = G2elemGUI.PickElement(G2frame,oneOnly=True)
if PE.ShowModal() == wx.ID_OK:
Atype2 = PE.Elem.strip()
AtomInfo2 = G2elem.GetAtomInfo(Atype2)
FF2 = G2elem.GetFFtable([Atype2])[Atype2]
for iso in AtomInfo2['Isotopes']:
B2[iso] = AtomInfo2['Isotopes'][iso]['SL'][0]
PE.Destroy()
SQ = 0.0
PE2 = G2G.SingleFloatDialog(G2frame,'form factor','Enter sinth/lam for atom frac split',SQ)
if PE2.ShowModal() == wx.ID_OK:
SQ = PE2.GetValue()
PE2.Destroy()
ff2 = G2elem.ScatFac(FF2,SQ**2)
print(' X-ray site fractions for sin(th)/lam = %.3f'%SQ)
for ind in indx:
Aname1 = atomData[ind][ct-1]
Atype1 = G2elem.FixValence(atomData[ind][ct])
if Atype1 == 'Q':
PE = G2elemGUI.PickElement(G2frame,oneOnly=False)
if PE.ShowModal() == wx.ID_OK:
Atype1 = PE.Elem.strip()
PE.Destroy()
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
FF1 = G2elem.GetFFtable([Atype1])[Atype1]
ff1 = G2elem.ScatFac(FF1,SQ**2)
if ff1 != ff2:
frac1 = (ff1*Afrac-ff2)/(ff1-ff2)
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))
B1 = AtomInfo1['Isotopes']['Nat. Abund.']['SL'][0]
for iso in B2:
if B1 != B2[iso]:
bfrac1 = (B1*Afrac-B2[iso])/(B1-B2[iso])
atype2 = Atype2
if 'nat' not in iso:
atype2 += '_%s'%iso
print(' neutron based site fractions %s = %.3f, %.3f/cell; %s = %.3f, %.3f/cell' \
%(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(G2frame,data)
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):
#from importlib import reload
#reload(G2cnstG)
#print(f'reloading {G2cnstG}')
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 OnReplacePhase(event):
'Called to replace the current phase with a new phase from a file'
reqrdr = G2frame.dataWindow.ReplaceMenuId.get(event.GetId())
rdlist = G2frame.OnImportGeneric(reqrdr,
G2frame.ImportPhaseReaderlist,'phase')
if len(rdlist) == 0: return
# rdlist is only expected to have one entry
rd = rdlist[0]
# Strict = True
# if 'rmc6f' in rd.readfilename:
# Strict = False
# idx = -1
phsnam = data['General']['Name']
# clear out stuff that in general should not be
# transferred from one phase to another
resId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Restraints')
Restraints = G2frame.GPXtree.GetItemPyData(resId)
# resId = G2gd.GetGPXtreeItemId(G2frame,resId,phsnam)
if phsnam in Restraints:
del Restraints[phsnam]
consId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
Constraints = G2frame.GPXtree.GetItemPyData(consId)
# TODO: would be cleaner to just delete constraints w/phase data['pId']
Constraints['Phase'] = []
if 'magPhases' in data: del data['magPhases']
data['MCSA'] = {'Models':
[{'Type': 'MD', 'Coef': [1.0, False, [0.8, 1.2]], 'axis': [0, 0, 1]}],
'Results': [], 'AtInfo': {}}
data['RMC'] = {'RMCProfile': {}, 'fullrmc': {}, 'PDFfit': {}}
data['ISODISTORT'] = {}
data['Deformations'] = {}
# copy over most of the data from the reader object
# but keep original name, pId & ranId
for key in ['General', 'Atoms', 'Drawing', 'Histograms', 'Pawley ref', 'RBModels']:
data[key] = rd.Phase[key]
# TODO: want to keep Histograms rather than wipe it out?
# If so, need to think about Dij & microstrain:
# UseList = newPhase['Histograms']
# for hist in UseList:
# # 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,]]
# restore existing phase name
newname = rd.Phase['General']['Name']
data['General']['Name'] = phsnam
# rename phase to new name from file
renamePhaseName(G2frame,data,G2frame.PickId, data['General'],newname)
# force a reload of current tree item
G2frame.PickIdText = []
wx.CallAfter(G2gd.SelectDataTreeItem,G2frame,G2frame.PickId)
def OnReImport(event):
'Called to replace the coordinates with "original" values from a file'
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 OnLoadDysnomia(event):
# print('Load MEM - might not be implemented')
# def OnSaveDysnomia(event):
# print('Save MEM - might not be implemented')
def OnRunDysnomia(event):
if sys.platform == "win32":
binimage = 'Dysnomia64.exe'
else:
binimage = 'Dysnomia'
is_exe = lambda fpath: os.path.isfile(fpath) and os.access(fpath, os.X_OK)
#path2GSAS2 = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
pathlist = (GSASIIpath.path2GSAS2,
os.path.expanduser('~'),
os.path.expanduser(os.path.join('~','.GSASII')))
locations = []
for path in pathlist:
DYSNOMIA = os.path.join(path,'Dysnomia',binimage)
locations.append(DYSNOMIA)
if not os.path.exists(DYSNOMIA): continue
if is_exe(DYSNOMIA):
break
else:
newline = '\n\t'
print(f"File {binimage!r} not found."
f"\nThe following locations were checked:\n\t{newline.join(locations)}")
msg = f'''Dysnomia is not installed. Please download it from
https://jp-minerals.org/dysnomia/en/ and install the
downloaded directory (which includes file {binimage!r})
at one of the following locations:
\t{newline.join(pathlist)}'''
G2G.ShowWebPage("https://jp-minerals.org/dysnomia/en/",G2frame)
G2G.ShowScrolledInfo(G2frame,msg,header='Install Dysnomia',
width=350,height=150)
return
DysData = data['Dysnomia']
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
treeId = G2gd.GetGPXtreeItemId(G2frame,pId,'Reflection Lists')
if treeId:
reflSets = G2frame.GPXtree.GetItemPyData(treeId)
reflData = reflSets[generalData['Name']]['RefList']
else:
wx.MessageBox('You must have PWDR reflections before running Dysnomia','Dysnomia Error',
style=wx.ICON_ERROR)
return
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
wx.MessageBox(' For use of Dysnomia, please cite:\n\n'+G2G.GetCite('Dysnomia'),
caption='Dysnomia (MEM)',style=wx.ICON_INFORMATION)
print('Run '+DYSNOMIA)
subp.call([DYSNOMIA,prfName])
DysData['DenStart'] = 'uniform'
DysData['prior'] = 'uniform'
wx.CallAfter(G2phsG2.UpdateDysnomia,G2frame,data)
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 OnSetupRMC(event):
written = lambda fil: print(f' {fil} written')
generalData = data['General']
if not G2frame.GSASprojectfile: #force a project save
G2frame.OnFileSaveas(event)
dName = G2frame.LastGPXdir
os.chdir(dName)
print(f'Writing input files in directory {dName!r}')
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
written(G2pwd.MakeInst(PWDdata,pName,Size,Mustrain,RMCPdict['UseSampBrd']))
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:
written(backfile)
written(G2pwd.MakeBragg(PWDdata,pName,data))
if RMCPdict['ReStart'][0]:
if os.path.isfile(pName+'.his6f'):
os.remove(pName+'.his6f')
RMC6f,reset = G2pwd.MakeRMC6f(PWDdata,pName,data,RMCPdict)
written(RMC6f)
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
written(fname)
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(G2rmcG.UpdateRMC,G2frame,data)
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:
written(fname)
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
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:\n\n'+
G2G.GetCite('PDFfit2'),
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)
G2rmcG.UpdateRMC(G2frame,data)
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:
shutil.rmtree(rmcname)
else:
return
G2G.G2MessageBox(G2frame,'For use of fullrmc, please cite:\n\n'+
G2G.GetCite('fullrmc')+
'\n\nNote: 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
G2rmcG.UpdateRMC(G2frame,data)
def RunRMCProfile(event):
generalData = data['General']
pName = generalData['Name'].replace(' ','_')
rmcfile = G2pwd.findrmcprofile()
wx.MessageBox(
' For use of RMCProfile, please cite:\n\n'+
G2G.GetCite("RMCProfile"),
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(' ','_')
if rmcfile is None:
wx.MessageBox('''RMCProfile is not correctly installed for use in GSAS-II
This software must be downloaded separately (from
https://rmcprofile.ornl.gov/download). Install the rmcprofile or
rmcprofile.exe file in a location where GSAS-II can find it
(see config variable rmcprofile_exec in preferences.)''',
caption='RMCProfile',style=wx.ICON_INFORMATION)
return
if sys.platform == "darwin":
script_file = os.path.join(os.getcwd(), "runrmc.sh")
with open(script_file, 'w') as f:
f.write("#!/bin/bash\n")
f.write(f'cd "{os.getcwd()}"\n')
f.write(f'export PATH="{os.path.dirname(rmcfile)}":$PATH\n')
f.write(f'"{rmcfile}" "{pName}"\n')
os.system("chmod +x runrmc.sh")
ascript_file = os.path.join(os.getcwd(), "runrmc.script")
with open(ascript_file, 'w') as f:
f.write('tell application "Terminal"\n')
f.write(' if not (exists window 1) then\n')
f.write(f' do script "bash {script_file}"\n')
f.write(' else\n')
f.write(f' do script "bash {script_file}" in window 1\n')
f.write(' end if\n')
f.write(' activate\n')
f.write("end tell\n")
subp.Popen(['osascript', ascript_file])
elif sys.platform.startswith("linux"):
script_file = os.path.join(os.getcwd(), "runrmc.sh")
with open(script_file, 'w') as frmc:
frmc.write("#!/bin/bash\n")
frmc.write(f"export LD_LIBRARY_PATH={Path(rmcfile).parent.parent}/exe/libs\n")
frmc.write(f"export LIBRARY_PATH={Path(rmcfile).parent.parent}/exe/libs\n")
frmc.write(f"export PATH=$PATH:{Path(rmcfile).parent.parent}/exe\n")
frmc.write(f'"rmcprofile" "{pName}"\n')
subp.Popen(['bash', script_file])
else:
script_file = os.path.join(os.getcwd(), "runrmc.bat")
with open(script_file,'w') as batch:
batch.write('Title RMCProfile\n') # BHT: is Title a Windows command?
batch.write(f'"{rmcfile}" "{pName}"\n')
batch.write('pause\n')
batch.close()
subp.Popen(script_file,creationflags=subp.CREATE_NEW_CONSOLE)
# Proc.wait() #for it to finish before continuing on
G2rmcG.UpdateRMC(G2frame,data)
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(' ','_')
if sys.platform == "darwin":
wildcard = 'RMCProfile result csv files|' + pName + '*.csv' + '|All files|*.*'
else:
wildcard = 'RMCProfile result csv files|' + pName + '*.csv'
dlg = wx.FileDialog(G2frame, "Choose any RMCProfile csv results file for "+pName+":",
defaultDir=G2frame.LastGPXdir,style=wx.FD_CHANGE_DIR,wildcard=wildcard)
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:
fileName = os.path.join(path,pName+item)
if os.path.exists(fileName):
OutFile = open(fileName,'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 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(G2phsG2.UpdateISODISTORT,G2frame,data)
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 ################################################################################
# Utility routines her
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(G2phsG2.UpdateLayerData,G2frame,data)
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(G2phsG2.UpdateLayerData,G2frame,data)
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:\n\n'+
G2G.GetCite('DIFFaX'),
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 = [item for item in data['Histograms'] if 'PWDR' in item]
if not UseList:
wx.MessageBox('No PWDR data for this phase to simulate',caption='Data error',style=wx.ICON_EXCLAMATION)
return
elif len(UseList) == 1: # don't ask questions when we know the answer!
HistName = UseList[0]
else:
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)
G2pwpl.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(G2phsG2.UpdateLayerData,G2frame,data)
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(G2phsG2.UpdateLayerData,G2frame,data)
G2pwpl.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(G2phsG2.UpdateLayerData,G2frame,data)
#### Wave Data page ################################################################################
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:
G2elem.AddWave2atm(atom)
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()
G2phsG2.UpdateWavesData(G2frame,data)
#### 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]],
'Line':[[0,0,1],False,False,1.0,[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
try: # patch of sorts; this had been set to a string; needs to be an int between 0 & 3
int(drawingData['showSlice'])
except:
drawingData['showSlice'] = 0
if 'sliceSize' not in drawingData:
drawingData['sliceSize'] = 5.0
if 'contourColor' not in drawingData:
drawingData['contourColor'] = 'RdYlGn'
drawingData['Plane'] = drawingData.get('Plane',[[0,0,1.],False,False,0.0,[255,255,0]])
drawingData['Line'] = drawingData.get('Line',[[0,0,1.],False,False,1.0,[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(G2frame.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(G2frame.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(G2frame,data,atomStyle=''):
# save pointers to window and routines
G2frame.drawAtoms.UpdateDrawAtoms = UpdateDrawAtoms
G2frame.drawAtoms.OnReloadDrawAtoms = OnReloadDrawAtoms
drawAtoms = G2frame.drawAtoms
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':
DrawAtomStyle(event)
elif drawAtoms.GetColLabelValue(c) == 'Label':
DrawAtomLabel(event)
elif drawAtoms.GetColLabelValue(c) == 'Color':
DrawAtomColor(event)
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(G2frame,data)
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
topSizer = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
lbl= f"Draw Atom list for {data['General']['Name']!r}"[:60]
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
G2frame.GetStatusBar().SetStatusText('',1)
oldSizer = G2frame.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 = DrawStyleChoice
# 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 = None
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)
drawAtoms.SetRowLabelSize(45)
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,AddBox,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)
mainSizer.Add(drawAtoms,1,wx.EXPAND)
drawAtoms.SetScrollRate(10,10) # allow grid to scroll
SetPhaseWindow(G2frame.drawAtomsList,mainSizer)
FindBondsDraw(data)
drawAtoms.ClearSelection()
G2frame.drawAtoms = drawAtoms
def DrawAtomStyle(event):
cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True)
indx = getAtomSelections(G2frame.drawAtoms,ct-1)
if not indx: return
generalData = data['General']
atomData = data['Drawing']['Atoms']
styleChoice = DrawStyleChoice
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
G2frame.drawAtoms.SetCellValue(r,cs,parms)
dlg.Destroy()
FindBondsDraw(data)
G2frame.drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
def DrawAtomLabel(event):
cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True)
indx = getAtomSelections(G2frame.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
G2frame.drawAtoms.SetCellValue(r,cs+1,parms)
dlg.Destroy()
G2frame.drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
def DrawAtomColor(event):
cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True)
indx = getAtomSelections(G2frame.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)
G2frame.drawAtoms.SetAttr(r,cs+2,attr)
data['Drawing']['Atoms'][r][cs+2] = color
dlg.Destroy()
G2frame.drawAtoms.ClearSelection()
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(G2frame,data)
G2frame.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(G2frame.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):
drawAtoms = G2frame.drawAtoms
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(G2frame,data)
drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
def AddBox(event):
print('Box of enclosure, TBD')
def AddSphere(event=None,selection=None,radius=None,targets=None):
drawAtoms = G2frame.drawAtoms
cx,ct,cs,ci = G2mth.getAtomPtrs(data,draw=True)
if selection:
indx = selection
else:
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()
if radius is None or targets is None:
dlg = SphereEnclosure(G2frame,data['General'],data['Drawing'],indx)
try:
if dlg.ShowModal() == wx.ID_OK:
centers,radius,targets = dlg.GetSelection()
else:
return
finally:
dlg.Destroy()
else:
centers = []
for Id in indx:
if Id < len(data['Drawing']['Atoms']):
atom = data['Drawing']['Atoms'][Id]
centers.append(atom[cx:cx+3])
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()
UpdateDrawAtoms(G2frame,data)
G2frame.drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
def TransformSymEquiv(event):
drawAtoms = G2frame.drawAtoms
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(G2frame,data)
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.
'''
drawAtoms = G2frame.drawAtoms
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(G2frame,data)
# G2plt.PlotStructure(G2frame,data)
pgbar.Destroy()
UpdateDrawAtoms(G2frame,data)
drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
def FillCoordSphere(event=None,selection=None):
if selection:
indx = selection
else:
indx = getAtomSelections(G2frame.drawAtoms)
if not indx: return
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
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(G2frame,data)
G2frame.drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
else:
G2G.G2MessageBox(G2frame,'Select atoms first')
def FillCoordSphereNew(event):
time0 = time.time()
drawAtoms = G2frame.drawAtoms
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(G2frame,data)
drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
def FillUnitCell(event,selectAll=None):
drawAtoms = G2frame.drawAtoms
if selectAll is not None:
indx = list(range(drawAtoms.NumberRows))
else:
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(G2frame,data)
drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
def DrawAtomsDelete(event):
indx = getAtomSelections(G2frame.drawAtoms)
if not indx: return
indx.sort()
atomData = data['Drawing']['Atoms']
indx.reverse()
for ind in indx:
del atomData[ind]
UpdateDrawAtoms(G2frame,data)
G2frame.drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
event.StopPropagation()
def SelDrawList(event):
'select atoms using a filtered listbox'
drawAtoms = G2frame.drawAtoms
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(G2frame,data)
G2frame.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(G2frame,data)
G2frame.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):
drawAtoms = G2frame.drawAtoms
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
drawAtoms = G2frame.drawAtoms
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
drawAtoms = G2frame.drawAtoms
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):
def onColor(event):
'respond to color button press'
c = event.GetEventObject().GetValue() # RGBA
voidPar['color'] = [int(i*c.alpha/255) for i in (
c.red,c.green,c.blue)] # RGB w/black background
event.GetEventObject().SetValue(voidPar['color'])
import wx.lib.colourselect as csel
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,
'drawsize':0.05,'brightness':3.0, 'color':[50,50,255]}
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))
G2G.HorizontalLine(mainSizer,voidDlg)
mainSizer.Add(wx.StaticText(voidDlg,wx.ID_ANY,
'Void map visualization parameters'))
mainSizer.Add(G2G.G2SliderWidget(voidDlg,voidPar,'drawsize',
'Brightness: ',0.001,1.0,500))
mainSizer.Add(G2G.G2SliderWidget(voidDlg,voidPar,'brightness',
'Brightness: ',0.1,5.0,50))
hSizer = wx.BoxSizer(wx.HORIZONTAL)
hSizer.Add(wx.StaticText(voidDlg,wx.ID_ANY,'Void map color:'))
cbut = csel.ColourSelect(voidDlg, wx.ID_ANY, '',
tuple(voidPar['color']),
size = wx.DefaultSize)
cbut.Bind(csel.EVT_COLOURSELECT, onColor)
hSizer.Add(cbut)
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'])
for key in ('drawsize','brightness','color'):
drawingData['void'+key] = voidPar[key]
drawingData['showVoids'] = True
G2plt.PlotStructure(G2frame,data)
def RandomizedAction(event):
'''perform a selected action on a random sequence from a selected
list of atoms. After each selection, one chooses if the
action should be performed on the selected atom
'''
ranDrwDict['opt'] = 1
ranDrwDict['optList'] = ['Delete selection',
'Change color of selection',
'Atom drawing style for selection',
'Add sphere of atoms around selection',
'Add coordination-sphere around selection']
dlg = G2G.G2SingleChoiceDialog(G2frame,'Select option from list',
'Select option',ranDrwDict['optList'])
dlg.CenterOnParent()
try:
if dlg.ShowModal() == wx.ID_OK:
ranDrwDict['opt'] = dlg.GetSelection()
ranDrwDict['optList'][dlg.GetSelection()]
else:
return
finally:
dlg.Destroy()
if ranDrwDict['opt'] == 1:
colors = wx.ColourData()
colors.SetChooseFull(True)
try:
dlg = wx.ColourDialog(G2frame.GetParent(),colors)
if dlg.ShowModal() == wx.ID_OK:
ranDrwDict['color'] = dlg.GetColourData().GetColour()[:3]
else:
return
finally:
dlg.Destroy()
elif ranDrwDict['opt'] == 2:
styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
if data['General']['Type'] == 'macromolecular':
styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
'backbone','ribbons','schematic']
try:
dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',
styleChoice)
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
ranDrwDict['style'] = styleChoice[sel]
else:
return
finally:
dlg.Destroy()
elif ranDrwDict['opt'] == 3:
dlg = SphereEnclosure(G2frame,data['General'],data['Drawing'],None)
try:
if dlg.ShowModal() == wx.ID_OK:
centers,ranDrwDict['radius'],ranDrwDict['targets'] = dlg.GetSelection()
ranDrwDict['2call'] = AddSphere
else:
return
finally:
dlg.Destroy()
elif ranDrwDict['opt'] == 4:
ranDrwDict['2call'] = FillCoordSphere
indx = getAtomSelections(G2frame.drawAtoms)
if not indx: return
ranDrwDict['atomList'] = list(indx)
ran.shuffle(ranDrwDict['atomList'])
i = ranDrwDict['atomList'][0]
cx,ct = data['Drawing']['atomPtrs'][:2]
data['Drawing']['viewPoint'][0] = data['Drawing']['Atoms'][i][cx:cx+3]
G2frame.drawAtoms.SelectRow(i)
G2plt.PlotStructure(G2frame,data)
msg = f"Atom #{i} selected ({data['Drawing']['Atoms'][i][ct-1]})"
print(msg)
ranDrwDict['delAtomsList'] = []
ranDrwDict['msgWin'] = wx.Frame(G2frame, wx.ID_ANY, size=(300, 300),
style=wx.DEFAULT_FRAME_STYLE|wx.FRAME_FLOAT_ON_PARENT|
wx.STAY_ON_TOP)
ranDrwDict['msgWin'].SetTitle("Random action messages")
siz = wx.BoxSizer(wx.VERTICAL)
ranDrwDict['msgWin'].text1 = wx.StaticText(ranDrwDict['msgWin'], wx.ID_ANY,
f"For random Draw Atoms action, in plot window press: \n\t'Y' to {ranDrwDict['optList'][ranDrwDict['opt']]}\n\t'N' to advance to the next atom\n\t'Q' to end\n"
)
siz.Add(ranDrwDict['msgWin'].text1)
ranDrwDict['msgWin'].text2 = wx.StaticText(ranDrwDict['msgWin'], wx.ID_ANY, msg)
siz.Add(ranDrwDict['msgWin'].text2)
ranDrwDict['msgWin'].SetSizer(siz)
siz.Fit(ranDrwDict['msgWin'])
ranDrwDict['msgWin'].CentreOnParent()
ranDrwDict['msgWin'].Show()
UpdateDrawAtoms(G2frame,data)
# #### Draw Options page ################################################################################
def UpdateDrawOptions(G2frame,data):
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.ChangeValue(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 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)
return showSizer
def MapSizer():
def OnShowMap(event):
drawingData['showMap'] = showMap.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 OnSliceSize(invalid,value,tc):
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)
mapSizer = wx.BoxSizer(wx.VERTICAL)
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)
line3Sizer.Add(wx.StaticText(drawOptions,label=' Slice size 2X(2-20)A: '),0,WACV)
line3Sizer.Add(G2G.ValidatedTxtCtrl(drawOptions,drawingData,'sliceSize',nDig=(10,2),xmin=2.0,xmax=20.0,OnLeave=OnSliceSize),0,WACV)
mapSizer.Add(line3Sizer)
line4Sizer = wx.BoxSizer(wx.HORIZONTAL)
contourMaxTxt = wx.StaticText(drawOptions,label=' Rho max: '+'%.2f'%(drawingData['contourMax']*generalData['Map']['rhoMax']))
line4Sizer.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)
line4Sizer.Add(contourMax,1,wx.EXPAND|wx.RIGHT)
mapSizer.Add(line4Sizer)
valSize = (50,20)
showMap = wx.CheckBox(drawOptions,label=' Show 3D 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',
'Radius of displayed map: ',0.1,10.,5.,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 LineSizer():
def OnLine(event):
event.Skip()
vals = line.GetValue().split()
try:
xyz = [float(vals[i]) for i in range(3)]
if not any(xyz): #can't be all zeros!
raise ValueError
except (ValueError,IndexError):
xyz = drawingData['Line'][0]
drawingData['Line'][0] = xyz
line.SetValue('%5.3f %5.3f %5.3f'%(xyz[0],xyz[1],xyz[2]))
G2plt.PlotStructure(G2frame,data)
def OnShowLine(event):
drawingData['Line'][1] = showLine.GetValue()
G2plt.PlotStructure(G2frame,data)
def OnShowBoth(event):
drawingData['Line'][2] = showBoth.GetValue()
G2plt.PlotStructure(G2frame,data)
def OnLength(invalid,value,tc):
G2plt.PlotStructure(G2frame,data)
lineSizer = wx.BoxSizer(wx.VERTICAL)
lineSizer1 = wx.BoxSizer(wx.HORIZONTAL)
lineSizer1.Add(wx.StaticText(drawOptions,label=' Line from view point: '),0,WACV)
X = drawingData['Line'][0]
line = wx.TextCtrl(drawOptions,value='%5.3f %5.3f %5.3f'%(X[0],X[1],X[2]),
style=wx.TE_PROCESS_ENTER,size=(140,20))
line.Bind(wx.EVT_TEXT_ENTER,OnLine)
line.Bind(wx.EVT_KILL_FOCUS,OnLine)
lineSizer1.Add(line,0,WACV)
showLine = wx.CheckBox(drawOptions,label=' Show line?')
showLine.SetValue(drawingData['Line'][1])
showLine.Bind(wx.EVT_CHECKBOX, OnShowLine)
lineSizer1.Add(showLine,0,WACV)
showBoth = wx.CheckBox(drawOptions,label=' Extend negative?')
showBoth.SetValue(drawingData['Line'][2])
showBoth.Bind(wx.EVT_CHECKBOX, OnShowBoth)
lineSizer1.Add(showBoth,0,WACV)
lineSizer2 = wx.BoxSizer(wx.HORIZONTAL)
lineSizer2.Add(wx.StaticText(drawOptions,label=' Length multiplier: '),0,WACV)
length = G2G.ValidatedTxtCtrl(drawOptions,drawingData['Line'],3,nDig=(10,2),OnLeave=OnLength)
lineSizer2.Add(length,0,WACV)
lineSizer2.Add(wx.StaticText(drawOptions,-1,' Line color: '),0,WACV)
lineColor = G2G.setColorButton(drawOptions,drawingData['Line'], 4,
G2plt.PlotStructure,[G2frame,data])
lineSizer2.Add(lineColor,0,WACV)
lineSizer.Add(lineSizer1)
lineSizer.Add(lineSizer2)
return lineSizer
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),
typeHint=float,OnLeave=onLeave))
mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,"\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),
typeHint=float,OnLeave=onLeave))
mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,"\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),
typeHint=float,OnLeave=onLeave))
mapSizer.Add(wx.StaticText(drawOptions,wx.ID_ANY,"\u212B"),0,WACV)
return mapSizer
# UpdateDrawOptions exectable code starts here
drawOptions = G2frame.drawOptions
topSizer = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
lbl= f"Drawing controls for phase {data['General']['Name']!r}"
if len(lbl) > 60: lbl = lbl[:60] + '...'
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
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)
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,)
mainSizer.Add(LineSizer(),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()
G2phsG2.UpdateDeformation(G2frame,data,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 = []
sytsyms = []
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])
sytsyms.append(atom[cs])
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:
fxchoice = []
orbs = atmdata.OrbFF[types[indx]]
data['Deformations'][Ids[indx]] = []
newj0 = True
newjn = True
radial = ''
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
if 'Bessel' not in fxchoice:
fxchoice.append('Bessel')
radial = 'Bessel'
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(sytsyms[indx],'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])
elif 'Sl ' in orb:
if 'Slater' not in fxchoice:
fxchoice.append('Slater')
if not radial:
radial = 'Slater'
if 'Sl val' in orb: #valence; no harmonics
data['Deformations'][Ids[indx]].append([orb,{'Ne':[float(orbs[orb]['Ne']),False],'kappa':[1.0,False]}])
break
# else: #p, d or f
# orbDict = {}
# Order = 'spdf'.index(orb[-1])
# cofNames,cofSgns = G2lat.GenRBCoeff(sytsyms[indx],'1',Order) #sytsym, RBsym = '1'
# 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)
# orbDict.update({'Ne':[float(orbs[orb]['Ne']),False]})
# data['Deformations'][Ids[indx]].append([orb,orbDict])
data['Deformations'][-Ids[indx]] = {'U':'X','V':'Y','UVmat':np.eye(3),'PtGrp':'1',
'MUV':"A: X'=U, Y'=(UxV)xU & Z'=UxV",'Radial':radial,'fxchoice':fxchoice}
dlg.Destroy()
if not len(indxes):
return
G2frame.drawAtoms.ClearSelection()
G2frame.drawAtoms.SelectRow(indx,True)
G2plt.PlotStructure(G2frame,data)
G2phsG2.UpdateDeformation(G2frame,data,None)
event.StopPropagation()
#### DData routines - GUI stuff in GSASIIddataGUI.py. Used for Phase/data "Edit Phase" menu
def OnHklfAdd(event):
'''Called to link a Single Xtal (HKLF) dataset to the current phase.
Most commonly, the histogram and phase are linked when the latter
item is read in (routines OnImportPhase or OnImportSfact in
func:`GSASIIdataGUI.GSASIImain`, but one can defer this or change
the linking later using this routine.
Note that the capability here is duplicated in routine OnHklfAdd
inside :func:`GSASIIddataGUI.MakeHistPhaseWin`.
'''
result = CheckAddHKLF(G2frame,data)
if result is None: return
wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
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)
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','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,'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,'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','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,'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:
pth = G2G.GetImportPath(G2frame)
dlg = G2G.gpxFileSelector(parent=G2frame,startdir=pth)
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','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,
'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],
'Flack':[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'
cia = data['General']['AtomPtrs'][3]
for i,Id in enumerate(RBObj['Ids']):
data['Atoms'][AtLookUp[Id]][cia] = Ttype
resId,vecId,spnId = None,None,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]
data['Drawing']['Atoms'] = []
UpdateDrawAtoms(G2frame,data)
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']
#patch - remove 'None' as option
if model[0] == 'None':
model[0] = 'Uiso'
model[1][0] = 0.01
#end patch
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,rbId):
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(G2frame,data)
G2plt.PlotStructure(G2frame,data)
def ApplyAV(A,V):
Q = G2mth.AVdeg2Q(A,V)
if not any(Q):
raise ValueError
RBObj['Orient'][0] = Q
if rbType != 'Spin':
newXYZ,Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)
Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
maxFrac = 0.0
for i,Id in enumerate(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]
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]
data['Atoms'][AtLookUp[Id]][cx+3] = maxFrac
data['Atoms'] = G2lat.RBsymCheck(data['Atoms'],ct,cx,cs,AtLookUp,Amat,RBObj['Ids'],SGData)
def OnAng(event):
move = Ang.GetValue()*2.0
Ang.SetValue(0)
A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
A += move
Indx['Ang'].ChangeValue(A)
try:
ApplyAV(A,V)
data['Drawing']['Atoms'] = []
UpdateDrawAtoms(G2frame,data)
G2plt.PlotStructure(G2frame,data)
except ValueError:
pass
def OnOrien(*args, **kwargs):
'''Called when the orientation info is changed (vector
or azimuth). When called after a move of RB with alt key pressed,
an optional keyword arg is provided with the mode to draw atoms
(lines, ball & sticks,...)
'''
orient = [float(Indx['Orien'][i].GetValue()) for i in range(4)]
A = orient[0]
V = np.inner(Amat,orient[1:]) # normalized in AVdeg2Q
try:
ApplyAV(A,V)
data['Drawing']['Atoms'] = []
if 'mode' in kwargs:
UpdateDrawAtoms(G2frame,data,kwargs['mode'])
else:
UpdateDrawAtoms(G2frame,data)
G2plt.PlotStructure(G2frame,data)
except ValueError:
pass
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
A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
ApplyAV(A,V)
data['Drawing']['Atoms'] = []
UpdateDrawAtoms(G2frame,data)
G2plt.PlotStructure(G2frame,data)
SGData = data['General']['SGData']
rbSizer = wx.BoxSizer(wx.VERTICAL)
topSizer = wx.FlexGridSizer(0,7,5,5)
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))
Xsizers = []
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)
Xsizers.append(origX)
G2frame.testRBObjSizers.update({'Xsizers':Xsizers})
Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
Ocheck.SetValue(RBObj['Orig'][1])
topSizer.Add(Ocheck,0,WACV)
topSizer.Add((-1,-1))
Name = 'Origin'
G2frame.testRBObjSizers['OnOrien'] = OnOrien
G2frame.testRBObjSizers['FillUnitCell'] = FillUnitCell
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.
OrientVecSiz = []
for ix,x in enumerate(Orien):
if not ix: #add spinner to angle
Ang = wx.SpinButton(RigidBodies,style=wx.SP_VERTICAL,size=(20,24))
Ang.SetValue(0)
Ang.SetRange(-1,1)
Ang.Bind(wx.EVT_SPIN, OnAng)
OrientVecSiz.append(Ang)
topSizer.Add(Ang,0,WACV)
orien = G2G.ValidatedTxtCtrl(RigidBodies,Orien,ix,nDig=(8,dp),
typeHint=float,OnLeave=OnOrien,xmin=xmin,xmax=xmax,size=(70,-1))
if not ix:
Indx['Ang'] = orien
OrientVecSiz.append(orien)
dp, xmin,xmax = 4,-1.,1.
Indx['Orien'][ix] = orien
topSizer.Add(orien,0,WACV)
G2frame.testRBObjSizers.update({'OrientVecSiz':OrientVecSiz})
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)
choices = [' x ',' y ',' z ','x+y','x+y+z']
RBObj['symAxis'] = RBObj.get('symAxis',[0,0,1]) #set default as 'z'
try:
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'])]
except KeyError:
symax = ' z '
if rbType == 'Spin':
symRadioSet = wx.RadioBox(RigidBodies,choices=choices,label='RB polar axis is aligned along:')
symRadioSet.SetStringSelection(symax)
symRadioSet.Bind(wx.EVT_RADIOBOX, OnSymRadioSet)
Indx[symRadioSet.GetId()] = rbId
rbSizer.Add(symRadioSet)
else:
rbSizer.Add(wx.StaticText(RigidBodies,label='Rigid body symmetry axis is %s'%symax))
return rbSizer
def SpnrbSizer(RBObj,spnIndx):
'''Displays details for selected spinning rigid body'''
def OnShowAx(event):
RBObj['showAxes'] = not RBObj['showAxes']
G2frame.selectRB['showAxes'] = RBObj['showAxes']
G2plt.PlotStructure(G2frame,data)
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 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']:
RBObj[name].append(rbData[name])
RBObj['Radius'].append([1.0,False])
RBObj['hide'].append(False)
RBData['Spin'][rbIds[selection]]['useCount'] += 1
G2plt.PlotStructure(G2frame,data)
wx.CallAfter(FillRigidBodyGrid,True,spnId=rbId)
def OnSymSel(event):
Obj = event.GetEventObject()
iSh = Indx[Obj.GetId()]
RBObj['RBsym'][iSh] = Obj.GetValue()
RBObj['SHC'][iSh] = SetSHCoef(iSh,RBObj['nSH'][iSh])
rbId = RBObj['RBId']
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 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 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: ' \
%(iSh,RBObj['RBname'][iSh],RBObj['atType'][iSh])),0,WACV)
simsel = wx.ComboBox(RigidBodies,choices=symchoice,value=RBObj['RBsym'][iSh],
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[simsel.GetId()] = iSh
simsel.Bind(wx.EVT_COMBOBOX,OnSymSel)
subLine.Add(simsel,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]) > 24:
shSizer.Add(wx.StaticText(RigidBodies,
label=' WARNING: More than 24 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,xmin=-1.0,xmax=1.0))
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)
def OnAtColor(event):
RBObj['useAtColor'] = not RBObj['useAtColor']
G2plt.PlotStructure(G2frame,data)
def OnFadeShell(event):
RBObj['fadeSh'] = not RBObj['fadeSh']
G2plt.PlotStructure(G2frame,data)
def OnSliceShell(event):
RBObj['sliceSh'] = not RBObj['sliceSh']
G2plt.PlotStructure(G2frame,data)
symchoice = ['53m','m3m','-43m','6/mmm','-6m2','-3m','3m','32','-3','3','4/mmm','-42m',
'mmm','2/m','2','m','-1','1']
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)
G2G.HorizontalLine(sprbSizer,RigidBodies)
topLine = wx.BoxSizer(wx.HORIZONTAL)
secLine = wx.BoxSizer(wx.HORIZONTAL)
plotLine = 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)
simsel = wx.ComboBox(RigidBodies,choices=symchoice,value=RBObj['RBsym'][0],
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[simsel.GetId()] = 0
simsel.Bind(wx.EVT_COMBOBOX,OnSymSel)
topLine.Add(simsel,0,WACV)
showAx = wx.CheckBox(RigidBodies,label='Show RB axes on plot?')
showAx.SetValue(RBObj['showAxes'])
showAx.Bind(wx.EVT_CHECKBOX,OnShowAx)
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)
RBObj['noNeg'] = RBObj.get('noNeg',[False,0.01])
addShell = wx.Button(RigidBodies,wx.ID_ANY,'Add shell',style=wx.BU_EXACTFIT)
addShell.Bind(wx.EVT_BUTTON,OnAddShell)
Indx[addShell.GetId()] = rbId
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(wx.StaticText(RigidBodies,label='Spinning RB orientation parameters for %s:'%RBObj['RBname'][0]))
sprbSizer.Add(LocationSizer(RBObj,'Spin',rbId))
RBObj['useAtColor'] = RBObj.get('useAtColor',True)
atColor = wx.CheckBox(RigidBodies,label='Use atom color?')
atColor.SetValue(RBObj['useAtColor'])
atColor.Bind(wx.EVT_CHECKBOX,OnAtColor)
RBObj['fadeSh'] = RBObj.get('fadeSh',True)
fadeShell = wx.CheckBox(RigidBodies,label='Fade shells?')
fadeShell.SetValue(RBObj['fadeSh'])
fadeShell.Bind(wx.EVT_CHECKBOX,OnFadeShell)
RBObj['sliceSh'] = RBObj.get('sliceSh',False)
sliceShell = wx.CheckBox(RigidBodies,label='Slice shells?')
sliceShell.SetValue(RBObj['sliceSh'])
sliceShell.Bind(wx.EVT_CHECKBOX,OnSliceShell)
plotLine.Add(atColor,0,WACV)
plotLine.Add(showAx,0,WACV)
plotLine.Add(fadeShell,0,WACV)
plotLine.Add(sliceShell,0,WACV)
plotLine.Add(addShell,0,WACV)
sprbSizer.Add(plotLine)
G2G.HorizontalLine(sprbSizer,RigidBodies)
sprbSizer.Add(topLine)
sprbSizer.Add(secLine)
sprbSizer.Add(SHsizer())
return sprbSizer
def ResrbSizer(RBObj,resIndx):
'''Displays details for selected residue rigid body'''
def OnShowAx(event):
RBObj['showAxes'] = not RBObj['showAxes']
G2frame.selectRB['showAxes'] = RBObj['showAxes']
G2plt.PlotStructure(G2frame,data)
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(G2frame,data,atomStyle)
G2frame.drawAtoms.ClearSelection()
G2plt.PlotStructure(G2frame,data)
def OnTang(event):
Obj = event.GetEventObject()
Tid,torsTxt = Indx[Obj.GetId()]
move = Obj.GetValue()*5.0
Obj.SetValue(0)
RBObj['Torsions'][Tid][0] += move
torsTxt.ChangeValue(RBObj['Torsions'][Tid][0])
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(G2frame,data,atomStyle)
G2frame.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)
G2G.HorizontalLine(resrbSizer,RigidBodies)
topLine = wx.BoxSizer(wx.HORIZONTAL)
topLine.Add(wx.StaticText(RigidBodies,-1,'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,WACV)
showAx = wx.CheckBox(RigidBodies,label='Show RB axes on plot?')
showAx.SetValue(RBObj['showAxes'])
showAx.Bind(wx.EVT_CHECKBOX,OnShowAx)
topLine.Add(showAx,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)
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',rbId))
if len(RBObj['Torsions']):
resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0)
torSizer = wx.FlexGridSizer(0,8,5,5)
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)
Tang = wx.SpinButton(RigidBodies,style=wx.SP_VERTICAL,size=(20,24))
Tang.SetValue(0)
Tang.SetRange(-1,1)
Tang.Bind(wx.EVT_SPIN, OnTang)
Indx[Tang.GetId()] = [itors,torsTxt]
torSizer.Add(Tang,0,WACV)
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 = ['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)
resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
dragSizer = wx.BoxSizer(wx.HORIZONTAL)
dragSizer.Add(wx.StaticText(RigidBodies,wx.ID_ANY,'Draw mode after dragging the rigid body: '),0,WACV)
RBObj['drawMode'] = RBObj.get('drawMode',DrawStyleChoice[4])
modeOpt = G2G.G2ChoiceButton(RigidBodies, DrawStyleChoice[1:],strLoc=RBObj,strKey='drawMode')
dragSizer.Add(modeOpt)
modeOpt.Enable(False) # not implemented yet
G2frame.testRBObjSizers['fillMode'] = G2frame.testRBObjSizers.get('fillMode',False)
dragSizer.Add(G2G.G2CheckBoxFrontLbl(RigidBodies, ' Fill cell on mouse up?', G2frame.testRBObjSizers, 'fillMode'))
resrbSizer.Add((-1,5))
resrbSizer.Add(dragSizer)
return resrbSizer
def VecrbSizer(RBObj,resIndx):
'''Displays details for selected vector rigid body'''
def OnShowAx(event):
RBObj['showAxes'] = not RBObj['showAxes']
G2frame.selectRB['showAxes'] = RBObj['showAxes']
G2plt.PlotStructure(G2frame,data)
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)
G2G.HorizontalLine(vecrbSizer,RigidBodies)
topLine = wx.BoxSizer(wx.HORIZONTAL)
topLine.Add(wx.StaticText(RigidBodies,-1,
'Name: '+RBObj['RBname']+' '),0,WACV)
showAx = wx.CheckBox(RigidBodies,label='Show RB axes on plot?')
showAx.SetValue(RBObj['showAxes'])
showAx.Bind(wx.EVT_CHECKBOX,OnShowAx)
topLine.Add(showAx,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',rbId))
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 = ['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)
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
# # define the parameters needed to drag the RB with the mouse
# data['testRBObj'] = {}
# rbType = 'Residue'
# data['testRBObj']['rbObj'] = copy.deepcopy(data['RBModels'][rbType][prevResId])
# rbId = data['RBModels'][rbType][prevResId]['RBId']
# RBdata = G2frame.GPXtree.GetItemPyData(
# G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies'))
# data['testRBObj']['rbData'] = RBdata
# data['testRBObj']['rbType'] = rbType
# 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']['Sizers'] = {}
# data['testRBObj']['rbRef'] = RBData[rbType][rbId]['rbRef']
# refType = []
# for ref in data['testRBObj']['rbRef'][:3]:
# reftype = data['testRBObj']['rbAtTypes'][ref]
# refType.append(reftype)
# #refName.append(reftype+' '+str(rbRef[0]))
# atNames = [{},{},{}]
# AtNames = {}
# cx,ct,cs,cia = data['General']['AtomPtrs']
# for iatm,atom in enumerate(data['Atoms']):
# 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']['torAtms'] = []
# # unclear why these torsion entries are being added to rbObj.
# for item in RBData[rbType][rbId].get('rbSeq',[]):
# data['testRBObj']['rbObj']['Torsions'].append([item[2],False]) # Needed?
# data['testRBObj']['torAtms'].append([-1,-1,-1])
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]
rbObj['showAxes'] = rbObj.get('showAxes',False)
Quad = rbObj['Orient'][0]
data['Drawing']['Quaternion'] = G2mth.invQ(Quad)
if rbType == 'Residue':
G2frame.GetStatusBar().SetStatusText('Alt RB: drag RB, ALT MB: Z rotate RB, ALT LB: Q rotate RB',1)
data['Drawing']['viewPoint'][0] = rbObj['Orig'][0]
G2frame.selectRB = {item:rbObj[item] for item in ['Orig','Orient','showAxes']}
G2frame.bottomSizer = ResrbSizer(rbObj,rbIndx)
elif rbType == 'Spin':
text = ''
for ish,pMax in enumerate(rbObj.get('Pmax',[])):
text += 'Shell %d: Pmax %.3f Pmin %.3f '%(ish,pMax,rbObj['Pmin'][ish])
G2frame.GetStatusBar().SetStatusText(text,1)
G2frame.selectRB = {item:rbObj[item] for item in ['Orient','symAxis','showAxes']}
G2frame.selectRB['Orig'] = [data['Atoms'][AtLookUp[rbObj['Ids'][0]]][cx:cx+3],False]
data['Drawing']['viewPoint'][0] = data['Atoms'][AtLookUp[rbObj['Ids'][0]]][cx:cx+3]
G2frame.bottomSizer = SpnrbSizer(rbObj,rbIndx)
else: #Vector
G2frame.GetStatusBar().SetStatusText('Alt RB: drag RB, ALT MB: Z rotate RB, ALT LB: Q rotate RB',1)
data['Drawing']['viewPoint'][0] = rbObj['Orig'][0]
G2frame.selectRB = {item:rbObj[item] for item in ['Orig','Orient','symAxis','showAxes']}
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)
if oldFocus: wx.CallAfter(oldFocus.SetFocus)
#### FillRigidBodyGrid main
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'
mainSizer = wx.BoxSizer(wx.VERTICAL)
topSizer = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
lbl= f"Select rigid body to view for {data['General']['Name']!r}"[:60]
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
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:
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=(-1,80))
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:
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=(-1,80))
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:
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=(-1,80))
if spnId != -1:
spnSelect.SetSelection(spnId)
OnSpnSelect(None)
spnSelect.Bind(wx.EVT_LISTBOX,OnSpnSelect)
spnSizer.Add(spnSelect,0)
rbSizer.Add(spnSizer)
try:
rbObj['showAxes'] = rbObj.get('showAxes',False)
G2frame.selectRB = {item:rbObj[item] for item in ['Orig','Orient','OrientVec','symAxis','showAxes']}
except:
G2frame.selectRB = {}
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):
#### copy implies setting equal but not same, is what is intended here is make all parms the same?
RBObjs = []
for rbType in ['Vector',]:
RBObjs += data['RBModels'].get(rbType,[])
if not len(RBObjs):
print ('**** ERROR - only allowed for defined Vector rigid bodies ****')
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','Duplicate 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','Duplicate rigid body parameters',Source)
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelections()
for x in sel:
RBObjs[x].update(sourceRB) #NB: this duplicates the objects; not make independent copies!
# RBObjs[x].update(copy.copy(sourceRB)) #NB: this duplicates the objects; not make independent copies!
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']
rbObj['Invert'] = rbObj.get('Invert',False)
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()
data['Drawing']['Atoms'] = []
UpdateDrawAtoms(G2frame,data)
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'] = ['Uiso',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
rbObj['ThermalMotion'][1][0] = 0.01 #Uiso default
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','RBId','RBname','RBsym']:
item = rbObj[name]
rbObj[name] = [rbObj[name],]
rbObj['Radius'] = [[1.0,False],]
rbObj['symAxis'] = data['testRBObj']['symAxis']
rbObj['showAxes'] = False
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.ChangeValue(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.ChangeValue(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]
if not i: #in that BoxSizer from G2SpinWidget
BSI = G2frame.testRBObjSizers['OrientVecSiz'][i].GetChildren()[-2].GetWindow()
else:
BSI = G2frame.testRBObjSizers['OrientVecSiz'][i]
BSI.ChangeValue(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
azSlide.SetValue(int(10*rbObj['OrientVec'][0]))
# G2frame.testRBObjSizers['OrientVecSiz'][4].ChangeValue(
# 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))
G2plt.PlotStructure(G2frame,data,False,UpdateTable)
UpdateTable()
# 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])
item.ChangeValue(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])
item.ChangeValue(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 = ([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.ChangeValue(data['testRBObj']['rbObj']['Orig'][0][i])
UpdateSytSym()
UpdateTablePlot()
def OnInvert(event):
UpdateTable()
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']
rbObj['Invert'] = rbObj.get('Invert',False)
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(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)
topSizer.Add((-1,-1),1,wx.EXPAND,1)
topSizer.Add(G2G.HelpButton(RigidBodies,helpText,wrap=700),0,wx.RIGHT,5)
mainSizer.Add(topSizer,0,wx.EXPAND,0)
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'] = [180.,0.,0.,1.]
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))
Orientvec = G2G.G2SpinWidget(RigidBodies,rbObj['OrientVec'],0,nDig=(10,2),typeHint=float,
label='Orientation azimuth: ',xmin=0.,xmax=360.,onChange=UpdateOrientation)
OrientVecSiz.append(Orientvec)
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)
if data['testRBObj']['rbType'] == 'Vector':
OriSizer4.Add(wx.StaticText(RigidBodies,label='Rigid body symmetry axis: '),0, WACV)
symax = dict(zip([str(x) for x in [[1,0,0],[0,1,0],[0,0,1],[1,1,0],[1,1,1]]],RBdirlbl))[str(data['testRBObj']['symAxis'])]
symRadioSet = wx.RadioBox(RigidBodies,choices=RBdirlbl)
symRadioSet.SetStringSelection(symax)
symRadioSet.Bind(wx.EVT_RADIOBOX, OnSymRadioSet)
OriSizer4.Add(symRadioSet)
else:
OriSizer4.Add(wx.StaticText(RigidBodies,label='Rigid body symmetry axis is z'),0, WACV)
Invert = G2G.G2CheckBox(RigidBodies,'Invert',rbObj,'Invert',OnInvert)
OriSizer4.Add(Invert,0,WACV)
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'])
else:
lbl = rbAssignments[i]
displayTable.append([l[0],l[5],l[6],l[10],lbl])
else:
if rbType == 'Spin':
displayTable.append([l[1],-1,l[1]+str(i),-1,'Create new'])
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]
data['testRBObj']['symAxis'] = RBData[rbType][rbId].get('symAxis',[0,0,1])
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'] = ['Uiso',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
rbObj['ThermalMotion'][1][0] = 0.01 #Uiso default
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']:
RBData[RBType] = RBData.get(RBType,[])
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
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)
topSizer = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
lbl= f"Monte Carlo/Simulated Annealing for {data['General']['Name']!r}"[:60]
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
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)
mainSizer.Add(wx.StaticText(G2frame.MCSA,label='MC/SA models:'))
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
#wx.CallAfter(FillPawleyReflectionsGrid)
G2frame.PawleyRefl.ForceRefresh()
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 = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
if len(PawleyPeaks) and generalData['doPawley']:
lbl= f"Pawley reflections for {data['General']['Name']!r}"[:60]
else:
lbl= f"There are no Pawley reflections for {data['General']['Name']!r}"[:60]
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
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)
G2frame.PawleyRefl.SetRowLabelSize(50)
G2frame.PawleyRefl.SetScrollRate(10,10) # allow grid to scroll
mainSizer.Add(G2frame.PawleyRefl,1,wx.EXPAND)
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 = (
'''Pawley refinement has not yet been setup. Use the
Operations->"Pawley setttings" menu command to change this.
(Or, if Pawley settings have already been set on the General
tab, use Operations->"Pawley create")''')
mainSizer.Add(wx.StaticText(PawleyRefList,label=msg),0,wx.ALIGN_CENTER)
SetPhaseWindow(PawleyRefList,mainSizer)
def OnPawleySet(event):
'''Open dialog to set Pawley parameters and optionally recompute reflections.
This is called from the Phase/Pawley Reflections "Pawley Settings"
menu command. These settings are also available on the Phase/General tab.
'''
def DisablePawleyOpts(*args):
'dis-/enable Pawley options'
for c in PawleyCtrlsList:
c.Enable(generalData['doPawley'])
PawleyCtrlsList = []
dmin,dmax,nhist,lbl,chist = 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)
PawleyCtrlsList.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)
#PawleyCtrlsList.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)
PawleyCtrlsList.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)
PawleyCtrlsList.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
# If Pawley is on, turn off Le Bail settings (since they will
# be hidden)
if generalData['doPawley']:
Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.GPXtree.root, 'Controls'))
Controls['newLeBail'] = False
for h in data['Histograms']:
data['Histograms'][h]['LeBail'] = False
# 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 G2frame.MapPeaks.IsSelection():
G2frame.MapPeaks.ClearSelection()
else:
for row in range(G2frame.MapPeaks.GetNumberRows()):
G2frame.MapPeaks.SelectRow(row,True)
elif c < 0: #only row clicks
if event.ControlDown():
if r in getAtomSelections(G2frame.MapPeaks):
G2frame.MapPeaks.DeselectRow(r)
else:
G2frame.MapPeaks.SelectRow(r,True)
elif event.ShiftDown():
indxs = getAtomSelections(G2frame.MapPeaks)
G2frame.MapPeaks.ClearSelection()
ibeg = 0
if indxs:
ibeg = indxs[-1]
for row in range(ibeg,r+1):
G2frame.MapPeaks.SelectRow(row,True)
else:
G2frame.MapPeaks.ClearSelection()
G2frame.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)
topSizer = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
lbl= f"Fourier map peak positions for {data['General']['Name']!r}"[:60]
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
mainSizer = wx.BoxSizer(wx.VERTICAL)
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)
G2frame.MapPeaks.Show(True)
G2frame.MapPeaks.SetTable(G2frame.MapPeaksTable, True)
G2frame.MapPeaks.Unbind(wg.EVT_GRID_LABEL_LEFT_CLICK)
G2frame.MapPeaks.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
for r in range(G2frame.MapPeaks.GetNumberRows()):
for c in range(G2frame.MapPeaks.GetNumberCols()):
G2frame.MapPeaks.SetCellStyle(r,c,VERY_LIGHT_GREY,True)
G2frame.MapPeaks.SetMargins(0,0)
G2frame.MapPeaks.AutoSizeColumns(False)
G2frame.MapPeaks.SetRowLabelSize(40)
mainSizer.Add(G2frame.MapPeaks,1,wx.EXPAND)
G2frame.MapPeaks.SetScrollRate(10,10) # allow grid to scroll
else:
mainSizer.Add(wx.StaticText(MapPeakList,label=' Map peak list is empty'),0,wx.ALL,10)
G2frame.MapPeaks.Show(False)
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(G2frame.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 = np.array(data['Map Peaks'])
Ind = getAtomSelections(G2frame.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:
#mapPeaks = np.array(data['Map Peaks'])
Ind = getAtomSelections(G2frame.MapPeaks)
if Ind:
wx.BeginBusyCursor()
try:
Ind = G2mth.PeaksEquiv(data,Ind)
for r in range(G2frame.MapPeaks.GetNumberRows()):
if r in Ind:
G2frame.MapPeaks.SelectRow(r,addToSelected=True)
else:
G2frame.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 = np.array(data['Map Peaks'])
Ind = getAtomSelections(G2frame.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 = G2frame.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(G2frame.MapPeaks.GetNumberRows()):
if r < len(Ind):
G2frame.MapPeaks.SelectRow(r,addToSelected=True)
else:
G2frame.MapPeaks.DeselectRow(r)
G2frame.MapPeaks.ForceRefresh()
G2plt.PlotStructure(G2frame,data)
def OnPeaksViewPoint(event):
# set view point
indx = getAtomSelections(G2frame.MapPeaks)
if not indx:
G2frame.ErrorDialog('Set view point','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(G2frame.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 = [G2frame.MapPeaks.GetColLabelValue(c) for c in range(G2frame.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(G2frame.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'] = 4.
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,'FM')
UpdateDrawAtoms(G2frame,data)
G2plt.PlotStructure(G2frame,data)
def OnFourClear(event):
generalData = data['General']
generalData['Map'] = G2elem.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(G2frame,data)
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(f'4D Charge flip: {result[2]}\n{result[3]}','CF')
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'] = 4.
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(f'Charge flip: {result[2]}\n{result[3]}','CF')
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'] = 4.
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,labelX='POobs',labelY='POcalc',lines=False,newPlot=False,Title='Texture fit error')
G2phsG2.UpdateTexture(G2frame,data)
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
# force edits in open grids to complete
newlist = []
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 lis
# let the pending events clear before posting the new NB page
wx.CallAfter(ChangePage,page)
def ChangePage(page):
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)
G2phsG2.UpdateLayerData(G2frame,data)
elif text == 'Wave Data' and data['General']['Modulated']:
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.WavesData)
G2plt.PlotStructure(G2frame,data,firstCall=True)
G2phsG2.UpdateWavesData(G2frame,data)
elif text == 'Dysnomia':
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.MEMMenu)
G2phsG2.UpdateDysnomia(G2frame,data)
elif text == 'RMC':
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.FRMCMenu)
G2rmcG.UpdateRMC(G2frame,data)
G2rmcG.UpdateRMC(G2frame,data) #TODO: apparently needs to be done twice to get a working GUI. Find a better fix.
elif text == 'ISODISTORT':
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.ISODData)
G2phsG2.UpdateISODISTORT(G2frame,data)
elif text == 'Draw Options':
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DataDrawOptions)
G2plt.PlotStructure(G2frame,data,firstCall=True)
UpdateDrawOptions(G2frame,data)
elif text == 'Draw Atoms':
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DrawAtomsMenu)
G2plt.PlotStructure(G2frame,data,firstCall=True)
UpdateDrawAtoms(G2frame,data)
elif text == 'Deformation':
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.DeformationMenu)
G2plt.PlotStructure(G2frame,data,firstCall=True)
G2phsG2.UpdateDeformation(G2frame,data,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)
G2phsG2.UpdateTexture(G2frame,data)
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, OnSubSearch, id=G2G.wxID_SUBSRCH)
# G2frame.Bind(wx.EVT_MENU, OnNISTLatSym, id=G2G.wxID_NISTLATCELL)
G2frame.Bind(wx.EVT_MENU, OnCompare, id=G2G.wxID_COMPARESTRUCTURE)
G2frame.Bind(wx.EVT_MENU, TestBilbao, id=G2G.wxID_TESTBCS)
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)
for Id in G2frame.dataWindow.ReplaceMenuId: #loop over submenu items
G2frame.Bind(wx.EVT_MENU, OnReplacePhase, id=Id)
# 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, OnSaveDAHist, id=G2G.wxID_ATOMSSAVEHIST)
G2frame.Bind(wx.EVT_MENU, OnClearDAHist, id=G2G.wxID_ATOMSCLEARHIST)
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, AddBox, id=G2G.wxID_DRAWADDBOX)
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, OnShowIsoDistortCalc, id=G2G.wxID_DRAWISO)
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)
G2frame.Bind(wx.EVT_MENU, RandomizedAction, id=G2G.wxID_DRAWRANDOM)
# 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, 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
'''
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
# make sure that the phase menu bars get created before selecting
# any (this will only be true on the first call to UpdatePhaseData)
if callable(G2frame.dataWindow.DataGeneral):
wx.BeginBusyCursor()
G2frame.dataWindow.DataGeneral()
wx.EndBusyCursor()
#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)
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.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.Panel(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')
G2frame.drawOptions = wx.ScrolledWindow(G2frame.phaseDisplay)
G2frame.phaseDisplay.AddPage(G2frame.drawOptions,'Draw Options')
Pages.append('Draw Options')
G2frame.drawAtomsList = wx.Panel(G2frame.phaseDisplay)
G2frame.drawAtoms = G2G.GSGrid(G2frame.drawAtomsList)
G2frame.phaseDisplay.gridList.append(G2frame.drawAtoms)
G2frame.phaseDisplay.AddPage(G2frame.drawAtomsList,'Draw Atoms')
Pages.append('Draw Atoms')
dmin,dmax,nhist,lbl,chist = getPawleydRange(G2frame,data)
dataGeneral = data['General']
if any('X' in item for item in G2frame.GetHistogramTypes()):
G2frame.deformation = wx.ScrolledWindow(G2frame.phaseDisplay)
G2frame.phaseDisplay.AddPage(G2frame.deformation,'Deformation')
Pages.append('Deformation')
if dataGeneral['Type'] not in ['faulted',] and not dataGeneral['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')
if ('Map' in dataGeneral and dataGeneral['Map']['MapType']) or 'Flip' in dataGeneral:
MapPeakList = wx.Panel(G2frame.phaseDisplay)
G2frame.phaseDisplay.AddPage(MapPeakList,'Map peaks')
# create the grid once; N.B. need to reference at this scope
G2frame.MapPeaks = G2G.GSGrid(MapPeakList)
G2frame.phaseDisplay.gridList.append(G2frame.MapPeaks)
Pages.append('Map peaks')
if data['General']['doDysnomia']:
G2frame.MEMData = wx.ScrolledWindow(G2frame.phaseDisplay)
G2frame.phaseDisplay.AddPage(G2frame.MEMData,'Dysnomia')
Pages.append('Dysnomia')
if dataGeneral['Type'] not in ['faulted',] and not dataGeneral['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 dataGeneral['Type'] == 'nuclear':
G2frame.ISODIST = wx.ScrolledWindow(G2frame.phaseDisplay)
G2frame.phaseDisplay.AddPage(G2frame.ISODIST,'ISODISTORT')
Pages.append('ISODISTORT')
if nhist > 0:
G2frame.Texture = wx.ScrolledWindow(G2frame.phaseDisplay)
G2frame.phaseDisplay.AddPage(G2frame.Texture,'Texture')
Pages.append('Texture')
PawleyRefList = wx.Panel(G2frame.phaseDisplay)
G2frame.PawleyRefl = None # grid now created when needed
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))
if len(UCdata) >5:
flag = not any(['magAtms' in i for i in UCdata[5]])
else:
del data['magPhases']
G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_USEBILBAOSUB,flag)
if not flag and 'SUBGROUPS' in data:
G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_USEBILBAOSUB,True)
G2frame.dataWindow.GeneralCalc.Enable(G2G.wxID_USEBILBAOMAG,True)
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)
# on windows, need to wait for previous to finish before
# going to selected tab
wx.CallAfter(G2frame.phaseDisplay.SetSelection,ind)
return
ChangePage(0)
[docs]
def CheckAddHKLF(G2frame,data):
'''GUI actions associated with linking a Phase to a HKLF histogram.
This gets called in two routines named OnHklfAdd (one inside
:func:`GSASIIphsGUI.UpdatePhaseData` and the other inside
:func:`GSASIIddataGUI.MakeHistPhaseWin`).
'''
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 HKLF histograms')
return
dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select HKLF reflection sets to use',
'Use data',TextList)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
else:
print('Nothing selected')
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)[:2]
G2mth.UpdateHKLFvals(histoName, data, reflData)
wx.EndBusyCursor()
return result
[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.
: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
PdfFit
return True
except:
pass
# Last effort: With conda we should be able to create a separate
# Python in a separate environment
try: # have conda. Can we access it programmatically?
import conda.cli.python_api
conda.cli.python_api
except:
G2G.G2MessageBox(G2frame,'You are running a directly installed Python. You will need to install PDFfit2 directly as well, preferably in a separate virtual environment.')
return
msg = ('Do you want to use 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=1.3.4 -c conda-forge -c diffpy
res,PDFpython = GSASIIpath.condaEnvCreate('pdffit2',
['python', 'conda', 'gsl', 'diffpy.pdffit2>=1.4.3',
'-c', 'conda-forge']) # not needed , '-c', 'diffpy'])
finally:
wx.EndBusyCursor()
if os.path.exists(PDFpython) and is_exe(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'))
print('\n\nSuccess: PDFfit2 installed.')
return True
else:
print(f'Failed to install PDFfit2 with error:\n{PDFpython}')
if ('PackagesNotFoundError' in PDFpython
and 'darwin' in sys.platform
and 'arm' in platform.machine()):
msg = ('It appears that PDFfit2 is not yet available as a conda package for Macs with arm processors. '+
'\n\nYou could install PDFfit2 with x86 Python and use that '+
'in compatibility mode.')
else:
msg = ('An attempt to install PDFfit2 has failed. '+
'Do you have write access to where GSAS-II is installed? '+
'You may be able to install PDFfit2 manually.')
msg += '\n\nIf you install PDFfit2 yourself, set the pdffit2_exec config variable to the install location'
G2G.G2MessageBox(G2frame,
'PDFfit2 Install failed. See console for error message\n\n'+msg,
'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
[docs]
def renamePhaseName(G2frame,data,phaseItem,generalData,newName):
'''Called to rename the phase. Updates the tree and items that
reference the file name.
'''
oldName = generalData['Name']
phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree()
phaseNameList = usedHistograms.keys() # phase names in use
if newName and newName != oldName:
newName = G2obj.MakeUniqueLabel(newName,list(phaseNameList))
generalData['Name'] = newName
G2frame.G2plotNB.Rename(oldName,generalData['Name'])
G2frame.GPXtree.SetItemText(phaseItem,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]
# 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)
if len(Restraints) and oldName in Restraints:
Restraints[newName] = Restraints[oldName]
del Restraints[oldName]
[docs]
def showFinalResults(G2frame,msgs,pagelist,fileList):
'''Show a summary with info from a search of supergroups in
:func:`OnSuperSearch` (in :func:`UpdatePhaseData`)
'''
def _showWebPage(event):
import tempfile
f = event.GetEventObject().webFile
tmp = tempfile.NamedTemporaryFile(suffix='.html',
delete=False)
with open(tmp.name,'w') as fp:
fp.write(f.replace(
'<head>',
f'<head><base href="{SUBGROUPS.bilbaoURL}/">',
))
fileList.append(tmp.name)
G2G.ShowWebPage('file://'+tmp.name,G2frame)
width = 700
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,
f'''Summary of results from the Bilbao Crystallographic Server Pseudosymmetry
search (PSEUDO) program; Please cite:
{G2G.GetCite('Bilbao: PSEUDO',wrap=70,indent=5)}'''))
txt = wx.StaticText(dlg,wx.ID_ANY,'Starting from '+msgs[0].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 = pagelist[0]
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))
spanel = wxscroll.ScrolledPanel(dlg, wx.ID_ANY, size=(width, 400))
txtSizer = wx.BoxSizer(wx.VERTICAL)
level = -1
while True:
level += 1
keys = [i for i in pagelist if i !=0 and i.count('-') == level and 'R' not in i]
if not keys: break
txtSizer.Add((-1,10))
G2G.HorizontalLine(txtSizer,spanel)
G2G.HorizontalLine(txtSizer,spanel)
txt = wx.StaticText(spanel,wx.ID_ANY,f'Level {level} supergroups',style=wx.ALIGN_CENTER)
txtSizer.Add(txt,0,wx.EXPAND)
for num in keys:
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
if num in pagelist:
txtSizer.Add((-1,5))
showSizer = wx.BoxSizer(wx.HORIZONTAL)
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+'R' in pagelist:
txtSizer.Add((-1,5))
showSizer = wx.BoxSizer(wx.HORIZONTAL)
btn = wx.Button(spanel, wx.ID_ANY,label='Show')
btn.webFile = pagelist[num+'R']
btn.Bind(wx.EVT_BUTTON,_showWebPage)
showSizer.Add(btn)
showSizer.Add(wx.StaticText(spanel,wx.ID_ANY,' Web page with supergroup search info'))
txtSizer.Add(showSizer)
txtSizer.Add((-1,10))
if level == 0:
mainSizer.Add((-1,10))
mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,
'No matching supergroups were found'))
spanel.Destroy()
else:
spanel.SetSizer(txtSizer)
mainSizer.Add(spanel,1,wx.ALL|wx.EXPAND,1)
spanel.SetAutoLayout(1)
spanel.SetupScrolling()
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)
dlg.CenterOnParent()
ans = dlg.ShowModal()
dlg.Destroy()
return ans
def TestBilbao(event):
G2frame = wx.GetApp().GetMainTopWindow()
SUBGROUPS.do_once = None # force reinitialization
if SUBGROUPS.BCS_init():
msg = 'Bilbao key (BCS_API_KEY) has not been defined.'
G2G.G2MessageBox(G2frame,msg,'Bilbao access failed')
return
try:
sgnum,sgsym,xmat,xoff = SUBGROUPS.GetStdSGset(G2spc.SpcGroup('R 3 C r')[1])
if sgnum != 161:
G2G.G2MessageBox(G2frame,'Bilbao problem: unexpected result','Bilbao problem')
except Exception as msg:
if GSASIIpath.GetConfigValue('debug'): print(msg)
G2G.G2MessageBox(G2frame,'Bilbao access failed. Invalid key?','Bilbao access failed')
return
G2G.G2MessageBox(G2frame,'Bilbao accessed OK','Bilbao accessed')
print('done')