def PrintDistAngle(DisAglCtls,DisAglData,out=sys.stdout):
'''Print distances and angles
:param dict DisAglCtls: contains distance/angle radii usually defined using
:func:`GSASIIgrid.DisAglDialog`
:param dict DisAglData: contains phase data:
Items 'OrigAtoms' and 'TargAtoms' contain the atoms to be used
for distance/angle origins and atoms to be used as targets.
Item 'SGData' has the space group information (see :ref:`Space Group object<SGData_table>`)
:param file out: file object for output. Defaults to sys.stdout.
'''
import numpy.ma as ma
def MyPrint(s):
out.write(s+'\n')
# print(s,file=out) # use in Python 3
def ShowBanner(name):
MyPrint(80*'*')
MyPrint(' Interatomic Distances and Angles for phase '+name)
MyPrint((80*'*')+'\n')
ShowBanner(DisAglCtls['Name'])
SGData = DisAglData['SGData']
SGtext,SGtable = G2spc.SGPrint(SGData)
for line in SGtext: MyPrint(line)
if len(SGtable):
for i,item in enumerate(SGtable[::2]):
line = ' %s %s'%(item.ljust(30),SGtable[2*i+1].ljust(30))
MyPrint(line)
else:
MyPrint(' ( 1) %s'%(SGtable[0]))
Cell = DisAglData['Cell']
Amat,Bmat = G2lat.cell2AB(Cell[:6])
covData = {}
if 'covData' in DisAglData:
covData = DisAglData['covData']
covMatrix = covData['covMatrix']
varyList = covData['varyList']
pfx = str(DisAglData['pId'])+'::'
A = G2lat.cell2A(Cell[:6])
cellSig = G2stIO.getCellEsd(pfx,SGData,A,covData)
names = [' a = ',' b = ',' c = ',' alpha = ',' beta = ',' gamma = ',' Volume = ']
valEsd = [G2mth.ValEsd(Cell[i],cellSig[i],True) for i in range(7)]
line = '\n Unit cell:'
for name,vals in zip(names,valEsd):
line += name+vals
MyPrint(line)
else:
MyPrint('\n Unit cell: a = '+('%.5f'%Cell[0])+' b = '+('%.5f'%Cell[1])+' c = '+('%.5f'%Cell[2])+
' alpha = '+('%.3f'%Cell[3])+' beta = '+('%.3f'%Cell[4])+' gamma = '+
('%.3f'%Cell[5])+' volume = '+('%.3f'%Cell[6]))
AtomLabels,DistArray,AngArray = RetDistAngle(DisAglCtls,DisAglData)
origAtoms = DisAglData['OrigAtoms']
targAtoms = DisAglData['TargAtoms']
for Oatom in origAtoms:
i = Oatom[0]
Dist = DistArray[i]
nDist = len(Dist)
angles = np.zeros((nDist,nDist))
angsig = np.zeros((nDist,nDist))
for k,j,tup in AngArray[i]:
angles[k][j],angsig[k][j] = angles[j][k],angsig[j][k] = tup
line = ''
for i,x in enumerate(Oatom[3:6]):
line += ('%12.5f'%x).rstrip('0')
MyPrint('\n Distances & angles for '+Oatom[1]+' at '+line.rstrip())
MyPrint(80*'*')
line = ''
for dist in Dist[:-1]:
line += '%12s'%(AtomLabels[dist[0]].center(12))
MyPrint(' To cell +(sym. op.) dist. '+line.rstrip())
for i,dist in enumerate(Dist):
line = ''
for j,angle in enumerate(angles[i][0:i]):
sig = angsig[i][j]
if angle:
if sig:
line += '%12s'%(G2mth.ValEsd(angle,sig,True).center(12))
else:
val = '%.3f'%(angle)
line += '%12s'%(val.center(12))
else:
line += 12*' '
if dist[4]: #sig exists!
val = G2mth.ValEsd(dist[3],dist[4])
else:
val = '%8.4f'%(dist[3])
tunit = '[%2d%2d%2d]'% dist[1]
MyPrint((' %8s%10s+(%4d) %12s'%(AtomLabels[dist[0]].ljust(8),tunit.ljust(10),dist[2],val.center(12)))+line.rstrip())
def PrintDistAngle(DisAglCtls,DisAglData,out=sys.stdout):
'''Print distances and angles
:param dict DisAglCtls: contains distance/angle radii usually defined using
:func:`GSASIIctrlGUI.DisAglDialog`
:param dict DisAglData: contains phase data:
Items 'OrigAtoms' and 'TargAtoms' contain the atoms to be used
for distance/angle origins and atoms to be used as targets.
Item 'SGData' has the space group information (see :ref:`Space Group object<SGData_table>`)
:param file out: file object for output. Defaults to sys.stdout.
'''
def MyPrint(s):
out.write(s+'\n')
# print(s,file=out) # use in Python 3
def ShowBanner(name):
MyPrint(80*'*')
MyPrint(' Interatomic Distances and Angles for phase '+name)
MyPrint((80*'*')+'\n')
ShowBanner(DisAglCtls['Name'])
SGData = DisAglData['SGData']
SGtext,SGtable = G2spc.SGPrint(SGData)
for line in SGtext: MyPrint(line)
if len(SGtable) > 1:
for i,item in enumerate(SGtable[::2]):
if 2*i+1 == len(SGtable):
line = ' %s'%(item.ljust(30))
else:
line = ' %s %s'%(item.ljust(30),SGtable[2*i+1].ljust(30))
MyPrint(line)
else:
MyPrint(' ( 1) %s'%(SGtable[0])) #triclinic case
Cell = DisAglData['Cell']
Amat,Bmat = G2lat.cell2AB(Cell[:6])
covData = {}
if 'covData' in DisAglData:
covData = DisAglData['covData']
pfx = str(DisAglData['pId'])+'::'
A = G2lat.cell2A(Cell[:6])
cellSig = G2stIO.getCellEsd(pfx,SGData,A,covData)
names = [' a = ',' b = ',' c = ',' alpha = ',' beta = ',' gamma = ',' Volume = ']
valEsd = [G2mth.ValEsd(Cell[i],cellSig[i],True) for i in range(7)]
line = '\n Unit cell:'
for name,vals in zip(names,valEsd):
line += name+vals
MyPrint(line)
else:
MyPrint('\n Unit cell: a = '+('%.5f'%Cell[0])+' b = '+('%.5f'%Cell[1])+' c = '+('%.5f'%Cell[2])+
' alpha = '+('%.3f'%Cell[3])+' beta = '+('%.3f'%Cell[4])+' gamma = '+
('%.3f'%Cell[5])+' Volume = '+('%.3f'%Cell[6]))
AtomLabels,DistArray,AngArray = RetDistAngle(DisAglCtls,DisAglData)
origAtoms = DisAglData['OrigAtoms']
for Oatom in origAtoms:
i = Oatom[0]
Dist = DistArray[i]
nDist = len(Dist)
angles = np.zeros((nDist,nDist))
angsig = np.zeros((nDist,nDist))
for k,j,tup in AngArray[i]:
angles[k][j],angsig[k][j] = angles[j][k],angsig[j][k] = tup
line = ''
for i,x in enumerate(Oatom[3:6]):
line += ('%12.5f'%x).rstrip('0')
MyPrint('\n Distances & angles for '+Oatom[1]+' at '+line.rstrip())
MyPrint(80*'*')
line = ''
for dist in Dist[:-1]:
line += '%12s'%(AtomLabels[dist[0]].center(12))
MyPrint(' To cell +(sym. op.) dist. '+line.rstrip())
for i,dist in enumerate(Dist):
line = ''
for j,angle in enumerate(angles[i][0:i]):
sig = angsig[i][j]
if angle:
if sig:
line += '%12s'%(G2mth.ValEsd(angle,sig,True).center(12))
else:
val = '%.3f'%(angle)
line += '%12s'%(val.center(12))
else:
line += 12*' '
if dist[4]: #sig exists!
val = G2mth.ValEsd(dist[3],dist[4])
else:
val = '%8.4f'%(dist[3])
tunit = '[%2d%2d%2d]'% dist[1]
MyPrint((' %8s%10s+(%4d) %12s'%(AtomLabels[dist[0]].ljust(8),tunit.ljust(10),dist[2],val.center(12)))+line.rstrip())
def RetDistAngle(DisAglCtls,DisAglData):
'''Compute and return distances and angles
:param dict DisAglCtls: contains distance/angle radii usually defined using
:func:`GSASIIgrid.DisAglDialog`
:param dict DisAglData: contains phase data:
Items 'OrigAtoms' and 'TargAtoms' contain the atoms to be used
for distance/angle origins and atoms to be used as targets.
Item 'SGData' has the space group information (see :ref:`Space Group object<SGData_table>`)
:returns: AtomLabels,DistArray,AngArray where:
**AtomLabels** is a dict of atom labels, keys are the atom number
**DistArray** is a dict keyed by the origin atom number where the value is a list
of distance entries. The value for each distance is a list containing:
0) the target atom number (int);
1) the unit cell offsets added to x,y & z (tuple of int values)
2) the symmetry operator number (which may be modified to indicate centering and center of symmetry)
3) an interatomic distance in A (float)
4) an uncertainty on the distance in A or 0.0 (float)
**AngArray** is a dict keyed by the origin (central) atom number where
the value is a list of
angle entries. The value for each angle entry consists of three values:
0) a distance item reference for one neighbor (int)
1) a distance item reference for a second neighbor (int)
2) a angle, uncertainty pair; the s.u. may be zero (tuple of two floats)
The AngArray distance reference items refer directly to the index of the items in the
DistArray item for the list of distances for the central atom.
'''
import numpy.ma as ma
SGData = DisAglData['SGData']
Cell = DisAglData['Cell']
Amat,Bmat = G2lat.cell2AB(Cell[:6])
covData = {}
if 'covData' in DisAglData:
covData = DisAglData['covData']
covMatrix = covData['covMatrix']
varyList = covData['varyList']
pfx = str(DisAglData['pId'])+'::'
A = G2lat.cell2A(Cell[:6])
cellSig = G2stIO.getCellEsd(pfx,SGData,A,covData)
names = [' a = ',' b = ',' c = ',' alpha = ',' beta = ',' gamma = ',' Volume = ']
valEsd = [G2mth.ValEsd(Cell[i],cellSig[i],True) for i in range(7)]
Factor = DisAglCtls['Factors']
Radii = dict(zip(DisAglCtls['AtomTypes'],zip(DisAglCtls['BondRadii'],DisAglCtls['AngleRadii'])))
indices = (-1,0,1)
Units = np.array([[h,k,l] for h in indices for k in indices for l in indices])
origAtoms = DisAglData['OrigAtoms']
targAtoms = DisAglData['TargAtoms']
AtomLabels = {}
for Oatom in origAtoms:
AtomLabels[Oatom[0]] = Oatom[1]
for Oatom in targAtoms:
AtomLabels[Oatom[0]] = Oatom[1]
DistArray = {}
AngArray = {}
for Oatom in origAtoms:
DistArray[Oatom[0]] = []
AngArray[Oatom[0]] = []
OxyzNames = ''
IndBlist = []
Dist = []
Vect = []
VectA = []
angles = []
for Tatom in targAtoms:
Xvcov = []
TxyzNames = ''
if 'covData' in DisAglData:
OxyzNames = [pfx+'dAx:%d'%(Oatom[0]),pfx+'dAy:%d'%(Oatom[0]),pfx+'dAz:%d'%(Oatom[0])]
TxyzNames = [pfx+'dAx:%d'%(Tatom[0]),pfx+'dAy:%d'%(Tatom[0]),pfx+'dAz:%d'%(Tatom[0])]
Xvcov = G2mth.getVCov(OxyzNames+TxyzNames,varyList,covMatrix)
result = G2spc.GenAtom(Tatom[3:6],SGData,False,Move=False)
BsumR = (Radii[Oatom[2]][0]+Radii[Tatom[2]][0])*Factor[0]
AsumR = (Radii[Oatom[2]][1]+Radii[Tatom[2]][1])*Factor[1]
for Txyz,Top,Tunit in result:
Dx = (Txyz-np.array(Oatom[3:6]))+Units
dx = np.inner(Amat,Dx)
dist = ma.masked_less(np.sqrt(np.sum(dx**2,axis=0)),0.5)
IndB = ma.nonzero(ma.masked_greater(dist-BsumR,0.))
if np.any(IndB):
for indb in IndB:
for i in range(len(indb)):
if str(dx.T[indb][i]) not in IndBlist:
IndBlist.append(str(dx.T[indb][i]))
unit = Units[indb][i]
tunit = (unit[0]+Tunit[0],unit[1]+Tunit[1],unit[2]+Tunit[2])
pdpx = G2mth.getDistDerv(Oatom[3:6],Tatom[3:6],Amat,unit,Top,SGData)
sig = 0.0
if len(Xvcov):
sig = np.sqrt(np.inner(pdpx,np.inner(Xvcov,pdpx)))
Dist.append([Oatom[0],Tatom[0],tunit,Top,ma.getdata(dist[indb])[i],sig])
if (Dist[-1][-2]-AsumR) <= 0.:
Vect.append(dx.T[indb][i]/Dist[-1][-2])
VectA.append([OxyzNames,np.array(Oatom[3:6]),TxyzNames,np.array(Tatom[3:6]),unit,Top])
else:
Vect.append([0.,0.,0.])
VectA.append([])
for D in Dist:
DistArray[Oatom[0]].append(D[1:])
Vect = np.array(Vect)
angles = np.zeros((len(Vect),len(Vect)))
angsig = np.zeros((len(Vect),len(Vect)))
for i,veca in enumerate(Vect):
if np.any(veca):
for j,vecb in enumerate(Vect):
if np.any(vecb):
angles[i][j],angsig[i][j] = G2mth.getAngSig(VectA[i],VectA[j],Amat,SGData,covData)
if i <= j: continue
AngArray[Oatom[0]].append((i,j,
G2mth.getAngSig(VectA[i],VectA[j],Amat,SGData,covData)))
return AtomLabels,DistArray,AngArray