myAtoms = ['Mg', 'B', 'B']
myLattice = Lattice()
theta = -30. * math.pi / 180.
rotMatrix = [[math.cos(theta), -math.sin(theta), 0],
[math.sin(theta), math.cos(theta), 0], [0, 0, 1]]
#myLattice.setLatPar(1., 1, 1.,gamma=120.0)#,baserot = rotMatrix)
print myLattice.base
a = 5.2
c = 6.3
base = [[1, 0, 0], [-1. / 2., math.sqrt(3.) / 2., 0.], [0, 0, c / a]]
myLattice.setLatBase(base)
print myLattice.base
print "baserot:"
print myLattice.baserot
myLattice.setLatPar(5.2, 5.2, 6.3, gamma=120.0, baserot=myLattice.baserot)
print myLattice.base
#myLattice.setLatBase(numpy.array(base)*a)
#print myLattice
#print myLattice.abcABG()
myStruct = Structure(myAtoms, myLattice)
# fractional coordinates:
myStruct[0].xyz[:] = [
0,
0,
0,
]
myStruct[1].xyz[:] = [
class QELattice(object):
"""Class QELattice for working with crystal lattices in QE notation
Uses diffpy.Lattice class for storage
Following parameters are dynamically linked to other properties
(E.g. lattice vectors):
ibrav - lattice type
if ibrav = 0, only 'a' prameter is relevant
a, b, c, cBC, cAC ,cAB - lattice parameters
type - lattice type to save into PWSCF cfg file ('celldm');
'traditional' - using a,b,c,cosAC, cosAB, cosBC;
'generic cubic', 'generic hexagonal' - assume exiasting
section 'CELL_PARAMETERS', 'generic' types also
assume/set ibrav = 0
setLattice() will set everything at once
"""
def __init__(self, ibrav = 1,a = 1. ,b = 1.,c = 1.,
cBC = 0.,cAC = 0. ,cAB = 0., fname = None, base = None ):
# Lattice.__init__(self)
self.filename = fname
self._type = 'celldm'
self.qeConf = None # should be none if nothing to parse
self._primitiveLattice = Lattice()
self._standardLattice = Lattice()
self._base = None
self._a0 = None
if self.filename != None:
self.setLatticeFromPWSCF(self.filename)
else:
if ibrav > 0 and base != None:
self.setLatticeFromQEVectors(ibrav, base)
else:
self.setLattice(ibrav ,a ,b , c, cBC ,cAC ,cAB, base)
def setLatticeFromQEVectors(self, ibrav, vectors):
""" Will extract conventional lattice parameters from primitive vectors.
'vectors' - is a list with primitive vectors (in QE notation),
including lattice parameters. For example from PWSCF output"""
from numpy import dot
# default values:
a = b = c = 1.0
cBC = cAC = cAB = 0.0
v = numpy.array(vectors, dtype = float)
if ibrav == 0:
raise NotImplementedError
# sc simple cubic:
if ibrav == 1:
a = v[0,0]
if ibrav == 2:
a = b = c = sqrt( 2.0*dot(v[0,:],v[0,:]) )
if ibrav == 3:
a = b = c = 2.0*sqrt( dot(v[0,:],v[0,:])/3.0)
if ibrav == 4:
a = b = sqrt( dot(v[0,:],v[0,:]))
c = sqrt( dot(v[2,:],v[2,:]))
cAB = cosd(120.0)
if ibrav == 5:
a = b = c = sqrt( dot(v[0,:],v[0,:]))
cBC = cAC = cAB = dot(v[0,:],v[2,:])/a**2
if ibrav == 6:
a = b = sqrt( dot(v[0,:],v[0,:]))
c = sqrt( dot(v[2,:],v[2,:]))
if ibrav == 7:
a = b = v[1,0] - v[2,0]
c = v[1,2] + v[2,2]
if ibrav == 8:
a = v[0,0]
b = v[1,1]
c = v[2,2]
if ibrav == 9:
a = v[0,0] - v[1,0]
b = v[0,1] + v[1,1]
c = v[2,2]
if ibrav == 10:
a = v[2,0] - v[0,0] - v[1,0]
b = v[2,1] - v[0,1] + v[1,1]
c = v[0,2] - v[1,2] + v[2,2]
if ibrav == 11:
a = v[0,0] - v[1,0]
b = v[1,1] - v[2,1]
c = v[0,2] - v[2,2]
if ibrav == 12:
a = v[0,0]
b = sqrt( dot(v[1,:],v[1,:]))
cAB = v[1,0]/b
c = v[2,2]
if ibrav == 13:
a = v[0,0] + v[2,0]
b = sqrt( dot(v[1,:],v[1,:]))
c = v[2,2] - v[0,2]
cAB = v[1,0]/b
if ibrav == 14:
a = v[0,0]
b = sqrt( dot(v[1,:],v[1,:]))
cAB = v[1,0]/b
c = sqrt( dot(v[2,:],v[2,:]))
cAC = v[2,0]/c
cBC = v[2,1]*sqrt(1.0 - cAB**2)/c + cAC*cAB
self.setLattice(ibrav, a, b, c, cBC, cAC, cAB)
def setLatticeFromPWSCF(self, fname = None):
if fname != None:
self.filename = fname
self.qeConf = QEConfig(fname)
self.qeConf.parse()
if 'ibrav' in self.qeConf.namelists['system'].params:
ibrav = int(self.qeConf.namelist('system').param('ibrav'))
if ibrav >= 0:
a, b, c, cBC, cAC, cAB, base = self.getLatticeParamsFromPWSCF(ibrav, fname)
else:
raise NotImplementedError("ibrav should be integer >= 0")
else:
raise NotImplementedError("config file should have ibrav defined")
self.setLattice(ibrav, a, b, c, cBC, cAC, cAB, base)
def setLattice(self, ibrav, a = None, b = None, c = None,
cBC = None, cAC = None, cAB = None, base = None):
""" 'base', numpy array of lattice vectors, and 'a' will only be used
if ibrav == 0. Otherwise, ibrav + lattice parameters will be used"""
from math import acos
# if [ibrav, a,b,c,cBC,cAC,cAB, base] == 8*[None]:
# return None
if ibrav == None:
raise NonImplementedError('ibrav should be specified')
self._ibrav = ibrav
self._a0 = a
if self._ibrav == 0:
# print 'Found "generic" cell:'
if base == None:
raise NonImplementedError('base must be specified')
if a == None: a = 1.0
qeBase = numpy.array(base, dtype = float)*a
# print qeBase
self._a = 1.0
self._primitiveLattice.setLatBase(qeBase)
self._standardLattice.setLatBase(qeBase)
else:
# Make sure all lattice parameters are mutually consistent
# according to ibrav. base array is not used:
if ibrav < 4 or ibrav == 5:
if a is not None:
self._a = self._b = self._c = a
else:
if b is not None:
self._a = self._b = self._c = b
else:
if c is not None:
self._a = self._b = self._c = c
else:
self._b = self._c = self._a
if ibrav < 4:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 4 or ibrav == 6 or ibrav == 7:
if a is not None:
self._a = self._b = a
else:
if b is not None:
self._a = self._b = b
else:
self._b = self._a
if c is not None:
self._c = c
if ibrav == 4:
self._cAB = cosd(120.0)
self._cBC = self._cAC = 0.0
if ibrav == 5:
if cBC is not None:
self._cBC = self._cAC = self._cAB = cBC
else:
if cAC is not None:
self._cBC = self._cAC = self._cAB = cAC
else:
if cAB is not None:
self._cBC = self._cAC = self._cAB = cAB
else:
self._cAC = self._cAB = self._cBC
if ibrav == 6 or ibrav == 7:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav > 7 and ibrav <= 14:
if a is not None:
self._a = a
if b is not None:
self._b = b
if c is not None:
self._c = c
if ibrav > 7 and ibrav < 12:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 12 or ibrav == 13:
if cAB is not None:
self._cAB = cAB
else:
if cBC is not None or cAC is not None:
raise Exception("Should specify cos(AB) only for" + \
" ibrav = 12 or ibrav = 13" )
self._cBC = self._cAC = 0.0
if ibrav == 14:
if cBC is not None:
self._cBC = cBC
if cAC is not None:
self._cAC = cAC
if cAB is not None:
self._cAB = cAB
# if a is not None: self._a = a
# if b is not None: self._b = b
# if c is not None: self._c = c
# if cBC is not None: self._cBC = cBC
# if cAC is not None: self._cAC = cAC
# if cAB is not None: self._cAB = cAB
qeBaseTuple = self._getQEBaseFromParCos(self._ibrav, self._a, self._b,
self._c, self._cBC, self._cAC, self._cAB)
qeBase = numpy.array(qeBaseTuple[1], dtype = float)*qeBaseTuple[0]
# print 'Found "' + qeBaseTuple[2] + '" cell'
# print 'Setting the base vectors according to QE conventions:'
# print qeBase
self._primitiveLattice.setLatBase(qeBase)
alpha = degrees(acos(self._cBC))
beta = degrees(acos(self._cAC))
gamma = degrees(acos(self._cAB))
self._standardLattice.setLatPar(self._a,self._b,self._c,alpha,beta,gamma)
# print "Standard Lattice:"
# print self._standardLattice.base
self._base = qeBase
def printBase(self):
if self._ibrav == 0:
print '"generic" cell:'
else:
qeBaseTuple = self._getQEBaseFromParCos(self._ibrav, self._a, self._b,
self._c, self._cBC, self._cAC, self._cAB)
qeBase = numpy.array(qeBaseTuple[1], dtype = float)*qeBaseTuple[0]
print '"' + qeBaseTuple[2] + '" cell:'
print qeBase
def latticeParams(self):
return [self._a, self._b,self._c, self._cBC, self._cAC, self._cAB]
def diffpy(self):
'''Returns diffpy.Lattice object. Do not use it for reading QE
(standard cell) lattice parameters. Use latticeParams, or a, b, c , ...
instead'''
return self._primitiveLattice
def getLatticeParamsFromPWSCF(self, ibrav, fname):
qeConf = QEConfig(fname)
qeConf.parse()
cBC = 0.0
cAC = 0.0
cAB = 0.0
if 'celldm(1)' in qeConf.namelists['system'].params:
self._type = 'celldm' # celldm(i), i=1,6
a = float(qeConf.namelist('system').param('celldm(1)'))
if ibrav == 0:
# lattice is set in the units of celldm(1)
# need to parse CELL_PARAMETERS
cellParLines = qeConf.card('cell_parameters').getLines()
cellParType = qeConf.card('cell_parameters').argument()
if cellParType == 'cubic' or cellParType == None:
self._type = 'generic cubic'
else:
if cellParType == 'hexagonal':
self._type = 'generic hexagonal'
# convert card into list
base = []
for line in cellParLines:
if '!' not in line:
words = line.split()
base.append([float(w) for w in words])
return a, None, None, None, None, None, numpy.array(base)
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, a, c_a*a, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
if ibrav == 14:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cBC = float(qeConf.namelist('system').param('celldm(4)'))
cAC = float(qeConf.namelist('system').param('celldm(5)'))
cAB = float(qeConf.namelist('system').param('celldm(6)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
else:
if ibrav == 0:
print "Should specify celldm(1) if use 'generic' lattice"
raise NotImplementedError
a = float(qeConf.namelist('system').param('A'))
self._type = 'traditional' # A, B, C, cosAB, cosAC, cosBC
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c = float(qeConf.namelist('system').param('C'))
return a, a, c, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 14:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cBC = float(qeConf.namelist('system').param('cosBC'))
cAC = float(qeConf.namelist('system').param('cosAC'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
def saveLatticeToPWSCF(self, fname = None):
"""Will save the lattice either into its own file or into supplied with fname.
It will also create all relevant sections/cards"""
if fname != None:
filename = fname
qeConf = QEConfig(fname)
qeConf.parse()
else:
if self.filename != None:
filename = self.filename
qeConf = self.qeConf
else:
raise # saveLatticeToPWSCF, filename was not supplied
if qeConf == None:
raise NotImplementedError("writeLatticeToPWSCF: qeConf was not properly initialized")
if 'system' not in qeConf.namelists:
qeConf.createNamelist('system')
# clear geometry from qeConf:
qeConf.namelist('system').removeParam('a')
qeConf.namelist('system').removeParam('b')
qeConf.namelist('system').removeParam('c')
qeConf.namelist('system').removeParam('cosab')
qeConf.namelist('system').removeParam('cosbc')
qeConf.namelist('system').removeParam('cosac')
qeConf.namelist('system').removeParam('celldm(1)')
qeConf.namelist('system').removeParam('celldm(2)')
qeConf.namelist('system').removeParam('celldm(3)')
qeConf.namelist('system').removeParam('celldm(4)')
qeConf.namelist('system').removeParam('celldm(5)')
qeConf.namelist('system').removeParam('celldm(6)')
if 'cell_parameters' in qeConf.cards:
qeConf.removeCard('cell_parameters')
if self._type == 'celldm':
qeConf.namelist('system').addParam('ibrav', self._ibrav)
qeConf.namelist('system').addParam('celldm(1)', self._a)
qeConf.namelist('system').addParam('celldm(2)', self._b/self._a)
qeConf.namelist('system').addParam('celldm(3)', self._c/self._a)
if self._ibrav < 14:
qeConf.namelist('system').addParam('celldm(4)', self._cAB)
else:
qeConf.namelist('system').addParam('celldm(4)', self._cBC)
qeConf.namelist('system').addParam('celldm(5)', self._cAC)
qeConf.namelist('system').addParam('celldm(6)', self._cAB)
else:
if self._type == 'traditional':
qeConf.namelist('system').addParam('ibrav', self._ibrav)
qeConf.namelist('system').addParam('A', self._a)
qeConf.namelist('system').addParam('B', self._b)
qeConf.namelist('system').addParam('C', self._c)
qeConf.namelist('system').addParam('cosAB', self._cAB)
qeConf.namelist('system').addParam('cosAC', self._cAC)
qeConf.namelist('system').addParam('cosBC', self._cBC)
else:
if 'generic' in self._type:
qeConf.namelist('system').addParam('celldm(1)', 1.0)
self._ibrav = 0
qeConf.namelist('system').addParam('ibrav', self._ibrav)
if self._type == 'generic hexagonal':
cardArg = 'hexagonal'
if self._type == 'generic cubic' or self._type == None:
cardArg = 'cubic'
qeConf.createCard('cell_parameters')
qeConf.card('cell_parameters').setArgument(cardArg)
qeConf.card('cell_parameters').removeLines()
for i in range(3):
v = self._primitiveLattice.base[i,:]
qeConf.card('cell_parameters').addLine(str(v)[1:-1])
qeConf.save(filename)
def recipCartesian(self, kPoint):
"""Conversts vector on fractional coordinates in reciprocal space into
a vector in cartesian coordinates"""
recip_base = self.diffpy().reciprocal().base*self._a
return numpy.dot( kPoint, recip_base)
def _getQEBaseFromParCos( self, ibrav = 1, a = 1., b = 1., c = 1.,
cBC = 0.,cAC = 0. ,cAB = 0.):
c_a = float(c)/a
# description dictionary of QE base vectors:
QEBase = {
# sc simple cubic:
1 : (a, [[1, 0, 0],
[0, 1, 0],
[0, 0, 1]],
'Simple Cubic'),
# fcc face centered cubic:
2 : (a/2., [[-1, 0, 1],
[0, 1, 1],
[-1, 1, 0]],
'Face Centered Cubic'),
# bcc body entered cubic:
3 : (a/2., [[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1]],
'Body Centered Cubic'),
# simple hexagonal and trigonal(p):
4 : (a, [[1, 0, 0],
[-0.5, sqrt(3.0)/2.0, 0.],
[0, 0, c_a]],
'Simple Hexagonal or Trigonal(P)'),
# trigonal(r):
5 : (a, [[sqrt((1.-cAB)/2.),-sqrt((1.-cAB)/6.), sqrt((1.+2.*cAB)/3.)],
[0, 2.*sqrt((1.-cAB)/6.), sqrt((1.+2.*cAB)/3.)],
[-sqrt((1.-cAB)/2.), -sqrt((1.-cAB)/6.), sqrt((1.+2.*cAB)/3.)]],
'Trigonal(R)'),
# simple tetragonal (p):
6 : (a, [[1, 0, 0],
[0, 1, 0.],
[0, 0, c_a]],
'Simple Tetragonal(P)'),
# body centered tetragonal (i):
7 : (a/2., [[1, -1, c_a],
[1, 1, c_a],
[-1, -1, c_a]],
'Body Centered Tetragonal (I)'),
# simple orthorhombic (p):
8 : (1.0, [[a, 0., 0.],
[0., b, 0.],
[0., 0., c]],
'Simple Orthorhombic (P)'),
# bco base centered orthorhombic:
9: (1.0, [[a/2., b/2., 0.],
[-a/2., b/2., 0.],
[0., 0., c]],
'Base Centered Orthorhombic'),
# face centered orthorhombic:
10: (1.0, [[a/2., 0., c/2.],
[a/2., b/2., 0.],
[0., b/2., c/2.]],
'Face Centered Orthorhombic' ),
# body centered orthorhombic:
11: (1.0, [[a/2., b/2., c/2.],
[-a/2., b/2., c/2.],
[-a/2., -b/2., c/2.]],
'Body Centered Orthorhombic'),
# monoclinic (p):
12: (1.0, [[a, 0, 0],
[b*cAB, b*sqrt(1.0 - cAB**2), 0],
[0, 0, c]],
'Monoclinic (P)'),
# base centered monoclinic:
13: (1.0, [[a/2., 0, -c/2.],
[b*cAB, b*sqrt(1.0 - cAB**2), 0],
[a/2., 0, c/2.]],
'Base Centered Monoclinic'),
# triclinic:
14: (1.0, [[a, 0, 0],
[b*cAB, b*sqrt(1.0 - cAB**2), 0],
[c*cAC, c*( cBC-cAC*cAB )/sqrt(1.-cAB**2), c*sqrt( 1. +
2.*cBC*cAC*cAB - cBC**2 - cAC**2 - cAB**2)/sqrt(1.-cAB**2)]],
'Triclinic')
}
return QEBase[ibrav]
####################################################################
# property handlers
####################################################################
# lattice parameters
def _get_a0(self):
if self._a0 != None:
return self._a0
else:
return self._a
a0 = property(_get_a0, doc ="old lattice parameter a0")
def _get_a(self):
return self._a
def _set_a(self, value):
self._a = value
self.setLattice(ibrav = self._ibrav, a = self._a)
a = property(_get_a, _set_a, doc ="lattice parameter a")
def _get_b(self):
return self._b
def _set_b(self, value):
self._b = value
self.setLattice(ibrav = self._ibrav, b = self._b)
b = property(_get_b, _set_b, doc ="""lattice parameter b""")
def _get_c(self):
return self._c
def _set_c(self, value):
self._c = value
self.setLattice(ibrav = self._ibrav, c = self._c)
c = property(_get_c, _set_c, doc ="""lattice parameter c""")
def _get_cBC(self):
return self._cBC
def _set_cBC(self, value):
self._cBC = value
self.setLattice(ibrav = self._ibrav, cBC = self._cBC)
cBC = property(_get_cBC, _set_cBC, doc ="""lattice parameter cBC""")
def _get_cAC(self):
return self._cAC
def _set_cAC(self, value):
self._cAC = value
self.setLattice(ibrav = self._ibrav, cAC = self._cAC)
cAC = property(_get_cAC, _set_cAC, doc ="""lattice parameter cAC""")
def _get_cAB(self):
return self._cAB
def _set_cAB(self, value):
self._cAB = value
self.setLattice(ibrav = self._ibrav, cAB = self._cAB)
cAB = property(_get_cAB, _set_cAB, doc ="""lattice parameter cAB""")
def _get_ibrav(self):
return self._ibrav
def _set_ibrav(self, value):
if value < 0: value = 0
ibravOld = self._ibrav
self._ibrav = value
if value == 0:
base = self._base/self._a
if ibravOld != 4:
self._type = 'generic cubic'
else:
self._type = 'generic hexagonal'
self.setLattice(ibrav = self._ibrav, a = self._a, base = base)
else:
if 'generic' in self._type:
self._type = 'celldm'
self.setLatticeFromQEVectors(self._ibrav, self.diffpy().base)
# self.setLattice(self._ibrav)
ibrav = property(_get_ibrav, _set_ibrav, doc ="""Lattice symmetry parameter
ibrav""")
def _get_type(self):
return self._type
def _set_type(self, value):
if 'generic' in value:
self._type = value
self._ibrav = 0
base = self._base/self._a
self.setLattice(ibrav = self._ibrav, a = self._a, base = base)
else:
if self._ibrav == 0:
pass
else:
self._type = value
type = property(_get_type, _set_type, doc ="""QE lattice type: 'celldm',
'traditional' or 'generic cubic', 'generic hexagonal'(implies ibrav = 0""")
myAtoms = ['Mg', 'B', 'B'] myLattice = Lattice() theta = -30.*math.pi/180. rotMatrix = [[math.cos(theta),-math.sin(theta),0],[math.sin(theta),math.cos(theta),0],[0,0,1]] #myLattice.setLatPar(1., 1, 1.,gamma=120.0)#,baserot = rotMatrix) print myLattice.base a = 5.2 c = 6.3 base = [[1,0,0],[-1./2.,math.sqrt(3.)/2.,0.],[0,0,c/a]] myLattice.setLatBase(base) print myLattice.base print "baserot:" print myLattice.baserot myLattice.setLatPar(5.2, 5.2, 6.3,gamma=120.0,baserot = myLattice.baserot) print myLattice.base #myLattice.setLatBase(numpy.array(base)*a) #print myLattice #print myLattice.abcABG() myStruct = Structure(myAtoms, myLattice) # fractional coordinates: myStruct[0].xyz[:] = [0, 0, 0,] myStruct[1].xyz[:] = [1, 2, 3,] print myStruct
