class QEStructure():
def __init__(self, qeConf):
"""the structure is initialized from PWSCF config file
'lattice' and 'structure' are automatically updated"""
self.filename = qeConf.filename
self.atomicSpecies = OrderedDict()
self.formatString = '%# .8f %# .8f %# .8f'
# optConstraints three 1/0 for each coordinate of each atom
self.optConstraints = []
self.qeConf = qeConf
#self.qeConf.parse()
#self.setStructureFromQEInput()
self.lattice = None
self.structure = None
self.nat = None
self.ntyp = None
def parseInput(self):
self.setStructureFromQEInput()
def parseOutput(self, pwscfOutputFile):
self.setStructureFromPWOutput(pwscfOutputFile)
# def _parseAtomicPositions(self, pwscfOut):
# for n in range(self.nat):
# words = pwscfOut[i + n + 1].split()
# atomSymbol = words[0]
# coords = [float(w) for w in words[1:4]]
# constraint = []
# if len(words) > 4:
# constraint = [int(c) for c in words[4:7]]
# self.optConstraints.append(numpy.array(constraint, dtype = int))
# print numpy.array(coords[0:3])*a_0
# coords = self.lattice.matter().fractional(numpy.array(coords[0:3])*a_0)
# self.structure.addNewAtom(atomSymbol, xyz = numpy.array(coords[0:3]))
def setStructureFromPWOutput(self, pwscfOutputFile):
"""
Loads structure from PWSCF output file. If there was geometry
optimization (relax or vc-relax), the structure will be reinitialized
from the last step of the optimization
"""
file = open(pwscfOutputFile)
pwscfOut = file.readlines()
pseudoList = []
atomList = []
massList = []
self.atomicSpecies = OrderedDict()
self.atomicPositionsType = 'alat'
# parse beginning:
for i, line in enumerate(pwscfOut):
if 'lattice parameter (a_0)' in line:
a_0 = float(line.split()[4])
if 'bravais-lattice index' in line:
ibrav = int(line.split('=')[1])
if 'number of atoms/cell' in line:
self.nat = int(line.split('=')[1])
if 'number of atomic types' in line:
self.ntyp = int(line.split('=')[1])
if 'PseudoPot.' in line:
pseudoList.append(line.split('read from file')[1].strip())
if 'atomic species valence mass pseudopotential' in line:
for j in range(self.ntyp):
atomList.append(pwscfOut[i+j+1].split()[0])
massList.append(float(pwscfOut[i+j+1].split()[2]))
if 'crystal axes: (cart. coord. in units of a_0)' in line:
latticeVectors = [[float(f)*a_0 for f in pwscfOut[i + 1].split()[3:6] ],
[float(f)*a_0 for f in pwscfOut[i + 2].split()[3:6] ],
[float(f)*a_0 for f in pwscfOut[i + 3].split()[3:6] ]]
self.lattice = QELattice(ibrav = ibrav, base = latticeVectors)
if 'site n. atom positions (a_0 units)' in line:
self.structure = Structure(lattice = self.lattice.matter())
for n in range(self.nat):
words = pwscfOut[i + n + 1].split()
atomSymbol = words[1]
coords = [float(w) for w in words[6:9]]
constraint = []
self.optConstraints.append(numpy.array(constraint, dtype = int))
#print numpy.array(coords[0:3])*a_0
coords = self.lattice.matter().fractional(numpy.array(coords[0:3])*a_0)
self.structure.addNewAtom(atomSymbol, xyz = numpy.array(coords[0:3]))
for a, m, p in zip(atomList, massList, pseudoList):
self.atomicSpecies[a] = AtomicSpecies(a, m, p)
#print 'Input structure from output file: ', self.toString()
#Parse end:
# Find all geometry optimization steps
posList = [i for i,line in enumerate(pwscfOut) if '! total energy' in line]
lastSection = pwscfOut[posList[-1]:]
for i, line in enumerate(lastSection):
if 'CELL_PARAMETERS (alat)' in line:
latticeVectors = [[float(f)*a_0 for f in lastSection[i + 1].split() ],
[float(f)*a_0 for f in lastSection[i + 2].split() ],
[float(f)*a_0 for f in lastSection[i + 3].split() ]]
self.lattice = QELattice(ibrav = ibrav, base = latticeVectors)
print self.lattice.matter().base
if 'ATOMIC_POSITIONS (alat)' in line:
self.structure = Structure(lattice = self.lattice.matter())
for n in range(self.nat):
words = lastSection[i + n + 1].split()
atomSymbol = words[0]
coords = [float(w) for w in words[1:4]]
constraint = []
if len(words) > 4:
constraint = [int(c) for c in words[4:7]]
self.optConstraints.append(numpy.array(constraint, dtype = int))
#print numpy.array(coords[0:3])*a_0
coords = self.lattice.matter().fractional(numpy.array(coords[0:3])*a_0)
self.structure.addNewAtom(atomSymbol, xyz = numpy.array(coords[0:3]))
#self.lattice.ibrav = ibrav
#print 'Output structure from output file: ', self.toString()
def setStructureFromQEInput(self):
""" Loads structure from PWSCF config file"""
self.atomicSpecies = OrderedDict()
self.lattice = QELattice(qeConf = self.qeConf)
self.structure = Structure(lattice = self.lattice.matter())
self.nat = int(self.qeConf.namelist('system').param('nat'))
self.ntyp = int(self.qeConf.namelist('system').param('ntyp'))
atomicLines = self.qeConf.card('atomic_positions').lines()
self.atomicPositionsType = self.qeConf.card('atomic_positions').arg()
if self.atomicPositionsType == 'bohr' or self.atomicPositionsType == 'angstrom':
raise NotImplementedError
if self.atomicPositionsType == None:
self.atomicPositionsType = 'alat'
for line in atomicLines:
if '!' not in line:
words = line.split()
coords = [float(w) for w in words[1:4]]
constraint = []
if len(words) > 4:
constraint = [int(c) for c in words[4:7]]
self.optConstraints.append(numpy.array(constraint, dtype = int))
atomSymbol = words[0]
if self.atomicPositionsType == 'alat':
coords = self.lattice.matter().fractional(numpy.array(coords[0:3])*self.lattice.a0)
if self.atomicPositionsType == 'crystal':
coords = numpy.array(coords[0:3])
self.structure.addNewAtom(atomSymbol, xyz = numpy.array(coords[0:3]))
# parse mass ATOMIC_SPECIES section:
atomicSpeciesLines = self.qeConf.card('atomic_species').lines()
for line in atomicSpeciesLines:
if '!' not in line:
atomicSpeciesWords = line.split()
element = atomicSpeciesWords[0]
mass = float(atomicSpeciesWords[1])
ps = atomicSpeciesWords[2]
self.atomicSpecies[element] = AtomicSpecies(element, mass, ps)
def toString(self):
s = self.lattice.toString() + '\n'
if self.atomicPositionsType == 'alat':
s = s + 'Atomic positions in units of lattice parametr "a":\n'
if self.atomicPositionsType == 'crystal':
s = s + 'Atomic positions in crystal coordinates:\n'
for atom, constraint in zip(self.structure, self.optConstraints):
if self.atomicPositionsType == 'alat':
coords = self.lattice.matter().cartesian(atom.xyz)/self.lattice.a
coords = self.formatString%(coords[0], coords[1], coords[2])
#coords = str(coords/self.lattice.a)[1:-1]
else:
if self.atomicPositionsType == 'crystal':
#coords = str(atom.xyz)[1:-1]
coords = self.formatString%(v[0], v[1], v[2])%(atom.xyz[0], atom.xyz[1], atom.xyz[2])
else:
raise NonImplementedError
s = s + '%-3s'%atom.element + ' ' + coords + ' ' \
+ str(constraint)[1:-1] + '\n'
s = s + '\n'
for element, specie in self.atomicSpecies.items():
s = s + specie.toString() + '\n'
return s
def updatePWInput(self, qeConf = None):
if qeConf == None:
qeConf = self.qeConf
self.lattice.updatePWInput(qeConf)
qeConf.namelist('system').remove('ntyp')
qeConf.namelist('system').remove('nat')
qeConf.namelist('system').add('ntyp', self.ntyp)
qeConf.namelist('system').add('nat', self.nat)
if 'atomic_positions' in qeConf.cards:
qeConf.removeCard('atomic_positions')
qeConf.createCard('atomic_positions')
qeConf.card('atomic_positions').setArg(self.atomicPositionsType)
for atom, constraint in zip(self.structure, self.optConstraints):
if self.atomicPositionsType == 'alat':
coords = self.lattice.matter().cartesian(atom.xyz)/self.lattice.a
coords = self.formatString%(coords[0], coords[1], coords[2])
else:
if self.atomicPositionsType == 'crystal':
#coords = str(atom.xyz)[1:-1]
coords = self.formatString%(atom.xyz[0], atom.xyz[1], atom.xyz[2])
else:
raise NonImplementedError
line = '%-3s'%atom.element + ' ' + coords + ' ' + str(constraint)[1:-1]
# line = atom.element + ' ' + coords + ' ' + str(constraint)[1:-1]
qeConf.card('atomic_positions').addLine(line)
# update ATOMIC_SPECIES card
if 'atomic_species' in qeConf.cards:
qeConf.removeCard('atomic_species')
qeConf.createCard('atomic_species')
for element, specie in self.atomicSpecies.items():
qeConf.card('atomic_species').addLine(specie.toString())
def save(self, fname = None):
"""Writes/updates structure into PW config file,
if the file does not exist, new one will be created"""
if fname != None:
filename = fname
self.lattice.save(filename)
qeConf = QEInput(fname)
qeConf.parse()
else:
filename = self.filename
self.lattice.save(filename)
qeConf = self.qeConf
#qeConf.parse()
self.updatePWInput(qeConf )
qeConf.save(filename)
def diffpy(self):
return self.structure
class QEStructure():
def __init__(self, qeConf):
"""the structure is initialized from PWSCF config file
'lattice' and 'structure' are automatically updated"""
self.filename = qeConf.filename
self.atomicSpecies = OrderedDict()
self.formatString = '%# .8f %# .8f %# .8f'
# optConstraints three 1/0 for each coordinate of each atom
self.optConstraints = []
self.qeConf = qeConf
self.lattice = QELattice()
self.structure = Structure(lattice=self.lattice.diffpy())
self.nat = None
self.ntyp = None
def parseInput(self):
self.setStructureFromQEInput()
def parseOutput(self, pwscfOutputFile):
self.setStructureFromPWOutput(pwscfOutputFile)
def setStructureFromPWOutput(self, pwscfOutputFile):
"""
Loads structure from PWSCF output file. If there was geometry
optimization (relax or vc-relax), the structure will be reinitialized
from the last step of the optimization
"""
file = open(pwscfOutputFile)
pwscfOut = file.readlines()
pseudoList = []
atomList = []
massList = []
self.atomicSpecies = OrderedDict()
self.atomicPositionsType = 'alat'
# parse beginning:
for i, line in enumerate(pwscfOut):
if 'lattice parameter (a_0)' in line:
a_0 = float(line.split()[4])
if 'bravais-lattice index' in line:
ibrav = int(line.split('=')[1])
if 'number of atoms/cell' in line:
self.nat = int(line.split('=')[1])
if 'number of atomic types' in line:
self.ntyp = int(line.split('=')[1])
if 'PseudoPot.' in line:
pseudoList.append(line.split('read from file')[1].strip())
if 'atomic species valence mass pseudopotential' in line:
for j in range(self.ntyp):
atomList.append(pwscfOut[i + j + 1].split()[0])
massList.append(float(pwscfOut[i + j + 1].split()[2]))
if 'crystal axes: (cart. coord. in units of a_0)' in line:
latticeVectors = [
[float(f) * a_0 for f in pwscfOut[i + 1].split()[3:6]],
[float(f) * a_0 for f in pwscfOut[i + 2].split()[3:6]],
[float(f) * a_0 for f in pwscfOut[i + 3].split()[3:6]]
]
self.lattice.setLatticeFromQEVectors(ibrav, latticeVectors)
if 'site n. atom positions (a_0 units)' in line:
self.structure = Structure(lattice=self.lattice.diffpy())
for n in range(self.nat):
words = pwscfOut[i + n + 1].split()
atomSymbol = words[1]
coords = [float(w) for w in words[6:9]]
constraint = []
self.optConstraints.append(
numpy.array(constraint, dtype=int))
#print numpy.array(coords[0:3])*a_0
coords = self.lattice.diffpy().fractional(
numpy.array(coords[0:3]) * a_0)
self.structure.addNewAtom(atomSymbol,
xyz=numpy.array(coords[0:3]))
for a, m, p in zip(atomList, massList, pseudoList):
self.atomicSpecies[a] = AtomicSpecies(a, m, p)
#print 'Input structure from output file: ', self.toString()
#Parse end:
# Find all geometry optimization steps
posList = [
i for i, line in enumerate(pwscfOut) if '! total energy' in line
]
lastSection = pwscfOut[posList[-1]:]
for i, line in enumerate(lastSection):
if 'CELL_PARAMETERS (alat)' in line:
latticeVectors = [
[float(f) * a_0 for f in lastSection[i + 1].split()],
[float(f) * a_0 for f in lastSection[i + 2].split()],
[float(f) * a_0 for f in lastSection[i + 3].split()]
]
self.lattice.setLatticeFromQEVectors(ibrav, latticeVectors)
#self.lattice = QELattice(ibrav = ibrav, base = latticeVectors)
print self.lattice.diffpy().base
if 'ATOMIC_POSITIONS (alat)' in line:
self.structure = Structure(lattice=self.lattice.diffpy())
for n in range(self.nat):
words = lastSection[i + n + 1].split()
atomSymbol = words[0]
coords = [float(w) for w in words[1:4]]
constraint = []
if len(words) > 4:
constraint = [int(c) for c in words[4:7]]
self.optConstraints.append(
numpy.array(constraint, dtype=int))
coords = self.lattice.diffpy().fractional(
numpy.array(coords[0:3]) * a_0)
self.structure.addNewAtom(atomSymbol,
xyz=numpy.array(coords[0:3]))
def setStructureFromQEInput(self):
""" Loads structure from PWSCF config file"""
self.atomicSpecies = OrderedDict()
self.lattice.setLatticeFromPWInput(self.qeConf)
#self.lattice = QELattice(qeConf = self.qeConf)
self.structure = Structure(lattice=self.lattice.diffpy())
self.nat = int(self.qeConf.namelist('system').param('nat'))
self.ntyp = int(self.qeConf.namelist('system').param('ntyp'))
atomicLines = self.qeConf.card('atomic_positions').lines()
self.atomicPositionsType = self.qeConf.card('atomic_positions').arg()
if self.atomicPositionsType == 'bohr' or self.atomicPositionsType == 'angstrom':
raise NotImplementedError
if self.atomicPositionsType == None:
self.atomicPositionsType = 'alat'
for line in atomicLines:
if '!' not in line:
words = line.split()
coords = [float(w) for w in words[1:4]]
constraint = []
if len(words) > 4:
constraint = [int(c) for c in words[4:7]]
self.optConstraints.append(numpy.array(constraint, dtype=int))
atomSymbol = words[0]
if self.atomicPositionsType == 'alat':
coords = self.lattice.diffpy().fractional(
numpy.array(coords[0:3]) * self.lattice.a0)
if self.atomicPositionsType == 'crystal':
coords = numpy.array(coords[0:3])
self.structure.addNewAtom(atomSymbol,
xyz=numpy.array(coords[0:3]))
# parse mass ATOMIC_SPECIES section:
atomicSpeciesLines = self.qeConf.card('atomic_species').lines()
for line in atomicSpeciesLines:
if '!' not in line:
atomicSpeciesWords = line.split()
element = atomicSpeciesWords[0]
mass = float(atomicSpeciesWords[1])
ps = atomicSpeciesWords[2]
self.atomicSpecies[element] = AtomicSpecies(
element, mass, ps)
def toString(self):
s = self.lattice.toString() + '\n'
if self.atomicPositionsType == 'alat':
s = s + 'Atomic positions in units of lattice parametr "a":\n'
if self.atomicPositionsType == 'crystal':
s = s + 'Atomic positions in crystal coordinates:\n'
for atom, constraint in zip(self.structure, self.optConstraints):
if self.atomicPositionsType == 'alat':
coords = self.lattice.diffpy().cartesian(
atom.xyz) / self.lattice.a
coords = self.formatString % (coords[0], coords[1], coords[2])
else:
if self.atomicPositionsType == 'crystal':
coords = self.formatString % (v[0], v[1], v[2]) % (
atom.xyz[0], atom.xyz[1], atom.xyz[2])
else:
raise NonImplementedError
s = s + '%-3s'%atom.element + ' ' + coords + ' ' \
+ str(constraint)[1:-1] + '\n'
s = s + '\n'
for element, specie in self.atomicSpecies.items():
s = s + specie.toString() + '\n'
return s
def updatePWInput(self, qeConf=None):
if qeConf == None:
qeConf = self.qeConf
self.lattice.updatePWInput(qeConf)
qeConf.namelist('system').remove('ntyp')
qeConf.namelist('system').remove('nat')
qeConf.namelist('system').add('ntyp', self.ntyp)
qeConf.namelist('system').add('nat', self.nat)
if 'atomic_positions' in qeConf.cards:
qeConf.removeCard('atomic_positions')
qeConf.createCard('atomic_positions')
qeConf.card('atomic_positions').setArg(self.atomicPositionsType)
for atom, constraint in zip(self.structure, self.optConstraints):
if self.atomicPositionsType == 'alat':
coords = self.lattice.diffpy().cartesian(
atom.xyz) / self.lattice.a
coords = self.formatString % (coords[0], coords[1], coords[2])
else:
if self.atomicPositionsType == 'crystal':
coords = self.formatString % (atom.xyz[0], atom.xyz[1],
atom.xyz[2])
else:
raise NonImplementedError
line = '%-3s' % atom.element + ' ' + coords + ' ' + str(
constraint)[1:-1]
qeConf.card('atomic_positions').addLine(line)
# update ATOMIC_SPECIES card
if 'atomic_species' in qeConf.cards:
qeConf.removeCard('atomic_species')
qeConf.createCard('atomic_species')
for element, specie in self.atomicSpecies.items():
qeConf.card('atomic_species').addLine(specie.toString())
def save(self, fname=None):
"""Writes/updates structure into PW config file,
if the file does not exist, new one will be created"""
if fname != None:
filename = fname
self.lattice.save(filename)
qeConf = QEInput(fname)
qeConf.parse()
else:
filename = self.filename
self.lattice.save(filename)
qeConf = self.qeConf
self.updatePWInput(qeConf)
qeConf.save(filename)
def diffpy(self):
return self.structure
class QEStructure():
def __init__(self, qeConf):
"""the structure is initialized from PWSCF config file
'lattice' and 'structure' are automatically updated"""
self.filename = qeConf.filename
self.atomicSpecies = OrderedDict()
self.formatString = '%# .8f %# .8f %# .8f'
# optConstraints three 1/0 for each coordinate of each atom
self.optConstraints = []
self.qeConf = qeConf
self.lattice = QELattice()
self.structure = Structure(lattice = self.lattice.diffpy())
self.nat = None
self.ntyp = None
self.atomicPositionsType = 'crystal'
def atomLabels(self):
labels = []
for l in self.atomicSpecies:
labels.append(l)
return labels
def parseInput(self):
self.setStructureFromQEInput()
def parseOutput(self, pwscfOutputFile):
self.setStructureFromPWOutput(pwscfOutputFile)
def setStructureFromPWOutput(self, pwscfOutputFile):
"""
Loads structure from PWSCF output file. If there was geometry
optimization (relax or vc-relax), the structure will be reinitialized
from the last step of the optimization
"""
file = open(pwscfOutputFile)
pwscfOut = file.readlines()
pseudoList = []
atomList = []
massList = []
self.atomicSpecies = OrderedDict()
self.atomicPositionsType = 'alat'
# parse beginning:
for i, line in enumerate(pwscfOut):
if 'lattice parameter (a_0)' in line:
a_0 = float(line.split()[4])
if 'bravais-lattice index' in line:
ibrav = int(line.split('=')[1])
if 'number of atoms/cell' in line:
self.nat = int(line.split('=')[1])
if 'number of atomic types' in line:
self.ntyp = int(line.split('=')[1])
if 'PseudoPot.' in line:
pseudoList.append(line.split('read from file')[1].strip())
if 'atomic species valence mass pseudopotential' in line:
for j in range(self.ntyp):
atomList.append(pwscfOut[i+j+1].split()[0])
massList.append(float(pwscfOut[i+j+1].split()[2]))
if 'crystal axes: (cart. coord. in units of a_0)' in line:
latticeVectors = [[float(f)*a_0 for f in pwscfOut[i + 1].split()[3:6] ],
[float(f)*a_0 for f in pwscfOut[i + 2].split()[3:6] ],
[float(f)*a_0 for f in pwscfOut[i + 3].split()[3:6] ]]
self.lattice.setLatticeFromQEVectors(ibrav, latticeVectors)
if 'site n. atom positions (a_0 units)' in line:
self.structure = Structure(lattice = self.lattice.diffpy())
for n in range(self.nat):
words = pwscfOut[i + n + 1].split()
atomSymbol = words[1]
coords = [float(w) for w in words[6:9]]
constraint = []
self.optConstraints.append(numpy.array(constraint, dtype = int))
#print numpy.array(coords[0:3])*a_0
coords = self.lattice.diffpy().fractional(numpy.array(coords[0:3])*a_0)
self.structure.addNewAtom(atomSymbol, xyz = numpy.array(coords[0:3]))
for a, m, p in zip(atomList, massList, pseudoList):
self.atomicSpecies[a] = AtomicSpecies(a, m, p)
#print 'Input structure from output file: ', self.toString()
#Parse end:
# Find all geometry optimization steps
posList = [i for i,line in enumerate(pwscfOut) if '! total energy' in line]
lastSection = pwscfOut[posList[-1]:]
for i, line in enumerate(lastSection):
if 'CELL_PARAMETERS (alat)' in line:
latticeVectors = [[float(f)*a_0 for f in lastSection[i + 1].split() ],
[float(f)*a_0 for f in lastSection[i + 2].split() ],
[float(f)*a_0 for f in lastSection[i + 3].split() ]]
self.lattice.setLatticeFromQEVectors(ibrav, latticeVectors)
#self.lattice = QELattice(ibrav = ibrav, base = latticeVectors)
#print self.lattice.diffpy().base
if 'ATOMIC_POSITIONS (alat)' in line:
self.structure = Structure(lattice = self.lattice.diffpy())
for n in range(self.nat):
words = lastSection[i + n + 1].split()
atomSymbol = words[0]
coords = [float(w) for w in words[1:4]]
constraint = []
if len(words) > 4:
constraint = [int(c) for c in words[4:7]]
self.optConstraints.append(numpy.array(constraint, dtype = int))
coords = self.lattice.diffpy().fractional(numpy.array(coords[0:3])*a_0)
self.structure.addNewAtom(atomSymbol, xyz = numpy.array(coords[0:3]))
def setStructureFromQEInput(self):
""" Loads structure from PWSCF config file"""
self.atomicSpecies = OrderedDict()
self.lattice.setLatticeFromPWInput(self.qeConf)
#self.lattice = QELattice(qeConf = self.qeConf)
self.structure = Structure(lattice = self.lattice.diffpy())
self.nat = self.ntyp = None
self.filename = self.qeConf.filename
self.optConstraints = []
if 'system' in self.qeConf.namelists:
self.nat = int(self.qeConf.namelist('system').param('nat'))
self.ntyp = int(self.qeConf.namelist('system').param('ntyp'))
if 'atomic_positions' in self.qeConf.cards:
atomicLines = self.qeConf.card('atomic_positions').lines()
self.atomicPositionsType = self.qeConf.card('atomic_positions').arg()
if self.atomicPositionsType == 'bohr' or self.atomicPositionsType == 'angstrom':
raise NotImplementedError
if self.atomicPositionsType == None:
self.atomicPositionsType = 'alat'
for line in atomicLines:
if '!' not in line:
words = line.split()
coords = [float(w) for w in words[1:4]]
constraint = []
if len(words) > 4:
constraint = [int(c) for c in words[4:7]]
self.optConstraints.append(numpy.array(constraint, dtype = int))
atomSymbol = words[0]
if self.atomicPositionsType == 'alat':
coords = self.lattice.diffpy().fractional(numpy.array(coords[0:3])*self.lattice.a0)
if self.atomicPositionsType == 'crystal':
coords = numpy.array(coords[0:3])
self.structure.addNewAtom(atomSymbol, xyz = numpy.array(coords[0:3]))
# parse mass ATOMIC_SPECIES section:
if 'atomic_species' in self.qeConf.cards:
atomicSpeciesLines = self.qeConf.card('atomic_species').lines()
for line in atomicSpeciesLines:
if '!' not in line:
if line.strip() != '':
atomicSpeciesWords = line.split()
element = atomicSpeciesWords[0]
mass = 0
ps = ''
if len(atomicSpeciesWords) > 1 :
mass = float(atomicSpeciesWords[1])
if len(atomicSpeciesWords) > 2:
ps = atomicSpeciesWords[2]
self.atomicSpecies[element] = AtomicSpecies(element, mass, ps)
def load(self, source, **args):
task = {
'diffpy': self.setStructureFromDiffpyStructure
}
if source == 'diffpy':
if 'ibrav' in args and args['ibrav'] != 0:
task['diffpy'] = self.setReducedStructureFromDiffpyStructure
task[source](**args)
self.updatePWInput(qeConf = self.qeConf)
def setStructureFromDiffpyStructure(self, structure, massList = [], psList = [], ibrav = 0):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with pseudopotential names
diffpyStructure object will be modified with reduced atomic positions
"""
diffpyLattice = structure.lattice
self.structure = structure
#set lattice and convert to bohr units
qeLattice = QELattice(ibrav = 0, a = 1.889725989, base = diffpyLattice.base)
self.lattice = qeLattice
self.lattice.type = 'generic cubic'
atomNames = []
for a in structure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
#print atomNames
#print len(massList)
for i, elem in enumerate(atomNames):
if len(massList) - 1 < i:
mass = 0
else:
mass = massList[i]
if len(psList) - 1 < i:
ps = ''
else:
ps = psList[i]
self.atomicSpecies[elem] = AtomicSpecies(elem, mass, ps)
for atom in structure:
self.optConstraints.append([])
# for i, atom in enumerate(structure):
# elem = self._element(atom)
# if len(massList) - 1 < i:
# mass = 0
# else:
# mass = massList[i]
# if len(psList) - 1 < i:
# ps = ''
# else:
# ps = psList[i]
# self.atomicSpecies[elem] = AtomicSpecies(elem, mass, ps)
# self.optConstraints.append([])
# for atom, mass, ps in zip(structure, massList, psList):
# elem = self._element(atom)
# self.atomicSpecies[elem] = AtomicSpecies(elem, mass, ps)
# self.optConstraints.append([])
self.nat = len(structure)
self.ntyp = len(self.atomicSpecies)
def setReducedStructureFromDiffpyStructure(self, structure, ibrav, massList = [], psList = []):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with pseudopotential names
diffpyStructure object will be modified with reduced atomic positions
"""
#self.atomicSpecies = OrderedDict()
#self.optConstraints = []
#self.atomicPositionsType = 'crystal'
diffpyLattice = structure.lattice
a = diffpyLattice.a
b = diffpyLattice.b
c = diffpyLattice.c
cAB = cosd(diffpyLattice.gamma)
cBC = cosd(diffpyLattice.alpha)
cAC = cosd(diffpyLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
self.lattice = qeLattice
# make a deep copy (does not wok now)
#reducedStructure = Structure(diffpyStructure)
reducedStructure = structure
reducedStructure.placeInLattice(Lattice(base=qeLattice.diffpy().base))
# collect atoms that are at equivalent position to some previous atom
duplicates = set([a1
for i0, a0 in enumerate(reducedStructure) for a1 in reducedStructure[i0+1:]
if self._element(a0) == self._element(a1) and equalPositions(a0.xyz, a1.xyz, eps=1e-4)])
# Filter out duplicate atoms. Use slice assignment so that
# reducedStructure is not replaced with a list.
reducedStructure[:] = [a for a in reducedStructure if not a in duplicates]
self.structure = reducedStructure
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
#print atomNames
#print len(massList)
for i, elem in enumerate(atomNames):
if len(massList) - 1 < i:
mass = 0
else:
mass = massList[i]
if len(psList) - 1 < i:
ps = ''
else:
ps = psList[i]
#print mass, ps
# atomDict[a] =
# for i, atom in enumerate(reducedStructure):
# elem = self._element(atom)
# if len(massList) - 1 < i:
# mass = 0
# else:
# mass = massList[i]
# if len(psList) - 1 < i:
# ps = ''
# else:
# ps = psList[i]
self.atomicSpecies[elem] = AtomicSpecies(elem, mass, ps)
for atom in reducedStructure:
self.optConstraints.append([])
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
self.nat = len(reducedStructure)
self.ntyp = len(self.atomicSpecies)
# use rstrip to avoid duplicate line feed
#print reducedStructure.writeStr(format='discus').rstrip()
#print reducedStructure.writeStr(format='discus')
#print reducedStructure.writeStr().rstrip()
#print reducedStructure
#self.lattice = setLatticeFromDiffpyLattice(structure.lattice, ibrav)
# def toString(self):
# s = self.lattice.toString() + '\n'
# if self.atomicPositionsType == 'alat':
# s = s + 'Atomic positions in units of lattice parametr "a":\n'
# if self.atomicPositionsType == 'crystal':
# s = s + 'Atomic positions in crystal coordinates:\n'
# for atom, constraint in zip(self.structure, self.optConstraints):
# if self.atomicPositionsType == 'alat':
# coords = self.lattice.diffpy().cartesian(atom.xyz)/self.lattice.a
# coords = self.formatString%(coords[0], coords[1], coords[2])
# else:
# if self.atomicPositionsType == 'crystal':
# coords = self.formatString%(atom.xyz[0], atom.xyz[1], atom.xyz[2])
# else:
# raise NonImplementedError
# s = s + '%-3s'%self._element(atom) + ' ' + coords + ' ' \
# + str(constraint)[1:-1] + '\n'
# s = s + '\n'
# for element, specie in self.atomicSpecies.items():
# s = s + specie.toString() + '\n'
# return s
def toString(self, string = None):
if string != None:
string = self.lattice.toString(string = string)
qeConf = QEInput(config = string)
qeConf.parse()
else:
if self.qeConf != None:
qeConf = self.qeConf
else:
qeConf = QEInput(config = '')
self.updatePWInput(qeConf)
return qeConf.toString()
def updatePWInput(self, qeConf = None):
if qeConf == None:
qeConf = self.qeConf
self.lattice.updatePWInput(qeConf)
if 'system' not in qeConf.namelists:
qeConf.addNamelist('system')
qeConf.namelist('system').remove('ntyp')
qeConf.namelist('system').remove('nat')
if self.ntyp != None:
qeConf.namelist('system').add('ntyp', self.ntyp)
if self.nat != None:
qeConf.namelist('system').add('nat', self.nat)
if len(qeConf.namelist('system').params) == 0:
qeConf.removeNamelist('system')
if 'atomic_positions' in qeConf.cards:
qeConf.removeCard('atomic_positions')
qeConf.createCard('atomic_positions')
qeConf.card('atomic_positions').setArg(self.atomicPositionsType)
for atom, constraint in zip(self.structure, self.optConstraints):
if self.atomicPositionsType == 'alat':
coords = self.lattice.diffpy().cartesian(atom.xyz)/self.lattice.a
coords = self.formatString%(coords[0], coords[1], coords[2])
else:
if self.atomicPositionsType == 'crystal':
coords = self.formatString%(atom.xyz[0], atom.xyz[1], atom.xyz[2])
else:
raise NonImplementedError
line = '%-3s'%self._element(atom) + ' ' + coords + ' ' + str(constraint)[1:-1]
qeConf.card('atomic_positions').addLine(line)
if len(qeConf.card('atomic_positions').lines()) == 0:
qeConf.removeCard('atomic_positions')
# update ATOMIC_SPECIES card
if 'atomic_species' in qeConf.cards:
qeConf.removeCard('atomic_species')
qeConf.createCard('atomic_species')
for element, specie in self.atomicSpecies.items():
qeConf.card('atomic_species').addLine(specie.toString())
if len(qeConf.card('atomic_species').lines()) == 0:
qeConf.removeCard('atomic_species')
def save(self, fname = None):
"""Writes/updates structure into PW config file,
if the file does not exist, new one will be created"""
filename = fname
if fname != None:
self.lattice.save(filename)
qeConf = QEInput(fname)
qeConf.parse()
else:
filename = self.filename
self.lattice.save(filename)
qeConf = self.qeConf
self.updatePWInput(qeConf)
qeConf.save(filename)
def diffpy(self):
return self.structure
def _element(self, atom):
"""
Is needed for suport both diffpy and matter classess
"""
if 'element' in dir(atom):
return atom.element
else:
if 'symbol' in dir(atom):
return atom.symbol
else:
raise