def getLatticeParameters(self):
"""Extract lattice parameters after pwscf geometry optimization
Returns a list of 6 parameters: A, B, C, cos(BC), cos(AC), cos(AB)"""
from qelattice import QELattice
# obtain lattice from PWSCF input file:
lat = QELattice(fname=self.pwscfInput)
pwscfOut = read_file(self.pwscfOutput)
key_a_0 = find_key_from_string(pwscfOut, 'lattice parameter (a_0)')
a_0 = float(string.split(pwscfOut[key_a_0])[4])
if lat.type == 'traditional':
a_0 = a_0 * 0.529177249 # convert back to angstrom
keyEnd = max(
find_all_keys_from_marker_string(pwscfOut, '!', 'total energy'))
keyCellPar = find_key_from_string_afterkey(pwscfOut, keyEnd, \
'CELL_PARAMETERS (alat)') + 1
latticeVectors = [
[
float(valstr) * a_0
for valstr in string.split(pwscfOut[keyCellPar])
],
[
float(valstr) * a_0
for valstr in string.split(pwscfOut[keyCellPar + 1])
],
[
float(valstr) * a_0
for valstr in string.split(pwscfOut[keyCellPar + 2])
]
]
lat.setLatticeFromQEVectors(lat.ibrav, latticeVectors)
return [lat.a, lat.b, lat.c, lat.cBC, lat.cAC, lat.cAB]
def reduce(self, ibrav = None):
"""
Reduces a structure instance with nonprimitive lattice ( i.e. solves
for equivalent atomic positions) according to specified lattice type (ibrav).
Each ibrav number corresponds to a specific primitive lattice
(see QE documentation).
"""
ib = self.lattice.ibrav
if ibrav != None:
ib = ibrav
a = self.lattice.matter().a
b = self.lattice.matter().b
c = self.lattice.matter().c
cAB = cosd(self.lattice.matter().gamma)
cBC = cosd(self.lattice.matter().alpha)
cAC = cosd(self.lattice.matter().beta)
if ib > 0:
qeLattice = QELattice(ibrav = ib, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
else:
qeLattice = QELattice(ibrav = ib, base = self.lattice.base)
qeLattice._qeInput = self._qeInput
reducedStructure = QEStructure(self)
reducedStructure.placeInLattice( qeLattice )
# 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 a0.symbol == a1.symbol 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.
self.lattice = qeLattice
self[:] = [a for a in reducedStructure if not a in duplicates]
self._qeInput.structure = self
return
def _setStructureFromMatterStructure(self, structure, massList = [], psList = [], ibrav = 0):
"""
structure - matter.Structure object
ibrav - Lattice index
psList - list of strings with potential names
matterStructure object will be modified with reduced atomic positions
"""
matterLattice = structure.lattice
qeLattice = QELattice(ibrav = 0, base = matterLattice.base)
qeLattice.a = 1.889725989*qeLattice.a
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
self.lattice.type = 'generic cubic'
atomNames = []
for a in structure:
if a.symbol not in atomNames:
atomNames.append(a.symbol)
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
for atom in structure:
self.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
mass = atomicSpecies[atom.symbol][0], \
potential = atomicSpecies[atom.symbol][1],\
lattice = self.lattice, optConstraint = [])
def __init__(self, atoms = [], lattice = None, filename = None, qeInput = None):
"""
atoms -- list of QEAtom atom instances or a QEStructure object
lattice -- QELattice object
filename -- filename QE input file
qeInput -- pointer to a PWInput parsing object. If not None,
its PWInput.structure and PWInput.structure.lattice
will be reset to the current instance of the structure
"""
Structure.__init__(self)
self.formatString = '%# .8f %# .8f %# .8f'
self._atomicPositionsType = 'crystal'
self._qeInput = qeInput
self.lattice = QELattice()
self.lattice._qeInput = self._qeInput
if lattice != None:
if self.lattice._qeInput != None:
self._qeInput = self.lattice._qeInput
else:
self.lattice._qeInput = self._qeInput
self.lattice = QELattice( lattice = lattice )
# CP and PW inputs are compatible
from pwinput import PWInput
from cpinput import CPInput
if isinstance( atoms, PWInput) or isinstance( atoms, CPInput):
qeInput = atoms
elif isinstance( atoms, QEStructure):
stru = atoms
self.__dict__.update( stru.__dict__ )
# deep copy of the lattice will deep copy PWInput as well
self.lattice = QELattice(lattice = stru.lattice)
self._qeInput = self.lattice._qeInput
self[:] = stru
else:
if self.lattice == None:
raise "Lattice must be provided"
self[:] = atoms
if filename != None:
qeInput = PWInput(filename = filename)
qeInput.parse()
self.parseInput(qeInput)
if qeInput != None:
self.lattice._qeInput = qeInput
self._qeInput = qeInput
if self.lattice._qeInput != None:
self.lattice._qeInput.structure = self
self.lattice._qeInput.structure.lattice = self.lattice
return
def _setReducedStructureFromMatterStructure(self, structure, ibrav, massList = [], psList = []):
"""
structure - matter.Structure object
ibrav - Lattice index
psList - list of strings with potential names
matterStructure object will be modified with reduced atomic positions
"""
import copy
matterLattice = copy.deepcopy(structure.lattice)
# there is a big problem with what Nikolay is doing because he is initializing QELattice with abcalbega which
# leaves room for errors in how the basis vectors are chosen compared to the old lattice
a = matterLattice.a
b = matterLattice.b
c = matterLattice.c
cAB = cosd(matterLattice.gamma)
cBC = cosd(matterLattice.alpha)
cAC = cosd(matterLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
#what he should do is initialize the vectors of QELattice with the vectors of matterLattice
#
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms = structure)
reducedStructure.placeInLattice(Lattice(base=qeLattice.matter().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 a0.symbol==a1.symbol 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]
atomNames = []
for a in reducedStructure:
if a.symbol not in atomNames:
atomNames.append(a.symbol)
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
self.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
mass = atomicSpecies[atom.symbol][0], \
potential = atomicSpecies[atom.symbol][1],\
lattice = self.lattice, optConstraint = [])
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 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 getLatticeParameters(self):
"""Extract lattice parameters after pwscf geometry optimization
Returns a list of 6 parameters: A, B, C, cos(BC), cos(AC), cos(AB)"""
from qelattice import QELattice
# obtain lattice from PWSCF input file:
lat = QELattice(fname = self.pwscfInput)
pwscfOut = read_file(self.pwscfOutput)
key_a_0 = find_key_from_string(pwscfOut, 'lattice parameter (a_0)')
a_0 = float( string.split( pwscfOut[key_a_0] )[4] )
if lat.type == 'traditional': a_0 = a_0*0.529177249 # convert back to angstrom
keyEnd = max( find_all_keys_from_marker_string(pwscfOut, '!', 'total energy') )
keyCellPar = find_key_from_string_afterkey(pwscfOut, keyEnd, \
'CELL_PARAMETERS (alat)') + 1
latticeVectors = [[float(valstr)*a_0 for valstr in string.split( pwscfOut[keyCellPar] ) ],
[ float(valstr)*a_0 for valstr in string.split( pwscfOut[keyCellPar+1] ) ],
[ float(valstr)*a_0 for valstr in string.split( pwscfOut[keyCellPar+2] ) ]]
lat.setLatticeFromQEVectors(lat.ibrav, latticeVectors)
return [lat.a, lat.b, lat.c, lat.cBC ,lat.cAC , lat.cAB]
def reduce(self, ibrav=None):
"""
Reduces a structure instance with nonprimitive lattice ( i.e. solves
for equivalent atomic positions) according to specified lattice type (ibrav).
Each ibrav number corresponds to a specific primitive lattice
(see QE documentation).
"""
ib = self.lattice.ibrav
if ibrav != None:
ib = ibrav
a = self.lattice.diffpy().a
b = self.lattice.diffpy().b
c = self.lattice.diffpy().c
cAB = cosd(self.lattice.diffpy().gamma)
cBC = cosd(self.lattice.diffpy().alpha)
cAC = cosd(self.lattice.diffpy().beta)
if ib > 0:
qeLattice = QELattice(ibrav = ib, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
else:
qeLattice = QELattice(ibrav=ib, base=self.lattice.base)
qeLattice._qeInput = self._qeInput
reducedStructure = QEStructure(self)
reducedStructure.placeInLattice(qeLattice)
# 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 a0.element == a1.element
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.
self.lattice = qeLattice
self[:] = [a for a in reducedStructure if not a in duplicates]
self._qeInput.structure = self
return
def _setStructureFromDiffpyStructure(self,
structure,
massList=[],
psList=[],
ibrav=0):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
diffpyLattice = structure.lattice
qeLattice = QELattice(ibrav=0, base=diffpyLattice.base)
qeLattice.a = 1.889725989 * qeLattice.a
qeLattice._qeInput = self._qeInput
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))
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
for atom in structure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
def setStructureFromPWSCF(self):
""" Loads structure from PWSCF config file"""
self.lattice = QELattice(fname=self.filename)
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').getLines()
self.atomicPositionsType = self.qeConf.card(
'atomic_positions').argument()
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').getLines()
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 __init__(self, atype=None, xyz=None, mass = None, \
potential = None, lattice=None, optConstraint = None, name=None):
"""Create atom of a specified type at given lattice coordinates.
Atom(a) creates a copy of Atom instance a.
atype -- element symbol string or Atom instance
xyz -- fractional(crystal) coordinates
name -- atom label
mass -- atom mass
potential -- pseudopotential file name
lattice -- QE coordinate system for fractional coordinates
optConstraint -- list of up to three constraints for each coordinate
for QE geometry optimization (0 or 1)
"""
# declare data members
self.element = None
self._xyz = numpy.zeros(3, dtype=float)
self.name = ''
self._mass = 0
self._potential = ''
self.lattice = QELattice()
from pwinput import PWInput
self.lattice._qeInput = PWInput()
self._optConstraint = numpy.array([], dtype = int)
# assign them as needed
if isinstance(atype, QEAtom):
atype_dup = atype.__copy__()
self.__dict__.update(atype_dup.__dict__)
else:
self.element = atype
# take care of remaining arguments
if xyz is not None: self._xyz[:] = xyz
if name is not None: self.name = name
if mass is not None: self._mass = mass
if potential is not None: self._potential = potential
if lattice is not None: self.lattice = lattice
if optConstraint is not None: self._optConstraint = \
numpy.array(optConstraint, dtype = int)
return
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 __init__(self, atoms=[], lattice=None, filename=None, qeInput=None):
"""
atoms -- list of QEAtom atom instances or a QEStructure object
lattice -- QELattice object
filename -- filename QE input file
qeInput -- pointer to a PWInput parsing object. If not None,
its PWInput.structure and PWInput.structure.lattice
will be reset to the current instance of the structure
"""
Structure.__init__(self)
self.formatString = '%# .8f %# .8f %# .8f'
self._atomicPositionsType = 'crystal'
self._qeInput = qeInput
self.lattice = QELattice()
self.lattice._qeInput = self._qeInput
if lattice != None:
if self.lattice._qeInput != None:
self._qeInput = self.lattice._qeInput
else:
self.lattice._qeInput = self._qeInput
self.lattice = QELattice(lattice=lattice)
# CP and PW inputs are compatible
from pwinput import PWInput
from cpinput import CPInput
if isinstance(atoms, PWInput) or isinstance(atoms, CPInput):
qeInput = atoms
elif isinstance(atoms, QEStructure):
stru = atoms
self.__dict__.update(stru.__dict__)
# deep copy of the lattice will deep copy PWInput as well
self.lattice = QELattice(lattice=stru.lattice)
self._qeInput = self.lattice._qeInput
self[:] = stru
else:
if self.lattice == None:
raise "Lattice must be provided"
self[:] = atoms
if filename != None:
qeInput = PWInput(filename=filename)
qeInput.parse()
self.parseInput(qeInput)
if qeInput != None:
self.lattice._qeInput = qeInput
self._qeInput = qeInput
if self.lattice._qeInput != None:
self.lattice._qeInput.structure = self
self.lattice._qeInput.structure.lattice = self.lattice
return
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 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]))
def _setReducedStructureFromDiffpyStructure(self,
structure,
ibrav,
massList=[],
psList=[]):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
import copy
diffpyLattice = copy.deepcopy(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)
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms=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
]
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
def _setReducedStructureFromMatterStructure(self,
structure,
ibrav,
massList=[],
psList=[]):
"""
structure - matter.Structure object
ibrav - Lattice index
psList - list of strings with potential names
matterStructure object will be modified with reduced atomic positions
"""
import copy
matterLattice = copy.deepcopy(structure.lattice)
# there is a big problem with what Nikolay is doing because he is initializing QELattice with abcalbega which
# leaves room for errors in how the basis vectors are chosen compared to the old lattice
a = matterLattice.a
b = matterLattice.b
c = matterLattice.c
cAB = cosd(matterLattice.gamma)
cBC = cosd(matterLattice.alpha)
cAC = cosd(matterLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
#what he should do is initialize the vectors of QELattice with the vectors of matterLattice
#
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms=structure)
reducedStructure.placeInLattice(Lattice(base=qeLattice.matter().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 a0.symbol == a1.symbol
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
]
atomNames = []
for a in reducedStructure:
if a.symbol not in atomNames:
atomNames.append(a.symbol)
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
self.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
mass = atomicSpecies[atom.symbol][0], \
potential = atomicSpecies[atom.symbol][1],\
lattice = self.lattice, optConstraint = [])
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)
class QEStructure(Structure):
"""
Parses and handles Quantum Espresso structure information.
QEStructure is inherited from a diffpy.Structure, which is in turn
inherited from a Python list.
QEStructure is a list of QEAtom object instances.
All list functionality is preserved. setitem and
setslice methods are overloaded so that the lattice attribute
of atoms get set to lattice.
QEStructure, QELattice and QEAtom objects contain a hidden QEInput
pointer to current Quantum Espresso parsing object.
if QEInput.autoUpdate = True (default),any change in a property from
QEStructure, QELattice, or QEAtom will automatically invoke
QEInput.update(). In that case, QEInput.save() or QEInput.toString() will
immediately yield updated QE input file or a string
All properties are mutually synchronized. E.g. change in a lattice parameter
will also affect other lattice parameters as well as atomic positions
according to the lattice type (ibrav)
All relevant methods from diffpy.Structure are redefined.
QEStructure read only properties, automatically synchronized with current
list of Atoms:
nat -- "number of atoms" (integer)
ntyp -- "number of atomic types" (integer)
atomicSpecies -- OrderedDic of AtomicSpecies class instances
(see AtomicSpecies class definition)
Other properties:
atomicPositionsType -- 'crystal' (default), 'alat', 'bohr', and 'angstrom'
Note: This version of QEStructure does not support multiple images from
QE input files
"""
def __init__(self, atoms=[], lattice=None, filename=None, qeInput=None):
"""
atoms -- list of QEAtom atom instances or a QEStructure object
lattice -- QELattice object
filename -- filename QE input file
qeInput -- pointer to a PWInput parsing object. If not None,
its PWInput.structure and PWInput.structure.lattice
will be reset to the current instance of the structure
"""
Structure.__init__(self)
self.formatString = '%# .8f %# .8f %# .8f'
self._atomicPositionsType = 'crystal'
self._qeInput = qeInput
self.lattice = QELattice()
self.lattice._qeInput = self._qeInput
if lattice != None:
if self.lattice._qeInput != None:
self._qeInput = self.lattice._qeInput
else:
self.lattice._qeInput = self._qeInput
self.lattice = QELattice(lattice=lattice)
# CP and PW inputs are compatible
from pwinput import PWInput
from cpinput import CPInput
if isinstance(atoms, PWInput) or isinstance(atoms, CPInput):
qeInput = atoms
elif isinstance(atoms, QEStructure):
stru = atoms
self.__dict__.update(stru.__dict__)
# deep copy of the lattice will deep copy PWInput as well
self.lattice = QELattice(lattice=stru.lattice)
self._qeInput = self.lattice._qeInput
self[:] = stru
else:
if self.lattice == None:
raise "Lattice must be provided"
self[:] = atoms
if filename != None:
qeInput = PWInput(filename=filename)
qeInput.parse()
self.parseInput(qeInput)
if qeInput != None:
self.lattice._qeInput = qeInput
self._qeInput = qeInput
if self.lattice._qeInput != None:
self.lattice._qeInput.structure = self
self.lattice._qeInput.structure.lattice = self.lattice
return
def addNewAtom(self, *args, **kwargs):
"""Add new Atom instance to the end of this Structure.
All arguments are forwarded to Atom constructor.
No return value.
"""
kwargs['lattice'] = self.lattice
a = QEAtom(*args, **kwargs)
list.append(self, a)
self._uncache('labels')
return
def placeInLattice(self, new_lattice):
"""place structure into new_lattice coordinate system
sets lattice to new_lattice and recalculate fractional coordinates
of all atoms so their absolute positionls remain the same
return self
"""
Tx = numpy.dot(self.lattice.diffpy().base,
new_lattice.diffpy().recbase)
Tu = numpy.dot(self.lattice.diffpy().normbase,
new_lattice.diffpy().recnormbase)
for a in self:
a.xyz = numpy.dot(a.xyz, Tx)
tmpInput = self.lattice._qeInput
self.lattice = new_lattice
self.lattice._qeInput = tmpInput
self.lattice._qeInput.structure = self
return self
##############################################################################
# overloaded list methods - taken from diffpy.Structure
##############################################################################
def append(self, a, copy=True):
"""Append atom to a structure and update its lattice attribute.
a -- instance of QEAtom
copy -- flag for appending a copy of a.
When False, append a and update a.owner.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.append(self, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def insert(self, idx, a, copy=True):
"""Insert atom a before position idx in this Structure.
idx -- position in atom list
a -- instance of QEAtom
copy -- flag for inserting a copy of a.
When False, append a and update a.lattice.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.insert(self, idx, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def extend(self, atoms, copy=True):
"""Extend Structure by appending copies from a list of atoms.
atoms -- list of QEAtom instances
copy -- flag for extending with copies of QEAtom instances.
When False extend with atoms and update their lattice
attributes.
No return value.
"""
self._uncache('labels')
if copy: adups = [QEAtom(a) for a in atoms]
else: adups = atoms
for a in adups:
a.lattice = self.lattice
list.extend(self, adups)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def __setitem__(self, idx, a, copy=True):
"""Set idx-th atom to a.
idx -- index of atom in this Structure
a -- instance of QEAtom
copy -- flag for setting to a copy of a.
When False, set to a and update a.lattice.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.__setitem__(self, idx, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def __setslice__(self, lo, hi, atoms, copy=True):
"""Set Structure slice from lo to hi-1 to the sequence of atoms.
lo -- low index for the slice
hi -- high index of the slice
atoms -- sequence of Atom instances
copy -- flag for using copies of Atom instances. When False, set
to existing instances and update their lattice attributes.
No return value.
"""
self._uncache('labels')
if copy: adups = [QEAtom(a) for a in atoms]
else: adups = atoms
for a in adups:
a.lattice = self.lattice
list.__setslice__(self, lo, hi, adups)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def _get_nat(self):
return len(self)
nat = property(_get_nat, doc="number of atoms")
def _get_ntyp(self):
return len(self.atomicSpecies)
ntyp = property(_get_ntyp, doc="number of types")
def _get_atomicPositionsType(self):
return self._atomicPositionsType
def _set_atomicPositionsType(self, value):
self._atomicPositionsType = value
self.lattice._qeInput.update()
atomicPositionsType = property(_get_atomicPositionsType, \
_set_atomicPositionsType, \
doc ="type of atomic positions (crystal, alat ...)")
def _get_atomicSpecies(self):
atomicSpecies = OrderedDict()
for a in self:
atomicSpecies[a.element] = AtomicSpecies(element = a.element, \
mass = a.mass, potential = a.potential)
return atomicSpecies
atomicSpecies = property(_get_atomicSpecies, \
doc ="returns an ordered dictionary with atomic species' objects")
def __str__(self):
"""simple string representation"""
s = str(self.lattice) + '\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 in self:
constraint = atom.optConstraint
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 atomLabels(self):
labels = []
for l in self.atomicSpecies:
labels.append(l)
return labels
def parseInput(self, qeInput):
from qecalc.qetask.qeparser.qestructureparser.qestructureparser import QEStructureParser
new_structure = QEStructureParser(qeInput).parseqeInput()
self.__Init(new_structure)
def __Init(self, structure):
QEStructure.__init__(self)
if structure is not None:
self.__dict__.update(structure.__dict__)
self.lattice.__dict__.update(structure.lattice.__dict__)
self[:] = structure
def read(self, filename, format='pwinput'):
"""Load structure from a file, any original data become lost.
l
filename -- file to be loaded
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
from qecalc.qetask.qeparser.qestructureparser import parser_index
if self._qeInput == None:
from qecalc.qetask.qeparser.pwinput import PWInput
self._qeInput = PWInput()
self._qeInput.structure = self
#self._qeInput.parse()
if format in parser_index:
module = __import__("qestructureparser.P_" + format, globals(), \
locals(), ['P_' + format], -1)
parser = module.getParser(self._qeInput)
new_structure = parser.parse(filename)
else:
diffpyStruct = Structure()
parser = diffpyStruct.read(filename, format=format)
new_structure = QEStructure(qeInput=self._qeInput)
new_structure._setStructureFromDiffpyStructure(diffpyStruct, \
massList = [], psList = [], ibrav = 0)
new_structure.lattice._qeInput.update(forceUpdate=True)
self.__Init(new_structure)
return parser
def readStr(self, s, format='pwinput'):
"""Load structure from a string, any original data become lost.
filename -- file to be loaded
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
from qecalc.qetask.qeparser.qestructureparser import parser_index
#from qecalc.qetask.qeparser.pwinput import PWInput
if self._qeInput == None:
from qecalc.qetask.qeparser.pwinput import PWInput
self._qeInput = PWInput()
self._qeInput.structure = self
#if self._qeInput == None:
# self._qeInput = PWInput()
#self._qeInput.parse()
if format in parser_index:
module = __import__("qestructureparser.P_" + format, globals(), \
locals(), ['P_' + format], -1)
parser = module.getParser(self._qeInput)
new_structure = parser.parseStr(s)
else:
diffpyStruct = Structure()
parser = diffpyStruct.readStr(s, format=format)
new_structure = QEStructure(qeInput=self._qeInput)
new_structure._setStructureFromDiffpyStructure(diffpyStruct, \
massList = [], psList = [], ibrav = 0)
new_structure.lattice._qeInput.update(forceUpdate=True)
#new_structure._qeInput = new_structure.lattice._qeInput
#print 'toString: ', new_structure._qeInput.toString()
#self = QEStructure(new_structure)
self.__Init(new_structure)
return parser
def write(self, filename=None, format="pwinput"):
"""Save structure to file in the specified format
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
No return value.
"""
if format == "pwinput":
self._qeInput.update(forceUpdate=True)
if filename == None:
filename = self._qeInput.filename
input = QEInput(config=self._qeInput.toString(), type='pw')
input.save(filename=filename)
else:
self.diffpy().write(filename=filename, format=format)
return
def writeStr(self, format='pwinput'):
"""return string representation of the structure in specified format
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
"""
if format == 'pwinput':
self._qeInput.update(forceUpdate=True)
return self.toString()
else:
return self.diffpy().writeStr(format=format)
def toString(self, string=None):
"""Writes/updates structure into PW config string.
If the string is None, one, based on current structure
will be generated
"""
if string != None:
stru = QEStructure()
stru.readStr(string, format='pwinput')
qeInput = stru._qeInput
else:
qeInput = self._qeInput
self._qeInput.update(qeInput=qeInput, forceUpdate=True)
return qeInput.toString()
def save(self, filename=None):
"""Writes/updates structure into PW config file,
if the file does not exist, new one will be created"""
from os.path import exists
from qecalc.qetask.qeparser.pwinput import PWInput
if filename != None:
if not exists(filename):
f = open(filename, 'w')
qeInput = PWInput()
qeInput.readFile(filename)
else:
qeInput = self._qeInput
self._qeInput.update(qeInput=qeInput, forceUpdate=True)
qeInput.save()
def reduce(self, ibrav=None):
"""
Reduces a structure instance with nonprimitive lattice ( i.e. solves
for equivalent atomic positions) according to specified lattice type (ibrav).
Each ibrav number corresponds to a specific primitive lattice
(see QE documentation).
"""
ib = self.lattice.ibrav
if ibrav != None:
ib = ibrav
a = self.lattice.diffpy().a
b = self.lattice.diffpy().b
c = self.lattice.diffpy().c
cAB = cosd(self.lattice.diffpy().gamma)
cBC = cosd(self.lattice.diffpy().alpha)
cAC = cosd(self.lattice.diffpy().beta)
if ib > 0:
qeLattice = QELattice(ibrav = ib, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
else:
qeLattice = QELattice(ibrav=ib, base=self.lattice.base)
qeLattice._qeInput = self._qeInput
reducedStructure = QEStructure(self)
reducedStructure.placeInLattice(qeLattice)
# 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 a0.element == a1.element
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.
self.lattice = qeLattice
self[:] = [a for a in reducedStructure if not a in duplicates]
self._qeInput.structure = self
return
def load(self, source, **args):
task = {
'diffpy': self._setStructureFromDiffpyStructure,
'matter': self._setStructureFromMatter,
}
if source == 'matter':
if 'ibrav' in args and args['ibrav'] != 0:
task['matter'] = self._setReducedStructureFromMatter
if source == 'diffpy':
if 'ibrav' in args and args['ibrav'] != 0:
task['diffpy'] = self._setReducedStructureFromDiffpyStructure
task[source](**args)
self.lattice._qeInput.update()
def _matter_diffpy(self, structure):
"""
converts matter Structure object to diffpy.Structure
returns diffpy.Structure object
"""
l = structure.lattice
lat = Lattice( a=l.a, b=l.b, c=l.c, alpha=l.alpha, \
beta=l.beta, gamma=l.gamma)
stru = Structure(lattice=lat)
for a in structure:
stru.addNewAtom(atype = a.symbol, xyz = a.xyz, name = a.symbol, \
anisotropy=a.anisotropy, U=a.U, Uisoequiv=a.Uisoequiv, \
lattice=lat)
return stru
def _setStructureFromMatter(self,
structure,
massList=[],
psList=[],
ibrav=0):
stru = self._matter_diffpy(structure)
self._setStructureFromDiffpyStructure(structure=stru,\
massList=massList, psList=psList,ibrav=ibrav)
def _setReducedStructureFromMatter(self,
structure,
ibrav,
massList=[],
psList=[]):
stru = self._matter_diffpy(structure)
self._setReducedStructureFromDiffpyStructure(structure = stru, \
ibrav=ibrav, massList=massList,psList=psList)
def _setStructureFromDiffpyStructure(self,
structure,
massList=[],
psList=[],
ibrav=0):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
diffpyLattice = structure.lattice
qeLattice = QELattice(ibrav=0, base=diffpyLattice.base)
qeLattice.a = 1.889725989 * qeLattice.a
qeLattice._qeInput = self._qeInput
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))
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
for atom in structure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
def _setReducedStructureFromDiffpyStructure(self,
structure,
ibrav,
massList=[],
psList=[]):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
import copy
diffpyLattice = copy.deepcopy(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)
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms=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
]
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
def updatePWInput(self, qeInput=None):
"""
Deprecated
"""
self._qeInput.update()
def diffpy(self):
stru = Structure(lattice=self.lattice.diffpy())
for atom in self:
stru.addNewAtom(atype = atom.element, xyz = atom.xyz, \
lattice = self.lattice.diffpy() )
return stru
def _element(self, atom):
"""
Is needed for support both diffpy and matter classes
"""
if 'element' in dir(atom):
return atom.element
else:
if 'symbol' in dir(atom):
return atom.symbol
else:
raise
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
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
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]))
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 QEAtom(object):
"""Atom --> class for storing atom information
Data members:
element -- type of the atom
xyz -- fractional coordinates
name -- atom label
xyz_cartn -- absolute Cartesian coordinates, property synced with xyz
lattice -- coordinate system for fractional coordinates,
an instance of Lattice or None for Cartesian system
"""
def __init__(self, atype=None, xyz=None, mass = None, \
potential = None, lattice=None, optConstraint = None, name=None):
"""Create atom of a specified type at given lattice coordinates.
Atom(a) creates a copy of Atom instance a.
atype -- element symbol string or Atom instance
xyz -- fractional(crystal) coordinates
name -- atom label
mass -- atom mass
potential -- pseudopotential file name
lattice -- QE coordinate system for fractional coordinates
optConstraint -- list of up to three constraints for each coordinate
for QE geometry optimization (0 or 1)
"""
# declare data members
self.element = None
self._xyz = numpy.zeros(3, dtype=float)
self.name = ''
self._mass = 0
self._potential = ''
self.lattice = QELattice()
from pwinput import PWInput
self.lattice._qeInput = PWInput()
self._optConstraint = numpy.array([], dtype = int)
# assign them as needed
if isinstance(atype, QEAtom):
atype_dup = atype.__copy__()
self.__dict__.update(atype_dup.__dict__)
else:
self.element = atype
# take care of remaining arguments
if xyz is not None: self._xyz[:] = xyz
if name is not None: self.name = name
if mass is not None: self._mass = mass
if potential is not None: self._potential = potential
if lattice is not None: self.lattice = lattice
if optConstraint is not None: self._optConstraint = \
numpy.array(optConstraint, dtype = int)
return
def __repr__(self):
"""simple string representation"""
xyz = self.xyz
s = "%-4s %8.6f %8.6f %8.6f %8.6f %s" % \
(self.element, xyz[0], xyz[1], xyz[2], self.mass, self.potential)
return s
def __copy__(self):
"""Return a copy of this instance.
"""
adup = QEAtom(self.element)
adup.__dict__.update(self.__dict__)
# create copies for what should be copied
adup.xyz = numpy.array(self.xyz)
return adup
####################################################################
# property handlers
####################################################################
# xyz_cartn
def _get_xyz_cartn(self):
if not self.lattice:
rv = self.xyz
else:
rv = CartesianCoordinatesArray(self.lattice, self.xyz)
return rv
def _set_xyz_cartn(self, value):
if not self.lattice:
self.xyz[:] = value
else:
self.xyz = self.lattice.fractional(value)
self.lattice._qeInput.update()
return
xyz_cartn = property(_get_xyz_cartn, _set_xyz_cartn, doc =
"""absolute Cartesian coordinates of an atom
""" )
def _get_xyz(self):
return self._xyz
def _set_xyz(self, value):
self._xyz = value
self.lattice._qeInput.update()
xyz = property(_get_xyz, _set_xyz, doc =
"""fractional coordinates of an atom
""" )
def _get_mass(self):
return self._mass
def _set_mass(self, value):
self._mass = value
self.lattice._qeInput.update()
mass = property(_get_mass, _set_mass, doc =
"""mass of an atom """ )
def _get_potential(self):
return self._potential
def _set_potential(self, value):
self._potential = value
self.lattice._qeInput.update()
potential = property(_get_potential, _set_potential, doc =
"""property. Name of paseudopotential of an atom """)
def _get_optConstraint(self):
return self._optConstraint
def _set_optConstraint(self, value):
self._optConstraints = value
self.lattice._qeInput.update()
optConstraint = property(_get_optConstraint, _set_optConstraint, doc =
"""optimization constraint, e.g. [1, 0, 1] of an atom for QE geometry
optimization""")
def _setReducedStructureFromDiffpyStructure(self, structure, ibrav, massList = [], psList = []):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
import copy
diffpyLattice = copy.deepcopy(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)
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms = 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]
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
class QEStructure( Structure ):
"""
Parses and handles Quantum Espresso structure information.
QEStructure is inherited from a diffpy.Structure, which is in turn
inherited from a Python list.
QEStructure is a list of QEAtom object instances.
All list functionality is preserved. setitem and
setslice methods are overloaded so that the lattice attribute
of atoms get set to lattice.
QEStructure, QELattice and QEAtom objects contain a hidden QEInput
pointer to current Quantum Espresso parsing object.
if QEInput.autoUpdate = True (default),any change in a property from
QEStructure, QELattice, or QEAtom will automatically invoke
QEInput.update(). In that case, QEInput.save() or QEInput.toString() will
immediately yield updated QE input file or a string
All properties are mutually synchronized. E.g. change in a lattice parameter
will also affect other lattice parameters as well as atomic positions
according to the lattice type (ibrav)
All relevant methods from diffpy.Structure are redefined.
QEStructure read only properties, automatically synchronized with current
list of Atoms:
nat -- "number of atoms" (integer)
ntyp -- "number of atomic types" (integer)
atomicSpecies -- OrderedDic of AtomicSpecies class instances
(see AtomicSpecies class definition)
Other properties:
atomicPositionsType -- 'crystal' (default), 'alat', 'bohr', and 'angstrom'
Note: This version of QEStructure does not support multiple images from
QE input files
"""
def __init__(self, atoms = [], lattice = None, filename = None, qeInput = None):
"""
atoms -- list of QEAtom atom instances or a QEStructure object
lattice -- QELattice object
filename -- filename QE input file
qeInput -- pointer to a PWInput parsing object. If not None,
its PWInput.structure and PWInput.structure.lattice
will be reset to the current instance of the structure
"""
Structure.__init__(self)
self.formatString = '%# .8f %# .8f %# .8f'
self._atomicPositionsType = 'crystal'
self._qeInput = qeInput
self.lattice = QELattice()
self.lattice._qeInput = self._qeInput
if lattice != None:
self.lattice = QELattice( lattice = lattice )
self._qeInput = self.lattice._qeInput
# CP and PW inputs are compatible
from pwinput import PWInput
from cpinput import CPInput
if isinstance( atoms, PWInput) or isinstance( atoms, CPInput):
qeInput = atoms
elif isinstance( atoms, QEStructure):
stru = atoms
self.__dict__.update( stru.__dict__ )
# deep copy of the lattice will deep copy PWInput as well
self.lattice = QELattice(lattice = stru.lattice)
self._qeInput = self.lattice._qeInput
self[:] = stru
else:
if self.lattice == None:
raise "Lattice must be provided"
self[:] = atoms
if filename != None:
qeInput = PWInput(filename = filename)
qeInput.parse()
self.parseInput(qeInput)
if qeInput != None:
self.lattice._qeInput = qeInput
self._qeInput = qeInput
if self.lattice._qeInput != None:
self.lattice._qeInput.structure = self
self.lattice._qeInput.structure.lattice = self.lattice
return
def addNewAtom(self, *args, **kwargs):
"""Add new Atom instance to the end of this Structure.
All arguments are forwarded to Atom constructor.
No return value.
"""
kwargs['lattice'] = self.lattice
a = QEAtom(*args, **kwargs)
list.append(self, a)
self._uncache('labels')
return
def placeInLattice(self, new_lattice):
"""place structure into new_lattice coordinate system
sets lattice to new_lattice and recalculate fractional coordinates
of all atoms so their absolute positionls remain the same
return self
"""
Tx = numpy.dot(self.lattice.diffpy().base, new_lattice.diffpy().recbase)
Tu = numpy.dot(self.lattice.diffpy().normbase, new_lattice.diffpy().recnormbase)
for a in self:
a.xyz = numpy.dot(a.xyz, Tx)
tmpInput = self.lattice._qeInput
self.lattice = new_lattice
self.lattice._qeInput = tmpInput
self.lattice._qeInput.structure = self
return self
##############################################################################
# overloaded list methods - taken from diffpy.Structure
##############################################################################
def append(self, a, copy=True):
"""Append atom to a structure and update its lattice attribute.
a -- instance of QEAtom
copy -- flag for appending a copy of a.
When False, append a and update a.owner.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.append(self, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def insert(self, idx, a, copy=True):
"""Insert atom a before position idx in this Structure.
idx -- position in atom list
a -- instance of QEAtom
copy -- flag for inserting a copy of a.
When False, append a and update a.lattice.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.insert(self, idx, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def extend(self, atoms, copy=True):
"""Extend Structure by appending copies from a list of atoms.
atoms -- list of QEAtom instances
copy -- flag for extending with copies of QEAtom instances.
When False extend with atoms and update their lattice
attributes.
No return value.
"""
self._uncache('labels')
if copy: adups = [QEAtom(a) for a in atoms]
else: adups = atoms
for a in adups: a.lattice = self.lattice
list.extend(self, adups)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def __setitem__(self, idx, a, copy=True):
"""Set idx-th atom to a.
idx -- index of atom in this Structure
a -- instance of QEAtom
copy -- flag for setting to a copy of a.
When False, set to a and update a.lattice.
No return value.
"""
self._uncache('labels')
adup = copy and QEAtom(a) or a
adup.lattice = self.lattice
list.__setitem__(self, idx, adup)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def __setslice__(self, lo, hi, atoms, copy=True):
"""Set Structure slice from lo to hi-1 to the sequence of atoms.
lo -- low index for the slice
hi -- high index of the slice
atoms -- sequence of Atom instances
copy -- flag for using copies of Atom instances. When False, set
to existing instances and update their lattice attributes.
No return value.
"""
self._uncache('labels')
if copy: adups = [QEAtom(a) for a in atoms]
else: adups = atoms
for a in adups: a.lattice = self.lattice
list.__setslice__(self, lo, hi, adups)
if hasattr(self, '_qeInput') and self._qeInput != None:
self._qeInput.update()
return
def _get_nat(self):
return len(self)
nat = property(_get_nat, doc ="number of atoms")
def _get_ntyp(self):
return len(self.atomicSpecies)
ntyp = property(_get_ntyp, doc ="number of types")
def _get_atomicPositionsType(self):
return self._atomicPositionsType
def _set_atomicPositionsType(self, value):
self._atomicPositionsType = value
self.lattice._qeInput.update()
atomicPositionsType = property(_get_atomicPositionsType, \
_set_atomicPositionsType, \
doc ="type of atomic positions (crystal, alat ...)")
def _get_atomicSpecies(self):
atomicSpecies = OrderedDict()
for a in self:
atomicSpecies[a.element] = AtomicSpecies(element = a.element, \
mass = a.mass, potential = a.potential)
return atomicSpecies
atomicSpecies = property(_get_atomicSpecies, \
doc ="returns an ordered dictionary with atomic species' objects")
def __str__(self):
"""simple string representation"""
s = str(self.lattice) + '\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 in self:
constraint = atom.optConstraint
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 atomLabels(self):
labels = []
for l in self.atomicSpecies:
labels.append(l)
return labels
def parseInput(self, qeInput):
from qecalc.qetask.qeparser.qestructureparser.qestructureparser import QEStructureParser
new_structure = QEStructureParser(qeInput).parseqeInput()
self.__Init(new_structure)
def __Init(self, structure):
QEStructure.__init__(self)
if structure is not None:
self.__dict__.update(structure.__dict__)
self.lattice.__dict__.update(structure.lattice.__dict__)
self[:] = structure
def read(self, filename, format = 'pwinput'):
"""Load structure from a file, any original data become lost.
l
filename -- file to be loaded
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
from qecalc.qetask.qeparser.qestructureparser import parser_index
if self._qeInput == None:
from qecalc.qetask.qeparser.pwinput import PWInput
self._qeInput = PWInput()
#self._qeInput.parse()
if format in parser_index:
module = __import__("qestructureparser.P_" + format, globals(), \
locals(), ['P_' + format], -1)
parser = module.getParser(self._qeInput)
new_structure = parser.parse(filename)
else:
diffpyStruct = Structure()
parser = diffpyStruct.read(filename, format = format)
new_structure = QEStructure(qeInput = self._qeInput)
new_structure._setStructureFromDiffpyStructure(diffpyStruct, \
massList = [], psList = [], ibrav = 0)
new_structure.lattice._qeInput.update( forceUpdate = True )
self.__Init(new_structure)
return parser
def readStr(self, s, format = 'pwinput'):
"""Load structure from a string, any original data become lost.
filename -- file to be loaded
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
from qecalc.qetask.qeparser.qestructureparser import parser_index
from qecalc.qetask.qeparser.pwinput import PWInput
#if self._qeInput == None:
# self._qeInput = PWInput()
#self._qeInput.parse()
if format in parser_index:
module = __import__("qestructureparser.P_" + format, globals(), \
locals(), ['P_' + format], -1)
parser = module.getParser(self._qeInput)
new_structure = parser.parseStr(s)
else:
diffpyStruct = Structure()
parser = diffpyStruct.readStr(s, format = format)
new_structure = QEStructure(qeInput = self._qeInput)
new_structure._setStructureFromDiffpyStructure(diffpyStruct, \
massList = [], psList = [], ibrav = 0)
new_structure.lattice._qeInput.update( forceUpdate = True )
#new_structure._qeInput = new_structure.lattice._qeInput
#print 'toString: ', new_structure._qeInput.toString()
#self = QEStructure(new_structure)
self.__Init(new_structure)
return parser
def write(self, filename = None, format = "pwinput"):
"""Save structure to file in the specified format
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
No return value.
"""
if format == "pwinput":
self._qeInput.update( qeInput = qeInput, forceUpdate = True )
if filename == None:
filename = self._qeInput.filename
input = QEInput(config = self._qeInput.toString(), type='pw')
input.save( filename = filename)
else:
self.diffpy().write( filename = filename, format = format )
return
def writeStr(self, format = 'pwinput'):
"""return string representation of the structure in specified format
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
"""
if format == 'pwinput':
return self.toString()
else:
return self.diffpy().writeStr(format = format)
def toString(self, string = None):
"""Writes/updates structure into PW config string.
If the string is None, one, based on current structure
will be generated
"""
if string != None:
stru = QEStructure()
stru.readStr(string, format = 'pwinput')
qeInput = stru._qeInput
else:
qeInput = self._qeInput
self._qeInput.update( qeInput = qeInput, forceUpdate = True )
return qeInput.toString()
def save(self, filename = None):
"""Writes/updates structure into PW config file,
if the file does not exist, new one will be created"""
from os.path import exists
from qecalc.qetask.qeparser.pwinput import PWInput
if filename != None:
if not exists(filename):
f = open(filename, 'w')
qeInput = PWInput()
qeInput.readFile(filename)
else:
qeInput = self._qeInput
self._qeInput.update( qeInput = qeInput, forceUpdate = True )
qeInput.save()
def reduce(self, ibrav = None):
"""
Reduces a structure instance with nonprimitive lattice ( i.e. solves
for equivalent atomic positions) according to specified lattice type (ibrav).
Each ibrav number corresponds to a specific primitive lattice
(see QE documentation).
"""
ib = self.lattice.ibrav
if ibrav != None:
ib = ibrav
a = self.lattice.diffpy().a
b = self.lattice.diffpy().b
c = self.lattice.diffpy().c
cAB = cosd(self.lattice.diffpy().gamma)
cBC = cosd(self.lattice.diffpy().alpha)
cAC = cosd(self.lattice.diffpy().beta)
if ib > 0:
qeLattice = QELattice(ibrav = ib, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
else:
qeLattice = QELattice(ibrav = ib, base = self.lattice.base)
qeLattice._qeInput = self._qeInput
reducedStructure = QEStructure(self)
reducedStructure.placeInLattice( qeLattice )
# 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 a0.element == a1.element 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.
self.lattice = qeLattice
self[:] = [a for a in reducedStructure if not a in duplicates]
return
def load(self, source, **args):
task = {
'diffpy': self._setStructureFromDiffpyStructure,
'matter': self._setStructureFromMatter,
}
if source == 'matter':
if 'ibrav' in args and args['ibrav'] != 0:
task['matter'] = self._setReducedStructureFromMatter
if source == 'diffpy':
if 'ibrav' in args and args['ibrav'] != 0:
task['diffpy'] = self._setReducedStructureFromDiffpyStructure
task[source](**args)
self.lattice._qeInput.update()
def _matter_diffpy(self, structure):
"""
converts matter Structure object to diffpy.Structure
returns diffpy.Structure object
"""
l = structure.lattice
lat = Lattice( a=l.a, b=l.b, c=l.c, alpha=l.alpha, \
beta=l.beta, gamma=l.gamma)
stru = Structure( lattice = lat)
for a in structure:
stru.addNewAtom(atype = a.symbol, xyz = a.xyz, name = a.symbol, \
anisotropy=a.anisotropy, U=a.U, Uisoequiv=a.Uisoequiv, \
lattice=lat)
return stru
def _setStructureFromMatter(self, structure, massList = [], psList = [], ibrav = 0):
stru = self._matter_diffpy( structure )
self._setStructureFromDiffpyStructure(structure=stru,\
massList=massList, psList=psList,ibrav=ibrav)
def _setReducedStructureFromMatter(self, structure, ibrav, massList = [], psList = []):
stru = self._matter_diffpy( structure )
self._setReducedStructureFromDiffpyStructure(structure = stru, \
ibrav=ibrav, massList=massList,psList=psList)
def _setStructureFromDiffpyStructure(self, structure, massList = [], psList = [], ibrav = 0):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
diffpyLattice = structure.lattice
qeLattice = QELattice(ibrav = 0, base = diffpyLattice.base)
qeLattice.a = 1.889725989*qeLattice.a
qeLattice._qeInput = self._qeInput
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))
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
for atom in structure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
def _setReducedStructureFromDiffpyStructure(self, structure, ibrav, massList = [], psList = []):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
import copy
diffpyLattice = copy.deepcopy(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)
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms = 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]
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
atomicSpecies = {}
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]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
def updatePWInput(self, qeInput = None):
"""
Deprecated
"""
self._qeInput.update()
def diffpy(self):
stru = Structure(lattice = self.lattice.diffpy())
for atom in self:
stru.addNewAtom(atype = atom.element, xyz = atom.xyz, \
lattice = self.lattice.diffpy() )
return stru
def _element(self, atom):
"""
Is needed for support both diffpy and matter classes
"""
if 'element' in dir(atom):
return atom.element
else:
if 'symbol' in dir(atom):
return atom.symbol
else:
raise
class QEStructure():
def __init__(self, fname):
"""the structure is initialized from PWSCF config file
'lattice' and 'structure' are automatically updated"""
self.filename = fname
self.atomicSpecies = OrderedDict()
self.lattice = None
# optConstraints three 1/0 for each coordinate of each atom
self.optConstraints = []
self.qeConf = QEConfig(fname)
self.qeConf.parse()
self.setStructureFromPWSCF()
def setStructureFromPWSCF(self):
""" Loads structure from PWSCF config file"""
self.lattice = QELattice(fname=self.filename)
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').getLines()
self.atomicPositionsType = self.qeConf.card(
'atomic_positions').argument()
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').getLines()
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 saveStructureToPWSCF(self, fname=None):
"""Writes/updates structure into PWSCF config file,
if the file does not exist, new one will be created"""
if fname != None:
filename = fname
self.lattice.saveLatticeToPWSCF(filename)
qeConf = QEConfig(fname)
qeConf.parse()
else:
filename = self.filename
self.lattice.saveLatticeToPWSCF(filename)
qeConf = self.qeConf
qeConf.parse()
qeConf.namelist('system').removeParam('ntyp')
qeConf.namelist('system').removeParam('nat')
qeConf.namelist('system').addParam('ntyp', self.ntyp)
qeConf.namelist('system').addParam('nat', self.nat)
if 'atomic_positions' in qeConf.cards:
qeConf.removeCard('atomic_positions')
qeConf.createCard('atomic_positions')
qeConf.card('atomic_positions').setArgument(self.atomicPositionsType)
for atom, constraint in zip(self.structure, self.optConstraints):
if self.atomicPositionsType == 'alat':
coords = self.lattice.diffpy().cartesian(atom.xyz)
coords = str(coords / self.lattice.a)[1:-1]
else:
if self.atomicPositionsType == 'crystal':
#coords = str(atom.xyz)[1:-1]
coords = '%f.8 %f.8 %f.8' % (atom.xyz[0], atom.xyz[1],
atom.xyz[2])
else:
raise NonImplementedError
line = 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())
qeConf.save(filename)
def diffpy(self):
return self.structure