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 = [])
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
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 = [])
class QEStructure(Structure):
"""
Parses and handles Quantum Espresso structure information.
QEStructure is inherited from a matter.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 matter.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
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')
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.matter().base,
new_lattice.matter().recbase)
Tu = numpy.dot(self.lattice.matter().normbase,
new_lattice.matter().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.symbol] = AtomicSpecies(symbol = a.symbol, \
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.matter().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 NotImplementedError
s = s + '%-3s'%self._symbol(atom) + ' ' + coords + ' ' \
+ str(constraint)[1:-1] + '\n'
s = s + '\n'
for symbol, 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.
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:
struct = Structure()
parser = struct.read(filename, format=format)
new_structure = QEStructure(qeInput=self._qeInput)
new_structure._setStructureFromMatterStructure(struct, \
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:
#print 'cannot use format '+format
struct = Structure()
parser = struct.readStr(s, format=format)
new_structure = QEStructure(qeInput=self._qeInput)
new_structure._setStructureFromMatterStructure(struct, \
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.matter().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.matter().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.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 load(self, **args):
#def load(self, source, **args):
if 'ibrav' in args and args['ibrav'] != 0:
self._setReducedStructureFromMatterStructure(**args)
else:
self._setStructureFromMatterStructure(**args)
# task = {
# 'diffpy': self._setStructureFromDiffpyStructure,
# 'matter': self._setStructureFromMatterStructure,
# }
# if source == 'matter':
# if 'ibrav' in args and args['ibrav'] != 0:
# task['matter'] = self._setReducedStructureFromMatterStructure
# 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 _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 _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._symbol(a) not in atomNames:
# atomNames.append(self._symbol(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._symbol(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 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.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 self._symbol(a0) == self._symbol(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._symbol(a) not in atomNames:
# atomNames.append(self._symbol(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._symbol(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 matter(self):
stru = Structure(lattice=self.lattice.matter())
for atom in self:
stru.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
lattice = self.lattice.matter() )
return stru
def _symbol(self, atom):
"""
Is needed for support both diffpy and matter classes
"""
if 'symbol' in dir(atom):
return atom.symbol
else:
if 'symbol' in dir(atom):
return atom.symbol
else:
raise
class QEStructure( Structure ):
"""
Parses and handles Quantum Espresso structure information.
QEStructure is inherited from a matter.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 matter.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
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')
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.matter().base, new_lattice.matter().recbase)
Tu = numpy.dot(self.lattice.matter().normbase, new_lattice.matter().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.symbol] = AtomicSpecies(symbol = a.symbol, \
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.matter().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 NotImplementedError
s = s + '%-3s'%self._symbol(atom) + ' ' + coords + ' ' \
+ str(constraint)[1:-1] + '\n'
s = s + '\n'
for symbol, 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.
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:
struct = Structure()
parser = struct.read(filename, format = format)
new_structure = QEStructure(qeInput = self._qeInput)
new_structure._setStructureFromMatterStructure(struct, \
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:
#print 'cannot use format '+format
struct = Structure()
parser = struct.readStr(s, format = format)
new_structure = QEStructure(qeInput = self._qeInput)
new_structure._setStructureFromMatterStructure(struct, \
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.matter().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.matter().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.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 load(self, **args):
#def load(self, source, **args):
if 'ibrav' in args and args['ibrav'] != 0:
self._setReducedStructureFromMatterStructure(**args)
else:
self._setStructureFromMatterStructure(**args)
# task = {
# 'diffpy': self._setStructureFromDiffpyStructure,
# 'matter': self._setStructureFromMatterStructure,
# }
# if source == 'matter':
# if 'ibrav' in args and args['ibrav'] != 0:
# task['matter'] = self._setReducedStructureFromMatterStructure
# 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 _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 _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._symbol(a) not in atomNames:
# atomNames.append(self._symbol(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._symbol(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 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.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 self._symbol(a0) == self._symbol(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._symbol(a) not in atomNames:
# atomNames.append(self._symbol(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._symbol(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 matter(self):
stru = Structure(lattice = self.lattice.matter())
for atom in self:
stru.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
lattice = self.lattice.matter() )
return stru
def _symbol(self, atom):
"""
Is needed for support both diffpy and matter classes
"""
if 'symbol' in dir(atom):
return atom.symbol
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.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
