def __init__(self, filename=None, config=None, type = 'pw', setting = None,\
parse = True):
self._structure = QEStructure(self)
self.kpoints = PWKpoints(self)
# Boolean flag, if True, QEInput is updated on change of any property in
# structure, lattice, or atom
self.autoUpdate = True
QESInput.__init__(self,filename, config, type = type, setting = setting,\
parse = parse)
class PWInput(QESInput):
"""
pw.x input
"""
def __init__(self, filename=None, config=None, type = 'pw', setting = None,\
parse = True):
self._structure = QEStructure(self)
self.kpoints = PWKpoints(self)
# Boolean flag, if True, QEInput is updated on change of any property in
# structure, lattice, or atom
self.autoUpdate = True
QESInput.__init__(self,filename, config, type = type, setting = setting,\
parse = parse)
def parse(self):
""" Parses the configuration file and stores the values in qe dictionary
Initializes structure as well"""
#(self.header, self.namelists, self.cards, self.attach) = self.parser.parse()
QESInput.parse(self)
self.structure.parseInput(self)
self.kpoints.parse()
def _get_structure(self):
return self._structure
def _set_structure(self, structure):
self._structure = structure
self._structure._qeInput = self._structure.lattice._qeInput = self
structure = property(_get_structure, _set_structure)
def update(self, qeInput = None, forceUpdate = False):
"""
Loads current mathematical representation of Structure and Lattice
into QEInput parsing object.
Will be deprecated soon. Currently it is already automatically called \
for most of Lattice and structure operations.
E.g. 'input.structure.lattice.a = new_a' will automatically update
input
"""
if qeInput == None:
qeInput = self
if self.autoUpdate is False and forceUpdate is False:
return
lattice = self._structure.lattice
structure = self._structure
#************************* updateLattice:*******************************
#if 'system' not in qeInput.namelists:
# qeInput.createNamelist('system')
nlSystem = qeInput.namelist('system')
# clear geometry from qeInput:
nlSystem.remove('a')
nlSystem.remove('b')
nlSystem.remove('c')
nlSystem.remove('cosab')
nlSystem.remove('cosbc')
nlSystem.remove('cosac')
nlSystem.remove('celldm(1)')
nlSystem.remove('celldm(2)')
nlSystem.remove('celldm(3)')
nlSystem.remove('celldm(4)')
nlSystem.remove('celldm(5)')
nlSystem.remove('celldm(6)')
#if 'cell_parameters' in qeInput.cards:
# qeInput.removeCard('cell_parameters')
qeInput.removeCard('cell_parameters')
if lattice._type == 'celldm':
nlSystem.set('ibrav', lattice._ibrav)
nlSystem.set('celldm(1)', lattice._a)
nlSystem.set('celldm(2)', float(lattice._b)/lattice._a)
nlSystem.set('celldm(3)', float(lattice._c)/lattice._a)
if lattice._ibrav < 14:
nlSystem.set('celldm(4)', lattice._cAB)
else:
nlSystem.set('celldm(4)', lattice._cBC)
nlSystem.set('celldm(5)', lattice._cAC)
nlSystem.set('celldm(6)', lattice._cAB)
else:
if lattice._type == 'traditional':
nlSystem.set('ibrav', lattice._ibrav)
nlSystem.set('A', lattice._a)
nlSystem.set('B', lattice._b)
nlSystem.set('C', lattice._c)
nlSystem.set('cosAB', lattice._cAB)
nlSystem.set('cosAC', lattice._cAC)
nlSystem.set('cosBC', lattice._cBC)
else:
if 'generic' in lattice._type:
nlSystem.set('celldm(1)', lattice._a)
lattice._ibrav = 0
nlSystem.set('ibrav', lattice._ibrav)
if lattice._type == 'generic hexagonal':
cardArg = 'hexagonal'
if lattice._type == 'generic cubic' or lattice._type == None:
cardArg = 'cubic'
card = qeInput.card('cell_parameters')
card.setArg(cardArg)
card.removeLines()
for i in range(3):
v = lattice.diffpy().base[i,:]/float(lattice._a)
card.addLine(\
lattice.formatString%(v[0], v[1], v[2]))
#************************* updateStructure:*****************************
#if 'system' not in qeInput.namelists:
# qeInput.addNamelist('system')
nlSystem.remove('ntyp')
nlSystem.remove('nat')
if structure.ntyp != None:
nlSystem.set('ntyp', structure.ntyp)
if structure.nat != None:
nlSystem.set('nat', structure.nat)
if len(nlSystem.paramlist()) == 0:
qeInput.removeNamelist('system')
#if 'atomic_positions' in qeInput.cards:
#qeInput.removeCard('atomic_positions')
qeInput.removeCard('atomic_positions')
#qeInput.card('atomic_positions')
qeInput.card('atomic_positions').setArg(structure.atomicPositionsType)
for atom in structure:
constraint = atom.optConstraint
if structure.atomicPositionsType == 'alat':
coords = structure.lattice.diffpy().cartesian(atom.xyz)/structure.lattice.a
coords = structure.formatString%(coords[0], coords[1], coords[2])
else:
if structure.atomicPositionsType == 'crystal':
coords = structure.formatString%(atom.xyz[0], atom.xyz[1], atom.xyz[2])
else:
if structure.atomicPositionsType == 'bohr' or structure.atomicPositionsType == 'angstrom':
coords = structure.lattice.diffpy().cartesian(atom.xyz)
coords = structure.formatString%(coords[0], coords[1], coords[2])
else:
raise NonImplementedError
line = '%-3s'%structure._element(atom) + ' ' + coords + ' ' + str(constraint)[1:-1]
qeInput.card('atomic_positions').addLine(line)
if len(qeInput.card('atomic_positions').lines()) == 0:
qeInput.removeCard('atomic_positions')
# update ATOMIC_SPECIES card
#if 'atomic_species' in qeInput.cards:
#qeInput.removeCard('atomic_species')
qeInput.removeCard('atomic_species')
qeInput.card('atomic_species')
for element, specie in structure.atomicSpecies.items():
qeInput.card('atomic_species').addLine(specie.toString())
if len(qeInput.card('atomic_species').lines()) == 0:
qeInput.removeCard('atomic_species')
def outDir(self):
self.parse()
return self.namelist('control').get('outdir', quotes = False)
