/usr/share/pyshared/ase/tasks/bulk.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
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import numpy as np
from ase.lattice import bulk
from ase.tasks.task import OptimizeTask
from ase.data import chemical_symbols, reference_states
from ase.utils.eos import EquationOfState
from ase.io.trajectory import PickleTrajectory
import ase.units as units
class BulkTask(OptimizeTask):
taskname = 'bulk'
def __init__(self, crystal_structure=None, lattice_constant=None,
c_over_a=None, cubic=False, orthorhombic=False, fit=None,
**kwargs):
"""Bulk task."""
self.crystal_structure = crystal_structure
self.lattice_constant = lattice_constant
self.c_over_a = c_over_a
self.cubic = cubic
self.orthorhombic = orthorhombic
self.fit = fit
self.repeat = None
OptimizeTask.__init__(self, **kwargs)
self.summary_header += [('V0', 'Ang^3'),
('B', 'GPa')]
def expand(self, names):
"""Expand fcc, bcc, hcp and diamond.
The name fcc will be expanded to all the elements with the fcc
stucture and so on."""
names = OptimizeTask.expand(self, names)
newnames = []
for name in names:
if name in ['fcc', 'bcc', 'hcp', 'diamond']:
for Z in range(1, 95):
x = reference_states[Z]
if x is not None and x['symmetry'] == name:
newnames.append(chemical_symbols[Z])
else:
newnames.append(name)
return newnames
def build_system(self, name):
atoms = bulk(name, crystalstructure=self.crystal_structure,
a=self.lattice_constant, covera=self.c_over_a,
orthorhombic=self.orthorhombic, cubic=self.cubic)
M = {'Fe': 2.3, 'Co': 1.2, 'Ni': 0.6}.get(name)
if M is not None:
atoms.set_initial_magnetic_moments([M] * len(atoms))
if self.repeat is not None:
r = self.repeat.split(',')
if len(r) == 1:
r = 3 * r
atoms = atoms.repeat([int(c) for c in r])
return atoms
def fit_volume(self, name, atoms):
N, x = self.fit
cell0 = atoms.get_cell()
strains = np.linspace(1 - x, 1 + x, N)
energies = []
traj = PickleTrajectory(self.get_filename(name, '-fit.traj'), 'w')
for s in strains:
atoms.set_cell(cell0 * s, scale_atoms=True)
energies.append(atoms.get_potential_energy())
traj.write(atoms)
traj.close()
assert N % 2 == 1
data = {'energy': energies[N // 2],
'strains': strains,
'energies': energies}
return data
def calculate(self, name, atoms):
#????
if self.fit:
return self.fit_volume(name, atoms)
else:
return OptimizeTask.calculate(self, name, atoms)
def analyse(self):
OptimizeTask.analyse(self)
for name, data in self.data.items():
if 'strains' in data:
atoms = self.create_system(name)
volumes = data['strains']**3 * atoms.get_volume()
energies = data['energies']
eos = EquationOfState(volumes, energies)
try:
v, e, B = eos.fit()
except ValueError:
self.results[name].extend([None, None])
else:
self.results[name][1:] = [energies[2] - e, v,
B * 1e24 / units.kJ]
else:
self.results[name].extend([None, None])
def add_options(self, parser):
OptimizeTask.add_options(self, parser)
bulk = optparse.OptionGroup(parser, 'Bulk')
bulk.add_option('-F', '--fit', metavar='N,x',
help='Find optimal volume and bulk modulus ' +
'using N points and variations of the lattice ' +
'constants from -x % to +x %.')
bulk.add_option('-x', '--crystal-structure',
help='Crystal structure.',
choices=['sc', 'fcc', 'bcc', 'diamond', 'hcp',
'rocksalt', 'zincblende'])
bulk.add_option('-a', '--lattice-constant', type='float',
help='Lattice constant in Angstrom.')
bulk.add_option('--c-over-a', type='float',
help='c/a ratio.')
bulk.add_option('-O', '--orthorhombic', action='store_true',
help='Use orthorhombic unit cell.')
bulk.add_option('-C', '--cubic', action='store_true',
help='Use cubic unit cell.')
bulk.add_option('-r', '--repeat',
help='Repeat unit cell. Use "-r 2" or "-r 2,3,1".')
parser.add_option_group(bulk)
def parse(self, opts, args):
OptimizeTask.parse(self, opts, args)
if opts.fit:
points, strain = opts.fit.split(',')
self.fit = (int(points), float(strain) * 0.01)
self.crystal_structure = opts.crystal_structure
self.lattice_constant = opts.lattice_constant
self.c_over_a = opts.c_over_a
self.orthorhombic = opts.orthorhombic
self.cubic = opts.cubic
self.repeat = opts.repeat
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