def atoms(self):
""" Returns ase.atoms.Atoms object. """
atoms = Atoms(cell=self.cell,
pbc=self.pbc,
info=self.info,
celldisp=self._celldisp.copy())
atoms.arrays = {}
for name, a in self.arrays.items():
atoms.arrays[name] = a.copy()
atoms.constraints = copy.deepcopy(self.constraints)
self._atoms = atoms
return self._atoms
def copy(self):
"""Return a copy."""
atoms = Atoms(cell=self.cell,
pbc=self.pbc,
info=self.info,
celldisp=self._celldisp.copy())
atoms.arrays = {}
for name, a in self.arrays.items():
atoms.arrays[name] = a.copy()
atoms.constraints = copy.deepcopy(self.constraints)
strc = self.__class__(atoms)
return strc
def run(argv=None):
if argv is None:
argv = sys.argv[1:]
elif isinstance(argv, str):
argv = argv.split()
parser = build_parser()
opt, args = parser.parse_args(argv)
if len(args) != 1:
parser.error("incorrect number of arguments")
name = args[0]
if world.rank == 0:
out = sys.stdout#open('%s-%s.results' % (name, opt.identifier), 'w')
else:
out = devnull
a = None
try:
symbols = string2symbols(name)
except ValueError:
# name was not a chemical formula - must be a file name:
atoms = read(name)
else:
if opt.crystal_structure:
a = opt.lattice_constant
if a is None:
a = estimate_lattice_constant(name, opt.crystal_structure,
opt.c_over_a)
out.write('Using an estimated lattice constant of %.3f Ang\n' %
a)
atoms = bulk(name, opt.crystal_structure, a, covera=opt.c_over_a,
orthorhombic=opt.orthorhombic, cubic=opt.cubic)
else:
try:
# Molecule?
atoms = molecule(name)
except NotImplementedError:
if len(symbols) == 1:
# Atom
atoms = Atoms(name)
elif len(symbols) == 2:
# Dimer
atoms = Atoms(name, positions=[(0, 0, 0),
(opt.bond_length, 0, 0)])
else:
raise ValueError('Unknown molecule: ' + name)
if opt.magnetic_moment:
magmom = opt.magnetic_moment.split(',')
atoms.set_initial_magnetic_moments(np.tile(magmom,
len(atoms) // len(magmom)))
if opt.repeat is not None:
r = opt.repeat.split(',')
if len(r) == 1:
r = 3 * r
atoms = atoms.repeat([int(c) for c in r])
if opt.gui:
view(atoms)
return
if opt.write_to_file:
write(opt.write_to_file, atoms)
return
if opt.effective_medium_theory:
Runner = EMTRunner
else:
Runner = GPAWRunner
if opt.fit:
strains = np.linspace(0.98, 1.02, 5)
else:
strains = None
if opt.constrain_tags:
tags = [int(t) for t in opt.constrain_tags.split(',')]
constrain = FixAtoms(mask=[t in tags for t in atoms.get_tags()])
atoms.constraints = [constrain]
runner = Runner(name, atoms, strains, tag=opt.identifier,
clean=not opt.read,
fmax=opt.relax, out=out)
if not opt.effective_medium_theory:
# Import stuff that eval() may need to know:
from gpaw.wavefunctions.pw import PW
from gpaw.occupations import FermiDirac, MethfesselPaxton
if opt.parameters:
input_parameters = eval(open(opt.parameters).read())
else:
input_parameters = {}
for key in defaults:
value = getattr(opt, key)
if value is not None:
try:
input_parameters[key] = eval(value)
except (NameError, SyntaxError):
input_parameters[key] = value
runner.set_parameters(vacuum=opt.vacuum,
write_gpw_file=opt.write_gpw_file,
**input_parameters)
runner.run()
runner.summary(plot=opt.plot, a0=a)
return runner
