def add_arguments(cls, parser):
RunCommand.add_arguments(parser)
parser.add_argument('-f', '--maximum-force', default=0.05, type=float,
help='Relax internal coordinates.')
parser.add_argument('--constrain-tags',
metavar='T1,T2,...',
help='Constrain atoms with tags T1, T2, ...')
parser.add_argument('-s', '--maximum-stress', type=float,
help='Relax unit-cell and internal coordinates.')
def calculate(self, atoms, name):
args = self.args
if args.constrain_tags:
tags = [int(t) for t in args.constrain_tags.split(',')]
mask = [t in tags for t in atoms.get_tags()]
atoms.constraints = FixAtoms(mask=mask)
trajectory = PickleTrajectory(self.get_filename(name, 'traj'), 'w',
atoms)
if args.maximum_stress:
optimizer = LBFGS(UnitCellFilter(atoms), logfile=self.logfile)
fmax = args.maximum_stress
else:
optimizer = LBFGS(atoms, logfile=self.logfile)
fmax = args.maximum_force
optimizer.attach(trajectory)
optimizer.run(fmax=fmax)
data = RunCommand.calculate(self, atoms, name)
if hasattr(optimizer, 'force_calls'):
data['force calls'] = optimizer.force_calls
return data
def add_arguments(cls, parser):
RunCommand.add_arguments(parser)
parser.add_argument(
'--interactive-python-session', action='store_true',
help=argparse.SUPPRESS)
def set_calculator(self, atoms, name):
if self.args.interactive_python_session:
RunCommand.set_calculator(self, atoms, name)
def __init__(self, logfile, args, calculate_function):
RunCommand.__init__(self, logfile, args)
self.calculate_function = calculate_function
