def _write_atoms(self, atoms, **kwargs):
b = self.backend
if self.header_data is None:
b.write(version=1, ase_version=__version__)
if self.description:
b.write(description=self.description)
# Atomic numbers and periodic boundary conditions are written
# in the header in the beginning.
#
# If an image later on has other numbers/pbc, we write a new
# header. All subsequent images will then have their own header
# whether or not their numbers/pbc change.
self.header_data = get_header_data(atoms)
write_header = True
else:
if not self.multiple_headers:
header_data = get_header_data(atoms)
self.multiple_headers = not headers_equal(
self.header_data, header_data)
write_header = self.multiple_headers
write_atoms(b, atoms, write_header=write_header)
calc = atoms.calc
if calc is None and len(kwargs) > 0:
calc = SinglePointCalculator(atoms)
if calc is not None:
if not hasattr(calc, 'get_property'):
calc = OldCalculatorWrapper(calc)
c = b.child('calculator')
c.write(name=calc.name)
if hasattr(calc, 'todict'):
c.write(parameters=calc.todict())
for prop in all_properties:
if prop in kwargs:
x = kwargs[prop]
else:
if self.properties is not None:
if prop in self.properties:
x = calc.get_property(prop, atoms)
else:
x = None
else:
try:
x = calc.get_property(prop,
atoms,
allow_calculation=False)
except (PropertyNotImplementedError, KeyError):
# KeyError is needed for Jacapo.
# XXX We can perhaps remove this.
x = None
if x is not None:
if prop in ['stress', 'dipole']:
x = x.tolist()
c.write(prop, x)
info = {}
for key, value in atoms.info.items():
try:
encode(value)
except TypeError:
warnings.warn('Skipping "{0}" info.'.format(key))
else:
info[key] = value
if info:
b.write(info=info)
b.sync()
def write(self, atoms=None, **kwargs):
"""Write the atoms to the file.
If the atoms argument is not given, the atoms object specified
when creating the trajectory object is used.
Use keyword arguments to add extra properties::
writer.write(atoms, energy=117, dipole=[0, 0, 1.0])
"""
b = self.backend
if atoms is None:
atoms = self.atoms
if hasattr(atoms, 'interpolate'):
# seems to be a NEB
neb = atoms
assert not neb.parallel or world.size == 1
for image in neb.images:
self.write(image)
return
while hasattr(atoms, 'atoms_for_saving'):
# Seems to be a Filter or similar, instructing us to
# save the original atoms.
atoms = atoms.atoms_for_saving
if len(b) == 0:
b.write(version=1, ase_version=__version__)
if self.description:
b.write(description=self.description)
# Atomic numbers and periodic boundary conditions are only
# written once - in the header. Store them here so that we can
# check that they are the same for all images:
self.numbers = atoms.get_atomic_numbers()
self.pbc = atoms.get_pbc()
else:
if (atoms.pbc != self.pbc).any():
raise ValueError('Bad periodic boundary conditions!')
elif len(atoms) != len(self.numbers):
raise ValueError('Bad number of atoms!')
elif (atoms.numbers != self.numbers).any():
raise ValueError('Bad atomic numbers!')
write_atoms(b, atoms, write_header=(len(b) == 0))
calc = atoms.get_calculator()
if calc is None and len(kwargs) > 0:
calc = SinglePointCalculator(atoms)
if calc is not None:
if not hasattr(calc, 'get_property'):
calc = OldCalculatorWrapper(calc)
c = b.child('calculator')
c.write(name=calc.name)
if hasattr(calc, 'todict'):
d = calc.todict()
if d:
c.write(parameters=d)
for prop in all_properties:
if prop in kwargs:
x = kwargs[prop]
else:
if self.properties is not None:
if prop in self.properties:
x = calc.get_property(prop, atoms)
else:
x = None
else:
try:
x = calc.get_property(prop, atoms,
allow_calculation=False)
except (PropertyNotImplementedError, KeyError):
# KeyError is needed for Jacapo.
x = None
if x is not None:
if prop in ['stress', 'dipole']:
x = x.tolist()
c.write(prop, x)
info = {}
for key, value in atoms.info.items():
try:
encode(value)
except TypeError:
warnings.warn('Skipping "{0}" info.'.format(key))
else:
info[key] = value
if info:
b.write(info=info)
b.sync()
def write(self, atoms=None, **kwargs):
"""Write the atoms to the file.
If the atoms argument is not given, the atoms object specified
when creating the trajectory object is used.
Use keyword arguments to add extra properties::
writer.write(atoms, energy=117, dipole=[0, 0, 1.0])
"""
b = self.backend
if atoms is None:
atoms = self.atoms
if hasattr(atoms, 'interpolate'):
# seems to be a NEB
neb = atoms
assert not neb.parallel or world.size == 1
for image in neb.images:
self.write(image)
return
while hasattr(atoms, 'atoms_for_saving'):
# Seems to be a Filter or similar, instructing us to
# save the original atoms.
atoms = atoms.atoms_for_saving
if self.header_data is None:
b.write(version=1, ase_version=__version__)
if self.description:
b.write(description=self.description)
# Atomic numbers and periodic boundary conditions are written
# in the header in the beginning.
#
# If an image later on has other numbers/pbc, we write a new
# header. All subsequent images will then have their own header
# whether or not their numbers/pbc change.
self.header_data = get_header_data(atoms)
write_header = True
else:
if not self.multiple_headers:
header_data = get_header_data(atoms)
self.multiple_headers = not headers_equal(
self.header_data, header_data)
write_header = self.multiple_headers
write_atoms(b, atoms, write_header=write_header)
calc = atoms.get_calculator()
if calc is None and len(kwargs) > 0:
calc = SinglePointCalculator(atoms)
if calc is not None:
if not hasattr(calc, 'get_property'):
calc = OldCalculatorWrapper(calc)
c = b.child('calculator')
c.write(name=calc.name)
if hasattr(calc, 'todict'):
d = calc.todict()
if d:
c.write(parameters=d)
for prop in all_properties:
if prop in kwargs:
x = kwargs[prop]
else:
if self.properties is not None:
if prop in self.properties:
x = calc.get_property(prop, atoms)
else:
x = None
else:
try:
x = calc.get_property(prop,
atoms,
allow_calculation=False)
except (PropertyNotImplementedError, KeyError):
# KeyError is needed for Jacapo.
x = None
if x is not None:
if prop in ['stress', 'dipole']:
x = x.tolist()
c.write(prop, x)
info = {}
for key, value in atoms.info.items():
try:
encode(value)
except TypeError:
warnings.warn('Skipping "{0}" info.'.format(key))
else:
info[key] = value
if info:
b.write(info=info)
b.sync()
def write(self, atoms=None, **kwargs):
"""Write the atoms to the file.
If the atoms argument is not given, the atoms object specified
when creating the trajectory object is used.
Use keyword arguments to add extra properties::
writer.write(atoms, energy=117, dipole=[0, 0, 1.0])
"""
b = self.backend
if atoms is None:
atoms = self.atoms
if hasattr(atoms, 'interpolate'):
# seems to be a NEB
neb = atoms
assert not neb.parallel or world.size == 1
for image in neb.images:
self.write(image)
return
while hasattr(atoms, 'atoms_for_saving'):
# Seems to be a Filter or similar, instructing us to
# save the original atoms.
atoms = atoms.atoms_for_saving
if self.header_data is None:
b.write(version=1, ase_version=__version__)
if self.description:
b.write(description=self.description)
# Atomic numbers and periodic boundary conditions are written
# in the header in the beginning.
#
# If an image later on has other numbers/pbc, we write a new
# header. All subsequent images will then have their own header
# whether or not their numbers/pbc change.
self.header_data = get_header_data(atoms)
write_header = True
else:
if not self.multiple_headers:
header_data = get_header_data(atoms)
self.multiple_headers = not headers_equal(self.header_data,
header_data)
write_header = self.multiple_headers
write_atoms(b, atoms, write_header=write_header)
calc = atoms.get_calculator()
if calc is None and len(kwargs) > 0:
calc = SinglePointCalculator(atoms)
if calc is not None:
if not hasattr(calc, 'get_property'):
calc = OldCalculatorWrapper(calc)
c = b.child('calculator')
c.write(name=calc.name)
if hasattr(calc, 'todict'):
d = calc.todict()
if d:
c.write(parameters=d)
for prop in all_properties:
if prop in kwargs:
x = kwargs[prop]
else:
if self.properties is not None:
if prop in self.properties:
x = calc.get_property(prop, atoms)
else:
x = None
else:
try:
x = calc.get_property(prop, atoms,
allow_calculation=False)
except (PropertyNotImplementedError, KeyError):
# KeyError is needed for Jacapo.
x = None
if x is not None:
if prop in ['stress', 'dipole']:
x = x.tolist()
c.write(prop, x)
info = {}
for key, value in atoms.info.items():
try:
encode(value)
except TypeError:
warnings.warn('Skipping "{0}" info.'.format(key))
else:
info[key] = value
if info:
b.write(info=info)
b.sync()