def check_atoms_type(atoms: ase.Atoms) -> None:
"""Check that the passed atoms object is in fact an Atoms object.
Raises CalculatorSetupError.
"""
if not isinstance(atoms, ase.Atoms):
raise calculator.CalculatorSetupError(
('Expected an Atoms object, '
'instead got object of type {}'.format(type(atoms))))
def check_pbc(atoms: ase.Atoms) -> None:
"""Check if any boundaries are not PBC, as VASP
cannot handle non-PBC.
Raises CalculatorSetupError.
"""
if not atoms.pbc.all():
raise calculator.CalculatorSetupError(
"Vasp cannot handle non-periodic boundaries. "
"Please enable all PBC, e.g. atoms.pbc=True")
def check_cell(atoms: ase.Atoms) -> None:
"""Check if there is a zero unit cell.
Raises CalculatorSetupError if the cell is wrong.
"""
if atoms.cell.rank < 3:
raise calculator.CalculatorSetupError(
"The lattice vectors are zero! "
"This is the default value - please specify a "
"unit cell.")
def make_command(self, command=None):
"""Return command if one is passed, otherwise try to find
ASE_VASP_COMMAND, VASP_COMMAND or VASP_SCRIPT.
If none are set, a CalculatorSetupError is raised"""
if command:
cmd = command
else:
# Search for the environment commands
for env in self.env_commands:
if env in os.environ:
cmd = os.environ[env].replace('PREFIX', self.prefix)
if env == 'VASP_SCRIPT':
# Make the system python exe run $VASP_SCRIPT
exe = sys.executable
cmd = ' '.join([exe, cmd])
break
else:
msg = ('Please set either command in calculator'
' or one of the following environment '
'variables (prioritized as follows): {}').format(
', '.join(self.env_commands))
raise calculator.CalculatorSetupError(msg)
return cmd