def calculate(self,
atoms=None,
properties=('energy', ),
system_changes=tuple(calculator.all_changes)):
"""Do a VASP calculation in the specified directory.
This will generate the necessary VASP input files, and then
execute VASP. After execution, the energy, forces. etc. are read
from the VASP output files.
"""
self.clear_results()
if atoms is not None:
self.atoms = atoms.copy()
self.check_cell() # Check for zero-length lattice vectors
command = self.make_command(self.command)
self.write_input(self.atoms, properties, system_changes)
with self._txt_outstream() as out:
errorcode = self._run(command=command,
out=out,
directory=self.directory)
if errorcode:
raise calculator.CalculationFailed(
'{} in {} returned an error: {:d}'.format(
self.name, self.directory, errorcode))
# Read results from calculation
self.update_atoms(atoms)
self.read_results()
def calculate(
self,
atoms: Optional[Atoms] = None,
properties: List[str] = None,
system_changes: List[str] = ase_calc.all_changes,
) -> None:
"""Perform actual calculation with by calling the xtb API"""
if not properties:
properties = ["energy"]
ase_calc.Calculator.calculate(self, atoms, properties, system_changes)
self._check_api_calculator(system_changes)
if self._xtb is None:
self._xtb = self._create_api_calculator()
try:
self._res = self._xtb.singlepoint(self._res)
except XTBException:
raise ase_calc.CalculationFailed("xtb could not evaluate input")
# Check if a wavefunction object is present in results
_wfn = self._res.get_number_of_orbitals() > 0
# These properties are garanteed to exist for all implemented calculators
self.results["energy"] = self._res.get_energy() * Hartree
self.results["free_energy"] = self.results["energy"]
self.results["forces"] = -self._res.get_gradient() * Hartree / Bohr
self.results["dipole"] = self._res.get_dipole() * Bohr
# stress tensor is only returned for periodic systems
if self.atoms.pbc.any():
_stress = self._res.get_virial() * Hartree / self.atoms.get_volume(
)
self.results["stress"] = _stress.flat[[0, 4, 8, 5, 2, 1]]
# Not all xtb calculators provide access to partial charges yet,
# this is mainly an issue for the GFN-FF calculator
if _wfn:
self.results["charges"] = self._res.get_charges()