def get_structure(self, job_specifier, iteration_step=-1, wrap_atoms=True):
"""
Gets the structure from a given iteration step of the simulation (MD/ionic relaxation). For static calculations
there is only one ionic iteration step
Args:
job_specifier (str, int): name of the job or job ID
iteration_step (int): Step for which the structure is requested
wrap_atoms (bool): True if the atoms are to be wrapped back into the unit cell
Returns:
atomistics.structure.atoms.Atoms object
"""
job = self.inspect(job_specifier)
snapshot = Atoms().from_hdf(job["input"], "structure")
if "output" in job.project_hdf5.list_groups() and iteration_step != 0:
snapshot.cell = job.get("output/generic/cells")[iteration_step]
snapshot.positions = job.get("output/generic/positions")[iteration_step]
if "indices" in job.get("output/generic").list_nodes():
snapshot.indices = job.get("output/generic/indices")[iteration_step]
if (
"dft" in job["output/generic"].list_groups()
and "atom_spins" in job["output/generic/dft"].list_nodes()
):
snapshot.set_initial_magnetic_moments(
job.get("output/generic/dft/atom_spins")[iteration_step]
)
if wrap_atoms:
return snapshot.center_coordinates_in_unit_cell()
else:
return snapshot
def get_structure(self, job_specifier, iteration_step=-1):
"""
Gets the structure from a given iteration step of the simulation (MD/ionic relaxation). For static calculations
there is only one ionic iteration step
Args:
job_specifier (str, int): name of the job or job ID
iteration_step (int): Step for which the structure is requested
Returns:
atomistics.structure.atoms.Atoms object
"""
job = self.inspect(job_specifier)
snapshot = Atoms().from_hdf(job['input'], 'structure')
if 'output' in job.project_hdf5.list_groups() and iteration_step != 0:
snapshot.cell = job.get("output/generic/cells")[iteration_step]
snapshot.positions = job.get(
"output/generic/positions")[iteration_step]
if 'indices' in job.get('output/generic').list_nodes():
snapshot.indices = job.get(
"output/generic/indices")[iteration_step]
if 'dft' in job['output/generic'].list_groups(
) and 'atom_spins' in job['output/generic/dft'].list_nodes():
snapshot.set_initial_magnetic_moments(
job.get("output/generic/dft/atom_spins")[iteration_step])
return snapshot