def test_center_coordinates(self):
cell = 2.2 * np.identity(3)
NaCl = Atoms('NaCl',
scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)],
cell=cell)
NaCl.set_repeat([3, 3, 3])
NaCl.positions += [2.2, 2.2, 2.2]
NaCl.center_coordinates_in_unit_cell(origin=-0.5)
self.assertTrue(-0.5 < np.min(NaCl.scaled_positions))
self.assertTrue(np.max(NaCl.scaled_positions < 0.5))
NaCl.center_coordinates_in_unit_cell(origin=0.)
self.assertTrue(0 <= np.min(NaCl.positions))
self.assertTrue(np.max(NaCl.scaled_positions < 1))
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, 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:
iteration_step (int): Step for which the structure is requested
wrap_atoms (bool):
Returns:
atomistics.structure.atoms.Atoms object
"""
if (self.server.run_mode.interactive
or self.server.run_mode.interactive_non_modal):
# Warning: We only copy symbols, positions and cell information - no tags.
if self.output.indices is not None and len(
self.output.indices) != 0:
indices = self.output.indices[iteration_step]
else:
return None
if len(self._interactive_species_lst) == 0:
el_lst = [el.Abbreviation for el in self.structure.species]
else:
el_lst = self._interactive_species_lst.tolist()
if indices is not None:
if wrap_atoms:
positions = self.output.positions[iteration_step]
else:
if len(self.output.unwrapped_positions) > max(
[iteration_step, 0]):
positions = self.output.unwrapped_positions[
iteration_step]
else:
positions = (
self.output.positions[iteration_step] +
self.output.total_displacements[iteration_step])
atoms = Atoms(
symbols=np.array([el_lst[el] for el in indices]),
positions=positions,
cell=self.output.cells[iteration_step],
pbc=self.structure.pbc,
)
# Update indicies to match the indicies in the cache.
atoms.set_species(
[self._periodic_table.element(el) for el in el_lst])
atoms.indices = indices
if wrap_atoms:
atoms = atoms.center_coordinates_in_unit_cell()
return atoms
else:
return None
else:
if (self.get("output/generic/cells") is not None
and len(self.get("output/generic/cells")) != 0):
return super(GenericInteractive,
self).get_structure(iteration_step=iteration_step,
wrap_atoms=wrap_atoms)
else:
return None