def interactive_forces_getter(self):
if self._interactive_vasprun is not None:
file_name = os.path.join(self.working_directory, "OUTCAR")
forces = self._interactive_vasprun.get_forces(filename=file_name)[-1]
forces[vasp_sorter(self.structure)] = forces.copy()
return forces
else:
return None
def test_vasp_sorter(self):
write_poscar(structure=self.structure,
filename=posixpath.join(self.file_location,
"POSCAR_test"))
test_atoms = read_atoms(
posixpath.join(self.file_location, "POSCAR_test"))
vasp_order = vasp_sorter(self.structure)
self.assertEqual(len(self.structure), len(test_atoms))
self.assertEqual(self.structure[vasp_order], test_atoms)
os.remove(posixpath.join(self.file_location, "POSCAR_test"))
def test_manip_contcar(self):
for f in self.file_list:
if "CONTCAR_Mg" in f:
struct = read_atoms(f)
Mg_indices = struct.select_index("Mg")
add_pos = np.zeros_like(struct.positions)
max_Mg = np.argmax(struct.positions[Mg_indices, 2])
init_z = struct.positions[max_Mg, 2]
add_pos[np.argsort(vasp_sorter(struct))[max_Mg], 2] += 5.0
manip_contcar(filename=f,
new_filename="manip_file",
add_pos=add_pos)
new_struct = read_atoms("manip_file")
Mg_indices = new_struct.select_index("Mg")
max_Mg = np.argmax(new_struct.positions[Mg_indices, 2])
final_z = new_struct.positions[max_Mg, 2]
self.assertEqual(round(final_z - init_z, 3), 5.0)
os.remove("manip_file")
break
positions = np.ones((3, 3))
positions[0] = [5., 5., 5.]
positions[1] = [5., 5.7, 5.7]
positions[2] = [5., -5.7, -5.7]
struct = Atoms(["O", "H", "H"],
positions=positions,
cell=10. * np.eye(3))
write_poscar(structure=struct, filename="simple_water")
add_pos = np.zeros_like(positions)
poscar_order = np.argsort(vasp_sorter(struct))
add_pos[poscar_order[struct.select_index("O")], 2] += 3
manip_contcar("simple_water", "simple_water_new", add_pos)
new_struct = read_atoms("simple_water_new")
self.assertEqual(new_struct.positions[new_struct.select_index("O"), 2],
8)
os.remove("simple_water")
os.remove("simple_water_new")
