def test_as_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'HEADER')
header = Header.from_file(file_name)
struct = header.struct
pot = Potential(struct, 'O')
d=pot.as_dict()
pot2 = Potential.from_dict(d)
self.assertEqual(str(pot), str(pot2),
"Potential to and from dict does not match")
def test_as_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'HEADER')
header = Header.from_file(file_name)
struct = header.struct
pot = Potential(struct, 'O')
d=pot.as_dict()
pot2 = Potential.from_dict(d)
self.assertEqual(str(pot), str(pot2),
"Potential to and from dict does not match")
def test_as_dict_and_from_dict(self):
file_name = os.path.join(PymatgenTest.TEST_FILES_DIR, "HEADER")
header = Header.from_file(file_name)
struct = header.struct
pot = Potential(struct, "O")
d = pot.as_dict()
pot2 = Potential.from_dict(d)
self.assertEqual(str(pot), str(pot2),
"Potential to and from dict does not match")
def potential(self):
"""
FEFF potential
Returns:
Potential
"""
return Potential(self.structure, self.absorbing_atom)
def test_init(self):
filepath = os.path.join(test_dir, 'POTENTIALS')
feffpot = Potential.pot_string_from_file(filepath)
d, dr = Potential.pot_dict_from_string(feffpot)
self.assertEqual(d['Co'], 1, "Wrong symbols read in for Potential")
def test_get_feffPot(self):
POT = str(self.mp_xanes.potential)
d, dr = Potential.pot_dict_from_string(POT)
self.assertEqual(d["Co"], 1, "Wrong symbols read in for Potential")
def test_get_feffPot(self):
POT = str(self.mp_xanes.potential)
d, dr = Potential.pot_dict_from_string(POT)
self.assertEqual(d['Co'], 1, "Wrong symbols read in for Potential")
def test_init(self):
filepath = os.path.join(test_dir, 'POTENTIALS')
feffpot = Potential.pot_string_from_file(filepath)
d, dr = Potential.pot_dict_from_string(feffpot)
self.assertEqual(d['Co'], 1, "Wrong symbols read in for Potential")
def test_init(self):
filepath = os.path.join(PymatgenTest.TEST_FILES_DIR, "POTENTIALS")
feffpot = Potential.pot_string_from_file(filepath)
d, dr = Potential.pot_dict_from_string(feffpot)
self.assertEqual(d["Co"], 1, "Wrong symbols read in for Potential")
def init_potentials(self):
if self.is_load_potentials_from_file:
self._potentials = Potential(struct=self.structure, absorbing_atom=self.absorbing_atom). \
pot_string_from_file(self.path_to_src_feff_input)
else:
self._potentials = Potential(struct=self.structure, absorbing_atom=self.absorbing_atom)
[1 / 3, 2 / 3, 0.00000],
[1 / 3, 2 / 3, 0.37780],
],
coords_are_cartesian=False,
tol=1e-9,
)
print(zno_structure)
print(zno_structure.get_space_group_info())
out_file_name = '/home/yugin/PycharmProjects/neurons/data/src/feff.inp.new2'
file_name = '/home/yugin/PycharmProjects/neurons/data/src/feff.inp.old'
atoms_obj = Atoms(zno_structure, 'O', 12)
pprint(atoms_obj.struct.cart_coords)
pprint(atoms_obj.get_lines())
header_obj = Header(struct=zno_structure)
pot_obj = Potential(zno_structure, 'O')
tags_obj = Tags().from_file(filename=file_name)
pprint(tags_obj.as_dict())
pot_obj.pot_string_from_file(filename=file_name)
pprint(pot_obj)
atoms_obj.atoms_string_from_file(filename=file_name)
pprint(atoms_obj.as_dict())
header_obj.write_file(out_file_name)
tags_obj.write_file(out_file_name)
pot_obj.write_file(out_file_name)
atoms_obj.write_file(out_file_name)
# paths_obj = Paths()
