def test_as_dict_and_from_dict(self):
file_name = os.path.join(PymatgenTest.TEST_FILES_DIR, "HEADER")
header = Header.from_file(file_name)
d = header.as_dict()
header2 = Header.from_dict(d)
self.assertEqual(str(header), str(header2),
"Header failed to and from dict test")
def test_as_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'HEADER')
header = Header.from_file(file_name)
d = header.as_dict()
header2 = Header.from_dict(d)
self.assertEqual(str(header), str(header2),
"Header failed to and from dict test")
def test_as_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'HEADER')
header = Header.from_file(file_name)
d = header.as_dict()
header2 = Header.from_dict(d)
self.assertEqual(str(header), str(header2),
"Header failed to and from dict test")
def test_from_string(self):
header = Header.from_string(header_string)
self.assertEqual(
header.struct.composition.reduced_formula,
"CoO",
"Failed to generate structure from HEADER string",
)
def test_post_distdiff(self):
feff_dict_input = FEFFDictSet.from_directory(
os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test"))
self.assertTrue(feff_dict_input.tags == Tags.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"feff_dist_test/feff.inp")))
self.assertTrue(
str(feff_dict_input.header()) == str(
Header.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"feff_dist_test/HEADER"))))
feff_dict_input.write_input("feff_dist_regen")
origin_tags = Tags.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"feff_dist_test/PARAMETERS"))
output_tags = Tags.from_file(
os.path.join(".", "feff_dist_regen/PARAMETERS"))
origin_mole = Atoms.cluster_from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"feff_dist_test/feff.inp"))
output_mole = Atoms.cluster_from_file(
os.path.join(".", "feff_dist_regen/feff.inp"))
original_mole_dist = np.array(
origin_mole.distance_matrix[0, :]).astype(np.float64)
output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(
np.float64)
original_mole_shell = [x.species_string for x in origin_mole]
output_mole_shell = [x.species_string for x in output_mole]
self.assertTrue(np.allclose(original_mole_dist, output_mole_dist))
self.assertTrue(origin_tags == output_tags)
self.assertTrue(original_mole_shell == output_mole_shell)
shutil.rmtree(os.path.join(".", "feff_dist_regen"))
def test_get_string(self):
cif_file = os.path.join(test_dir, 'CoO19128.cif')
h = Header.from_cif_file(cif_file)
head = str(h)
self.assertEqual(head.splitlines()[3].split()[-1],
header_string.splitlines()[3].split()[-1],
"Failed to generate HEADER from structure")
def test_get_string(self):
cif_file = os.path.join(test_dir, 'CoO19128.cif')
h = Header.from_cif_file(cif_file)
head = str(h)
self.assertEqual(head.splitlines()[3].split()[-1],
header_string.splitlines()[3].split()[-1],
"Failed to generate HEADER from structure")
def test_get_string(self):
header = Header.from_string(header_string)
struc = header.struct
central_atom = 'O'
a = Atoms(struc, central_atom, radius=10.)
atoms = str(a)
self.assertEqual(atoms.splitlines()[3].split()[4], central_atom,
"failed to create ATOMS string")
def test_get_string(self):
header = Header.from_string(header_string)
struc = header.struct
central_atom = 'O'
a = Atoms(struc, central_atom, radius=10.)
atoms = str(a)
self.assertEqual(atoms.splitlines()[3].split()[4], central_atom,
"failed to create ATOMS string")
def test_postfeffset(self):
self.mp_xanes.write_input(os.path.join(".", "xanes_3"))
feff_dict_input = FEFFDictSet.from_directory(os.path.join(".", "xanes_3"))
self.assertTrue(
feff_dict_input.tags
== Tags.from_file(os.path.join(".", "xanes_3/feff.inp"))
)
self.assertTrue(
str(feff_dict_input.header())
== str(Header.from_file(os.path.join(".", "xanes_3/HEADER")))
)
feff_dict_input.write_input("xanes_3_regen")
origin_tags = Tags.from_file(os.path.join(".", "xanes_3/PARAMETERS"))
output_tags = Tags.from_file(os.path.join(".", "xanes_3_regen/PARAMETERS"))
origin_mole = Atoms.cluster_from_file(os.path.join(".", "xanes_3/feff.inp"))
output_mole = Atoms.cluster_from_file(
os.path.join(".", "xanes_3_regen/feff.inp")
)
original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(
np.float64
)
output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(
np.float64
)
original_mole_shell = [x.species_string for x in origin_mole]
output_mole_shell = [x.species_string for x in output_mole]
self.assertTrue(np.allclose(original_mole_dist, output_mole_dist))
self.assertTrue(origin_tags == output_tags)
self.assertTrue(original_mole_shell == output_mole_shell)
shutil.rmtree(os.path.join(".", "xanes_3"))
shutil.rmtree(os.path.join(".", "xanes_3_regen"))
reci_mp_xanes = MPXANESSet(
self.absorbing_atom, self.structure, user_tag_settings={"RECIPROCAL": ""}
)
reci_mp_xanes.write_input("xanes_reci")
feff_reci_input = FEFFDictSet.from_directory(os.path.join(".", "xanes_reci"))
self.assertTrue("RECIPROCAL" in feff_reci_input.tags)
feff_reci_input.write_input("Dup_reci")
self.assertTrue(os.path.exists(os.path.join(".", "Dup_reci", "HEADER")))
self.assertTrue(os.path.exists(os.path.join(".", "Dup_reci", "feff.inp")))
self.assertTrue(os.path.exists(os.path.join(".", "Dup_reci", "PARAMETERS")))
self.assertFalse(os.path.exists(os.path.join(".", "Dup_reci", "ATOMS")))
self.assertFalse(os.path.exists(os.path.join(".", "Dup_reci", "POTENTIALS")))
tags_original = Tags.from_file(os.path.join(".", "xanes_reci/feff.inp"))
tags_output = Tags.from_file(os.path.join(".", "Dup_reci/feff.inp"))
self.assertTrue(tags_original == tags_output)
stru_orig = Structure.from_file(os.path.join(".", "xanes_reci/Co2O2.cif"))
stru_reci = Structure.from_file(os.path.join(".", "Dup_reci/Co2O2.cif"))
self.assertTrue(stru_orig.__eq__(stru_reci))
shutil.rmtree(os.path.join(".", "Dup_reci"))
shutil.rmtree(os.path.join(".", "xanes_reci"))
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
atoms = Atoms(struct, 'O', radius=10.)
d = atoms.as_dict()
atoms2 = Atoms.from_dict(d)
self.assertEqual(str(atoms), str(atoms2),
"Atoms failed to and from dict test")
def test_get_string(self):
cif_file = os.path.join(PymatgenTest.TEST_FILES_DIR, "CoO19128.cif")
h = Header.from_cif_file(cif_file)
head = str(h)
self.assertEqual(
head.splitlines()[3].split()[-1],
header_string.splitlines()[3].split()[-1],
"Failed to generate HEADER from structure",
)
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 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
atoms = Atoms(struct, "O", radius=10.0)
d = atoms.as_dict()
atoms2 = Atoms.from_dict(d)
self.assertEqual(str(atoms), str(atoms2),
"Atoms failed to and from dict test")
def test_init(self):
filepath = os.path.join(test_dir, 'HEADER')
header = Header.header_string_from_file(filepath)
h = header.splitlines()
hs = header_string.splitlines()
for i, line in enumerate(h):
self.assertEqual(line, hs[i])
self.assertEqual(header_string.splitlines(), header.splitlines(),
"Failed to read HEADER file")
def test_init(self):
filepath = os.path.join(test_dir, 'HEADER')
header = Header.header_string_from_file(filepath)
h = header.splitlines()
hs = header_string.splitlines()
for i, line in enumerate(h):
self.assertEqual(line, hs[i])
self.assertEqual(header_string.splitlines(), header.splitlines(),
"Failed to read HEADER file")
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
atoms = Atoms(struct, 'O', radius=10.)
d = atoms.as_dict()
atoms2 = Atoms.from_dict(d)
self.assertEqual(str(atoms), str(atoms2),
"Atoms failed to and from dict test")
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_init(self):
filepath = os.path.join(PymatgenTest.TEST_FILES_DIR, "HEADER")
header = Header.header_string_from_file(filepath)
h = header.splitlines()
hs = header_string.splitlines()
for i, line in enumerate(h):
self.assertEqual(line, hs[i])
self.assertEqual(
header_string.splitlines(),
header.splitlines(),
"Failed to read HEADER file",
)
def header(self, source='', comment=''):
"""
Creates header string from structure object
Args:
source: Source identifier used to create structure, can be defined
however user wants to organize structures, calculations, etc.
example would be Materials Project material ID number.
comment: comment to include in header
Returns:
Header
"""
return Header(self.structure, source, comment)
def test_postfeffset(self):
self.mp_xanes.write_input(os.path.join('.', 'xanes_3'))
feff_dict_input = FEFFDictSet.from_directory(os.path.join('.', 'xanes_3'))
self.assertTrue(feff_dict_input.tags == Tags.from_file(os.path.join('.', 'xanes_3/feff.inp')))
self.assertTrue(str(feff_dict_input.header()) == str(Header.from_file(os.path.join('.', 'xanes_3/HEADER'))))
feff_dict_input.write_input('xanes_3_regen')
origin_tags = Tags.from_file(os.path.join('.', 'xanes_3/PARAMETERS'))
output_tags = Tags.from_file(os.path.join('.', 'xanes_3_regen/PARAMETERS'))
origin_mole = Atoms.cluster_from_file(os.path.join('.', 'xanes_3/feff.inp'))
output_mole = Atoms.cluster_from_file(os.path.join('.', 'xanes_3_regen/feff.inp'))
original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(np.float64)
output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(np.float64)
original_mole_shell = [x.species_string for x in origin_mole]
output_mole_shell = [x.species_string for x in output_mole]
self.assertTrue(np.allclose(original_mole_dist, output_mole_dist))
self.assertTrue(origin_tags == output_tags)
self.assertTrue(original_mole_shell == output_mole_shell)
shutil.rmtree(os.path.join('.', 'xanes_3'))
shutil.rmtree(os.path.join('.', 'xanes_3_regen'))
reci_mp_xanes = MPXANESSet(self.absorbing_atom, self.structure,
user_tag_settings={"RECIPROCAL": ""})
reci_mp_xanes.write_input('xanes_reci')
feff_reci_input = FEFFDictSet.from_directory(os.path.join('.', 'xanes_reci'))
self.assertTrue("RECIPROCAL" in feff_reci_input.tags)
feff_reci_input.write_input('Dup_reci')
self.assertTrue(os.path.exists(os.path.join('.', 'Dup_reci', 'HEADER')))
self.assertTrue(os.path.exists(os.path.join('.', 'Dup_reci', 'feff.inp')))
self.assertTrue(os.path.exists(os.path.join('.', 'Dup_reci', 'PARAMETERS')))
self.assertFalse(os.path.exists(os.path.join('.', 'Dup_reci', 'ATOMS')))
self.assertFalse(os.path.exists(os.path.join('.', 'Dup_reci', 'POTENTIALS')))
tags_original = Tags.from_file(os.path.join('.', 'xanes_reci/feff.inp'))
tags_output = Tags.from_file(os.path.join('.', 'Dup_reci/feff.inp'))
self.assertTrue(tags_original == tags_output)
stru_orig = Structure.from_file(os.path.join('.', 'xanes_reci/Co2O2.cif'))
stru_reci = Structure.from_file(os.path.join('.', 'Dup_reci/Co2O2.cif'))
self.assertTrue(stru_orig.__eq__(stru_reci))
shutil.rmtree(os.path.join('.', 'Dup_reci'))
shutil.rmtree(os.path.join('.', 'xanes_reci'))
def test_post_distdiff(self):
feff_dict_input = FEFFDictSet.from_directory(os.path.join(test_dir, 'feff_dist_test'))
self.assertTrue(feff_dict_input.tags == Tags.from_file(os.path.join(test_dir, 'feff_dist_test/feff.inp')))
self.assertTrue(
str(feff_dict_input.header()) == str(Header.from_file(os.path.join(test_dir, 'feff_dist_test/HEADER'))))
feff_dict_input.write_input('feff_dist_regen')
origin_tags = Tags.from_file(os.path.join(test_dir, 'feff_dist_test/PARAMETERS'))
output_tags = Tags.from_file(os.path.join('.', 'feff_dist_regen/PARAMETERS'))
origin_mole = Atoms.cluster_from_file(os.path.join(test_dir, 'feff_dist_test/feff.inp'))
output_mole = Atoms.cluster_from_file(os.path.join('.', 'feff_dist_regen/feff.inp'))
original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(np.float64)
output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(np.float64)
original_mole_shell = [x.species_string for x in origin_mole]
output_mole_shell = [x.species_string for x in output_mole]
self.assertTrue(np.allclose(original_mole_dist, output_mole_dist))
self.assertTrue(origin_tags == output_tags)
self.assertTrue(original_mole_shell == output_mole_shell)
shutil.rmtree(os.path.join('.', 'feff_dist_regen'))
coords=[
[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)
def init_header(self):
self._header = Header(struct=self.structure, source=self.header_user_identifier, comment=self.header_comment)
def test_from_string(self):
header = Header.from_string(header_string)
self.assertEqual(header.struct.composition.reduced_formula, "CoO",
"Failed to generate structure from HEADER string")
