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_user_tag_settings(self):
tags_dict_ans = self.mp_xanes.tags.as_dict()
tags_dict_ans["COREHOLE"] = "RPA"
tags_dict_ans["EDGE"] = "L1"
user_tag_settings = {"COREHOLE": "RPA", "EDGE": "L1"}
mp_xanes_2 = MPXANESSet(self.absorbing_atom, self.structure,
user_tag_settings=user_tag_settings)
self.assertEqual(mp_xanes_2.tags.as_dict(), tags_dict_ans)
print(mp_xanes_2.as_dict().keys())
def test_user_tag_settings(self):
tags_dict_ans = self.mp_xanes.tags.as_dict()
tags_dict_ans["COREHOLE"] = "RPA"
tags_dict_ans["EDGE"] = "L1"
user_tag_settings = {"COREHOLE": "RPA", "EDGE": "L1"}
mp_xanes_2 = MPXANESSet(self.absorbing_atom,
self.structure,
user_tag_settings=user_tag_settings)
self.assertEqual(mp_xanes_2.tags.as_dict(), tags_dict_ans)
print(mp_xanes_2.as_dict().keys())
def main():
"""
Main method.
"""
parser = argparse.ArgumentParser(description='''
Example script to generate FEFF input files from a cif file
Author: Alan Dozier
Version: 1.0
Last updated: August, 2012''')
parser.add_argument('cif_file',
metavar='cif_file',
type=str,
nargs=1,
help='cif_file to use')
parser.add_argument('central_atom',
metavar='central_atom',
type=str,
nargs=1,
help='symbol of absorbing atom')
parser.add_argument('calc_type',
metavar='calc_type',
type=str,
nargs=1,
help='type of calc, currently XANES or EXAFS')
args = parser.parse_args()
cif_file = args.cif_file[0]
central_atom = args.central_atom[0]
calc_type = args.calc_type[0]
r = CifParser(cif_file)
structure = r.get_structures()[0]
x = MPXANESSet("MaterialsProject")
source = os.path.basename(cif_file)
comment = 'From cif file'
header = MPXANESSet.get_header(x, structure, source, comment)
print("\n\nHEADER\n")
print(header)
tags = MPXANESSet.get_feff_tags(x, calc_type)
print("\n\nPARAMETERS\n")
print(tags)
POT = MPXANESSet.get_feff_pot(x, structure, central_atom)
print("\n\nPOTENTIALS\n")
print(POT)
ATOMS = MPXANESSet.get_feff_atoms(x, structure, central_atom)
print("\n\nATOMS\n")
print(ATOMS)
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 setUpClass(cls):
cls.header_string = """* This FEFF.inp file generated by pymatgen
TITLE comment: From cif file
TITLE Source: CoO19128.cif
TITLE Structure Summary: Co2 O2
TITLE Reduced formula: CoO
TITLE space group: (P6_3mc), space number: (186)
TITLE abc: 3.297078 3.297078 5.254213
TITLE angles: 90.000000 90.000000 120.000000
TITLE sites: 4
* 1 Co 0.333333 0.666667 0.503676
* 2 Co 0.666667 0.333333 0.003676
* 3 O 0.333333 0.666667 0.121324
* 4 O 0.666667 0.333333 0.621325"""
cif_file = os.path.join(PymatgenTest.TEST_FILES_DIR, "CoO19128.cif")
cls.structure = CifParser(cif_file).get_structures()[0]
cls.absorbing_atom = "O"
cls.mp_xanes = MPXANESSet(cls.absorbing_atom, cls.structure)
def test_to_and_from_dict(self):
f1_dict = self.mp_xanes.as_dict()
f2 = MPXANESSet.from_dict(f1_dict)
self.assertEqual(f1_dict, f2.as_dict())
def test_to_and_from_dict(self):
f1_dict = self.mp_xanes.as_dict()
f2 = MPXANESSet.from_dict(f1_dict)
self.assertEqual(f1_dict, f2.as_dict())
