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(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 correct(self):
backup(FEFF_BACKUP_FILES)
feff_input = FEFFDictSet.from_directory(".")
scf_values = feff_input.tags.get("SCF")
nscmt = scf_values[2]
ca = scf_values[3]
nmix = scf_values[4]
actions = []
#Add RESTART card to PARAMETERS
if not "RESTART" in feff_input.tags:
actions.append({"dict": "PARAMETERS",
"action": {"_set": {"RESTART": []}}})
if nscmt < 100 and ca == 0.2:
scf_values[2] = 100
scf_values[4] = 3 # Set nmix = 3
actions.append({"dict": "PARAMETERS",
"action": {"_set": {"SCF": scf_values}}})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
elif nscmt == 100 and nmix == 3 and ca > 0.01:
# Reduce the convergence accelerator factor
scf_values[3] = round(ca / 2, 2)
actions.append({"dict": "PARAMETERS",
"action": {"_set": {"SCF": scf_values}}})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
elif nmix == 3 and ca == 0.01:
# Set ca = 0.05 and set nmix
scf_values[3] = 0.05
scf_values[4] = 5
actions.append({"dict": "PARAMETERS",
"action": {"_set": {"SCF": scf_values}}})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
elif nmix == 5 and ca == 0.05:
# Set ca = 0.05 and set nmix
scf_values[3] = 0.05
scf_values[4] = 10
actions.append({"dict": "PARAMETERS",
"action": {"_set": {"SCF": scf_values}}})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
elif nmix == 10 and ca < 0.2:
# loop through ca with nmix = 10
scf_values[3] = round(ca * 2, 2)
actions.append({"dict": "PARAMETERS",
"action": {"_set": {"SCF": scf_values}}})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
# Unfixable error. Just return None for actions.
else:
return {"errors": ["Non-converging job"], "actions": None}
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 __init__(self, actions=None, strict=True, feffinp=None):
"""
Args:
actions ([Action]): A sequence of supported actions. See
actions ([Action]): A sequence of supported actions. See
:mod:`custodian.ansible.actions`. Default is None,
which means DictActions and FileActions are supported.
strict (bool): Indicating whether to use strict mode. In non-strict
mode, unsupported actions are simply ignored without any
errors raised. In strict mode, if an unsupported action is
supplied, a ValueError is raised. Defaults to True.
feffinp (FEFFInput): A FeffInput object from the current directory.
Initialized automatically if not passed (but passing it will
avoid having to reparse the directory).
"""
self.feffinp = feffinp or FEFFDictSet.from_directory(".")
self.feffinp = self.feffinp.all_input()
actions = actions or [FileActions, DictActions]
super().__init__(actions, strict)
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'))
def __init__(self, actions=None, strict=True, feffinp=None):
"""
Initializes a Modder for FeffInput sets
Args:
actions ([Action]): A sequence of supported actions. See
actions ([Action]): A sequence of supported actions. See
:mod:`custodian.ansible.actions`. Default is None,
which means DictActions and FileActions are supported.
strict (bool): Indicating whether to use strict mode. In non-strict
mode, unsupported actions are simply ignored without any
errors raised. In strict mode, if an unsupported action is
supplied, a ValueError is raised. Defaults to True.
feffinp (FEFFInput): A FeffInput object from the current directory.
Initialized automatically if not passed (but passing it will
avoid having to reparse the directory).
"""
self.feffinp = feffinp or FEFFDictSet.from_directory('.')
self.feffinp = self.feffinp.all_input()
actions = actions or [FileActions, DictActions]
super(FeffModder, self).__init__(actions, strict)
def correct(self):
backup(FEFF_BACKUP_FILES)
feff_input = FEFFDictSet.from_directory(".")
scf_values = feff_input.tags.get("SCF")
nscmt = scf_values[2]
ca = scf_values[3]
nmix = scf_values[4]
actions = []
if nscmt < 100 and ca == 0.2:
scf_values[2] = 100
scf_values[4] = 3 # Set nmix = 3
actions.append({
"dict": "PARAMETERS",
"action": {
"_set": {
"SCF": scf_values
}
}
})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
elif nscmt == 100 and nmix == 3 and ca > 0.01:
# Reduce the convergence accelerator factor
scf_values[3] = round(ca / 2, 2)
actions.append({
"dict": "PARAMETERS",
"action": {
"_set": {
"SCF": scf_values
}
}
})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
elif nmix == 3 and ca == 0.01:
# Set ca = 0.05 and set nmix
scf_values[3] = 0.05
scf_values[4] = 5
actions.append({
"dict": "PARAMETERS",
"action": {
"_set": {
"SCF": scf_values
}
}
})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
elif nmix == 5 and ca == 0.05:
# Set ca = 0.05 and set nmix
scf_values[3] = 0.05
scf_values[4] = 10
actions.append({
"dict": "PARAMETERS",
"action": {
"_set": {
"SCF": scf_values
}
}
})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
elif nmix == 10 and ca < 0.2:
# loop through ca with nmix = 10
scf_values[3] = round(ca * 2, 2)
actions.append({
"dict": "PARAMETERS",
"action": {
"_set": {
"SCF": scf_values
}
}
})
FeffModder().apply_actions(actions)
return {"errors": ["Non-converging job"], "actions": actions}
# Unfixable error. Just return None for actions.
else:
return {"errors": ["Non-converging job"], "actions": None}