def test_init(self):
# nosetests pymatgen/io/vasp/tests/test_outputs.py:DynmatTest.test_init
filepath = os.path.join(test_dir, 'DYNMAT')
d = Dynmat(filepath)
self.assertEqual(d.nspecs, 2)
self.assertEqual(d.natoms, 6)
self.assertEqual(d.ndisps, 3)
self.assertTrue(np.allclose(d.masses, [63.546, 196.966]))
self.assertTrue(4 in d.data)
self.assertTrue(2 in d.data[4])
self.assertTrue(np.allclose(d.data[4][2]['dispvec'], [0., 0.05, 0.]))
self.assertTrue(
np.allclose(d.data[4][2]['dynmat'][3], [0.055046, -0.298080, 0.]))
def assimilate(self, path):
files = os.listdir(path)
try:
files_to_parse = {}
if "relax1" in files and "relax2" in files:
for filename in ("INCAR", "POTCAR", "POSCAR"):
search_str = os.path.join(path, "relax1", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[0]
for filename in ("CONTCAR", "OSZICAR"):
search_str = os.path.join(path, "relax2", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[-1]
else:
for filename in (
"INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR", "DYNMAT"
):
files = glob.glob(os.path.join(path, filename + "*"))
if len(files) < 1:
continue
if len(files) == 1 or filename == "INCAR" or \
filename == "POTCAR" or filename == "DYNMAT":
files_to_parse[filename] = files[-1]\
if filename == "POTCAR" else files[0]
elif len(files) > 1:
"""
This is a bit confusing, since there maybe be
multiple steps. By default, assimilate will try to find
a file simply named filename, filename.bz2, or
filename.gz. Failing which it will try to get a relax2
from a custodian double relaxation style run if
possible. Or else, a random file is chosen.
"""
for fname in files:
if fnmatch.fnmatch(os.path.basename(fname),
"{}(\.gz|\.bz2)*"
.format(filename)):
files_to_parse[filename] = fname
break
if fname == "POSCAR" and \
re.search("relax1", fname):
files_to_parse[filename] = fname
break
if (fname in ("CONTCAR", "OSZICAR") and
re.search("relax2", fname)):
files_to_parse[filename] = fname
break
files_to_parse[filename] = fname
poscar, contcar, incar, potcar, oszicar, dynmat = [None]*6
if 'POSCAR' in files_to_parse:
poscar = Poscar.from_file(files_to_parse["POSCAR"])
if 'CONTCAR' in files_to_parse:
contcar = Poscar.from_file(files_to_parse["CONTCAR"])
if 'INCAR' in files_to_parse:
incar = Incar.from_file(files_to_parse["INCAR"])
if 'POTCAR' in files_to_parse:
potcar = Potcar.from_file(files_to_parse["POTCAR"])
if 'OSZICAR' in files_to_parse:
oszicar = Oszicar(files_to_parse["OSZICAR"])
if 'DYNMAT' in files_to_parse:
dynmat = Dynmat(files_to_parse["DYNMAT"])
param = {"hubbards":{}}
if poscar is not None and incar is not None and "LDAUU" in incar:
param["hubbards"] = dict(zip(poscar.site_symbols,
incar["LDAUU"]))
param["is_hubbard"] = (
incar.get("LDAU", False) and sum(param["hubbards"].values()) > 0
) if incar is not None else False
param["run_type"] = None
if incar is not None:
param["run_type"] = "GGA+U" if param["is_hubbard"] else "GGA"
param["history"] = _get_transformation_history(path)
param["potcar_spec"] = potcar.spec if potcar is not None else None
energy = oszicar.final_energy if oszicar is not None else 1e10
structure = contcar.structure if contcar is not None\
else poscar.structure
initial_vol = poscar.structure.volume if poscar is not None else \
None
final_vol = contcar.structure.volume if contcar is not None else \
None
delta_volume = None
if initial_vol is not None and final_vol is not None:
delta_volume = (final_vol / initial_vol - 1)
data = {"filename": path, "delta_volume": delta_volume}
if dynmat is not None:
data['phonon_frequencies'] = dynmat.get_phonon_frequencies()
if self._inc_structure:
entry = ComputedStructureEntry(
structure, energy, parameters=param, data=data
)
else:
entry = ComputedEntry(
structure.composition, energy, parameters=param, data=data
)
return entry
except Exception as ex:
logger.debug("error in {}: {}".format(path, ex))
return None
def assimilate(self, path):
"""
Assimilate data in a directory path into a ComputedEntry object.
Args:
path: directory path
Returns:
ComputedEntry
"""
files = os.listdir(path)
try:
files_to_parse = {}
if "relax1" in files and "relax2" in files:
for filename in ("INCAR", "POTCAR", "POSCAR"):
search_str = os.path.join(path, "relax1", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[0]
for filename in ("CONTCAR", "OSZICAR"):
search_str = os.path.join(path, "relax2", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[-1]
else:
for filename in (
"INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR", "DYNMAT"
):
files = sorted(glob.glob(os.path.join(path, filename + "*")))
if len(files) < 1:
continue
if len(files) == 1 or filename == "INCAR" or \
filename == "POTCAR" or filename == "DYNMAT":
files_to_parse[filename] = files[-1] \
if filename == "POTCAR" else files[0]
elif len(files) > 1:
# Since multiple files are ambiguous, we will always
# use the first one for POSCAR and the last one
# alphabetically for CONTCAR and OSZICAR.
if filename == "POSCAR":
files_to_parse[filename] = files[0]
else:
files_to_parse[filename] = files[-1]
warnings.warn(
"%d files found. %s is being parsed." %
(len(files), files_to_parse[filename]))
poscar, contcar, incar, potcar, oszicar, dynmat = [None] * 6
if 'POSCAR' in files_to_parse:
poscar = Poscar.from_file(files_to_parse["POSCAR"])
if 'CONTCAR' in files_to_parse:
contcar = Poscar.from_file(files_to_parse["CONTCAR"])
if 'INCAR' in files_to_parse:
incar = Incar.from_file(files_to_parse["INCAR"])
if 'POTCAR' in files_to_parse:
potcar = Potcar.from_file(files_to_parse["POTCAR"])
if 'OSZICAR' in files_to_parse:
oszicar = Oszicar(files_to_parse["OSZICAR"])
if 'DYNMAT' in files_to_parse:
dynmat = Dynmat(files_to_parse["DYNMAT"])
param = {"hubbards": {}}
if poscar is not None and incar is not None and "LDAUU" in incar:
param["hubbards"] = dict(zip(poscar.site_symbols, incar["LDAUU"]))
param["is_hubbard"] = (incar.get("LDAU", True) and sum(param["hubbards"].values()) > 0) \
if incar is not None else False
param["run_type"] = None
param["potcar_spec"] = potcar.spec if potcar is not None else None
energy = oszicar.final_energy if oszicar is not None else Vasprun.final_energy
structure = contcar.structure if contcar is not None \
else poscar.structure
initial_vol = poscar.structure.volume if poscar is not None else \
None
final_vol = contcar.structure.volume if contcar is not None else \
None
delta_volume = None
if initial_vol is not None and final_vol is not None:
delta_volume = (final_vol / initial_vol - 1)
data = {"filename": path, "delta_volume": delta_volume}
if dynmat is not None:
data['phonon_frequencies'] = dynmat.get_phonon_frequencies()
if self._inc_structure:
entry = ComputedStructureEntry(
structure, energy, parameters=param, data=data
)
else:
entry = ComputedEntry(
structure.composition, energy, parameters=param, data=data
)
return entry
except Exception as ex:
logger.debug("error in {}: {}".format(path, ex))
return None
def assimilate(self, path):
files = os.listdir(path)
try:
files_to_parse = {}
if "relax1" in files and "relax2" in files:
for filename in ("INCAR", "POTCAR", "POSCAR"):
search_str = os.path.join(path, "relax1", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[0]
for filename in ("CONTCAR", "OSZICAR"):
search_str = os.path.join(path, "relax2", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[-1]
else:
for filename in (
"INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR", "DYNMAT"
):
files = sorted(glob.glob(os.path.join(path, filename + "*")))
if len(files) < 1:
continue
if len(files) == 1 or filename == "INCAR" or \
filename == "POTCAR" or filename == "DYNMAT":
files_to_parse[filename] = files[-1]\
if filename == "POTCAR" else files[0]
elif len(files) > 1:
# Since multiple files are ambiguous, we will always
# use the first one for POSCAR and the last one
# alphabetically for CONTCAR and OSZICAR.
if filename == "POSCAR":
files_to_parse[filename] = files[0]
else:
files_to_parse[filename] = files[-1]
warnings.warn(
"%d files found. %s is being parsed." %
(len(files), files_to_parse[filename]))
poscar, contcar, incar, potcar, oszicar, dynmat = [None]*6
if 'POSCAR' in files_to_parse:
poscar = Poscar.from_file(files_to_parse["POSCAR"])
if 'CONTCAR' in files_to_parse:
contcar = Poscar.from_file(files_to_parse["CONTCAR"])
if 'INCAR' in files_to_parse:
incar = Incar.from_file(files_to_parse["INCAR"])
if 'POTCAR' in files_to_parse:
potcar = Potcar.from_file(files_to_parse["POTCAR"])
if 'OSZICAR' in files_to_parse:
oszicar = Oszicar(files_to_parse["OSZICAR"])
if 'DYNMAT' in files_to_parse:
dynmat = Dynmat(files_to_parse["DYNMAT"])
param = {"hubbards":{}}
if poscar is not None and incar is not None and "LDAUU" in incar:
param["hubbards"] = dict(zip(poscar.site_symbols,
incar["LDAUU"]))
param["is_hubbard"] = (
incar.get("LDAU", False) and sum(param["hubbards"].values()) > 0
) if incar is not None else False
param["run_type"] = None
if incar is not None:
param["run_type"] = "GGA+U" if param["is_hubbard"] else "GGA"
# param["history"] = _get_transformation_history(path)
param["potcar_spec"] = potcar.spec if potcar is not None else None
energy = oszicar.final_energy if oszicar is not None else 1e10
structure = contcar.structure if contcar is not None\
else poscar.structure
initial_vol = poscar.structure.volume if poscar is not None else \
None
final_vol = contcar.structure.volume if contcar is not None else \
None
delta_volume = None
if initial_vol is not None and final_vol is not None:
delta_volume = (final_vol / initial_vol - 1)
data = {"filename": path, "delta_volume": delta_volume}
if dynmat is not None:
data['phonon_frequencies'] = dynmat.get_phonon_frequencies()
if self._inc_structure:
entry = ComputedStructureEntry(
structure, energy, parameters=param, data=data
)
else:
entry = ComputedEntry(
structure.composition, energy, parameters=param, data=data
)
return entry
except Exception as ex:
logger.debug("error in {}: {}".format(path, ex))
return None
def assimilate(self, path):
"""
Assimilate data in a directory path into a ComputedEntry object.
Args:
path: directory path
Returns:
ComputedEntry
"""
files = os.listdir(path)
try:
files_to_parse = {}
filenames = {"INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR", "DYNMAT"}
if "relax1" in files and "relax2" in files:
for filename in ("INCAR", "POTCAR", "POSCAR"):
search_str = os.path.join(path, "relax1", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[0]
for filename in ("CONTCAR", "OSZICAR"):
search_str = os.path.join(path, "relax2", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[-1]
else:
for filename in filenames:
files = sorted(glob.glob(os.path.join(path, filename + "*")))
if len(files) == 1 or filename in ("INCAR", "POTCAR"):
files_to_parse[filename] = files[0]
elif len(files) == 1 and filename == "DYNMAT":
files_to_parse[filename] = files[0]
elif len(files) > 1:
# Since multiple files are ambiguous, we will always
# use the first one for POSCAR and the last one
# alphabetically for CONTCAR and OSZICAR.
files_to_parse[filename] = files[0] if filename == "POSCAR" else files[-1]
warnings.warn("%d files found. %s is being parsed." % (len(files), files_to_parse[filename]))
if not set(files_to_parse.keys()).issuperset({"INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR"}):
raise ValueError(
"Unable to parse %s as not all necessary files are present! "
"SimpleVaspToComputedEntryDrone requires INCAR, POTCAR, CONTCAR, OSZICAR, POSCAR "
"to be present. Only %s detected" % str(files_to_parse.keys())
)
poscar = Poscar.from_file(files_to_parse["POSCAR"])
contcar = Poscar.from_file(files_to_parse["CONTCAR"])
incar = Incar.from_file(files_to_parse["INCAR"])
potcar = Potcar.from_file(files_to_parse["POTCAR"])
oszicar = Oszicar(files_to_parse["OSZICAR"])
param = {"hubbards": {}}
if "LDAUU" in incar:
param["hubbards"] = dict(zip(poscar.site_symbols, incar["LDAUU"]))
param["is_hubbard"] = incar.get("LDAU", True) and sum(param["hubbards"].values()) > 0
param["run_type"] = None
param["potcar_spec"] = potcar.spec
energy = oszicar.final_energy
structure = contcar.structure
initial_vol = poscar.structure.volume
final_vol = contcar.structure.volume
delta_volume = final_vol / initial_vol - 1
data = {"filename": path, "delta_volume": delta_volume}
if "DYNMAT" in files_to_parse:
dynmat = Dynmat(files_to_parse["DYNMAT"])
data["phonon_frequencies"] = dynmat.get_phonon_frequencies()
if self._inc_structure:
return ComputedStructureEntry(structure, energy, parameters=param, data=data)
return ComputedEntry(structure.composition, energy, parameters=param, data=data)
except Exception as ex:
logger.debug(f"error in {path}: {ex}")
return None
def assimilate(self, path):
files = os.listdir(path)
try:
files_to_parse = {}
if "relax1" in files and "relax2" in files:
for filename in ("INCAR", "POTCAR", "POSCAR"):
search_str = os.path.join(path, "relax1", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[0]
for filename in ("CONTCAR", "OSZICAR"):
search_str = os.path.join(path, "relax2", filename + "*")
files_to_parse[filename] = glob.glob(search_str)[-1]
else:
for filename in (
"INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR", "DYNMAT"
):
files = glob.glob(os.path.join(path, filename + "*"))
if len(files) < 1:
continue
if len(files) == 1 or filename == "INCAR" or \
filename == "POTCAR" or filename == "DYNMAT":
files_to_parse[filename] = files[-1]\
if filename == "POTCAR" else files[0]
elif len(files) > 1:
"""
This is a bit confusing, since there maybe be
multiple steps. By default, assimilate will try to find
a file simply named filename, filename.bz2, or
filename.gz. Failing which it will try to get a relax2
from a custodian double relaxation style run if
possible. Or else, a random file is chosen.
"""
for fname in files:
if fnmatch.fnmatch(os.path.basename(fname),
r"{}(\.gz|\.bz2)*"
.format(filename)):
files_to_parse[filename] = fname
break
if fname == "POSCAR" and \
re.search(r"relax1", fname):
files_to_parse[filename] = fname
break
if (fname in ("CONTCAR", "OSZICAR") and
re.search(r"relax2", fname)):
files_to_parse[filename] = fname
break
files_to_parse[filename] = fname
poscar, contcar, incar, potcar, oszicar, dynmat = [None]*6
if 'POSCAR' in files_to_parse:
poscar = Poscar.from_file(files_to_parse["POSCAR"])
if 'CONTCAR' in files_to_parse:
contcar = Poscar.from_file(files_to_parse["CONTCAR"])
if 'INCAR' in files_to_parse:
incar = Incar.from_file(files_to_parse["INCAR"])
if 'POTCAR' in files_to_parse:
potcar = Potcar.from_file(files_to_parse["POTCAR"])
if 'OSZICAR' in files_to_parse:
oszicar = Oszicar(files_to_parse["OSZICAR"])
if 'DYNMAT' in files_to_parse:
dynmat = Dynmat(files_to_parse["DYNMAT"])
param = {"hubbards":{}}
if poscar is not None and incar is not None and "LDAUU" in incar:
param["hubbards"] = dict(zip(poscar.site_symbols,
incar["LDAUU"]))
param["is_hubbard"] = (
incar.get("LDAU", False) and sum(param["hubbards"].values()) > 0
) if incar is not None else False
param["run_type"] = None
if incar is not None:
param["run_type"] = "GGA+U" if param["is_hubbard"] else "GGA"
param["history"] = _get_transformation_history(path)
param["potcar_spec"] = potcar.spec if potcar is not None else None
energy = oszicar.final_energy if oszicar is not None else 1e10
structure = contcar.structure if contcar is not None\
else poscar.structure
initial_vol = poscar.structure.volume if poscar is not None else \
None
final_vol = contcar.structure.volume if contcar is not None else \
None
delta_volume = None
if initial_vol is not None and final_vol is not None:
delta_volume = (final_vol / initial_vol - 1)
data = {"filename": path, "delta_volume": delta_volume}
if dynmat is not None:
data['phonon_frequencies'] = dynmat.get_phonon_frequencies()
if self._inc_structure:
entry = ComputedStructureEntry(
structure, energy, parameters=param, data=data
)
else:
entry = ComputedEntry(
structure.composition, energy, parameters=param, data=data
)
return entry
except Exception as ex:
logger.debug("error in {}: {}".format(path, ex))
return None