def test_init(self):
filepath = os.path.join(test_dir, 'OSZICAR')
oszicar = Oszicar(filepath)
self.assertEqual(len(oszicar.electronic_steps),
len(oszicar.ionic_steps))
self.assertEqual(len(oszicar.all_energies), 60)
self.assertAlmostEqual(oszicar.final_energy, -526.63928)
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:
files_to_parse["INCAR"] = glob.glob(
os.path.join(path, "INCAR*"))[0]
files_to_parse["POTCAR"] = glob.glob(
os.path.join(path, "POTCAR*"))[-1]
for filename in ("CONTCAR", "OSZICAR", "POSCAR"):
files = glob.glob(os.path.join(path, filename + "*"))
if len(files) == 1:
files_to_parse[filename] = 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 an aflow style run if possible. Or else, a
randomly chosen 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 = Poscar.from_file(files_to_parse["POSCAR"])
contcar = Poscar.from_file(files_to_parse["CONTCAR"])
param = {}
incar = Incar.from_file(files_to_parse["INCAR"])
if "LDAUU" in incar:
param["hubbards"] = dict(
zip(poscar.site_symbols, incar["LDAUU"]))
else:
param["hubbards"] = {}
param["is_hubbard"] = (incar.get("LDAU", False)
and sum(param["hubbards"].values()) > 0)
param["run_type"] = "GGA+U" if param["is_hubbard"] else "GGA"
param["history"] = _get_transformation_history(path)
potcar = Potcar.from_file(files_to_parse["POTCAR"])
param["potcar_symbols"] = potcar.symbols
oszicar = Oszicar(files_to_parse["OSZICAR"])
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 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