def setup(self):
"""
Method is identical to custodian.vasp.jobs.setup(), except that the
environment variable PBS_NUM_PPN is checked first when auto_npar =
True.
"""
files = os.listdir(".")
num_structures = 0
if not set(files).issuperset(VASP_INPUT_FILES):
for f in files:
try:
struct = read_structure(f)
num_structures += 1
except:
pass
if num_structures != 1:
raise RuntimeError("{} structures found. Unable to continue."
.format(num_structures))
else:
self.default_vis.write_input(struct, ".")
if self.backup:
for f in VASP_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
if self.auto_npar:
try:
incar = Incar.from_file("INCAR")
# Only optimized NPAR for non-HF and non-RPA calculations.
if not (incar.get("LHFCALC") or incar.get("LRPA") or
incar.get("LEPSILON")):
if incar.get("IBRION") in [5, 6, 7, 8]:
# NPAR should not be set for Hessian matrix
# calculations, whether in DFPT or otherwise.
del incar["NPAR"]
else:
import multiprocessing
# try pbs environment variable first
# try sge environment variable second
# Note!
# multiprocessing.cpu_count() will include hyperthreads
# in the CPU count, which will set NPAR to be too large
# and can cause the job to hang if you use compute
# nodes with scratch partitions.
ncores = (os.environ.get("PBS_NUM_PPN") or
os.environ.get('NSLOTS') or
multiprocessing.cpu_count())
ncores = int(ncores)
for npar in range(int(math.sqrt(ncores)),
ncores):
if ncores % npar == 0:
incar["NPAR"] = npar
break
incar.write_file("INCAR")
except:
pass
if self.settings_override is not None:
VaspModder().apply_actions(self.settings_override)
def setup(self):
"""
Method is identical to custodian.vasp.jobs.setup(), except that the
environment variable PBS_NUM_PPN is checked first when auto_npar =
True.
"""
files = os.listdir(".")
num_structures = 0
if not set(files).issuperset(VASP_INPUT_FILES):
for f in files:
try:
struct = read_structure(f)
num_structures += 1
except:
pass
if num_structures != 1:
raise RuntimeError(
"{} structures found. Unable to continue.".format(
num_structures))
else:
self.default_vis.write_input(struct, ".")
if self.backup:
for f in VASP_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
if self.auto_npar:
try:
incar = Incar.from_file("INCAR")
# Only optimized NPAR for non-HF and non-RPA calculations.
if not (incar.get("LHFCALC") or incar.get("LRPA")
or incar.get("LEPSILON")):
if incar.get("IBRION") in [5, 6, 7, 8]:
# NPAR should not be set for Hessian matrix
# calculations, whether in DFPT or otherwise.
del incar["NPAR"]
else:
import multiprocessing
# try pbs environment variable first
# try sge environment variable second
# Note!
# multiprocessing.cpu_count() will include hyperthreads
# in the CPU count, which will set NPAR to be too large
# and can cause the job to hang if you use compute
# nodes with scratch partitions.
ncores = (os.environ.get("PBS_NUM_PPN")
or os.environ.get('NSLOTS')
or multiprocessing.cpu_count())
ncores = int(ncores)
for npar in range(int(math.sqrt(ncores)), ncores):
if ncores % npar == 0:
incar["NPAR"] = npar
break
incar.write_file("INCAR")
except:
pass
if self.settings_override is not None:
VaspModder().apply_actions(self.settings_override)
def test_read_structure(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
for fname in ("Li2O.cif", "vasprun.xml",
"vasprun_Si_bands.xml", "Si.cssr"):
filename = os.path.join(test_dir, fname)
struct = read_structure(filename)
self.assertIsInstance(struct, Structure)
prim = read_structure(filename, primitive=True)
self.assertLessEqual(len(prim), len(struct))
sorted_s = read_structure(filename, sort=True)
self.assertEqual(sorted_s, sorted_s.get_sorted_structure())
m = StructureMatcher()
for ext in [".cif", ".json", ".cssr"]:
fn = "smartio_structure_test" + ext
write_structure(struct, fn)
back = read_structure(fn)
self.assertTrue(m.fit(back, struct))
os.remove(fn)
def test_read_structure(self):
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
for fname in ("Li2O.cif", "vasprun.xml", "vasprun_Si_bands.xml",
"Si.cssr"):
filename = os.path.join(test_dir, fname)
struct = read_structure(filename)
self.assertIsInstance(struct, Structure)
prim = read_structure(filename, primitive=True)
self.assertLessEqual(len(prim), len(struct))
sorted_s = read_structure(filename, sort=True)
self.assertEqual(sorted_s, sorted_s.get_sorted_structure())
m = StructureMatcher()
for ext in [".cif", ".json", ".cssr"]:
fn = "smartio_structure_test" + ext
write_structure(struct, fn)
back = read_structure(fn)
self.assertTrue(m.fit(back, struct))
os.remove(fn)
def setup(self):
"""
Performs initial setup for VaspJob, including overriding any settings
and backing up.
"""
files = os.listdir(".")
num_structures = 0
if not set(files).issuperset(VASP_INPUT_FILES):
for f in files:
try:
struct = read_structure(f)
num_structures += 1
except:
pass
if num_structures != 1:
raise RuntimeError(
"{} structures found. Unable to continue.".format(
num_structures))
else:
self.default_vis.write_input(struct, ".")
if self.backup:
for f in VASP_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
if self.auto_npar:
try:
incar = Incar.from_file("INCAR")
#Only optimized NPAR for non-HF and non-RPA calculations.
if not (incar.get("LHFCALC") or incar.get("LRPA")
or incar.get("LEPSILON")):
if incar.get("IBRION") in [5, 6, 7, 8]:
# NPAR should not be set for Hessian matrix
# calculations, whether in DFPT or otherwise.
del incar["NPAR"]
else:
import multiprocessing
# try sge environment variable first
# (since multiprocessing counts cores on the current machine only)
ncores = os.environ.get(
'NSLOTS') or multiprocessing.cpu_count()
ncores = int(ncores)
for npar in range(int(round(math.sqrt(ncores))),
ncores):
if ncores % npar == 0:
incar["NPAR"] = npar
break
incar.write_file("INCAR")
except:
pass
if self.settings_override is not None:
VaspModder().apply_actions(self.settings_override)
def setup(self):
"""
Performs initial setup for VaspJob, including overriding any settings
and backing up.
"""
files = os.listdir(".")
num_structures = 0
if not set(files).issuperset(VASP_INPUT_FILES):
for f in files:
try:
struct = read_structure(f)
num_structures += 1
except:
pass
if num_structures != 1:
raise RuntimeError("{} structures found. Unable to continue."
.format(num_structures))
else:
self.default_vis.write_input(struct, ".")
if self.backup:
for f in VASP_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
if self.auto_npar:
try:
incar = Incar.from_file("INCAR")
#Only optimized NPAR for non-HF and non-RPA calculations.
if not (incar.get("LHFCALC") or incar.get("LRPA") or
incar.get("LEPSILON")):
if incar.get("IBRION") in [5, 6, 7, 8]:
# NPAR should not be set for Hessian matrix
# calculations, whether in DFPT or otherwise.
del incar["NPAR"]
else:
import multiprocessing
# try sge environment variable first
# (since multiprocessing counts cores on the current machine only)
ncores = os.environ.get('NSLOTS') or multiprocessing.cpu_count()
ncores = int(ncores)
for npar in range(int(math.sqrt(ncores)),
ncores):
if ncores % npar == 0:
incar["NPAR"] = npar
break
incar.write_file("INCAR")
except:
pass
if self.settings_override is not None:
VaspModder().apply_actions(self.settings_override)
