def setup(self):
"""
Performs initial setup for VaspJob, including overriding any settings
and backing up.
"""
decompress_dir('.')
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.auto_continue:
if os.path.exists("continue.json"):
actions = loadfn("continue.json").get("actions")
logger.info("Continuing previous VaspJob. Actions: {}".format(actions))
backup(VASP_BACKUP_FILES, prefix="prev_run")
VaspModder().apply_actions(actions)
else:
# Default functionality is to copy CONTCAR to POSCAR and set
# ISTART to 1 in the INCAR, but other actions can be specified
if self.auto_continue is True:
actions = [{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}},
{"dict": "INCAR",
"action": {"_set": {"ISTART": 1}}}]
else:
actions = self.auto_continue
dumpfn({"actions": actions}, "continue.json")
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.
"""
decompress_dir('.')
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.auto_continue:
if os.path.exists("continue.json"):
actions = loadfn("continue.json").get("actions")
logger.info("Continuing previous VaspJob. Actions: {}".format(actions))
backup(VASP_BACKUP_FILES, prefix="prev_run")
VaspModder().apply_actions(actions)
else:
# Default functionality is to copy CONTCAR to POSCAR and set
# ISTART to 1 in the INCAR, but other actions can be specified
if self.auto_continue is True:
actions = [{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}},
{"dict": "INCAR",
"action": {"_set": {"ISTART": 1}}}]
else:
actions = self.auto_continue
dumpfn({"actions": actions}, "continue.json")
if self.settings_override is not None:
VaspModder().apply_actions(self.settings_override)
def run_task(self, fw_spec):
ignore_errors = self.get("ignore_errors", False)
dest = self.get("dest", os.getcwd())
try:
decompress_dir(dest)
except:
if not ignore_errors:
raise ValueError("There was an error performing decompression in %s." % dest)
def run_task(self, fw_spec):
ignore_errors = self.get('ignore_errors', False)
dest = self.get("dest", os.getcwd())
try:
decompress_dir(dest)
except:
if not ignore_errors:
raise ValueError(
"There was an error performing decompression in %s." % dest)
def setup(self):
"""
Performs initial setup for AimsJob, including overriding any settings
and backing up.
"""
decompress_dir('.')
actions = []
if self.backup:
for f in AIMS_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
return actions
def setup(self):
"""
Performs initial setup for FeffJob, do backing up.
Returns:
"""
decompress_dir('.')
if self.backup:
for f in FEFF_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
for f in FEFF_BACKUP_FILES:
if os.path.isfile(f):
shutil.copy(f, "{}.orig".format(f))
def test_recursive_copy_and_compress(self):
copy_r(os.path.join(test_dir, "cpr_src"), os.path.join(test_dir, "cpr_dst"))
self.assertTrue(os.path.exists(os.path.join(test_dir, "cpr_dst", "test")))
self.assertTrue(os.path.exists(os.path.join(test_dir, "cpr_dst", "sub", "testr")))
compress_dir(os.path.join(test_dir, "cpr_src"))
self.assertTrue(os.path.exists(os.path.join(test_dir, "cpr_src", "test.gz")))
self.assertTrue(os.path.exists(os.path.join(test_dir, "cpr_src", "sub", "testr.gz")))
decompress_dir(os.path.join(test_dir, "cpr_src"))
self.assertTrue(os.path.exists(os.path.join(test_dir, "cpr_src", "test")))
self.assertTrue(os.path.exists(os.path.join(test_dir, "cpr_src", "sub", "testr")))
with open(os.path.join(test_dir, "cpr_src", "test")) as f:
txt = f.read()
self.assertEqual(txt, "what")
def setup(self):
"""
Performs initial setup for FeffJob, do backing up.
Returns:
"""
decompress_dir('.')
if self.backup:
for f in FEFF_INPUT_FILES:
shutil.copy(f, "{}.orig".format(f))
for f in FEFF_BACKUP_FILES:
if os.path.isfile(f):
shutil.copy(f, "{}.orig".format(f))
def _setup_file_for_parsing(self, path):
#make a "kyle_file" for parsing out relevant data
#returns True if file setup correctly
files_to_copy = [
'CONTCAR', 'OUTCAR', 'POTCAR', 'WAVECAR', 'vasprun.xml'
]
kyle_path = os.path.join(path, 'kyle_file')
if os.path.exists(kyle_path):
print('KYLE FILE ALREADY! Removing and rebuilding...')
rmtree(kyle_path)
#make kyle file
os.makedirs(kyle_path)
#copy relevant files to kyle path
for file in files_to_copy:
filepat = os.path.join(path, file + '.relax2.gz')
if not os.path.exists(filepat):
filepat = os.path.join(path, file + '.relax1.gz')
if not os.path.exists(filepat):
filepat = os.path.join(path, file + '.gz')
if not os.path.exists(filepat):
filepat = os.path.join(path, file)
if not os.path.exists(filepat):
print(
'Could not find {}! Skipping this defect...'.format(file))
return False
#COPY file to kyle_file
if '.gz' in filepat:
shutil.copy(filepat, os.path.join(kyle_path, file + '.gz'))
else:
shutil.copy(filepat, os.path.join(kyle_path, file))
decompress_dir(kyle_path)
return True
def _setup_file_for_parsing(self, path):
# make a "kyle_file" for parsing out relevant data
# returns True if file setup correctly
files_to_copy = [
"CONTCAR", "OUTCAR", "POTCAR", "WAVECAR", "vasprun.xml"
]
kyle_path = os.path.join(path, "kyle_file")
if os.path.exists(kyle_path):
print("KYLE FILE ALREADY! Removing and rebuilding...")
rmtree(kyle_path)
# make kyle file
os.makedirs(kyle_path)
# copy relevant files to kyle path
for file in files_to_copy:
filepat = os.path.join(path, file + ".relax2.gz")
if not os.path.exists(filepat):
filepat = os.path.join(path, file + ".relax1.gz")
if not os.path.exists(filepat):
filepat = os.path.join(path, file + ".gz")
if not os.path.exists(filepat):
filepat = os.path.join(path, file)
if not os.path.exists(filepat):
print(f"Could not find {file}! Skipping this defect...")
return False
# COPY file to kyle_file
if ".gz" in filepat:
shutil.copy(filepat, os.path.join(kyle_path, file + ".gz"))
else:
shutil.copy(filepat, os.path.join(kyle_path, file))
decompress_dir(kyle_path)
return True
def test_recursive_copy_and_compress(self):
copy_r(os.path.join(test_dir, "cpr_src"),
os.path.join(test_dir, "cpr_dst"))
self.assertTrue(
os.path.exists(os.path.join(test_dir, "cpr_dst", "test")))
self.assertTrue(
os.path.exists(os.path.join(test_dir, "cpr_dst", "sub", "testr")))
compress_dir(os.path.join(test_dir, "cpr_src"))
self.assertTrue(
os.path.exists(os.path.join(test_dir, "cpr_src", "test.gz")))
self.assertTrue(
os.path.exists(os.path.join(test_dir, "cpr_src", "sub",
"testr.gz")))
decompress_dir(os.path.join(test_dir, "cpr_src"))
self.assertTrue(
os.path.exists(os.path.join(test_dir, "cpr_src", "test")))
self.assertTrue(
os.path.exists(os.path.join(test_dir, "cpr_src", "sub",
"testr")))
with open(os.path.join(test_dir, "cpr_src", "test")) as f:
txt = f.read()
self.assertEqual(txt, "what")
def test_compress_dir(self):
c = CompressDirTask(compression="gz")
c.run_task({})
self.assertTrue(os.path.exists("delete.yaml.gz"))
self.assertFalse(os.path.exists("delete.yaml"))
decompress_dir(".")
def test_compress_dir(self):
c = CompressDirTask(compression="gz")
c.run_task({})
self.assertTrue(os.path.exists("delete.yaml.gz"))
self.assertFalse(os.path.exists("delete.yaml"))
decompress_dir(".")
