def test_setup(self):
if "VASP_PSP_DIR" not in os.environ:
os.environ["VASP_PSP_DIR"] = test_dir
os.chdir(os.path.join(test_dir, 'setup_neb'))
v = VaspNEBJob("hello", half_kpts=True)
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 1:
self.assertGreater(incar["NPAR"], 1)
kpt = Kpoints.from_file("KPOINTS")
kpt_pre = Kpoints.from_file("KPOINTS.orig")
self.assertEqual(kpt_pre.style.name, "Monkhorst")
self.assertEqual(kpt.style.name, "Gamma")
shutil.copy("KPOINTS.orig", "KPOINTS")
os.remove("INCAR.orig")
os.remove("KPOINTS.orig")
os.remove("POTCAR.orig")
poscars = glob.glob("[0-9][0-9]/POSCAR.orig")
for p in poscars:
os.remove(p)
def test_postprocess(self):
neb_outputs = ['INCAR', 'KPOINTS', 'POTCAR', 'vasprun.xml']
neb_sub_outputs = [
'CHG', 'CHGCAR', 'CONTCAR', 'DOSCAR', 'EIGENVAL', 'IBZKPT',
'PCDAT', 'POSCAR', 'REPORT', 'PROCAR', 'OSZICAR', 'OUTCAR',
'WAVECAR', 'XDATCAR'
]
os.chdir(os.path.join(test_dir, 'postprocess_neb'))
postprocess_neb = os.path.abspath(".")
v = VaspNEBJob("hello", final=False, suffix=".test")
v.postprocess()
for f in neb_outputs:
self.assertTrue(os.path.isfile('{}.test'.format(f)))
os.remove('{}.test'.format(f))
sub_folders = glob.glob("[0-9][0-9]")
for sf in sub_folders:
os.chdir(os.path.join(postprocess_neb, sf))
for f in neb_sub_outputs:
if os.path.exists(f):
self.assertTrue(os.path.isfile('{}.test'.format(f)))
os.remove('{}.test'.format(f))
def test_setup(self):
if "VASP_PSP_DIR" not in os.environ:
os.environ["VASP_PSP_DIR"] = test_dir
os.chdir(os.path.join(test_dir, 'setup_neb'))
v = VaspNEBJob("hello", half_kpts=True)
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 1:
self.assertGreater(incar["NPAR"], 1)
kpt = Kpoints.from_file("KPOINTS")
kpt_pre = Kpoints.from_file("KPOINTS.orig")
self.assertEqual(kpt_pre.style.name, "Monkhorst")
self.assertEqual(kpt.style.name, "Gamma")
shutil.copy("KPOINTS.orig", "KPOINTS")
os.remove("INCAR.orig")
os.remove("KPOINTS.orig")
os.remove("POTCAR.orig")
poscars = glob.glob("[0-9][0-9]/POSCAR.orig")
for p in poscars:
os.remove(p)
def test_setup(self):
with cd(os.path.join(test_dir, 'setup_neb')):
with ScratchDir('.', copy_from_current_on_enter=True) as d:
v = VaspNEBJob("hello", half_kpts=True)
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 3:
self.assertGreater(incar["NPAR"], 1)
kpt = Kpoints.from_file("KPOINTS")
kpt_pre = Kpoints.from_file("KPOINTS.orig")
self.assertEqual(kpt_pre.style.name, "Monkhorst")
self.assertEqual(kpt.style.name, "Gamma")
def test_setup(self):
with cd(os.path.join(test_dir, 'setup_neb')):
with ScratchDir('.', copy_from_current_on_enter=True) as d:
v = VaspNEBJob("hello", half_kpts=True)
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 3:
self.assertGreater(incar["NPAR"], 1)
kpt = Kpoints.from_file("KPOINTS")
kpt_pre = Kpoints.from_file("KPOINTS.orig")
self.assertEqual(kpt_pre.style.name, "Monkhorst")
self.assertEqual(kpt.style.name, "Gamma")
def test_postprocess(self):
neb_outputs = ["INCAR", "KPOINTS", "POTCAR", "vasprun.xml"]
neb_sub_outputs = [
"CHG",
"CHGCAR",
"CONTCAR",
"DOSCAR",
"EIGENVAL",
"IBZKPT",
"PCDAT",
"POSCAR",
"REPORT",
"PROCAR",
"OSZICAR",
"OUTCAR",
"WAVECAR",
"XDATCAR",
]
with cd(os.path.join(test_dir, "postprocess_neb")):
postprocess_neb = os.path.abspath(".")
v = VaspNEBJob("hello", final=False, suffix=".test")
v.postprocess()
for f in neb_outputs:
self.assertTrue(os.path.isfile(f"{f}.test"))
os.remove(f"{f}.test")
sub_folders = glob.glob("[0-9][0-9]")
for sf in sub_folders:
os.chdir(os.path.join(postprocess_neb, sf))
for f in neb_sub_outputs:
if os.path.exists(f):
self.assertTrue(os.path.isfile(f"{f}.test"))
os.remove(f"{f}.test")
def test_postprocess(self):
neb_outputs = ['INCAR', 'KPOINTS', 'POTCAR', 'vasprun.xml']
neb_sub_outputs = ['CHG', 'CHGCAR', 'CONTCAR', 'DOSCAR',
'EIGENVAL', 'IBZKPT', 'PCDAT', 'POSCAR',
'REPORT', 'PROCAR', 'OSZICAR', 'OUTCAR',
'WAVECAR', 'XDATCAR']
with cd(os.path.join(test_dir, 'postprocess_neb')):
postprocess_neb = os.path.abspath(".")
v = VaspNEBJob("hello", final=False, suffix=".test")
v.postprocess()
for f in neb_outputs:
self.assertTrue(os.path.isfile('{}.test'.format(f)))
os.remove('{}.test'.format(f))
sub_folders = glob.glob("[0-9][0-9]")
for sf in sub_folders:
os.chdir(os.path.join(postprocess_neb, sf))
for f in neb_sub_outputs:
if os.path.exists(f):
self.assertTrue(os.path.isfile('{}.test'.format(f)))
os.remove('{}.test'.format(f))
def test_to_from_dict(self):
v = VaspNEBJob("hello")
v2 = VaspNEBJob.from_dict(v.as_dict())
self.assertEqual(type(v2), type(v))
self.assertEqual(v2.vasp_cmd, "hello")
def run_task(self, fw_spec):
handler_groups = {
"default": [
VaspErrorHandler(),
MeshSymmetryErrorHandler(),
UnconvergedErrorHandler(),
NonConvergingErrorHandler(),
PotimErrorHandler(),
PositiveEnergyErrorHandler(),
FrozenJobErrorHandler(),
StdErrHandler(),
DriftErrorHandler()
],
"strict": [
VaspErrorHandler(),
MeshSymmetryErrorHandler(),
UnconvergedErrorHandler(),
NonConvergingErrorHandler(),
PotimErrorHandler(),
PositiveEnergyErrorHandler(),
FrozenJobErrorHandler(),
StdErrHandler(),
AliasingErrorHandler(),
DriftErrorHandler()
],
"md": [VaspErrorHandler(),
NonConvergingErrorHandler()],
"no_handler": []
}
vasp_cmd = env_chk(self["vasp_cmd"], fw_spec)
if isinstance(vasp_cmd, str):
vasp_cmd = os.path.expandvars(vasp_cmd)
vasp_cmd = shlex.split(vasp_cmd)
# initialize variables
job_type = self.get("job_type", "normal")
scratch_dir = env_chk(self.get("scratch_dir"), fw_spec)
gzip_output = self.get("gzip_output", True)
max_errors = self.get("max_errors", CUSTODIAN_MAX_ERRORS)
auto_npar = env_chk(self.get("auto_npar"),
fw_spec,
strict=False,
default=False)
gamma_vasp_cmd = env_chk(self.get("gamma_vasp_cmd"),
fw_spec,
strict=False,
default=None)
if gamma_vasp_cmd:
gamma_vasp_cmd = shlex.split(gamma_vasp_cmd)
# construct jobs
if job_type == "normal":
jobs = [
VaspJob(vasp_cmd,
auto_npar=auto_npar,
gamma_vasp_cmd=gamma_vasp_cmd)
]
elif job_type == "double_relaxation_run":
jobs = VaspJob.double_relaxation_run(
vasp_cmd,
auto_npar=auto_npar,
ediffg=self.get("ediffg"),
half_kpts_first_relax=self.get("half_kpts_first_relax",
HALF_KPOINTS_FIRST_RELAX))
elif job_type == "metagga_opt_run":
jobs = VaspJob.metagga_opt_run(vasp_cmd,
auto_npar=auto_npar,
ediffg=self.get("ediffg"),
half_kpts_first_relax=self.get(
"half_kpts_first_relax",
HALF_KPOINTS_FIRST_RELAX))
elif job_type == "full_opt_run":
jobs = VaspJob.full_opt_run(vasp_cmd,
auto_npar=auto_npar,
ediffg=self.get("ediffg"),
max_steps=9,
half_kpts_first_relax=self.get(
"half_kpts_first_relax",
HALF_KPOINTS_FIRST_RELAX))
elif job_type == "neb":
# TODO: @shyuep @HanmeiTang This means that NEB can only be run (i) in reservation mode
# and (ii) when the queueadapter parameter is overridden and (iii) the queue adapter
# has a convention for nnodes (with that name). Can't the number of nodes be made a
# parameter that the user sets differently? e.g., fw_spec["neb_nnodes"] must be set
# when setting job_type=NEB? Then someone can use this feature in non-reservation
# mode and without this complication. -computron
nnodes = int(fw_spec["_queueadapter"]["nnodes"])
# TODO: @shyuep @HanmeiTang - I am not sure what the code below is doing. It looks like
# it is trying to override the number of processors. But I tried running the code
# below after setting "vasp_cmd = 'mpirun -n 16 vasp'" and the code fails.
# (i) Is this expecting an array vasp_cmd rather than String? If so, that's opposite to
# the rest of this task's convention and documentation
# (ii) can we get rid of this hacking in the first place? e.g., allowing the user to
# separately set the NEB_VASP_CMD as an env_variable and not rewriting the command
# inside this.
# -computron
# Index the tag "-n" or "-np"
index = [i for i, s in enumerate(vasp_cmd) if '-n' in s]
ppn = int(vasp_cmd[index[0] + 1])
vasp_cmd[index[0] + 1] = str(nnodes * ppn)
# Do the same for gamma_vasp_cmd
if gamma_vasp_cmd:
index = [i for i, s in enumerate(gamma_vasp_cmd) if '-n' in s]
ppn = int(gamma_vasp_cmd[index[0] + 1])
gamma_vasp_cmd[index[0] + 1] = str(nnodes * ppn)
jobs = [
VaspNEBJob(vasp_cmd,
final=False,
auto_npar=auto_npar,
gamma_vasp_cmd=gamma_vasp_cmd)
]
else:
raise ValueError("Unsupported job type: {}".format(job_type))
# construct handlers
handler_group = self.get("handler_group", "default")
if isinstance(handler_group, str):
handlers = handler_groups[handler_group]
else:
handlers = handler_group
if self.get("max_force_threshold"):
handlers.append(
MaxForceErrorHandler(
max_force_threshold=self["max_force_threshold"]))
if self.get("wall_time"):
handlers.append(WalltimeHandler(wall_time=self["wall_time"]))
if job_type == "neb":
validators = [
] # CINEB vasprun.xml sometimes incomplete, file structure different
else:
validators = [VasprunXMLValidator(), VaspFilesValidator()]
c = Custodian(handlers,
jobs,
validators=validators,
max_errors=max_errors,
scratch_dir=scratch_dir,
gzipped_output=gzip_output)
c.run()
if os.path.exists(zpath("custodian.json")):
stored_custodian_data = {
"custodian": loadfn(zpath("custodian.json"))
}
return FWAction(stored_data=stored_custodian_data)
def test_to_from_dict(self):
v = VaspNEBJob("hello")
v2 = VaspNEBJob.from_dict(v.as_dict())
self.assertEqual(type(v2), type(v))
self.assertEqual(v2.vasp_cmd, "hello")