def test_eddrmm(self):
h = VaspErrorHandler("vasp.eddrmm")
self.assertEqual(h.check(), True)
self.assertEqual(h.correct()["errors"], ["eddrmm"])
i = Incar.from_file("INCAR")
self.assertEqual(i["ALGO"], "Normal")
self.assertEqual(h.correct()["errors"], ["eddrmm"])
i = Incar.from_file("INCAR")
self.assertEqual(i["POTIM"], 0.25)
def make_hex_lattice_input(path,
atomic_sep,
kpointdivs,
comment,
forbid_symmetry=True):
pb = hexagonal_unitcell('C', atomic_sep, layersep=25.)
incar = Incar()
incar['SYSTEM'] = comment
incar['ALGO'] = 'Fast'
incar['NSW'] = 1000
incar['IBRION'] = 2
incar['EDIFF'] = 1E-8
if forbid_symmetry:
incar['ISYM'] = 0
kpoints = Kpoints.gamma_automatic(kpointdivs, [0, 0, 0])
metadata = {'atomic_sep': atomic_sep, 'kpointdivs': kpointdivs}
ws = VaspInput(
poscar=pb.poscar(comment=comment),
potcar=pb.potcar(functional='PBE'),
incar=incar,
kpoints=kpoints,
# additional files
metadata=json.dumps(metadata),
)
ws.write_input(path)
def _vasp_incar_setup(self, my_potcar, my_poscar):
"""Set up the INCAR, including MAGMOM string, ENCUT, and NELECT."""
name=self.keywords['name']
myd = dict()
myd = self._vasp_incar_get_non_mast_keywords()
try:
myd.pop("IMAGES")
except KeyError:
pass
if 'mast_multiplyencut' in self.keywords['program_keys'].keys():
mymult = float(self.keywords['program_keys']['mast_multiplyencut'])
else:
mymult = 1.5
if 'ENCUT' in myd.keys():
pass
else:
myd['ENCUT']=self._get_max_enmax_from_potcar(my_potcar)*mymult
if 'mast_setmagmom' in self.keywords['program_keys'].keys():
magstr = str(self.keywords['program_keys']['mast_setmagmom'])
magmomstr=""
maglist = magstr.split()
numatoms = sum(my_poscar.natoms)
if len(maglist) < numatoms:
magct=0
while magct < len(maglist):
magmomstr = magmomstr + str(my_poscar.natoms[magct]) + "*" + maglist[magct] + " "
magct = magct + 1
else:
magmomstr = magstr
myd['MAGMOM']=magmomstr
if 'mast_charge' in self.keywords['program_keys'].keys():
myelectrons = self.get_total_electrons(my_poscar, my_potcar)
newelectrons=0.0
try:
adjustment = float(self.keywords['program_keys']['mast_charge'])
except (ValueError, TypeError):
raise MASTError("vasp_checker, vasp_incar_setup","Could not parse adjustment")
#newelectrons = myelectrons + adjustment
newelectrons = myelectrons - adjustment
myd['NELECT']=str(newelectrons)
if self.metafile.read_data('nbands'):
myd['NBANDS']=self.metafile.read_data('nbands')
my_incar = Incar(myd)
dirutil.lock_directory(name)
my_incar.write_file(name + "/INCAR")
dirutil.unlock_directory(name)
return my_incar
def test_potim_correction(self):
shutil.copy("OSZICAR.one_step", "OSZICAR")
s1 = Structure.from_file("POSCAR")
h = VaspErrorHandler("vasp.out")
self.assertEqual(h.check(), True)
d = h.correct()
self.assertEqual(d['errors'], ['zpotrf'])
s2 = Structure.from_file("POSCAR")
self.assertAlmostEqual(s2.volume, s1.volume, 3)
self.assertAlmostEqual(Incar.from_file("INCAR")['POTIM'], 0.25)
def make_vasp_input(path, *, kpointdivs, comment, forbid_symmetry, functional,
perturb_dist, **kwargs):
assert hasattr(kpointdivs, '__iter__')
assert isinstance(comment, str)
assert isinstance(forbid_symmetry, bool)
assert isinstance(perturb_dist, float)
pb = carbon_chain_poxcar(**kwargs)
incar = Incar()
incar['SYSTEM'] = comment
incar['ALGO'] = 'Fast'
incar['NSW'] = 1000
incar['NPAR'] = 4
incar['IBRION'] = 2
incar['EDIFF'] = 1E-8
incar['EDIFFG'] = -0.001
if forbid_symmetry:
incar['ISYM'] = 0
kpoints = Kpoints.gamma_automatic(kpointdivs, [0, 0, 0])
metadata = {
'kpointdivs': kpointdivs,
'functional': functional,
'perturb_dist': perturb_dist,
'forbid_symmetry': forbid_symmetry,
}
# FIXME FIXME FIXME
# Here, we insert all structure parameters into the metadata. The purpose is because
# oftentimes those parameters are the ones we're most interested in (such as scale).
#
# However, this is all kinds of bad:
# * Not all structure arguments are necessarily desirable to have in the metadata.
# * What if we want a structure argument to be of a non JSON-encodable type?
# * It creates a dependency between names of function arguments in code, and the output file.
# In other words, madness.
metadata = dict_union(metadata, kwargs)
ws = VaspInput(
poscar=pb.poscar(
perturb_dist=perturb_dist,
comment=comment,
),
potcar=pb.potcar(functional=functional, ),
incar=incar,
kpoints=kpoints,
# additional files
metadata=json.dumps(metadata),
)
ws.write_input(path)
def get_incar(self, structure):
incar = Incar()
symamt = structure.composition.to_dict
poscar = Poscar(structure)
for key, setting in self.incar_settings.items():
if key == "MAGMOM":
mag = []
for site in structure:
if hasattr(site, 'magmom'):
mag.append(site.magmom)
elif hasattr(site.specie, 'spin'):
mag.append(site.specie.spin)
else:
mag.append(setting.get(site.specie.symbol, 0.6))
incar[key] = mag
elif key in ['LDAUU', 'LDAUJ', 'LDAUL']:
if symamt.get("O", 0) > 0 or symamt.get("F", 0) > 0:
incar[key] = [setting.get(sym, 0) for sym in poscar.site_symbols]
else:
incar[key] = [0 for sym in poscar.site_symbols]
elif key == "EDIFF":
incar[key] = float(setting) * structure.num_sites
else:
incar[key] = setting
has_u = ("LDAUU" in incar and sum(incar['LDAUU']) > 0)
if has_u:
# modify LMAXMIX if LSDA+U and you have d or f electrons
# note that if the user explicitly sets LMAXMIX in settings it will override this logic
if 'LMAXMIX' not in self.incar_settings.keys():
if any([el.Z > 56 for el in structure.composition]): # contains f-electrons
incar['LMAXMIX'] = 6
elif any([el.Z > 20 for el in structure.composition]): # contains d-electrons
incar['LMAXMIX'] = 4
else:
for key in incar.keys():
if key.startswith('LDAU'):
del incar[key]
return incar
def test_check_correct(self):
subdir = os.path.join(test_dir, "potim")
os.chdir(subdir)
shutil.copy("INCAR", "INCAR.orig")
shutil.copy("POSCAR", "POSCAR.orig")
incar = Incar.from_file('INCAR')
original_potim = incar['POTIM']
h = PotimErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['POTIM'])
os.remove(os.path.join(subdir, "error.1.tar.gz"))
incar = Incar.from_file('INCAR')
new_potim = incar['POTIM']
shutil.move("INCAR.orig", "INCAR")
shutil.move("POSCAR.orig", "POSCAR")
self.assertEqual(original_potim, new_potim)
self.assertEqual(incar['IBRION'], 3)
def test_setup(self):
if "VASP_PSP_DIR" not in os.environ:
os.environ["VASP_PSP_DIR"] = test_dir
os.chdir(test_dir)
v = VaspJob("hello")
v.setup()
incar = Incar.from_file("INCAR")
count = multiprocessing.cpu_count()
if count > 1:
self.assertGreater(incar["NPAR"], 1)
shutil.copy("INCAR.orig", "INCAR")
os.remove("INCAR.orig")
os.remove("KPOINTS.orig")
os.remove("POTCAR.orig")
os.remove("POSCAR.orig")
def test_aliasing_incar(self):
os.chdir(os.path.join(test_dir, "aliasing"))
shutil.copy("INCAR", "INCAR.orig")
h = VaspErrorHandler("vasp.aliasing_incar")
h.check()
d = h.correct()
incar = Incar.from_file('INCAR')
shutil.move("INCAR.orig", "INCAR")
clean_dir()
os.chdir(test_dir)
self.assertEqual(d["errors"], ['aliasing_incar'])
self.assertEqual(d["actions"],
[{'action': {'_unset': {'NGY':1, 'NGZ': 1}},
'dict': 'INCAR'}, {"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}},
{"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}}])
def test_check_correct(self):
subdir = os.path.join(test_dir, "positive_energy")
os.chdir(subdir)
shutil.copy("INCAR", "INCAR.orig")
shutil.copy("POSCAR", "POSCAR.orig")
h = PositiveEnergyErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Positive energy'])
os.remove(os.path.join(subdir, "error.1.tar.gz"))
incar = Incar.from_file('INCAR')
shutil.move("INCAR.orig", "INCAR")
shutil.move("POSCAR.orig", "POSCAR")
self.assertEqual(incar['ALGO'], 'Normal')
def test_check_correct(self):
#NOTE: the vasprun here has had projected and partial eigenvalues removed
subdir = os.path.join(test_dir, "max_force")
os.chdir(subdir)
shutil.copy("INCAR", "INCAR.orig")
shutil.copy("POSCAR", "POSCAR.orig")
h = MaxForceErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['MaxForce'])
os.remove(os.path.join(subdir, "error.1.tar.gz"))
incar = Incar.from_file('INCAR')
poscar = Poscar.from_file('POSCAR')
contcar = Poscar.from_file('CONTCAR')
shutil.move("INCAR.orig", "INCAR")
shutil.move("POSCAR.orig", "POSCAR")
self.assertEqual(poscar.structure, contcar.structure)
self.assertAlmostEqual(incar['EDIFF'], 0.00075)
from pymatgen.io.vaspio import Incar
from pymatgen.util.string_utils import str_aligned
parser = argparse.ArgumentParser(description='''Convenient INCAR diff.
Author: Shyue Ping Ong
Version: 1.0
Last updated: Oct 26 2011''')
parser.add_argument('incar_file', metavar='filename', type=str, nargs=2,
help='files to process')
args = parser.parse_args()
filepath1 = args.incar_file[0]
filepath2 = args.incar_file[1]
incar1 = Incar.from_file(filepath1)
incar2 = Incar.from_file(filepath2)
def format_lists(v):
if isinstance(v, (tuple, list)):
return " ".join(["%d*%.2f" % (len(tuple(group)), i)
for (i, group) in itertools.groupby(v)])
return v
d = incar1.diff(incar2)
output = [['SAME PARAMS', '', '']]
output.append(['---------------', '', ''])
output.extend([(k, format_lists(d['Same'][k]), format_lists(d['Same'][k]))
for k in sorted(d['Same'].keys()) if k != "SYSTEM"])
output.append(['', '', ''])
def process_killed_run(cls, dir_name):
"""
Process a killed vasp run.
"""
fullpath = os.path.abspath(dir_name)
logger.info("Processing Killed run " + fullpath)
d = {"dir_name": fullpath, "state": "killed", "oszicar": {}}
for f in os.listdir(dir_name):
filename = os.path.join(dir_name, f)
if fnmatch(f, "INCAR*"):
try:
incar = Incar.from_file(filename)
d["incar"] = incar.to_dict
d["is_hubbard"] = incar.get("LDAU", False)
if d["is_hubbard"]:
us = incar.get("LDAUU", [])
js = incar.get("LDAUJ", [])
if sum(us) == 0 and sum(js) == 0:
d["is_hubbard"] = False
d["hubbards"] = {}
else:
d["hubbards"] = {}
if d["is_hubbard"]:
d["run_type"] = "GGA+U"
elif incar.get("LHFCALC", False):
d["run_type"] = "HF"
else:
d["run_type"] = "GGA"
except Exception as ex:
print str(ex)
logger.error("Unable to parse INCAR for killed run {}.".format(dir_name))
elif fnmatch(f, "KPOINTS*"):
try:
kpoints = Kpoints.from_file(filename)
d["kpoints"] = kpoints.to_dict
except:
logger.error("Unable to parse KPOINTS for killed run {}.".format(dir_name))
elif fnmatch(f, "POSCAR*"):
try:
s = Poscar.from_file(filename).structure
comp = s.composition
el_amt = s.composition.get_el_amt_dict()
d.update(
{
"unit_cell_formula": comp.to_dict,
"reduced_cell_formula": comp.to_reduced_dict,
"elements": list(el_amt.keys()),
"nelements": len(el_amt),
"pretty_formula": comp.reduced_formula,
"anonymous_formula": comp.anonymized_formula,
"nsites": comp.num_atoms,
"chemsys": "-".join(sorted(el_amt.keys())),
}
)
d["poscar"] = s.to_dict
except:
logger.error("Unable to parse POSCAR for killed run {}.".format(dir_name))
elif fnmatch(f, "POTCAR*"):
try:
potcar = Potcar.from_file(filename)
d["pseudo_potential"] = {"functional": "pbe", "pot_type": "paw", "labels": potcar.symbols}
except:
logger.error("Unable to parse POTCAR for killed run in {}.".format(dir_name))
elif fnmatch(f, "OSZICAR"):
try:
d["oszicar"]["root"] = Oszicar(os.path.join(dir_name, f)).to_dict
except:
logger.error("Unable to parse OSZICAR for killed run in {}.".format(dir_name))
elif re.match("relax\d", f):
if os.path.exists(os.path.join(dir_name, f, "OSZICAR")):
try:
d["oszicar"][f] = Oszicar(os.path.join(dir_name, f, "OSZICAR")).to_dict
except:
logger.error("Unable to parse OSZICAR for killed " "run in {}.".format(dir_name))
return d
def test_to_dict_and_from_dict(self):
file_name = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(file_name)
d = incar.to_dict
incar2 = Incar.from_dict(d)
self.assertEqual(incar, incar2)
def process_killed_run(cls, dir_name):
"""
Process a killed vasp run.
"""
fullpath = os.path.abspath(dir_name)
logger.info("Processing Killed run " + fullpath)
d = {"dir_name": fullpath, "state": "killed", "oszicar": {}}
for f in os.listdir(dir_name):
filename = os.path.join(dir_name, f)
if fnmatch(f, "INCAR*"):
try:
incar = Incar.from_file(filename)
d["incar"] = incar.to_dict
d["is_hubbard"] = incar.get("LDAU", False)
if d["is_hubbard"]:
us = incar.get("LDAUU", [])
js = incar.get("LDAUJ", [])
if sum(us) == 0 and sum(js) == 0:
d["is_hubbard"] = False
d["hubbards"] = {}
else:
d["hubbards"] = {}
if d["is_hubbard"]:
d["run_type"] = "GGA+U"
elif incar.get("LHFCALC", False):
d["run_type"] = "HF"
else:
d["run_type"] = "GGA"
except Exception as ex:
print str(ex)
logger.error(
"Unable to parse INCAR for killed run {}.".format(
dir_name))
elif fnmatch(f, "KPOINTS*"):
try:
kpoints = Kpoints.from_file(filename)
d["kpoints"] = kpoints.to_dict
except:
logger.error(
"Unable to parse KPOINTS for killed run {}.".format(
dir_name))
elif fnmatch(f, "POSCAR*"):
try:
s = Poscar.from_file(filename).structure
comp = s.composition
el_amt = s.composition.get_el_amt_dict()
d.update({
"unit_cell_formula": comp.to_dict,
"reduced_cell_formula": comp.to_reduced_dict,
"elements": list(el_amt.keys()),
"nelements": len(el_amt),
"pretty_formula": comp.reduced_formula,
"anonymous_formula": comp.anonymized_formula,
"nsites": comp.num_atoms,
"chemsys": "-".join(sorted(el_amt.keys()))
})
d["poscar"] = s.to_dict
except:
logger.error(
"Unable to parse POSCAR for killed run {}.".format(
dir_name))
elif fnmatch(f, "POTCAR*"):
try:
potcar = Potcar.from_file(filename)
d["pseudo_potential"] = {
"functional": "pbe",
"pot_type": "paw",
"labels": potcar.symbols
}
except:
logger.error(
"Unable to parse POTCAR for killed run in {}.".format(
dir_name))
elif fnmatch(f, "OSZICAR"):
try:
d["oszicar"]["root"] = \
Oszicar(os.path.join(dir_name, f)).to_dict
except:
logger.error(
"Unable to parse OSZICAR for killed run in {}.".format(
dir_name))
elif re.match("relax\d", f):
if os.path.exists(os.path.join(dir_name, f, "OSZICAR")):
try:
d["oszicar"][f] = Oszicar(
os.path.join(dir_name, f, "OSZICAR")).to_dict
except:
logger.error("Unable to parse OSZICAR for killed "
"run in {}.".format(dir_name))
return d
def test_frozen_job(self):
h = FrozenJobErrorHandler()
d = h.correct()
self.assertEqual(d['errors'], ['Frozen job'])
self.assertEqual(Incar.from_file("INCAR")['ALGO'], "Normal")
def test_init(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
incar["LDAU"] = "T"
self.assertEqual(incar["ALGO"], "Damped", "Wrong Algo")
self.assertEqual(float(incar["EDIFF"]), 1e-4, "Wrong EDIFF")
def test_pssyevx(self):
h = VaspErrorHandler("vasp.pssyevx")
self.assertEqual(h.check(), True)
self.assertEqual(h.correct()["errors"], ["pssyevx"])
i = Incar.from_file("INCAR")
self.assertEqual(i["ALGO"], "Normal")
parser = argparse.ArgumentParser(description='''Convenient INCAR diff.
Author: Shyue Ping Ong
Version: 1.0
Last updated: Oct 26 2011''')
parser.add_argument('incar_file',
metavar='filename',
type=str,
nargs=2,
help='files to process')
args = parser.parse_args()
filepath1 = args.incar_file[0]
filepath2 = args.incar_file[1]
incar1 = Incar.from_file(filepath1)
incar2 = Incar.from_file(filepath2)
def format_lists(v):
if isinstance(v, (tuple, list)):
return " ".join([
"%d*%.2f" % (len(tuple(group)), i)
for (i, group) in itertools.groupby(v)
])
return v
d = incar1.diff(incar2)
output = [['SAME PARAMS', '', '']]
output.append(['---------------', '', ''])
def test_diff(self):
filepath1 = os.path.join(test_dir, 'INCAR')
incar1 = Incar.from_file(filepath1)
filepath2 = os.path.join(test_dir, 'INCAR.2')
incar2 = Incar.from_file(filepath2)
self.assertEqual(incar1.diff(incar2), {'Different': {'NELM': {'INCAR1': 'Default', 'INCAR2': 100}, 'ISPIND': {'INCAR1': 2, 'INCAR2': 'Default'}, 'LWAVE': {'INCAR1': True, 'INCAR2': False}, 'LDAUPRINT': {'INCAR1': 'Default', 'INCAR2': 1}, 'MAGMOM': {'INCAR1': [6, -6, -6, 6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6], 'INCAR2': 'Default'}, 'NELMIN': {'INCAR1': 'Default', 'INCAR2': 3}, 'ENCUTFOCK': {'INCAR1': 0.0, 'INCAR2': 'Default'}, 'HFSCREEN': {'INCAR1': 0.207, 'INCAR2': 'Default'}, 'LSCALU': {'INCAR1': False, 'INCAR2': 'Default'}, 'ENCUT': {'INCAR1': 500, 'INCAR2': 'Default'}, 'NSIM': {'INCAR1': 1, 'INCAR2': 'Default'}, 'ICHARG': {'INCAR1': 'Default', 'INCAR2': 1}, 'NSW': {'INCAR1': 99, 'INCAR2': 51}, 'NKRED': {'INCAR1': 2, 'INCAR2': 'Default'}, 'NUPDOWN': {'INCAR1': 0, 'INCAR2': 'Default'}, 'LCHARG': {'INCAR1': True, 'INCAR2': 'Default'}, 'LPLANE': {'INCAR1': True, 'INCAR2': 'Default'}, 'ISMEAR': {'INCAR1': 0, 'INCAR2':-5}, 'NPAR': {'INCAR1': 8, 'INCAR2': 1}, 'SYSTEM': {'INCAR1': 'Id=[0] dblock_code=[97763-icsd] formula=[li mn (p o4)] sg_name=[p n m a]', 'INCAR2': 'Id=[91090] dblock_code=[20070929235612linio-59.53134651-vasp] formula=[li3 ni3 o6] sg_name=[r-3m]'}, 'ALGO': {'INCAR1': 'Damped', 'INCAR2': 'Fast'}, 'LHFCALC': {'INCAR1': True, 'INCAR2': 'Default'}, 'TIME': {'INCAR1': 0.4, 'INCAR2': 'Default'}}, 'Same': {'IBRION': 2, 'PREC': 'Accurate', 'ISIF': 3, 'LMAXMIX': 4, 'LREAL': 'Auto', 'ISPIN': 2, 'EDIFF': 0.0001, 'LORBIT': '11', 'SIGMA': 0.05}})
