def generate_files(args):
from pymatgen.io.vaspio.vasp_input import Potcar
if args.symbols:
try:
p = Potcar(args.symbols, functional=args.functional)
p.write_file("POTCAR")
except Exception as ex:
print("An error has occurred: {}".format(str(ex)))
else:
print("No valid options selected.")
def generate_files(args):
from pymatgen.io.vaspio.vasp_input import Potcar
if args.symbols:
try:
p = Potcar(args.symbols, functional=args.functional)
p.write_file("POTCAR")
except Exception as ex:
print "An error has occurred: {}".format(str(ex))
else:
print "No valid options selected."
def get_potcar(self, structure):
"""
Method for getting LDA potcars
"""
if self.sort_structure:
structure = structure.get_sorted_structure()
return Potcar(self.get_potcar_symbols(structure), functional=self.functional)
def setUp(self):
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
self.potcar = Potcar.from_file(filepath)
def setUp(self):
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..", "test_files")
)
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, "POTCAR")
self.potcar = Potcar.from_file(filepath)
def test_potcar_map(self):
fe_potcar = zopen(os.path.join(test_dir, "POT_GGA_PAW_PBE",
"POTCAR.Fe_pv.gz")).read()
#specify V instead of Fe - this makes sure the test won't pass if the
#code just grabs the POTCAR from the config file (the config file would
#grab the V POTCAR)
potcar = Potcar(["V"], sym_potcar_map={"V": fe_potcar})
self.assertEqual(potcar.symbols, ["Fe_pv"], "Wrong symbols read in "
"for POTCAR")
def get_POTCAR(poscar):
list_postfix = ['_pv','_sv','']
potcar = Potcar()
list_potcar_singles = []
for symbol in poscar.site_symbols:
for postfix in list_postfix:
potcar_path = PSEUDOPOTENTIALS_DIRECTORY+'%s%s/POTCAR'%(symbol,postfix)
if os.path.isfile(potcar_path):
single = PotcarSingle.from_file(potcar_path)
list_potcar_singles.append(single)
potcar.insert(-1,single)
break
return list_potcar_singles, potcar
def __init__(self, chgcar_filename, potcar_filename=None):
"""
Args:
chgcar_filename:
The filename of the CHGCAR.
potcar_filename:
Optional: the filename of the corresponding POTCAR file. Used
for calculating the charge transfer. If None, the
get_charge_transfer method will raise a ValueError.
"""
temp_dir = tempfile.mkdtemp()
self.chgcar = Chgcar.from_file(chgcar_filename)
self.potcar = Potcar.from_file(potcar_filename) \
if potcar_filename is not None else None
self.natoms = self.chgcar.poscar.natoms
try:
shutil.copy(chgcar_filename, os.path.join(temp_dir, "CHGCAR"))
current_dir = os.getcwd()
os.chdir(temp_dir)
rs = subprocess.Popen(["bader", "CHGCAR"],
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
close_fds=True)
rs.communicate()
data = []
with open("ACF.dat") as f:
raw = f.readlines()
headers = [s.lower() for s in raw.pop(0).split()]
raw.pop(0)
while True:
l = raw.pop(0).strip()
if l.startswith("-"):
break
vals = map(float, l.split()[1:])
data.append(dict(zip(headers[1:], vals)))
for l in raw:
toks = l.strip().split(":")
if toks[0] == "VACUUM CHARGE":
self.vacuum_charge = float(toks[1])
elif toks[0] == "VACUUM VOLUME":
self.vacuum_volume = float(toks[1])
elif toks[0] == "NUMBER OF ELECTRONS":
self.nelectrons = float(toks[1])
self.data = data
os.chdir(current_dir)
except Exception as ex:
print str(ex)
finally:
shutil.rmtree(temp_dir)
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def setUp(self):
filepath = os.path.join(test_dir, "INCAR")
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..", "test_files")
)
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, "POTCAR")
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, "KPOINTS.auto")
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def __init__(self, chgcar_filename, potcar_filename=None):
"""
Args:
chgcar_filename:
The filename of the CHGCAR.
potcar_filename:
Optional: the filename of the corresponding POTCAR file. Used
for calculating the charge transfer. If None, the
get_charge_transfer method will raise a ValueError.
"""
temp_dir = tempfile.mkdtemp()
self.chgcar = Chgcar.from_file(chgcar_filename)
self.potcar = Potcar.from_file(potcar_filename) \
if potcar_filename is not None else None
self.natoms = self.chgcar.poscar.natoms
try:
shutil.copy(chgcar_filename, os.path.join(temp_dir, "CHGCAR"))
current_dir = os.getcwd()
os.chdir(temp_dir)
rs = subprocess.Popen(["bader", "CHGCAR"],
stdout=subprocess.PIPE,
stdin=subprocess.PIPE, close_fds=True)
rs.communicate()
data = []
with open("ACF.dat") as f:
raw = f.readlines()
headers = [s.lower() for s in raw.pop(0).split()]
raw.pop(0)
while True:
l = raw.pop(0).strip()
if l.startswith("-"):
break
vals = map(float, l.split()[1:])
data.append(dict(zip(headers[1:], vals)))
for l in raw:
toks = l.strip().split(":")
if toks[0] == "VACUUM CHARGE":
self.vacuum_charge = float(toks[1])
elif toks[0] == "VACUUM VOLUME":
self.vacuum_volume = float(toks[1])
elif toks[0] == "NUMBER OF ELECTRONS":
self.nelectrons = float(toks[1])
self.data = data
os.chdir(current_dir)
except Exception as ex:
print str(ex)
finally:
shutil.rmtree(temp_dir)
def buildPOTCAR(atname, fpotcar="POTCAR"):
"""
Build POTCAR file according to atom for wich CL calculation is required. The POTCAR of
the atom is placed in first postion.
"""
potcar = Potcar.from_file(fpotcar)
add = False
for pot in potcar:
if pot.symbol == atname:
newpot = pot
add = True
break
if not add:
print("Atom " + atname + " not found in POTCAR")
exit(1)
else:
potcar.insert(0, newpot)
potcar.write_file("POTCAR_CL")
def buildPOTCAR(atname, fpotcar="POTCAR"):
"""
Build POTCAR file according to atom for wich CL calculation is required. The POTCAR of
the atom is placed in first postion.
"""
from pymatgen.io.vaspio.vasp_input import Potcar
potcar = Potcar.from_file(fpotcar)
add = False
for pot in potcar:
if pot.symbol == atname:
newpot = pot
add = True
break
if not add:
print("Atom " + atname + " not found in POTCAR")
exit(1)
else:
potcar.insert(0, newpot)
potcar.write_file("POTCAR_CL")
def test_to_from_dict(self):
d = self.potcar.to_dict
potcar = Potcar.from_dict(d)
self.assertEqual(potcar.symbols, ["Fe", "P", "O"])
def run_task(self, fw_spec):
Incar.from_dict(fw_spec['vasp']['incar']).write_file('INCAR')
Poscar.from_dict(fw_spec['vasp']['poscar']).write_file('POSCAR')
Potcar.from_dict(fw_spec['vasp']['potcar']).write_file('POTCAR')
Kpoints.from_dict(fw_spec['vasp']['kpoints']).write_file('KPOINTS')
def get_ModifiedMaterialsProject_VASP_inputs(structure, workdir, job_name, nproc=16,
U_strategy_instance = None, supplementary_incar_dict = None):
"""
Inputs will be inspired by MaterialsProject, but this function is appropriate
when we are seriously modifying the inputs such that they no longer conform to Materials Project.
"""
if os.path.exists(workdir):
print 'WORKDIR ALREADY EXISTS. DELETE TO LAUNCH NEW JOB'
return -1
os.mkdir(workdir)
# let's start with MP
input_set = MPVaspInputSet()
incar = input_set.get_incar(structure)
if U_strategy_instance != None:
# reading the structure here insures consistency, rather
# than having the strategy read the structure outside this driver.
U_strategy_instance.read_structure(structure)
# Generate all LDAU-related variables according to specified strategy.
LDAU_dict, poscar_need_hack, potcar_need_hack = U_strategy_instance.get_LDAU()
incar.update(LDAU_dict)
# set the number of parallel processors to sqrt(nproc),
# as recommended in manual.
incar.update({'NPAR':int(np.sqrt(nproc))})
if supplementary_incar_dict != None:
incar.update(supplementary_incar_dict)
poscar = input_set.get_poscar(structure)
kpoints = input_set.get_kpoints(structure)
potcar = input_set.get_potcar(structure)
incar.write_file(workdir+'INCAR')
poscar.write_file(workdir+'POSCAR', vasp4_compatible = True)
kpoints.write_file(workdir+'KPOINTS')
potcar.write_file(workdir+'POTCAR')
if poscar_need_hack:
# do we need specialized hacking of the poscar because of the U strategy?
new_poscar_lines = U_strategy_instance.get_new_poscar_lines()
with open(workdir+'POSCAR','w') as f:
for line in new_poscar_lines:
print >>f, line.strip()
if potcar_need_hack:
# do we need specialized hacking of the potcar because of the U strategy?
new_potcar_symbols = U_strategy_instance.get_new_potcar_symbols(potcar)
new_potcar = Potcar(new_potcar_symbols)
# overwrite the previous potcar
new_potcar.write_file(workdir+'POTCAR')
with open(workdir+'job.sh','w') as f:
f.write(submit_template.format(job_name,nproc))
with open(workdir+'clean.sh','w') as f:
f.write(clean_template)
return 0
def test_to_from_dict(self):
d = self.potcar.to_dict
potcar = Potcar.from_dict(d)
self.assertEqual(potcar.symbols, ["Fe", "P", "O"])
def test_init(self):
self.assertEqual(self.potcar.symbols, ["Fe", "P", "O"],
"Wrong symbols read in for POTCAR")
potcar = Potcar(["Fe_pv", "O"])
self.assertEqual(potcar[0].enmax, 293.238)
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:
for filename in (
"INCAR", "POTCAR", "CONTCAR", "OSZICAR", "POSCAR", "DYNMAT"
):
files = glob.glob(os.path.join(path, filename + "*"))
if len(files) < 1:
continue
if len(files) == 1 or filename == "INCAR" or \
filename == "POTCAR" or filename == "DYNMAT":
files_to_parse[filename] = files[-1]\
if filename == "POTCAR" else 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 a custodian double relaxation style run if
possible. Or else, a random 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, contcar, incar, potcar, oszicar, dynmat = [None]*6
if 'POSCAR' in files_to_parse:
poscar = Poscar.from_file(files_to_parse["POSCAR"])
if 'CONTCAR' in files_to_parse:
contcar = Poscar.from_file(files_to_parse["CONTCAR"])
if 'INCAR' in files_to_parse:
incar = Incar.from_file(files_to_parse["INCAR"])
if 'POTCAR' in files_to_parse:
potcar = Potcar.from_file(files_to_parse["POTCAR"])
if 'OSZICAR' in files_to_parse:
oszicar = Oszicar(files_to_parse["OSZICAR"])
if 'DYNMAT' in files_to_parse:
dynmat = Dynmat(files_to_parse["DYNMAT"])
param = {"hubbards":{}}
if poscar is not None and incar is not None and "LDAUU" in incar:
param["hubbards"] = dict(zip(poscar.site_symbols,
incar["LDAUU"]))
param["is_hubbard"] = (
incar.get("LDAU", False) and sum(param["hubbards"].values()) > 0
) if incar is not None else False
param["run_type"] = None
if incar is not None:
param["run_type"] = "GGA+U" if param["is_hubbard"] else "GGA"
param["history"] = _get_transformation_history(path)
param["potcar_spec"] = potcar.spec if potcar is not None else None
energy = oszicar.final_energy if oszicar is not None else 1e10
structure = contcar.structure if contcar is not None\
else poscar.structure
initial_vol = poscar.structure.volume if poscar is not None else \
None
final_vol = contcar.structure.volume if contcar is not None else \
None
delta_volume = None
if initial_vol is not None and final_vol is not None:
delta_volume = (final_vol / initial_vol - 1)
data = {"filename": path, "delta_volume": delta_volume}
if dynmat is not None:
data['phonon_frequencies'] = dynmat.get_phonon_frequencies()
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
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"
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
def test_write(self):
tempfname = "POTCAR.testing"
self.potcar.write_file(tempfname)
p = Potcar.from_file(tempfname)
self.assertEqual(p.symbols, self.potcar.symbols)
os.remove(tempfname)
def run_task(self, fw_spec):
Incar.from_dict(fw_spec['vasp']['incar']).write_file('INCAR')
Poscar.from_dict(fw_spec['vasp']['poscar']).write_file('POSCAR')
Potcar.from_dict(fw_spec['vasp']['potcar']).write_file('POTCAR')
Kpoints.from_dict(fw_spec['vasp']['kpoints']).write_file('KPOINTS')
iface_slab = iface.slab
iface_slab.sort()
#set selective dynamics flags as required
true_site= [1, 1, 1]
false_site= [0, 0, 0]
sd_flag_iface= []
j= 0
sd_flag_slab= []
for i in iface.sites:
sd_flag_iface.append(false_site)
for i in iface_slab.sites:
sd_flag_slab.append(false_site)
#POSCAR and POTCAR construction, pending setting of exact flags for POSCAR
interface_poscar = Poscar(iface, selective_dynamics= sd_flag_iface)
interface_potcar= Potcar(interface_poscar.site_symbols)
slab_poscar = Poscar(iface_slab, selective_dynamics= sd_flag_slab)
slab_potcar= Potcar(slab_poscar.site_symbols)
#write the files in appropriate directories
interface_poscar.write_file("./Interface/POSCAR_PbS100DMF_interface_with_sd.vasp")
slab_poscar.write_file("./Slab/POSCAR_PbS100_slab_with_sd.vasp")
interface_potcar.write_file("./Interface_with_vdw/POTCAR")
slab_potcar.write_file("./Slab_with_vdw/POTCAR")
#set the common INCAR file and KPOINTS
incar_dict = {
'SYSTEM': 'ligand_PbS',
'ENCUT': 600,
'ISIF': 2,
'IBRION': 2,
def get_potcar(self, structure):
if self.sort_structure:
structure = structure.get_sorted_structure()
return Potcar(self.get_potcar_symbols(structure))
def get_potcar(self, structure):
return Potcar(self.get_potcar_symbols(structure))
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
def test_write(self):
tempfname = "POTCAR.testing"
self.potcar.write_file(tempfname)
p = Potcar.from_file(tempfname)
self.assertEqual(p.symbols, self.potcar.symbols)
os.remove(tempfname)
