def _vasp_potcar_setup(self, my_poscar):
"""Set up the POTCAR file."""
name = self.keywords['name']
if 'mast_xc' in self.keywords['program_keys'].keys():
myxc = self.keywords['program_keys']['mast_xc'].upper() #Uppercase
else:
raise MASTError("vasp_checker, _vasp_potcar_setup","Exchange correlation functional needs to be specified in ingredients keyword mast_xc")
if ('mast_pp_setup' in self.keywords['program_keys'].keys()):
sites = my_poscar.site_symbols
setup = self.keywords['program_keys']['mast_pp_setup']
pp_sites = list()
for site in sites:
try:
pp_sites.append(setup[site])
except KeyError:
pp_sites.append(site)
my_potcar = Potcar(symbols=pp_sites, functional=myxc, sym_potcar_map=None)
else:
my_potcar = Potcar(symbols=my_poscar.site_symbols, functional=myxc, sym_potcar_map=None)
dirutil.lock_directory(name)
my_potcar.write_file(name + "/POTCAR")
dirutil.unlock_directory(name)
return my_potcar
def gen_potcar(dirname, filename):
if filename == "POTCAR.spec":
fullpath = os.path.join(dirname, filename)
f = open(fullpath, "r")
elements = f.readlines()
f.close()
symbols = [el.strip() for el in elements if el.strip() != ""]
potcar = Potcar(symbols)
potcar.write_file(os.path.join(dirname, "POTCAR"))
def gen_potcar(dirname, filename):
if filename == "POTCAR.spec":
fullpath = os.path.join(dirname, filename)
f = open(fullpath, "r")
elements = f.readlines()
f.close()
symbols = [el.strip() for el in elements if el.strip() != ""]
potcar = Potcar(symbols)
potcar.write_file(os.path.join(dirname, "POTCAR"))
def scaleCell(path,volume):
poscar = os.path.join(path,'POSCAR')
refcar = os.path.join(path,'REFCAR')
potcar = Potcar()
assert os.path.isfile(poscar)
struct = read_structure(poscar)
struct.scale_lattice(volume)
species = [ pot.element for pot in potcar.from_file('POTCAR') ]
reprule = { old:new for old,new in zip(struct.composition.elements,species) }
struct.replace_species(reprule)
p = Poscar(struct)
with open(poscar) as f:
poscomment = f.readline().strip()
p.comment = poscomment
p.write_file(poscar,vasp4_compatible=True)
if os.path.isfile(refcar):
tmp = os.path.join(path,'POSCARtmp')
# copy Poscar to temporary file and refcar to poscar
copyfile(poscar,tmp)
copyfile(refcar,poscar)
struct = read_structure(poscar)
struct.scale_lattice(volume)
species = [ pot.element for pot in potcar.from_file('POTCAR') ]
reprule = { old:new for old,new in zip(struct.composition.elements,species) }
struct.replace_species(reprule)
r = Poscar(struct)
with open(poscar) as f:
poscomment = f.readline().strip()
r.comment = poscomment
r.write_file(poscar,vasp4_compatible=True)
with open(refcar) as f:
poscomment = f.readline().strip()
r.comment = poscomment
r.write_file(refcar,vasp4_compatible=True)
# replace poscar with its original
move(tmp,poscar)
else:
print 'No REFCAR found.'
def __init__(self,
acf_path='./ACF.dat',
chgcar_filename="./CHGCAR",
aecar0="./AECCAR0",
aecar2="./AECCAR2",
potcar_filename="./POTCAR",
bader_path="./bader CHGCAR -ref Charge_sum"):
print "Reading CHGCAR"
self.chgcar = Chgcar.from_file(chgcar_filename)
##uncomment if you have to run from scratch##
# self.contcar = Structure.from_file(contcar_filename)
# print "Reading AECCAR0"
# Vol_obj_1 = Chgcar.from_file(aecar0)
# print "Reading AECCAR2"
# Vol_obj_2 = Chgcar.from_file(aecar2)
# print "Summing"
# Vol_obj_sum = Vol_obj_1.linear_add(Vol_obj_2)
# print "Writing Combined Sum"
# Vol_obj_sum.write_file("./Charge_sum")
# self.exe = bader_path
# os.system(self.exe)
self.potcar = Potcar.from_file(
potcar_filename) if potcar_filename is not None else None
self.natoms = self.chgcar.poscar.natoms
chgcarpath = os.path.abspath(chgcar_filename)
data = []
with open(acf_path) as f:
print "Reading ACF"
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
def __init__(self, acf_path='./ACF.dat', chgcar_filename="./CHGCAR",
aecar0="./AECCAR0", aecar2="./AECCAR2",
potcar_filename="./POTCAR",
bader_path="./bader CHGCAR -ref Charge_sum"):
print "Reading CHGCAR"
self.chgcar = Chgcar.from_file(chgcar_filename)
##uncomment if you have to run from scratch##
# self.contcar = Structure.from_file(contcar_filename)
# print "Reading AECCAR0"
# Vol_obj_1 = Chgcar.from_file(aecar0)
# print "Reading AECCAR2"
# Vol_obj_2 = Chgcar.from_file(aecar2)
# print "Summing"
# Vol_obj_sum = Vol_obj_1.linear_add(Vol_obj_2)
# print "Writing Combined Sum"
# Vol_obj_sum.write_file("./Charge_sum")
# self.exe = bader_path
# os.system(self.exe)
self.potcar = Potcar.from_file(
potcar_filename) if potcar_filename is not None else None
self.natoms = self.chgcar.poscar.natoms
chgcarpath = os.path.abspath(chgcar_filename)
data = []
with open(acf_path) as f:
print "Reading ACF"
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
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 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_init(self):
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
self.assertEqual(potcar.symbols, ["Fe", "P", "O"], "Wrong symbols read in for POTCAR")