def plot_chgint(args):
chgcar = Chgcar.from_file(args.filename[0])
s = chgcar.structure
if args.inds:
atom_ind = map(int, args.inds[0].split(","))
else:
finder = SymmetryFinder(s, symprec=0.1)
sites = [
sites[0]
for sites in finder.get_symmetrized_structure().equivalent_sites
]
atom_ind = [s.sites.index(site) for site in sites]
from pymatgen.util.plotting_utils import get_publication_quality_plot
plt = get_publication_quality_plot(12, 8)
for i in atom_ind:
d = chgcar.get_integrated_diff(i, args.radius, 30)
plt.plot(d[:, 0],
d[:, 1],
label="Atom {} - {}".format(i, s[i].species_string))
plt.legend(loc="upper left")
plt.xlabel("Radius (A)")
plt.ylabel("Integrated charge (e)")
plt.tight_layout()
plt.show()
def read_structure(filename):
"""
Reads a structure based on file extension. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR and pymatgen's JSON serialized structures.
Args:
filename (str): A filename to read from.
Returns:
A Structure object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
return parser.get_structures(True)[0]
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
return Poscar.from_file(filename, False).structure
elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
return Chgcar.from_file(filename).structure
elif fnmatch(fname, "vasprun*.xml*"):
return Vasprun(filename).final_structure
elif fnmatch(fname.lower(), "*.cssr*"):
cssr = Cssr.from_file(filename)
return cssr.structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
return s
raise ValueError("Unrecognized file extension!")
def read_structure(filename):
"""
Reads a structure based on file extension. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Args:
filename:
A filename to read from.
Returns:
A Structure object.
"""
lower_filename = os.path.basename(filename).lower()
if re.search("\.cif", lower_filename):
parser = CifParser(filename)
return parser.get_structures(True)[0]
elif lower_filename.startswith("poscar") \
or lower_filename.startswith("contcar"):
return Poscar.from_file(filename, False).structure
elif lower_filename.startswith("chgcar") \
or lower_filename.startswith("locpot"):
return Chgcar.from_file(filename).structure
elif re.search("vasprun", lower_filename) \
and re.search("xml", lower_filename):
return Vasprun(filename).final_structure
elif re.search("\.cssr", lower_filename):
cssr = Cssr.from_file(filename)
return cssr.structure
raise ValueError("Unrecognized file extension!")
def read_structure(filename):
"""
Reads a structure based on file extension. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR and pymatgen's JSON serialized structures.
Args:
filename:
A filename to read from.
Returns:
A Structure object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
return parser.get_structures(True)[0]
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
return Poscar.from_file(filename, False).structure
elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
return Chgcar.from_file(filename).structure
elif fnmatch(fname, "vasprun*.xml*"):
return Vasprun(filename).final_structure
elif fnmatch(fname.lower(), "*.cssr*"):
cssr = Cssr.from_file(filename)
return cssr.structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
return s
raise ValueError("Unrecognized file extension!")
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 read_structure(filename, primitive=True, sort=False):
"""
Reads a structure based on file extension. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR and pymatgen's JSON serialized structures.
Args:
filename (str): A filename to read from.
primitive (bool): Whether to convert to a primitive cell for cifs.
Defaults to True.
sort (bool): Whether to sort sites. Default to False.
Returns:
A Structure object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
s = parser.get_structures(primitive=primitive)[0]
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
s = Poscar.from_file(filename, False).structure
elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
s = Chgcar.from_file(filename).structure
elif fnmatch(fname, "vasprun*.xml*"):
s = Vasprun(filename).final_structure
elif fnmatch(fname.lower(), "*.cssr*"):
cssr = Cssr.from_file(filename)
s = cssr.structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=MontyDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
else:
raise ValueError("Unrecognized file extension!")
if sort:
s = s.get_sorted_structure()
return s
def read_structure(filename, primitive=True, sort=False):
"""
Reads a structure based on file extension. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR and pymatgen's JSON serialized structures.
Args:
filename (str): A filename to read from.
primitive (bool): Whether to convert to a primitive cell for cifs.
Defaults to False.
sort (bool): Whether to sort sites. Default to False.
Returns:
A Structure object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.cif*"):
parser = CifParser(filename)
s = parser.get_structures(primitive=primitive)[0]
elif fnmatch(fname, "POSCAR*") or fnmatch(fname, "CONTCAR*"):
s = Poscar.from_file(filename, False).structure
elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
s = Chgcar.from_file(filename).structure
elif fnmatch(fname, "vasprun*.xml*"):
s = Vasprun(filename).final_structure
elif fnmatch(fname.lower(), "*.cssr*"):
cssr = Cssr.from_file(filename)
s = cssr.structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
else:
raise ValueError("Unrecognized file extension!")
if sort:
s = s.get_sorted_structure()
return s
def plot_chgint(args):
chgcar = Chgcar.from_file(args.filename[0])
s = chgcar.structure
if args.inds:
atom_ind = map(int, args.inds[0].split(","))
else:
finder = SymmetryFinder(s, symprec=0.1)
sites = [sites[0] for sites in finder.get_symmetrized_structure().equivalent_sites]
atom_ind = [s.sites.index(site) for site in sites]
from pymatgen.util.plotting_utils import get_publication_quality_plot
plt = get_publication_quality_plot(12, 8)
for i in atom_ind:
d = chgcar.get_integrated_diff(i, args.radius, 30)
plt.plot(d[:, 0], d[:, 1], label="Atom {} - {}".format(i, s[i].species_string))
plt.legend(loc="upper left")
plt.xlabel("Radius (A)")
plt.ylabel("Integrated charge (e)")
plt.tight_layout()
plt.show()
def read_structure(filename):
"""
Reads a structure based on file extension. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR and pymatgen's JSON serialized structures.
Args:
filename:
A filename to read from.
Returns:
A Structure object.
"""
lower_filename = os.path.basename(filename).lower()
if re.search("\.cif", lower_filename):
parser = CifParser(filename)
return parser.get_structures(True)[0]
elif lower_filename.startswith("poscar") \
or lower_filename.startswith("contcar"):
return Poscar.from_file(filename, False).structure
elif lower_filename.startswith("chgcar") \
or lower_filename.startswith("locpot"):
return Chgcar.from_file(filename).structure
elif re.search("vasprun", lower_filename) \
and re.search("xml", lower_filename):
return Vasprun(filename).final_structure
elif re.search("\.cssr", lower_filename):
cssr = Cssr.from_file(filename)
return cssr.structure
elif re.search("\.[mj]son", lower_filename):
with zopen(lower_filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Structure:
raise IOError("File does not contain a valid serialized "
"structure")
return s
raise ValueError("Unrecognized file extension!")
def chgcar_test():
from pymatgen.io.vaspio import Chgcar
c = Chgcar.from_file("../test_files/CHGCAR.noncubic")
print c.get_integrated_diff(1, 2.5, 3)
def run_task(self, fw_spec):
MyDB.db_access().connect()
collection = MyDB.db_access().collection(fw_spec['collection'])
with open('vasp.out', 'r') as output:
content = output.readlines()
examine = content[-2].strip()
if examine[0:3] == '1 F':
chgcar = Chgcar.from_file('CHGCAR')
s1 = self['struct_s1']
s2 = self['struct_s2']
relax_sites = []
for site_i, site in enumerate(s1.sites):
if site.specie == fw_spec['moving_cation']:
relax_sites.append(site_i)
pf = NEBPathfinder(s1,
s2,
relax_sites=relax_sites,
v=ChgcarPotential(chgcar).get_v(),
n_images=8)
images = pf.images
doc = collection.find_one({
'mp-id': fw_spec["mp-id"],
'pair_index': fw_spec["pair_index"]
})
path = []
coordination_number = []
for image in images:
struct = Structure.from_dict(doc["gamma_structure"])
site_index = image.species.index(fw_spec['moving_cation'])
cation_site = image[site_index]
struct.insert(0,
cation_site.specie,
cation_site.frac_coords,
properties=cation_site.properties)
path.append(image[site_index].as_dict())
voro_cn = VoronoiCoordFinder(struct)
cn = voro_cn.get_coordination_number(0)
coordination_number.append(cn)
collection.update(
{
"mp-id": fw_spec["mp-id"],
"pair_index": fw_spec["pair_index"]
}, {
"$set": {
"status": "success",
"CN_path": coordination_number,
"path": path
}
})
else:
collection.update(
{
"mp-id": fw_spec["mp-id"],
"pair_index": fw_spec["pair_index"]
}, {"$set": {
"status": "error"
}})
MyDB.db_access().close()
return FWAction()
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-s1', type=str, help='starting point CONTCAR')
parser.add_argument('-s2', type=str, help='ending point CONTCAR')
parser.add_argument('-e', type=str, help='diffusing cation')
parser.add_argument('-n',
type=int,
default=8,
help='number of interpolated images')
parser.add_argument('-chg', type=str, help='CHGCAR for pathFinder')
arg = parser.parse_args()
s1 = Poscar.from_file(arg.s1).structure
s2 = Poscar.from_file(arg.s2).structure
chg = Chgcar.from_file(arg.chg)
relax_sites = []
for i, site in enumerate(s1.sites):
if site.specie == Element(arg.e):
relax_sites.append(i)
pf = NEBPathfinder(s1,
s2,
relax_sites=relax_sites,
v=ChgcarPotential(chg).get_v(),
n_images=(3 * arg.n))
images = pf.images
for i, image in enumerate(images):
__email__ = '*****@*****.**'
from PathFinder.pathFinder import NEBPathfinder, ChgcarPotential
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-s1', type=str, help='starting point CONTCAR')
parser.add_argument('-s2', type=str, help='ending point CONTCAR')
parser.add_argument('-e', type=str, help='diffusing cation')
parser.add_argument('-n', type=int, default=8, help='number of interpolated images')
parser.add_argument('-chg', type=str, help='CHGCAR for pathFinder')
arg = parser.parse_args()
s1 = Poscar.from_file(arg.s1).structure
s2 = Poscar.from_file(arg.s2).structure
chg = Chgcar.from_file(arg.chg)
relax_sites = []
for i, site in enumerate(s1.sites):
if site.specie == Element(arg.e):
relax_sites.append(i)
pf = NEBPathfinder(s1, s2, relax_sites=relax_sites, v=ChgcarPotential(chg).get_v(), n_images=(3*arg.n))
images = pf.images
for i, image in enumerate(images):
if i % 3 == 0:
p = Poscar(image)
directory = "0" + str(i/3)
if not os.path.exists(directory):
