def setUp(self):
path = os.path.join(test_dir, "cohp", "complete_cohp_lobster.json")
with open(os.path.join(path), "r") as f:
self.cohp = CompleteCohp.from_dict(json.load(f))
path = os.path.join(test_dir, "cohp", "complete_coop_lobster.json")
with open(os.path.join(path), "r") as f:
self.coop = CompleteCohp.from_dict(json.load(f))
self.cohp_plot = CohpPlotter(zero_at_efermi=False)
self.coop_plot = CohpPlotter(are_coops=True)
def setUp(self):
path = os.path.join(test_dir, "cohp", "complete_cohp_lobster.json")
with open(os.path.join(path), "r") as f:
self.cohp = CompleteCohp.from_dict(json.load(f))
path = os.path.join(test_dir, "cohp", "complete_coop_lobster.json")
with open(os.path.join(path), "r") as f:
self.coop = CompleteCohp.from_dict(json.load(f))
self.cohp_plot = CohpPlotter(zero_at_efermi=False)
self.coop_plot = CohpPlotter(are_coops=True)
warnings.simplefilter("ignore")
def setUp(self):
path = os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp",
"complete_cohp_lobster.json")
with open(os.path.join(path)) as f:
self.cohp = CompleteCohp.from_dict(json.load(f))
path = os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp",
"complete_coop_lobster.json")
with open(os.path.join(path)) as f:
self.coop = CompleteCohp.from_dict(json.load(f))
self.cohp_plot = CohpPlotter(zero_at_efermi=False)
self.coop_plot = CohpPlotter(are_coops=True)
warnings.simplefilter("ignore")
def setUp(self):
filepath = os.path.join(test_dir, "complete_cohp_lobster.json")
with open(filepath, "r") as f:
self.cohp_lobster_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "complete_coop_lobster.json")
with open(filepath, "r") as f:
self.coop_lobster_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "complete_cohp_lmto.json")
with open(filepath, "r") as f:
self.cohp_lmto_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "COPL.BiSe")
structure = os.path.join(test_dir, "CTRL.BiSe")
self.cohp_lmto = CompleteCohp.from_file("lmto",
filename=filepath,
structure_file=structure)
filepath = os.path.join(test_dir, "COHPCAR.lobster")
structure = os.path.join(test_dir, "POSCAR")
self.cohp_lobster = CompleteCohp.from_file("lobster",
filename=filepath,
structure_file=structure)
filepath = os.path.join(test_dir, "COOPCAR.lobster.BiSe")
structure = os.path.join(test_dir, "POSCAR.BiSe")
self.coop_lobster = CompleteCohp.from_file("lobster",
filename=filepath,
structure_file=structure,
are_coops=True)
def setUp(self):
filepath = os.path.join(test_dir, "complete_cohp_lobster.json")
with open(filepath, "r") as f:
self.cohp_lobster_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "complete_coop_lobster.json")
with open(filepath, "r") as f:
self.coop_lobster_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "complete_cohp_lmto.json")
with open(filepath, "r") as f:
self.cohp_lmto_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "complete_cohp_orbitalwise.json")
with open(filepath, "r") as f:
self.cohp_orb_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "COPL.BiSe")
structure = os.path.join(test_dir, "CTRL.BiSe")
self.cohp_lmto = CompleteCohp.from_file("lmto", filename=filepath,
structure_file=structure)
filepath = os.path.join(test_dir, "COHPCAR.lobster")
structure = os.path.join(test_dir, "POSCAR")
self.cohp_lobster = CompleteCohp.from_file("lobster",
filename=filepath,
structure_file=structure)
filepath = os.path.join(test_dir, "COOPCAR.lobster.BiSe")
structure = os.path.join(test_dir, "POSCAR.BiSe")
self.coop_lobster = CompleteCohp.from_file("lobster",
filename=filepath,
structure_file=structure,
are_coops=True)
filepath = os.path.join(test_dir, "COHPCAR.lobster.orbitalwise")
structure = os.path.join(test_dir, "POSCAR.orbitalwise")
self.cohp_orb = CompleteCohp.from_file("lobster",
filename=filepath,
structure_file=structure)
filepath = os.path.join(test_dir, "COHPCAR.lobster.notot.orbitalwise")
self.cohp_notot = CompleteCohp.from_file("lobster",
filename=filepath,
structure_file=structure)
def get_COOP_from_folder(folder, bond="O_O"):
folders = check_valid_folder(folder, bond=bond)
if len(folders) == 0:
print("No COOP in this folder")
return (None)
os.chdir(folders[0])
complete_coop = CompleteCohp.from_file("LOBSTER", are_coops=True)
print("cohp sucessfully read from {}".format(folders[0]))
for key, bond_dict in complete_coop.bonds.items():
print(key, bond_dict)
# for key, bond_dict in complete_coop.bonds.items():
# print(" /\/\/\ ")
# print(key, bond_dict)
# # \D matches non digit characters
# [ind_a, ind_b] = [(int(re.sub(r"\D", "", ind_str)) - 1)
# for ind_str in key.split("-")]
# bond_dict["atom_pair"] = [ind_a, ind_b]
# # print(complete_coop.bonds)
return (complete_coop)
def setUp(self):
filepath = os.path.join(test_dir, "complete_cohp_lobster.json")
with open(filepath, "r") as f:
self.cohp_lobster_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "complete_coop_lobster.json")
with open(filepath, "r") as f:
self.coop_lobster_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "complete_cohp_lmto.json")
with open(filepath, "r") as f:
self.cohp_lmto_dict = CompleteCohp.from_dict(json.load(f))
filepath = os.path.join(test_dir, "complete_cohp_orbitalwise.json")
with open(filepath, "r") as f:
self.cohp_orb_dict = CompleteCohp.from_dict(json.load(f))
# Lobster 3.0
filepath = os.path.join(test_dir, "complete_cohp_forb.json")
with open(filepath, "r") as f:
self.cohp_lobster_forb_dict = CompleteCohp.from_dict(json.load(f))
# Lobster 2.0
filepath = os.path.join(test_dir, "COPL.BiSe")
structure = os.path.join(test_dir, "CTRL.BiSe")
self.cohp_lmto = CompleteCohp.from_file(
"lmto", filename=filepath, structure_file=structure
)
filepath = os.path.join(test_dir, "COHPCAR.lobster")
structure = os.path.join(test_dir, "POSCAR")
self.cohp_lobster = CompleteCohp.from_file(
"lobster", filename=filepath, structure_file=structure
)
filepath = os.path.join(test_dir, "COOPCAR.lobster.BiSe")
structure = os.path.join(test_dir, "POSCAR.BiSe")
self.coop_lobster = CompleteCohp.from_file(
"lobster", filename=filepath, structure_file=structure, are_coops=True
)
filepath = os.path.join(test_dir, "COHPCAR.lobster.orbitalwise")
structure = os.path.join(test_dir, "POSCAR.orbitalwise")
self.cohp_orb = CompleteCohp.from_file(
"lobster", filename=filepath, structure_file=structure
)
filepath = os.path.join(test_dir, "COHPCAR.lobster.notot.orbitalwise")
self.cohp_notot = CompleteCohp.from_file(
"lobster", filename=filepath, structure_file=structure
)
# Lobster 3.0
filepath = os.path.join(test_dir, "COHPCAR.lobster.Na2UO4")
structure = os.path.join(test_dir, "POSCAR.Na2UO4")
self.cohp_lobster_forb = CompleteCohp.from_file(
"lobster", filename=filepath, structure_file=structure
)
"""
Plot COHP
"""
from pymatgen.electronic_structure.plotter import CohpPlotter
from pymatgen.electronic_structure.cohp import CompleteCohp
from pymatgen.io.lobster import Icohplist
file_list = [file for file in os.listdir() if file.endswith('.lobster')]
if file_list != []:
COHPCAR_path = os.getcwd() + "/COHPCAR.lobster"
POSCAR_path = os.getcwd() + "/POSCAR"
completecohp = CompleteCohp.from_file(fmt="LOBSTER",
filename=COHPCAR_path,
structure_file=POSCAR_path)
# Read in ICOHPLIST.lobster and get lcohpcollection object
icohplist = Icohplist(filename=os.getcwd() + '/ICOHPLIST.lobster')
idx_list = [idx for idx in list(icohplist.icohplist)]
# search for the number of the COHP you would like to plot in ICOHPLIST.lobster
# (the numbers in COHPCAR.lobster are different!)
cp = CohpPlotter()
# make COHPs directory
try:
if not (os.path.isdir('COHPs')):
def get_info_cohps_to_neighbors(
self,
path_to_COHPCAR="COHPCAR.lobster",
isites=[],
only_bonds_to=None,
onlycation_isites=True,
per_bond=True,
summed_spin_channels=False,
):
"""
will return info about the cohps from all sites mentioned in isites with neighbors
Args:
path_to_COHPCAR: str, path to COHPCAR
isites: list of int that indicate the number of the site
only_bonds_to: list of str, e.g. ["O"] to only show cohps of anything to oxygen
onlycation_isites: if isites=[], only cation sites will be returned
per_bond: will normalize per bond
summed_spin_channels: will sum all spin channels
Returns: label for cohp (str), CompleteCohp object which describes all cohps of the sites as given by isites
and the other parameters
"""
# TODO: add options for orbital-resolved cohps
summed_icohps, list_icohps, number_bonds, labels, atoms = self.get_info_icohps_to_neighbors(
isites=isites, onlycation_isites=onlycation_isites
)
import tempfile
with tempfile.TemporaryDirectory() as t:
path = os.path.join(t, "POSCAR.vasp")
self.structure.to(filename=path, fmt="POSCAR")
completecohp = CompleteCohp.from_file(fmt="LOBSTER", filename=path_to_COHPCAR, structure_file=path)
# will check that the number of bonds in ICOHPLIST and COHPCAR are identical
# further checks could be implemented
if len(self.Icohpcollection._list_atom1) != len(completecohp.bonds.keys()):
raise ValueError("COHPCAR and ICOHPLIST do not fit together")
is_spin_completecohp = Spin.down in completecohp.get_cohp_by_label("1").cohp
if self.Icohpcollection.is_spin_polarized != is_spin_completecohp:
raise ValueError("COHPCAR and ICOHPLIST do not fit together")
if only_bonds_to is None:
# sort by anion type
if per_bond:
divisor = len(labels)
else:
divisor = 1
plotlabel = self._get_plot_label(atoms, per_bond)
summed_cohp = completecohp.get_summed_cohp_by_label_list(
label_list=labels, divisor=divisor, summed_spin_channels=summed_spin_channels
)
else:
# labels of the COHPs that will be summed!
# iterate through labels and atoms and check which bonds can be included
new_labels = []
new_atoms = []
for label, atompair in zip(labels, atoms):
# durchlaufe only_bonds_to=[] und sage ja, falls eines der Labels in atompair ist, dann speichere
# new_label
present = False
for atomtype in only_bonds_to:
if atomtype in (self._split_string(atompair[0])[0], self._split_string(atompair[1])[0]):
present = True
if present:
new_labels.append(label)
new_atoms.append(atompair)
if len(new_labels) > 0:
if per_bond:
divisor = len(new_labels)
else:
divisor = 1
plotlabel = self._get_plot_label(new_atoms, per_bond)
summed_cohp = completecohp.get_summed_cohp_by_label_list(
label_list=new_labels, divisor=divisor, summed_spin_channels=summed_spin_channels
)
else:
plotlabel = None
summed_cohp = None
return plotlabel, summed_cohp
def get_cohp(self, xlim=[-4, 4], ylim=[-10, 6]):
cohp = CompleteCohp.from_file('LOBSTER', filename=os.path.join(self.path, "COHPCAR.lobster"),
structure_file=os.path.join(self.path, "CONTCAR"))
plotter = CohpPlotter()
plotter.add_cohp(self.name, cohp)
plotter.save_plot(f'{self.path}.png', xlim=xlim, ylim=ylim, img_format='png')
