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(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 plot_cohps_of_neighbors(
self,
path_to_COHPCAR="COHPCAR.lobster",
isites=[],
onlycation_isites=True,
only_bonds_to=None,
per_bond=False,
summed_spin_channels=False,
xlim=None,
ylim=[-10, 6],
integrated=False,
):
"""
will plot summed cohps (please be careful in the spin polarized case (plots might overlap (exactly!))
Args:
isites: list of site ids, if isite==[], all isites will be used to add the icohps of the neighbors
onlycation_isites: bool, will only use cations, if isite==[]
only_bonds_to: list of str, only anions in this list will be considered
per_bond: bool, will lead to a normalization of the plotted COHP per number of bond if True,
otherwise the sum
will be plotted
xlim: list of float, limits of x values
ylim: list of float, limits of y values
integrated: bool, if true will show integrated cohp instead of cohp
Returns:
plt of the cohps
"""
# include COHPPlotter and plot a sum of these COHPs
# might include option to add Spin channels
# implement only_bonds_to
cp = CohpPlotter()
plotlabel, summed_cohp = self.get_info_cohps_to_neighbors(
path_to_COHPCAR,
isites,
only_bonds_to,
onlycation_isites,
per_bond,
summed_spin_channels=summed_spin_channels,
)
cp.add_cohp(plotlabel, summed_cohp)
plot = cp.get_plot(integrated=integrated)
if xlim is not None:
plot.xlim(xlim)
if ylim is not None:
plot.ylim(ylim)
return plot
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')):
os.makedirs(os.path.join('COHPs'))
except OSError as e:
if e.errno != errno.EEXIST:
print("WARNING: COHPs directory already exists")
raise
for idx in idx_list:
species1 = completecohp.bonds[idx]['sites'][0]
species2 = completecohp.bonds[idx]['sites'][1]
plotlabel = str(species1.species_string) + '-' + str(
species2.species_string)
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')