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
# 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)
cp.add_cohp(plotlabel, completecohp.get_cohp_by_label(label=idx))
# check which COHP you are plotting
print("This is a COHP between the following sites: " + str(species1) +
' and' + str(species2))
cohpplot = cp.get_plot(integrated=False)
cohpplot.ylim([-10, 6])
cohpplot.savefig(
'COHPs/cohp_no_%s_%s-%s.pdf' %
(idx, species1.species_string, species2.species_string))
else:
print('lobster files are not found !!')
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')