Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

snakecase whichbonds arg and update tests #161

Merged
merged 3 commits into from
Oct 5, 2023
Merged

snakecase whichbonds arg and update tests #161

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
50dd6cf
snakecase whichbonds arg and update tests
naik-aakash Sep 29, 2023
30ac9e2
fix input string for which_bonds as before
naik-aakash Sep 29, 2023
c4cbd75
Merge branch 'JaGeo:main' into snake_case_bond_type
naik-aakash Oct 5, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions lobsterpy/cli.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -666,16 +666,16 @@ def run(args):
"autoplotia",
]:
if args.allbonds:
whichbonds = "all"
which_bonds = "all"
else:
whichbonds = "cation-anion"
which_bonds = "cation-anion"

analyse = Analysis(
path_to_poscar=args.poscar,
path_to_charge=args.charge,
path_to_cohpcar=args.cohpcar,
path_to_icohplist=args.icohplist,
whichbonds=whichbonds,
which_bonds=which_bonds,
are_coops=args.coops,
are_cobis=args.cobis,
noise_cutoff=args.noisecutoff,
Expand Down
44 changes: 22 additions & 22 deletions lobsterpy/cohp/analyze.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ class Analysis:
spg: space group information
structure: Structure object
type_charge: which charges are considered here
whichbonds: which bonds will be considered in analysis
which_bonds: which bonds will be considered in analysis
"""

Expand All @@ -62,7 +62,7 @@ def __init__(
path_to_cohpcar: str,
path_to_charge: str | None = None,
path_to_madelung: str | None = None,
whichbonds: str = "cation-anion",
which_bonds: str = "cation-anion",
cutoff_icohp: float = 0.1,
noise_cutoff: float = 0.1,
summed_spins=True,
Expand All @@ -83,7 +83,7 @@ def __init__(
are_cobis : bool indicating if file contains COBI/ICOBI data
are_coops : bool indicating if file contains COOP/ICOOP data
noise_cutoff : float that sets the lower limit of icohps or icoops or icobis considered
whichbonds: selects which kind of bonds are analyzed. "cation-anion" is the default
which_bonds: selects which kind of bonds are analyzed. "cation-anion" is the default
cutoff_icohp: only bonds that are stronger than cutoff_icohp*strongest ICOHP will be considered
summed_spins: if true, spins will be summed
type_charge: If no path_to_charge is given, Valences will be used. Otherwise, Mulliken charges.
Expand All @@ -94,7 +94,7 @@ def __init__(
self.path_to_poscar = path_to_poscar
self.path_to_icohplist = path_to_icohplist
self.path_to_cohpcar = path_to_cohpcar
self.whichbonds = whichbonds
self.which_bonds = which_bonds
self.cutoff_icohp = cutoff_icohp
self.path_to_charge = path_to_charge
self.path_to_madelung = path_to_madelung
Expand Down Expand Up @@ -142,7 +142,7 @@ def setup_env(self):
self.set_equivalent_sites = list(set(equivalent_sites))
self.spg = symmetry_dataset["international"]

if self.whichbonds == "cation-anion":
if self.which_bonds == "cation-anion":
try:
self.chemenv = LobsterNeighbors(
filename_ICOHP=self.path_to_icohplist,
Expand All @@ -167,7 +167,7 @@ def setup_env(self):
" It looks like no cations are detected."
)
raise err
elif self.whichbonds == "all":
elif self.which_bonds == "all":
# raise ValueError("only cation anion bonds implemented so far")
self.chemenv = LobsterNeighbors(
filename_ICOHP=self.path_to_icohplist,
Expand All @@ -187,11 +187,11 @@ def setup_env(self):

# determine cations and anions
try:
if self.whichbonds == "cation-anion":
if self.which_bonds == "cation-anion":
self.lse = self.chemenv.get_light_structure_environment(
only_cation_environments=True
)
elif self.whichbonds == "all":
elif self.which_bonds == "all":
self.lse = self.chemenv.get_light_structure_environment(
only_cation_environments=False
)
Expand Down Expand Up @@ -226,9 +226,9 @@ def __init__(self, chemenv, valences=None):
[{"ce_symbol": None}]
)

if self.whichbonds == "all":
if self.which_bonds == "all":
self.lse = Lse(self.chemenv.list_coords)
elif self.whichbonds == "cation-anion":
elif self.which_bonds == "cation-anion":
# make a new list
self.lse = Lse(self.chemenv.list_coords, self.chemenv.valences)

Expand All @@ -240,7 +240,7 @@ def get_information_all_bonds(self, summed_spins=True):
None
"""
if self.whichbonds == "cation-anion":
if self.which_bonds == "cation-anion":
# this will only analyze cation anion bonds which simplifies the analysis
self.seq_ineq_ions = []
self.seq_coord_ions = []
Expand Down Expand Up @@ -281,7 +281,7 @@ def get_information_all_bonds(self, summed_spins=True):
self.seq_labels_cohps.append(aniontype_labels)
self.seq_cohps.append(aniontype_cohps)

elif self.whichbonds == "all":
elif self.which_bonds == "all":
# this will only analyze all bonds

self.seq_ineq_ions = []
Expand Down Expand Up @@ -681,14 +681,14 @@ def set_condensed_bonding_analysis(self):
"""
self.condensed_bonding_analysis = {}
# which icohps are considered
if self.whichbonds == "cation-anion":
if self.which_bonds == "cation-anion":
limit_icohps = self.chemenv._get_limit_from_extremum(
self.chemenv.Icohpcollection,
self.cutoff_icohp,
adapt_extremum_to_add_cond=True,
additional_condition=1,
)
elif self.whichbonds == "all":
elif self.which_bonds == "all":
limit_icohps = self.chemenv._get_limit_from_extremum(
self.chemenv.Icohpcollection,
self.cutoff_icohp,
Expand All @@ -700,9 +700,9 @@ def set_condensed_bonding_analysis(self):
# set population type
type_pop = self._get_pop_type()
# how many inequivalent cations are in the structure
if self.whichbonds == "cation-anion":
if self.which_bonds == "cation-anion":
number_considered_ions = len(self.seq_ineq_ions)
elif self.whichbonds == "all":
elif self.which_bonds == "all":
number_considered_ions = len(self.seq_ineq_ions)

# what was the maximum bond lengths that was considered
Expand All @@ -713,7 +713,7 @@ def set_condensed_bonding_analysis(self):

# dictionary including bonding information for each site
site_dict = {}
if self.whichbonds == "cation-anion":
if self.which_bonds == "cation-anion":
for ication, ce, cation_anion_infos, labels, cohps in zip(
self.seq_ineq_ions,
self.seq_coord_ions,
Expand Down Expand Up @@ -755,7 +755,7 @@ def set_condensed_bonding_analysis(self):
"charge": charge_list[ication],
"relevant_bonds": cation_anion_infos[3],
}
elif self.whichbonds == "all":
elif self.which_bonds == "all":
for iion, ce, bond_infos, labels, cohps in zip(
self.seq_ineq_ions,
self.seq_coord_ions,
Expand Down Expand Up @@ -798,7 +798,7 @@ def set_condensed_bonding_analysis(self):
}

if self.path_to_madelung is None:
if self.whichbonds == "cation-anion":
if self.which_bonds == "cation-anion":
# This sets the dictionary including the most important information on the compound
self.condensed_bonding_analysis = {
"formula": formula,
Expand All @@ -808,7 +808,7 @@ def set_condensed_bonding_analysis(self):
"sites": site_dict,
"type_charges": self.type_charge,
}
elif self.whichbonds == "all":
elif self.which_bonds == "all":
self.condensed_bonding_analysis = {
"formula": formula,
"max_considered_bond_length": max_bond_lengths,
Expand All @@ -826,7 +826,7 @@ def set_condensed_bonding_analysis(self):
elif self.type_charge == "Löwdin":
madelung_energy = madelung.madelungenergies_Loewdin
# This sets the dictionary including the most important information on the compound
if self.whichbonds == "cation-anion":
if self.which_bonds == "cation-anion":
self.condensed_bonding_analysis = {
"formula": formula,
"max_considered_bond_length": max_bond_lengths,
Expand All @@ -836,7 +836,7 @@ def set_condensed_bonding_analysis(self):
"type_charges": self.type_charge,
"madelung_energy": madelung_energy,
}
elif self.whichbonds == "all":
elif self.which_bonds == "all":
self.condensed_bonding_analysis = {
"formula": formula,
"max_considered_bond_length": max_bond_lengths,
Expand Down
8 changes: 4 additions & 4 deletions lobsterpy/cohp/describe.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ def set_description(self):
type_pop = self.analysis_object._get_pop_type()
# set units for populations
units = " eV" if type_pop == "COHP" else ""
if self.analysis_object.whichbonds == "cation-anion":
if self.analysis_object.which_bonds == "cation-anion":
relevant_cations = ", ".join(
[
str(site.specie) + str(isite + 1)
Expand Down Expand Up @@ -119,7 +119,7 @@ def set_description(self):
+ str(bonds)
+ " bonds."
)
elif self.analysis_object.whichbonds == "all":
elif self.analysis_object.which_bonds == "all":
relevant_ions = ", ".join(
[
str(site.specie) + str(isite + 1)
Expand Down Expand Up @@ -236,9 +236,9 @@ def plot_cohps(
"""
seq_cohps = self.analysis_object.seq_cohps
if self.analysis_object.whichbonds == "cation-anion":
if self.analysis_object.which_bonds == "cation-anion":
seq_ineq_cations = self.analysis_object.seq_ineq_ions
elif self.analysis_object.whichbonds == "all":
elif self.analysis_object.which_bonds == "all":
seq_ineq_cations = self.analysis_object.seq_ineq_ions
seq_labels = self.analysis_object.seq_labels_cohps
structure = self.analysis_object.structure
Expand Down
Loading