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[WIP] Lobsterenv improvements (#3624)
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* add args to work with pymatgen objs

* adapt and add test
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@naik-aakash
naik-aakash committed Feb 18, 2024
1 parent ff45527 commit bd88e0d
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Showing 2 changed files with 154 additions and 105 deletions.
100 changes: 61 additions & 39 deletions pymatgen/io/lobster/lobsterenv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,17 +57,19 @@ class LobsterNeighbors(NearNeighbors):
def __init__(
self,
structure: Structure,
filename_ICOHP: str = "ICOHPLIST.lobster",
filename_icohp: str | None = "ICOHPLIST.lobster",
obj_icohp: Icohplist | None = None,
are_coops: bool = False,
are_cobis: bool = False,
valences: list[float] | None = None,
limits: tuple[float, float] | None = None,
additional_condition: int = 0,
only_bonds_to: list[str] | None = None,
perc_strength_ICOHP: float = 0.15,
perc_strength_icohp: float = 0.15,
noise_cutoff: float = 0.1,
valences_from_charges: bool = False,
filename_CHARGE: str | None = None,
filename_charge: str | None = None,
obj_charge: Charge | None = None,
which_charge: str = "Mulliken",
adapt_extremum_to_add_cond: bool = False,
add_additional_data_sg: bool = False,
Expand All @@ -79,7 +81,8 @@ def __init__(
"""
Args:
filename_ICOHP: (str) Path to ICOHPLIST.lobster or ICOOPLIST.lobster or ICOBILIST.lobster
filename_icohp: (str) Path to ICOHPLIST.lobster or ICOOPLIST.lobster or ICOBILIST.lobster
obj_icohp: Icohplist object
structure: (Structure) typically constructed by Structure.from_file("POSCAR")
are_coops: (bool) if True, the file is a ICOOPLIST.lobster and not a ICOHPLIST.lobster; only tested for
ICOHPLIST.lobster so far
Expand All @@ -95,13 +98,14 @@ def __init__(
DO_NOT_CONSIDER_ANION_CATION_BONDS=5
ONLY_CATION_CATION_BONDS=6
only_bonds_to: (list[str]) will only consider bonds to certain elements (e.g. ["O"] for oxygen)
perc_strength_ICOHP: if no limits are given, this will decide which icohps will still be considered (
perc_strength_icohp: if no limits are given, this will decide which icohps will still be considered (
relative to
the strongest ICOHP (ICOOP or ICOBI)
noise_cutoff: if provided hardcodes the lower limit of icohps considered
valences_from_charges: if True and path to CHARGE.lobster is provided, will use Lobster charges (
Mulliken) instead of valences
filename_CHARGE: (str) Path to Charge.lobster
filename_charge: (str) Path to Charge.lobster
obj_charge: Charge object
which_charge: (str) "Mulliken" or "Loewdin"
adapt_extremum_to_add_cond: (bool) will adapt the limits to only focus on the bonds determined by the
additional condition
Expand All @@ -113,7 +117,12 @@ def __init__(
id_blist_sg2: (str) Identity of data in filename_blist_sg2,
e.g., "icoop" or "icobi".
"""
self.ICOHP = Icohplist(are_coops=are_coops, are_cobis=are_cobis, filename=filename_ICOHP)
if filename_icohp is not None:
self.ICOHP = Icohplist(are_coops=are_coops, are_cobis=are_cobis, filename=filename_icohp)
elif obj_icohp is not None:
self.ICOHP = obj_icohp
else:
raise ValueError("Please provide either filename_icohp or obj_icohp")
self.Icohpcollection = self.ICOHP.icohpcollection
self.structure = structure
self.limits = limits
Expand Down Expand Up @@ -167,8 +176,10 @@ def __init__(
# will read in valences, will prefer manual setting of valences
self.valences: list[float] | None
if valences is None:
if valences_from_charges and filename_CHARGE is not None:
chg = Charge(filename=filename_CHARGE)
if valences_from_charges and filename_charge is not None:
chg = Charge(filename=filename_charge)
if valences_from_charges and obj_charge is not None:
chg = obj_charge
if which_charge == "Mulliken":
self.valences = chg.Mulliken
elif which_charge == "Loewdin":
Expand Down Expand Up @@ -199,7 +210,7 @@ def __init__(
upperlimit=self.upperlimit,
only_bonds_to=only_bonds_to,
additional_condition=self.additional_condition,
perc_strength_ICOHP=perc_strength_ICOHP,
perc_strength_icohp=perc_strength_icohp,
adapt_extremum_to_add_cond=adapt_extremum_to_add_cond,
)

Expand Down Expand Up @@ -235,7 +246,7 @@ def anion_types(self):
def get_anion_types(self):
return self.anion_types

def get_nn_info(self, structure: Structure, n, use_weights=False):
def get_nn_info(self, structure: Structure, n, use_weights: bool = False):
"""
Get coordination number, CN, of site with index n in structure.
Expand Down Expand Up @@ -408,21 +419,24 @@ def get_info_icohps_to_neighbors(self, isites=None, onlycation_isites=True):

def plot_cohps_of_neighbors(
self,
path_to_COHPCAR="COHPCAR.lobster",
isites=None,
onlycation_isites=True,
only_bonds_to=None,
per_bond=False,
summed_spin_channels=False,
path_to_cohpcar: str | None = "COHPCAR.lobster",
obj_cohpcar: CompleteCohp | None = None,
isites: list[int] | None = None,
onlycation_isites: bool = True,
only_bonds_to: list[str] | None = None,
per_bond: bool = False,
summed_spin_channels: bool = False,
xlim=None,
ylim=(-10, 6),
integrated=False,
integrated: bool = False,
):
"""
Will plot summed cohps or cobis or coops
(please be careful in the spin polarized case (plots might overlap (exactly!)).
Args:
path_to_cohpcar: str, path to COHPCAR or COOPCAR or COBICAR
obj_cohpcar: CompleteCohp object
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
Expand All @@ -442,7 +456,8 @@ def plot_cohps_of_neighbors(
cp = CohpPlotter(are_cobis=self.are_cobis, are_coops=self.are_coops)

plotlabel, summed_cohp = self.get_info_cohps_to_neighbors(
path_to_COHPCAR,
path_to_cohpcar,
obj_cohpcar,
isites,
only_bonds_to,
onlycation_isites,
Expand All @@ -462,19 +477,21 @@ def plot_cohps_of_neighbors(

def get_info_cohps_to_neighbors(
self,
path_to_COHPCAR="COHPCAR.lobster",
isites=None,
only_bonds_to=None,
onlycation_isites=True,
per_bond=True,
summed_spin_channels=False,
path_to_cohpcar: str | None = "COHPCAR.lobster",
obj_cohpcar: CompleteCohp | None = None,
isites: list[int] | None = None,
only_bonds_to: list[str] | None = None,
onlycation_isites: bool = True,
per_bond: bool = True,
summed_spin_channels: bool = False,
):
"""
Return info about the cohps (coops or cobis) as a summed cohp object and a label
from all sites mentioned in isites with neighbors.
Args:
path_to_COHPCAR: str, path to COHPCAR or COOPCAR or COBICAR
path_to_cohpcar: str, path to COHPCAR or COOPCAR or COBICAR
obj_cohpcar: CompleteCohp object
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=None, only cation sites will be returned
Expand All @@ -493,16 +510,21 @@ def get_info_cohps_to_neighbors(
with tempfile.TemporaryDirectory() as t:
path = f"{t}/POSCAR.vasp"

self.structure.to(filename=path, fmt="POSCAR")
self.structure.to(filename=path, fmt="poscar")

if not hasattr(self, "completecohp"):
self.completecohp = CompleteCohp.from_file(
fmt="LOBSTER",
filename=path_to_COHPCAR,
structure_file=path,
are_coops=self.are_coops,
are_cobis=self.are_cobis,
)
if path_to_cohpcar is not None and obj_cohpcar is None:
self.completecohp = CompleteCohp.from_file(
fmt="LOBSTER",
filename=path_to_cohpcar,
structure_file=path,
are_coops=self.are_coops,
are_cobis=self.are_cobis,
)
elif obj_cohpcar is not None:
self.completecohp = obj_cohpcar
else:
raise ValueError("Please provide either path_to_cohpcar or obj_cohpcar")

# will check that the number of bonds in ICOHPLIST and COHPCAR are identical
# further checks could be implemented
Expand Down Expand Up @@ -681,9 +703,9 @@ def _evaluate_ce(
lowerlimit,
upperlimit,
only_bonds_to=None,
additional_condition=0,
perc_strength_ICOHP=0.15,
adapt_extremum_to_add_cond=False,
additional_condition: int = 0,
perc_strength_icohp: float = 0.15,
adapt_extremum_to_add_cond: bool = False,
) -> None:
"""
Args:
Expand All @@ -693,7 +715,7 @@ def _evaluate_ce(
neighbors
only_bonds_to: restricts the types of bonds that will be considered
additional_condition: Additional condition for the evaluation
perc_strength_ICOHP: will be used to determine how strong the ICOHPs (percentage*strongest ICOHP) will be
perc_strength_icohp: will be used to determine how strong the ICOHPs (percentage*strongest ICOHP) will be
that are still considered for the evaluation
adapt_extremum_to_add_cond: will recalculate the limit based on the bonding type and not on the overall
extremum.
Expand All @@ -702,7 +724,7 @@ def _evaluate_ce(
if lowerlimit is None and upperlimit is None:
lowerlimit, upperlimit = self._get_limit_from_extremum(
self.Icohpcollection,
percentage=perc_strength_ICOHP,
percentage=perc_strength_icohp,
adapt_extremum_to_add_cond=adapt_extremum_to_add_cond,
additional_condition=additional_condition,
)
Expand Down

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