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WIP: Fix consideration of translation symmetry for some (extremely rare) edge cases in LobsterEnv #4148

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WIP: Fix consideration of translation symmetry for some (extremely rare) edge cases in LobsterEnv #4148

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7e5b838
partially test translations in lobsterenv
JaGeo Oct 30, 2024
0778527
pre-commit auto-fixes
pre-commit-ci[bot] Oct 30, 2024
44047b4
Merge branch 'materialsproject:master' into fix_icohp
naik-aakash Dec 3, 2024
8cc5c8f
Merge branch 'master' into fix_icohp
JaGeo Jan 14, 2025
0d5ff55
Merge branch 'master' of github.com:JaGeo/pymatgen into fix_icohp
JaGeo Jan 24, 2025
e7b558a
merge current mastr
JaGeo Jan 24, 2025
8a8003e
pre-commit auto-fixes
pre-commit-ci[bot] Jan 24, 2025
a922572
Merge branch 'materialsproject:master' into fix_icohp
naik-aakash Feb 6, 2025
aa1fda5
add new test data
JaGeo Feb 6, 2025
bc1aa7b
merge conflict
JaGeo Feb 6, 2025
9ac8003
pre-commit auto-fixes
pre-commit-ci[bot] Feb 6, 2025
527e675
fix some more
JaGeo Feb 6, 2025
8af3352
Merge branch 'fix_icohp' of github.com:JaGeo/pymatgen into fix_icohp
JaGeo Feb 6, 2025
df3589a
pre-commit auto-fixes
pre-commit-ci[bot] Feb 6, 2025
5520121
fix nearly everything except for two inter neighbor things
JaGeo Feb 6, 2025
5921ed8
Merge branch 'fix_icohp' of github.com:JaGeo/pymatgen into fix_icohp
JaGeo Feb 6, 2025
8c27943
pre-commit auto-fixes
pre-commit-ci[bot] Feb 6, 2025
e908e47
add more fixes
JaGeo Feb 7, 2025
17037c2
add more fixes
JaGeo Feb 7, 2025
5436d40
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
cfdd0ea
fix the just introduced bug and add a warning for very rare cases tha…
JaGeo Feb 7, 2025
bf1b7fd
fix the just introduced bug and add a warning for very rare cases tha…
JaGeo Feb 7, 2025
47aca41
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
53a2a67
fix next test by adapting cutoff
JaGeo Feb 7, 2025
9154b3c
Merge branch 'fix_icohp' of github.com:JaGeo/pymatgen into fix_icohp
JaGeo Feb 7, 2025
413ed2f
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
c474ff8
fix some bugs
JaGeo Feb 7, 2025
43ea1fc
Merge branch 'fix_icohp' of github.com:JaGeo/pymatgen into fix_icohp
JaGeo Feb 7, 2025
ebe4bc1
pre-commit auto-fixes
pre-commit-ci[bot] Feb 7, 2025
0acbb0c
fix some bugs
JaGeo Feb 7, 2025
5646066
remove translation correction
JaGeo Feb 7, 2025
d195474
Merge branch 'materialsproject:master' into fix_icohp
naik-aakash Feb 24, 2025
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4 changes: 4 additions & 0 deletions src/pymatgen/electronic_structure/cohp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1042,6 +1042,10 @@ def is_spin_polarized(self) -> bool:
"""
return self._is_spin_polarized

@property
def translation(self) -> list[int, int, int]:
return self._translation

def icohpvalue(self, spin: Spin = Spin.up) -> float:
"""
Args:
Expand Down
70 changes: 53 additions & 17 deletions src/pymatgen/io/lobster/lobsterenv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -790,14 +790,9 @@ def _evaluate_ce(
raise ValueError("Please give two limits or leave them both at None")

# Find environments based on ICOHP values
(
list_icohps,
list_keys,
list_lengths,
list_neighisite,
list_neighsite,
list_coords,
) = self._find_environments(additional_condition, lowerlimit, upperlimit, only_bonds_to)
(list_icohps, list_keys, list_lengths, list_neighisite, list_neighsite, list_coords) = self._find_environments(
additional_condition, lowerlimit, upperlimit, only_bonds_to
)

self.list_icohps = list_icohps
self.list_lengths = list_lengths
Expand Down Expand Up @@ -939,11 +934,14 @@ def _find_environments(
lengths_from_ICOHPs,
neighbors_from_ICOHPs,
selected_ICOHPs,
translations_ICOHPs,
) = additional_conds

if len(neighbors_from_ICOHPs) > 0:
centralsite = site

copysite = copy.copy(centralsite)
cell_start = centralsite.frac_coords - copysite.to_unit_cell().frac_coords
print(cell_start)
neighbors_by_distance_start = self.structure.get_sites_in_sphere(
pt=centralsite.coords,
r=np.max(lengths_from_ICOHPs) + 0.5,
Expand All @@ -955,50 +953,71 @@ def _find_environments(
list_distances = []
index_here_list = []
coords = []
translations_by_distance = []
for neigh_new in sorted(neighbors_by_distance_start, key=lambda x: x[1]):
site_here = neigh_new[0].to_unit_cell()
index_here = neigh_new[2]
index_here_list.append(index_here)
cell_here = neigh_new[3]

new_coords = [
site_here.frac_coords[0] + float(cell_here[0]),
site_here.frac_coords[1] + float(cell_here[1]),
site_here.frac_coords[2] + float(cell_here[2]),
]
coords.append(site_here.lattice.get_cartesian_coords(new_coords))

# new_site = PeriodicSite(
# species=site_here.species_string,
# coords=site_here.lattice.get_cartesian_coords(new_coords),
# lattice=site_here.lattice,
# to_unit_cell=False,
# coords_are_cartesian=True,
# )
neighbors_by_distance.append(neigh_new[0])
list_distances.append(neigh_new[1])
translations_by_distance.append(cell_here)
_list_neighsite = []
_list_neighisite = []
copied_neighbors_from_ICOHPs = copy.copy(neighbors_from_ICOHPs)
copied_distances_from_ICOHPs = copy.copy(lengths_from_ICOHPs)
copied_translations_from_ICOHPs = copy.copy(translations_ICOHPs)
_neigh_coords = []
_neigh_frac_coords = []

for neigh_idx, neigh in enumerate(neighbors_by_distance):
index_here2 = index_here_list[neigh_idx]

print(index_here2)
for dist_idx, dist in enumerate(copied_distances_from_ICOHPs):
if (
np.isclose(dist, list_distances[neigh_idx], rtol=1e-4)
and copied_neighbors_from_ICOHPs[dist_idx] == index_here2
and (
(
copied_translations_from_ICOHPs[dist_idx][0]
== -translations_by_distance[neigh_idx][0]
and copied_translations_from_ICOHPs[dist_idx][1]
== -translations_by_distance[neigh_idx][1]
and copied_translations_from_ICOHPs[dist_idx][2]
== -translations_by_distance[neigh_idx][2]
)
or (
copied_translations_from_ICOHPs[dist_idx][0]
== translations_by_distance[neigh_idx][0]
and copied_translations_from_ICOHPs[dist_idx][1]
== translations_by_distance[neigh_idx][1]
and copied_translations_from_ICOHPs[dist_idx][2]
== translations_by_distance[neigh_idx][2]
)
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We could raise a warning if this fall-back option is taken. I think with updating to reading the CONTCAR, most issues should be fixed, however.

)
):
_list_neighsite.append(neigh)
_list_neighisite.append(index_here2)
_neigh_coords.append(coords[neigh_idx])
_neigh_frac_coords.append(neigh.frac_coords)
print("test")
print(copied_translations_from_ICOHPs[dist_idx])
print(translations_by_distance[neigh_idx])
print(cell_start)
del copied_distances_from_ICOHPs[dist_idx]
del copied_neighbors_from_ICOHPs[dist_idx]
del copied_translations_from_ICOHPs[dist_idx]
break

print(_list_neighsite)
list_neighisite.append(_list_neighisite)
list_neighsite.append(_list_neighsite)
list_lengths.append(lengths_from_ICOHPs)
Expand Down Expand Up @@ -1042,6 +1061,7 @@ def _find_relevant_atoms_additional_condition(
lengths_from_ICOHPs: list[float] = []
neighbors_from_ICOHPs: list[int] = []
icohps_from_ICOHPs: list[IcohpValue] = []
translation_from_ICOHPs: list[list[int, int, int]] = []

for key, icohp in icohps.items():
atomnr1 = self._get_atomnumber(icohp._atom1)
Expand All @@ -1062,11 +1082,14 @@ def _find_relevant_atoms_additional_condition(
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
# add translation to icohp value
translation_from_ICOHPs.append(icohp.translation)
elif atomnr2 == site_idx:
neighbors_from_ICOHPs.append(atomnr1)
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

# ONLY_ANION_CATION_BONDS
elif additional_condition == 1:
Expand All @@ -1076,12 +1099,14 @@ def _find_relevant_atoms_additional_condition(
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

elif atomnr2 == site_idx:
neighbors_from_ICOHPs.append(atomnr1)
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

# NO_ELEMENT_TO_SAME_ELEMENT_BONDS
elif additional_condition == 2:
Expand All @@ -1091,12 +1116,14 @@ def _find_relevant_atoms_additional_condition(
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

elif atomnr2 == site_idx:
neighbors_from_ICOHPs.append(atomnr1)
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

# ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS
elif additional_condition == 3:
Expand All @@ -1108,12 +1135,14 @@ def _find_relevant_atoms_additional_condition(
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

elif atomnr2 == site_idx:
neighbors_from_ICOHPs.append(atomnr1)
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

# ONLY_ELEMENT_TO_OXYGEN_BONDS
elif additional_condition == 4:
Expand All @@ -1123,12 +1152,14 @@ def _find_relevant_atoms_additional_condition(
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

elif atomnr2 == site_idx:
neighbors_from_ICOHPs.append(atomnr1)
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

# DO_NOT_CONSIDER_ANION_CATION_BONDS
elif additional_condition == 5:
Expand All @@ -1138,12 +1169,14 @@ def _find_relevant_atoms_additional_condition(
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

elif atomnr2 == site_idx:
neighbors_from_ICOHPs.append(atomnr1)
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

# ONLY_CATION_CATION_BONDS
elif additional_condition == 6 and val1 > 0.0 and val2 > 0.0: # type: ignore[operator]
Expand All @@ -1152,18 +1185,21 @@ def _find_relevant_atoms_additional_condition(
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

elif atomnr2 == site_idx:
neighbors_from_ICOHPs.append(atomnr1)
lengths_from_ICOHPs.append(icohp._length)
icohps_from_ICOHPs.append(icohp.summed_icohp)
keys_from_ICOHPs.append(key)
translation_from_ICOHPs.append(icohp.translation)

return (
keys_from_ICOHPs,
lengths_from_ICOHPs,
neighbors_from_ICOHPs,
icohps_from_ICOHPs,
translation_from_ICOHPs,
)

@staticmethod
Expand Down
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