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list offending elements in BVAnalyzer.get_valences error message #3225

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merged 3 commits into from
Aug 5, 2023
Merged

list offending elements in BVAnalyzer.get_valences error message #3225

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546b690
list offending elements in BVAnalyzer.get_valences err msg
janosh Aug 5, 2023
294f033
test err msg in TestBVAnalyzer.test_get_valences()
janosh Aug 5, 2023
2108262
Merge branch 'master' into BVAnalyzer.get_valences-err-msg
janosh Aug 5, 2023
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6 changes: 3 additions & 3 deletions pymatgen/analysis/bond_valence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -221,10 +221,10 @@ def get_valences(self, structure: Structure):
Raises:
A ValueError if the valences cannot be determined.
"""
els = [Element(el.symbol) for el in structure.composition.elements]
els = [Element(el.symbol) for el in structure.elements]

if not set(els).issubset(set(BV_PARAMS)):
raise ValueError("Structure contains elements not in set of BV parameters!")
if diff := set(els) - set(BV_PARAMS):
raise ValueError(f"Structure contains elements not in set of BV parameters: {diff}")

# Perform symmetry determination and get sites grouped by symmetry.
if self.symm_tol:
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13 changes: 9 additions & 4 deletions tests/analysis/test_bond_valence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import os

import pytest
from pytest import approx

from pymatgen.analysis.bond_valence import BVAnalyzer, calculate_bv_sum, calculate_bv_sum_unordered
Expand All @@ -15,7 +16,7 @@ class TestBVAnalyzer(PymatgenTest):
def setUp(self):
self.analyzer = BVAnalyzer()

def test_get_valence(self):
def test_get_valences(self):
struct = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "LiMn2O4.json"))
ans = [1, 1, 3, 3, 4, 4, -2, -2, -2, -2, -2, -2, -2, -2]
assert self.analyzer.get_valences(struct) == ans
Expand All @@ -31,11 +32,15 @@ def test_get_valence(self):
struct = self.get_structure("NaFePO4")
assert self.analyzer.get_valences(struct) == ans

# trigger ValueError Structure contains elements not in set of BV parameters
with pytest.raises(ValueError, match="Structure contains elements not in set of BV parameters: {Element Xe}"):
self.analyzer.get_valences(self.get_structure("Li10GeP2S12").replace_species({"Li": "Xe"}, in_place=False))

def test_get_oxi_state_structure(self):
struct = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "LiMn2O4.json"))
news = self.analyzer.get_oxi_state_decorated_structure(struct)
assert Species("Mn", 3) in news.composition.elements
assert Species("Mn", 4) in news.composition.elements
oxi_struct = self.analyzer.get_oxi_state_decorated_structure(struct)
assert Species("Mn", 3) in oxi_struct.composition.elements
assert Species("Mn", 4) in oxi_struct.composition.elements


class TestBondValenceSum(PymatgenTest):
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2 changes: 1 addition & 1 deletion tests/files/.pytest-split-durations
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Expand Up @@ -219,7 +219,7 @@
"tests/analysis/test_bond_dissociation.py::TestBondDissociation::test_pc_neutral_pcm_65": 0.0004544589319266379,
"tests/analysis/test_bond_dissociation.py::TestBondDissociation::test_tfsi_neg_no_pcm": 0.0004278330015949905,
"tests/analysis/test_bond_valence.py::TestBVAnalyzer::test_get_oxi_state_structure": 0.005586749990470707,
"tests/analysis/test_bond_valence.py::TestBVAnalyzer::test_get_valence": 0.05632162501569837,
"tests/analysis/test_bond_valence.py::TestBVAnalyzer::test_get_valences": 0.05632162501569837,
"tests/analysis/test_bond_valence.py::TestBondValenceSum::test_calculate_bv_sum": 0.0013919160119257867,
"tests/analysis/test_bond_valence.py::TestBondValenceSum::test_calculate_bv_sum_unordered": 0.0008953339420258999,
"tests/analysis/test_chempot_diagram.py::TestChemicalPotentialDiagram::test_border_hyperplanes": 0.07804387499345466,
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