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fix TypeError when attr force_field not exists #3495

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merged 3 commits into from
Dec 6, 2023
Merged

fix TypeError when attr force_field not exists #3495

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7882be4
fix TypeError when attr force_field not exists
xjf729 Dec 5, 2023
82bc048
add test for CombinedData with different ff type
xjf729 Dec 6, 2023
55a6e55
refactor new tests
janosh Dec 6, 2023
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2 changes: 1 addition & 1 deletion pymatgen/io/lammps/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1277,7 +1277,7 @@ def __init__(
self.force_field = {}
for kw in ff_kws:
self.force_field[kw] = pd.concat(
[mol.force_field[kw].copy() for mol in self.mols if kw in mol.force_field],
[mol.force_field[kw].copy() for mol in self.mols if kw in (mol.force_field or [])],
ignore_index=True,
)
self.force_field[kw].index += 1
Expand Down
19 changes: 16 additions & 3 deletions tests/io/lammps/test_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -823,6 +823,9 @@ def setUpClass(cls):
cls.ec_li = CombinedData.from_lammpsdata([cls.ec, cls.li], ["EC", "Li"], [1, 1], cls.small_coord_2)
cls.li_2 = CombinedData.from_lammpsdata([cls.li], ["Li"], [2], cls.small_coord_3)
cls.li_2_minimal = CombinedData.from_lammpsdata([cls.li_minimal], ["Li_minimal"], [2], cls.small_coord_3)
cls.ec_li_minimal = CombinedData.from_lammpsdata(
[cls.ec, cls.li_minimal], ["EC", "Li"], [1, 1], cls.small_coord_2
)

def test_from_files(self):
# general tests
Expand Down Expand Up @@ -957,7 +960,7 @@ def test_from_lammpsdata(self):
assert topo["Impropers"].loc[1, "atom3"] == 3
assert topo["Impropers"].loc[1, "atom4"] == 6

# tests for data objects with different number of ff kw
# test data objects with different number of FF keywords
li_ec = self.li_ec
ec_li = self.ec_li
assert li_ec.force_field["Pair Coeffs"].loc[6, "coeff2"] == 2.42
Expand All @@ -971,15 +974,25 @@ def test_from_lammpsdata(self):
assert li_ec.force_field["Improper Coeffs"].loc[1, "coeff1"] == 10.5
assert ec_li.force_field["Improper Coeffs"].loc[1, "coeff1"] == 10.5

# tests for combining data with no topo info
# test combining data with no topo info
li_2 = self.li_2
assert li_2.topology is None, "Empty topo info should be none"

# tests for combining data with no topo and ff info
# test combining data with no topo info but FF info
li_2_minimal = self.li_2_minimal
assert li_2_minimal.force_field is None, "Empty ff info should be none"
assert li_2_minimal.topology is None, "Empty topo info should be none"

# test combining data with no FF info and existing FF info
ec_li_minimal = self.ec_li_minimal
for key in ("Bonds", "Angles", "Dihedrals", "Impropers"):
pd.testing.assert_frame_equal(ec_li_minimal.topology[key], ec_li_minimal.topology[key])
pd.testing.assert_frame_equal(
ec_li_minimal.force_field["Pair Coeffs"], ec_li.force_field["Pair Coeffs"].loc[1:5]
)
for key in ("Bond Coeffs", "Angle Coeffs", "Dihedral Coeffs", "Improper Coeffs"):
pd.testing.assert_frame_equal(ec_li_minimal.force_field[key], ec_li.force_field[key])

def test_get_str(self):
# general tests
ec_fec_lines = self.ec_fec1.get_str().splitlines()
Expand Down