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fix: infer optional CALYPSO inputs #383

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fix: infer optional CALYPSO inputs #383

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17 changes: 12 additions & 5 deletions dpgen2/exploration/task/caly_task_group.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,12 +144,19 @@ def set_params(
self.atomic_number = [atomic_symbols.index(i) for i in self.name_of_atoms]
else:
self.name_of_atoms = name_of_atoms
self.atomic_number = atomic_number

if isinstance(distance_of_ions, dict):
self.atomic_number = (
[atomic_number_map[name] for name in self.name_of_atoms]
if atomic_number is None
else atomic_number
)

if distance_of_ions is None or isinstance(distance_of_ions, dict):
# Generate a complete distance matrix from the maintained
# covalent-radius table when the optional matrix is omitted.
updated_table = copy.deepcopy(covalent_radii)
for key, value in distance_of_ions.items():
updated_table[atomic_number_map[key]] = value
if isinstance(distance_of_ions, dict):
for key, value in distance_of_ions.items():
updated_table[atomic_number_map[key]] = value

temp_distance_mtx = np.zeros((numb_of_species, numb_of_species))
for i in range(numb_of_species):
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15 changes: 15 additions & 0 deletions tests/exploration/test_make_task_group_from_config.py
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Expand Up @@ -126,3 +126,18 @@ def test_make_caly_input(self):
def test_caly_task_group(self):
tgroup = make_calypso_task_group_from_config(self.config)
self.assertTrue(isinstance(tgroup, CalyTaskGroup))

def test_infers_optional_atomic_numbers_and_distances(self):
"""Generate CALYPSO-required values when optional fields are absent."""
config = {
"name_of_atoms": ["Li", "La"],
"numb_of_atoms": [10, 10],
"numb_of_species": 2,
}

task_group = make_calypso_task_group_from_config(config)

self.assertEqual(task_group.atomic_number, [3, 57])
self.assertEqual(task_group.distance_of_ions.shape, (2, 2))

@wanghan-iapcm wanghan-iapcm Sep 2, 2026

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These two assertions only establish that a square, positive matrix was produced. I mutated the source four ways (0.7 -> 7.0; radius index +1; dict-override loop replaced by if False; matrix replaced by a constant 0.01) and all five tests stayed green each time.

Please pin the values instead. For this Li/La config:

np.testing.assert_allclose(
    task_group.distance_of_ions, [[1.79, 2.34], [2.34, 2.90]]
)

and one dict case, since no test in the repo pins an override value and this PR restructures that loop: distance_of_ions={"Li": 2.0} on the same config gives [[2.8, 2.85], [2.85, 2.9]].

The atomic_number == [3, 57] line above is fine; it does catch an off-by-one in the symbol table.

self.assertTrue(np.all(task_group.distance_of_ions > 0))
self.assertEqual(len(task_group.make_task()), 1)