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Fix species test #55

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merged 2 commits into from
Jan 6, 2024
Merged

Fix species test #55

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ac80d60
Fix species test
sivonxay Jan 6, 2024
69293d2
Fix failing graph data tests
sivonxay Jan 6, 2024
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4 changes: 3 additions & 1 deletion src/NanoParticleTools/species_data/species.py
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Original file line number Diff line number Diff line change
Expand Up @@ -204,14 +204,16 @@
with open(os.path.join(SPECIES_DATA_PATH, f'{symbol}.json'),
'r') as f:
species_data = json.load(f)
except FileNotFoundError:
except FileNotFoundError as e:
# File was not found, check if it is a legacy calc
if self.symbol in self.LEGACY_SURFACE_NAMES:
# This is a legacy calc. Load the corresponding calc
symbol = self.LEGACY_SURFACE_NAMES[self.symbol]
with open(os.path.join(SPECIES_DATA_PATH, f'{symbol}.json'),

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src/NanoParticleTools/species_data/species.py#L211-L212 

Added lines #L211 - L212 were not covered by tests
'r') as f:
species_data = json.load(f)

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src/NanoParticleTools/species_data/species.py#L214 

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else:
raise e

return species_data

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28 changes: 14 additions & 14 deletions tests/machine_learning/models/gnn_model/test_graph_data.py
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Expand Up @@ -166,9 +166,9 @@ def test_graph_interaction_feature_processor(doc_one):
data = feature_processor.data_cls(**_data_dict)
assert data.radii.shape == (3, )
assert data.constraint_radii_idx.shape == (2, 2)
assert torch.allclose(data.constraint_indices, torch.tensor([0, 0, 1, 1]))
assert data.x.shape == (4, )
assert torch.allclose(data.x, torch.tensor([0.499, 0.25, 0.2, 0.1]))
assert torch.allclose(data.dopant_constraint_indices, torch.tensor([0, 0, 1, 1]))
assert data.dopant_concs.shape == (4, )
assert torch.allclose(data.dopant_concs, torch.tensor([0.499, 0.25, 0.2, 0.1]))
assert data.edge_index.shape == (2, 32)


Expand All @@ -180,10 +180,10 @@ def test_graph_interaction_feature_processor_zeros(doc_one):
data = feature_processor.data_cls(**_data_dict)
assert data.radii.shape == (3, )
assert data.constraint_radii_idx.shape == (2, 2)
assert torch.allclose(data.constraint_indices,
assert torch.allclose(data.dopant_constraint_indices,
torch.tensor([0, 0, 0, 1, 1, 1]))
assert data.x.shape == (6, )
assert torch.allclose(data.x, torch.tensor([0.499, 0.25, 0, 0.2, 0.1, 0]))
assert data.dopant_concs.shape == (6, )
assert torch.allclose(data.dopant_concs, torch.tensor([0.499, 0.25, 0, 0.2, 0.1, 0]))
assert data.edge_index.shape == (2, 72)


Expand All @@ -195,10 +195,10 @@ def test_invalid_doc(doc_one_invalid):
data = feature_processor.data_cls(**_data_dict)
assert data.radii.shape == (3, )
assert data.constraint_radii_idx.shape == (2, 2)
assert torch.allclose(data.constraint_indices,
assert torch.allclose(data.dopant_constraint_indices,
torch.tensor([0, 0, 0, 1, 1, 1]))
assert data.x.shape == (6, )
assert torch.allclose(data.x, torch.tensor([0.499, 0.25, 0, 0.2, 0.1, 0]))
assert data.dopant_concs.shape == (6, )
assert torch.allclose(data.dopant_concs, torch.tensor([0.499, 0.25, 0, 0.2, 0.1, 0]))
assert data.edge_index.shape == (2, 72)

feature_processor = GraphInteractionFeatureProcessor(
Expand All @@ -207,9 +207,9 @@ def test_invalid_doc(doc_one_invalid):
data = feature_processor.data_cls(**_data_dict)
assert data.radii.shape == (3, )
assert data.constraint_radii_idx.shape == (2, 2)
assert torch.allclose(data.constraint_indices, torch.tensor([0, 0, 1, 1]))
assert data.x.shape == (4, )
assert torch.allclose(data.x, torch.tensor([0.499, 0.25, 0.2, 0.1]))
assert torch.allclose(data.dopant_constraint_indices, torch.tensor([0, 0, 1, 1]))
assert data.dopant_concs.shape == (4, )
assert torch.allclose(data.dopant_concs, torch.tensor([0.499, 0.25, 0.2, 0.1]))
assert data.edge_index.shape == (2, 32)


Expand All @@ -220,12 +220,12 @@ def test_grad(doc_four):
_data_dict = feature_processor.process_doc(doc_four)
data = feature_processor.data_cls(**_data_dict)
assert data.radii.requires_grad
assert data.x.requires_grad
assert data.dopant_concs.requires_grad

feature_processor = GraphInteractionFeatureProcessor(
possible_elements=['Yb', 'Er', 'Mg'], input_grad=False)

_data_dict = feature_processor.process_doc(doc_four)
data = feature_processor.data_cls(**_data_dict)
assert not data.radii.requires_grad
assert not data.x.requires_grad
assert not data.dopant_concs.requires_grad
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