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Cherry-pick roitberg-group#23 #544

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Nov 13, 2020
Merged

Cherry-pick roitberg-group#23 #544

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2 changes: 1 addition & 1 deletion torchani/nn.py
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,7 @@ class SpeciesConverter(torch.nn.Module):

def __init__(self, species):
super().__init__()
rev_idx = {s: k for k, s in enumerate(utils.PERIODIC_TABLE, 1)}
rev_idx = {s: k for k, s in enumerate(utils.PERIODIC_TABLE)}
maxidx = max(rev_idx.values())
self.register_buffer('conv_tensor', torch.full((maxidx + 2,), -1, dtype=torch.long))
for i, s in enumerate(species):
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5 changes: 4 additions & 1 deletion torchani/utils.py
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Expand Up @@ -377,7 +377,10 @@ def get_atomic_masses(species):
return masses


PERIODIC_TABLE = """
# This constant, when indexed with the corresponding atomic number, gives the
# element associated with it. Note that there is no element with atomic number
# 0, so 'Dummy' returned in this case.
PERIODIC_TABLE = ['Dummy'] + """
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
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