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Fix the empty neighbor distance array in neighbor_stat.py #882

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Merged
amcadmus merged 2 commits into from
Jul 26, 2021
Merged

Fix the empty neighbor distance array in neighbor_stat.py #882

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ad305fd
Update neighbor_stat.py
nicklin96 Jul 23, 2021
04cc1b5
Update neighbor_stat.py
nicklin96 Jul 23, 2021
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7 changes: 6 additions & 1 deletion deepmd/utils/neighbor_stat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,12 @@ def get_stat(self,
self.place_holders['box']: np.array(data_set['box'])[kk].reshape([-1, 9]),
self.place_holders['default_mesh']: np.array(data.default_mesh[ii]),
})
dt = np.min(dt)
if dt.size != 0:
dt = np.min(dt)
else:
dt = self.rcut
log.warning("Atoms with no neighbors found in %s. Please make sure it's what you expected."%jj)

if dt < self.min_nbor_dist:
self.min_nbor_dist = dt
for ww in range(self.ntypes):
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