Fix v-site coordinate stacking

leeping · Jun 30, 2021 · 20b4ae5 · 20b4ae5
1 parent 8ea4e0a
commit 20b4ae5
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/src/smirnoffio.py b/src/smirnoffio.py
@@ -519,7 +519,10 @@ def _update_positions(self, X1, disable_vsite):
  )
 
  # Add placeholder positions for an v-sites.
- X1 = (X1 + [Vec3(0.0, 0.0, 0.0)] * n_v_sites) * angstrom
+ if isinstance(X1, np.ndarray):
+ X1 = numpy.vstack([X1, np.zeros((n_v_sites, 3))]) * angstrom
+ else:
+ X1 = (X1 + [Vec3(0.0, 0.0, 0.0)] * n_v_sites) * angstrom
 
  self.simulation.context.setPositions(X1)
  self.simulation.context.computeVirtualSites()