Merge pull request #382 from marrink-lab/speedopt

Optimisation of Speed
marrink-lab · Sep 6, 2024 · f8fff22 · f8fff22
2 parents c820aaa + 6f168af
commit f8fff22
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/polyply/src/build_system.py b/polyply/src/build_system.py
@@ -221,7 +221,11 @@ def _compose_system(self, molecules):
                                                                    vector_sphere)
             if success:
                 self.nonbond_matrix = new_nonbond_matrix
-                self.nonbond_matrix.concatenate_trees()
+                # concatanation only makes sense for polymers
+                # longer than 10; it really hurts performance
+                # for for example 1 monomer solvents
+                if len(molecule) > 10:
+                    self.nonbond_matrix.concatenate_trees()
                 mol_idx += 1
                 pbar.update(1)
 

diff --git a/polyply/src/random_walk.py b/polyply/src/random_walk.py
@@ -356,8 +356,8 @@ def update_positions(self, vector_bundle, current_node, prev_node):
             if fulfill_geometrical_constraints(new_point, self.molecule.nodes[current_node])\
                 and self.checks_milestones(current_node, new_point, step_length)\
                 and is_restricted(new_point, last_point, self.molecule.nodes[current_node])\
-                and not self._is_overlap(new_point, current_node)\
-                and self.bendiness(new_point, current_node):
+                and self.bendiness(new_point, current_node)\
+                and not self._is_overlap(new_point, current_node):
 
                     self.nonbond_matrix.add_positions(new_point,
                                                       self.mol_idx,