Skip to content

HTF speed up #128

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ijpulidos merged 1 commit into from
Oct 17, 2025
Merged

HTF speed up #128

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions feflow/utils/hybrid_topology.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2698,14 +2698,17 @@ def _create_hybrid_topology(self):
# In the first instance, create a list of necessary atoms from
# both old & new Topologies
atom_list = []
# iterate once over the topologies for speed
old_topology_atoms = list(self._old_topology.atoms())
new_topology_atoms = list(self._new_topology.atoms())

for pidx in range(self.hybrid_system.getNumParticles()):
if pidx in self._hybrid_to_old_map:
idx = self._hybrid_to_old_map[pidx]
atom_list.append(list(self._old_topology.atoms())[idx])
atom_list.append(old_topology_atoms[idx])
else:
idx = self._hybrid_to_new_map[pidx]
atom_list.append(list(self._new_topology.atoms())[idx])
atom_list.append(new_topology_atoms[idx])

# Now we loop over the atoms and add them in alongside chains & resids

Expand Down
Loading