Skip to content

Backport fixes from PR #100 #101

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
lohedges merged 1 commit into from
Dec 2, 2025
Merged

Backport fixes from PR #100 #101

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
20 changes: 11 additions & 9 deletions src/somd2/runner/_base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,8 @@ def __init__(self, system, config):

# Flag whether frames are being saved.
if (
self._config.frame_frequency > 0
self._config.save_trajectories
and self._config.frame_frequency > 0
and self._config.frame_frequency <= self._config.runtime
):
self._save_frames = True
Expand Down Expand Up @@ -1241,7 +1242,6 @@ def _compare_configs(config1, config2):
"equilibration_timestep",
"equilibration_constraints",
"energy_frequency",
"save_trajectory",
"frame_frequency",
"save_velocities",
"platform",
Expand Down Expand Up @@ -1646,15 +1646,17 @@ def _checkpoint(
_copyfile(traj_filename, f"{traj_filename}.prev")
traj_chunks = [f"{traj_filename}.prev"] + traj_chunks

# Load the topology and chunked trajectory files.
mols = _sr.load([topology0] + traj_chunks)
# Make sure there are trajectory chunks to process.
if len(traj_chunks) > 0:
# Load the topology and chunked trajectory files.
mols = _sr.load([topology0] + traj_chunks)

# Save the final trajectory to a single file.
_sr.save(mols.trajectory(), traj_filename, format=["DCD"])
# Save the final trajectory to a single file.
_sr.save(mols.trajectory(), traj_filename, format=["DCD"])

# Now remove the chunked trajectory files.
for chunk in traj_chunks:
_Path(chunk).unlink()
# Now remove the chunked trajectory files.
for chunk in traj_chunks:
_Path(chunk).unlink()

# Add config and lambda value to the system properties.
system.set_property("config", self._config.as_dict(sire_compatible=True))
Expand Down