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Bugfix rename equil files #36

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merged 2 commits into from
Feb 23, 2025
Merged

Bugfix rename equil files #36

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dc3c866
Ensure somd.rst7 is correctly named during equilibration
fjclark Feb 21, 2025
53d2c61
Update changelog
fjclark Feb 21, 2025
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6 changes: 4 additions & 2 deletions a3fe/run/leg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -645,9 +645,11 @@ def run_ensemble_equilibration(
)

# Give the output files unique names
for i, outdir in enumerate(outdirs_to_run):
equil_numbers = [int(outdir.split("_")[-1]) for outdir in outdirs_to_run]
for equil_number, outdir in zip(equil_numbers, outdirs_to_run):
_subprocess.run(
["mv", f"{outdir}/somd.rst7", f"{outdir}/somd_{i + 1}.rst7"], check=True
["mv", f"{outdir}/somd.rst7", f"{outdir}/somd_{equil_number}.rst7"],
check=True,
)

# Load the system and mark the ligand to be decoupled
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2 changes: 1 addition & 1 deletion a3fe/run/system_prep.py
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Expand Up @@ -675,7 +675,7 @@ def run_ensemble_equilibration(

# Run - assuming that this will be in the appropriate ensemble equilibration directory
print(
f"Running SOMD ensemble equilibration simulation for {cfg.ensemble_equilibration_time} ps"
f"Running ensemble equilibration simulation with GROMACS for {cfg.ensemble_equilibration_time} ps"
)
if leg_type == _LegType.BOUND:
work_dir = output_dir
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4 changes: 4 additions & 0 deletions docs/CHANGELOG.rst
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Expand Up @@ -2,6 +2,10 @@
Change Log
===============

0.3.2
====================
- Fix bug which caused somd.rst7 files in the ensemble equilibration directories to be incorrectly numbered in some cases.

0.3.1
====================
- Modified the SimulationRunnerIterator to ensure that the state of sub-simulation runners is saved before they are torn down. This means that setting the equilibration time at the CalcSet level will now work as expected (previously the state of the calculations was not saved, causing the analysis to fail).
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