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Address review comments.
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src/somd2/runner/_runner.py

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -377,6 +377,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
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if self._config.equilibration_time.value() > 0.0 and not is_restart:
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try:
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# Run without saving energies or frames.
380+
_logger.info(f"Equilibrating at {_lam_sym} = {lambda_value:.5f}")
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# Copy the dynamics kwargs.
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dynamics_kwargs = self._dynamics_kwargs.copy()
@@ -416,8 +417,10 @@ def generate_lam_vals(lambda_base, increment=0.001):
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# Commit the system.
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system = dynamics.commit()
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420+
from sire import u
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# Reset the timer to zero.
420-
system.set_time(_sr.u("0ps"))
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system.set_time(u("0ps"))
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# Perform minimisation at the end of equilibration only if the
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# timestep is increasing, or the constraint is changing.
@@ -427,7 +430,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
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):
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self._minimisation(
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system,
430-
lambda_min=lambda_value,
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lambda_value=lambda_value,
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rest2_scale=rest2_scale,
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device=device,
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constraint=self._config.constraint,

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