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Replacing Fire minimization with LocalEnergyMinimizer #672

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Replacing Fire minimization with LocalEnergyMinimizer #672

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88bd0bf
Replacing FireMinimizer with LocalEnergyMinimizer
ijpulidos Mar 28, 2023
0782749
Removing unnecessary import
ijpulidos Mar 29, 2023
cc49fbc
shoudn't need to delete the context here
ijpulidos Apr 6, 2023
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30 changes: 3 additions & 27 deletions openmmtools/multistate/multistatesampler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,6 @@
from openmmtools.multistate.utils import SimulationNaNError
from openmmtools.multistate.pymbar import ParameterError

from openmmtools.integrators import FIREMinimizationIntegrator

logger = logging.getLogger(__name__)


Expand Down Expand Up @@ -1356,11 +1354,8 @@ def _minimize_replica(self, replica_id, tolerance, max_iterations):
thermodynamic_state = self._thermodynamic_states[thermodynamic_state_id]
sampler_state = self._sampler_states[replica_id]

# Use the FIRE minimizer
integrator = FIREMinimizationIntegrator(tolerance=tolerance)

# Get context and bound integrator from energy_context_cache
context, integrator = self.energy_context_cache.get_context(thermodynamic_state, integrator)
context, integrator = self.energy_context_cache.get_context(thermodynamic_state)
# inform of platform used in current context
logger.debug(f"{type(integrator).__name__}: Minimize using {context.getPlatform().getName()} platform.")

Expand All @@ -1373,33 +1368,14 @@ def _minimize_replica(self, replica_id, tolerance, max_iterations):
replica_id + 1, self.n_replicas, initial_energy))

# Minimize energy.
try:
if max_iterations == 0:
logger.debug('Using FIRE: tolerance {} minimizing to convergence'.format(tolerance))
while integrator.getGlobalVariableByName('converged') < 1:
integrator.step(50)
else:
logger.debug('Using FIRE: tolerance {} max_iterations {}'.format(tolerance, max_iterations))
integrator.step(max_iterations)
except Exception as e:
if str(e) == 'Particle coordinate is nan':
logger.debug('NaN encountered in FIRE minimizer; falling back to L-BFGS after resetting positions')
sampler_state.apply_to_context(context)
openmm.LocalEnergyMinimizer.minimize(context, tolerance, max_iterations)
else:
raise e
openmm.LocalEnergyMinimizer.minimize(context, tolerance, max_iterations)

# Get the minimized positions.
sampler_state.update_from_context(context)

# Compute the final energy of the system for logging.
final_energy = thermodynamic_state.reduced_potential(sampler_state)
logger.debug('Replica {}/{}: final energy {:8.3f}kT'.format(
replica_id + 1, self.n_replicas, final_energy))
# TODO if energy > 0, use slower openmm minimizer

# Clean up the integrator
del context
logger.debug(f'Replica {replica_id + 1}/{self.n_replicas}: final energy {final_energy:8.3f}kT')

# Return minimized positions.
return sampler_state.positions
Expand Down