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Fixing FIREMinimizerIntegrator #420

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Fixing FIREMinimizerIntegrator #420

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a85076e
fixing nan check in fire minimizer and relaxing test requirements
hannahbrucemacdonald Apr 29, 2019
4e6f1e8
removing print statements
hannahbrucemacdonald Apr 29, 2019
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8 changes: 5 additions & 3 deletions openmmtools/integrators.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2198,8 +2198,10 @@ def __init__(self, timestep=1.0 * unit.femtoseconds, tolerance=None, alpha=0.1,
self.addPerDofVariable("x1", 0)
self.addGlobalVariable("E0", 0) # old energy associated with x0
self.addGlobalVariable("dE", 0)
self.addGlobalVariable("is_nan",0)
self.addGlobalVariable("restart", 0)
self.addGlobalVariable("delta_t", timestep.value_in_unit_system(unit.md_unit_system))
self.addGlobalVariable("dt_min", 1.0e-5*timestep.value_in_unit_system(unit.md_unit_system))

# Update context state.
self.addUpdateContextState()
Expand Down Expand Up @@ -2256,7 +2258,8 @@ def __init__(self, timestep=1.0 * unit.femtoseconds, tolerance=None, alpha=0.1,

# Back up if the energy went up, protecing against NaNs
self.addComputeGlobal('restart', '1')
self.beginIfBlock('dE < 0')
self.addComputeGlobal('is_nan','step( exp(-dE)/kT - uniform)')
self.beginIfBlock('is_nan = 1')
self.addComputeGlobal('restart', '0')
self.endBlock()
self.beginIfBlock('restart > 0')
Expand All @@ -2266,8 +2269,7 @@ def __init__(self, timestep=1.0 * unit.femtoseconds, tolerance=None, alpha=0.1,
self.endBlock()

# If dt goes to zero, signal we've converged!
dt_min = 1.0e-5 * timestep
self.beginIfBlock('delta_t <= %f' % dt_min.value_in_unit_system(unit.md_unit_system))
self.beginIfBlock('delta_t <= dt_min')
self.addComputeGlobal('converged', '1')
self.endBlock()

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4 changes: 2 additions & 2 deletions openmmtools/multistate/multistatesampler.py
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Expand Up @@ -544,8 +544,8 @@ def create(self, thermodynamic_states: list, sampler_states, storage,
self._initialize_reporter()

@utils.with_timer('Minimizing all replicas')
def minimize(self, tolerance=1.0 * unit.kilojoules_per_mole / unit.nanometers,
max_iterations=0):
def minimize(self, tolerance=2.0 * unit.kilojoules_per_mole / unit.nanometers,
max_iterations=1000):
"""Minimize all replicas.

Minimized positions are stored at the end.
Expand Down