from molsysmt._private.exceptions import *
from molsysmt import pyunitwizard as puw
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class Simulation():
def __init__(self, molecular_system=None, remove_cm_motion=True,
integrator=None, temperature=None, collisions_rate=None, integration_timestep=None,
initial_velocities_to_temperature = True, constraint_tolerance=0.00001,
platform='CUDA', cuda_precision='mixed'):
self._molecular_system = molecular_system
self.remove_cm_motion = remove_cm_motion
self.integrator = integrator
self.temperature = temperature
self.collisions_rate = collisions_rate
self.integration_timestep = integration_timestep
self.initial_velocities_to_temperature = initial_velocities_to_temperature
self.constraint_tolerance = constraint_tolerance
self.platform = platform
self.cuda_precision = cuda_precision
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def to_dict(self):
tmp_dict = {
'remove_cm_motion' : self.remove_cm_motion,
'integrator' : self.integrator,
'temperature' : self.temperature,
'collisions_rate' : self.collisions_rate,
'integration_timestep' : self.integration_timestep,
'initial_velocities_to_temperature' : self.initial_velocities_to_temperature,
'constraint_tolerance' : self.constraint_tolerance,
'platform' : self.platform,
'cuda_precision' : self.cuda_precision,
}
return tmp_dict
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def copy(self):
tmp_simulation = Simulation()
tmp_simulation._molecular_system = self._molecular_system
tmp_simulation.remove_cm_motion = self.remove_cm_motion
tmp_simulation.integrator = self.integrator
tmp_simulation.temperature = self.temperature
tmp_simulation.collisions_rate = self.collisions_rate
tmp_simulation.integration_timestep = self.integration_timestep
tmp_simulation.initial_velocities_to_temperature = self.initial_velocities_to_temperature
tmp_constraint_tolerance = self.constraint_tolerance
tmp_simulation.platform = self.platform
tmp_simulation.cuda_precision = self.cuda_precision
return tmp_simulation
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def set_parameters(self, return_non_processed=False, **kwargs):
for argument, value in kwargs.items():
if argument.lower() in self.__dict__.keys():
self.__dict__[argument]=puw.standardize(value)
del(kwargs[argment.lower()])
if return_non_processed:
return kwargs
else:
pass
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def to_openmm_Integrator(self):
from openmm import LangevinIntegrator
temperature = puw.convert(self.temperature, to_unit='K', to_form='openmm.unit')
collisions_rate = puw.convert(self.collisions_rate, to_unit='1/ps', to_form='openmm.unit')
integration_timestep = puw.convert(self.integration_timestep, to_unit='fs', to_form='openmm.unit')
if self.integrator=='Langevin':
integrator = LangevinIntegrator(temperature, collisions_rate, integration_timestep)
if self.constraint_tolerance is not None:
integrator.setConstraintTolerance(self.constraint_tolerance)
else:
raise NotImplementedError()
return integrator
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def get_openmm_Context_parameters(self):
parameters = {}
if self.platform=='CUDA':
parameters['CudaPrecision']=self.cuda_precision
return parameters
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def to_openmm_Context(self, molecular_system=None, selection='all', structure_indices='all'):
from molsysmt.basic import convert
if molecular_system is None:
molecular_system = self._molecular_system
else:
molecular_system = digest_molecular_system(molecular_system)
if molecular_system is None:
raise NoMolecularSystemError()
context = convert(molecular_system, to_form='openmm.Context', selection=selection, simulation=self)
return context
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def get_openmm_Simulation_parameters(self):
parameters = {}
if self.platform=='CUDA':
parameters['CudaPrecision']=self.cuda_precision
return parameters
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def to_openmm_Simulation(self, molecular_system=None, selection='all', structure_indices='all'):
from molsysmt.basic import convert
if molecular_system is None:
molecular_system = self._molecular_system
else:
molecular_system = digest_molecular_system(molecular_system)
if molecular_system is None:
raise NoMolecularSystemError()
simulation = convert(molecular_system, to_form='openmm.Simulation', selection=selection, simulation=self)
return simulation
simulation_to_potential_energy_minimization = Simulation(integrator='Langevin', temperature='0 K',
collisions_rate='1.0 1/ps', integration_timestep='2fs',
initial_velocities_to_temperature = False,
platform='CUDA', cuda_precision='mixed')
