示例#1
0
文件: mcmc.py 项目: swails/repex
    def minimize(self, tolerance=None, maxIterations=None, platform=None):
        """
        Minimize the current configuration.

        Parameters
        ----------
        tolerance : simtk.unit.Quantity compatible with kilocalories_per_mole/anstroms, optional, default = 1*kilocalories_per_mole/anstrom
           Tolerance to use for minimization termination criterion.

        maxIterations : int, optional, default = 100
           Maximum number of iterations to use for minimization.

        platform : simtk.openmm.Platform, optional
           Platform to use for minimization.

        Examples
        --------
        
        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Minimize
        >>> sampler_state.minimize()

        """
        timer = Timer()

        if (tolerance is None):
            tolerance = 1.0 * u.kilocalories_per_mole / u.angstroms

        if (maxIterations is None):
            maxIterations = 100

        # Use LocalEnergyMinimizer
        from simtk.openmm import LocalEnergyMinimizer
        timer.start("Context creation")
        context = self.createContext(platform=platform)
        logger.debug("LocalEnergyMinimizer: platform is %s" %
                     context.getPlatform().getName())
        logger.debug("Minimizing with tolerance %s and %d max. iterations." %
                     (tolerance, maxIterations))
        timer.stop("Context creation")
        timer.start("LocalEnergyMinimizer minimize")
        LocalEnergyMinimizer.minimize(context, tolerance, maxIterations)
        timer.stop("LocalEnergyMinimizer minimize")

        # Retrieve data.
        sampler_state = SamplerState.createFromContext(context)
        self.positions = sampler_state.positions
        self.potential_energy = sampler_state.potential_energy
        self.total_energy = sampler_state.total_energy

        del context

        timer.report_timing()

        return
示例#2
0
文件: mcmc.py 项目: swails/repex
    def minimize(self, tolerance=None, maxIterations=None, platform=None):
        """
        Minimize the current configuration.

        Parameters
        ----------
        tolerance : simtk.unit.Quantity compatible with kilocalories_per_mole/anstroms, optional, default = 1*kilocalories_per_mole/anstrom
           Tolerance to use for minimization termination criterion.

        maxIterations : int, optional, default = 100
           Maximum number of iterations to use for minimization.

        platform : simtk.openmm.Platform, optional
           Platform to use for minimization.

        Examples
        --------
        
        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Minimize
        >>> sampler_state.minimize()

        """
        timer = Timer()

        if (tolerance is None):
            tolerance = 1.0 * u.kilocalories_per_mole / u.angstroms

        if (maxIterations is None):
            maxIterations = 100

        # Use LocalEnergyMinimizer
        from simtk.openmm import LocalEnergyMinimizer
        timer.start("Context creation")
        context = self.createContext(platform=platform)
        logger.debug("LocalEnergyMinimizer: platform is %s" % context.getPlatform().getName())
        logger.debug("Minimizing with tolerance %s and %d max. iterations." % (tolerance, maxIterations))
        timer.stop("Context creation")
        timer.start("LocalEnergyMinimizer minimize")
        LocalEnergyMinimizer.minimize(context, tolerance, maxIterations)
        timer.stop("LocalEnergyMinimizer minimize")

        # Retrieve data.
        sampler_state = SamplerState.createFromContext(context)
        self.positions = sampler_state.positions
        self.potential_energy = sampler_state.potential_energy
        self.total_energy = sampler_state.total_energy

        del context

        timer.report_timing()

        return
示例#3
0
文件: mcmc.py 项目: swails/repex
    def apply(self, thermodynamic_state, sampler_state, platform=None):
        """
        Apply the GHMC MCMC move.

        Parameters
        ----------
        thermodynamic_state : ThermodynamicState
           The thermodynamic state to use when applying the MCMC move
        sampler_state : SamplerState
           The sampler state to apply the move to
        platform : simtk.openmm.Platform, optional, default = None
           If not None, the specified platform will be used.

        Returns
        -------
        updated_sampler_state : SamplerState
           The updated sampler state

        Examples
        --------
        
        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
        >>> # Create a LangevinDynamicsMove
        >>> move = GHMCMove(nsteps=10, timestep=1.0*u.femtoseconds, collision_rate=20.0/u.picoseconds)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        """
        
        timer = Timer()
        
        # Create integrator.
        integrator = integrators.GHMCIntegrator(temperature=thermodynamic_state.temperature, collision_rate=self.collision_rate, timestep=self.timestep)

        # Random number seed.
        seed = np.random.randint(_RANDOM_SEED_MAX)
        integrator.setRandomNumberSeed(seed)

        # Create context.
        timer.start("Context Creation")
        context = sampler_state.createContext(integrator, platform=platform)
        timer.stop("Context Creation")

        # TODO: Enforce constraints?
        #tol = 1.0e-8
        #context.applyConstraints(tol)
        #context.applyVelocityConstraints(tol)

        # Run dynamics.
        timer.start("step()")
        integrator.step(self.nsteps)
        timer.stop("step()")
        
        # Get updated sampler state.
        timer.start("update_sampler_state")
        updated_sampler_state = SamplerState.createFromContext(context)
        timer.start("update_sampler_state")
        
        # Accumulate acceptance statistics.
        ghmc_global_variables = { integrator.getGlobalVariableName(index) : index for index in range(integrator.getNumGlobalVariables()) }
        naccepted = integrator.getGlobalVariable(ghmc_global_variables['naccept'])
        nattempted = integrator.getGlobalVariable(ghmc_global_variables['ntrials'])
        self.naccepted += naccepted
        self.nattempted += nattempted

        # DEBUG.
        #print "  GHMC accepted %d / %d (%.1f%%)" % (naccepted, nattempted, float(naccepted) / float(nattempted) * 100.0)

        # Clean up.
        del context
        
        timer.report_timing()
        
        return updated_sampler_state
示例#4
0
文件: mcmc.py 项目: swails/repex
    def apply(self, thermodynamic_state, sampler_state, platform=None):
        """
        Apply the Langevin dynamics MCMC move.

        Parameters
        ----------
        thermodynamic_state : ThermodynamicState
           The thermodynamic state to use when applying the MCMC move
        sampler_state : SamplerState
           The sampler state to apply the move to
        platform : simtk.openmm.Platform, optional, default = None
           If not None, the specified platform will be used.

        Returns
        -------
        updated_sampler_state : SamplerState
           The updated sampler state

        Examples
        --------

        Alanine dipeptide in vacuum.

        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
        >>> # Create a LangevinDynamicsMove
        >>> move = LangevinDynamicsMove(nsteps=10, timestep=0.5*u.femtoseconds, collision_rate=20.0/u.picoseconds)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        Ideal gas.

        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.IdealGas()
        >>> # Add a MonteCarloBarostat.
        >>> barostat = mm.MonteCarloBarostat(1*u.atmospheres, 298*u.kelvin, 25)
        >>> force_index = test.system.addForce(barostat)
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
        >>> # Create a LangevinDynamicsMove
        >>> move = LangevinDynamicsMove(nsteps=500, timestep=0.5*u.femtoseconds, collision_rate=20.0/u.picoseconds)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        """

        timer = Timer()
        
        # Check if the system contains a barostat.
        system = sampler_state.system
        forces = { system.getForce(index).__class__.__name__ : system.getForce(index) for index in range(system.getNumForces()) }
        barostat = None
        if 'MonteCarloBarostat' in forces:
            barostat = forces['MonteCarloBarostat']
            barostat.setTemperature(thermodynamic_state.temperature)            
            parameter_name = barostat.Pressure()

        # Create integrator.
        integrator = mm.LangevinIntegrator(thermodynamic_state.temperature, self.collision_rate, self.timestep)

        # Random number seed.
        seed = np.random.randint(_RANDOM_SEED_MAX)
        integrator.setRandomNumberSeed(seed)

        # Create context.
        timer.start("Context Creation")
        context = sampler_state.createContext(integrator, platform=platform)
        timer.stop("Context Creation")
        logger.debug("LangevinDynamicMove: Context created, platform is %s" % context.getPlatform().getName())

        # Set pressure, if barostat is included.
        if barostat is not None:
            context.setParameter(parameter_name, thermodynamic_state.pressure)

        if self.reassign_velocities:
            # Assign Maxwell-Boltzmann velocities.        
            context.setVelocitiesToTemperature(thermodynamic_state.temperature)
        
        # Run dynamics.
        timer.start("step()")
        integrator.step(self.nsteps)
        timer.stop("step()")

        # Get updated sampler state.
        timer.start("update_sampler_state")
        updated_sampler_state = SamplerState.createFromContext(context)
        timer.start("update_sampler_state")

        # Clean up.
        del context

        timer.report_timing()

        return updated_sampler_state
示例#5
0
文件: mcmc.py 项目: swails/repex
    def apply(self, thermodynamic_state, sampler_state, platform=None):
        """
        Apply the MCMC move.

        Parameters
        ----------
        thermodynamic_state : ThermodynamicState
           The thermodynamic state to use when applying the MCMC move
        sampler_state : SamplerState
           The sampler state to apply the move to
        platform : simtk.openmm.Platform, optional, default = None
           If not None, the specified platform will be used.

        Returns
        -------
        updated_sampler_state : SamplerState
           The updated sampler state

        Examples
        --------

        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.LennardJonesFluid()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions, box_vectors=test.system.getDefaultPeriodicBoxVectors())
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin, pressure=1*u.atmospheres)
        >>> # Create a Monte Carlo Barostat move.
        >>> move = MonteCarloBarostatMove(nattempts=5)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        """
        
        timer = Timer()

        # Make sure system contains a barostat.
        system = sampler_state.system
        forces = { system.getForce(index).__class__.__name__ : system.getForce(index) for index in range(system.getNumForces()) }
        old_barostat_frequency = None
        if 'MonteCarloBarostat' in forces:
            force = forces['MonteCarloBarostat']
            force.setTemperature(thermodynamic_state.temperature)            
            old_barostat_frequency = force.getFrequency()
            force.setFrequency(1)
            parameter_name = force.Pressure()
        else:
            # Add MonteCarloBarostat.
            force = mm.MonteCarloBarostat(thermodynamic_state.pressure, thermodynamic_state.temperature, 1)
            system.addForce(force)
            parameter_name = force.Pressure()

        # Create integrator.
        integrator = integrators.DummyIntegrator()

        # Random number seed.
        seed = np.random.randint(_RANDOM_SEED_MAX)
        force.setRandomNumberSeed(seed)

        # Create context.
        timer.start("Context Creation")
        context = sampler_state.createContext(integrator, platform=platform)
        timer.stop("Context Creation")

        # Set pressure.
        context.setParameter(parameter_name, thermodynamic_state.pressure)

        # Run update.
        # Note that ONE step of this integrator is equal to self.nsteps of velocity Verlet dynamics followed by Metropolis accept/reject.
        timer.start("step(1)")
        integrator.step(self.nattempts)
        timer.stop("step(1)")
        
        # Get sampler state.
        timer.start("update_sampler_state")
        updated_sampler_state = SamplerState.createFromContext(context)
        timer.stop("update_sampler_state")

        # DEBUG
        #print thermodynamics.volume(updated_sampler_state.box_vectors)
        
        # Clean up.
        del context

        # Restore frequency of barostat.
        if old_barostat_frequency:
            force.setFrequency(old_barostat_frequency)

        timer.report_timing()

        # Return updated sampler state.
        return updated_sampler_state
示例#6
0
文件: mcmc.py 项目: swails/repex
    def apply(self, thermodynamic_state, sampler_state, platform=None):
        """
        Apply the MCMC move.

        Parameters
        ----------
        thermodynamic_state : ThermodynamicState
           The thermodynamic state to use when applying the MCMC move
        sampler_state : SamplerState
           The sampler state to apply the move to
        platform : simtk.openmm.Platform, optional, default = None
           If not None, the specified platform will be used.

        Returns
        -------
        updated_sampler_state : SamplerState
           The updated sampler state

        Examples
        --------
        
        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
        >>> # Create an HMC move.
        >>> move = HMCMove(nsteps=10, timestep=0.5*u.femtoseconds)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        """
        
        timer = Timer()

        # Create integrator.
        integrator = integrators.HMCIntegrator(temperature=thermodynamic_state.temperature, timestep=self.timestep, nsteps=self.nsteps)

        # Random number seed.
        seed = np.random.randint(_RANDOM_SEED_MAX)
        integrator.setRandomNumberSeed(seed)

        # Create context.
        timer.start("Context Creation")
        context = sampler_state.createContext(integrator, platform=platform)
        timer.stop("Context Creation")

        # Run dynamics.
        # Note that ONE step of this integrator is equal to self.nsteps of velocity Verlet dynamics followed by Metropolis accept/reject.
        timer.start("HMC integration")
        integrator.step(1)
        timer.stop("HMC integration")
        
        # Get sampler state.
        timer.start("updated_sampler_state")
        updated_sampler_state = SamplerState.createFromContext(context)
        timer.stop("updated_sampler_state")

        # Clean up.
        del context

        timer.report_timing()
        
        # Return updated sampler state.
        return updated_sampler_state
示例#7
0
文件: mcmc.py 项目: swails/repex
    def apply(self, thermodynamic_state, sampler_state, platform=None):
        """
        Apply the GHMC MCMC move.

        Parameters
        ----------
        thermodynamic_state : ThermodynamicState
           The thermodynamic state to use when applying the MCMC move
        sampler_state : SamplerState
           The sampler state to apply the move to
        platform : simtk.openmm.Platform, optional, default = None
           If not None, the specified platform will be used.

        Returns
        -------
        updated_sampler_state : SamplerState
           The updated sampler state

        Examples
        --------
        
        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
        >>> # Create a LangevinDynamicsMove
        >>> move = GHMCMove(nsteps=10, timestep=1.0*u.femtoseconds, collision_rate=20.0/u.picoseconds)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        """

        timer = Timer()

        # Create integrator.
        integrator = integrators.GHMCIntegrator(
            temperature=thermodynamic_state.temperature,
            collision_rate=self.collision_rate,
            timestep=self.timestep)

        # Random number seed.
        seed = np.random.randint(_RANDOM_SEED_MAX)
        integrator.setRandomNumberSeed(seed)

        # Create context.
        timer.start("Context Creation")
        context = sampler_state.createContext(integrator, platform=platform)
        timer.stop("Context Creation")

        # TODO: Enforce constraints?
        #tol = 1.0e-8
        #context.applyConstraints(tol)
        #context.applyVelocityConstraints(tol)

        # Run dynamics.
        timer.start("step()")
        integrator.step(self.nsteps)
        timer.stop("step()")

        # Get updated sampler state.
        timer.start("update_sampler_state")
        updated_sampler_state = SamplerState.createFromContext(context)
        timer.start("update_sampler_state")

        # Accumulate acceptance statistics.
        ghmc_global_variables = {
            integrator.getGlobalVariableName(index): index
            for index in range(integrator.getNumGlobalVariables())
        }
        naccepted = integrator.getGlobalVariable(
            ghmc_global_variables['naccept'])
        nattempted = integrator.getGlobalVariable(
            ghmc_global_variables['ntrials'])
        self.naccepted += naccepted
        self.nattempted += nattempted

        # DEBUG.
        #print "  GHMC accepted %d / %d (%.1f%%)" % (naccepted, nattempted, float(naccepted) / float(nattempted) * 100.0)

        # Clean up.
        del context

        timer.report_timing()

        return updated_sampler_state
示例#8
0
文件: mcmc.py 项目: swails/repex
    def apply(self, thermodynamic_state, sampler_state, platform=None):
        """
        Apply the Langevin dynamics MCMC move.

        Parameters
        ----------
        thermodynamic_state : ThermodynamicState
           The thermodynamic state to use when applying the MCMC move
        sampler_state : SamplerState
           The sampler state to apply the move to
        platform : simtk.openmm.Platform, optional, default = None
           If not None, the specified platform will be used.

        Returns
        -------
        updated_sampler_state : SamplerState
           The updated sampler state

        Examples
        --------

        Alanine dipeptide in vacuum.

        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
        >>> # Create a LangevinDynamicsMove
        >>> move = LangevinDynamicsMove(nsteps=10, timestep=0.5*u.femtoseconds, collision_rate=20.0/u.picoseconds)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        Ideal gas.

        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.IdealGas()
        >>> # Add a MonteCarloBarostat.
        >>> barostat = mm.MonteCarloBarostat(1*u.atmospheres, 298*u.kelvin, 25)
        >>> force_index = test.system.addForce(barostat)
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
        >>> # Create a LangevinDynamicsMove
        >>> move = LangevinDynamicsMove(nsteps=500, timestep=0.5*u.femtoseconds, collision_rate=20.0/u.picoseconds)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        """

        timer = Timer()

        # Check if the system contains a barostat.
        system = sampler_state.system
        forces = {
            system.getForce(index).__class__.__name__: system.getForce(index)
            for index in range(system.getNumForces())
        }
        barostat = None
        if 'MonteCarloBarostat' in forces:
            barostat = forces['MonteCarloBarostat']
            barostat.setTemperature(thermodynamic_state.temperature)
            parameter_name = barostat.Pressure()

        # Create integrator.
        integrator = mm.LangevinIntegrator(thermodynamic_state.temperature,
                                           self.collision_rate, self.timestep)

        # Random number seed.
        seed = np.random.randint(_RANDOM_SEED_MAX)
        integrator.setRandomNumberSeed(seed)

        # Create context.
        timer.start("Context Creation")
        context = sampler_state.createContext(integrator, platform=platform)
        timer.stop("Context Creation")
        logger.debug("LangevinDynamicMove: Context created, platform is %s" %
                     context.getPlatform().getName())

        # Set pressure, if barostat is included.
        if barostat is not None:
            context.setParameter(parameter_name, thermodynamic_state.pressure)

        if self.reassign_velocities:
            # Assign Maxwell-Boltzmann velocities.
            context.setVelocitiesToTemperature(thermodynamic_state.temperature)

        # Run dynamics.
        timer.start("step()")
        integrator.step(self.nsteps)
        timer.stop("step()")

        # Get updated sampler state.
        timer.start("update_sampler_state")
        updated_sampler_state = SamplerState.createFromContext(context)
        timer.start("update_sampler_state")

        # Clean up.
        del context

        timer.report_timing()

        return updated_sampler_state
示例#9
0
文件: mcmc.py 项目: swails/repex
    def apply(self, thermodynamic_state, sampler_state, platform=None):
        """
        Apply the MCMC move.

        Parameters
        ----------
        thermodynamic_state : ThermodynamicState
           The thermodynamic state to use when applying the MCMC move
        sampler_state : SamplerState
           The sampler state to apply the move to
        platform : simtk.openmm.Platform, optional, default = None
           If not None, the specified platform will be used.

        Returns
        -------
        updated_sampler_state : SamplerState
           The updated sampler state

        Examples
        --------

        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.LennardJonesFluid()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions, box_vectors=test.system.getDefaultPeriodicBoxVectors())
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin, pressure=1*u.atmospheres)
        >>> # Create a Monte Carlo Barostat move.
        >>> move = MonteCarloBarostatMove(nattempts=5)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        """

        timer = Timer()

        # Make sure system contains a barostat.
        system = sampler_state.system
        forces = {
            system.getForce(index).__class__.__name__: system.getForce(index)
            for index in range(system.getNumForces())
        }
        old_barostat_frequency = None
        if 'MonteCarloBarostat' in forces:
            force = forces['MonteCarloBarostat']
            force.setTemperature(thermodynamic_state.temperature)
            old_barostat_frequency = force.getFrequency()
            force.setFrequency(1)
            parameter_name = force.Pressure()
        else:
            # Add MonteCarloBarostat.
            force = mm.MonteCarloBarostat(thermodynamic_state.pressure,
                                          thermodynamic_state.temperature, 1)
            system.addForce(force)
            parameter_name = force.Pressure()

        # Create integrator.
        integrator = integrators.DummyIntegrator()

        # Random number seed.
        seed = np.random.randint(_RANDOM_SEED_MAX)
        force.setRandomNumberSeed(seed)

        # Create context.
        timer.start("Context Creation")
        context = sampler_state.createContext(integrator, platform=platform)
        timer.stop("Context Creation")

        # Set pressure.
        context.setParameter(parameter_name, thermodynamic_state.pressure)

        # Run update.
        # Note that ONE step of this integrator is equal to self.nsteps of velocity Verlet dynamics followed by Metropolis accept/reject.
        timer.start("step(1)")
        integrator.step(self.nattempts)
        timer.stop("step(1)")

        # Get sampler state.
        timer.start("update_sampler_state")
        updated_sampler_state = SamplerState.createFromContext(context)
        timer.stop("update_sampler_state")

        # DEBUG
        #print thermodynamics.volume(updated_sampler_state.box_vectors)

        # Clean up.
        del context

        # Restore frequency of barostat.
        if old_barostat_frequency:
            force.setFrequency(old_barostat_frequency)

        timer.report_timing()

        # Return updated sampler state.
        return updated_sampler_state
示例#10
0
文件: mcmc.py 项目: swails/repex
    def apply(self, thermodynamic_state, sampler_state, platform=None):
        """
        Apply the MCMC move.

        Parameters
        ----------
        thermodynamic_state : ThermodynamicState
           The thermodynamic state to use when applying the MCMC move
        sampler_state : SamplerState
           The sampler state to apply the move to
        platform : simtk.openmm.Platform, optional, default = None
           If not None, the specified platform will be used.

        Returns
        -------
        updated_sampler_state : SamplerState
           The updated sampler state

        Examples
        --------
        
        >>> # Create a test system
        >>> import testsystems
        >>> test = testsystems.AlanineDipeptideVacuum()
        >>> # Create a sampler state.
        >>> sampler_state = SamplerState(system=test.system, positions=test.positions)
        >>> # Create a thermodynamic state.
        >>> from thermodynamics import ThermodynamicState
        >>> thermodynamic_state = ThermodynamicState(system=test.system, temperature=298*u.kelvin)
        >>> # Create an HMC move.
        >>> move = HMCMove(nsteps=10, timestep=0.5*u.femtoseconds)
        >>> # Perform one update of the sampler state.
        >>> updated_sampler_state = move.apply(thermodynamic_state, sampler_state)

        """

        timer = Timer()

        # Create integrator.
        integrator = integrators.HMCIntegrator(
            temperature=thermodynamic_state.temperature,
            timestep=self.timestep,
            nsteps=self.nsteps)

        # Random number seed.
        seed = np.random.randint(_RANDOM_SEED_MAX)
        integrator.setRandomNumberSeed(seed)

        # Create context.
        timer.start("Context Creation")
        context = sampler_state.createContext(integrator, platform=platform)
        timer.stop("Context Creation")

        # Run dynamics.
        # Note that ONE step of this integrator is equal to self.nsteps of velocity Verlet dynamics followed by Metropolis accept/reject.
        timer.start("HMC integration")
        integrator.step(1)
        timer.stop("HMC integration")

        # Get sampler state.
        timer.start("updated_sampler_state")
        updated_sampler_state = SamplerState.createFromContext(context)
        timer.stop("updated_sampler_state")

        # Clean up.
        del context

        timer.report_timing()

        # Return updated sampler state.
        return updated_sampler_state