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misc.py
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import numpy
from rexfw import Parcel
from rexfw.proposers import LMDRENSProposer, AMDRENSProposer, ParamInterpolationPDF, HMCStepRENSProposer
from rexfw.replicas import Replica
from csb.statistics.samplers import State
class GeneralTrajectory(list):
def __init__(self, items, work=0.0, heat=0.0, delta_Epot=0.0, delta_Ekin=0.0):
super(GeneralTrajectory, self).__init__(items)
self.work = work
self.heat = heat
self.delta_Epot = delta_Epot
self.delta_Ekin = delta_Ekin
class TrajDumpLMDRENSProposer(LMDRENSProposer):
def propose(self, local_replica, partner_state, partner_energy, params):
pdf = self._pdf_factory(local_replica, params)
propagator = self._propagator_factory(pdf, params)
ps_pos = partner_state.position
traj = propagator.generate(State(ps_pos, numpy.random.normal(size=ps_pos.shape)), params.n_steps, True)
traj.work = self._calculate_work(local_replica, partner_energy, traj)
E_remote = partner_energy
E_local = -local_replica.pdf.log_prob(traj.final.position)
deltaE = (E_local - E_remote) + 0.5 * numpy.sum(traj.final.momentum ** 2) - 0.5 * numpy.sum(traj.initial.momentum ** 2)
traj = GeneralTrajectory([traj.initial, traj[len(traj)/2], traj.final],
work=traj.work, heat=traj.heat,
delta_Epot=E_local - E_remote,
delta_Ekin=.5*numpy.sum(traj.final.momentum**2)-.5*numpy.sum(traj.initial.momentum**2))
return traj
class TrajDumpAMDRENSProposer(AMDRENSProposer):
def propose(self, local_replica, partner_state, partner_energy, params):
pdf = self._pdf_factory(local_replica, params)
propagator = self._propagator_factory(pdf, params)
ps_pos = partner_state.position
traj = propagator.generate(State(ps_pos, numpy.random.normal(size=ps_pos.shape)), params.n_steps, True)
traj.work = self._calculate_work(local_replica, partner_energy, traj)
E_remote = partner_energy
E_local = -local_replica.pdf.log_prob(traj.final.position)
deltaE = (E_local - E_remote) + 0.5 * numpy.sum(traj.final.momentum ** 2) - 0.5 * numpy.sum(traj.initial.momentum ** 2)
traj = GeneralTrajectory([traj.initial, traj[len(traj)/2], traj.final],
work=traj.work, heat=traj.heat,
delta_Epot=E_local - E_remote, delta_Ekin=0.5 * numpy.sum(traj.final.momentum ** 2) - 0.5 * numpy.sum(traj.initial.momentum ** 2))
return traj
class TrajDumpHMCStepRENSProposer(HMCStepRENSProposer):
def propose(self, local_replica, partner_state, partner_energy, params):
pdf = self._pdf_factory(local_replica, params)
n_steps = params.n_steps
propagator = self._propagator_factory(local_replica.pdf, params)
ps_pos = partner_state.position
traj = propagator.generate(State(ps_pos), return_trajectory=True)
E_remote = partner_energy
E_local = -local_replica.pdf.log_prob(traj.final.position)
deltaE = (E_local - E_remote)
traj = GeneralTrajectory([traj.initial, traj[len(traj)/2], traj.final], work=traj.work, heat=traj.heat, delta_Epot=deltaE)
return traj
class TrajDumpReplica(Replica):
def _propose(self, request):
partner_name = request.partner
params = request.params
proposer_params = params.proposer_params
self._current_master = request.sender
proposer = list(set(self.proposers.keys()).intersection(set(params.proposers)))[-1]
self.proposers[proposer].partner_name = partner_name
proposal = self.proposers[proposer].propose(self,
self._buffered_partner_state,
self._buffered_partner_energy,
proposer_params)
self._comm.send(Parcel(self.name, self._current_master, proposal),
self._current_master)
self._buffered_proposal = proposal[-1]