def generateTrajectory(self, x0, nframes):
"""
Generate a velocity Verlet trajectory consisting of ntau segments of tau_steps in between storage of Snapshots and randomization of velocities.
ARGUMENTS
x0 (coordinate set) - initial coordinates; velocities will be assigned from Maxwell-Boltzmann distribution
nframes (int) - number of trajectory segments to generate
RETURNS
trajectory (list of Snapshot) - generated trajectory of initial conditions, including initial coordinate set
NOTES
This exists in OpenMM. Check with John on how to best get snapshots
This routine generates a velocity Verlet trajectory for systems without constraints by wrapping the OpenMM 'VerletIntegrator' in two half-kicks of the velocity.
"""
# Set initial positions
self.context.setPositions(x0)
# Store initial state for each trajectory segment in trajectory.
trajectory = Trajectory()
# Construct mass vector.
nparticles = self.system.getNumParticles()
mass = Quantity(numpy.zeros([nparticles, 3], numpy.float64), amu)
for particle_index in range(nparticles):
mass[particle_index, :] = self.system.getParticleMass(particle_index)
# Assign velocities from Maxwell-Boltzmann distribution
self.context.setVelocitiesToTemperature(self.temperature)
# Store initial snapshot of trajectory segment.
snapshot = Snapshot(context=self.context)
trajectory.forward(snapshot)
# Propagate dynamics by velocity Verlet.
in_void = True
self.frame = 0
while self.frame < self.xframes and in_void == True:
# Do integrator x steps
self.integrator.step()
# Check if reached a core set
in_void = self.check_void()
# Store final snapshot of trajectory.
snapshot = Snapshot(self.context)
trajectory.forward(snapshot)
return trajectory
def split_into_connections(self, traj):
c, i, d = self.assign_trajectory(traj)
l_traj = []
traj_mode = 0
t = Trajectory()
first = None
for index, snapshot in enumerate(traj):
if (c[index] != -1 and i[index]==0 and traj_mode == 0):
# core set
first = snapshot
elif (i[index] != 0 and first is not None):
# in void
t.forward(snapshot)
traj_mode = 1
elif (c[index] != -1 and i[index]==0 and traj_mode == 1):
t.insert(0, first)
t.forward(snapshot)
l_traj.forward(t)
t = Trajectory()
first = snapshot
traj_mode = 0
return l_traj
def _resume_from_netcdf(self):
"""
Resume execution by reading current positions and energies from a NetCDF file.
"""
# Open NetCDF file for reading
# ncfile = netcdf.NetCDFFile(self.store_filename, 'r') # for Scientific.IO.NetCDF
ncfile = netcdf.Dataset(self.store_filename, "r") # for netCDF4
# TODO: Perform sanity check on file before resuming
# Get current dimensions.
self.iteration = ncfile.variables["activities"].shape[0] - 1
self.nstates = ncfile.variables["activities"].shape[1]
self.n_frames = ncfile.variables["trajectory_coordinates"].shape[1]
self.natoms = ncfile.variables["trajectory_coordinates"].shape[2]
print "iteration = %d, nstates = %d, natoms = %d" % (self.iteration, self.nstates, self.natoms)
# Restore trajectories.
self.trajectories = list()
for replica_index in range(self.nstates):
trajectory = Trajectory()
for frame_index in range(self.n_frames):
x = (
ncfile.variables["trajectory_coordinates"][replica_index, frame_index, :, :]
.astype(numpy.float32)
.copy()
)
coordinates = Quantity(x, nanometers)
v = (
ncfile.variables["trajectory_velocities"][replica_index, frame_index, :, :]
.astype(numpy.float32)
.copy()
)
velocities = Quantity(v, nanometers / picoseconds)
V = ncfile.variables["trajectory_potential"][replica_index, frame_index]
potential_energy = Quantity(V, kilojoules_per_mole)
T = ncfile.variables["trajectory_kinetic"][replica_index, frame_index]
kinetic_energy = Quantity(T, kilojoules_per_mole)
snapshot = Snapshot(
coordinates=coordinates,
velocities=velocities,
kinetic_energy=kinetic_energy,
potential_energy=potential_energy,
)
trajectory.forward(snapshot)
self.trajectories.forward(trajectory)
# Restore state information.
self.replica_states = ncfile.variables["states"][self.iteration, :].copy()
# Restore log probabilities.
print "Reading log probabilities..." # DEBUG
print self.log_P_kl # DEBUG
self.log_P_kl = ncfile.variables["log_probabilities"][self.iteration, :, :]
print self.log_P_kl # DEBUG
# Restore activities
for replica_index in range(self.nstates):
state_index = self.replica_states[replica_index]
K_reduced_unit = self.ensembles[state_index].K_reduced_unit
K = ncfile.variables["activities"][self.iteration, replica_index]
self.activities[replica_index] = K * K_reduced_unit
# Restore path Hamiltonians
for replica_index in range(self.nstates):
state_index = self.replica_states[replica_index]
H_reduced_unit = self.ensembles[state_index].H_reduced_unit
H = ncfile.variables["path_hamiltonians"][self.iteration, replica_index]
self.path_hamiltonians[replica_index] = H * H_reduced_unit
# Close NetCDF file.
ncfile.close()
# Reopen NetCDF file for appending, and maintain handle.
# self.ncfile = netcdf.NetCDFFile(self.store_filename, 'a') # for Scientific.IO.NetCDF
self.ncfile = netcdf.Dataset(self.store_filename, "a") # for netCDF4
# DEBUG: Set number of iterations to be a bit more than we've done.
# self.number_of_iterations = self.iteration + 50
return