dcd = app.DCDFile(file=dcdfile, topology=topology, dt=timestep)
# The actual simulation
k = 0
for iteration in range(args.iterations):
# Propagate configurations and salt concentrations
t0 = time()
langevin.step(args.steps)
if not args.fix_salt:
salinator.update(nattempts=1)
iter_time = time() - t0
if iteration % args.save_freq == 0:
# Record the simulation data
Record.record_netcdf(ncfile,
context,
salinator.swapper,
k,
attempt=0,
sync=False)
ncfile.groups['Sample state data']['time'][k] = iter_time
ncfile.sync()
if args.save_configs:
# Record the simulation configurations
state = context.getState(getPositions=True,
enforcePeriodicBox=True)
positions = state.getPositions(asNumpy=True)
box_vectors = state.getPeriodicBoxVectors()
dcd.writeModel(positions=positions,
periodicBoxVectors=box_vectors)
k += 1
# Update SAMS estimator
nwater, ncation, nanion = mcdriver.get_identity_counts()
noisy = np.zeros(args.saltmax + 1)
noisy[ncation] = 1
state_counts[ncation] += 1
bias = adaptor.update(state=ncation,
noisy_observation=noisy,
histogram=state_counts)
# Save data
if iteration % args.save_freq == 0:
# Record the simulation data
Record.record_netcdf(ncfile,
context,
mcdriver,
k,
attempt=0,
sync=False)
ncfile.groups['Sample state data']['sams bias'][k, :] = bias
ncfile.sync()
if args.save_configs:
# Record the simulation configurations
state = context.getState(getPositions=True,
enforcePeriodicBox=True)
positions = state.getPositions(asNumpy=True)
box_vectors = state.getPeriodicBoxVectors()
dcd.writeModel(positions=positions,
periodicBoxVectors=box_vectors)
k += 1
dcdfile = open(args.out + '.dcd', 'wb')
dcd = app.DCDFile(file=dcdfile, topology=wbox.topology, dt=timestep)
# The actual simulation
k = 0
for iteration in range(args.iterations):
# Propagate configurations and salt concentrations, and update SAMS bias.
langevin.step(args.steps)
sams_salinator.update()
# Save data
if iteration % args.save_freq == 0:
# Record the simulation data
Record.record_netcdf(ncfile,
context,
sams_salinator.swapper,
k,
attempt=0,
sams_bias=sams_salinator.bias,
sync=True)
if args.save_configs:
# Record the simulation configurations
state = context.getState(getPositions=True,
enforcePeriodicBox=True)
positions = state.getPositions(asNumpy=True)
box_vectors = state.getPeriodicBoxVectors()
dcd.writeModel(positions=positions,
periodicBoxVectors=box_vectors)
k += 1