def pre_we(self):
starttime = time.time()
segments = self.sim_manager.segments.values()
bin_mapper = self.system.bin_mapper
self.find_mappers()
# For now, assume one wexploreMapper
wexploreMapper = self.wexploreMappers[0]['base_mapper']
final_pcoords = np.empty((len(segments), self.system.pcoord_ndim), dtype=self.system.pcoord_dtype)
for iseg, segment in enumerate(segments):
final_pcoords[iseg] = segment.pcoord[-1,:]
hash_init = wexploreMapper.last_graph
kwargs = {'add_bins': True, 'n_regions': self.system.n_regions}
assignments = bin_mapper.assign(final_pcoords, **kwargs)
# Re-assign segments to new bins if bin_mapper changes
if wexploreMapper.last_graph != hash_init:
# The mapper has updated; force an update to the system mapper.
bin_mapper.refresh_mappers()
self.target_counts()
# Reset we_driver internal data structures. This includes sending in the target states,
# as the bins have changed (we also need to feed in the initial states).
target_states = []
tstates = self.system.tstates
tstates_strio = cStringIO.StringIO('\n'.join(tstates).replace(',', ' '))
target_states.extend(TargetState.states_from_file(tstates_strio, self.system.pcoord_dtype))
initial_states = []
self.data_manager.save_target_states(target_states)
#self.sim_manager.report_target_states(target_states)
for key,value in self.we_driver.avail_initial_states.iteritems():
initial_states.append(value)
self.we_driver.new_iteration(target_states=target_states, initial_states=initial_states)
# Re-assign segments
self.we_driver.assign(segments)
# Reset target counts to account for new iteration.
self.target_counts(coords=final_pcoords, startup=False)
endtime = time.time()
# Report level statistics
s = 1
westpa.rc.pstatus('--wexplore-stats--------------------')
westpa.rc.pstatus('wallclock time: {:.3f} s'.format(endtime - starttime))
westpa.rc.pstatus('')
for li, level in enumerate(wexploreMapper.level_indices):
s *= wexploreMapper.n_regions[li]
westpa.rc.pstatus('Level {}: {} cells ({} max)'.format(li, len(level), s))
westpa.rc.pstatus('------------------------------------')
westpa.rc.pflush()
system = westpa.rc.get_system_driver()
sim_manager = westpa.rc.get_sim_manager()
propagator = westpa.rc.get_propagator()
data_manager = westpa.rc.get_data_manager()
h5file = data_manager.we_h5filename
data_manager.system = system
we_driver = westpa.rc.get_we_driver()
with work_manager:
if work_manager.is_master:
# Process target states
target_states = []
if args.tstate_file:
target_states.extend(TargetState.states_from_file(args.tstate_file, system.pcoord_dtype))
if args.tstates:
tstates_strio = cStringIO.StringIO('\n'.join(args.tstates).replace(',', ' '))
target_states.extend(TargetState.states_from_file(tstates_strio, system.pcoord_dtype))
del tstates_strio
# Process basis states
basis_states = []
if args.bstate_file:
basis_states.extend(BasisState.states_from_file(args.bstate_file))
if args.bstates:
for bstate_str in args.bstates:
fields = bstate_str.split(',')
label=fields[0]
probability=float(fields[1])
try:
system = westpa.rc.get_system_driver()
sim_manager = westpa.rc.get_sim_manager()
propagator = westpa.rc.get_propagator()
data_manager = westpa.rc.get_data_manager()
h5file = data_manager.we_h5filename
data_manager.system = system
we_driver = westpa.rc.get_we_driver()
with work_manager:
if work_manager.is_master:
# Process target states
target_states = []
if args.tstate_file:
target_states.extend(
TargetState.states_from_file(args.tstate_file,
system.pcoord_dtype))
if args.tstates:
tstates_strio = io.StringIO('\n'.join(args.tstates).replace(
',', ' '))
target_states.extend(
TargetState.states_from_file(tstates_strio,
system.pcoord_dtype))
del tstates_strio
# Process basis states
basis_states = []
if args.bstate_file:
basis_states.extend(BasisState.states_from_file(args.bstate_file))
if args.bstates:
for bstate_str in args.bstates:
fields = bstate_str.split(',')
tprob = sum(bstate.probability for bstate in basis_states)
if abs(1.0 - tprob) > len(basis_states) * EPS:
pscale = 1/tprob
log.warning('Basis state probabilities do not add to unity; rescaling by {:g}'.format(pscale))
for bstate in basis_states:
bstate.probability *= pscale
# Assign progress coordinates to basis states
sim_manager.get_bstate_pcoords(basis_states, n_iter)
data_manager.create_ibstate_group(basis_states, n_iter)
sim_manager.report_basis_states(basis_states)
# Now handle target states
target_states = []
if args.tstate_file:
target_states.extend(TargetState.states_from_file(args.tstate_file, system.pcoord_dtype))
if args.tstates:
tstates_strio = io.StringIO('\n'.join(args.tstates).replace(',', ' '))
target_states.extend(TargetState.states_from_file(tstates_strio, system.pcoord_dtype))
del tstates_strio
if not target_states:
westpa.rc.pstatus('No target states specified.')
else:
data_manager.save_target_states(target_states, n_iter)
sim_manager.report_target_states(target_states)
data_manager.update_iter_group_links(n_iter)
else: # args.mode == 'append'
if args.bstate_file or args.bstates:
