def test_recycle(self):
segments = [
self.segment(0.0, 1.5, weight=0.5),
self.segment(0.0, 0.5, weight=0.5)
]
tstate = TargetState('recycle', [1.5], 0)
istate = InitialState(0, 0, 0, pcoord=[0.0])
self.we_driver.new_iteration(initial_states=[istate],
target_states=[tstate])
n_needed = self.we_driver.assign(segments)
assert n_needed == 0
self.we_driver.construct_next()
n_recycled = len(list(self.we_driver.recycling_segments))
assert n_recycled == 1
assert len(self.we_driver.next_iter_binning[0]) == 4
assert len(self.we_driver.next_iter_binning[1]) == 0
assert abs(
sum(seg.weight for seg in self.we_driver.next_iter_binning[0]) -
1.0) < 4 * EPS
assert numpy.allclose(
[seg.weight for seg in self.we_driver.next_iter_binning[0]],
[0.25 for _i in xrange(4)])
assert segments[0].endpoint_type == Segment.SEG_ENDPOINT_RECYCLED
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(',')
n_iter = data_manager.current_iteration
assert args.mode in ('show', 'replace', 'append')
if args.mode == 'show':
basis_states = data_manager.get_basis_states(n_iter)
if basis_states:
bstate_file = sys.stdout if not args.bstate_file else open(args.bstate_file, 'wt')
bstate_file.write('# Basis states for iteration {:d}\n'.format(n_iter))
BasisState.states_to_file(basis_states, bstate_file)
target_states = data_manager.get_target_states(n_iter)
if target_states:
tstate_file = sys.stdout if not args.tstate_file else open(args.tstate_file, 'wt')
tstate_file.write('# Target states for iteration {:d}\n'.format(n_iter))
TargetState.states_to_file(target_states, tstate_file)
elif args.mode == 'replace':
seg_index = data_manager.get_seg_index(n_iter)
if (seg_index['status'] == Segment.SEG_STATUS_COMPLETE).any():
print('Iteration {:d} has completed segments; applying new states to iteration {:d}'.format(n_iter,n_iter+1))
n_iter += 1
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])
