westpa 2022.12__cp312-cp312-macosx_10_13_x86_64.whl

westpa/core/we_driver.py

@@ -0,0 +1,910 @@
+import logging
+import math
+import operator
+
+import numpy as np
+from numpy.random import Generator, MT19937
+
+import westpa
+from .segment import Segment
+from .states import InitialState
+
+log = logging.getLogger(__name__)
+
+
+def _group_walkers_identity(we_driver, ibin, **kwargs):
+    log.debug('using we_driver._group_walkers_identity')
+    bin_set = we_driver.next_iter_binning[ibin]
+    list_bins = [set()]
+    for i in bin_set:
+        list_bins[0].add(i)
+    return list_bins
+
+
+class ConsistencyError(RuntimeError):
+    pass
+
+
+class AccuracyError(RuntimeError):
+    pass
+
+
+class NewWeightEntry:
+    NW_SOURCE_RECYCLED = 0
+
+    def __init__(
+        self,
+        source_type,
+        weight,
+        prev_seg_id=None,
+        prev_init_pcoord=None,
+        prev_final_pcoord=None,
+        new_init_pcoord=None,
+        target_state_id=None,
+        initial_state_id=None,
+    ):
+        self.source_type = source_type
+        self.weight = weight
+        self.prev_seg_id = prev_seg_id
+        self.prev_init_pcoord = np.asarray(prev_init_pcoord) if prev_init_pcoord is not None else None
+        self.prev_final_pcoord = np.asarray(prev_final_pcoord) if prev_final_pcoord is not None else None
+        self.new_init_pcoord = np.asarray(new_init_pcoord) if new_init_pcoord is not None else None
+        self.target_state_id = target_state_id
+        self.initial_state_id = initial_state_id
+
+    def __repr__(self):
+        return '<{} object at 0x{:x}: weight={self.weight:g} target_state_id={self.target_state_id} prev_final_pcoord={self.prev_final_pcoord}>'.format(
+            self.__class__.__name__, id(self), self=self
+        )
+
+
+class WEDriver:
+    '''A class implemented Huber & Kim's weighted ensemble algorithm over Segment objects.
+    This class handles all binning, recycling, and preparation of new Segment objects for the
+    next iteration. Binning is accomplished using system.bin_mapper, and per-bin target counts
+    are from system.bin_target_counts.
+
+    The workflow is as follows:
+
+      1) Call `new_iteration()` every new iteration, providing any recycling targets that are
+         in force and any available initial states for recycling.
+      2) Call `assign()` to assign segments to bins based on their initial and end points. This
+         returns the number of walkers that were recycled.
+      3) Call `run_we()`, optionally providing a set of initial states that will be used to
+         recycle walkers.
+
+    Note the presence of flux_matrix, transition_matrix,
+    current_iter_segments, next_iter_segments, recycling_segments,
+    initial_binning, final_binning, next_iter_binning, and new_weights (to be documented soon).
+    '''
+
+    weight_split_threshold = 2.0
+    weight_merge_cutoff = 1.0
+    largest_allowed_weight = 1.0
+    smallest_allowed_weight = 1e-310
+
+    def __init__(self, rc=None, system=None):
+        self.rc = rc or westpa.rc
+        self.system = system or self.rc.get_system_driver()
+
+        # Whether to adjust counts to exactly match target count
+        self.do_adjust_counts = True
+
+        # bin mapper and per-bin target counts (see new_iteration for initialization)
+        self.bin_mapper = None
+        self.bin_target_counts = None
+
+        # Mapping of bin index to target state
+        self.target_states = None
+
+        # binning on initial points
+        self.initial_binning = None
+
+        # binning on final points (pre-WE)
+        self.final_binning = None
+
+        # binning on initial points for next iteration
+        self.next_iter_binning = None
+
+        # Flux and rate matrices for the current iteration
+        self.flux_matrix = None
+        self.transition_matrix = None
+
+        # Information on new weights (e.g. from recycling) for the next iteration
+        self.new_weights = None
+
+        # Set of initial states passed to run_we() that are actually used for
+        # recycling targets
+        self.used_initial_states = None
+
+        self.avail_initial_states = None
+
+        self.rng = Generator(MT19937())
+
+        # Make property for subgrouping function.
+        self.subgroup_function = _group_walkers_identity
+        self.subgroup_function_kwargs = {}
+
+        self.process_config()
+        self.check_threshold_configs()
+
+    def process_config(self):
+        config = self.rc.config
+
+        config.require_type_if_present(['west', 'we', 'adjust_counts'], bool)
+
+        config.require_type_if_present(['west', 'we', 'thresholds'], bool)
+
+        self.do_adjust_counts = config.get(['west', 'we', 'adjust_counts'], True)
+        log.info('Adjust counts to exactly match target_counts: {}'.format(self.do_adjust_counts))
+
+        self.do_thresholds = config.get(['west', 'we', 'thresholds'], True)
+        log.info('Obey abolute weight thresholds: {}'.format(self.do_thresholds))
+
+        self.weight_split_threshold = config.get(['west', 'we', 'weight_split_threshold'], self.weight_split_threshold)
+        log.info('Split threshold: {}'.format(self.weight_split_threshold))
+
+        self.weight_merge_cutoff = config.get(['west', 'we', 'weight_merge_cutoff'], self.weight_merge_cutoff)
+        log.info('Merge cutoff: {}'.format(self.weight_merge_cutoff))
+
+        self.largest_allowed_weight = config.get(['west', 'we', 'largest_allowed_weight'], self.largest_allowed_weight)
+        log.info('Largest allowed weight: {}'.format(self.largest_allowed_weight))
+
+        self.smallest_allowed_weight = config.get(['west', 'we', 'smallest_allowed_weight'], self.smallest_allowed_weight)
+        log.info('Smallest allowed_weight: {}'.format(self.smallest_allowed_weight))
+
+    @property
+    def next_iter_segments(self):
+        '''Newly-created segments for the next iteration'''
+        if self.next_iter_binning is None:
+            raise RuntimeError('cannot access next iteration segments before running WE')
+
+        for _bin in self.next_iter_binning:
+            for walker in _bin:
+                yield walker
+
+    @property
+    def current_iter_segments(self):
+        '''Segments for the current iteration'''
+        for _bin in self.final_binning:
+            for walker in _bin:
+                yield walker
+
+    @property
+    def next_iter_assignments(self):
+        '''Bin assignments (indices) for initial points of next iteration.'''
+        if self.next_iter_binning is None:
+            raise RuntimeError('cannot access next iteration segments before running WE')
+
+        for ibin, _bin in enumerate(self.next_iter_binning):
+            for _walker in _bin:
+                yield ibin
+
+    @property
+    def current_iter_assignments(self):
+        '''Bin assignments (indices) for endpoints of current iteration.'''
+        for ibin, _bin in enumerate(self.final_binning):
+            for walker in _bin:
+                yield ibin
+
+    @property
+    def recycling_segments(self):
+        '''Segments designated for recycling'''
+        if len(self.target_states):
+            for ibin, tstate in self.target_states.items():
+                for segment in self.final_binning[ibin]:
+                    yield segment
+        else:
+            return
+
+    @property
+    def n_recycled_segs(self):
+        '''Number of segments recycled this iteration'''
+        count = 0
+        for _segment in self.recycling_segments:
+            count += 1
+        return count
+
+    @property
+    def n_istates_needed(self):
+        '''Number of initial states needed to support recycling for this iteration'''
+        n_istates_avail = len(self.avail_initial_states)
+        return max(0, self.n_recycled_segs - n_istates_avail)
+
+    def check_threshold_configs(self):
+        '''Check to see if weight thresholds parameters are valid'''
+        if (not np.issubdtype(type(self.largest_allowed_weight), np.floating)) or (
+            not np.issubdtype(type(self.smallest_allowed_weight), np.floating)
+        ):
+            try:
+                # Trying to self correct
+                self.largest_allowed_weight = float(self.largest_allowed_weight)
+                self.smallest_allowed_weight = float(self.smallest_allowed_weight)
+            except ValueError:
+                # Generate error saying thresholds are invalid
+                raise ValueError("Invalid weight thresholds specified. Please check your west.cfg.")
+
+        if np.isclose(self.largest_allowed_weight, self.smallest_allowed_weight):
+            raise ValueError("Weight threshold bounds cannot be identical.")
+        elif self.largest_allowed_weight < self.smallest_allowed_weight:
+            self.smallest_allowed_weight, self.largest_allowed_weight = self.largest_allowed_weight, self.smallest_allowed_weight
+            log.warning('Swapped largest allowed weight with smallest allowed weight to fulfill inequality (largest > smallest).')
+
+    def clear(self):
+        '''Explicitly delete all Segment-related state.'''
+
+        del self.initial_binning, self.final_binning, self.next_iter_binning
+        del self.flux_matrix, self.transition_matrix
+        del self.new_weights, self.used_initial_states, self.avail_initial_states
+
+        self.initial_binning = None
+        self.final_binning = None
+        self.next_iter_binning = None
+        self.flux_matrix = None
+        self.transition_matrix = None
+        self.avail_initial_states = None
+        self.used_initial_states = None
+        self.new_weights = None
+
+    def new_iteration(self, initial_states=None, target_states=None, new_weights=None, bin_mapper=None, bin_target_counts=None):
+        '''Prepare for a new iteration. ``initial_states`` is a sequence of all InitialState objects valid
+        for use in to generating new segments for the *next* iteration (after the one being begun with the call to
+        new_iteration); that is, these are states available to recycle to. Target states which generate recycling events
+        are specified in ``target_states``, a sequence of TargetState objects. Both ``initial_states``
+        and ``target_states`` may be empty as required.
+
+        The optional ``new_weights`` is a sequence of NewWeightEntry objects which will
+        be used to construct the initial flux matrix.
+
+        The given ``bin_mapper`` will be used for assignment, and ``bin_target_counts`` used for splitting/merging
+        target counts; each will be obtained from the system object if omitted or None.
+        '''
+
+        self.clear()
+
+        new_weights = new_weights or []
+        if initial_states is None:
+            initial_states = initial_states or []
+
+        # update mapper, in case it has changed on the system driver and has not been overridden
+        if bin_mapper is not None:
+            self.bin_mapper = bin_mapper
+        else:
+            self.bin_mapper = self.system.bin_mapper
+
+        if bin_target_counts is not None:
+            self.bin_target_counts = bin_target_counts
+        else:
+            self.bin_target_counts = np.array(self.system.bin_target_counts).copy()
+        nbins = self.bin_mapper.nbins
+        log.debug('mapper is {!r}, handling {:d} bins'.format(self.bin_mapper, nbins))
+
+        self.initial_binning = self.bin_mapper.construct_bins()
+        self.final_binning = self.bin_mapper.construct_bins()
+        self.next_iter_binning = None
+
+        flux_matrix = self.flux_matrix = np.zeros((nbins, nbins), dtype=np.float64)
+        transition_matrix = self.transition_matrix = np.zeros((nbins, nbins), np.uint)
+
+        # map target state specifications to bins
+        target_states = target_states or []
+        self.target_states = {}
+        for tstate in target_states:
+            tstate_assignment = self.bin_mapper.assign([tstate.pcoord])[0]
+            self.target_states[tstate_assignment] = tstate
+            log.debug('target state {!r} mapped to bin {}'.format(tstate, tstate_assignment))
+            self.bin_target_counts[tstate_assignment] = 0
+
+        # loop over recycled segments, adding entries to the flux matrix appropriately
+        if new_weights:
+            init_pcoords = np.empty((len(new_weights), self.system.pcoord_ndim), dtype=self.system.pcoord_dtype)
+            prev_init_pcoords = np.empty((len(new_weights), self.system.pcoord_ndim), dtype=self.system.pcoord_dtype)
+
+            for ientry, entry in enumerate(new_weights):
+                init_pcoords[ientry] = entry.new_init_pcoord
+                prev_init_pcoords[ientry] = entry.prev_init_pcoord
+
+            init_assignments = self.bin_mapper.assign(init_pcoords)
+            prev_init_assignments = self.bin_mapper.assign(prev_init_pcoords)
+
+            for entry, i, j in zip(new_weights, prev_init_assignments, init_assignments):
+                flux_matrix[i, j] += entry.weight
+                transition_matrix[i, j] += 1
+
+            del init_pcoords, prev_init_pcoords, init_assignments, prev_init_assignments
+
+        self.avail_initial_states = {state.state_id: state for state in initial_states}
+        self.used_initial_states = {}
+
+    def add_initial_states(self, initial_states):
+        '''Add newly-prepared initial states to the pool available for recycling.'''
+        for state in initial_states:
+            self.avail_initial_states[state.state_id] = state
+
+    @property
+    def all_initial_states(self):
+        '''Return an iterator over all initial states (available or used)'''
+        for state in self.avail_initial_states.values():
+            yield state
+        for state in self.used_initial_states.values():
+            yield state
+
+    def assign(self, segments, initializing=False):
+        '''Assign segments to initial and final bins, and update the (internal) lists of used and available
+        initial states. If ``initializing`` is True, then the "final" bin assignments will
+        be identical to the initial bin assignments, a condition required for seeding a new iteration from
+        pre-existing segments.'''
+
+        # collect initial and final coordinates into one place
+        all_pcoords = np.empty((2, len(segments), self.system.pcoord_ndim), dtype=self.system.pcoord_dtype)
+
+        for iseg, segment in enumerate(segments):
+            all_pcoords[0, iseg] = segment.pcoord[0, :]
+            all_pcoords[1, iseg] = segment.pcoord[-1, :]
+
+        # assign based on initial and final progress coordinates
+        initial_assignments = self.bin_mapper.assign(all_pcoords[0, :, :])
+        if initializing:
+            final_assignments = initial_assignments
+        else:
+            final_assignments = self.bin_mapper.assign(all_pcoords[1, :, :])
+
+        initial_binning = self.initial_binning
+        final_binning = self.final_binning
+        flux_matrix = self.flux_matrix
+        transition_matrix = self.transition_matrix
+        for segment, iidx, fidx in zip(segments, initial_assignments, final_assignments):
+            initial_binning[iidx].add(segment)
+            final_binning[fidx].add(segment)
+            flux_matrix[iidx, fidx] += segment.weight
+            transition_matrix[iidx, fidx] += 1
+
+        n_recycled_total = self.n_recycled_segs
+        n_new_states = n_recycled_total - len(self.avail_initial_states)
+
+        log.debug(
+            '{} walkers scheduled for recycling, {} initial states available'.format(
+                n_recycled_total, len(self.avail_initial_states)
+            )
+        )
+
+        if n_new_states > 0:
+            return n_new_states
+        else:
+            return 0
+
+    def _recycle_walkers(self):
+        '''Recycle walkers'''
+
+        # recall that every walker we deal with is already a new segment in the subsequent iteration,
+        # so to recycle, we actually move the appropriate Segment from the target bin to the initial state bin
+
+        self.new_weights = []
+
+        n_recycled_walkers = len(list(self.recycling_segments))
+        if not n_recycled_walkers:
+            return
+        elif n_recycled_walkers > len(self.avail_initial_states):
+            raise ConsistencyError(
+                'need {} initial states for recycling, but only {} present'.format(
+                    n_recycled_walkers, len(self.avail_initial_states)
+                )
+            )
+
+        used_istate_ids = set()
+        istateiter = iter(self.avail_initial_states.values())
+        for ibin, target_state in self.target_states.items():
+            target_bin = self.next_iter_binning[ibin]
+            for segment in set(target_bin):
+                initial_state = next(istateiter)
+                istate_assignment = self.bin_mapper.assign([initial_state.pcoord])[0]
+                parent = self._parent_map[segment.parent_id]
+                parent.endpoint_type = Segment.SEG_ENDPOINT_RECYCLED
+
+                if log.isEnabledFor(logging.DEBUG):
+                    log.debug(
+                        'recycling {!r} from target state {!r} to initial state {!r}'.format(segment, target_state, initial_state)
+                    )
+                    log.debug('parent is {!r}'.format(parent))
+
+                segment.parent_id = -(initial_state.state_id + 1)
+                segment.pcoord[0] = initial_state.pcoord
+
+                self.new_weights.append(
+                    NewWeightEntry(
+                        source_type=NewWeightEntry.NW_SOURCE_RECYCLED,
+                        weight=parent.weight,
+                        prev_seg_id=parent.seg_id,
+                        # the .copy() is crucial, otherwise the slice of pcoords will
+                        # keep the parent segments' pcoord data alive unnecessarily long
+                        prev_init_pcoord=parent.pcoord[0].copy(),
+                        prev_final_pcoord=parent.pcoord[-1].copy(),
+                        new_init_pcoord=initial_state.pcoord.copy(),
+                        target_state_id=target_state.state_id,
+                        initial_state_id=initial_state.state_id,
+                    )
+                )
+
+                if log.isEnabledFor(logging.DEBUG):
+                    log.debug('new weight entry is {!r}'.format(self.new_weights[-1]))
+
+                self.next_iter_binning[istate_assignment].add(segment)
+
+                initial_state.iter_used = segment.n_iter
+                log.debug('marking initial state {!r} as used'.format(initial_state))
+                used_istate_ids.add(initial_state.state_id)
+                target_bin.remove(segment)
+
+            assert len(target_bin) == 0
+
+        # Transfer newly-assigned states from "available" to "used"
+        for state_id in used_istate_ids:
+            self.used_initial_states[state_id] = self.avail_initial_states.pop(state_id)
+
+    def _split_walker(self, segment, m, bin):
+        '''Split the walker ``segment`` (in ``bin``) into ``m`` walkers'''
+        new_segments = []
+        for _inew in range(0, m):
+            new_segment = Segment(
+                n_iter=segment.n_iter,  # previously incremented
+                weight=segment.weight / m,
+                parent_id=segment.parent_id,
+                wtg_parent_ids=set(segment.wtg_parent_ids),
+                pcoord=segment.pcoord.copy(),
+                status=Segment.SEG_STATUS_PREPARED,
+            )
+            new_segment.pcoord[0, :] = segment.pcoord[0, :]
+            new_segments.append(new_segment)
+
+        if log.isEnabledFor(logging.DEBUG):
+            log.debug('splitting {!r} into {:d}:\n    {!r}'.format(segment, m, new_segments))
+
+        return new_segments
+
+    def _merge_walkers(self, segments, cumul_weight, bin):
+        '''Merge the given ``segments`` in ``bin``, previously sorted by weight, into one conglomerate segment.
+        ``cumul_weight`` is the cumulative sum of the weights of the ``segments``; this may be None to calculate here.'''
+
+        if cumul_weight is None:
+            cumul_weight = np.add.accumulate([segment.weight for segment in segments])
+
+        glom = Segment(
+            n_iter=segments[0].n_iter,  # assumed correct (and equal among all segments)
+            weight=cumul_weight[len(segments) - 1],
+            status=Segment.SEG_STATUS_PREPARED,
+            pcoord=self.system.new_pcoord_array(),
+        )
+
+        # Select the history to use
+        # The following takes a random number in the interval 0 <= x < glom.weight, then
+        # sees where this value falls among the (sorted) weights of the segments being merged;
+        # this ensures that a walker with (e.g.) twice the weight of its brethren has twice the
+        # probability of having its history selected for continuation
+        iparent = np.digitize((self.rng.uniform(0, glom.weight),), cumul_weight)[0]
+        gparent_seg = segments[iparent]
+
+        # Inherit history from this segment ("gparent" stands for "glom parent", as opposed to historical
+        # parent).
+        glom.parent_id = gparent_seg.parent_id
+        glom.pcoord[0, :] = gparent_seg.pcoord[0, :]
+
+        # Weight comes from all segments being merged, and therefore all their
+        # parent segments
+        glom.wtg_parent_ids = set()
+        for segment in segments:
+            glom.wtg_parent_ids |= segment.wtg_parent_ids
+
+        # The historical parent of gparent is continued; all others are marked as merged
+        for segment in segments:
+            if segment is gparent_seg:
+                # we must ignore initial states here...
+                if segment.parent_id >= 0:
+                    self._parent_map[segment.parent_id].endpoint_type = Segment.SEG_ENDPOINT_CONTINUES
+            else:
+                # and "unuse" an initial state here (recall that initial states are in 1:1 correspondence
+                # with the segments they initiate), except when a previously-split particle is being
+                # merged
+                if segment.parent_id >= 0:
+                    self._parent_map[segment.parent_id].endpoint_type = Segment.SEG_ENDPOINT_MERGED
+                else:
+                    if segment.initial_state_id in {segment.initial_state_id for segment in bin}:
+                        log.debug('initial state in use by other walker; not removing')
+                    else:
+                        initial_state = self.used_initial_states.pop(segment.initial_state_id)
+                        log.debug('freeing initial state {!r} for future use (merged)'.format(initial_state))
+                        self.avail_initial_states[initial_state.state_id] = initial_state
+                        initial_state.iter_used = None
+
+        if log.isEnabledFor(logging.DEBUG):
+            log.debug('merging ({:d}) {!r} into 1:\n    {!r}'.format(len(segments), segments, glom))
+
+        return glom, gparent_seg
+
+    def _split_by_weight(self, bin, target_count, ideal_weight):
+        '''Split overweight particles'''
+
+        segments = np.array(sorted(bin, key=operator.attrgetter('weight')), dtype=np.object_)
+        weights = np.array(list(map(operator.attrgetter('weight'), segments)))
+
+        if len(bin) > 0:
+            assert target_count > 0
+
+        to_split = segments[weights > self.weight_split_threshold * ideal_weight]
+
+        for segment in to_split:
+            m = int(math.ceil(segment.weight / ideal_weight))
+            bin.remove(segment)
+            new_segments_list = self._split_walker(segment, m, bin)
+            bin.update(new_segments_list)
+
+    def _merge_by_weight(self, bin, target_count, ideal_weight):
+        '''Merge underweight particles'''
+
+        while True:
+            segments = np.array(sorted(bin, key=operator.attrgetter('weight')), dtype=np.object_)
+            weights = np.array(list(map(operator.attrgetter('weight'), segments)))
+            cumul_weight = np.add.accumulate(weights)
+
+            to_merge = segments[cumul_weight <= ideal_weight * self.weight_merge_cutoff]
+            if len(to_merge) < 2:
+                return
+            bin.difference_update(to_merge)
+            new_segment, parent = self._merge_walkers(to_merge, cumul_weight, bin)
+            bin.add(new_segment)
+
+    def _adjust_count(self, bin, subgroups, target_count):
+        weight_getter = operator.attrgetter('weight')
+        # Order subgroups by the sum of their weights.
+        if len(subgroups) > target_count:
+            sorted_subgroups = [set()]
+            for i in bin:
+                sorted_subgroups[0].add(i)
+        else:
+            sorted_subgroups = sorted(subgroups, key=lambda gp: sum(seg.weight for seg in gp))
+        # Loops over the groups, splitting/merging until the proper count has been reached.  This way, no trajectories are accidentally destroyed.
+
+        # split
+        while len(bin) < target_count:
+            for i in sorted_subgroups:
+                log.debug('adjusting counts by splitting')
+                # always split the highest probability walker into two
+                segments = sorted(i, key=weight_getter)
+                bin.remove(segments[-1])
+                i.remove(segments[-1])
+                new_segments_list = self._split_walker(segments[-1], 2, bin)
+                i.update(new_segments_list)
+                bin.update(new_segments_list)
+
+                if len(bin) == target_count:
+                    break
+
+        # merge
+        while len(bin) > target_count:
+            sorted_subgroups.reverse()
+            # Adjust to go from lowest weight group to highest to merge
+            for i in sorted_subgroups:
+                # Ensures that there are least two walkers to merge
+                if len(i) > 1:
+                    log.debug('adjusting counts by merging')
+                    # always merge the two lowest-probability walkers
+                    segments = sorted(i, key=weight_getter)
+                    bin.difference_update(segments[:2])
+                    i.difference_update(segments[:2])
+                    merged_segment, parent = self._merge_walkers(segments[:2], cumul_weight=None, bin=bin)
+                    i.add(merged_segment)
+                    bin.add(merged_segment)
+
+                    # As long as we're changing the merge_walkers and split_walkers, adjust them so that they don't update the bin within the function
+                    # and instead update the bin here.  Assuming nothing else relies on those.  Make sure with grin.
+                    # in bash, "find . -name \*.py | xargs fgrep -n '_merge_walkers'"
+                    if len(bin) == target_count:
+                        break
+
+    def _merge_by_threshold(self, bin, subgroup):
+        # merge to satisfy weight thresholds
+        # this gets rid of weights that are too small
+        while True:
+            segments = np.array(sorted(subgroup, key=operator.attrgetter('weight')), dtype=np.object_)
+            weights = np.array(list(map(operator.attrgetter('weight'), segments)))
+            cumul_weight = np.add.accumulate(weights)
+
+            to_merge = segments[weights < self.smallest_allowed_weight]
+            if len(to_merge) < 2:
+                return
+            bin.difference_update(to_merge)
+            subgroup.difference_update(to_merge)
+            new_segment, parent = self._merge_walkers(to_merge, cumul_weight, bin)
+            bin.add(new_segment)
+            subgroup.add(new_segment)
+
+    def _split_by_threshold(self, bin, subgroup):
+        # split to satisfy weight thresholds
+        # this splits walkers that are too big
+        segments = np.array(sorted(subgroup, key=operator.attrgetter('weight')), dtype=np.object_)
+        weights = np.array(list(map(operator.attrgetter('weight'), segments)))
+
+        to_split = segments[weights > self.largest_allowed_weight]
+        for segment in to_split:
+            m = int(math.ceil(segment.weight / self.largest_allowed_weight))
+            bin.remove(segment)
+            subgroup.remove(segment)
+            new_segments_list = self._split_walker(segment, m, bin)
+            bin.update(new_segments_list)
+            subgroup.update(new_segments_list)
+
+    def _check_pre(self):
+        for ibin, _bin in enumerate(self.next_iter_binning):
+            if self.bin_target_counts[ibin] == 0 and len(_bin) > 0:
+                raise ConsistencyError('bin {:d} has target count of 0 but contains {:d} walkers'.format(ibin, len(_bin)))
+
+    def _check_post(self):
+        for segment in self.next_iter_segments:
+            if segment.weight == 0:
+                raise ConsistencyError('segment {!r} has weight of zero')
+
+    def _prep_we(self):
+        '''Prepare internal state for WE recycle/split/merge.'''
+        self._parent_map = {}
+        self.next_iter_binning = self.bin_mapper.construct_bins()
+
+    def _run_we(self):
+        '''Run recycle/split/merge. Do not call this function directly; instead, use
+        populate_initial(), rebin_current(), or construct_next().'''
+        self._recycle_walkers()
+
+        # sanity check
+        self._check_pre()
+
+        # Regardless of current particle count, always split overweight particles and merge underweight particles
+        # Then and only then adjust for correct particle count
+        total_number_of_subgroups = 0
+        total_number_of_particles = 0
+        for ibin, bin in enumerate(self.next_iter_binning):
+            if len(bin) == 0:
+                continue
+
+            # Splits the bin into subgroups as defined by the called function
+            target_count = self.bin_target_counts[ibin]
+            subgroups = self.subgroup_function(self, ibin, **self.subgroup_function_kwargs)
+            total_number_of_subgroups += len(subgroups)
+            # Clear the bin
+            segments = np.array(sorted(bin, key=operator.attrgetter('weight')), dtype=np.object_)
+            weights = np.array(list(map(operator.attrgetter('weight'), segments)))
+            ideal_weight = weights.sum() / target_count
+            bin.clear()
+            # Determines to see whether we have more sub bins than we have target walkers in a bin (or equal to), and then uses
+            # different logic to deal with those cases.  Should devolve to the Huber/Kim algorithm in the case of few subgroups.
+            if len(subgroups) >= target_count:
+                for i in subgroups:
+                    # Merges all members of set i.  Checks to see whether there are any to merge.
+                    if len(i) > 1:
+                        (segment, parent) = self._merge_walkers(
+                            list(i),
+                            np.add.accumulate(np.array(list(map(operator.attrgetter('weight'), i)))),
+                            i,
+                        )
+                        i.clear()
+                        i.add(segment)
+                    # Add all members of the set i to the bin.  This keeps the bins in sync for the adjustment step.
+                    bin.update(i)
+
+                if len(subgroups) > target_count:
+                    self._adjust_count(bin, subgroups, target_count)
+
+            if len(subgroups) < target_count:
+                for i in subgroups:
+                    self._split_by_weight(i, target_count, ideal_weight)
+                    self._merge_by_weight(i, target_count, ideal_weight)
+                    # Same logic here.
+                    bin.update(i)
+                if self.do_adjust_counts:
+                    # A modified adjustment routine is necessary to ensure we don't unnecessarily destroy trajectory pathways.
+                    self._adjust_count(bin, subgroups, target_count)
+            if self.do_thresholds:
+                for i in subgroups:
+                    self._split_by_threshold(bin, i)
+                    self._merge_by_threshold(bin, i)
+                for iseg in bin:
+                    if iseg.weight > self.largest_allowed_weight or iseg.weight < self.smallest_allowed_weight:
+                        log.warning(
+                            f'Unable to fulfill threshold conditions for {iseg}. The given threshold range is likely too small.'
+                        )
+            total_number_of_particles += len(bin)
+        log.debug('Total number of subgroups: {!r}'.format(total_number_of_subgroups))
+
+        self._check_post()
+
+        self.new_weights = self.new_weights or []
+
+        log.debug('used initial states: {!r}'.format(self.used_initial_states))
+        log.debug('available initial states: {!r}'.format(self.avail_initial_states))
+
+    def populate_initial(self, initial_states, weights, system=None):
+        '''Create walkers for a new weighted ensemble simulation.
+
+        One segment is created for each provided initial state, then binned and split/merged
+        as necessary. After this function is called, next_iter_segments will yield the new
+        segments to create, used_initial_states will contain data about which of the
+        provided initial states were used, and avail_initial_states will contain data about
+        which initial states were unused (because their corresponding walkers were merged
+        out of existence).
+        '''
+
+        # This has to be down here to avoid an import race
+        from westpa.core.data_manager import weight_dtype
+
+        EPS = np.finfo(weight_dtype).eps
+
+        system = system or westpa.rc.get_system_driver()
+        self.new_iteration(
+            initial_states=[], target_states=[], bin_mapper=system.bin_mapper, bin_target_counts=system.bin_target_counts
+        )
+
+        # Create dummy segments
+        segments = []
+        for seg_id, (initial_state, weight) in enumerate(zip(initial_states, weights)):
+            dummy_segment = Segment(
+                n_iter=0,
+                seg_id=seg_id,
+                parent_id=-(initial_state.state_id + 1),
+                weight=weight,
+                wtg_parent_ids=set([-(initial_state.state_id + 1)]),
+                pcoord=system.new_pcoord_array(),
+                status=Segment.SEG_STATUS_PREPARED,
+            )
+            dummy_segment.pcoord[[0, -1]] = initial_state.pcoord
+            segments.append(dummy_segment)
+
+        # Adjust weights, if necessary
+        tprob = sum(weights)
+        if abs(1.0 - tprob) > len(weights) * EPS:
+            pscale = 1.0 / tprob
+            log.warning('Weights of initial segments do not sum to unity; scaling by {:g}'.format(pscale))
+            for segment in segments:
+                segment.weight *= pscale
+
+        self.assign(segments, initializing=True)
+        self.construct_next()
+
+        # We now have properly-constructed initial segments, except for parent information,
+        # and we need to  mark initial states as used or unused
+        istates_by_id = {state.state_id: state for state in initial_states}
+        dummysegs_by_id = self._parent_map
+
+        # Don't add start states to the list of available initial states.
+        # They're only meant to be used in the first iteration, so nothing should ever be recycled into them.
+        # Thus, they're not available.
+        self.avail_initial_states = {
+            k: v for (k, v) in istates_by_id.items() if not v.istate_type == InitialState.ISTATE_TYPE_START
+        }
+
+        for state in self.avail_initial_states.keys():
+            if self.avail_initial_states[state].istate_type == InitialState.ISTATE_TYPE_START:
+                self.avail_initial_states.pop(state)
+
+        self.used_initial_states = {}
+        for segment in self.next_iter_segments:
+            segment.parent_id = dummysegs_by_id[segment.parent_id].parent_id
+            segment.wtg_parent_ids = set([segment.parent_id])
+            assert segment.initpoint_type == Segment.SEG_INITPOINT_NEWTRAJ
+            istate = istates_by_id[segment.initial_state_id]
+            try:
+                self.used_initial_states[istate.state_id] = self.avail_initial_states.pop(istate.state_id)
+            except KeyError:
+                # Shared by more than one segment, and already marked as used
+                pass
+
+        for used_istate in self.used_initial_states.values():
+            used_istate.iter_used = 1
+
+    def rebin_current(self, parent_segments):
+        '''Reconstruct walkers for the current iteration based on (presumably) new binning.
+        The previous iteration's segments must be provided (as ``parent_segments``) in order
+        to update endpoint types appropriately.'''
+
+        self._prep_we()
+        self._parent_map = {segment.seg_id: segment for segment in parent_segments}
+
+        # Create new segments for the next iteration
+        # We assume that everything is going to continue without being touched by recycling or WE, and
+        # adjust later
+        new_pcoord_array = self.system.new_pcoord_array
+        n_iter = None
+
+        for ibin, _bin in enumerate(self.final_binning):
+            for segment in _bin:
+                if n_iter is None:
+                    n_iter = segment.n_iter
+                else:
+                    assert segment.n_iter == n_iter
+
+                new_segment = Segment(
+                    n_iter=segment.n_iter,
+                    parent_id=segment.parent_id,
+                    weight=segment.weight,
+                    wtg_parent_ids=set(segment.wtg_parent_ids or []),
+                    pcoord=new_pcoord_array(),
+                    status=Segment.SEG_STATUS_PREPARED,
+                )
+                new_segment.pcoord[0] = segment.pcoord[0]
+                self.next_iter_binning[ibin].add(new_segment)
+
+        self._run_we()
+
+    def construct_next(self):
+        '''Construct walkers for the next iteration, by running weighted ensemble recycling
+        and bin/split/merge on the segments previously assigned to bins using ``assign``.
+        Enough unused initial states must be present in ``self.avail_initial_states`` for every recycled
+        walker to be assigned an initial state.
+
+        After this function completes, ``self.flux_matrix`` contains a valid flux matrix for this
+        iteration (including any contributions from recycling from the previous iteration), and
+        ``self.next_iter_segments`` contains a list of segments ready for the next iteration,
+        with appropriate values set for weight, endpoint type, parent walkers, and so on.
+        '''
+
+        self._prep_we()
+
+        # Create new segments for the next iteration
+        # We assume that everything is going to continue without being touched by recycling or WE, and
+        # adjust later
+        new_pcoord_array = self.system.new_pcoord_array
+        n_iter = None
+
+        for ibin, _bin in enumerate(self.final_binning):
+            for segment in _bin:
+                if n_iter is None:
+                    n_iter = segment.n_iter
+                else:
+                    assert segment.n_iter == n_iter
+
+                segment.endpoint_type = Segment.SEG_ENDPOINT_CONTINUES
+                new_segment = Segment(
+                    n_iter=segment.n_iter + 1,
+                    parent_id=segment.seg_id,
+                    weight=segment.weight,
+                    wtg_parent_ids=[segment.seg_id],
+                    pcoord=new_pcoord_array(),
+                    status=Segment.SEG_STATUS_PREPARED,
+                )
+                new_segment.pcoord[0] = segment.pcoord[-1]
+                self.next_iter_binning[ibin].add(new_segment)
+
+                # Store a link to the parent segment, so we can update its endpoint status as we need,
+                # based on its ID
+                self._parent_map[segment.seg_id] = segment
+
+        self._run_we()
+
+        log.debug('used initial states: {!r}'.format(self.used_initial_states))
+        log.debug('available initial states: {!r}'.format(self.avail_initial_states))
+
+    def _log_bin_stats(self, bin, heading=None, level=logging.DEBUG):
+        if log.isEnabledFor(level):
+            weights = sorted(np.array(list(map(operator.attrgetter('weight'), bin))))
+            bin_label = getattr(bin, 'label', None) or ''
+            log_fmt = '\n      '.join(
+                [
+                    '',
+                    'stats for bin {bin_label!r} {heading}',
+                    '  count: {bin.count:d}, target count: {bin.target_count:d}',
+                    '  total weight: {bin.weight:{weight_spec}},  ideal weight: {ideal_weight:{weight_spec}}',
+                    '  mean weight:  {mean_weight:{weight_spec}},  stdev weight: {stdev_weight:{weight_spec}}',
+                    '  min weight:   {min_weight:{weight_spec}},  med weight  : {median_weight:{weight_spec}}'
+                    + ', max weight: {max_weight:{weight_spec}}',
+                ]
+            )
+            log_msg = log_fmt.format(
+                log_fmt,
+                weight_spec='<12.6e',
+                bin_label=bin_label,
+                heading=heading,
+                bin=bin,
+                ideal_weight=bin.weight / bin.target_count,
+                mean_weight=weights.mean(),
+                stdev_weight=weights.std(),
+                min_weight=weights[0],
+                median_weight=np.median(weights),
+                max_weight=weights[-1],
+            )
+            log.log(level, log_msg)