westpa 2022.12__cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

westpa/core/binning/binless_manager.py

@@ -0,0 +1,190 @@
+import logging
+
+from westpa.core.binning.binless import BinlessMapper
+from westpa.core.sim_manager import WESimManager, grouper
+from westpa.core.states import InitialState, pare_basis_initial_states
+from westpa.core import wm_ops
+from westpa.core.segment import Segment
+import numpy as np
+
+log = logging.getLogger(__name__)
+
+
+class BinlessSimManager(WESimManager):
+    def initialize_simulation(self, basis_states, target_states, start_states, segs_per_state=1, suppress_we=False):
+        if len(target_states) > 0:
+            if isinstance(self.system.bin_mapper, BinlessMapper):
+                log.error("BinlessMapper cannot be an outer binning scheme with a target state\n")
+
+        super().initialize_simulation(
+            basis_states, target_states, start_states, segs_per_state=segs_per_state, suppress_we=suppress_we
+        )
+
+    def propagate(self):
+        log.debug("BinlessManager in use")
+        segments = list(self.incomplete_segments.values())
+        log.debug('iteration {:d}: propagating {:d} segments'.format(self.n_iter, len(segments)))
+
+        # all futures dispatched for this iteration
+        futures = set()
+        segment_futures = set()
+
+        # Immediately dispatch any necessary initial state generation
+        istate_gen_futures = self.get_istate_futures()
+        futures.update(istate_gen_futures)
+
+        # Dispatch propagation tasks using work manager
+        for segment_block in grouper(self.propagator_block_size, segments):
+            segment_block = [_f for _f in segment_block if _f]
+            pbstates, pistates = pare_basis_initial_states(
+                self.current_iter_bstates, list(self.current_iter_istates.values()), segment_block
+            )
+            future = self.work_manager.submit(wm_ops.propagate, args=(pbstates, pistates, segment_block))
+            futures.add(future)
+            segment_futures.add(future)
+
+        while futures:
+            # TODO: add capacity for timeout or SIGINT here
+            future = self.work_manager.wait_any(futures)
+            futures.remove(future)
+
+            if future in segment_futures:
+                segment_futures.remove(future)
+                incoming = future.get_result()
+                self.n_propagated += 1
+
+                self.segments.update({segment.seg_id: segment for segment in incoming})
+                self.completed_segments.update({segment.seg_id: segment for segment in incoming})
+
+                new_istate_futures = self.get_istate_futures()
+                istate_gen_futures.update(new_istate_futures)
+                futures.update(new_istate_futures)
+
+                with self.data_manager.expiring_flushing_lock():
+                    self.data_manager.update_segments(self.n_iter, incoming)
+
+            elif future in istate_gen_futures:
+                istate_gen_futures.remove(future)
+                _basis_state, initial_state = future.get_result()
+                log.debug('received newly-prepared initial state {!r}'.format(initial_state))
+                initial_state.istate_status = InitialState.ISTATE_STATUS_PREPARED
+                with self.data_manager.expiring_flushing_lock():
+                    self.data_manager.update_initial_states([initial_state], n_iter=self.n_iter + 1)
+                self.we_driver.avail_initial_states[initial_state.state_id] = initial_state
+            else:
+                log.error('unknown future {!r} received from work manager'.format(future))
+                raise AssertionError('untracked future {!r}'.format(future))
+
+        # Collectively assign all segments to their bins...
+        self.we_driver.assign(self.segments.values())
+
+        # For cases where we need even more istates for recycled trajectories
+        # futures should be empty at this point.
+        istate_gen_futures = self.get_istate_futures()
+        futures.update(istate_gen_futures)
+
+        # Wait for istate_gen_futures and catch untracked futures.
+        while futures:
+            future = self.work_manager.wait_any(futures)
+            futures.remove(future)
+
+            if future in istate_gen_futures:
+                istate_gen_futures.remove(future)
+                _basis_state, initial_state = future.get_result()
+                log.debug('received newly-prepared initial state {!r}'.format(initial_state))
+                initial_state.istate_status = InitialState.ISTATE_STATUS_PREPARED
+                with self.data_manager.expiring_flushing_lock():
+                    self.data_manager.update_initial_states([initial_state], n_iter=self.n_iter + 1)
+                self.we_driver.avail_initial_states[initial_state.state_id] = initial_state
+            else:
+                log.error('unknown future {!r} received from work manager'.format(future))
+                raise AssertionError('untracked future {!r}'.format(future))
+
+        log.debug('done with propagation')
+        self.save_bin_data()
+        self.data_manager.flush_backing()
+
+    def prepare_iteration(self):
+        log.debug('beginning iteration {:d}'.format(self.n_iter))
+
+        # the WE driver needs a list of all target states for this iteration
+        # along with information about any new weights introduced (e.g. by recycling)
+        target_states = self.data_manager.get_target_states(self.n_iter)
+        new_weights = self.data_manager.get_new_weight_data(self.n_iter)
+
+        self.we_driver.new_iteration(target_states=target_states, new_weights=new_weights)
+
+        # Get basis states used in this iteration
+        self.current_iter_bstates = self.data_manager.get_basis_states(self.n_iter)
+
+        # Get the segments for this iteration and separate into complete and incomplete
+        if self.segments is None:
+            segments = self.segments = {segment.seg_id: segment for segment in self.data_manager.get_segments()}
+            log.debug('loaded {:d} segments'.format(len(segments)))
+        else:
+            segments = self.segments
+            log.debug('using {:d} pre-existing segments'.format(len(segments)))
+
+        completed_segments = self.completed_segments = {}
+        incomplete_segments = self.incomplete_segments = {}
+        for segment in segments.values():
+            if segment.status == Segment.SEG_STATUS_COMPLETE:
+                completed_segments[segment.seg_id] = segment
+            else:
+                incomplete_segments[segment.seg_id] = segment
+        log.debug('{:d} segments are complete; {:d} are incomplete'.format(len(completed_segments), len(incomplete_segments)))
+
+        if len(incomplete_segments) == len(segments):
+            # Starting a new iteration
+            self.rc.pstatus('Beginning iteration {:d}'.format(self.n_iter))
+        elif incomplete_segments:
+            self.rc.pstatus('Continuing iteration {:d}'.format(self.n_iter))
+        self.rc.pstatus(
+            '{:d} segments remain in iteration {:d} ({:d} total)'.format(len(incomplete_segments), self.n_iter, len(segments))
+        )
+
+        # Get the initial states active for this iteration (so that the propagator has them if necessary)
+        self.current_iter_istates = {
+            state.state_id: state for state in self.data_manager.get_segment_initial_states(list(segments.values()))
+        }
+        log.debug('This iteration uses {:d} initial states'.format(len(self.current_iter_istates)))
+
+        # Assign this iteration's segments' initial points to bins and report on bin population
+        initial_pcoords = self.system.new_pcoord_array(len(segments))
+        initial_binning = self.system.bin_mapper.construct_bins()
+        for iseg, segment in enumerate(segments.values()):
+            initial_pcoords[iseg] = segment.pcoord[0]
+        initial_assignments = self.system.bin_mapper.assign(initial_pcoords)
+        for segment, assignment in zip(iter(segments.values()), initial_assignments):
+            initial_binning[assignment].add(segment)
+        self.report_bin_statistics(initial_binning, [], save_summary=True)
+        del initial_pcoords, initial_binning
+
+        self.rc.pstatus("Binless scheme in use")
+
+        self.rc.pstatus("Waiting for segments to complete...")
+
+        # Let the WE driver assign completed segments
+        if completed_segments and len(incomplete_segments) == 0:
+            self.we_driver.assign(list(completed_segments.values()))
+
+        # load restart data
+        self.data_manager.prepare_segment_restarts(
+            incomplete_segments.values(), self.current_iter_bstates, self.current_iter_istates
+        )
+
+        # Get the basis states and initial states for the next iteration, necessary for doing on-the-fly recycling
+        self.next_iter_bstates = self.data_manager.get_basis_states(self.n_iter + 1)
+        self.next_iter_bstate_cprobs = np.add.accumulate([bstate.probability for bstate in self.next_iter_bstates])
+
+        self.we_driver.avail_initial_states = {
+            istate.state_id: istate for istate in self.data_manager.get_unused_initial_states(n_iter=self.n_iter + 1)
+        }
+        log.debug('{:d} unused initial states found'.format(len(self.we_driver.avail_initial_states)))
+
+        # Invoke callbacks
+        self.invoke_callbacks(self.prepare_iteration)
+
+        # dispatch and immediately wait on result for prep_iter
+        log.debug('dispatching propagator prep_iter to work manager')
+        self.work_manager.submit(wm_ops.prep_iter, args=(self.n_iter, segments)).get_result()

westpa/core/binning/bins.py

@@ -0,0 +1,47 @@
+import logging
+
+import numpy as np
+
+log = logging.getLogger(__name__)
+
+EPS = np.finfo(np.float64).eps
+
+
+class Bin(set):
+    def __init__(self, iterable=None, label=None):
+        super().__init__(iterable or [])
+        self.label = label
+
+    def __repr__(self):
+        return '<{classname} at 0x{id:x}, label={label!r}, count={count:d}, weight={weight:g}>'.format(
+            classname=self.__class__.__name__, id=id(self), label=self.label, count=len(self), weight=self.weight
+        )
+
+    @property
+    def weight(self):
+        'Total weight of all walkers in this bin'
+
+        weight = 0.0
+        for particle in self:
+            weight += particle.weight
+        return weight
+
+    def reweight(self, new_weight):
+        """Reweight all walkers in this bin so that the total weight is new_weight"""
+
+        if len(self) == 0 and new_weight == 0:
+            return
+
+        if len(self) == 0 and new_weight != 0:
+            raise ValueError('cannot reweight empty ParticleCollection')
+
+        current_weight = self.weight
+        log.debug('reweighting collection of {:d} particles from {:g} to {:g}'.format(len(self), current_weight, new_weight))
+        assert (new_weight == 0 and current_weight == 0) or new_weight > 0
+
+        wrat = new_weight / current_weight
+        for p in self:
+            p.weight *= wrat
+
+        log.debug('new weight: {:g}'.format(self.weight))
+        assert abs(new_weight - self.weight) <= EPS * len(self)