Merge pull request #35 from dwhswenson/md

New command: `md`

Author: dwhswenson

README.md

@@ -22,6 +22,7 @@ miscellaneous operations on OPS output files.
 **Simulation Commands:**
 
 * `visit-all`:     Run MD to generate initial trajectories
+* `md`:            Run MD for fixed time or until a given ensemble is satisfied
 * `equilibrate`:   Run equilibration for path sampling
 * `pathsampling`:  Run any path sampling simulation, including TIS variants
 

paths_cli/commands/md.py

@@ -0,0 +1,203 @@
+import click
+
+import paths_cli.utils
+from paths_cli.parameters import (INPUT_FILE, OUTPUT_FILE, ENGINE,
+                                  MULTI_ENSEMBLE, INIT_SNAP)
+
+import logging
+logger = logging.getLogger(__name__)
+
+@click.command(
+    "md",
+    short_help=("Run MD for fixed time or until a given ensemble is "
+                "satisfied"),
+)
+@INPUT_FILE.clicked(required=True)
+@OUTPUT_FILE.clicked(required=True)
+@ENGINE.clicked(required=False)
+@MULTI_ENSEMBLE.clicked(required=False)
+@click.option('-n', '--nsteps', type=int,
+              help="number of MD steps to run")
+@INIT_SNAP.clicked(required=False)
+def md(input_file, output_file, engine, ensemble, nsteps, init_frame):
+    """Run MD for for time of steps or until ensembles are satisfied.
+
+    This can either take a --nsteps or --ensemble, but not both. If the
+    --ensemble option is specfied more than once, then this will attempt to
+    run until all ensembles are satisfied by a subtrajectory.
+
+    This still respects the maximum number of frames as set in the engine,
+    and will terminate if the trajectory gets longer than that.
+    """
+    storage = INPUT_FILE.get(input_file)
+    md_main(
+        output_storage=OUTPUT_FILE.get(output_file),
+        engine=ENGINE.get(storage, engine),
+        ensembles=MULTI_ENSEMBLE.get(storage, ensemble),
+        nsteps=nsteps,
+        initial_frame=INIT_SNAP.get(storage, init_frame)
+    )
+
+class ProgressReporter(object):
+    """Generic class for a callable that reports progress.
+
+    Base class for ends-with-ensemble and fixed-length tricks.
+
+    Parameters
+    ----------
+    timestep : Any
+        timestep, optionally with units
+    update_freq : int
+        how often to report updates
+    """
+    def __init__(self, timestep, update_freq):
+        self.timestep = timestep
+        self.update_freq = update_freq
+
+    def steps_progress_string(self, n_steps):
+        """Return string for number of frames run and time elapsed
+
+        Not newline-terminated.
+        """
+        report_str = "Ran {n_steps} frames"
+        if self.timestep is not None:
+            report_str += " [{}]".format(str(n_steps * self.timestep))
+        report_str += '.'
+        return report_str.format(n_steps=n_steps)
+
+    def progress_string(self, n_steps):
+        """Return the progress string. Subclasses may override.
+        """
+        report_str = self.steps_progress_string(n_steps) + "\n"
+        return report_str.format(n_steps=n_steps)
+
+    def report_progress(self, n_steps, force=False):
+        """Report the progress to the terminal.
+        """
+        import openpathsampling as paths
+        if (n_steps % self.update_freq == 0) or force:
+            string = self.progress_string(n_steps)
+            paths.tools.refresh_output(string)
+
+    def __call__(self, trajectory, trusted=False):
+        raise NotImplementedError()
+
+
+class EnsembleSatisfiedContinueConditions(ProgressReporter):
+    """Continuation condition for including subtrajs for each ensemble.
+
+    This object creates a continuation condition (a callable) analogous with
+    the ensemble ``can_append`` method. This will tell the trajectory to
+    keep running until, for each of the given ensembles, a subtrajectory has
+    been found that will satisfy the ensemble.
+
+    Parameters
+    ----------
+    ensembles: List[:class:`openpathsampling.Ensemble`]
+        the ensembles to satisfy
+    timestep : Any
+        timestep, optionally with units
+    update_freq : int
+        how often to report updates
+    """
+    def __init__(self, ensembles, timestep=None, update_freq=10):
+        super().__init__(timestep, update_freq)
+        self.satisfied = {ens: False for ens in ensembles}
+
+    def progress_string(self, n_steps):
+        report_str = self.steps_progress_string(n_steps)
+        report_str += (" Found ensembles [{found}]. "
+                       "Looking for [{missing}].\n")
+        found = [ens.name for ens, done in self.satisfied.items() if done]
+        missing = [ens.name for ens, done in self.satisfied.items()
+                   if not done]
+        found_str = ",".join(found)
+        missing_str = ",".join(missing)
+        return report_str.format(n_steps=n_steps,
+                                 found=found_str,
+                                 missing=missing_str)
+
+
+    def _check_previous_frame(self, trajectory, start, unsatisfied):
+        if -start > len(trajectory):
+            # we've done the whole traj; don't keep going
+            return False
+        subtraj = trajectory[start:]
+        logger.debug(str(subtraj) + "/" + str(trajectory))
+        for ens in unsatisfied:
+            if not ens.strict_can_prepend(subtraj, trusted=True):
+                # test if we can't prepend because we satsify
+                self.satisfied[ens] = ens(subtraj) or ens(subtraj[1:])
+                unsatisfied.remove(ens)
+        return bool(unsatisfied)
+
+    def _call_untrusted(self, trajectory):
+        self.satisfied = {ens: False for ens in self.satisfied}
+        for i in range(1, len(trajectory)):
+            keep_going = self(trajectory[:i], trusted=True)
+            if not keep_going:
+                return False
+        return self(trajectory, trusted=True)
+
+    def __call__(self, trajectory, trusted=False):
+        if not trusted:
+            return self._call_untrusted(trajectory)
+
+        # below here, trusted is True
+        self.report_progress(len(trajectory) - 1)
+
+        unsatisfied = [ens for ens, done in self.satisfied.items()
+                       if not done]
+        # TODO: update on how many ensembles left, what frame number we are
+
+        start = -1
+        while self._check_previous_frame(trajectory, start, unsatisfied):
+            start -= 1
+
+        return not all(self.satisfied.values())
+
+
+class FixedLengthContinueCondition(ProgressReporter):
+    """Continuation condition for fixed-length runs.
+
+    Parameters
+    ----------
+    length : int
+        final length of the trajectory in frames
+    timestep : Any
+        timestep, optionally with units
+    update_freq : int
+        how often to report updates
+    """
+    def __init__(self, length, timestep=None, update_freq=10):
+        super().__init__(timestep, update_freq)
+        self.length = length
+
+    def __call__(self, trajectory, trusted=False):
+        len_traj = len(trajectory)
+        self.report_progress(len_traj - 1)
+        return len_traj < self.length
+
+
+
+def md_main(output_storage, engine, ensembles, nsteps, initial_frame):
+    import openpathsampling as paths
+    if nsteps is not None and ensembles:
+        raise RuntimeError("Options --ensemble and --nsteps cannot both be"
+                           " used at once.")
+
+    if ensembles:
+        continue_cond = EnsembleSatisfiedContinueConditions(ensembles)
+    else:
+        continue_cond = FixedLengthContinueCondition(nsteps)
+
+    trajectory = engine.generate(initial_frame, running=continue_cond)
+    continue_cond.report_progress(len(trajectory) - 1, force=True)
+    paths_cli.utils.tag_final_result(trajectory, output_storage,
+                                     'final_conditions')
+    return trajectory, None
+
+CLI = md
+SECTION = "Simulation"
+REQUIRES_OPS = (1, 0)
+

paths_cli/commands/visit_all.py

@@ -1,5 +1,6 @@
 import click
 
+import paths_cli.utils
 from paths_cli.parameters import (INPUT_FILE, OUTPUT_FILE, ENGINE, STATES,
                                   INIT_SNAP)
 
@@ -34,9 +35,8 @@ def visit_all_main(output_storage, states, engine, initial_frame):
     timestep = getattr(engine, 'timestep', None)
     visit_all_ens = paths.VisitAllStatesEnsemble(states, timestep=timestep)
     trajectory = engine.generate(initial_frame, [visit_all_ens.can_append])
-    if output_storage is not None:
-        output_storage.save(trajectory)
-        output_storage.tags['final_conditions'] = trajectory
+    paths_cli.utils.tag_final_result(trajectory, output_storage,
+                                     'final_conditions')
 
     return trajectory, None  # no simulation object to return here
 

paths_cli/parameters.py

@@ -57,6 +57,12 @@
     store='engines'
 )
 
+MULTI_ENSEMBLE = OPSStorageLoadNames(
+    param=Option('--ensemble', type=str, multiple=True,
+                 help='name of index of ensemble' + HELP_MULTIPLE),
+    store='ensembles'
+)
+
 STATES = OPSStorageLoadNames(
     param=Option('-s', '--state', type=str, multiple=True,
                  help='name  of state' + HELP_MULTIPLE),