Add equil/pathsampling commands (no tests)

Author: dwhswenson

paths_cli/commands/equilibrate.py

@@ -0,0 +1,62 @@
+import click
+# import openpathsampling as paths
+
+from paths_cli.parameters import (
+    INPUT_FILE, OUTPUT_FILE, INIT_CONDS, SCHEME
+)
+
+@click.command(
+    "equilibrate",
+    short_help="Run equilibration for path sampling",
+)
+@INPUT_FILE.clicked(required=True)
+@OUTPUT_FILE.clicked(required=True)
+@SCHEME.clicked(required=False)
+@INIT_CONDS.clicked(required=False)
+@click.option('--multiplier', type=int, default=1,
+              help=("run number of steps equal to MULTIPLIER times the "
+                    + "number of stepss to decorrelate"))
+@click.option("--extra-steps", type=int, default=0,
+              help="run EXTRA-STEPS additional steps")
+def equilibrate(input_file, output_file, scheme, init_conds, multiplier,
+                extra_steps):
+    """Run path sampling equilibration, based on INPUT_FILE.
+
+    This just runs the normal path sampling simulation, but the number of
+    steps depends on how long it takes to create  a fully decorrelated
+    sample set (no frames from the initial trajectories are still active).
+
+    If N_DECORR is the number of steps to fully decorrelate, the total
+    number of steps run is: N_DECORR * MULTIPLIER + EXTRA_STEPS
+    """
+    storage = INPUT_FILE.get(input_file)
+    equilibrate_main(
+        output_storage=OUTPUT_FILE.get(output_file),
+        scheme=SCHEME.get(storage, scheme),
+        init_conds=INIT_CONDS.get(storage, init_conds),
+        multiplier=multiplier,
+        extra_steps=extra_steps
+    )
+
+
+def equilibrate_main(output_storage, scheme, init_conds, multiplier,
+                     extra_steps):
+    import openpathsampling as paths
+    init_conds = scheme.initial_conditions_from_trajectories(init_conds)
+    simulation = paths.PathSampling(
+        storage=output_storage,
+        move_scheme=scheme,
+        sample_set=init_conds
+    )
+    simulation.run_until_decorrelated()
+    n_decorr = simulation.step
+    simulation.run(n_decorr * (multiplier - 1) + extra_steps)
+    if output_storage:
+        output_storage.tags['final_conditions'] = simulation.sample_set
+        output_storage.tags['equilibrated'] = simulation.sample_set
+    return simulation.sample_set, simulation
+
+
+CLI = equilibrate
+SECTION = "Simulation"
+REQUIRES_OPS = (1, 2)

paths_cli/commands/pathsampling.py

@@ -0,0 +1,42 @@
+import click
+# import openpathsampling as paths
+
+from paths_cli.parameters import (
+    INPUT_FILE, OUTPUT_FILE, INIT_CONDS, SCHEME, N_STEPS_MC
+)
+
+
+@click.command(
+    "pathsampling",
+    short_help="Run any path sampling simulation, including TIS variants",
+)
+@INPUT_FILE.clicked(required=True)
+@OUTPUT_FILE.clicked(required=True)
+@SCHEME.clicked(required=False)
+@INIT_CONDS.clicked(required=False)
+@N_STEPS_MC
+def path_sampling(input_file, output_file, scheme, init_conds, nsteps):
+    """General path sampling, using setup in INPUT_FILE"""
+    storage = INPUT_FILE.get(input_file)
+    path_sampling_main(output_storage=OUTPUT_FILE.get(output_file),
+                       scheme=SCHEME.get(storage, scheme),
+                       init_conds=INIT_CONDS.get(storage, init_conds),
+                       n_steps=nsteps)
+
+def path_sampling_main(output_storage, scheme, init_conds, n_steps):
+    import openpathsampling as paths
+    init_conds = scheme.initial_conditions_from_trajectories(init_conds)
+    simulation = paths.PathSampling(
+        storage=output_storage,
+        move_scheme=scheme,
+        sample_set=init_conds
+    )
+    simulation.run(n_steps)
+    if output_storage:
+        output_storage.tags['final_conditions'] = simulation.sample_set
+    return simulation.sample_set, simulation
+
+
+CLI = path_sampling
+SECTION = "Simulation"
+REQUIRES_OPS = (1, 0)