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one_pot_tps.py

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one_pot_tps.py

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import click
from paths_cli.parameters import (INPUT_FILE, OUTPUT_FILE, ENGINE, STATES,
N_STEPS_MC, INIT_SNAP)
from paths_cli.commands.visit_all import visit_all_main
from paths_cli.commands.equilibrate import equilibrate_main
from paths_cli.commands.pathsampling import path_sampling_main
@click.command("one-pot-tps",
short_help="Start from a single frame and end with full TPS")
@INPUT_FILE.clicked(required=True)
@OUTPUT_FILE.clicked(required=True)
@STATES.clicked(required=True)
@ENGINE.clicked(required=False)
@click.option("--engine-hot", required=False,
help="high temperature engine for initial trajectory")
@INIT_SNAP.clicked(required=False)
@N_STEPS_MC
def one_pot_tps(input_file, output_file, state, nsteps, engine, engine_hot,
init_frame):
storage = INPUT_FILE.get(input_file)
engine = ENGINE.get(storage, engine)
engine_hot = engine if engine_hot is None else ENGINE.get(storage,
engine_hot)
one_pot_tps_main(output_storage=OUTPUT_FILE.get(output_file),
states=STATES.get(storage, state),
engine=engine,
engine_hot=engine_hot,
initial_frame=INIT_SNAP.get(storage, init_frame),
nsteps=nsteps)
def one_pot_tps_main(output_storage, states, engine, engine_hot,
initial_frame, nsteps):
import openpathsampling as paths
network = paths.TPSNetwork.from_states_all_to_all(states)
scheme = paths.OneWayShootingMoveScheme(network=network,
selector=paths.UniformSelector(),
engine=engine)
trajectory, _ = visit_all_main(None, states, engine_hot, initial_frame)
equil_multiplier = 1
equil_extra = 0
equil_set, _ = equilibrate_main(None, scheme, trajectory,
equil_multiplier, equil_extra)
return path_sampling_main(output_storage, scheme, equil_set, nsteps)
CLI = one_pot_tps
SECTION = "Workflow"
REQUIRES_OPS = (1, 2)
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