Source code for pyretis.initiation.initiate_restart

# -*- coding: utf-8 -*-
# Copyright (c) 2021, PyRETIS Development Team.
# Distributed under the LGPLv2.1+ License. See LICENSE for more info.
"""This file contains functions used for initiation of paths.

Important methods defined here

initiate_restart (:py:func:`.initiate_restart`)
    A method that will get the initial path from the output from
    a previous simulation.
import logging
import os
from pyretis.core.pathensemble import generate_ensemble_name
from pyretis.core.path import Path
from pyretis.inout import print_to_screen
from pyretis.inout.restart import read_restart_file
logger = logging.getLogger(__name__)  # pylint: disable=invalid-name

__all__ = ['initiate_restart']

[docs]def initiate_restart(simulation, cycle, settings): """Initialise paths by loading restart data. Parameters ---------- simulation : object like :py:class:`.Simulation` The simulation we are setting up. cycle : integer The simulation cycles we are starting at. settings : dictionary A dictionary with settings for the initiation. """ maxlen = settings['tis']['maxlength'] for ensemble in simulation.path_ensembles: name = ensemble.ensemble_name'Loading restart data for path ensemble %s:', name) print_to_screen( 'Loading restart data for path ensemble {}:'.format(name), level='warning' ) simulation.engine.exe_dir =['generate'] path = Path(rgen=simulation.rgen, maxlen=maxlen) restart_file = os.path.join( generate_ensemble_name(ensemble.ensemble_number), 'ensemble.restart' ) restart_info = read_restart_file(restart_file) ensemble.load_restart_info(path, restart_info, cycle=cycle) # The Force field is not part of the restart, just explicitly # set it: for point in path.phasepoints: point.forcefield = simulation.system.forcefield yield True, path, path.status, ensemble