Source code for espressomd.cell_system

# Copyright (C) 2013-2022 The ESPResSo project
# This file is part of ESPResSo.
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <>.
from . import utils
from . import particle_data
from .script_interface import ScriptInterfaceHelper, script_interface_register

[docs]@script_interface_register class CellSystem(ScriptInterfaceHelper): """ This class controls the particle decomposition. Attributes ---------- decomposition_type : :obj:`str` Name of the currently active particle decomposition. use_verlet_lists : :obj:`bool` Whether to use Verlet lists. skin : :obj:`float` Verlet list skin. node_grid : (3,) array_like of :obj:`int` MPI repartition for the regular decomposition cell system. max_cut_bonded : :obj:`float` Maximal range from bonded interactions. max_cut_nonbonded : :obj:`float` Maximal range from non-bonded interactions. interaction_range : :obj:`float` Maximal interaction range from all interactions, or -1 when no interactions are active (or their cutoff has no impact when only 1 MPI rank is used). Methods ------- resort() Resort the particles in the cell system. Parameters ---------- global_flag : :obj:`bool`, optional If true (default), a global resorting is done, otherwise particles are only exchanged between neighboring nodes. Returns ------- (N,) array_like of :obj:`int` The number of particles per node. tune_skin() Tune the skin by measuring the integration time and bisecting over the given range of skins. The best skin is set in the simulation core. Parameters ----------- min_skin : :obj:`float` Minimum skin to test. max_skin : :obj:`float` Maximum skin. tol : :obj:`float` Accuracy in skin to tune to. int_steps : :obj:`int` Integration steps to time. adjust_max_skin : :obj:`bool`, optional If ``True``, the value of ``max_skin`` is reduced to the maximum permissible skin (in case the passed value is too large). Defaults to ``False``. Returns ------- :obj:`float` : The :attr:`skin` get_state() Get the current state of the cell system. Returns ------- :obj:`dict` : The cell system state. """ _so_name = "CellSystem::CellSystem" _so_creation_policy = "GLOBAL" _so_bind_methods = ("get_state", "tune_skin", "resort") def __reduce__(self): so_callback, so_callback_args = super().__reduce__() return (CellSystem._restore_object, (so_callback, so_callback_args)) @classmethod def _restore_object(cls, so_callback, so_callback_args): return so_callback(*so_callback_args)
[docs] def set_regular_decomposition(self, **kwargs): """ Activate the regular decomposition cell system. Parameters ---------- use_verlet_lists : :obj:`bool`, optional Activates or deactivates the usage of Verlet lists. Defaults to ``True``. """ self.call_method("initialize", name="regular_decomposition", **kwargs)
[docs] def set_n_square(self, **kwargs): """ Activate the N-square cell system. Parameters ---------- use_verlet_lists : :obj:`bool`, optional Activates or deactivates the usage of Verlet lists. Defaults to ``True``. """ self.call_method("initialize", name="n_square", **kwargs)
[docs] def set_hybrid_decomposition(self, **kwargs): """ Activate the hybrid domain decomposition. Parameters ---------- cutoff_regular : :obj:`float` Maximum cutoff to consider in regular decomposition. Should be as low as the system permits. n_square_types : list of :obj:`int`, optional Particles types that should be handled in the N-square cell system. Defaults to an empty list. use_verlet_lists : :obj:`bool`, optional Activates or deactivates the usage of Verlet lists. Defaults to ``True``. """ self.call_method("initialize", name="hybrid_decomposition", **kwargs)
[docs] def get_pairs(self, distance, types='all'): """ Get pairs of particles closer than threshold value. Parameters ---------- distance : :obj:`float` Pairs of particles closer than ``distance`` are found. types : list of :obj:`int` or ``'all'``, optional Restrict the pair search to the specified types. Defaults to ``'all'``, in which case all particles are considered. Returns ------- list of tuples of :obj:`int` The particle pairs identified by their index Raises ------ Exception If the pair search distance is greater than the cell size """ pairs = self.call_method("get_pairs", distance=distance, types=types) return [tuple(pair) for pair in pairs]
[docs] def get_neighbors(self, particle, distance): """ Get neighbors of a given particle up to a certain distance. The choice of :ref:`cell systems <Cell systems>` has an impact on how far the algorithm can detect particle pairs: * N-square: no restriction on the search distance, no double counting if search distance is larger than the box size * regular decomposition: the search distance is bounded by half the local cell geometry * hybrid decomposition: not supported Parameters ---------- particle : :class:`~espressomd.particle_data.ParticleHandle` distance : :obj:`float` Pairs of particles closer than ``distance`` are found. Returns ------- (N,) array_like of :obj:`int` The list of neighbor particles surrounding the particle """ utils.check_type_or_throw_except( particle, 1, particle_data.ParticleHandle, "Parameter 'particle' must be a particle") utils.check_type_or_throw_except( distance, 1, float, "Parameter 'distance' must be a float") return self.call_method( "get_neighbors", distance=distance,
[docs] def non_bonded_loop_trace(self): pairs = self.call_method("non_bonded_loop_trace") res = [] for id1, id2, pos1, pos2, vec21, node in pairs: pos1 = utils.array_locked(pos1) pos2 = utils.array_locked(pos2) vec21 = utils.array_locked(vec21) res.append((id1, id2, pos1, pos2, vec21, node)) return res