Source code for espressomd.electrostatic_extensions

# 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 .script_interface import ScriptInterfaceHelper, script_interface_register
from .__init__ import has_features
import numpy as np

[docs]class ElectrostaticExtensions(ScriptInterfaceHelper): _so_creation_policy = "GLOBAL" def __init__(self, **kwargs): self._check_required_features() if 'sip' not in kwargs: params = self.default_params() params.update(kwargs) self.validate_params(params) super().__init__(**params) else: super().__init__(**kwargs) def _check_required_features(self): if not has_features("ELECTROSTATICS"): raise NotImplementedError("Feature ELECTROSTATICS not compiled in")
[docs] def validate_params(self, params): raise NotImplementedError("Derived classes must implement this method")
[docs] def default_params(self): raise NotImplementedError("Derived classes must implement this method")
[docs] def valid_keys(self): raise NotImplementedError("Derived classes must implement this method")
[docs] def required_keys(self): raise NotImplementedError("Derived classes must implement this method")
def _activate(self): self.call_method("check_charge_neutrality") self.call_method("activate") utils.handle_errors("Coulomb extension activation failed") def _deactivate(self): self.call_method("deactivate") utils.handle_errors("Coulomb extension deactivation failed")
[docs]@script_interface_register class ICC(ElectrostaticExtensions): """ Interface to the induced charge calculation scheme for dielectric interfaces. See :ref:`Dielectric interfaces with the ICC algorithm` for more details. Parameters ---------- n_icc : :obj:`int` Total number of ICC Particles. first_id : :obj:`int`, optional ID of the first ICC Particle. convergence : :obj:`float`, optional Abort criteria of the iteration. It corresponds to the maximum relative change of any of the interface particle's charge. relaxation : :obj:`float`, optional SOR relaxation parameter. ext_field : :obj:`float`, optional Homogeneous electric field added to the calculation of dielectric boundary forces. max_iterations : :obj:`int`, optional Maximal number of iterations. eps_out : :obj:`float`, optional Relative permittivity of the outer region (where the particles are). normals : (``n_icc``, 3) array_like :obj:`float` Normal vectors pointing into the outer region. areas : (``n_icc``, ) array_like :obj:`float` Areas of the discretized surface. sigmas : (``n_icc``, ) array_like :obj:`float`, optional Additional surface charge density in the absence of any charge induction. epsilons : (``n_icc``, ) array_like :obj:`float` Dielectric constant associated to the areas. """ _so_name = "Coulomb::ICCStar" _so_creation_policy = "GLOBAL"
[docs] def validate_params(self, params): utils.check_type_or_throw_except( params["n_icc"], 1, int, "Invalid parameter 'n_icc'") utils.check_type_or_throw_except( params["first_id"], 1, int, "Invalid parameter 'first_id'") utils.check_type_or_throw_except( params["convergence"], 1, float, "Invalid parameter 'convergence'") utils.check_type_or_throw_except( params["relaxation"], 1, float, "Invalid parameter 'relaxation'") utils.check_type_or_throw_except( params["ext_field"], 3, float, "Invalid parameter 'ext_field'") utils.check_type_or_throw_except( params["max_iterations"], 1, int, "Invalid parameter 'max_iterations'") utils.check_type_or_throw_except( params["eps_out"], 1, float, "Invalid parameter 'eps_out'") n_icc = params["n_icc"] if n_icc <= 0: raise ValueError("Parameter 'n_icc' must be >= 1") if n_icc: if np.shape(params["normals"]) != (n_icc, 3): raise ValueError("Parameter 'normals' has incorrect shape") utils.check_array_type_or_throw_except( np.reshape(params["normals"], (-1,)), 3 * n_icc, float, "Parameter 'normals' has incorrect type") if "sigmas" not in params: params["sigmas"] = np.zeros(n_icc) for key in ("areas", "sigmas", "epsilons"): if np.shape(params[key]) != (n_icc,): raise ValueError(f"Parameter '{key}' has incorrect shape") utils.check_array_type_or_throw_except( np.reshape(params[key], (-1,)), n_icc, float, f"Parameter '{key}' has incorrect type")
[docs] def valid_keys(self): return {"n_icc", "convergence", "relaxation", "ext_field", "max_iterations", "first_id", "eps_out", "normals", "areas", "sigmas", "epsilons", "check_neutrality"}
[docs] def required_keys(self): return {"n_icc", "normals", "areas", "epsilons"}
[docs] def default_params(self): return {"convergence": 1e-3, "relaxation": 0.7, "ext_field": [0., 0., 0.], "max_iterations": 100, "first_id": 0, "eps_out": 1, "check_neutrality": True}
[docs] def last_iterations(self): """ Number of iterations needed in last relaxation to reach the convergence criterion. Returns ------- iterations : :obj:`int` Number of iterations """ return self.citeration