EKReaction.hpp

Go to the documentation of this file.

/*
 * Copyright (C) 2022-2023 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
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * 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 <http://www.gnu.org/licenses/>.
 */
 
#pragma once
 
#include "config/config.hpp"
 
#ifdef WALBERLA
 
#include "EKReactant.hpp"
#include "LatticeIndices.hpp"
#include "LatticeWalberla.hpp"
 
#include <walberla_bridge/electrokinetics/ek_walberla_init.hpp>
#include <walberla_bridge/electrokinetics/reactions/EKReactionBase.hpp>
#include <walberla_bridge/electrokinetics/reactions/EKReactionBaseIndexed.hpp>
 
#include <script_interface/ScriptInterface.hpp>
#include <script_interface/auto_parameters/AutoParameters.hpp>
 
#include <utils/mpi/reduce_optional.hpp>
 
#include <algorithm>
#include <memory>
#include <sstream>
#include <stdexcept>
#include <string>
#include <vector>
 
namespace ScriptInterface::walberla {
 
class EKReaction : public AutoParameters<EKReaction, LatticeIndices> {
public:
  [[nodiscard]] std::shared_ptr<::walberla::EKReactionBase>
  get_instance() const {
    return m_ekreaction;
  }
 
  [[nodiscard]] auto get_conversion_coefficient() const noexcept {
    return m_conv_coefficient;
  }
 
protected:
  auto get_agrid(VariantMap const &args) const {
    auto lattice = get_value<std::shared_ptr<LatticeWalberla>>(args, "lattice");
    return get_value<double>(lattice->get_parameter("agrid"));
  }
 
  auto calculate_bulk_conversion_factor(VariantMap const &args) const {
    auto const tau = get_value<double>(args, "tau");
    auto const agrid = get_agrid(args);
    auto reactant = get_value<std::vector<Variant>>(args, "reactants");
 
    auto get_order = [](Variant const &v) {
      return get_value<double>(
          get_value<std::shared_ptr<EKReactant>>(v)->get_parameter("order"));
    };
    auto const sum_alphas =
        std::accumulate(reactant.begin(), reactant.end(), 0.,
                        [get_order](double sum, auto &element) {
                          return sum + get_order(element);
                        });
 
    return tau / std::pow(Utils::int_pow<3>(agrid), sum_alphas - 1.);
  }
 
  template <typename F>
  auto make_instance(VariantMap const &args, F &allocator) const {
    auto lattice = get_value<std::shared_ptr<LatticeWalberla>>(args, "lattice");
    auto reactants = get_value<std::vector<Variant>>(args, "reactants");
    auto output = ::walberla::EKReactionBase::reactants_type(reactants.size());
    auto get_instance = [](Variant const &v) {
      return get_value<std::shared_ptr<EKReactant>>(v)->get_instance();
    };
    std::transform(reactants.begin(), reactants.end(), output.begin(),
                   get_instance);
 
    auto const coefficient =
        get_value<double>(args, "coefficient") * get_conversion_coefficient();
 
    return allocator(lattice->lattice(), output, coefficient);
  }
 
  std::shared_ptr<::walberla::EKReactionBase> m_ekreaction;
  double m_conv_coefficient;
};
 
class EKBulkReaction : public EKReaction {
public:
  EKBulkReaction() {
    add_parameters({{"coefficient",
                     [this](Variant const &v) {
                       get_instance()->set_coefficient(
                           get_value<double>(v) * get_conversion_coefficient());
                     },
                     [this]() {
                       return get_instance()->get_coefficient() /
                              get_conversion_coefficient();
                     }}});
  }
 
  void do_construct(VariantMap const &args) override {
    m_conv_coefficient = calculate_bulk_conversion_factor(args);
    m_ekreaction = make_instance(args, ::walberla::new_ek_reaction_bulk);
  }
};
 
class EKIndexedReaction : public EKReaction {
public:
  EKIndexedReaction() {
    add_parameters(
        {{"coefficient",
          [this](Variant const &v) {
            get_instance()->set_coefficient(get_value<double>(v) *
                                            get_conversion_coefficient());
          },
          [this]() {
            return get_instance()->get_coefficient() /
                   get_conversion_coefficient();
          }},
         {"shape", AutoParameter::read_only, [this]() {
            return get_instance()->get_lattice()->get_grid_dimensions();
          }}});
  }
 
  void do_construct(VariantMap const &args) override {
    auto const agrid = get_agrid(args);
    m_conv_coefficient = calculate_bulk_conversion_factor(args) / agrid;
    m_ekreaction_impl =
        make_instance(args, ::walberla::new_ek_reaction_indexed);
    m_ekreaction = m_ekreaction_impl;
  }
 
  [[nodiscard]] Variant do_call_method(std::string const &method,
                                       VariantMap const &parameters) override {
    if (method == "set_node_is_boundary") {
      auto const index = get_mapped_index(
          get_value<Utils::Vector3i>(parameters, "node"),
          get_instance()->get_lattice()->get_grid_dimensions());
      m_ekreaction_impl->set_node_is_boundary(
          index, get_value<bool>(parameters, "is_boundary"));
      return none;
    }
    if (method == "get_node_is_boundary") {
      auto const index = get_mapped_index(
          get_value<Utils::Vector3i>(parameters, "node"),
          get_instance()->get_lattice()->get_grid_dimensions());
      auto const result = m_ekreaction_impl->get_node_is_boundary(index);
      return Utils::Mpi::reduce_optional(context()->get_comm(), result);
    }
    return {};
  }
 
private:
  std::shared_ptr<::walberla::EKReactionBaseIndexed> m_ekreaction_impl;
};
 
} // namespace ScriptInterface::walberla
 
#endif // WALBERLA