euler_depletion_grid.h

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// -----------------------------------------------------------------------------
//
// Copyright (C) 2021 CERN & University of Surrey for the benefit of the
// BioDynaMo collaboration. All Rights Reserved.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
//
// See the LICENSE file distributed with this work for details.
// See the NOTICE file distributed with this work for additional information
// regarding copyright ownership.
//
// -----------------------------------------------------------------------------
 
#ifndef CORE_DIFFUSION_EULER_DEPLETION_GRID_H_
#define CORE_DIFFUSION_EULER_DEPLETION_GRID_H_
 
#include <utility>
#include "core/diffusion/diffusion_grid.h"
#include "core/diffusion/euler_grid.h"
 
namespace bdm {
 
class EulerDepletionGrid : public EulerGrid {
 public:
  EulerDepletionGrid() = default;
  EulerDepletionGrid(int substance_id, std::string substance_name, real_t dc,
                     real_t mu, int resolution = 10,
                     std::vector<real_t> binding_coefficients = {},
                     std::vector<int> binding_substances = {})
      : EulerGrid(substance_id, std::move(substance_name), dc, mu, resolution),
        binding_coefficients_(std::move(binding_coefficients)),
        binding_substances_(std::move(binding_substances)) {}
 
  void DiffuseWithClosedEdge(real_t dt) override;
  void DiffuseWithOpenEdge(real_t dt) override;
  void DiffuseWithDirichlet(real_t dt) override;
  void DiffuseWithNeumann(real_t dt) override;
  void DiffuseWithPeriodic(real_t dt) override;
 
  // To avoid missing substances or coefficients, name of the sub and binding
  // coefficient must be set at the same time
 
  void SetBindingSubstance(int bnd_sub, real_t bnd_coeff) {
    binding_substances_.push_back(bnd_sub);
    binding_coefficients_.push_back(bnd_coeff);
  }
 
  std::vector<int> GetBindingSubstances() const { return binding_substances_; }
  std::vector<real_t> GetBindingCoefficients() const {
    return binding_coefficients_;
  }
 
 private:
  void ApplyDepletion(real_t dt);
 
  std::vector<real_t> binding_coefficients_ = {};
  std::vector<int> binding_substances_ = {};
 
  BDM_CLASS_DEF_OVERRIDE(EulerDepletionGrid, 1);
};
 
}  // namespace bdm
 
#endif  // CORE_DIFFUSION_EULER_DEPLETION_GRID_H_