chemotaxis.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_BEHAVIOR_CHEMOTAXIS_H_
#define CORE_BEHAVIOR_CHEMOTAXIS_H_
 
#include "core/agent/cell.h"
#include "core/behavior/behavior.h"
#include "core/diffusion/diffusion_grid.h"
#include "core/resource_manager.h"
 
namespace bdm {
 
class Chemotaxis : public Behavior {
  BDM_BEHAVIOR_HEADER(Chemotaxis, Behavior, 1);
 
 public:
  Chemotaxis() = default;
  Chemotaxis(const std::string& substance, real_t speed) : speed_(speed) {
    dgrid_ = Simulation::GetActive()->GetResourceManager()->GetDiffusionGrid(
        substance);
  }
 
  explicit Chemotaxis(DiffusionGrid* dgrid, real_t speed)
      : dgrid_(dgrid), speed_(speed) {}
 
  virtual ~Chemotaxis() = default;
 
  void Initialize(const NewAgentEvent& event) override {
    Base::Initialize(event);
    auto* other = bdm_static_cast<Chemotaxis*>(event.existing_behavior);
    dgrid_ = other->dgrid_;
    speed_ = other->speed_;
  }
 
  void Run(Agent* agent) override {
    auto* cell = bdm_static_cast<Cell*>(agent);
    auto& position = cell->GetPosition();
    Real3 gradient;
    dgrid_->GetGradient(position, &gradient);  // returns normalized gradient
    cell->UpdatePosition(gradient * speed_);
  }
 
 private:
  DiffusionGrid* dgrid_ = nullptr;
  real_t speed_;
};
 
}  // namespace bdm
 
#endif  // CORE_BEHAVIOR_CHEMOTAXIS_H_