continuum_op.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_OPERATION_DIFFUSION_OP_H_
#define CORE_OPERATION_DIFFUSION_OP_H_
 
#include <string>
#include <utility>
#include <vector>
 
#include "core/container/inline_vector.h"
#include "core/diffusion/diffusion_grid.h"
#include "core/environment/environment.h"
#include "core/operation/operation.h"
#include "core/operation/operation_registry.h"
#include "core/param/param.h"
#include "core/resource_manager.h"
#include "core/simulation.h"
#include "core/util/log.h"
 
namespace bdm {
 
class ContinuumOp : public StandaloneOperationImpl {
  BDM_OP_HEADER(ContinuumOp);
 
 public:
  void operator()() override {
    // Get active simulation and related pointers
    auto* sim = Simulation::GetActive();
    const auto* rm = sim->GetResourceManager();
    const auto* env = sim->GetEnvironment();
    const auto* param = sim->GetParam();
 
    // Compute the passed time to update the diffusion grid accordingly.
    real_t current_time = sim->GetScheduler()->GetSimulatedTime();
    delta_t_ = current_time - last_time_run_;
    last_time_run_ = current_time;
 
    // Avoid computation if delta_t_ is zero
    if (delta_t_ == 0.0) {
      return;
    }
 
    rm->ForEachContinuum([this, &env, &param](Continuum* cm) {
      // Update the diffusion grid dimension if the environment dimensions
      // have changed. If the space is bound, we do not need to update the
      // dimensions, because these should not be changing anyway
      if (env->HasGrown() &&
          param->bound_space == Param::BoundSpaceMode::kOpen) {
        cm->Update();
      }
      cm->IntegrateTimeAsynchronously(delta_t_);
      auto* dgrid = dynamic_cast<DiffusionGrid*>(cm);
      if (dgrid && param->calculate_gradients) {
        dgrid->CalculateGradient();
      }
    });
  }
 
 private:
  real_t last_time_run_ = 0.0;
  real_t delta_t_ = 0.0;
};
 
}  // namespace bdm
 
#endif  // CORE_OPERATION_DIFFUSION_OP_H_