cell_housekeep/Wortel.cpp

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/*
 * Copyright 2011-2016 Universiteit Antwerpen
 *
 * Licensed under the EUPL, Version 1.1 or  as soon they will be approved by
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at: http://ec.europa.eu/idabc/eupl5
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing
 * permissions and limitations under the Licence.
 */
#include "Wortel.h"

#include "bio/BoundaryType.h"
#include "bio/Cell.h"
#include "bio/Mesh.h"
#include "math/RandomEngine.h"

#include <trng/uniform01_dist.hpp>

namespace SimPT_Default {
namespace CellHousekeep {

using namespace std;
using namespace boost::property_tree;

Wortel::Wortel(const CoreData& cd)
{
        Initialize(cd);
}

void Wortel::Initialize(const CoreData& cd)
{
        m_cd = cd;

        const trng::uniform01_dist<double> dist;
        m_uniform_generator = m_cd.m_random_engine->GetGenerator(dist);

        const auto& p            = m_cd.m_parameters;
        m_ga_threshold           = p->get<double>("wortel.ga_threshold");
        m_shy2_threshold         = p->get<double>("wortel.shy2_threshold");
}

void Wortel::operator()(Cell* cell)
{
        const double chem2      = cell->GetChemical(2);
        const double chem3      = cell->GetChemical(3);
        const int celltype      = cell->GetCellType();
        const double t_area     = cell->GetTargetArea();
        const double a_area     = cell->GetArea();

//      if (/*sim->GetSimTime() m_mesh*/m_sim->GetSimTime() == 0)
//          {
//              cell->SetChemical(1,0.000);
//          }

        // DDV: EXPONENTIAL GROWTH WITH CHEMICAL 1 FOR START/STOP
//      if ( ( chem1 / a_area ) > 1./*1.0 0.085*/)
//      {
//              const double incr             = 0.1;
//              const double update_t_area    = t_area + incr;
//              cell->SetTargetArea(update_t_area);
//      }

        if (cell->GetBoundaryType() == BoundaryType::None)
        {
                if (celltype != 0 && (chem3 / a_area) >= m_ga_threshold) {
                        if ((chem2 / a_area) < m_shy2_threshold) {
                                const double incr = 0.02 * a_area;
                                const double update_t_area = t_area + incr;
                                cell->SetTargetArea(update_t_area);
                        } else {
                                const double incr = 0.2 * a_area;
                                const double update_t_area = t_area + incr;
                                cell->SetTargetArea(update_t_area);
                        }
                }

/*

        if (cell->GetBoundary() == BoundaryType::Type::None) {
                if (cell->GetArea() > threshold * m_cell_base_area) {
                        cell->SetChemical(0, 0);
                        must_divide = true;
                }

        // Updates
        const double incr = m_auxin_dependent_growth ? (chem / (1. + chem)) * rate : rate;
        const double update_t_area    = t_area + incr;
        const double update_factor    = update_t_area / t_area;
        const double update_t_length  = t_length * sqrt(update_factor);

        cell->SetTargetArea(update_t_area);
        cell->SetTargetLength(update_t_length);
        }
*/
        }

/*
        static ofstream myfile1;
        //    if ((int)m_mesh->GetSimTime() % 600 == 0)
        //    {
        myfile1.open("datadumpIUAP_1.txt",std::ios::app);
        myfile1 << (cell->GetChemical(0)) / (cell->GetArea()) << "\t";
        myfile1.close();
//
//      auto &transfer_map=m_cd.m_coupled_sim_transfer_data;

//      double transfer_value=0.0;

//      auto it=transfer_map.find(cell->GetIndex());
//      if (it!=transfer_map.end())
//      {
//              transfer_value=it->second;
//      }
*/

}

} // namespace
} // namespace