cell_chemistry/Blad.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 "Blad.h"

#include "bio/BoundaryType.h"
#include "bio/Cell.h"
#include "bio/ReduceCellWalls.h"

using namespace std;
using namespace SimPT_Sim::Util;
using boost::property_tree::ptree;

namespace SimPT_Blad {
namespace CellChemistry {

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

void Blad::Initialize(const CoreData& cd)
{
        m_cd = cd;
        const auto& p = m_cd.m_parameters->get_child("auxin_transport");

        const auto& q     = m_cd.m_parameters->get_child("blad");
        m_aux1prod        = p.get<double>("aux1prod");
        m_aux_breakdown   = p.get<double>("aux_breakdown");
        m_grid_size       = q.get<int>("grid_size");
        m_M_degradation   = q.get<double>("M_degradation");
        m_M_duration      = q.get<double>("M_duration");
        m_M_production    = q.get<double>("M_production");
}

void Blad::operator()(Cell* cell, double* dchem)
{

        double time_now         = m_cd.m_time_data->m_sim_time;
        const double chem1      = cell->GetChemical(1);
        //const double a_area   = cell->GetArea();

        bool produces_M = false;
        if (m_grid_size == 32) {
                if(cell->GetIndex() > 15 && cell->GetIndex() < 32) {
                        produces_M = true;
                }
        } else if (m_grid_size == 128) {
                if ((cell->GetIndex() > 15 && cell->GetIndex() < 32)
                        || (cell->GetIndex() > 52 && cell->GetIndex() < 61)
                        || (cell->GetIndex() > 63 && cell->GetIndex() < 72)
                        || (cell->GetIndex() > 81 && cell->GetIndex() < 86)
                        || (cell->GetIndex() > 93 && cell->GetIndex() < 98)
                        || (cell->GetIndex() > 103 && cell->GetIndex() < 128)) {
                        produces_M = true;
                }
        } else if (m_grid_size == 512) {
                if ((cell->GetIndex() > 15 && cell->GetIndex() < 32)
                        || (cell->GetIndex() > 52 && cell->GetIndex() < 61)
                        || (cell->GetIndex() > 63 && cell->GetIndex() < 72)
                        || (cell->GetIndex() > 81 && cell->GetIndex() < 86)
                        || (cell->GetIndex() > 93 && cell->GetIndex() < 98)
                        || (cell->GetIndex() > 103 && cell->GetIndex() < 128)
                        || (cell->GetIndex() > 135 && cell->GetIndex() < 144)
                        || (cell->GetIndex() > 187 && cell->GetIndex() < 196)
                        || (cell->GetIndex() > 207 && cell->GetIndex() < 256)
                        || (cell->GetIndex() > 280 && cell->GetIndex() < 297)
                        || (cell->GetIndex() > 375 && cell->GetIndex() < 392)
                        || (cell->GetIndex() > 395 && cell->GetIndex() < 412)
                        || (cell->GetIndex() > 431 && cell->GetIndex() < 512)) {
                        produces_M = true;
                }
        }

        if( produces_M && time_now < m_M_duration ) {
                dchem[1] = m_M_production - m_M_degradation * chem1;  //Half the production rate w.r.t. reference model
        } else {
                dchem[1] = -m_M_degradation * chem1;
        }
}

} // namespace
} // namespace