cell_housekeep/WrapperModel.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 "WrapperModel.h"

#include "bio/BoundaryType.h"
#include "bio/Cell.h"
#include "bio/Mesh.h"
#include "sim/CoreData.h"

#include <boost/property_tree/ptree.hpp>

namespace SimPT_Default {
namespace CellHousekeep {

using boost::property_tree::ptree;

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

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

        const auto& p = m_cd.m_parameters->get_child("wrapper_model");
        m_ch0_threshold = p.get<double>("ch0_threshold");
        m_expansion_rate = p.get<double>("expansion_rate");
}

void WrapperModel::operator()(Cell* cell)
{
        const double t_area = cell->GetTargetArea();
        const double a_area = cell->GetArea();

        // Prevent the 8 upper cells from expanding. They are used as a boundary
        // layer and are not supposed to grow / divide akin to regular cells.
        if (cell->GetIndex() > 7) {
                if ((cell->GetChemical(0) / a_area) > m_ch0_threshold /*|| (c->Chemical(6) / c->Area()) > 0.5  */) {
                        const double incr = m_expansion_rate * a_area; //Time step dependent
                        const double update_t_area = t_area + incr;
                        cell->SetTargetArea(update_t_area);
                }
        }
}

} // namespace
} // namespace