cell2cell_transport/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/Cell.h"
#include "bio/Wall.h"
 
namespace SimPT_Blad {
namespace CellToCellTransport {

using namespace std;
using namespace boost::property_tree;

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

void Blad::Initialize(const CoreData& cd)
{
        m_cd    = cd;
        const auto& p            = m_cd.m_parameters;
        m_M_diffusion_constant   = p->get<double>("blad.M_diffusion_constant");
}

void Blad::operator()(Wall* w, double* dchem_c1, double* dchem_c2)
{

        if ( !(w->GetC1()->IsBoundaryPolygon()) && !(w->GetC2()->IsBoundaryPolygon()) )
        {
                const double apoplast_thickness = 2.;

                //morphogen - chemical '1'
                const double phi2 = (w->GetLength() / ( apoplast_thickness ) ) * m_M_diffusion_constant * ( ( w->GetC2()->GetChemical(1) / (w->GetC2()->GetArea()) )
                        - ( w->GetC1()->GetChemical(1) / (w->GetC1()->GetArea()) ) );

                dchem_c1[1] += phi2 ;
                dchem_c2[1] -= phi2 ;
        }
}

} // namespace
} // namespace