hamiltonian/ModifiedGC.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 "ModifiedGC.h"

#include "HHelper.h"
#include "bio/Cell.h"
#include "sim/CoreData.h"

#include <cassert>

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

namespace SimPT_Default {
namespace Hamiltonian {

ModifiedGC::ModifiedGC(const CoreData& cd)
{
        assert( cd.Check() && "CoreData not ok in ModifiedGC Hamiltonian");
        Initialize(cd);
}

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

        m_lambda_bend                    = p.get<double>("lambda_bend");
        m_lambda_cell_length             = p.get<double>("lambda_celllength");
        m_lambda_length                  = p.get<double>("lambda_length");
        m_rp_stiffness                   = p.get<double>("relative_perimeter_stiffness");
        m_target_node_distance           = p.get<double>("target_node_distance");

}

double ModifiedGC::operator()(Cell* cell)
{
        double h = 0.0;

        if (!cell->IsBoundaryPolygon()) {

                // --------------------------------------------------------------------------------------------
                // Cell area:
                // --------------------------------------------------------------------------------------------
                // TODO: DDV: hidden factor 1000
                h += 1000.0 * pow((cell->GetArea() - cell->GetTargetArea()) / cell->GetArea(), 2);

                // --------------------------------------------------------------------------------------------
                // Wall length:
                // --------------------------------------------------------------------------------------------
                h += m_lambda_length
                        * HHelper::WallLengthTerm(cell, m_rp_stiffness, m_target_node_distance);
        }

        return h;
}

} // namespace
} // namespace