CardiacElectroMechProbRegularGeom.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2010
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 
00029 #ifndef CARDIACELECTROMECHPROBREGULARGEOM_HPP_
00030 #define CARDIACELECTROMECHPROBREGULARGEOM_HPP_
00031 
00032 #include "CardiacElectroMechanicsProblem.hpp"
00033 
00039 template<unsigned DIM>
00040 class CardiacElectroMechProbRegularGeom : public CardiacElectroMechanicsProblem<DIM>
00041 {
00042 public:
00043 
00058     CardiacElectroMechProbRegularGeom(ContractionModel contractionModel,
00059                                       double width,
00060                                       unsigned numMechanicsElementsEachDir,
00061                                       unsigned numElectricsElementsEachDir,
00062                                       AbstractCardiacCellFactory<DIM>* pCellFactory,
00063                                       double endTime,
00064                                       double electricsPdeTimeStep,
00065                                       unsigned numElecTimeStepsPerMechTimestep,
00066                                       double contractionModelOdeTimeStep,
00067                                       std::string outputDirectory = "")
00068         : CardiacElectroMechanicsProblem<DIM>(contractionModel,
00069                                               NULL, NULL, std::vector<unsigned>(), // all these set below
00070                                               pCellFactory, endTime,
00071                                               electricsPdeTimeStep,
00072                                               numElecTimeStepsPerMechTimestep,
00073                                               contractionModelOdeTimeStep, outputDirectory)
00074     {
00075         assert(DIM==2); // the below assumes DIM==2
00076 
00077         assert(width > 0.0);
00078         assert(numMechanicsElementsEachDir > 0);
00079         assert(numElectricsElementsEachDir > 0);
00080 
00081         // create electrics mesh
00082         this->mpElectricsMesh = new TetrahedralMesh<DIM,DIM>();
00083 
00084         this->mpElectricsMesh->ConstructRectangularMesh(numElectricsElementsEachDir,numElectricsElementsEachDir);
00085         this->mpElectricsMesh->Scale(width/numElectricsElementsEachDir,width/numElectricsElementsEachDir);
00086 
00087         // create mechanics mesh
00088         this->mpMechanicsMesh = new QuadraticMesh<DIM>(width,width,numMechanicsElementsEachDir,numMechanicsElementsEachDir);
00089         LOG(2, "Width of meshes is " << width);
00090         LOG(2, "Num nodes in electrical and mechanical meshes are: " << this->mpElectricsMesh->GetNumNodes() << ", " << this->mpMechanicsMesh->GetNumNodes() << "\n");
00091 
00092         // fix the nodes on x=0
00093         this->mFixedNodes.clear();
00094         for(unsigned i=0; i<this->mpMechanicsMesh->GetNumNodes(); i++)
00095         {
00096             if( fabs(this->mpMechanicsMesh->GetNode(i)->rGetLocation()[0])<1e-6)
00097             {
00098                 this->mFixedNodes.push_back(i);
00099             }
00100         }
00101 
00102         LOG(2, "Fixed the " << this->mFixedNodes.size() << " nodes on x=0");
00103     }
00104 
00105     ~CardiacElectroMechProbRegularGeom()
00106     {
00107         delete this->mpElectricsMesh;
00108         delete this->mpMechanicsMesh;
00109     }
00110 };
00111 
00112 #endif /*CARDIACELECTROMECHPROBREGULARGEOM_HPP_*/

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