AbstractCardiacCellFactory.cpp

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 #include "AbstractCardiacCellFactory.hpp"
00030 #include "HeartRegionCodes.hpp"
00031 
00032 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00033 AbstractCardiacCell*  AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::CreateCardiacCellForNode(
00034     unsigned nodeIndex)
00035 {
00036     if (mpMesh->GetNode(nodeIndex)->GetRegion() == HeartRegionCode::BATH)
00037     {
00038         return mpFakeCell;
00039     }
00040     else
00041     {
00042         return CreateCardiacCellForTissueNode(nodeIndex);
00043     }
00044 }
00045 
00046 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00047 void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::FinaliseCellCreation(
00048     std::vector< AbstractCardiacCell* >* pCellsDistributed,
00049     unsigned lo,
00050     unsigned hi)
00051 {
00052 }
00053 
00054 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00055 void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::FillInCellularTransmuralAreas()
00056 {
00057     //implemented in subclasses
00058 }
00059 
00060 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00061 unsigned AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetNumberOfCells()
00062 {
00063     assert(mpMesh != NULL);
00064     return mpMesh->GetNumNodes();
00065 }
00066 
00067 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00068 AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::AbstractCardiacCellFactory(
00069         boost::shared_ptr<AbstractIvpOdeSolver> pSolver)
00070     : mpMesh(NULL),
00071       mpHeartGeometryInformation(NULL),
00072       mpZeroStimulus(new ZeroStimulus),
00073       mpSolver(pSolver),
00074       mpFakeCell(new FakeBathCell(mpSolver, mpZeroStimulus))
00075 {
00076 }
00077 
00078 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00079 AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::~AbstractCardiacCellFactory()
00080 {
00081     delete mpFakeCell;
00082 }
00083 
00084 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00085 void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::SetMesh(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh)
00086 {
00087     mpMesh = pMesh;
00088 }
00089 
00090 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00091 AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetMesh()
00092 {
00093     if (mpMesh == NULL)
00094     {
00095         EXCEPTION("The mesh object has not been set in the cell factory");
00096     }
00097     return mpMesh;
00098 }
00099 
00100 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00101 void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::SetHeartGeometryInformation(HeartGeometryInformation<SPACE_DIM>* pHeartGeometryInformation)
00102 {
00103     mpHeartGeometryInformation = pHeartGeometryInformation;
00104 }
00105 
00106 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00107 HeartGeometryInformation<SPACE_DIM>* AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetHeartGeometryInformation()
00108 {
00109     if (mpHeartGeometryInformation == NULL)
00110     {
00111         EXCEPTION("HeartGeometryInformation object has not been set in the cell factory");
00112     }
00113     return mpHeartGeometryInformation;
00114 }
00116 // Explicit instantiation
00118 
00119 template class AbstractCardiacCellFactory<1,1>;
00120 template class AbstractCardiacCellFactory<1,2>;
00121 template class AbstractCardiacCellFactory<1,3>;
00122 template class AbstractCardiacCellFactory<2,2>;
00123 template class AbstractCardiacCellFactory<3,3>;