AbstractCardiacCellFactory.cpp

00001 /*
00002 
00003 Copyright (c) 2005-2015, University of Oxford.
00004 All rights reserved.
00005 
00006 University of Oxford means the Chancellor, Masters and Scholars of the
00007 University of Oxford, having an administrative office at Wellington
00008 Square, Oxford OX1 2JD, UK.
00009 
00010 This file is part of Chaste.
00011 
00012 Redistribution and use in source and binary forms, with or without
00013 modification, are permitted provided that the following conditions are met:
00014  * Redistributions of source code must retain the above copyright notice,
00015    this list of conditions and the following disclaimer.
00016  * Redistributions in binary form must reproduce the above copyright notice,
00017    this list of conditions and the following disclaimer in the documentation
00018    and/or other materials provided with the distribution.
00019  * Neither the name of the University of Oxford nor the names of its
00020    contributors may be used to endorse or promote products derived from this
00021    software without specific prior written permission.
00022 
00023 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
00024 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
00025 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
00026 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
00027 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
00028 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
00029 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
00030 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
00031 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
00032 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
00033 
00034 */
00035 
00036 #include "AbstractCardiacCellFactory.hpp"
00037 #include "FakeBathCell.hpp"
00038 #include "AbstractCvodeCell.hpp"
00039 #include "HeartConfig.hpp"
00040 
00041 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00042 AbstractCardiacCellInterface*  AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::CreateCardiacCellForNode(
00043     Node<SPACE_DIM>* pNode)
00044 {
00045     if (HeartRegionCode::IsRegionBath( pNode->GetRegion() ))
00046     {
00047         return new FakeBathCell(this->mpSolver, this->mpZeroStimulus);
00048     }
00049     else
00050     {
00051         AbstractCardiacCellInterface* p_cell = CreateCardiacCellForTissueNode(pNode);
00052 #ifdef CHASTE_CVODE
00053         if (dynamic_cast<AbstractCvodeCell*>(p_cell))
00054         {
00055 #if CHASTE_SUNDIALS_VERSION >= 20400
00056             // Tell the single cell model solver not to re-initialise on subsequent Solve calls.
00057             // Unfortunately the oldest CVODE we currently support (2.5.0 in Sundials 2.3.0) doesn't
00058             // work very well this this enabled, so we will go without and take a performance hit.
00059             static_cast<AbstractCvodeCell*>(p_cell)->SetMinimalReset(true);
00060 #endif // SUNDIALS_VERSION
00061             // Use the PDE timestep as the [maximum] CVODE timestep.
00062             static_cast<AbstractCvodeCell*>(p_cell)->SetTimestep(HeartConfig::Instance()->GetPdeTimeStep());
00063         }
00064 #endif // CHASTE_CVODE
00065         return p_cell;
00066     }
00067 }
00068 
00069 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00070 void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::FinaliseCellCreation(
00071     std::vector< AbstractCardiacCellInterface* >* pCellsDistributed,
00072     unsigned lo,
00073     unsigned hi)
00074 {
00075 }
00076 
00077 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00078 void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::FillInCellularTransmuralAreas()
00079 {
00080     //implemented in subclasses
00081 }
00082 
00083 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00084 unsigned AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetNumberOfCells()
00085 {
00086     assert(mpMesh != NULL);
00087     return mpMesh->GetNumNodes();
00088 }
00089 
00090 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00091 AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::AbstractCardiacCellFactory(
00092         boost::shared_ptr<AbstractIvpOdeSolver> pSolver)
00093     : mpMesh(NULL),
00094       mpHeartGeometryInformation(NULL),
00095       mpZeroStimulus(new ZeroStimulus),
00096       mpSolver(pSolver)
00097 {
00098 }
00099 
00100 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00101 AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::~AbstractCardiacCellFactory()
00102 {
00103 }
00104 
00105 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00106 void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::SetMesh(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh)
00107 {
00108     mpMesh = pMesh;
00109 }
00110 
00111 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00112 AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetMesh()
00113 {
00114     if (mpMesh == NULL)
00115     {
00116         EXCEPTION("The mesh object has not been set in the cell factory");
00117     }
00118     return mpMesh;
00119 }
00120 
00121 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00122 void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::SetHeartGeometryInformation(HeartGeometryInformation<SPACE_DIM>* pHeartGeometryInformation)
00123 {
00124     mpHeartGeometryInformation = pHeartGeometryInformation;
00125 }
00126 
00127 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00128 HeartGeometryInformation<SPACE_DIM>* AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetHeartGeometryInformation()
00129 {
00130     if (mpHeartGeometryInformation == NULL)
00131     {
00132         EXCEPTION("HeartGeometryInformation object has not been set in the cell factory");
00133     }
00134     return mpHeartGeometryInformation;
00135 }
00137 // Explicit instantiation
00139 
00140 template class AbstractCardiacCellFactory<1,1>;
00141 template class AbstractCardiacCellFactory<1,2>;
00142 template class AbstractCardiacCellFactory<1,3>;
00143 template class AbstractCardiacCellFactory<2,2>;
00144 template class AbstractCardiacCellFactory<3,3>;

Generated by  doxygen 1.6.2