MonodomainAssembler.cpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2011
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 MONODOMAINASSEMBLER_CPP_
00030 #define MONODOMAINASSEMBLER_CPP_
00031 
00032 #include "MonodomainAssembler.hpp"
00033 #include "PdeSimulationTime.hpp"
00034 
00035 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00036 c_matrix<double,1*(ELEMENT_DIM+1),1*(ELEMENT_DIM+1)> MonodomainAssembler<ELEMENT_DIM,SPACE_DIM>::ComputeMatrixTerm(
00037                 c_vector<double, ELEMENT_DIM+1> &rPhi,
00038                 c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> &rGradPhi,
00039                 ChastePoint<SPACE_DIM> &rX,
00040                 c_vector<double,1> &rU,
00041                 c_matrix<double, 1, SPACE_DIM> &rGradU /* not used */,
00042                 Element<ELEMENT_DIM,SPACE_DIM>* pElement)
00043 {
00045     return (PdeSimulationTime::GetPdeTimeStepInverse())*mMassMatrixAssembler.ComputeMatrixTerm(rPhi,rGradPhi,rX,rU,rGradU,pElement)
00046             + mStiffnessMatrixAssembler.ComputeMatrixTerm(rPhi,rGradPhi,rX,rU,rGradU,pElement);
00047 }
00048 
00049 
00050 
00051 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00052 c_vector<double,1*(ELEMENT_DIM+1)> MonodomainAssembler<ELEMENT_DIM,SPACE_DIM>::ComputeVectorTerm(
00053         c_vector<double, ELEMENT_DIM+1> &rPhi,
00054         c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> &rGradPhi /* not used */,
00055         ChastePoint<SPACE_DIM> &rX /* not used */,
00056         c_vector<double,1> &rU,
00057         c_matrix<double, 1, SPACE_DIM> &rGradU /* not used */,
00058         Element<ELEMENT_DIM,SPACE_DIM>* pElement /* not used */)
00059 {
00060     double Am = mpConfig->GetSurfaceAreaToVolumeRatio();
00061     double Cm = mpConfig->GetCapacitance();
00062     
00063     return  rPhi * (Am*Cm*rU(0)*PdeSimulationTime::GetPdeTimeStepInverse() - Am*mIionic - mIIntracellularStimulus);
00064 }
00065 
00066 
00067 
00068 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00069 c_vector<double, ELEMENT_DIM> MonodomainAssembler<ELEMENT_DIM,SPACE_DIM>::ComputeVectorSurfaceTerm(
00070        const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& rSurfaceElement,
00071        c_vector<double, ELEMENT_DIM>& rPhi,
00072        ChastePoint<SPACE_DIM>& rX)
00073 {
00074     // D_times_gradu_dot_n = [D grad(u)].n, D=diffusion matrix
00075     double D_times_gradu_dot_n = this->mpBoundaryConditions->GetNeumannBCValue(&rSurfaceElement, rX);
00076     return rPhi * D_times_gradu_dot_n;
00077 }
00078     
00079  
00080 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00081 void MonodomainAssembler<ELEMENT_DIM,SPACE_DIM>::IncrementInterpolatedQuantities(double phiI, const Node<SPACE_DIM>* pNode)
00082 {
00083     unsigned node_global_index = pNode->GetIndex();
00084     mIionic                 += phiI * this->mpCardiacTissue->rGetIionicCacheReplicated()[ node_global_index ];
00085     mIIntracellularStimulus += phiI * this->mpCardiacTissue->rGetIntracellularStimulusCacheReplicated()[ node_global_index ];
00086 }   
00087     
00088 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00089 MonodomainAssembler<ELEMENT_DIM,SPACE_DIM>::MonodomainAssembler(
00090                         AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
00091                         MonodomainTissue<ELEMENT_DIM,SPACE_DIM>* pTissue,
00092                         unsigned numQuadPoints)
00093     : AbstractCardiacFeObjectAssembler<ELEMENT_DIM,SPACE_DIM,1,true,true,CARDIAC>(pMesh,pTissue,numQuadPoints),
00094       mMassMatrixAssembler(pMesh, HeartConfig::Instance()->GetUseMassLumping(),
00095                            HeartConfig::Instance()->GetSurfaceAreaToVolumeRatio()*HeartConfig::Instance()->GetCapacitance()),
00096       mStiffnessMatrixAssembler(pMesh, pTissue)
00097 {
00098     assert(pTissue);
00099     mpConfig = HeartConfig::Instance();
00100 }
00101 
00102 
00103 
00105 // explicit instantiation
00107 
00108 
00109 template class MonodomainAssembler<1,1>;
00110 template class MonodomainAssembler<1,2>;
00111 template class MonodomainAssembler<1,3>;
00112 template class MonodomainAssembler<2,2>;
00113 template class MonodomainAssembler<3,3>;
00114 
00115 #endif /*MONODOMAINASSEMBLER_CPP_*/

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