BidomainAssembler.cpp

00001 
00002 /*
00003 
00004 Copyright (C) University of Oxford, 2005-2011
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 Chaste is free software: you can redistribute it and/or modify it
00013 under the terms of the GNU Lesser General Public License as published
00014 by the Free Software Foundation, either version 2.1 of the License, or
00015 (at your option) any later version.
00016 
00017 Chaste is distributed in the hope that it will be useful, but WITHOUT
00018 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00019 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00020 License for more details. The offer of Chaste under the terms of the
00021 License is subject to the License being interpreted in accordance with
00022 English Law and subject to any action against the University of Oxford
00023 being under the jurisdiction of the English Courts.
00024 
00025 You should have received a copy of the GNU Lesser General Public License
00026 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00027 
00028 */
00029 
00030 #include "BidomainAssembler.hpp"
00031 #include "PdeSimulationTime.hpp"
00032 #include "UblasIncludes.hpp"
00033 #include <boost/numeric/ublas/vector_proxy.hpp>
00034 
00035 
00036 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00037 c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)>
00038     BidomainAssembler<ELEMENT_DIM,SPACE_DIM>::ComputeMatrixTerm(
00039             c_vector<double, ELEMENT_DIM+1> &rPhi,
00040             c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> &rGradPhi,
00041             ChastePoint<SPACE_DIM> &rX,
00042             c_vector<double,2> &rU,
00043             c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
00044             Element<ELEMENT_DIM,SPACE_DIM>* pElement)
00045 {
00046     // get bidomain parameters
00047     double Am = mpConfig->GetSurfaceAreaToVolumeRatio();
00048     double Cm = mpConfig->GetCapacitance();
00049 
00050     const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_i = this->mpCardiacTissue->rGetIntracellularConductivityTensor(pElement->GetIndex());
00051     const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_e = this->mpCardiacTissue->rGetExtracellularConductivityTensor(pElement->GetIndex());
00052 
00053 
00054     c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> temp = prod(sigma_i, rGradPhi);
00055     c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_i_grad_phi =
00056         prod(trans(rGradPhi), temp);
00057 
00058     c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> basis_outer_prod =
00059         outer_prod(rPhi, rPhi);
00060 
00061     c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> temp2 = prod(sigma_e, rGradPhi);
00062     c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_e_grad_phi =
00063         prod(trans(rGradPhi), temp2);
00064 
00065 
00066     c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)> ret;
00067 
00068     // even rows, even columns
00069     matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
00070     slice00(ret, slice (0, 2, ELEMENT_DIM+1), slice (0, 2, ELEMENT_DIM+1));
00071     slice00 = (Am*Cm*PdeSimulationTime::GetPdeTimeStepInverse())*basis_outer_prod + grad_phi_sigma_i_grad_phi;
00072 
00073     // odd rows, even columns
00074     matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
00075     slice10(ret, slice (1, 2, ELEMENT_DIM+1), slice (0, 2, ELEMENT_DIM+1));
00076     slice10 = grad_phi_sigma_i_grad_phi;
00077 
00078     // even rows, odd columns
00079     matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
00080     slice01(ret, slice (0, 2, ELEMENT_DIM+1), slice (1, 2, ELEMENT_DIM+1));
00081     slice01 = grad_phi_sigma_i_grad_phi;
00082 
00083     // odd rows, odd columns
00084     matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
00085     slice11(ret, slice (1, 2, ELEMENT_DIM+1), slice (1, 2, ELEMENT_DIM+1));
00086     slice11 = grad_phi_sigma_i_grad_phi + grad_phi_sigma_e_grad_phi;
00087 
00088     return ret;
00089 }
00090 
00091 
00092 
00093 
00094 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00095 BidomainAssembler<ELEMENT_DIM,SPACE_DIM>::BidomainAssembler(
00096             AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
00097             BidomainTissue<SPACE_DIM>* pTissue,
00098             unsigned numQuadPoints)
00099     : AbstractCardiacFeVolumeIntegralAssembler<ELEMENT_DIM,SPACE_DIM,2,false,true,CARDIAC>(pMesh,pTissue,numQuadPoints)
00100 {
00101     assert(pTissue != NULL);
00102     mpConfig = HeartConfig::Instance();
00103 }
00104 
00105 
00106 
00108 // explicit instantiation
00110 
00111 template class BidomainAssembler<1,1>;
00112 template class BidomainAssembler<2,2>;
00113 template class BidomainAssembler<3,3>;