ExtendedBidomainNeumannSurfaceTermAssembler.hpp

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 EXTENDEDBIDOMAINNEUMANNSURFACETERMASSEMBLER_HPP_
00030 #define EXTENDEDBIDOMAINNEUMANNSURFACETERMASSEMBLER_HPP_
00031 
00032 #include "AbstractFeSurfaceIntegralAssembler.hpp"
00033 
00034 
00042 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00043 class ExtendedBidomainNeumannSurfaceTermAssembler : public AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM,SPACE_DIM,3>
00044 {
00045 protected:
00063     virtual c_vector<double, 3*ELEMENT_DIM> ComputeVectorSurfaceTerm(
00064         const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM> &rSurfaceElement,
00065         c_vector<double,ELEMENT_DIM> &rPhi,
00066         ChastePoint<SPACE_DIM> &rX);
00067 
00068 public:
00076     ExtendedBidomainNeumannSurfaceTermAssembler(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
00077                                         BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,3>* pBoundaryConditions,
00078                                         unsigned numQuadPoints = 2)
00079         : AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM,SPACE_DIM,3>(pMesh, pBoundaryConditions, numQuadPoints)
00080     {
00081     }
00082 };
00083 
00084 
00085 #define COVERAGE_IGNORE //no non-zero Neumann BC allowed at the moment in extended bidomain problems
00086 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00087 c_vector<double, 3*ELEMENT_DIM> ExtendedBidomainNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM>::ComputeVectorSurfaceTerm(
00088     const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM> &rSurfaceElement,
00089     c_vector<double,ELEMENT_DIM> &rPhi,
00090     ChastePoint<SPACE_DIM> &rX)
00091 {
00092     // D_times_gradu_dot_n = [D grad(u)].n, D=diffusion matrix
00093     double sigma_i_times_grad_phi_i_first_cell_dot_n = this->mpBoundaryConditions->GetNeumannBCValue(&rSurfaceElement, rX, 0);
00094     double sigma_i_times_grad_phi_i_second_cell_dot_n = this->mpBoundaryConditions->GetNeumannBCValue(&rSurfaceElement, rX, 1);
00095     double sigma_e_times_grad_phi_e_dot_n = this->mpBoundaryConditions->GetNeumannBCValue(&rSurfaceElement, rX, 2);
00096 
00097     c_vector<double, 3*ELEMENT_DIM> ret;
00098 
00099     for (unsigned i=0; i<3*ELEMENT_DIM; i = i + 3)
00100     {
00101         ret(i) = rPhi(i)*sigma_i_times_grad_phi_i_first_cell_dot_n;
00102         ret(i+1) = rPhi(i)*sigma_i_times_grad_phi_i_second_cell_dot_n;
00103         ret(i+2) = rPhi(i)*(sigma_i_times_grad_phi_i_first_cell_dot_n + sigma_i_times_grad_phi_i_second_cell_dot_n + sigma_e_times_grad_phi_e_dot_n);
00104     }
00105     return ret;
00106 }
00107 #undef COVERAGE_IGNORE
00108 
00109 #endif // EXTENDEDBIDOMAINNEUMANNSURFACETERMASSEMBLER_HPP_