AbstractConductivityTensors.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 #ifndef ABSTRACTCONDUCTIVITYTENSORS_HPP_
00029 #define ABSTRACTCONDUCTIVITYTENSORS_HPP_
00030 
00031 #include <vector>
00032 #include <string>
00033 #include <memory>
00034 #include "UblasIncludes.hpp"
00035 #include "AbstractTetrahedralMesh.hpp"
00036 #include "FibreReader.hpp"
00037 #include "Exception.hpp"
00038 #include "FileFinder.hpp"
00039 
00043 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00044 class AbstractConductivityTensors
00045 {
00046 protected:
00047     AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* mpMesh; 
00048     bool mUseNonConstantConductivities; 
00049     bool mUseFibreOrientation; 
00052     c_vector<double, SPACE_DIM> mConstantConductivities; // mS/cm
00053 
00058     std::vector<c_vector<double, SPACE_DIM> >* mpNonConstantConductivities; // mS/cm
00059 
00062     std::vector< c_matrix<double,SPACE_DIM,SPACE_DIM> > mTensors;
00063 
00065     bool mInitialised;
00066 
00068     FileFinder mFibreOrientationFile;
00069 
00071     std::auto_ptr<FibreReader<SPACE_DIM> > mFileReader;
00072 
00073 public:
00074 
00075     AbstractConductivityTensors();
00076 
00077     virtual ~AbstractConductivityTensors();
00078 
00084     void SetFibreOrientationFile(const FileFinder &rFibreOrientationFile);
00085 
00093     void SetConstantConductivities(c_vector<double, 1> constantConductivities);
00094 
00102     void SetConstantConductivities(c_vector<double, 2> constantConductivities);
00103 
00111     virtual void SetConstantConductivities(c_vector<double, 3> constantConductivities);
00112 
00113 
00118     void SetNonConstantConductivities(std::vector<c_vector<double, SPACE_DIM> >* pNonConstantConductivities);
00119 
00124     virtual void Init(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM> *pMesh) throw (Exception) = 0;
00125 
00131     c_matrix<double,SPACE_DIM,SPACE_DIM>& operator[](const unsigned global_index);
00132 };
00133 
00134 
00135 
00136 #endif /*ABSTRACTCONDUCTIVITYTENSORS_HPP_*/

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