DiffusionCaUpdateRule.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.
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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
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00034 */
00035 
00036 #include "DiffusionCaUpdateRule.hpp"
00037 
00038 template<unsigned DIM>
00039 DiffusionCaUpdateRule<DIM>::DiffusionCaUpdateRule()
00040     : AbstractCaUpdateRule<DIM>(),
00041       mDiffusionParameter(0.5)
00042 {
00043 }
00044 
00045 template<unsigned DIM>
00046 DiffusionCaUpdateRule<DIM>::~DiffusionCaUpdateRule()
00047 {
00048 }
00049 
00050 template<unsigned DIM>
00051 double DiffusionCaUpdateRule<DIM>::EvaluateProbability(unsigned currentNodeIndex,
00052                                                                unsigned targetNodeIndex,
00053                                                                CaBasedCellPopulation<DIM>& rCellPopulation,
00054                                                                double dt,
00055                                                                double deltaX,
00056                                                                CellPtr cell)
00057 {
00058    c_vector<double, DIM> node_index_location = rCellPopulation.GetNode(currentNodeIndex)->rGetLocation();
00059    c_vector<double, DIM> node_neighbour_location = rCellPopulation.GetNode(targetNodeIndex)->rGetLocation();
00060 
00061    return (mDiffusionParameter*dt/(2* pow(norm_2(rCellPopulation.rGetMesh().GetVectorFromAtoB(node_index_location, node_neighbour_location)), 2)));
00062 }
00063 
00064 template<unsigned DIM>
00065 double DiffusionCaUpdateRule<DIM>::GetDiffusionParameter()
00066 {
00067     return mDiffusionParameter;
00068 }
00069 
00070 template<unsigned DIM>
00071 void DiffusionCaUpdateRule<DIM>::SetDiffusionParameter(double diffusionParameter)
00072 {
00073     mDiffusionParameter = diffusionParameter;
00074 }
00075 
00076 //template<unsigned DIM>
00077 //double DiffusionCaUpdateRule<DIM>::GetTimeStep()
00078 //{
00079 //    return mDt;
00080 //}
00081 //
00082 //template<unsigned DIM>
00083 //void DiffusionCaUpdateRule<DIM>::SetTimeStep(double dt)
00084 //{
00085 //  mDt = dt;
00086 //}
00087 
00088 template<unsigned DIM>
00089 void DiffusionCaUpdateRule<DIM>::OutputUpdateRuleParameters(out_stream& rParamsFile)
00090 {
00091     *rParamsFile << "\t\t\t<DiffusionParameter>" << mDiffusionParameter << "</DiffusionParameter>\n";
00092 
00093     // Call method on direct parent class
00094     AbstractCaUpdateRule<DIM>::OutputUpdateRuleParameters(rParamsFile);
00095 }
00096 
00098 // Explicit instantiation
00100 
00101 template class DiffusionCaUpdateRule<1u>;
00102 template class DiffusionCaUpdateRule<2u>;
00103 template class DiffusionCaUpdateRule<3u>;
00104 
00105 // Serialization for Boost >= 1.36
00106 #include "SerializationExportWrapperForCpp.hpp"
00107 EXPORT_TEMPLATE_CLASS_SAME_DIMS(DiffusionCaUpdateRule)