Chaste
Commit::baa90ac2819b962188b7562f2326be23c47859a7
DiffusionCaUpdateRule.cpp
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/*
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Copyright (c) 2005-2024, University of Oxford.
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All rights reserved.
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University of Oxford means the Chancellor, Masters and Scholars of the
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University of Oxford, having an administrative office at Wellington
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Square, Oxford OX1 2JD, UK.
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This file is part of Chaste.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of the University of Oxford nor the names of its
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contributors may be used to endorse or promote products derived from this
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software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
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GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
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OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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#include "DiffusionCaUpdateRule.hpp"
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template
<
unsigned
DIM>
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DiffusionCaUpdateRule<DIM>::DiffusionCaUpdateRule
()
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:
AbstractCaUpdateRule
<DIM>(),
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mDiffusionParameter(0.5)
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{
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}
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template
<
unsigned
DIM>
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DiffusionCaUpdateRule<DIM>::~DiffusionCaUpdateRule
()
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{
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}
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template
<
unsigned
DIM>
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double
DiffusionCaUpdateRule<DIM>::EvaluateProbability
(
unsigned
currentNodeIndex,
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unsigned
targetNodeIndex,
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CaBasedCellPopulation<DIM>
& rCellPopulation,
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double
dt,
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double
deltaX,
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CellPtr cell)
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{
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c_vector<double, DIM> node_index_location = rCellPopulation.
GetNode
(currentNodeIndex)->
rGetLocation
();
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c_vector<double, DIM> node_neighbour_location = rCellPopulation.
GetNode
(targetNodeIndex)->
rGetLocation
();
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return
(mDiffusionParameter*dt/(2* pow(norm_2(rCellPopulation.
rGetMesh
().GetVectorFromAtoB(node_index_location, node_neighbour_location)), 2)));
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}
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template
<
unsigned
DIM>
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double
DiffusionCaUpdateRule<DIM>::GetDiffusionParameter
()
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{
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return
mDiffusionParameter;
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}
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template
<
unsigned
DIM>
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void
DiffusionCaUpdateRule<DIM>::SetDiffusionParameter
(
double
diffusionParameter)
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{
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mDiffusionParameter = diffusionParameter;
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}
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template
<
unsigned
DIM>
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void
DiffusionCaUpdateRule<DIM>::OutputUpdateRuleParameters
(out_stream& rParamsFile)
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{
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*rParamsFile <<
"\t\t\t<DiffusionParameter>"
<< mDiffusionParameter <<
"</DiffusionParameter>\n"
;
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// Call method on direct parent class
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AbstractCaUpdateRule<DIM>::OutputUpdateRuleParameters
(rParamsFile);
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}
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// Explicit instantiation
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template
class
DiffusionCaUpdateRule<1u>
;
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template
class
DiffusionCaUpdateRule<2u>
;
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template
class
DiffusionCaUpdateRule<3u>
;
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// Serialization for Boost >= 1.36
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#include "
SerializationExportWrapperForCpp.hpp
"
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EXPORT_TEMPLATE_CLASS_SAME_DIMS
(
DiffusionCaUpdateRule
)
SerializationExportWrapperForCpp.hpp
EXPORT_TEMPLATE_CLASS_SAME_DIMS
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
Definition
SerializationExportWrapper.hpp:352
AbstractCaUpdateRule
Definition
AbstractCaUpdateRule.hpp:50
AbstractCaUpdateRule::OutputUpdateRuleParameters
virtual void OutputUpdateRuleParameters(out_stream &rParamsFile)
Definition
AbstractCaUpdateRule.cpp:50
CaBasedCellPopulation
Definition
CaBasedCellPopulation.hpp:65
CaBasedCellPopulation::GetNode
Node< DIM > * GetNode(unsigned index)
Definition
CaBasedCellPopulation.cpp:159
CaBasedCellPopulation::rGetMesh
PottsMesh< DIM > & rGetMesh()
Definition
CaBasedCellPopulation.cpp:129
DiffusionCaUpdateRule
Definition
DiffusionCaUpdateRule.hpp:59
DiffusionCaUpdateRule::SetDiffusionParameter
void SetDiffusionParameter(double diffusionParameter)
Definition
DiffusionCaUpdateRule.cpp:71
DiffusionCaUpdateRule::GetDiffusionParameter
double GetDiffusionParameter()
Definition
DiffusionCaUpdateRule.cpp:65
DiffusionCaUpdateRule::~DiffusionCaUpdateRule
~DiffusionCaUpdateRule()
Definition
DiffusionCaUpdateRule.cpp:46
DiffusionCaUpdateRule::DiffusionCaUpdateRule
DiffusionCaUpdateRule()
Definition
DiffusionCaUpdateRule.cpp:39
DiffusionCaUpdateRule::EvaluateProbability
double EvaluateProbability(unsigned currentNodeIndex, unsigned targetNodeIndex, CaBasedCellPopulation< DIM > &rCellPopulation, double dt, double deltaX, CellPtr cell)
Definition
DiffusionCaUpdateRule.cpp:51
DiffusionCaUpdateRule::OutputUpdateRuleParameters
void OutputUpdateRuleParameters(out_stream &rParamsFile)
Definition
DiffusionCaUpdateRule.cpp:77
Node::rGetLocation
const c_vector< double, SPACE_DIM > & rGetLocation() const
Definition
Node.cpp:139
cell_based
src
population
update_rules
DiffusionCaUpdateRule.cpp
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