Chaste
Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
AbstractOffLatticeCellPopulation.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 "AbstractOffLatticeCellPopulation.hpp"
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::AbstractOffLatticeCellPopulation
(
AbstractMesh<ELEMENT_DIM, SPACE_DIM>
& rMesh,
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std::vector<CellPtr>& rCells,
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const
std::vector<unsigned> locationIndices)
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:
AbstractCellPopulation
<ELEMENT_DIM, SPACE_DIM>(rMesh, rCells, locationIndices),
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mDampingConstantNormal(1.0),
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mDampingConstantMutant(1.0),
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mAbsoluteMovementThreshold(2.0)
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{
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}
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::AbstractOffLatticeCellPopulation
(
AbstractMesh<ELEMENT_DIM, SPACE_DIM>
& rMesh)
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:
AbstractCellPopulation
<ELEMENT_DIM, SPACE_DIM>(rMesh)
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{
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}
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// LCOV_EXCL_START
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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void
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::UpdateNodeLocations
(
double
dt)
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{
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// This method is deprecated by the NumericalMethod class hierarchy; the only population that calls this method is the NodeBasedCellPopulationWithBuskeUpdate.
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NEVER_REACHED
;
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}
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// LCOV_EXCL_STOP
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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void
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetDampingConstantNormal
(
double
dampingConstantNormal)
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{
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assert(dampingConstantNormal > 0.0);
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mDampingConstantNormal = dampingConstantNormal;
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}
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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void
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetDampingConstantMutant
(
double
dampingConstantMutant)
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{
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assert(dampingConstantMutant > 0.0);
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mDampingConstantMutant = dampingConstantMutant;
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}
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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void
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::SetAbsoluteMovementThreshold
(
double
absoluteMovementThreshold)
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{
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mAbsoluteMovementThreshold = absoluteMovementThreshold;
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}
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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double
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetDampingConstantNormal
()
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{
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return
mDampingConstantNormal;
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}
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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double
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetDampingConstantMutant
()
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{
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return
mDampingConstantMutant;
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}
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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double
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::GetAbsoluteMovementThreshold
()
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{
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return
mAbsoluteMovementThreshold;
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}
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template
<
unsigned
ELEMENT_DIM,
unsigned
SPACE_DIM>
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void
AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>::OutputCellPopulationParameters
(out_stream& rParamsFile)
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{
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*rParamsFile <<
"\t\t<DampingConstantNormal>"
<< mDampingConstantNormal <<
"</DampingConstantNormal>\n"
;
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*rParamsFile <<
"\t\t<DampingConstantMutant>"
<< mDampingConstantMutant <<
"</DampingConstantMutant>\n"
;
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// Call method on direct parent class
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AbstractCellPopulation<ELEMENT_DIM, SPACE_DIM>::OutputCellPopulationParameters
(rParamsFile);
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}
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// Explicit instantiation
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template
class
AbstractOffLatticeCellPopulation<1,1>
;
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template
class
AbstractOffLatticeCellPopulation<1,2>
;
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template
class
AbstractOffLatticeCellPopulation<2,2>
;
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template
class
AbstractOffLatticeCellPopulation<1,3>
;
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template
class
AbstractOffLatticeCellPopulation<2,3>
;
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template
class
AbstractOffLatticeCellPopulation<3,3>
;
NEVER_REACHED
#define NEVER_REACHED
Definition
Exception.hpp:227
AbstractCellPopulation
Definition
AbstractCellPopulation.hpp:83
AbstractCellPopulation::OutputCellPopulationParameters
virtual void OutputCellPopulationParameters(out_stream &rParamsFile)=0
Definition
AbstractCellPopulation.cpp:803
AbstractMesh
Definition
AbstractMesh.hpp:61
AbstractOffLatticeCellPopulation
Definition
AbstractOffLatticeCellPopulation.hpp:54
AbstractOffLatticeCellPopulation::SetDampingConstantMutant
void SetDampingConstantMutant(double dampingConstantMutant)
Definition
AbstractOffLatticeCellPopulation.cpp:72
AbstractOffLatticeCellPopulation::AbstractOffLatticeCellPopulation
AbstractOffLatticeCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
Definition
AbstractOffLatticeCellPopulation.cpp:50
AbstractOffLatticeCellPopulation::GetDampingConstantMutant
double GetDampingConstantMutant()
Definition
AbstractOffLatticeCellPopulation.cpp:91
AbstractOffLatticeCellPopulation::GetDampingConstantNormal
double GetDampingConstantNormal()
Definition
AbstractOffLatticeCellPopulation.cpp:85
AbstractOffLatticeCellPopulation::GetAbsoluteMovementThreshold
double GetAbsoluteMovementThreshold()
Definition
AbstractOffLatticeCellPopulation.cpp:97
AbstractOffLatticeCellPopulation::OutputCellPopulationParameters
virtual void OutputCellPopulationParameters(out_stream &rParamsFile)
Definition
AbstractOffLatticeCellPopulation.cpp:103
AbstractOffLatticeCellPopulation::UpdateNodeLocations
virtual void UpdateNodeLocations(double dt)
Definition
AbstractOffLatticeCellPopulation.cpp:57
AbstractOffLatticeCellPopulation::SetAbsoluteMovementThreshold
void SetAbsoluteMovementThreshold(double absoluteMovementThreshold)
Definition
AbstractOffLatticeCellPopulation.cpp:79
AbstractOffLatticeCellPopulation::SetDampingConstantNormal
void SetDampingConstantNormal(double dampingConstantNormal)
Definition
AbstractOffLatticeCellPopulation.cpp:65
cell_based
src
population
AbstractOffLatticeCellPopulation.cpp
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