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Chaste Commit::30a3e656d4b131f8c595cc6eb2becd297337570f
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#include <CellwiseSourceParabolicPde.hpp>
Public Member Functions | |
CellwiseSourceParabolicPde (AbstractCellPopulation< DIM, DIM > &rCellPopulation, double constantSourceCoefficient=0.0, double linearSourceCoefficient=0.0, double diffusionCoefficient=1.0, double duDtCoefficient=1.0, bool scaleByCellVolume=false) | |
const AbstractCellPopulation< DIM > & | rGetCellPopulation () const |
double | GetConstantCoefficient () const |
double | GetLinearCoefficient () const |
double | GetDiffusionCoefficient () const |
double | GetDuDtCoefficient () const |
bool | GetScaleByCellVolume () const |
double | ComputeDuDtCoefficientFunction (const ChastePoint< DIM > &rX) override |
double | ComputeSourceTerm (const ChastePoint< DIM > &rX, double u, Element< DIM, DIM > *pElement) override |
double | ComputeSourceTermAtNode (const Node< DIM > &rNode, double u) override |
c_matrix< double, DIM, DIM > | ComputeDiffusionTerm (const ChastePoint< DIM > &rX, Element< DIM, DIM > *pElement=nullptr) override |
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AbstractLinearParabolicPde () | |
virtual | ~AbstractLinearParabolicPde () |
virtual double | ComputeDuDtCoefficientFunction (const ChastePoint< SPACE_DIM > &rX)=0 |
virtual double | ComputeSourceTerm (const ChastePoint< SPACE_DIM > &rX, double u, Element< ELEMENT_DIM, SPACE_DIM > *pElement=nullptr)=0 |
virtual double | ComputeSourceTermAtNode (const Node< SPACE_DIM > &rNode, double u) |
virtual c_matrix< double, SPACE_DIM, SPACE_DIM > | ComputeDiffusionTerm (const ChastePoint< SPACE_DIM > &rX, Element< ELEMENT_DIM, SPACE_DIM > *pElement)=0 |
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AbstractLinearPde () | |
virtual | ~AbstractLinearPde () |
Protected Attributes | |
AbstractCellPopulation< DIM, DIM > & | mrCellPopulation |
double | mConstantSourceCoefficient |
double | mLinearSourceCoefficient |
double | mDiffusionCoefficient |
double | mDuDtCoefficient |
bool | mScaleByCellVolume |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | TestCellBasedParabolicPdes |
class | boost::serialization::access |
A parabolic PDE to be solved numerically using the finite element method, for coupling to a cell-based simulation.
The PDE takes the form
c*du/dt = Grad.(D*Grad(u)) + a*u*rho(x) + b*rho(x),
where the scalars c, D, a and b are specified by the members mDuDtCoefficient, mDiffusionCoefficient, mLinearSourceCoefficient and mConstantSourceCoefficient, respectively. Their values must be set in the constructor.
For a node of the finite element mesh with location x, the function rho(x) equals one if there is a non-apoptotic cell associated with x, and zero otherwise. Here, 'associated with' takes a different meaning for each cell population class, and is encoded in the method IsPdeNodeAssociatedWithNonApoptoticCell().
Definition at line 63 of file CellwiseSourceParabolicPde.hpp.
CellwiseSourceParabolicPde< DIM >::CellwiseSourceParabolicPde | ( | AbstractCellPopulation< DIM, DIM > & | rCellPopulation, |
double | constantSourceCoefficient = 0.0 , |
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double | linearSourceCoefficient = 0.0 , |
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double | diffusionCoefficient = 1.0 , |
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double | duDtCoefficient = 1.0 , |
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bool | scaleByCellVolume = false |
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Constructor.
rCellPopulation | reference to the cell population |
constantSourceCoefficient | the constant source term coefficient (defaults to 0.0) |
linearSourceCoefficient | the linear source term coefficient (defaults to 0.0) |
diffusionCoefficient | the rate of diffusion (defaults to 1.0) |
duDtCoefficient | rate of reaction (defaults to 1.0) |
scaleByCellVolume | whether to scale by cell volume (defaults to false) |
Definition at line 39 of file CellwiseSourceParabolicPde.cpp.
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override |
Overridden ComputeDiffusionTerm() method.
rX | the point in space at which the diffusion term is computed |
pElement | the mesh element that x is contained in (optional; defaults to NULL). |
Definition at line 140 of file CellwiseSourceParabolicPde.cpp.
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override |
Overridden ComputeDuDtCoefficientFunction() method.
rX | the point in space at which the function c is computed |
Definition at line 91 of file CellwiseSourceParabolicPde.cpp.
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override |
Overridden ComputeSourceTerm() method. That is never called.
rX | the point in space at which the nonlinear source term is computed |
u | the value of the dependent variable at the point |
pElement | the mesh element that x is contained in (optional; defaults to NULL). |
Definition at line 98 of file CellwiseSourceParabolicPde.cpp.
References NEVER_REACHED.
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override |
Overridden ComputeSourceTermAtNode() method.
Note that for CellWise Parabolic PDEs used with CellBasedParabolicPdeSolver this method returns the coefficient of the linear component of the source term.
rNode | the node at which the nonlinear source term is computed |
u | the value of the dependent variable at the node |
Definition at line 105 of file CellwiseSourceParabolicPde.cpp.
References EXCEPTION, and Node< SPACE_DIM >::GetIndex().
double CellwiseSourceParabolicPde< DIM >::GetConstantCoefficient | ( | ) | const |
Definition at line 61 of file CellwiseSourceParabolicPde.cpp.
double CellwiseSourceParabolicPde< DIM >::GetDiffusionCoefficient | ( | ) | const |
Definition at line 73 of file CellwiseSourceParabolicPde.cpp.
double CellwiseSourceParabolicPde< DIM >::GetDuDtCoefficient | ( | ) | const |
Definition at line 79 of file CellwiseSourceParabolicPde.cpp.
double CellwiseSourceParabolicPde< DIM >::GetLinearCoefficient | ( | ) | const |
Definition at line 67 of file CellwiseSourceParabolicPde.cpp.
bool CellwiseSourceParabolicPde< DIM >::GetScaleByCellVolume | ( | ) | const |
Definition at line 85 of file CellwiseSourceParabolicPde.cpp.
const AbstractCellPopulation< DIM, DIM > & CellwiseSourceParabolicPde< DIM >::rGetCellPopulation | ( | ) | const |
Definition at line 55 of file CellwiseSourceParabolicPde.cpp.
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inlineprivate |
Serialize the PDE and its member variables.
archive | the archive |
version | the current version of this class |
Definition at line 78 of file CellwiseSourceParabolicPde.hpp.
References CellwiseSourceParabolicPde< DIM >::mConstantSourceCoefficient, CellwiseSourceParabolicPde< DIM >::mDiffusionCoefficient, CellwiseSourceParabolicPde< DIM >::mDuDtCoefficient, CellwiseSourceParabolicPde< DIM >::mLinearSourceCoefficient, and CellwiseSourceParabolicPde< DIM >::mScaleByCellVolume.
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friend |
Needed for serialization.
Definition at line 70 of file CellwiseSourceParabolicPde.hpp.
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friend |
Definition at line 65 of file CellwiseSourceParabolicPde.hpp.
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protected |
Coefficient of constant source term.
Definition at line 94 of file CellwiseSourceParabolicPde.hpp.
Referenced by CellwiseSourceParabolicPde< DIM >::serialize().
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Diffusion coefficient.
Definition at line 100 of file CellwiseSourceParabolicPde.hpp.
Referenced by CellwiseSourceParabolicPde< DIM >::serialize().
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Coefficient of rate of change term.
Definition at line 103 of file CellwiseSourceParabolicPde.hpp.
Referenced by CellwiseSourceParabolicPde< DIM >::serialize().
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Coefficient of linear source term.
Definition at line 97 of file CellwiseSourceParabolicPde.hpp.
Referenced by CellwiseSourceParabolicPde< DIM >::serialize().
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The cell population member.
Definition at line 91 of file CellwiseSourceParabolicPde.hpp.
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Whether to scale terms by cell volume.
Definition at line 106 of file CellwiseSourceParabolicPde.hpp.
Referenced by CellwiseSourceParabolicPde< DIM >::serialize().