#include <SurfaceAreaConstraintPottsUpdateRule.hpp>
Inheritance diagram for SurfaceAreaConstraintPottsUpdateRule< DIM >: Collaboration diagram for SurfaceAreaConstraintPottsUpdateRule< DIM >:Public Member Functions | |
| SurfaceAreaConstraintPottsUpdateRule () | |
| ~SurfaceAreaConstraintPottsUpdateRule () | |
| double | EvaluateHamiltonianContribution (unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation) |
| double | GetDeformationEnergyParameter () |
| void | SetDeformationEnergyParameter (double deformationEnergyParameter) |
| double | GetMatureCellTargetSurfaceArea () const |
| void | SetMatureCellTargetSurfaceArea (double matureCellTargetSurfaceArea) |
| void | OutputUpdateRuleParameters (out_stream &rParamsFile) |
| Public Member Functions inherited from AbstractPottsUpdateRule< DIM > | |
| AbstractPottsUpdateRule () | |
| virtual | ~AbstractPottsUpdateRule () |
| Public Member Functions inherited from AbstractUpdateRule< DIM > | |
| AbstractUpdateRule () | |
| virtual | ~AbstractUpdateRule () |
| void | OutputUpdateRuleInfo (out_stream &rParamsFile) |
| Public Member Functions inherited from Identifiable | |
| virtual | ~Identifiable () |
| std::string | GetIdentifier () const |
Private Member Functions | |
| template<class Archive > | |
| void | serialize (Archive &archive, const unsigned int version) |
Private Attributes | |
| double | mDeformationEnergyParameter |
| double | mMatureCellTargetSurfaceArea |
Friends | |
| class | TestPottsUpdateRules |
| class | boost::serialization::access |
Detailed Description
template<unsigned DIM>
class SurfaceAreaConstraintPottsUpdateRule< DIM >
A volume constraint update rule class for use in Potts based simulations.
Note this currently assumes cells don't grow, i.e the target volume is constant for each cell over time.
Definition at line 52 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
Constructor & Destructor Documentation
| SurfaceAreaConstraintPottsUpdateRule< DIM >::SurfaceAreaConstraintPottsUpdateRule | ( | ) |
Constructor.
- Todo:
- Default values don't apply in 3D.
Definition at line 39 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
| SurfaceAreaConstraintPottsUpdateRule< DIM >::~SurfaceAreaConstraintPottsUpdateRule | ( | ) |
Destructor.
Definition at line 48 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
Member Function Documentation
|
virtual |
Overridden EvaluateHamiltonianContribution() method
Uses sum_elements gamma (A_i - A_i^T)^2.
- Parameters
-
currentNodeIndex The index of the current node/lattice site targetNodeIndex The index of the target node/lattice site rCellPopulation The cell population
- Returns
- The difference in the Hamiltonian with the configuration of the target node having the same spin as the current node with the current configuration. i.e H_1-H_0
Implements AbstractPottsUpdateRule< DIM >.
Definition at line 53 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
References EXCEPTION, PottsBasedCellPopulation< DIM >::GetNode(), and PottsBasedCellPopulation< DIM >::rGetMesh().
| double SurfaceAreaConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter | ( | ) |
- Returns
- mDeformationEnergyParameter
Definition at line 176 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
| double SurfaceAreaConstraintPottsUpdateRule< DIM >::GetMatureCellTargetSurfaceArea | ( | ) | const |
- Returns
- mMatureCellTargetSurfaceArea
Definition at line 188 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
|
virtual |
Overridden OutputUpdateRuleParameters() method.
- Parameters
-
rParamsFile the file stream to which the parameters are output
Reimplemented from AbstractPottsUpdateRule< DIM >.
Definition at line 201 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
References AbstractPottsUpdateRule< DIM >::OutputUpdateRuleParameters().
|
inlineprivate |
Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.
- Parameters
-
archive The boost archive. version The current version of this class.
Definition at line 82 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, and SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.
| void SurfaceAreaConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter | ( | double | deformationEnergyParameter | ) |
Set mDeformationEnergyParameter.
- Parameters
-
deformationEnergyParameter the new value of mDeformationEnergyParameter
Definition at line 182 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
| void SurfaceAreaConstraintPottsUpdateRule< DIM >::SetMatureCellTargetSurfaceArea | ( | double | matureCellTargetSurfaceArea | ) |
Set mMatureCellTargetSurfaceArea.
- Parameters
-
matureCellTargetSurfaceArea the new value of mMatureCellTargetSurfaceArea
Definition at line 194 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
Member Data Documentation
|
private |
Cell deformation energy parameter. Set to the default value 0.5 in the constructor.
- Todo:
- provide units
Definition at line 63 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
Referenced by SurfaceAreaConstraintPottsUpdateRule< DIM >::serialize().
|
private |
- Todo:
- provide units #1829 Non-dimensional target surface area of a mature (fully-grown) cell, given in units of area of lattice site. Set to the default value 16 in the constructor.
Definition at line 71 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
Referenced by SurfaceAreaConstraintPottsUpdateRule< DIM >::serialize().
The documentation for this class was generated from the following files:
- cell_based/src/population/update_rules/SurfaceAreaConstraintPottsUpdateRule.hpp
- cell_based/src/population/update_rules/SurfaceAreaConstraintPottsUpdateRule.cpp
