SurfaceAreaConstraintPottsUpdateRule< DIM > Class Template Reference
#include <SurfaceAreaConstraintPottsUpdateRule.hpp>
Inherits AbstractPottsUpdateRule< 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) |
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 48 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
Constructor & Destructor Documentation
| SurfaceAreaConstraintPottsUpdateRule< DIM >::SurfaceAreaConstraintPottsUpdateRule | ( | ) | [inline] |
Constructor.
- Todo:
- Default values don't apply in 3D.
Definition at line 32 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
| SurfaceAreaConstraintPottsUpdateRule< DIM >::~SurfaceAreaConstraintPottsUpdateRule | ( | ) | [inline] |
Destructor.
Definition at line 41 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
Member Function Documentation
| double SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution | ( | unsigned | currentNodeIndex, | |
| unsigned | targetNodeIndex, | |||
| PottsBasedCellPopulation< DIM > & | rCellPopulation | |||
| ) | [inline, 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 46 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
References EXCEPTION, PottsBasedCellPopulation< DIM >::GetNode(), SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea, and PottsBasedCellPopulation< DIM >::rGetMesh().
| double SurfaceAreaConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter | ( | ) | [inline] |
- Returns:
- mDeformationEnergyParameter
Definition at line 139 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.
| double SurfaceAreaConstraintPottsUpdateRule< DIM >::GetMatureCellTargetSurfaceArea | ( | ) | const [inline] |
- Returns:
- mMatureCellTargetSurfaceArea
Definition at line 151 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
References SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.
| void SurfaceAreaConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters | ( | out_stream & | rParamsFile | ) | [inline, virtual] |
Overridden OutputUpdateRuleParameters() method.
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Implements AbstractPottsUpdateRule< DIM >.
Definition at line 164 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, and SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.
| void SurfaceAreaConstraintPottsUpdateRule< DIM >::serialize | ( | Archive & | archive, | |
| const unsigned int | version | |||
| ) | [inline, private] |
Serialize the object.
- Parameters:
-
archive the archive version the current version of this class
Reimplemented from AbstractPottsUpdateRule< DIM >.
Definition at line 71 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, and SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.
| void SurfaceAreaConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter | ( | double | deformationEnergyParameter | ) | [inline] |
Set mDeformationEnergyParameter.
- Parameters:
-
deformationEnergyParameter the new value of mDeformationEnergyParameter
Definition at line 145 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
References SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter.
| void SurfaceAreaConstraintPottsUpdateRule< DIM >::SetMatureCellTargetSurfaceArea | ( | double | matureCellTargetSurfaceArea | ) | [inline] |
Set mMatureCellTargetSurfaceArea.
- Parameters:
-
matureCellTargetSurfaceArea the new value of mMatureCellTargetSurfaceArea
Definition at line 157 of file SurfaceAreaConstraintPottsUpdateRule.cpp.
References SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractPottsUpdateRule< DIM >.
Definition at line 69 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
Member Data Documentation
double SurfaceAreaConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter [private] |
Cell deformation energy parameter. Set to the default value 0.5 in the constructor.
- Todo:
- provide units
Definition at line 59 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
Referenced by SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), SurfaceAreaConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter(), SurfaceAreaConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), SurfaceAreaConstraintPottsUpdateRule< DIM >::serialize(), and SurfaceAreaConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter().
double SurfaceAreaConstraintPottsUpdateRule< DIM >::mMatureCellTargetSurfaceArea [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 67 of file SurfaceAreaConstraintPottsUpdateRule.hpp.
Referenced by SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), SurfaceAreaConstraintPottsUpdateRule< DIM >::GetMatureCellTargetSurfaceArea(), SurfaceAreaConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), SurfaceAreaConstraintPottsUpdateRule< DIM >::serialize(), and SurfaceAreaConstraintPottsUpdateRule< DIM >::SetMatureCellTargetSurfaceArea().
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
