#include <VolumeConstraintPottsUpdateRule.hpp>
Inheritance diagram for VolumeConstraintPottsUpdateRule< DIM >:
Collaboration diagram for VolumeConstraintPottsUpdateRule< DIM >:
Public Member Functions | |
| VolumeConstraintPottsUpdateRule () | |
| ~VolumeConstraintPottsUpdateRule () | |
| double | EvaluateHamiltonianContribution (unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation) |
| double | GetDeformationEnergyParameter () |
| void | SetDeformationEnergyParameter (double deformationEnergyParameter) |
| double | GetMatureCellTargetVolume () const |
| void | SetMatureCellTargetVolume (double matureCellTargetVolume) |
| void | OutputUpdateRuleParameters (out_stream &rParamsFile) |
Private Member Functions | |
| template<class Archive > | |
| void | serialize (Archive &archive, const unsigned int version) |
Private Attributes | |
| double | mDeformationEnergyParameter |
| double | mMatureCellTargetVolume |
Friends | |
| class | TestPottsUpdateRules |
| class | boost::serialization::access |
Detailed Description
template<unsigned DIM>
class VolumeConstraintPottsUpdateRule< 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 55 of file VolumeConstraintPottsUpdateRule.hpp.
Constructor & Destructor Documentation
| VolumeConstraintPottsUpdateRule< DIM >::VolumeConstraintPottsUpdateRule | ( | ) |
Constructor.
- Todo:
- Default values don't apply in 3D.
Definition at line 39 of file VolumeConstraintPottsUpdateRule.cpp.
| VolumeConstraintPottsUpdateRule< DIM >::~VolumeConstraintPottsUpdateRule | ( | ) |
Destructor.
Definition at line 48 of file VolumeConstraintPottsUpdateRule.cpp.
Member Function Documentation
| double VolumeConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution | ( | unsigned | currentNodeIndex, |
| unsigned | targetNodeIndex, | ||
| PottsBasedCellPopulation< DIM > & | rCellPopulation | ||
| ) | [virtual] |
Overridden EvaluateHamiltonianContribution() method
Uses sum_elements alpha (V_i - V_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 VolumeConstraintPottsUpdateRule.cpp.
References EXCEPTION, PottsBasedCellPopulation< DIM >::GetNode(), and PottsBasedCellPopulation< DIM >::rGetMesh().
| double VolumeConstraintPottsUpdateRule< DIM >::GetDeformationEnergyParameter | ( | ) |
- Returns:
- mDeformationEnergyParameter
Definition at line 102 of file VolumeConstraintPottsUpdateRule.cpp.
| double VolumeConstraintPottsUpdateRule< DIM >::GetMatureCellTargetVolume | ( | ) | const |
- Returns:
- mMatureCellTargetVolume
Definition at line 114 of file VolumeConstraintPottsUpdateRule.cpp.
| void VolumeConstraintPottsUpdateRule< DIM >::OutputUpdateRuleParameters | ( | out_stream & | rParamsFile | ) | [virtual] |
Overridden OutputUpdateRuleParameters() method.
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Implements AbstractPottsUpdateRule< DIM >.
Definition at line 127 of file VolumeConstraintPottsUpdateRule.cpp.
References AbstractPottsUpdateRule< DIM >::OutputUpdateRuleParameters().
| void VolumeConstraintPottsUpdateRule< 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 77 of file VolumeConstraintPottsUpdateRule.hpp.
References VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter, and VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume.
| void VolumeConstraintPottsUpdateRule< DIM >::SetDeformationEnergyParameter | ( | double | deformationEnergyParameter | ) |
Set mDeformationEnergyParameter.
- Parameters:
-
deformationEnergyParameter the new value of mDeformationEnergyParameter
Definition at line 108 of file VolumeConstraintPottsUpdateRule.cpp.
| void VolumeConstraintPottsUpdateRule< DIM >::SetMatureCellTargetVolume | ( | double | matureCellTargetVolume | ) |
Set mMatureCellTargetVolume.
- Parameters:
-
matureCellTargetVolume the new value of mMatureCellTargetVolume
Definition at line 120 of file VolumeConstraintPottsUpdateRule.cpp.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractPottsUpdateRule< DIM >.
Definition at line 75 of file VolumeConstraintPottsUpdateRule.hpp.
Member Data Documentation
double VolumeConstraintPottsUpdateRule< DIM >::mDeformationEnergyParameter [private] |
Cell deformation energy parameter. Set to the default value 0.5 in the constructor.
- Todo:
- provide units
Definition at line 66 of file VolumeConstraintPottsUpdateRule.hpp.
Referenced by VolumeConstraintPottsUpdateRule< DIM >::serialize().
double VolumeConstraintPottsUpdateRule< DIM >::mMatureCellTargetVolume [private] |
Non-dimensional target volume of a mature (fully-grown) cell, given in number of lattice sites. Set to the default value 16 in the constructor.
Definition at line 73 of file VolumeConstraintPottsUpdateRule.hpp.
Referenced by VolumeConstraintPottsUpdateRule< DIM >::serialize().
The documentation for this class was generated from the following files:
- cell_based/src/population/update_rules/VolumeConstraintPottsUpdateRule.hpp
- cell_based/src/population/update_rules/VolumeConstraintPottsUpdateRule.cpp
