#include <AdhesionPottsUpdateRule.hpp>
Inheritance diagram for AdhesionPottsUpdateRule< DIM >:
Collaboration diagram for AdhesionPottsUpdateRule< DIM >:
Public Member Functions | |
| AdhesionPottsUpdateRule () | |
| ~AdhesionPottsUpdateRule () | |
| double | EvaluateHamiltonianContribution (unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation) |
| virtual double | GetCellCellAdhesionEnergy (CellPtr pCellA, CellPtr pCellB) |
| virtual double | GetCellBoundaryAdhesionEnergy (CellPtr pCell) |
| double | GetCellCellAdhesionEnergyParameter () |
| double | GetCellBoundaryAdhesionEnergyParameter () |
| void | SetCellCellAdhesionEnergyParameter (double cellCellAdhesionEnergyEnergyParameter) |
| void | SetCellBoundaryAdhesionEnergyParameter (double cellBoundaryAdhesionEnergyParameter) |
| void | OutputUpdateRuleParameters (out_stream &rParamsFile) |
Private Member Functions | |
| template<class Archive > | |
| void | serialize (Archive &archive, const unsigned int version) |
Private Attributes | |
| double | mCellCellAdhesionEnergyParameter |
| double | mCellBoundaryAdhesionEnergyParameter |
Friends | |
| class | TestPottsUpdateRules |
| class | boost::serialization::access |
Detailed Description
template<unsigned DIM>
class AdhesionPottsUpdateRule< DIM >
An adhesion update rule for use in cell-based simulations using the cellular Potts model.
Definition at line 53 of file AdhesionPottsUpdateRule.hpp.
Constructor & Destructor Documentation
| AdhesionPottsUpdateRule< DIM >::AdhesionPottsUpdateRule | ( | ) |
Constructor.
Definition at line 39 of file AdhesionPottsUpdateRule.cpp.
| AdhesionPottsUpdateRule< DIM >::~AdhesionPottsUpdateRule | ( | ) |
Destructor.
Definition at line 47 of file AdhesionPottsUpdateRule.cpp.
Member Function Documentation
| double AdhesionPottsUpdateRule< DIM >::EvaluateHamiltonianContribution | ( | unsigned | currentNodeIndex, |
| unsigned | targetNodeIndex, | ||
| PottsBasedCellPopulation< DIM > & | rCellPopulation | ||
| ) | [virtual] |
Overridden EvaluateHamiltonianContribution() method
Uses sum_adjacentsites (1-delta(spin(i),spin(j))) gamma(spin(i),spin(j))
- 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
Before the move, we have a negative contribution (H_0) to the Hamiltonian if: the target node and neighbouring node are NOT contained in the same Potts element; the neighbouring node is contained in a Potts element, but the target node is not; or the target node is contained in a Potts element, but the neighbouring node is not.
After the move, we have a positive contribution (H_1) to the Hamiltonian if: the current node and neighbouring node are contained in different Potts elements; the neighbouring node is contained in a Potts element, but the current node is not; or the current node is contained in a Potts element, but the neighbouring node is not.
Implements AbstractPottsUpdateRule< DIM >.
Definition at line 52 of file AdhesionPottsUpdateRule.cpp.
References EXCEPTION, AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), PottsBasedCellPopulation< DIM >::GetNode(), and PottsBasedCellPopulation< DIM >::rGetMesh().
| double AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergy | ( | CellPtr | pCell | ) | [virtual] |
Method to calculate the specific interaction between cell and medium can be overridden in child classes to implement differential adhesion .etc.
- Parameters:
-
pCell pointer to the cell
- Returns:
- Cell boundary interaction adhesion energy for the cell
Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.
Definition at line 162 of file AdhesionPottsUpdateRule.cpp.
| double AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergyParameter | ( | ) |
- Returns:
- mCellBoundaryAdhesionEnergyParameter
Definition at line 174 of file AdhesionPottsUpdateRule.cpp.
| double AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy | ( | CellPtr | pCellA, |
| CellPtr | pCellB | ||
| ) | [virtual] |
Method to calculate the specific interaction between 2 cells can be overridden in child classes to implement differential adhesion .etc.
- Parameters:
-
pCellA pointer to the 1st cell pCellB pointer to the 2nd cell
- Returns:
- The cell cell interaction adhesion energy between the two cells
Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.
Definition at line 156 of file AdhesionPottsUpdateRule.cpp.
| double AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergyParameter | ( | ) |
- Returns:
- mCellCellAdhesionEnergyParameter
Definition at line 168 of file AdhesionPottsUpdateRule.cpp.
| void AdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters | ( | out_stream & | rParamsFile | ) | [virtual] |
Overridden OutputUpdateRuleParameters() method.
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Implements AbstractPottsUpdateRule< DIM >.
Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.
Definition at line 192 of file AdhesionPottsUpdateRule.cpp.
References AbstractPottsUpdateRule< DIM >::OutputUpdateRuleParameters().
Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters().
| void AdhesionPottsUpdateRule< 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 >.
Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.
Definition at line 75 of file AdhesionPottsUpdateRule.hpp.
References AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter, and AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter.
| void AdhesionPottsUpdateRule< DIM >::SetCellBoundaryAdhesionEnergyParameter | ( | double | cellBoundaryAdhesionEnergyParameter | ) |
Set mCellBoundaryAdhesionEnergyParameter.
- Parameters:
-
cellBoundaryAdhesionEnergyParameter the new value of mCellBoundaryAdhesionEnergyParameter
Definition at line 186 of file AdhesionPottsUpdateRule.cpp.
| void AdhesionPottsUpdateRule< DIM >::SetCellCellAdhesionEnergyParameter | ( | double | cellCellAdhesionEnergyEnergyParameter | ) |
Set mCellCellAdhesionEnergyParameter.
- Parameters:
-
cellCellAdhesionEnergyEnergyParameter the new value of mCellCellAdhesionEnergyParameter
Definition at line 180 of file AdhesionPottsUpdateRule.cpp.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractPottsUpdateRule< DIM >.
Reimplemented in DifferentialAdhesionPottsUpdateRule< DIM >.
Definition at line 73 of file AdhesionPottsUpdateRule.hpp.
Member Data Documentation
double AdhesionPottsUpdateRule< DIM >::mCellBoundaryAdhesionEnergyParameter [private] |
Cell-boundary adhesion energy parameter. Set to the default value 0.2 in the constructor.
- Todo:
- provide units
Definition at line 71 of file AdhesionPottsUpdateRule.hpp.
Referenced by AdhesionPottsUpdateRule< DIM >::serialize().
double AdhesionPottsUpdateRule< DIM >::mCellCellAdhesionEnergyParameter [private] |
Cell-cell adhesion energy parameter. Set to the default value 0.1 in the constructor.
- Todo:
- provide units
Definition at line 64 of file AdhesionPottsUpdateRule.hpp.
Referenced by AdhesionPottsUpdateRule< DIM >::serialize().
The documentation for this class was generated from the following files:
- cell_based/src/population/update_rules/AdhesionPottsUpdateRule.hpp
- cell_based/src/population/update_rules/AdhesionPottsUpdateRule.cpp
