void CryptProjectionForce::UpdateNode3dLocationMap(AbstractCellPopulation<2>& rCellPopulation)
{
mNode3dLocationMap.clear();
c_vector<double, 2> node_location_2d;
c_vector<double, 3> node_location_3d;
// Only consider nodes corresponding to real cells
for (AbstractCellPopulation<2>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
// Get node index
unsigned node_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
// Get 3D location
node_location_2d = rCellPopulation.GetLocationOfCellCentre(*cell_iter);
node_location_3d[0] = node_location_2d[0];
node_location_3d[1] = node_location_2d[1];
node_location_3d[2] = CalculateCryptSurfaceHeightAtPoint(node_location_2d);
// Add to map
mNode3dLocationMap[node_index] = node_location_3d;
}
}
void VolumeTrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
// Make sure the cell population is updated
rCellPopulation.Update();
/**
* This hack is needed because in the case of a MeshBasedCellPopulation in which
* multiple cell divisions have occurred over one time step, the Voronoi tessellation
* (while existing) is out-of-date. Thus, if we did not regenerate the Voronoi
* tessellation here, an assertion may trip as we try to access a Voronoi element
* whose index exceeds the number of elements in the out-of-date tessellation.
*
* \todo work out how to properly fix this (#1986)
*/
if (bool(dynamic_cast<MeshBasedCellPopulation<DIM>*>(&rCellPopulation)))
{
static_cast<MeshBasedCellPopulation<DIM>*>(&(rCellPopulation))->CreateVoronoiTessellation();
}
// Iterate over cell population
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
// Get the volume of this cell
double cell_volume = rCellPopulation.GetVolumeOfCell(*cell_iter);
// Store the cell's volume in CellData
cell_iter->GetCellData()->SetItem("volume", cell_volume);
}
}
void GonadArmPositionTrackerModifier<DIM>::UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
if((SimulationTime::Instance()->GetTime())-(int)SimulationTime::Instance()->GetTime()==(1/250))
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
double id = cell_iter->GetCellId();
double position = cell_iter->GetCellData()->GetItem("DistanceAwayFromDTC");
double prolif = cell_iter->GetCellData()->GetItem("Proliferating");
fprintf(OutputPositionFile,"%e\t",SimulationTime::Instance()->GetTime());
fprintf(OutputPositionFile,"%f\t",id);
fprintf(OutputPositionFile,"%e\t",position);
fprintf(OutputPositionFile,"%e\t",prolif);
fprintf(OutputPositionFile,"\n");
}
if(SimulationTime::Instance()->IsFinished()){
//Close output file
fclose(OutputPositionFile);
}
}
/*
* Next, we define the {{{UpdateCellData()}}} method itself. This is a helper
* method that computes the height (y coordinate) of each cell in the population
* and stores this in the {{{CellData}}} property.
*/
void UpdateCellData(AbstractCellPopulation<2,2>& rCellPopulation)
{
/*
* We begin by calling {{{Update()}}} on the cell population, which ensures that
* it is in a coherent state.
*/
rCellPopulation.Update();
/*
* Next, we iterate over the cell population...
*/
for (AbstractCellPopulation<2>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
/*
* ...find its height...
*/
double cell_height = rCellPopulation.GetLocationOfCellCentre(*cell_iter)[1];
/*
* ...and store this in the {{{CellData}}} item "height".
*/
cell_iter->GetCellData()->SetItem("height", cell_height);
}
}
void TCellDiffusionForce<DIM>::AddForceContribution(AbstractCellPopulation<DIM>& rCellPopulation)
{
double dt = SimulationTime::Instance()->GetTimeStep();
// Iterate over the nodes
for (typename AbstractMesh<DIM, DIM>::NodeIterator node_iter = rCellPopulation.rGetMesh().GetNodeIteratorBegin();
node_iter != rCellPopulation.rGetMesh().GetNodeIteratorEnd();
++node_iter)
{
// Get the radius of this node
unsigned node_index = node_iter->GetIndex();
double node_radius = node_iter->GetRadius();
// Get cell associated with this index
CellPtr p_cell = rCellPopulation.GetCellUsingLocationIndex(node_index);
// Reject if no radius has been set
if (node_radius == 0.0)
{
EXCEPTION("SetRadius() must be called on each Node before calling TCellDiffusionForce::AddForceContribution() to avoid a division by zero error");
}
// If the selected cell is a Unlabelled Differentiated T Cell, apply diffusion force contribution.
if ( (p_cell->GetMutationState()->IsType<TCellMutationState>()) && (p_cell->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>())
&& !(p_cell->HasCellProperty<CellLabel>()) )
{
double nu = dynamic_cast<AbstractOffLatticeCellPopulation<DIM>*>(&rCellPopulation)->GetDampingConstant(node_index);
/* Compute the diffusion coefficient D as D = k*T/(6*pi*eta*r), where
*
* k = Boltzmann's constant,
* T = absolute temperature,
* eta = dynamic viscosity,
* r = cell radius. */
double diffusion_const_scaling = GetDiffusionScalingConstant();
double diffusion_constant = diffusion_const_scaling/node_radius;
c_vector<double, DIM> force_contribution;
for (unsigned i=0; i<DIM; i++)
{
/* The force on this cell is scaled with the timestep such that when it is
* used in the discretised equation of motion for the cell, we obtain the
* correct formula
*
* x_new = x_old + sqrt(2*D*dt)*W
*
* where W is a standard normal random variable. */
double xi = RandomNumberGenerator::Instance()->StandardNormalRandomDeviate();
force_contribution[i] = mStrengthParameter * ((nu*sqrt(2.0*diffusion_constant*dt)/dt)*xi);
}
node_iter->AddAppliedForceContribution(force_contribution);
}
}
}
void AbstractTargetAreaModifier<DIM>::UpdateTargetAreas(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
// Assume that SetupSolve() has already been called, so we must be using a VertexBasedCellPopulation
// Loop over the list of cells, rather than using the population iterator, so as to include dead cells
for (std::list<CellPtr>::iterator cell_iter = rCellPopulation.rGetCells().begin();
cell_iter != rCellPopulation.rGetCells().end();
++cell_iter)
{
UpdateTargetAreaOfCell(*cell_iter);
}
}
void CryptProjectionForce::AddForceContribution(AbstractCellPopulation<2>& rCellPopulation)
{
// First work out the 3D location of each cell
UpdateNode3dLocationMap(rCellPopulation);
// Throw an exception message if not using a MeshBasedCellPopulation
if (dynamic_cast<MeshBasedCellPopulation<2>*>(&rCellPopulation) == NULL)
{
EXCEPTION("CryptProjectionForce is to be used with a subclass of MeshBasedCellPopulation only");
}
MeshBasedCellPopulation<2>* p_static_cast_cell_population = static_cast<MeshBasedCellPopulation<2>*>(&rCellPopulation);
for (MeshBasedCellPopulation<2>::SpringIterator spring_iterator = p_static_cast_cell_population->SpringsBegin();
spring_iterator != p_static_cast_cell_population->SpringsEnd();
++spring_iterator)
{
unsigned nodeA_global_index = spring_iterator.GetNodeA()->GetIndex();
unsigned nodeB_global_index = spring_iterator.GetNodeB()->GetIndex();
c_vector<double, 2> force = CalculateForceBetweenNodes(nodeA_global_index, nodeB_global_index, rCellPopulation);
c_vector<double, 2> negative_force = -1.0 * force;
spring_iterator.GetNodeB()->AddAppliedForceContribution(negative_force);
spring_iterator.GetNodeA()->AddAppliedForceContribution(force);
}
if (mIncludeWntChemotaxis)
{
assert(WntConcentration<2>::Instance()->IsWntSetUp());
for (AbstractCellPopulation<2>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
if (cell_iter->GetCellProliferativeType()->IsType<StemCellProliferativeType>())
{
c_vector<double, 2> wnt_chemotactic_force = mWntChemotaxisStrength*WntConcentration<2>::Instance()->GetWntGradient(*cell_iter);
unsigned index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
rCellPopulation.GetNode(index)->AddAppliedForceContribution(wnt_chemotactic_force);
}
}
}
}
/* The second public method overrides {{{AddForceContribution()}}}.
* This method takes in one argument, a reference to the cell population itself.
*/
void AddForceContribution(AbstractCellPopulation<2>& rCellPopulation)
{
/* Inside the method, we loop over cells, and add a vector to
* each node associated with cells with the {{{MotileCellProperty}}}, which is proportional (with constant {{{mStrength}}}) to the negative of the position. Causing
* cells to move inwards towards the origin. Note that this will currently only work with subclasses of {{{AbstractCentreBasedCellPopulation}}}s as
* we associate cells with nodes in the force calculation. However, this could easily be modified to make it work for {{{VertexBasedCellPopulation}}}s.
*/
for (AbstractCellPopulation<2>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
if (cell_iter->HasCellProperty<MotileCellProperty>())
{
unsigned node_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
c_vector<double, 2> location = rCellPopulation.GetLocationOfCellCentre(*cell_iter);
c_vector<double, 2> force = -1.0 * mStrength * location;
rCellPopulation.GetNode(node_index)->AddAppliedForceContribution(force);
}
}
}
void PopulationTestingForce<ELEMENT_DIM, SPACE_DIM>::AddForceContribution(AbstractCellPopulation<ELEMENT_DIM,SPACE_DIM>& rCellPopulation)
{
for (unsigned i=0; i<rCellPopulation.GetNumNodes(); i++)
{
c_vector<double, SPACE_DIM> force;
for (unsigned j=0; j<SPACE_DIM; j++)
{
if (mWithPositionDependence)
{
force[j] = (j+1)*i*0.01*rCellPopulation.GetNode(i)->rGetLocation()[j];
}
else
{
force[j] = (j+1)*i*0.01;
}
}
rCellPopulation.GetNode(i)->ClearAppliedForce();
rCellPopulation.GetNode(i)->AddAppliedForceContribution(force);
}
}
c_vector<double, DIM> BuskeAdhesiveForce<DIM>::CalculateForceBetweenNodes(unsigned nodeAGlobalIndex,
unsigned nodeBGlobalIndex,
AbstractCellPopulation<DIM>& rCellPopulation)
{
// This force class is defined for NodeBasedCellPopulations only
assert(dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation) != NULL);
// We should only ever calculate the force between two distinct nodes
assert(nodeAGlobalIndex != nodeBGlobalIndex);
Node<DIM>* p_node_a = rCellPopulation.GetNode(nodeAGlobalIndex);
Node<DIM>* p_node_b = rCellPopulation.GetNode(nodeBGlobalIndex);
// Get the node locations
c_vector<double, DIM> node_a_location = p_node_a->rGetLocation();
c_vector<double, DIM> node_b_location = p_node_b->rGetLocation();
// Get the unit vector parallel to the line joining the two nodes (assuming no periodicities etc.)
c_vector<double, DIM> unit_vector = node_b_location - node_a_location;
// Calculate the distance between the two nodes
double distance_between_nodes = norm_2(unit_vector);
// Account for any cutoff in the force law
if (this->mUseCutOffLength)
{
if (distance_between_nodes >= this->GetCutOffLength())
{
return zero_vector<double>(DIM);
}
}
// Assert that the nodes are a finite, non-zero distance apart
assert(distance_between_nodes > 0);
assert(!std::isnan(distance_between_nodes));
// Normalize the unit vector
unit_vector /= distance_between_nodes;
double radius_of_cell_one = p_node_a->GetRadius();
double radius_of_cell_two = p_node_b->GetRadius();
// Compute the force vector
c_vector<double, DIM> force_between_nodes = GetMagnitudeOfForce(distance_between_nodes,radius_of_cell_one,radius_of_cell_two) * unit_vector;
return force_between_nodes;
}
void DeltaNotchTrackingModifier<DIM>::UpdateCellData(AbstractCellPopulation<DIM,DIM>& rCellPopulation)
{
// Make sure the cell population is updated
rCellPopulation.Update();
// First recover each cell's Notch and Delta concentrations from the ODEs and store in CellData
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
DeltaNotchCellCycleModel* p_model = static_cast<DeltaNotchCellCycleModel*>(cell_iter->GetCellCycleModel());
double this_delta = p_model->GetDelta();
double this_notch = p_model->GetNotch();
// Note that the state variables must be in the same order as listed in DeltaNotchOdeSystem
cell_iter->GetCellData()->SetItem("notch", this_notch);
cell_iter->GetCellData()->SetItem("delta", this_delta);
}
// Next iterate over the population to compute and store each cell's neighbouring Delta concentration in CellData
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
// Get the set of neighbouring location indices
std::set<unsigned> neighbour_indices = rCellPopulation.GetNeighbouringLocationIndices(*cell_iter);
// Compute this cell's average neighbouring Delta concentration and store in CellData
if (!neighbour_indices.empty())
{
double mean_delta = 0.0;
for (std::set<unsigned>::iterator iter = neighbour_indices.begin();
iter != neighbour_indices.end();
++iter)
{
CellPtr p_cell = rCellPopulation.GetCellUsingLocationIndex(*iter);
double this_delta = p_cell->GetCellData()->GetItem("delta");
mean_delta += this_delta/neighbour_indices.size();
}
cell_iter->GetCellData()->SetItem("mean delta", mean_delta);
}
else
{
// If this cell has no neighbours, such as an isolated cell in a CaBasedCellPopulation, store 0.0 for the cell data
cell_iter->GetCellData()->SetItem("mean delta", 0.0);
}
}
}
void BuskeCompressionForce<DIM>::AddForceContribution(AbstractCellPopulation<DIM>& rCellPopulation)
{
// This force class is defined for NodeBasedCellPopulations only
assert(dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation) != NULL);
NodeBasedCellPopulation<DIM>* p_static_cast_cell_population = static_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation);
c_vector<double, DIM> unit_vector;
// Loop over cells in the population
for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
cell_iter != rCellPopulation.End();
++cell_iter)
{
// Get the node index corresponding to this cell
unsigned node_index = rCellPopulation.GetLocationIndexUsingCell(*cell_iter);
Node<DIM>* p_node_i = rCellPopulation.GetNode(node_index);
// Get the location of this node
c_vector<double, DIM> node_i_location = p_node_i->rGetLocation();
// Get the radius of this cell
double radius_of_cell_i = p_node_i->GetRadius();
double delta_V_c = 0.0;
c_vector<double, DIM> dVAdd_vector = zero_vector<double>(DIM);
// Get the set of node indices corresponding to this cell's neighbours
std::set<unsigned> neighbouring_node_indices = p_static_cast_cell_population->GetNeighbouringNodeIndices(node_index);
// Loop over this set
for (std::set<unsigned>::iterator iter = neighbouring_node_indices.begin();
iter != neighbouring_node_indices.end();
++iter)
{
Node<DIM>* p_node_j = rCellPopulation.GetNode(*iter);
// Get the location of this node
c_vector<double, DIM> node_j_location = p_node_j->rGetLocation();
// Get the unit vector parallel to the line joining the two nodes (assuming no periodicities etc.)
unit_vector = node_j_location - node_i_location;
// Calculate the distance between the two nodes
double dij = norm_2(unit_vector);
unit_vector /= dij;
// Get the radius of the cell corresponding to this node
double radius_of_cell_j = p_node_j->GetRadius();
// If the cells are close enough to exert a force on each other...
if (dij < radius_of_cell_i + radius_of_cell_j)
{
// ...then compute the adhesion force and add it to the vector of forces...
double xij = 0.5*(radius_of_cell_i*radius_of_cell_i - radius_of_cell_j*radius_of_cell_j + dij*dij)/dij;
double dxijdd = 1.0 - xij/dij;
double dVAdd = M_PI*dxijdd*(5.0*pow(radius_of_cell_i,2.0) + 3.0*pow(xij,2.0) - 8.0*radius_of_cell_i*xij)/3.0;
dVAdd_vector += dVAdd*unit_vector;
// ...and add the contribution to the compression force acting on cell i
delta_V_c += M_PI*pow(radius_of_cell_i - xij,2.0)*(2*radius_of_cell_i - xij)/3.0;
}
}
double V_A = 4.0/3.0*M_PI*pow(radius_of_cell_i,3.0) - delta_V_c;
/**
* Target volume of the cell
* \todo Doesn't say in the Buske paper how they calculate this, so
* we need to look at this to be sure it's what we want (#1764)
*/
double V_T = 5.0;
// Note: the sign in force_magnitude is different from the one in equation (A3) in the Buske paper
c_vector<double, DIM> applied_force = -mCompressionEnergyParameter/V_T*(V_T - V_A)*dVAdd_vector;
p_node_i->AddAppliedForceContribution(applied_force);
}
}
void TCellTumorSpringForce<DIM>::AddForceContribution(AbstractCellPopulation<DIM>& rCellPopulation)
{
// Throw an exception message if not using a NodeBasedCellPopulation
if (dynamic_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation) == NULL)
{
EXCEPTION("TCellTumorSpringForce is to be used with a NodeBasedCellPopulation only");
}
std::vector< std::pair<Node<DIM>*, Node<DIM>* > >& r_node_pairs = (static_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation))->rGetNodePairs();
// Iterate over all pairs of nodes
for (typename std::vector< std::pair<Node<DIM>*, Node<DIM>* > >::iterator iter = r_node_pairs.begin();
iter != r_node_pairs.end();
iter++)
{
std::pair<Node<DIM>*, Node<DIM>* > pair = *iter;
Node<DIM>* p_node_a = pair.first;
Node<DIM>* p_node_b = pair.second;
// Get the node locations, radii and indices
c_vector<double, DIM> node_a_location = p_node_a->rGetLocation();
c_vector<double, DIM> node_b_location = p_node_b->rGetLocation();
double node_a_radius = p_node_a->GetRadius();
double node_b_radius = p_node_b->GetRadius();
unsigned node_a_index = p_node_a->GetIndex();
unsigned node_b_index = p_node_b->GetIndex();
// Get the cells associated with these node indices
CellPtr p_cell_a = rCellPopulation.GetCellUsingLocationIndex(node_a_index);
CellPtr p_cell_b = rCellPopulation.GetCellUsingLocationIndex(node_b_index);
/* --==-- 01: T Cell - T Cell Repulsion segment --==-- */
/* Applies RepulsionForce between Differentiated T-Cells (labelled and unlabelled) */
if ( (p_cell_a->GetMutationState()->IsType<TCellMutationState>()) && (p_cell_b->GetMutationState()->IsType<TCellMutationState>())
&& (p_cell_a->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>()) && (p_cell_b->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>()) )
{
c_vector<double, DIM> unit_difference;
unit_difference = (static_cast<NodeBasedCellPopulation<DIM>*>(&rCellPopulation))->rGetMesh().GetVectorFromAtoB(node_a_location, node_b_location);
double rest_length = node_a_radius+node_b_radius;
// Only apply force if the cells are close (repulsion force)
if (norm_2(unit_difference) < rest_length)
{
c_vector<double, DIM> force = this->CalculateForceBetweenNodes(p_node_a->GetIndex(), p_node_b->GetIndex(), rCellPopulation);
c_vector<double, DIM> negative_force = -1.0 * force;
for (unsigned j=0; j<DIM; j++)
{
assert(!std::isnan(force[j]));
}
p_node_a->AddAppliedForceContribution(force);
p_node_b->AddAppliedForceContribution(negative_force);
}
}
/* --==-- 02: T Cell - Tumor Cell Springs segment --==-- */
/* Applies GeneralisedLinearSpringForce between Labelled T-Cells and Tumor Cells */
if ( (p_cell_a->HasCellProperty<CellLabel>()) && (p_cell_b->GetMutationState()->IsType<TumorCellMutationState>())
|| (p_cell_b->HasCellProperty<CellLabel>()) && (p_cell_a->GetMutationState()->IsType<TumorCellMutationState>()) )
{
// Calculate the force between nodes
c_vector<double, DIM> force = this->CalculateForceBetweenNodes(p_node_a->GetIndex(), p_node_b->GetIndex(), rCellPopulation);
c_vector<double, DIM> negative_force = -1.0 * force;
for (unsigned j=0; j<DIM; j++)
{
assert(!std::isnan(force[j]));
}
// Add the force contribution to each node
p_node_a->AddAppliedForceContribution(force);
p_node_b->AddAppliedForceContribution(negative_force);
}
/* --==-- 03: Tumor Cell - Tumor Cell Springs segment --==-- */
/* Applies GeneralisedLinearSpringForce between Tumor Cells. Check both cells are Tumor Cells */
if ( (p_cell_a->GetMutationState()->IsType<TumorCellMutationState>()) && (p_cell_b->GetMutationState()->IsType<TumorCellMutationState>()) )
{
// Calculate the force between nodes
c_vector<double, DIM> force = this->CalculateForceBetweenNodes(p_node_a->GetIndex(), p_node_b->GetIndex(), rCellPopulation);
c_vector<double, DIM> negative_force = -1.0 * force;
for (unsigned j=0; j<DIM; j++)
{
assert(!std::isnan(force[j]));
}
// Add the force contribution to each node
p_node_a->AddAppliedForceContribution(force);
p_node_b->AddAppliedForceContribution(negative_force);
}
}
}
c_vector<double,2> CryptProjectionForce::CalculateForceBetweenNodes(unsigned nodeAGlobalIndex, unsigned nodeBGlobalIndex, AbstractCellPopulation<2>& rCellPopulation)
{
MeshBasedCellPopulation<2>* p_static_cast_cell_population = static_cast<MeshBasedCellPopulation<2>*>(&rCellPopulation);
// We should only ever calculate the force between two distinct nodes
assert(nodeAGlobalIndex != nodeBGlobalIndex);
// Get the node locations in 2D
c_vector<double,2> node_a_location_2d = rCellPopulation.GetNode(nodeAGlobalIndex)->rGetLocation();
c_vector<double,2> node_b_location_2d = rCellPopulation.GetNode(nodeBGlobalIndex)->rGetLocation();
// "Get the unit vector parallel to the line joining the two nodes" [GeneralisedLinearSpringForce]
// Create a unit vector in the direction of the 3D spring
c_vector<double,3> unit_difference = mNode3dLocationMap[nodeBGlobalIndex] - mNode3dLocationMap[nodeAGlobalIndex];
// Calculate the distance between the two nodes
double distance_between_nodes = norm_2(unit_difference);
assert(distance_between_nodes > 0);
assert(!std::isnan(distance_between_nodes));
unit_difference /= distance_between_nodes;
// If mUseCutOffLength has been set, then there is zero force between
// two nodes located a distance apart greater than mUseCutOffLength
if (this->mUseCutOffLength)
{
if (distance_between_nodes >= mMechanicsCutOffLength)
{
// Return zero (2D projected) force
return zero_vector<double>(2);
}
}
// Calculate the rest length of the spring connecting the two nodes
double rest_length = 1.0;
CellPtr p_cell_A = rCellPopulation.GetCellUsingLocationIndex(nodeAGlobalIndex);
CellPtr p_cell_B = rCellPopulation.GetCellUsingLocationIndex(nodeBGlobalIndex);
double ageA = p_cell_A->GetAge();
double ageB = p_cell_B->GetAge();
assert(!std::isnan(ageA));
assert(!std::isnan(ageB));
/*
* If the cells are both newly divided, then the rest length of the spring
* connecting them grows linearly with time, until mMeinekeSpringGrowthDuration hour after division.
*/
if (ageA < mMeinekeSpringGrowthDuration && ageB < mMeinekeSpringGrowthDuration)
{
/*
* The spring rest length increases from a predefined small parameter
* to a normal rest length of 1.0, over a period of one hour.
*/
std::pair<CellPtr,CellPtr> cell_pair = p_static_cast_cell_population->CreateCellPair(p_cell_A, p_cell_B);
if (p_static_cast_cell_population->IsMarkedSpring(cell_pair))
{
double lambda = mMeinekeDivisionRestingSpringLength;
rest_length = lambda + (1.0 - lambda) * ageA/mMeinekeSpringGrowthDuration;
}
if (ageA+SimulationTime::Instance()->GetTimeStep() >= mMeinekeSpringGrowthDuration)
{
// This spring is about to go out of scope
p_static_cast_cell_population->UnmarkSpring(cell_pair);
}
}
double a_rest_length = rest_length*0.5;
double b_rest_length = a_rest_length;
/*
* If either of the cells has begun apoptosis, then the length of the spring
* connecting them decreases linearly with time.
*/
if (p_cell_A->HasApoptosisBegun())
{
double time_until_death_a = p_cell_A->GetTimeUntilDeath();
a_rest_length = a_rest_length * time_until_death_a / p_cell_A->GetApoptosisTime();
}
if (p_cell_B->HasApoptosisBegun())
{
double time_until_death_b = p_cell_B->GetTimeUntilDeath();
b_rest_length = b_rest_length * time_until_death_b / p_cell_B->GetApoptosisTime();
}
rest_length = a_rest_length + b_rest_length;
// Assert that the rest length does not exceed 1
assert(rest_length <= 1.0+1e-12);
bool is_closer_than_rest_length = true;
if (distance_between_nodes - rest_length > 0)
{
is_closer_than_rest_length = false;
}
/*
* Although in this class the 'spring constant' is a constant parameter, in
* subclasses it can depend on properties of each of the cells.
*/
double multiplication_factor = 1.0;
multiplication_factor *= VariableSpringConstantMultiplicationFactor(nodeAGlobalIndex, nodeBGlobalIndex, rCellPopulation, is_closer_than_rest_length);
// Calculate the 3D force between the two points
c_vector<double,3> force_between_nodes = multiplication_factor * this->GetMeinekeSpringStiffness() * unit_difference * (distance_between_nodes - rest_length);
// Calculate an outward normal unit vector to the tangent plane of the crypt surface at the 3D point corresponding to node B
c_vector<double,3> outward_normal_unit_vector;
double dfdr = CalculateCryptSurfaceDerivativeAtPoint(node_b_location_2d);
double theta_B = atan2(node_b_location_2d[1], node_b_location_2d[0]); // use atan2 to determine the quadrant
double normalization_factor = sqrt(1 + dfdr*dfdr);
outward_normal_unit_vector[0] = dfdr*cos(theta_B)/normalization_factor;
outward_normal_unit_vector[1] = dfdr*sin(theta_B)/normalization_factor;
outward_normal_unit_vector[2] = -1.0/normalization_factor;
// Calculate the projection of the force onto the plane z=0
c_vector<double,2> projected_force_between_nodes_2d;
double force_dot_normal = inner_prod(force_between_nodes, outward_normal_unit_vector);
for (unsigned i=0; i<2; i++)
{
projected_force_between_nodes_2d[i] = force_between_nodes[i]
- force_dot_normal*outward_normal_unit_vector[i]
+ force_dot_normal*outward_normal_unit_vector[2];
}
return projected_force_between_nodes_2d;
}