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 MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>::Update(bool hasHadBirthsOrDeaths)
{
///\todo check if there is a more efficient way of keeping track of node velocity information (#2404)
bool output_node_velocities = (this-> template HasWriter<NodeVelocityWriter>());
/**
* If node radii are set, then we must keep a record of these, since they will be cleared during
* the remeshing process. We then restore these attributes to the nodes after calling ReMesh().
*
* At present, we check whether node radii are set by interrogating the radius of the first node
* in the mesh and asking if it is strictly greater than zero (the default value, as set in the
* NodeAttributes constructor). Hence, we assume that either ALL node radii are set, or NONE are.
*
* \todo There may be a better way of checking if node radii are set (#2694)
*/
std::map<unsigned, double> old_node_radius_map;
old_node_radius_map.clear();
if (this->mrMesh.GetNodeIteratorBegin()->HasNodeAttributes())
{
if (this->mrMesh.GetNodeIteratorBegin()->GetRadius() > 0.0)
{
for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrMesh.GetNodeIteratorBegin();
node_iter != this->mrMesh.GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
old_node_radius_map[node_index] = node_iter->GetRadius();
}
}
}
std::map<unsigned, c_vector<double, SPACE_DIM> > old_node_applied_force_map;
old_node_applied_force_map.clear();
if (output_node_velocities)
{
/*
* If outputting node velocities, we must keep a record of the applied force at each
* node, since this will be cleared during the remeshing process. We then restore
* these attributes to the nodes after calling ReMesh().
*/
for (typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::NodeIterator node_iter = this->mrMesh.GetNodeIteratorBegin();
node_iter != this->mrMesh.GetNodeIteratorEnd();
++node_iter)
{
unsigned node_index = node_iter->GetIndex();
old_node_applied_force_map[node_index] = node_iter->rGetAppliedForce();
}
}
NodeMap node_map(this->mrMesh.GetNumAllNodes());
// We must use a static_cast to call ReMesh() as this method is not defined in parent mesh classes
static_cast<MutableMesh<ELEMENT_DIM,SPACE_DIM>&>((this->mrMesh)).ReMesh(node_map);
if (!node_map.IsIdentityMap())
{
UpdateGhostNodesAfterReMesh(node_map);
// Update the mappings between cells and location indices
std::map<Cell*, unsigned> old_cell_location_map = this->mCellLocationMap;
// Remove any dead pointers from the maps (needed to avoid archiving errors)
this->mLocationCellMap.clear();
this->mCellLocationMap.clear();
for (std::list<CellPtr>::iterator it = this->mCells.begin(); it != this->mCells.end(); ++it)
{
unsigned old_node_index = old_cell_location_map[(*it).get()];
// This shouldn't ever happen, as the cell vector only contains living cells
assert(!node_map.IsDeleted(old_node_index));
unsigned new_node_index = node_map.GetNewIndex(old_node_index);
this->SetCellUsingLocationIndex(new_node_index,*it);
if (old_node_radius_map[old_node_index] > 0.0)
{
this->GetNode(new_node_index)->SetRadius(old_node_radius_map[old_node_index]);
}
if (output_node_velocities)
{
this->GetNode(new_node_index)->AddAppliedForceContribution(old_node_applied_force_map[old_node_index]);
}
}
this->Validate();
}
else
{
if (old_node_radius_map[this->mCellLocationMap[(*(this->mCells.begin())).get()]] > 0.0)
{
for (std::list<CellPtr>::iterator it = this->mCells.begin(); it != this->mCells.end(); ++it)
{
unsigned node_index = this->mCellLocationMap[(*it).get()];
this->GetNode(node_index)->SetRadius(old_node_radius_map[node_index]);
}
}
if (output_node_velocities)
{
for (std::list<CellPtr>::iterator it = this->mCells.begin(); it != this->mCells.end(); ++it)
{
unsigned node_index = this->mCellLocationMap[(*it).get()];
this->GetNode(node_index)->AddAppliedForceContribution(old_node_applied_force_map[node_index]);
}
}
}
// Purge any marked springs that are no longer springs
std::vector<const std::pair<CellPtr,CellPtr>*> springs_to_remove;
for (std::set<std::pair<CellPtr,CellPtr> >::iterator spring_it = this->mMarkedSprings.begin();
spring_it != this->mMarkedSprings.end();
++spring_it)
{
CellPtr p_cell_1 = spring_it->first;
CellPtr p_cell_2 = spring_it->second;
Node<SPACE_DIM>* p_node_1 = this->GetNodeCorrespondingToCell(p_cell_1);
Node<SPACE_DIM>* p_node_2 = this->GetNodeCorrespondingToCell(p_cell_2);
bool joined = false;
// For each element containing node1, if it also contains node2 then the cells are joined
std::set<unsigned> node2_elements = p_node_2->rGetContainingElementIndices();
for (typename Node<SPACE_DIM>::ContainingElementIterator elem_iter = p_node_1->ContainingElementsBegin();
elem_iter != p_node_1->ContainingElementsEnd();
++elem_iter)
{
if (node2_elements.find(*elem_iter) != node2_elements.end())
{
joined = true;
break;
}
}
// If no longer joined, remove this spring from the set
if (!joined)
{
springs_to_remove.push_back(&(*spring_it));
}
}
// Remove any springs necessary
for (std::vector<const std::pair<CellPtr,CellPtr>* >::iterator spring_it = springs_to_remove.begin();
spring_it != springs_to_remove.end();
++spring_it)
{
this->mMarkedSprings.erase(**spring_it);
}
// Tessellate if needed
TessellateIfNeeded();
static_cast<MutableMesh<ELEMENT_DIM,SPACE_DIM>&>((this->mrMesh)).SetMeshHasChangedSinceLoading();
}