void ExtendedBidomainTissue<SPACE_DIM>::CreateExtracellularConductivityTensors()
{
if (this->mpConfig->IsMeshProvided() && this->mpConfig->GetLoadMesh())
{
assert(this->mFibreFilePathNoExtension != "");
switch (this->mpConfig->GetConductivityMedia())
{
case cp::media_type::Orthotropic:
{
mpExtracellularConductivityTensors = new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
FileFinder ortho_file(this->mFibreFilePathNoExtension + ".ortho", RelativeTo::AbsoluteOrCwd);
assert(ortho_file.Exists());
mpExtracellularConductivityTensors->SetFibreOrientationFile(ortho_file);
break;
}
case cp::media_type::Axisymmetric:
{
mpExtracellularConductivityTensors = new AxisymmetricConductivityTensors<SPACE_DIM,SPACE_DIM>;
FileFinder axi_file(this->mFibreFilePathNoExtension + ".axi", RelativeTo::AbsoluteOrCwd);
assert(axi_file.Exists());
mpExtracellularConductivityTensors->SetFibreOrientationFile(axi_file);
break;
}
case cp::media_type::NoFibreOrientation:
mpExtracellularConductivityTensors = new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
break;
default :
NEVER_REACHED;
}
}
else // no fibre orientation assumed
{
mpExtracellularConductivityTensors = new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
}
c_vector<double, SPACE_DIM> extra_conductivities;
this->mpConfig->GetExtracellularConductivities(extra_conductivities);
// this definition must be here (and not inside the if statement) because SetNonConstantConductivities() will keep
// a pointer to it and we don't want it to go out of scope before Init() is called
unsigned num_elements = this->mpMesh->GetNumElements();
std::vector<c_vector<double, SPACE_DIM> > hetero_extra_conductivities;
if (this->mpConfig->GetConductivityHeterogeneitiesProvided())
{
try
{
assert(hetero_extra_conductivities.size()==0);
//initialise with the values of teh default conductivity tensor
hetero_extra_conductivities.resize(num_elements, extra_conductivities);
}
catch(std::bad_alloc &badAlloc)
{
#define COVERAGE_IGNORE
std::cout << "Failed to allocate std::vector of size " << num_elements << std::endl;
PetscTools::ReplicateException(true);
throw badAlloc;
#undef COVERAGE_IGNORE
}
PetscTools::ReplicateException(false);
std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > conductivities_heterogeneity_areas;
std::vector< c_vector<double,3> > intra_h_conductivities;
std::vector< c_vector<double,3> > extra_h_conductivities;
HeartConfig::Instance()->GetConductivityHeterogeneities(conductivities_heterogeneity_areas,
intra_h_conductivities,
extra_h_conductivities);
unsigned local_element_index = 0;
for (typename AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>::ElementIterator iter = (this->mpMesh)->GetElementIteratorBegin();
iter != (this->mpMesh)->GetElementIteratorEnd();
++iter)
{
//unsigned element_index = iter->GetIndex();
// if element centroid is contained in the region
ChastePoint<SPACE_DIM> element_centroid(iter->CalculateCentroid());
for (unsigned region_index=0; region_index< conductivities_heterogeneity_areas.size(); region_index++)
{
// if element centroid is contained in the region
if ( conductivities_heterogeneity_areas[region_index]->DoesContain( element_centroid ) )
{
//We don't use ublas vector assignment here, because we might be getting a subvector of a 3-vector
for (unsigned i=0; i<SPACE_DIM; i++)
{
hetero_extra_conductivities[local_element_index][i] = extra_h_conductivities[region_index][i];
}
}
}
local_element_index++;
}
mpExtracellularConductivityTensors->SetNonConstantConductivities(&hetero_extra_conductivities);
}
else
{
mpExtracellularConductivityTensors->SetConstantConductivities(extra_conductivities);
}
mpExtracellularConductivityTensors->Init(this->mpMesh);
}
void ExtendedBidomainTissue<SPACE_DIM>::CreateIntracellularConductivityTensorSecondCell()
{
HeartEventHandler::BeginEvent(HeartEventHandler::READ_MESH);
this->mpConfig = HeartConfig::Instance();
mpIntracellularConductivityTensorsSecondCell = new OrthotropicConductivityTensors<SPACE_DIM,SPACE_DIM>;
// this definition must be here (and not inside the if statement) because SetNonConstantConductivities() will keep
// a pointer to it and we don't want it to go out of scope before Init() is called
unsigned num_elements = this->mpMesh->GetNumElements();
std::vector<c_vector<double, SPACE_DIM> > hetero_intra_conductivities;
c_vector<double, SPACE_DIM> intra_conductivities;
this->mpConfig->GetIntracellularConductivities(intra_conductivities);//this one is used just for resizing
if (this->mpConfig->GetConductivityHeterogeneitiesProvided())
{
try
{
assert(hetero_intra_conductivities.size()==0);
hetero_intra_conductivities.resize(num_elements, intra_conductivities);
}
catch(std::bad_alloc &badAlloc)
{
#define COVERAGE_IGNORE
std::cout << "Failed to allocate std::vector of size " << num_elements << std::endl;
PetscTools::ReplicateException(true);
throw badAlloc;
#undef COVERAGE_IGNORE
}
PetscTools::ReplicateException(false);
std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > conductivities_heterogeneity_areas;
std::vector< c_vector<double,3> > intra_h_conductivities;
std::vector< c_vector<double,3> > extra_h_conductivities;
HeartConfig::Instance()->GetConductivityHeterogeneities(conductivities_heterogeneity_areas,
intra_h_conductivities,
extra_h_conductivities);
unsigned local_element_index = 0;
for (typename AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>::ElementIterator it = this->mpMesh->GetElementIteratorBegin();
it != this->mpMesh->GetElementIteratorEnd();
++it)
{
//unsigned element_index = it->GetIndex();
// if element centroid is contained in the region
ChastePoint<SPACE_DIM> element_centroid(it->CalculateCentroid());
for (unsigned region_index=0; region_index< conductivities_heterogeneity_areas.size(); region_index++)
{
if ( conductivities_heterogeneity_areas[region_index]->DoesContain(element_centroid) )
{
//We don't use ublas vector assignment here, because we might be getting a subvector of a 3-vector
for (unsigned i=0; i<SPACE_DIM; i++)
{
hetero_intra_conductivities[local_element_index][i] = intra_h_conductivities[region_index][i];
}
}
}
local_element_index++;
}
mpIntracellularConductivityTensorsSecondCell->SetNonConstantConductivities(&hetero_intra_conductivities);
}
else
{
mpIntracellularConductivityTensorsSecondCell->SetConstantConductivities(mIntracellularConductivitiesSecondCell);
}
mpIntracellularConductivityTensorsSecondCell->Init(this->mpMesh);
HeartEventHandler::EndEvent(HeartEventHandler::READ_MESH);
}