SemMesh.cpp

/*

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*/

#include "SemMesh.hpp"
#include "RandomNumberGenerator.hpp"
#include "UblasCustomFunctions.hpp"
#include <list>

template<unsigned DIM>
SemMesh<DIM>::SemMesh( std::vector<Node<DIM>*> nodes,
                        std::vector<PottsElement<DIM>*> pottsElements)
{
    // SEM model only defined in 2 and 3D
    assert(DIM > 1);

    // Reset member variables and clear mNodes, mElements.
    Clear();

    // Populate mNodes and mElements
    for (unsigned node_index=0; node_index<nodes.size(); node_index++)
    {
        Node<DIM>* p_temp_node = nodes[node_index];
        this->mNodes.push_back(p_temp_node);
    }
    for (unsigned elem_index=0; elem_index<pottsElements.size(); elem_index++)
    {
        PottsElement<DIM>* p_temp_element = pottsElements[elem_index];
        mElements.push_back(p_temp_element);
    }

    // Register elements with nodes
    for (unsigned index=0; index<mElements.size(); index++)
    {
        PottsElement<DIM>* p_element = mElements[index];

        unsigned element_index = p_element->GetIndex();
        unsigned num_nodes_in_element = p_element->GetNumNodes();

        for (unsigned node_index=0; node_index<num_nodes_in_element; node_index++)
        {
            p_element->GetNode(node_index)->AddElement(element_index);
        }
    }

    this->mMeshChangesDuringSimulation = true;
}

template<unsigned DIM>
SemMesh<DIM>::SemMesh()
{
    assert(DIM > 1);
    this->mMeshChangesDuringSimulation = true;
    Clear();
}

template<unsigned DIM>
SemMesh<DIM>::~SemMesh()
{
    Clear();
}

template<unsigned DIM>
unsigned SemMesh<DIM>::SolveNodeMapping(unsigned index) const
{
    assert(index < this->mNodes.size());
    return index;
}

template<unsigned DIM>
unsigned SemMesh<DIM>::SolveElementMapping(unsigned index) const
{
    assert(index < this->mElements.size());
    return index;
}

template<unsigned DIM>
unsigned SemMesh<DIM>::SolveBoundaryElementMapping(unsigned index) const
{
    return index;
}

template<unsigned DIM>
void SemMesh<DIM>::Clear()
{
    // Delete elements
    for (unsigned i=0; i<mElements.size(); i++)
    {
        delete mElements[i];
    }
    mElements.clear();

    // Delete nodes
    for (unsigned i=0; i<this->mNodes.size(); i++)
    {
        delete this->mNodes[i];
    }
    this->mNodes.clear();

    mDeletedElementIndices.clear();
    mDeletedNodeIndices.clear();
}

template<unsigned DIM>
void SemMesh<DIM>::ConstructFromMeshReader(AbstractMeshReader<DIM, DIM>& rMeshReader)
{
    // Store numbers of nodes and elements
    unsigned num_nodes = rMeshReader.GetNumNodes();
    unsigned num_elements = rMeshReader.GetNumElements();

    // Reserve memory for nodes
    this->mNodes.reserve(num_nodes);

    rMeshReader.Reset();

    // Add nodes
    std::vector<double> node_data;
    for (unsigned i=0; i<num_nodes; i++)
    {
        node_data = rMeshReader.GetNextNode();
        unsigned is_boundary_node = (unsigned) node_data[DIM];
        node_data.pop_back();
        this->mNodes.push_back(new Node<DIM>(i, node_data, is_boundary_node));
    }

    rMeshReader.Reset();

    // Reserve memory for nodes
    mElements.reserve(rMeshReader.GetNumElements());

    // Add elements
    for (unsigned elem_index=0; elem_index<num_elements; elem_index++)
    {
     // Get the data for this element
     ElementData element_data = rMeshReader.GetNextElementData();

     // Get the nodes owned by this element
     std::vector<Node<DIM>*> nodes;
     unsigned num_nodes_in_element = element_data.NodeIndices.size();
     for (unsigned j=0; j<num_nodes_in_element; j++)
     {
         assert(element_data.NodeIndices[j] < this->mNodes.size());
         nodes.push_back(this->mNodes[element_data.NodeIndices[j]]);
     }

     // Use nodes and index to construct this element
     PottsElement<DIM>* p_element = new PottsElement<DIM>(elem_index, nodes);
     mElements.push_back(p_element);

     if (rMeshReader.GetNumElementAttributes() > 0)
     {
         assert(rMeshReader.GetNumElementAttributes() == 1);
         unsigned attribute_value = element_data.AttributeValue;
         p_element->SetAttribute(attribute_value);
     }
    }
}

template<unsigned DIM>
unsigned SemMesh<DIM>::GetNumNodes() const
{
    return this->mNodes.size() - mDeletedNodeIndices.size();
}

template<unsigned DIM>
unsigned SemMesh<DIM>::GetNumAllNodes() const
{
    return this->mNodes.size();
}

template<unsigned DIM>
unsigned SemMesh<DIM>::GetNumElements() const
{
    return mElements.size() - mDeletedElementIndices.size();
}

template<unsigned DIM>
unsigned SemMesh<DIM>::GetNumAllElements() const
{
    return mElements.size();
}

template<unsigned DIM>
PottsElement<DIM>* SemMesh<DIM>::GetElement(unsigned index) const
{
    assert(index < mElements.size());
    return mElements[index];
}

template<unsigned DIM>
void SemMesh<DIM>::ReMesh()
{
    std::vector<unsigned> old_element_indices;
    std::vector< std::vector<unsigned> > old_element_node_indices;
    std::vector< std::vector<c_vector<double, DIM> > > old_element_node_location;

    // For each element either note that it was deleted, or store the information needed to re-construct it, i.e. index and nodes.
    for (typename std::vector<PottsElement<DIM>* >::iterator element_iterator = this->mElements.begin();
         element_iterator != this->mElements.end();
         ++element_iterator)
    {
        if ((*element_iterator)->IsDeleted())
        {
            // Marked as deleted - don't store the nodes.
        }
        else
        {
            // Store the index and node location.
            old_element_indices.push_back( (*element_iterator)->GetIndex() );

            std::vector<unsigned> local_node_indices;
            std::vector< c_vector<double, DIM> > local_node_locations;
            for (unsigned local_index=0; local_index < (*element_iterator)->GetNumNodes(); local_index++)
            {
                Node<DIM>* p_node = (*element_iterator)->GetNode(local_index);
                local_node_indices.push_back(p_node->GetIndex());
                local_node_locations.push_back(p_node->rGetLocation());
            }
            old_element_node_indices.push_back(local_node_indices);
            old_element_node_location.push_back(local_node_locations);
        }
    }

    // Clear all the local information.
    Clear();

    // Reconstruct the elements
    for (unsigned index=0; index < old_element_indices.size(); index++)
    {
        std::vector<Node<DIM>* > new_element_nodes;
        for (unsigned node=0; node < old_element_node_indices[index].size(); node++)
        {
            c_vector<double, DIM> new_location = old_element_node_location[index][node];
            unsigned new_index = old_element_node_indices[index][node];
            Node<DIM>* p_new_node = new Node<DIM>(new_index, new_location);
            new_element_nodes.push_back(p_new_node);
            this->mNodes.push_back(p_new_node);
        }

        this->mElements.push_back(new PottsElement<DIM>(old_element_indices[index], new_element_nodes));
    }

    // Register elements with nodes
    for (unsigned index=0; index < this->mElements.size(); index++)
    {
        PottsElement<DIM>* p_element = this->mElements[index];

        unsigned element_index = p_element->GetIndex();
        unsigned num_nodes_in_element = p_element->GetNumNodes();

        for (unsigned node_index=0; node_index<num_nodes_in_element; node_index++)
        {
            p_element->GetNode(node_index)->AddElement(element_index);
        }
    }
}

template<unsigned DIM>
void SemMesh<DIM>::DeleteElement(unsigned index)
{
    // Delete the nodes
    for (unsigned node_index=0; node_index<this->mElements[index]->GetNumNodes(); node_index++)
    {
        Node<DIM>* p_node = this->mElements[index]->GetNode(node_index);
        p_node->MarkAsDeleted();
        mDeletedNodeIndices.push_back(node_index);
    }

    // Mark this element as deleted; this also updates the nodes containing element indices
    this->mElements[index]->MarkAsDeleted();
    mDeletedElementIndices.push_back(index);
}

template<unsigned DIM>
unsigned SemMesh<DIM>::AddElement(PottsElement<DIM>* pNewElement, std::vector<Node<DIM>* > newNodes)
{
    unsigned new_element_index = pNewElement->GetIndex();

    if (new_element_index == this->mElements.size())
    {
        this->mElements.push_back(pNewElement);
    }
    else
    {
        delete this->mElements[new_element_index];
        this->mElements[new_element_index] = pNewElement;
    }

    // Add the nodes
    for (unsigned index=0; index<newNodes.size(); index++)
    {
        // Set index of the node correctly
        newNodes[index]->SetIndex(this->mNodes.size());
        this->mNodes.push_back(newNodes[index]);
    }

    pNewElement->RegisterWithNodes();
    return pNewElement->GetIndex();
}

// Explicit instantiation

template class SemMesh<1>;
template class SemMesh<2>;
template class SemMesh<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(SemMesh)