AbstractMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2009

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#ifndef ABSTRACTMESH_HPP_
#define ABSTRACTMESH_HPP_

#include "Node.hpp"
#include "BoundaryElement.hpp"
#include "Element.hpp"
#include "AbstractMeshReader.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractMesh
{
private:
    virtual unsigned SolveNodeMapping(unsigned index) const = 0;
    virtual unsigned SolveElementMapping(unsigned index) const = 0;        
    virtual unsigned SolveBoundaryElementMapping(unsigned index) const = 0; 
    
protected:  // Give access of these variables to subclasses
    std::vector<Node<SPACE_DIM> *> mNodes;
    std::vector<Node<SPACE_DIM> *> mBoundaryNodes;

    std::vector<Element<ELEMENT_DIM, SPACE_DIM> *> mElements;
    std::vector<BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *> mBoundaryElements;
    
    std::vector<unsigned> mNodesPerProcessor;

    std::vector<unsigned> mNodesPermutation;
    
    std::string mMeshFileBaseName;

public:
    typedef typename std::vector<Element<ELEMENT_DIM, SPACE_DIM> *>::const_iterator ElementIterator;
    typedef typename std::vector<BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *>::const_iterator BoundaryElementIterator;
    typedef typename std::vector<Node<SPACE_DIM> *>::const_iterator BoundaryNodeIterator;

    AbstractMesh();

    virtual ~AbstractMesh();

    virtual unsigned GetNumNodes() const;
    virtual unsigned GetNumElements() const;
    virtual unsigned GetNumBoundaryElements() const;
    unsigned GetNumBoundaryNodes();// should this be overloaded and virtual too?

    unsigned GetNumAllNodes() const;
    unsigned GetNumAllElements();
    unsigned GetNumAllBoundaryElements();

    Node<SPACE_DIM> *GetNode(unsigned index) const;    
    Element<ELEMENT_DIM, SPACE_DIM>* GetElement(unsigned index) const;
    BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* GetBoundaryElement(unsigned index) const;
    
    virtual void SetElementOwnerships(unsigned lo, unsigned hi);
    
    virtual void ConstructFromMeshReader(AbstractMeshReader<ELEMENT_DIM,SPACE_DIM> &rMeshReader,
                                         bool cullInternalFaces=false)=0;
    
    virtual void ReadNodesPerProcessorFile(const std::string& nodesPerProcessorFile);

    std::vector<unsigned>& rGetNodesPerProcessor();
    
    virtual void PermuteNodes();      
    
    ElementIterator GetElementIteratorBegin() const;

    ElementIterator GetElementIteratorEnd() const;

    BoundaryElementIterator GetBoundaryElementIteratorBegin() const;

    BoundaryElementIterator GetBoundaryElementIteratorEnd() const;

    BoundaryNodeIterator GetBoundaryNodeIteratorBegin() const;

    BoundaryNodeIterator GetBoundaryNodeIteratorEnd() const;

    virtual void GetInverseJacobianForElement(unsigned elementIndex, c_matrix<double, SPACE_DIM, SPACE_DIM>& rJacobian, double &rJacobianDeterminant, c_matrix<double, SPACE_DIM, SPACE_DIM>& rInverseJacobian) const;

    virtual void GetWeightedDirectionForBoundaryElement(unsigned elementIndex, c_vector<double, SPACE_DIM>& rWeightedDirection, double &rJacobianDeterminant) const;
    
    std::string GetMeshFileBaseName() const;
    
    std::vector<unsigned>& rGetNodePermutation();
};

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::SetElementOwnerships(unsigned lo, unsigned hi)
{
    assert(hi>=lo);
    for (unsigned element_index=0; element_index<this->mElements.size(); element_index++)
    {
        Element<ELEMENT_DIM, SPACE_DIM>* p_element=this->mElements[element_index];
        p_element->SetOwnership(false);
        for (unsigned local_node_index=0; local_node_index< p_element->GetNumNodes(); local_node_index++)
        {
            unsigned global_node_index = p_element->GetNodeGlobalIndex(local_node_index);
            if (lo<=global_node_index && global_node_index<hi)
            {
                p_element->SetOwnership(true);
                break;
            }
        }

    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractMesh<ELEMENT_DIM, SPACE_DIM>::AbstractMesh()
: mMeshFileBaseName("")
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractMesh<ELEMENT_DIM, SPACE_DIM>::~AbstractMesh()
{
    // Iterate over nodes and free the memory
    for (unsigned i=0; i<this->mNodes.size(); i++)
    {
        delete this->mNodes[i];
    }
    // Iterate over elements and free the memory
    for (unsigned i=0; i<this->mElements.size(); i++)
    {
        delete this->mElements[i];
    }
    // Iterate over boundary elements and free the memory
    for (unsigned i=0; i<this->mBoundaryElements.size(); i++)
    {
        delete this->mBoundaryElements[i];
    }
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNumNodes() const
{
    return this->mNodes.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNumElements() const
{
    return this->mElements.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNumBoundaryNodes()
{
    return this->mBoundaryNodes.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNumAllNodes() const
{
    return this->mNodes.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNumAllElements()
{
    return this->mElements.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNumAllBoundaryElements()
{
    return this->mBoundaryElements.size();
}



template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNumBoundaryElements() const
{
    return this->mBoundaryElements.size();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node<SPACE_DIM>* AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNode(unsigned index) const
{
    unsigned local_index = SolveNodeMapping(index);
    return this->mNodes[local_index];
}
    
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Element<ELEMENT_DIM, SPACE_DIM>* AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetElement(unsigned index) const
{
    unsigned local_index = SolveElementMapping(index);
    return this->mElements[local_index];
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BoundaryElement<ELEMENT_DIM-1, SPACE_DIM>* AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetBoundaryElement(unsigned index) const
{
    unsigned local_index = SolveBoundaryElementMapping(index);
    return this->mBoundaryElements[local_index];
}    

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::ReadNodesPerProcessorFile(const std::string& nodesPerProcessorFile)
{
    NEVER_REACHED;
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<unsigned>& AbstractMesh<ELEMENT_DIM, SPACE_DIM>::rGetNodesPerProcessor()
{
    return mNodesPerProcessor;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::PermuteNodes()
{
    NEVER_REACHED;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorBegin() const
{
    return mElements.begin();
}
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetElementIteratorEnd() const
{
    return mElements.end();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::BoundaryElementIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetBoundaryElementIteratorBegin() const
{
    return mBoundaryElements.begin();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::BoundaryElementIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetBoundaryElementIteratorEnd() const
{
    return mBoundaryElements.end();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::BoundaryNodeIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetBoundaryNodeIteratorBegin() const
{
    return mBoundaryNodes.begin();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
typename AbstractMesh<ELEMENT_DIM, SPACE_DIM>::BoundaryNodeIterator AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetBoundaryNodeIteratorEnd() const
{
    return mBoundaryNodes.end();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetInverseJacobianForElement(unsigned elementIndex, c_matrix<double, SPACE_DIM, SPACE_DIM>& rJacobian, double &rJacobianDeterminant, c_matrix<double, SPACE_DIM, SPACE_DIM>& rInverseJacobian) const
{
    mElements[SolveElementMapping(elementIndex)]->CalculateInverseJacobian(rJacobian, rJacobianDeterminant, rInverseJacobian);
}    

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetWeightedDirectionForBoundaryElement(unsigned elementIndex, c_vector<double, SPACE_DIM>& rWeightedDirection, double &rJacobianDeterminant) const
{
    mBoundaryElements[SolveBoundaryElementMapping(elementIndex)]->CalculateWeightedDirection(rWeightedDirection, rJacobianDeterminant );
}    

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::string AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetMeshFileBaseName() const
{
    if (mMeshFileBaseName == "")
    {
        EXCEPTION("This mesh was not constructed from a file.");
    }
    
    return mMeshFileBaseName;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<unsigned>& AbstractMesh<ELEMENT_DIM, SPACE_DIM>::rGetNodePermutation()
{
    return mNodesPermutation;
}

#endif /*ABSTRACTMESH_HPP_*/

---