AbstractMesh.cpp

/*

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 * Redistributions of source code must retain the above copyright notice,
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 * Redistributions in binary form must reproduce the above copyright notice,
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   software without specific prior written permission.

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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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*/

#include "AbstractMesh.hpp"
#include "Exception.hpp"

// Implementation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractMesh<ELEMENT_DIM, SPACE_DIM>::AbstractMesh()
    : mpDistributedVectorFactory(NULL),
      mMeshFileBaseName(""),
      mMeshChangesDuringSimulation(false)
{
}

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<mNodes.size(); i++)
    {
        delete mNodes[i];
    }
    if (mpDistributedVectorFactory)
    {
        delete mpDistributedVectorFactory;
    }
}

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

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNumNodeAttributes() const
{
    /* Note, this implementation assumes that all nodes have the same number of attributes
     * so that the first node in the container is indicative of the others.*/
    assert(mNodes.size() != 0u);
    return mNodes[0]->GetNumNodeAttributes();
}

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 mNodes[local_index];
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node<SPACE_DIM>* AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNodeOrHaloNode(unsigned index) const
{
    return GetNode(index);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Node<SPACE_DIM>* AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetNodeFromPrePermutationIndex(unsigned index) const
{
    if (mNodePermutation.empty())
    {
        return GetNode(index);
    }
    else
    {
        return GetNode(mNodePermutation[index]);
    }
}

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


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::SetElementOwnerships()
{
    //Does nothing, since an AbstractMesh has no elements
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
DistributedVectorFactory* AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetDistributedVectorFactory()
{
    if (mpDistributedVectorFactory == NULL)
    {
        mpDistributedVectorFactory = new DistributedVectorFactory(GetNumNodes());
        if (PetscTools::IsParallel())
        {
            SetElementOwnerships(); // So any parallel implementation with shared mesh has owners set
        }
    }
    return mpDistributedVectorFactory;
}
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::SetDistributedVectorFactory(DistributedVectorFactory *pFactory)
{
    if (mpDistributedVectorFactory)
    {
        EXCEPTION("Cannot change the mesh's distributed vector factory once it has been set.");
    }
    if (pFactory->GetNumProcs() != PetscTools::GetNumProcs())
    {
        EXCEPTION("The distributed vector factory provided to the mesh is for the wrong number of processes.");
    }
    mpDistributedVectorFactory = pFactory;
}

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

    return mMeshFileBaseName;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractMesh<ELEMENT_DIM, SPACE_DIM>::IsMeshOnDisk() const
{
    return (mMeshFileBaseName != "");
}

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

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetVectorFromAtoB(
    const c_vector<double, SPACE_DIM>& rLocationA, const c_vector<double, SPACE_DIM>& rLocationB)
{
    c_vector<double, SPACE_DIM> vector = rLocationB - rLocationA;
    return vector;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetDistanceBetweenNodes(unsigned indexA, unsigned indexB)
{
    c_vector<double, SPACE_DIM> vector = GetVectorFromAtoB(mNodes[indexA]->rGetLocation(),
                                                           mNodes[indexB]->rGetLocation());
    return norm_2(vector);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double AbstractMesh<ELEMENT_DIM, SPACE_DIM>::GetWidth(const unsigned& rDimension) const
{
    assert(rDimension < SPACE_DIM);
    return CalculateBoundingBox(mNodes).GetWidth(rDimension);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ChasteCuboid<SPACE_DIM> AbstractMesh<ELEMENT_DIM, SPACE_DIM>::CalculateBoundingBox(const std::vector<Node<SPACE_DIM> *>& rNodes) const
{
    // Work out the max and min location in each co-ordinate direction.
    c_vector<double, SPACE_DIM> minimum_point;
    c_vector<double, SPACE_DIM> maximum_point;

    // Deal with the special case of no nodes by returning a cuboid with zero volume.
    if (rNodes.empty())
    {
        minimum_point = scalar_vector<double>(SPACE_DIM, 0.0);
        maximum_point = scalar_vector<double>(SPACE_DIM, 0.0);
    }
    else
    {
        minimum_point = scalar_vector<double>(SPACE_DIM, DBL_MAX);
        maximum_point = scalar_vector<double>(SPACE_DIM, -DBL_MAX);

        // Iterate through nodes
        for (unsigned index=0; index<rNodes.size(); index++)
        {
            if (!rNodes[index]->IsDeleted())
            {
                // Note that we define this vector before setting it as otherwise the profiling build will break (see #2367)
                c_vector<double, SPACE_DIM> position;
                position = rNodes[index]->rGetLocation();

                // Update max/min
                for (unsigned i=0; i<SPACE_DIM; i++)
                {
                    if (position[i] < minimum_point[i])
                    {
                        minimum_point[i] = position[i];
                    }
                    if (position[i] > maximum_point[i])
                    {
                        maximum_point[i] = position[i];
                    }
                }
            }
        }
    }

    ChastePoint<SPACE_DIM> min(minimum_point);
    ChastePoint<SPACE_DIM> max(maximum_point);

    return ChasteCuboid<SPACE_DIM>(min, max);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ChasteCuboid<SPACE_DIM> AbstractMesh<ELEMENT_DIM, SPACE_DIM>::CalculateBoundingBox() const
{
    ChasteCuboid<SPACE_DIM> bounding_cuboid = CalculateBoundingBox(mNodes);

    return bounding_cuboid;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::Scale(const double xScale, const double yScale, const double zScale)
{
    unsigned num_nodes = mNodes.size();

    for (unsigned i=0; i<num_nodes; i++)
    {
        c_vector<double, SPACE_DIM>& r_location = mNodes[i]->rGetModifiableLocation();
        if (SPACE_DIM>=3)
        {
            r_location[2] *= zScale;
        }
        if (SPACE_DIM>=2)
        {
            r_location[1] *= yScale;
        }
        r_location[0] *= xScale;
    }

    RefreshMesh();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::Translate(
    const double xMovement,
    const double yMovement,
    const double zMovement)
{
    c_vector<double, SPACE_DIM> displacement;

    switch (SPACE_DIM)
    {
        case 3:
            displacement[2] = zMovement;
        case 2:
            displacement[1] = yMovement;
        case 1:
            displacement[0] = xMovement;
    }

    Translate(displacement);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::Translate(const c_vector<double, SPACE_DIM>& rTransVec)
{
    unsigned num_nodes = this->GetNumAllNodes();

    for (unsigned i=0; i<num_nodes; i++)
    {
        c_vector<double, SPACE_DIM>& r_location = this->mNodes[i]->rGetModifiableLocation();
        r_location += rTransVec;
    }

    RefreshMesh();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::Rotate(c_matrix<double , SPACE_DIM, SPACE_DIM> rotationMatrix)
{
    unsigned num_nodes = this->GetNumAllNodes();

    for (unsigned i=0; i<num_nodes; i++)
    {
        c_vector<double, SPACE_DIM>& r_location = this->mNodes[i]->rGetModifiableLocation();
        r_location = prod(rotationMatrix, r_location);
    }

    RefreshMesh();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::Rotate(c_vector<double,3> axis, double angle)
{
    assert(SPACE_DIM == 3);
    double norm = norm_2(axis);
    c_vector<double,3> unit_axis=axis/norm;

    c_matrix<double, SPACE_DIM,SPACE_DIM> rotation_matrix;

    double c = cos(angle);
    double s = sin(angle);

    rotation_matrix(0,0) = unit_axis(0)*unit_axis(0)+c*(1-unit_axis(0)*unit_axis(0));
    rotation_matrix(0,1) = unit_axis(0)*unit_axis(1)*(1-c) - unit_axis(2)*s;
    rotation_matrix(1,0) = unit_axis(0)*unit_axis(1)*(1-c) + unit_axis(2)*s;
    rotation_matrix(1,1) = unit_axis(1)*unit_axis(1)+c*(1-unit_axis(1)*unit_axis(1));
    rotation_matrix(0,2) = unit_axis(0)*unit_axis(2)*(1-c)+unit_axis(1)*s;
    rotation_matrix(1,2) = unit_axis(1)*unit_axis(2)*(1-c)-unit_axis(0)*s;
    rotation_matrix(2,0) = unit_axis(0)*unit_axis(2)*(1-c)-unit_axis(1)*s;
    rotation_matrix(2,1) = unit_axis(1)*unit_axis(2)*(1-c)+unit_axis(0)*s;
    rotation_matrix(2,2) = unit_axis(2)*unit_axis(2)+c*(1-unit_axis(2)*unit_axis(2));

    Rotate(rotation_matrix);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::RotateX(const double theta)
{
    if (SPACE_DIM != 3)
    {
        EXCEPTION("This rotation is only valid in 3D");
    }
    c_matrix<double , SPACE_DIM, SPACE_DIM> x_rotation_matrix=identity_matrix<double>(SPACE_DIM);

    x_rotation_matrix(1,1) = cos(theta);
    x_rotation_matrix(1,2) = sin(theta);
    x_rotation_matrix(2,1) = -sin(theta);
    x_rotation_matrix(2,2) = cos(theta);
    Rotate(x_rotation_matrix);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::RotateY(const double theta)
{
    if (SPACE_DIM != 3)
    {
        EXCEPTION("This rotation is only valid in 3D");
    }
    c_matrix<double , SPACE_DIM, SPACE_DIM> y_rotation_matrix=identity_matrix<double>(SPACE_DIM);

    y_rotation_matrix(0,0) = cos(theta);
    y_rotation_matrix(0,2) = -sin(theta);
    y_rotation_matrix(2,0) = sin(theta);
    y_rotation_matrix(2,2) = cos(theta);


    Rotate(y_rotation_matrix);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::RotateZ(const double theta)
{
    if (SPACE_DIM < 2)
    {
        EXCEPTION("This rotation is not valid in less than 2D");
    }
    c_matrix<double , SPACE_DIM, SPACE_DIM> z_rotation_matrix=identity_matrix<double>(SPACE_DIM);


    z_rotation_matrix(0,0) = cos(theta);
    z_rotation_matrix(0,1) = sin(theta);
    z_rotation_matrix(1,0) = -sin(theta);
    z_rotation_matrix(1,1) = cos(theta);

    Rotate(z_rotation_matrix);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::Rotate(double theta)
{
    RotateZ(theta);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::RefreshMesh()
{
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractMesh<ELEMENT_DIM, SPACE_DIM>::IsMeshChanging() const
{
    return mMeshChangesDuringSimulation;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractMesh<ELEMENT_DIM, SPACE_DIM>::CalculateMaximumContainingElementsPerProcess() const
{
    unsigned max_num=0u;
    for (unsigned local_node_index=0; local_node_index<mNodes.size(); local_node_index++)
    {
        unsigned num=mNodes[local_node_index]->GetNumContainingElements();
        if (num>max_num)
        {
            max_num=num;
        }
    }
    return max_num;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractMesh<ELEMENT_DIM, SPACE_DIM>::SetMeshHasChangedSinceLoading()
{
    // We just forget what the original file was, which has the desired effect
    mMeshFileBaseName = "";
}

// Explicit instantiation

template class AbstractMesh<1,1>;
template class AbstractMesh<1,2>;
template class AbstractMesh<1,3>;
template class AbstractMesh<2,2>;
template class AbstractMesh<2,3>;
template class AbstractMesh<3,3>;