AbstractMesh.cpp

/*

Copyright (C) University of Oxford, 2005-2011

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/>.

*/

#include "AbstractMesh.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>
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 (mNodesPermutation.empty())
    {
        return GetNode(index);
    }
    else
    {
        return GetNode(mNodesPermutation[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 mNodesPermutation;
}

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().GetWidth(rDimension);
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ChasteCuboid<SPACE_DIM> AbstractMesh<ELEMENT_DIM, SPACE_DIM>::CalculateBoundingBox() const
{
    //Set min to DBL_MAX etc.
    c_vector<double, SPACE_DIM> minimum_point = scalar_vector<double>(SPACE_DIM, DBL_MAX);
    //Set max to -DBL_MAX etc.
    c_vector<double, SPACE_DIM> maximum_point=-minimum_point;

    //Iterate through nodes
    for (unsigned i=0; i<mNodes.size(); i++)
    {
        if (!mNodes[i]->IsDeleted())
        {
            c_vector<double, SPACE_DIM> position  = mNodes[i]->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>
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>;

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