Geometry3D.cpp

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////////////////////////////////////////////////////////////////////////////////
//
//  File:  Geometry3D.cpp
//
//  For more information, please see: http://www.nektar.info/
//
//  The MIT License
//
//  Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
//  Department of Aeronautics, Imperial College London (UK), and Scientific 
//  Computing and Imaging Institute, University of Utah (USA).
//
//  License for the specific language governing rights and limitations under
//  Permission is hereby granted, free of charge, to any person obtaining a
//  copy of this software and associated documentation files (the "Software"),
//  to deal in the Software without restriction, including without limitation
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//  and/or sell copies of the Software, and to permit persons to whom the
//  Software is furnished to do so, subject to the following conditions:
//
//  The above copyright notice and this permission notice shall be included
//  in all copies or substantial portions of the Software.
//
//  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
//  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
//  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
//  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
//  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
//  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
//  DEALINGS IN THE SOFTWARE.
//
//  Description: 3D geometry information.
//
////////////////////////////////////////////////////////////////////////////////

#include <SpatialDomains/Geometry3D.h>

#include <SpatialDomains/Geometry2D.h>
#include <SpatialDomains/GeomFactors.h>
#include <SpatialDomains/PointGeom.h>
#include <SpatialDomains/SegGeom.h>

#include <iomanip>

using namespace std;

namespace Nektar
{
namespace SpatialDomains
{
    Geometry3D::Geometry3D()
    {
    }

    Geometry3D::Geometry3D(const int coordim):
      Geometry(coordim)
    {
      ASSERTL0(m_coordim > 2,
               "Coordinate dimension should be at least 3 for a 3D geometry.");
    }

    Geometry3D::~Geometry3D()
    {
    }


    //---------------------------------------
    // Helper functions
    //---------------------------------------

    /**
    * @brief Return the ID of edge i in this element.
    */
    int Geometry3D::GetEid(int i) const
    {
      return v_GetEid(i);
    }

    /**
    * @brief Return face i in this element.
    */
    Geometry2DSharedPtr Geometry3D::GetFace(int i)
    {
      return v_GetFace(i);
    }

    /**
    * @brief Returns the element coordinate direction corresponding to a
    * given face coordinate direction
    */
    int Geometry3D::GetDir(const int faceidx, const int facedir) const
    {
      return v_GetDir(faceidx, facedir);
    }

    //---------------------------------------
    // 3D Geometry Methods
    //---------------------------------------
    void Geometry3D::NewtonIterationForLocCoord(
      const Array<OneD, const NekDouble> &coords,
      const Array<OneD, const NekDouble> &ptsx,
      const Array<OneD, const NekDouble> &ptsy,
      const Array<OneD, const NekDouble> &ptsz,
            Array<OneD,       NekDouble> &Lcoords,
      NekDouble                          &resid)
    {
        // maximum iterations for convergence
        const int MaxIterations   = 51;
        // |x-xp|^2 < EPSILON  error tolerance
        const NekDouble Tol       = 1.e-8;
        // |r,s|    > LcoordDIV stop the search
        const NekDouble LcoordDiv = 15.0;

        Array<OneD, const NekDouble > Jac =
                            m_geomFactors->GetJac(m_xmap->GetPointsKeys());

        NekDouble ScaledTol = Vmath::Vsum(Jac.num_elements(), Jac, 1) /
                                        ((NekDouble)Jac.num_elements());
        ScaledTol *= Tol;

        NekDouble xmap,ymap,zmap, F1,F2, F3;

        NekDouble derx_1, derx_2, derx_3, dery_1, dery_2, dery_3,
                  derz_1, derz_2, derz_3, jac;

        // save intiial guess for later reference if required.
        NekDouble init0 = Lcoords[0], init1 = Lcoords[1], init2 = Lcoords[2];

        Array<OneD, NekDouble> DxD1(ptsx.num_elements());
        Array<OneD, NekDouble> DxD2(ptsx.num_elements());
        Array<OneD, NekDouble> DxD3(ptsx.num_elements());
        Array<OneD, NekDouble> DyD1(ptsx.num_elements());
        Array<OneD, NekDouble> DyD2(ptsx.num_elements());
        Array<OneD, NekDouble> DyD3(ptsx.num_elements());
        Array<OneD, NekDouble> DzD1(ptsx.num_elements());
        Array<OneD, NekDouble> DzD2(ptsx.num_elements());
        Array<OneD, NekDouble> DzD3(ptsx.num_elements());

        // Ideally this will be stored in m_geomfactors
        m_xmap->PhysDeriv(ptsx,DxD1,DxD2,DxD3);
        m_xmap->PhysDeriv(ptsy,DyD1,DyD2,DyD3);
        m_xmap->PhysDeriv(ptsz,DzD1,DzD2,DzD3);

        int cnt=0;
        Array<OneD, DNekMatSharedPtr > I(3);
        Array<OneD, NekDouble>       eta(3);

        F1 = F2 = F3 = 2000; // Starting value of Function

        while(cnt++ < MaxIterations)
        {
            //  evaluate lagrange interpolant at Lcoords
            m_xmap->LocCoordToLocCollapsed(Lcoords,eta);
            I[0] = m_xmap->GetBasis(0)->GetI(eta  );
            I[1] = m_xmap->GetBasis(1)->GetI(eta+1);
            I[2] = m_xmap->GetBasis(2)->GetI(eta+2);

            //calculate the global point `corresponding to Lcoords
            xmap = m_xmap->PhysEvaluate(I, ptsx);
            ymap = m_xmap->PhysEvaluate(I, ptsy);
            zmap = m_xmap->PhysEvaluate(I, ptsz);

            F1 = coords[0] - xmap;
            F2 = coords[1] - ymap;
            F3 = coords[2] - zmap;

            if(F1*F1 + F2*F2 + F3*F3 < ScaledTol)
            {
              resid = sqrt(F1*F1 + F2*F2 + F3*F3);
              break;
            }

            //Interpolate derivative metric at Lcoords
            derx_1 = m_xmap->PhysEvaluate(I, DxD1);
            derx_2 = m_xmap->PhysEvaluate(I, DxD2);
            derx_3 = m_xmap->PhysEvaluate(I, DxD3);
            dery_1 = m_xmap->PhysEvaluate(I, DyD1);
            dery_2 = m_xmap->PhysEvaluate(I, DyD2);
            dery_3 = m_xmap->PhysEvaluate(I, DyD3);
            derz_1 = m_xmap->PhysEvaluate(I, DzD1);
            derz_2 = m_xmap->PhysEvaluate(I, DzD2);
            derz_3 = m_xmap->PhysEvaluate(I, DzD3);

            jac = derx_1*(dery_2*derz_3 - dery_3*derz_2)
                - derx_2*(dery_1*derz_3 - dery_3*derz_1)
                + derx_3*(dery_1*derz_2 - dery_2*derz_1);

            // use analytical inverse of derivitives which are also similar to
            // those of metric factors.
            Lcoords[0] = Lcoords[0]
                             +((dery_2*derz_3 - dery_3*derz_2)*(coords[0]-xmap)
                             - (derx_2*derz_3 - derx_3*derz_2)*(coords[1]-ymap)
                             + (derx_2*dery_3 - derx_3*dery_2)*(coords[2]-zmap)
                               )/jac;

            Lcoords[1] = Lcoords[1]
                             -((dery_1*derz_3 - dery_3*derz_1)*(coords[0]-xmap)
                             - (derx_1*derz_3 - derx_3*derz_1)*(coords[1]-ymap)
                             + (derx_1*dery_3 - derx_3*dery_1)*(coords[2]-zmap)
                               )/jac;

            Lcoords[2] = Lcoords[2]
                             +((dery_1*derz_2 - dery_2*derz_1)*(coords[0]-xmap)
                             - (derx_1*derz_2 - derx_2*derz_1)*(coords[1]-ymap)
                             + (derx_1*dery_2 - derx_2*dery_1)*(coords[2]-zmap)
                               )/jac;

            if (fabs(Lcoords[0]) > LcoordDiv || fabs(Lcoords[1]) > LcoordDiv ||
                fabs(Lcoords[0]) > LcoordDiv)
            {
                break; // lcoords have diverged so stop iteration
            }
        }

        resid = sqrt(F1*F1 + F2*F2 + F3*F3);

        if(cnt >= MaxIterations)
        {
            Array<OneD, NekDouble> collCoords(3);
            m_xmap->LocCoordToLocCollapsed(Lcoords,collCoords);

            // if coordinate is inside element dump error!
            if((collCoords[0] >=  -1.0 && collCoords[0] <= 1.0)&&
               (collCoords[1] >=  -1.0 && collCoords[1] <= 1.0)&&
               (collCoords[2] >=  -1.0 && collCoords[2] <= 1.0))
            {
                std::ostringstream ss;

                ss << "Reached MaxIterations (" << MaxIterations << ") in Newton iteration ";
                ss << "Init value ("<< setprecision(4) << init0 << "," << init1<< "," << init2 <<") ";
                ss << "Fin  value ("<<Lcoords[0] << "," << Lcoords[1]<< "," << Lcoords[2] << ") ";
                ss << "Resid = " << resid << " Tolerance = " << sqrt(ScaledTol) ;

                WARNINGL1(cnt < MaxIterations,ss.str());
            }
        }
    }

    /**
    * @brief Put all quadrature information into face/edge structure and
    * backward transform.
    *
    * Note verts, edges, and faces are listed according to anticlockwise
    * convention but points in _coeffs have to be in array format from left
    * to right.
    */
    void Geometry3D::v_FillGeom()
    {
      if (m_state == ePtsFilled)
          return;

      int i,j,k;

      for(i = 0; i < m_forient.size(); i++)
      {
          m_faces[i]->FillGeom();

          int nFaceCoeffs = m_faces[i]->GetXmap()->GetNcoeffs();

          Array<OneD, unsigned int> mapArray (nFaceCoeffs);
          Array<OneD,          int> signArray(nFaceCoeffs);

          if (m_forient[i] < 9)
          {
              m_xmap->GetFaceToElementMap(
                  i, m_forient[i], mapArray, signArray,
                  m_faces[i]->GetXmap()->GetEdgeNcoeffs(0),
                  m_faces[i]->GetXmap()->GetEdgeNcoeffs(1));
          }
          else
          {
              m_xmap->GetFaceToElementMap(
                  i, m_forient[i], mapArray, signArray,
                  m_faces[i]->GetXmap()->GetEdgeNcoeffs(1),
                  m_faces[i]->GetXmap()->GetEdgeNcoeffs(0));
          }

          for (j = 0; j < m_coordim; j++)
          {
              const Array<OneD, const NekDouble> &coeffs =
                  m_faces[i]->GetCoeffs(j);

              for (k = 0; k < nFaceCoeffs; k++)
              {
                  NekDouble v = signArray[k] * coeffs[k];
                  m_coeffs[j][mapArray[k]] = v;
              }
          }
      }

      m_state = ePtsFilled;
    }

    /**
     * Generate the geometry factors for this element.
     */
    void Geometry3D::v_GenGeomFactors()
    {
        if (m_geomFactorsState != ePtsFilled)
        {
            GeomType      Gtype  = eRegular;

            v_FillGeom();

            // check to see if expansions are linear
            for(int i = 0; i < m_coordim; ++i)
            {
                if (m_xmap->GetBasisNumModes(0) != 2 ||
                    m_xmap->GetBasisNumModes(1) != 2 ||
                    m_xmap->GetBasisNumModes(2) != 2)
                {
                    Gtype = eDeformed;
                }
            }

            m_geomFactors = MemoryManager<GeomFactors>::AllocateSharedPtr(
                Gtype, m_coordim, m_xmap, m_coeffs);
            m_geomFactorsState = ePtsFilled;
        }
    }

    /**
    * @brief Given local collapsed coordinate Lcoord return the value of
    * physical coordinate in direction i.
    */
    NekDouble Geometry3D::v_GetCoord(
      const int i, const Array<OneD, const NekDouble> &Lcoord)
    {
      ASSERTL1(m_state == ePtsFilled,
               "Geometry is not in physical space");

      Array<OneD, NekDouble> tmp(m_xmap->GetTotPoints());
      m_xmap->BwdTrans(m_coeffs[i], tmp);

      return m_xmap->PhysEvaluate(Lcoord, tmp);
    }


    //---------------------------------------
    // Helper functions
    //---------------------------------------

    /**
    * @brief Return the dimension of this element.
    */
    int Geometry3D::v_GetShapeDim() const
    {
      return 3;
    }

    /**
    * @brief Return the vertex ID of vertex i.
    */
    int Geometry3D::v_GetVid(const int i) const
    {
      ASSERTL2(i >= 0 && i <= m_verts.size() - 1,
               "Vertex ID must be between 0 and "+
               boost::lexical_cast<string>(m_verts.size() - 1));
      return m_verts[i]->GetVid();
    }
      
    /**
     * @brief Return vertex i in this element.
     */
    PointGeomSharedPtr Geometry3D::v_GetVertex(int i) const
    {
        return m_verts[i];
    }

    /**
    * @brief Return edge i of this element.
    */
    const SegGeomSharedPtr Geometry3D::v_GetEdge(int i) const
    {
      ASSERTL2(i >= 0 && i <= m_edges.size() - 1,
               "Edge ID must be between 0 and "+
               boost::lexical_cast<string>(m_edges.size() - 1));
      return m_edges[i];
    }

    /**
    * @brief Return the orientation of edge i in this element.
    */
    inline StdRegions::Orientation Geometry3D::v_GetEorient(
      const int i) const
    {
      ASSERTL2(i >= 0 && i <= m_edges.size() - 1,
               "Edge ID must be between 0 and "+
               boost::lexical_cast<string>(m_edges.size() - 1));
      return m_eorient[i];
    }

    /**
    * @brief Return the ID of edge i in this element.
    */
    int Geometry3D::v_GetEid(int i) const
    {
      ASSERTL2(i >= 0 && i <= m_edges.size() - 1,
               "Edge ID must be between 0 and "+
               boost::lexical_cast<string>(m_edges.size() - 1));
      return m_edges[i]->GetEid();
    }

    /**
    * @brief Return face i in this element.
    */
    const Geometry2DSharedPtr Geometry3D::v_GetFace(int i) const
    {
      ASSERTL2((i >=0) && (i <= 5),"Edge id must be between 0 and 4");
      return m_faces[i];
    }

    /**
    * @brief Return the orientation of face i in this element.
    */
    StdRegions::Orientation Geometry3D::v_GetForient(const int i) const
    {
      ASSERTL2(i >= 0 && i <= m_faces.size() - 1,
               "Face ID must be between 0 and "+
               boost::lexical_cast<string>(m_faces.size() - 1));
      return m_forient[i];
    }

    /**
    * @brief Return the ID of face i in this element.
    */
    int Geometry3D::v_GetFid(int i) const
    {
      ASSERTL2(i >= 0 && i <= m_faces.size() - 1,
               "Face ID must be between 0 and "+
               boost::lexical_cast<string>(m_faces.size() - 1));
      return m_faces[i]->GetFid();
    }

    /**
    * @brief Return the ID of this element.
    */
    int Geometry3D::v_GetEid() const
    {
      return m_eid;
    }

    /**
    * @brief Return the j-th basis of the i-th co-ordinate dimension.
    */
    const LibUtilities::BasisSharedPtr Geometry3D::v_GetBasis(
      const int i)
    {
      return m_xmap->GetBasis(i);
    }

    /**
    * @brief Return the local ID of a given edge.
    *
    * The local ID of an edge is a number between 0 and the number of edges
    * in this element. If the edge is not found, this function returns -1.
    */
    int Geometry3D::v_WhichEdge(SegGeomSharedPtr edge)
    {
      int returnval = -1;

      SegGeomVector::iterator edgeIter;
      int i;

      for (i=0,edgeIter = m_edges.begin(); edgeIter != m_edges.end(); ++edgeIter,++i)
      {
          if (*edgeIter == edge)
          {
              returnval = i;
              break;
          }
      }

      return returnval;
    }

    /**
    * @brief Return the local ID of a given face.
    *
    * The local ID of a face is a number between 0 and the number of faces
    * in this element. If the face is not found, this function returns -1.
    */
    int Geometry3D::v_WhichFace(Geometry2DSharedPtr face)
    {
      int i = 0;

      Geometry2DVector::iterator f;
      for (i = 0, f = m_faces.begin(); f != m_faces.end(); ++f,++i)
      {
          if (*f == face)
          {
              break;
          }
      }
      return i;
    }

    //---------------------------------------
    // Element connection functions
    //---------------------------------------

    void Geometry3D::v_AddElmtConnected(int gvo_id, int locid)
    {
      CompToElmt ee(gvo_id,locid);
      m_elmtmap.push_back(ee);
    }

    int Geometry3D::v_NumElmtConnected() const
    {
      return int(m_elmtmap.size());
    }

    bool Geometry3D::v_IsElmtConnected(int gvo_id, int locid) const
    {
      std::list<CompToElmt>::const_iterator def;
      CompToElmt ee(gvo_id,locid);

      def = find(m_elmtmap.begin(),m_elmtmap.end(),ee);

      // Found the element connectivity object in the list
      return (def != m_elmtmap.end());
    }

    void Geometry3D::v_SetOwnData()
    {
      m_owndata = true;
    }

}; //end of namespace
}; //end of namespace