SundancePeanoMesh3D.cpp

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//                              Sundance
//                 Copyright (2005) Sandia Corporation
//
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// of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
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/*
 * SundancePeanoMesh3D.cpp
 *
 *  Created on: Sep 8, 2009
 *      Author: benk
 */

#include "SundancePeanoMesh3D.hpp"

#include "SundanceMeshType.hpp"
#include "SundanceCellJacobianBatch.hpp"
#include "SundanceMaximalCofacetBatch.hpp"
#include "SundanceMeshSource.hpp"
#include "SundanceDebug.hpp"
#include "SundanceOut.hpp"
#include "PlayaMPIContainerComm.hpp"
#include "Teuchos_Time.hpp"
#include "Teuchos_TimeMonitor.hpp"
#include "SundanceObjectWithVerbosity.hpp"
#include "SundanceCollectiveExceptionCheck.hpp"

#ifdef HAVE_SUNDANCE_PEANO

using namespace Sundance;
using namespace Teuchos;
using Playa::MPIComm;
using Playa::MPIContainerComm;

//#define printf(msg)
//#define SUNDANCE_VERB_HIGH(msg) printf(msg);printf("\n");

Point PeanoMesh3D::returnPoint(0.0 , 0.0 , 0.0);

PeanoMesh3D::PeanoMesh3D(int dim, const MPIComm& comm,
      const MeshEntityOrder& order )
: MeshBase(dim, comm , order),_dimension(dim), _comm(comm)
 ,_peanoMesh(NULL)
{
  _uniqueResolution = 1.0;
}

void PeanoMesh3D::createMesh(
                      double position_x,
                double position_y,
                double position_z,
                double offset_x,
                double offset_y,
                double offset_z,
                double resolution
){
      double position[3];
      double offset[3];
      double res[3];

      // setting the values of the ctor argument
      position[0] = position_x; position[1] = position_y;  position[2] = position_z;
      offset[0] = offset_x;     offset[1] = offset_y;      offset[2] = offset_z;
      res[0] = resolution;      res[1] = resolution;       res[2] = resolution;


      // this is a 2D case
      // call the ctor for the Peano mesh
      SUNDANCE_VERB_LOW(" create Peano Mesh 3D ... ");
      _dimension = 3;
      // here we create the Peano grid
      _peanoMesh = new SundancePeanoInterface3D( position , offset , res );
      _uniqueResolution = _peanoMesh->returnResolution(0);

      SUNDANCE_VERB_LOW(" Peano Mesh created 3D ... \n");
      _peanoMesh->plotVTK("Peano3D");
      SUNDANCE_VERB_LOW(" After Plot 3D ... \n");
}

PeanoMesh3D::~PeanoMesh3D() {
  //delete _peanoMesh;
}


int PeanoMesh3D::numCells(int dim) const  {
  //printf("PeanoMesh3D::numCells(int dim):%d   dim:%d \n",_peanoMesh->numCells(dim),dim);
  return _peanoMesh->numCells(dim);
}

Point PeanoMesh3D::nodePosition(int i) const {
  //SUNDANCE_VERB_HIGH("nodePosition(int i)");
  //printf("PeanoMesh3D::nodePosition(int i)   i:%d \n", i);
  double* coords;
  coords = _peanoMesh->nodePositionView(i);
  // set the values
  PeanoMesh3D::returnPoint[0] = coords[0];
  PeanoMesh3D::returnPoint[1] = coords[1];
  PeanoMesh3D::returnPoint[2] = coords[2];
    return PeanoMesh3D::returnPoint;
}

const double* PeanoMesh3D::nodePositionView(int i) const {
  //printf("PeanoMesh3D::nodePositionView(int i)   i:%d \n", i);
  //SUNDANCE_VERB_HIGH("nodePosition(int i)");
  nodePosition(i);
  return &(PeanoMesh3D::returnPoint[0]);
}

void PeanoMesh3D::getJacobians(int cellDim, const Array<int>& cellLID,
                          CellJacobianBatch& jBatch) const
{
    //printf("cellDim:%d  _uniqueResolution:%f ",cellDim, _uniqueResolution);
    SUNDANCE_VERB_HIGH("getJacobians()");
    TEUCHOS_TEST_FOR_EXCEPTION(cellDim < 0 || cellDim > spatialDim(), std::logic_error,
      "cellDim=" << cellDim << " is not in expected range [0, " << spatialDim() << "]");
    int nCells = cellLID.size();
    int tmp_index , tmp;
    int tmp_index1 , tmp_index2;
    Point pnt(0.0,0.0,0.0);
    Point pnt1(0.0,0.0,0.0);
    Point pnt2(0.0,0.0,0.0);
    jBatch.resize(cellLID.size(), spatialDim(), cellDim);
    if (cellDim < spatialDim()) // they need the Jacobian of a lower dinemsional element
    {
      //printf("PeanoMesh3D::getJacobians() cellDim < spatialDim() \n");
       for (int i=0; i<nCells; i++)
        {
          //printf("PeanoMesh3D::getJacobian() cellDim < spatialDim() cellDim:%d , ret:%f \n",cellDim , _uniqueResolution);
          double* detJ = jBatch.detJ(i);
          switch(cellDim)
          {
            case 0: *detJ = 1.0;
              break;
            case 1:
             tmp_index = this->facetLID(cellDim,  cellLID[i] , 0 , 0 , tmp );
             tmp_index1= this->facetLID(cellDim,  cellLID[i] , 0 , 1 , tmp );
             pnt = nodePosition(tmp_index);
             pnt1 = nodePosition(tmp_index1);
             pnt = pnt1 - pnt;
                 *detJ = sqrt(pnt * pnt); // the length of the edge
            break;
            case 2:{
             tmp_index = this->facetLID(cellDim,  cellLID[i] , 0 , 0 , tmp );
             tmp_index1= this->facetLID(cellDim,  cellLID[i] , 0 , 1 , tmp );
             tmp_index2= this->facetLID(cellDim,  cellLID[i] , 0 , 2 , tmp );
             pnt = nodePosition(tmp_index);
             pnt1 = nodePosition(tmp_index1);
             pnt2 = nodePosition(tmp_index2);
             Point directedArea = cross( pnt1 - pnt , pnt2 - pnt );
                 *detJ = sqrt(directedArea * directedArea); // the are of the face
            break;}
            default:
              TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error, "impossible switch value "
                "cellDim=" << cellDim << " in PeanoMesh3D::getJacobians()");
          }
        }
    }else{ // they request the complete Jacoby matrix for this bunch of elements
        //Array<double> J(cellDim*cellDim);
        SUNDANCE_VERB_HIGH("cellDim == spatialDim()");
        for (unsigned int i=0; i<(unsigned int)cellLID.size(); i++)
        {
        //printf("PeanoMesh3D::getJacobian() cellDim == spatialDim() cellDim:%d , ret:%f \n",cellDim , _uniqueResolution);
          double* J = jBatch.jVals(i);
          switch(cellDim)
          {
            case 3:
              J[0] = _peanoMesh->returnResolution(0);
              J[1] = 0.0; J[2] = 0.0; J[3] = 0.0;
              J[4] = _peanoMesh->returnResolution(1);
              J[5] = 0.0; J[6] = 0.0; J[7] = 0.0;
              J[8] = _peanoMesh->returnResolution(2); // the Jacobi of the tet
            break;
            default:
              TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error, "impossible switch value "
                "cellDim=" << cellDim
                << " in PeanoMesh3D::getJacobians()");
          }
        }
    }
}

void PeanoMesh3D::getCellDiameters(int cellDim, const Array<int>& cellLID,
                              Array<double>& cellDiameters) const {
   TEUCHOS_TEST_FOR_EXCEPTION(cellDim < 0 || cellDim > spatialDim(), std::logic_error,
      "cellDim=" << cellDim << " is not in expected range [0, " << spatialDim() << "]");
   SUNDANCE_VERB_HIGH("getCellDiameters()");
    cellDiameters.resize(cellLID.size());

    int tmp_index , tmp;
    int tmp_index1;
    Point pnt(0.0,0.0,0.0);
    Point pnt1(0.0,0.0,0.0);

    if (cellDim < spatialDim())
    {
    //printf("PeanoMesh3D::getCellDiameters(), cellDim < spatialDim() \n ");
      for (unsigned int i=0; i<(unsigned int)cellLID.size(); i++)
      {
        switch(cellDim)
        {
          case 0:
            cellDiameters[i] = 1.0;
            break;
          case 1:
          tmp_index = this->facetLID(cellDim,  cellLID[i] , 0 , 0 , tmp );
          tmp_index1= this->facetLID(cellDim,  cellLID[i] , 0 , 1 , tmp );
          pnt = nodePosition(tmp_index);
          pnt1 = nodePosition(tmp_index1);
          pnt = pnt1 - pnt;
          cellDiameters[i] = sqrt(pnt * pnt); // the length of the edge
          break;
          case 2:
          tmp_index = this->facetLID(cellDim,  cellLID[i] , 0 , 0 , tmp );
          tmp_index1= this->facetLID(cellDim,  cellLID[i] , 0 , 3 , tmp );
          pnt = nodePosition(tmp_index);
          pnt1 = nodePosition(tmp_index1);
          pnt = pnt1 - pnt;
          cellDiameters[i] = sqrt(pnt * pnt); // the length of the edge
          break;
          default:
            TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error, "impossible switch value "
              "cellDim=" << cellDim << " in PeanoMesh3D::getCellDiameters()");
        }
      }
    }
    else
    {
    //printf("PeanoMesh3D::getCellDiameters(), cellDim == spatialDim() \n ");
      for (unsigned int i=0; i<(unsigned int)cellLID.size(); i++)
      {
        switch(cellDim)
        {
      case 3:
            cellDiameters[i] = (_peanoMesh->returnResolution(0) + _peanoMesh->returnResolution(1)
                          + _peanoMesh->returnResolution(2))/3.0;
          break;
          default:
            TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error, "impossible switch value "
              "cellDim=" << cellDim
              << " in PeanoMesh3D::getCellDiameters()");
        }
      }
    }
}

void PeanoMesh3D::pushForward(int cellDim, const Array<int>& cellLID,
                         const Array<Point>& refQuadPts,
                         Array<Point>& physQuadPts) const {

    //printf("PeanoMesh3D::pushForward cellDim:%d\n",cellDim);
    TEUCHOS_TEST_FOR_EXCEPTION(cellDim < 0 || cellDim > spatialDim(), std::logic_error,
      "cellDim=" << cellDim
      << " is not in expected range [0, " << spatialDim()
      << "]");

    int nQuad = refQuadPts.size();
    double start_point[3] , end_point[3];
    Array<double> J(cellDim*cellDim);

    if (physQuadPts.size() > 0) physQuadPts.resize(0);
    physQuadPts.reserve(cellLID.size() * refQuadPts.size());
    for (unsigned int i=0; i<(unsigned int)cellLID.size(); i++)
    {
      int lid = cellLID[i];
      _peanoMesh->pushForward( cellDim, lid ,start_point , end_point );
      //std::cout << "_peanoMesh->pushForward: " << cellDim << "," << lid << std::endl;
      //std::cout << "Start Point: "<< start_point[0] << " , " << start_point[1] << " , " << start_point[2] << std::endl;
      //std::cout << "End Point: "<< end_point[0] <<" , " << end_point[1] << " , "<< end_point[2] << std::endl;
        Point pnt( start_point[0] , start_point[1] , start_point[2] );
        Point pnt1( end_point[0] , end_point[1] , end_point[2]);
      switch(cellDim)
      {
        case 0: // integrate one point
           physQuadPts.append(pnt);
          break;
        case 1:{ // integrate on one line
           for (int q=0; q<nQuad; q++) {
             physQuadPts.append(pnt + refQuadPts[q][0]*(pnt1 - pnt));
           }
        break;}
        case 2:{
           for (int q=0; q<nQuad; q++) {
             if (fabs(pnt[0] - pnt1[0]) < 1e-8)
                    physQuadPts.append( pnt + Point(pnt[0] - pnt1[0],
                                                refQuadPts[q][0]*_peanoMesh->returnResolution(1),
                                                refQuadPts[q][1]*_peanoMesh->returnResolution(2)));
             else
               if (fabs(pnt[1] - pnt1[1]) < 1e-8)
                      physQuadPts.append( pnt + Point(refQuadPts[q][0]*_peanoMesh->returnResolution(0),
                                                  pnt[1] - pnt1[1],
                                                  refQuadPts[q][1]*_peanoMesh->returnResolution(2)));
               else
                      physQuadPts.append( pnt + Point(refQuadPts[q][0]*_peanoMesh->returnResolution(0),
                                                  refQuadPts[q][1]*_peanoMesh->returnResolution(1),
                                                  pnt[2] - pnt1[2]));
           }
        break;}
        case 3:{
            for (int q=0; q<nQuad; q++) {
                    physQuadPts.append( pnt
                       + Point(refQuadPts[q][0]*_peanoMesh->returnResolution(0),
                              refQuadPts[q][1]*_peanoMesh->returnResolution(1),
                                refQuadPts[q][2]*_peanoMesh->returnResolution(2)));
            }
        break;}
        default:
          TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error, "impossible switch value "
            "in PeanoMesh3D::getJacobians()");
      }
    }
}

int PeanoMesh3D::ownerProcID(int cellDim, int cellLID) const  {
   SUNDANCE_VERB_HIGH("ownerProcID()"); return 0; }


int PeanoMesh3D::numFacets(int cellDim, int cellLID,
                      int facetDim) const  {
  SUNDANCE_VERB_HIGH("numFacets()");
    return _peanoMesh->numFacets(cellDim, cellLID, facetDim);
}


int PeanoMesh3D::facetLID(int cellDim, int cellLID,
                     int facetDim, int facetIndex,
                     int& facetOrientation) const  {
    int LID;
    LID = _peanoMesh->facetLID( cellDim,cellLID, facetDim, facetIndex, facetOrientation);
    //printf("PeanoMesh3D::facetLID  cellDim: %d , cellLID: %d , facetDim %d , facetIndex:%d  %d\n" , cellDim , cellLID , facetDim , facetIndex , LID );
  return LID;
}

void PeanoMesh3D::getFacetLIDs(int cellDim,
                          const Array<int>& cellLID,
                          int facetDim,
                          Array<int>& facetLID,
                          Array<int>& facetSign) const {
    SUNDANCE_VERB_HIGH("getFacetLIDs()");
    //printf("PeanoMesh3D::getFacetLIDs()  cellDim:%d  cellLID.size():%d  facetDim:%d\n" , cellDim, (int)cellLID.size() , facetDim);
      int LID = 0 , cLID , facetOrientation ;
      int ptr = 0;

      int nf = numFacets(cellDim, cellLID[0], facetDim);
      facetLID.resize(cellLID.size() * nf);
      facetSign.resize(cellLID.size() * nf);
    // At this moment we just use the previous function
    for (unsigned int i = 0 ; i < (unsigned int)cellLID.size() ; i++){
      cLID = cellLID[i];
        for (int f=0; f<nf; f++, ptr++) {
          // we use this->facetLID caz facetLID is already used as variable
        LID = this->facetLID( cellDim, cLID, facetDim, f , facetOrientation);
        //printf("LID:%d , cellDim:%d , cLID:%d , facetDim:%d , f:%d , facetOrientation:%d \n"
        //    ,LID , cellDim, cLID, facetDim, f , facetOrientation );
            facetLID[ptr] = LID;
            facetSign[ptr] = facetOrientation;
        }
    }
}

const int* PeanoMesh3D::elemZeroFacetView(int cellLID) const {
  return _peanoMesh->elemZeroFacetView(cellLID);
}

int PeanoMesh3D::numMaxCofacets(int cellDim, int cellLID) const  {
    //SUNDANCE_VERB_HIGH("numMaxCofacets()");
      int coFacetCounter;
      coFacetCounter = _peanoMesh->numMaxCofacets( cellDim, cellLID);
    //printf("numMaxCofacets:  cellDim:%d cellLID:%d ret:%d\n",cellDim, cellLID, coFacetCounter);
    return coFacetCounter;
}

int PeanoMesh3D::maxCofacetLID(int cellDim, int cellLID,
                       int cofacetIndex,
                       int& facetIndex) const  {
    int rtn;
    rtn = _peanoMesh->maxCofacetLID(cellDim, cellLID, cofacetIndex, facetIndex);
    //printf("maxCofacetLID() cellDim:%d,  cellLID:%d, cofacetIndex:%d , rtn:%d , facetIndex:%d\n",
    //    cellDim,  cellLID, cofacetIndex , rtn , facetIndex);
    return rtn;
}

void PeanoMesh3D::getMaxCofacetLIDs(const Array<int>& cellLIDs,
  MaximalCofacetBatch& cofacets) const {
    TEUCHOS_TEST_FOR_EXCEPTION(true, std::logic_error," PeanoMesh3D::getMaxCofacetLIDs() not implemented yet");
  //TODO: Implement this, uses only in ExodusWriter::writeMesh
}


void PeanoMesh3D::getCofacets(int cellDim, int cellLID,
                 int cofacetDim, Array<int>& cofacetLIDs) const {
    int tmpVect[12] , nrCofacets;
    _peanoMesh->getCofacets( cellDim, cellLID, cofacetDim, &tmpVect[0], nrCofacets);
    cofacetLIDs.resize(nrCofacets);
    for (int ii = 0 ; ii < nrCofacets ; ii++ ) cofacetLIDs[ii] = tmpVect[ii];
}


int PeanoMesh3D::mapGIDToLID(int cellDim, int globalIndex) const  {
  SUNDANCE_VERB_HIGH("mapGIDToLID()");
  // in the serial implementation GID = LID
  // in the parallel version this should be done differently
  return globalIndex;
}

bool PeanoMesh3D::hasGID(int cellDim, int globalIndex) const {
  SUNDANCE_VERB_HIGH("hasGID()");
  // since currently we have a serial implementation , this is always true
  // in the parallel version this function has to be implemented differetly
  return true;
}

int PeanoMesh3D::mapLIDToGID(int cellDim, int localIndex) const  {
  SUNDANCE_VERB_HIGH("mapLIDToGID()");
  // at the current stage we have only serial implementation,
  // parallel implementation will(should) come soon
  return localIndex;
}

CellType PeanoMesh3D::cellType(int cellDim) const  {
  //printf("cellType() cellDim:%d\n",cellDim);
   switch(cellDim)
    {
      case 0:  return PointCell;
      case 1:  return LineCell;
      case 2:  return QuadCell;
      case 3:  return BrickCell;
      default:
        return NullCell; // -Wall
    }
}

int PeanoMesh3D::label(int cellDim, int cellLID) const {
   return _peanoMesh->label( cellDim, cellLID);
}

void PeanoMesh3D::getLabels(int cellDim, const Array<int>& cellLID,
    Array<int>& labels) const {
    int tmpIndex;
    SUNDANCE_VERB_HIGH("getLabels()");
    // resize the array
  labels.resize(cellLID.size());

    for (tmpIndex = 0 ; tmpIndex < (int)cellLID.size() ; tmpIndex++){
      labels[tmpIndex] = _peanoMesh->label( cellDim, cellLID[tmpIndex]);
    }
}

Set<int> PeanoMesh3D::getAllLabelsForDimension(int cellDim) const {
    Set<int>                 rtn;
    int                      tmpIndex;
    SUNDANCE_VERB_HIGH("getAllLabelsForDimension()");

    for (tmpIndex = 0 ; tmpIndex < _peanoMesh->numCells(cellDim) ; tmpIndex++){
      rtn.put( _peanoMesh->label( cellDim, tmpIndex) );
    }
    return rtn;
}

void PeanoMesh3D::getLIDsForLabel(int cellDim, int label, Array<int>& cellLIDs) const {
    int                      tmpIndex , tmpLabel;
  SUNDANCE_VERB_HIGH("getLIDsForLabel()");
    for (tmpIndex = 0 ; tmpIndex < _peanoMesh->numCells(cellDim) ; tmpIndex++){
      tmpLabel = this->label( cellDim , tmpIndex);
      if (tmpLabel == label) cellLIDs.append( tmpIndex );
    }
}

void PeanoMesh3D::setLabel(int cellDim, int cellLID, int label) {
  _peanoMesh->setLabel(cellDim, cellLID, label);
}


void PeanoMesh3D::assignIntermediateCellGIDs(int cellDim) {
  SUNDANCE_VERB_HIGH("assignIntermediateCellGIDs()");
  // in this method we could do synchronization between processors, not usede now
}


bool PeanoMesh3D::hasIntermediateGIDs(int dim) const {
  SUNDANCE_VERB_HIGH("hasIntermediateGIDs()");
  return true; // true means they have been synchronized ... not used now
}

#endif