TempestOnlineMap.hpp

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///////////////////////////////////////////////////////////////////////////////
///
/// \file    TempestOnlineMap.h
/// \author  Vijay Mahadevan
/// \version November 20, 2017
///
 
#ifndef _TEMPESTONLINEMAP_H_
#define _TEMPESTONLINEMAP_H_
 
#include "moab/MOABConfig.h"
#ifndef MOAB_HAVE_TEMPESTREMAP
#error Re-configure with TempestRemap
#endif
 
#include "moab/Remapping/TempestRemapper.hpp"
 
// Tempest includes
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused-but-set-variable"
#pragma GCC diagnostic ignored "-Wunused-variable"
#include "OfflineMap.h"
 
#ifdef MOAB_HAVE_EIGEN3
// #ifdef MOAB_HAVE_BLAS
// #define EIGEN_USE_BLAS
// #endif
// #define EIGEN_DONT_PARALLELIZE
// #define EIGEN_DONT_VECTORIZE
// #define EIGEN_STRONG_INLINE
#define EIGEN_DEFAULT_TO_ROW_MAJOR
#define EIGEN_RUNTIME_NO_MALLOC
// #define EIGEN_UNROLLING_LIMIT 0
#include <Eigen/Sparse>
#endif
 
#include <unordered_set>
 
#pragma GCC diagnostic pop
 
///////////////////////////////////////////////////////////////////////////////
 
#if !defined( RECTANGULAR_TRUNCATION ) && !defined( TRIANGULAR_TRUNCATION )
#define RECTANGULAR_TRUNCATION
// #define TRIANGULAR_TRUNCATION
#endif
 
///////////////////////////////////////////////////////////////////////////////
 
// Forward declarations
class Mesh;
 
///////////////////////////////////////////////////////////////////////////////
 
namespace moab
{
 
/// <summary>
///     An offline map between two Meshes.
/// </summary>
class TempestOnlineMap : public OfflineMap
{
 
  public:
    /// <summary>
    ///     Generate the metadata associated with the offline map.
    /// </summary>
    TempestOnlineMap( moab::TempestRemapper* remapper );
 
    /// <summary>
    ///     Define a virtual destructor.
    /// </summary>
    virtual ~TempestOnlineMap();
 
  public:
    // Input / Output types
    enum DiscretizationType
    {
        DiscretizationType_FV     = 0,
        DiscretizationType_CGLL   = 1,
        DiscretizationType_DGLL   = 2,
        DiscretizationType_PCLOUD = 3
    };
 
    // Type of limiter
    enum CAASType
    {
        CAAS_NONE           = 0,
        CAAS_GLOBAL         = 1,
        CAAS_LOCAL          = 2,
        CAAS_LOCAL_ADJACENT = 3,
        CAAS_QLT            = 4
    };
 
    /// <summary>
    ///     Generate the offline map, given the source and target mesh and discretization details.
    ///     This method generates the mapping between the two meshes based on the overlap and stores
    ///     the result in the SparseMatrix.
    /// </summary>
    moab::ErrorCode GenerateRemappingWeights( std::string strInputType,
                                              std::string strOutputType,
                                              const GenerateOfflineMapAlgorithmOptions& mapOptions,
                                              const std::string& srcDofTagName = "GLOBAL_ID",
                                              const std::string& tgtDofTagName = "GLOBAL_ID" );
 
    /// <summary>
    ///     Generate the metadata associated with the offline map.
    /// </summary>
    // moab::ErrorCode GenerateMetaData();
 
    /// <summary>
    ///     Read the OfflineMap from a NetCDF file.
    /// </summary>
    moab::ErrorCode ReadParallelMap( const char* strSource,
                                     const std::vector< int >& tgt_dof_ids,
                                     int arearead,
                                     std::vector< double >& areaA,
                                     int& nA,
                                     std::vector< double >& areaB,
                                     int& nB );
 
    /// <summary>
    ///     Write the TempestOnlineMap to a parallel NetCDF file.
    /// </summary>
    moab::ErrorCode WriteParallelMap( const std::string& strTarget,
                                      const std::map< std::string, std::string >& attrMap );
 
    /// <summary>
    ///     Determine if the map is first-order accurate.
    /// </summary>
    virtual int IsConsistent( double dTolerance );
 
    /// <summary>
    ///     Determine if the map is conservative.
    /// </summary>
    virtual int IsConservative( double dTolerance );
 
    /// <summary>
    ///     Determine if the map is monotone.
    /// </summary>
    virtual int IsMonotone( double dTolerance );
 
    /// <summary>
    ///     If we computed the reduction, get the vector representing the source areas for all entities
    /// in the mesh
    /// </summary>
    const DataArray1D< double >& GetGlobalSourceAreas() const;
 
    /// <summary>
    ///     If we computed the reduction, get the vector representing the target areas for all entities
    /// in the mesh
    /// </summary>
    const DataArray1D< double >& GetGlobalTargetAreas() const;
 
    /// <summary>
    ///     Print information and metadata about the remapping weights.
    /// </summary>
    void PrintMapStatistics();
 
  private:
    /// <summary>
    ///     Compute the remapping weights as a permutation matrix that relates DoFs on the source
    /// mesh
    ///     to DoFs on the target mesh.
    /// </summary>
    moab::ErrorCode LinearRemapNN_MOAB( bool use_GID_matching = false, bool strict_check = false );
 
    /// <summary>
    ///     Compute the remapping weights for a FV field defined on the source to a
    ///     FV field defined on the target mesh.
    /// </summary>
    void LinearRemapFVtoFV_Tempest_MOAB( int nOrder );
 
    /// <summary>
    ///     Generate the OfflineMap for linear conserative element-average
    ///     spectral element to element average remapping.
    /// </summary>
    void LinearRemapSE0_Tempest_MOAB( const DataArray3D< int >& dataGLLNodes,
                                      const DataArray3D< double >& dataGLLJacobian );
 
    /// <summary>
    ///     Generate the OfflineMap for cubic conserative element-average
    ///     spectral element to element average remapping.
    /// </summary>
    void LinearRemapSE4_Tempest_MOAB( const DataArray3D< int >& dataGLLNodes,
                                      const DataArray3D< double >& dataGLLJacobian,
                                      int nMonotoneType,
                                      bool fContinuousIn,
                                      bool fNoConservation );
 
    /// <summary>
    ///     Generate the OfflineMap for remapping from finite volumes to finite
    ///     elements.
    /// </summary>
    void LinearRemapFVtoGLL_MOAB( const DataArray3D< int >& dataGLLNodes,
                                  const DataArray3D< double >& dataGLLJacobian,
                                  const DataArray1D< double >& dataGLLNodalArea,
                                  int nOrder,
                                  int nMonotoneType,
                                  bool fContinuous,
                                  bool fNoConservation );
 
    /// <summary>
    ///     Generate the OfflineMap for remapping from finite elements to finite
    ///     elements.
    /// </summary>
    void LinearRemapGLLtoGLL2_MOAB( const DataArray3D< int >& dataGLLNodesIn,
                                    const DataArray3D< double >& dataGLLJacobianIn,
                                    const DataArray3D< int >& dataGLLNodesOut,
                                    const DataArray3D< double >& dataGLLJacobianOut,
                                    const DataArray1D< double >& dataNodalAreaOut,
                                    int nPin,
                                    int nPout,
                                    int nMonotoneType,
                                    bool fContinuousIn,
                                    bool fContinuousOut,
                                    bool fNoConservation );
 
    /// <summary>
    ///     Generate the OfflineMap for remapping from finite elements to finite
    ///     elements (pointwise interpolation).
    /// </summary>
    void LinearRemapGLLtoGLL2_Pointwise_MOAB( const DataArray3D< int >& dataGLLNodesIn,
                                              const DataArray3D< double >& dataGLLJacobianIn,
                                              const DataArray3D< int >& dataGLLNodesOut,
                                              const DataArray3D< double >& dataGLLJacobianOut,
                                              const DataArray1D< double >& dataNodalAreaOut,
                                              int nPin,
                                              int nPout,
                                              int nMonotoneType,
                                              bool fContinuousIn,
                                              bool fContinuousOut );
 
    /// <summary>
    ///     Copy the local matrix from Tempest SparseMatrix representation (ELL)
    ///     to the parallel CSR Eigen Matrix for scalable application of matvec
    ///     needed for projections.
    /// </summary>
#ifdef MOAB_HAVE_EIGEN3
    void copy_tempest_sparsemat_to_eigen3();
#endif
 
    /// <summary>
    ///     Parallel I/O with HDF5 to write out the remapping weights from multiple processors.
    /// </summary>
    moab::ErrorCode WriteSCRIPMapFile( const std::string& strOutputFile,
                                       const std::map< std::string, std::string >& attrMap );
 
    /// <summary>
    ///     Parallel I/O with NetCDF to write out the SCRIP file from multiple processors.
    /// </summary>
    moab::ErrorCode WriteHDF5MapFile( const std::string& filename );
 
  public:
    /// <summary>
    ///    Store the tag names associated with global DoF ids for source and target meshes to be used for mapping.
    ///   <param name="srcDofTagName">The tag name associated with global DoF ids for the source mesh</param>
    ///   <param name="tgtDofTagName">The tag name associated with global DoF ids for the target mesh</param>
    /// </summary>
    moab::ErrorCode SetDOFmapTags( const std::string srcDofTagName, const std::string tgtDofTagName );
 
    /// <summary>
    ///     @brief Compute the association between the solution tag global DoF numbering and
    ///     the local matrix numbering so that matvec operations can be performed
    ///     consistently.
    ///    <param name="srcType">The discretization type of the source mesh</param>
    ///    <param name="srcOrder">The order of the discretization on the source mesh</param>
    ///    <param name="isSrcContinuous">The continuity of the discretization on the source mesh</param>
    ///    <param name="srcdataGLLNodes">The GLL nodes on the source mesh</param>
    ///    <param name="srcdataGLLNodesSrc">The GLL nodes on the source mesh</param>
    ///    <param name="destType">The discretization type of the destination mesh</param>
    ///    <param name="destOrder">The order of the discretization on the destination mesh</param>
    ///    <param name="isTgtContinuous">The continuity of the discretization on the destination mesh</param>
    ///    <param name="tgtdataGLLNodes">The GLL nodes on the destination mesh</param>
    /// </summary>
    moab::ErrorCode SetDOFmapAssociation( DiscretizationType srcType,
                                          int srcOrder,
                                          bool isSrcContinuous,
                                          DataArray3D< int >* srcdataGLLNodes,
                                          DataArray3D< int >* srcdataGLLNodesSrc,
                                          DiscretizationType destType,
                                          int destOrder,
                                          bool isTgtContinuous,
                                          DataArray3D< int >* tgtdataGLLNodes );
 
    /// <summary>
    /// @brief ApplyBoundsLimiting - Apply bounds limiting to the data field
    /// @param dataInDouble - input data field
    /// @param dataOutDouble - output data field
    /// @param caasType - type of limiter
    /// @param caasIteration - iteration number of limiter
    /// @return - pair of mass defect pre and post limiter application
    /// </summary>
    std::pair< double, double > ApplyBoundsLimiting( std::vector< double >& dataInDouble,
                                                     std::vector< double >& dataOutDouble,
                                                     CAASType caasType = CAAS_GLOBAL,
                                                     int caasIteration = 0,
                                                     double mismatch   = 0.0 );
 
    /// @brief
    /// @param vecAdjFaces
    /// @param nrings
    /// @param entities
    /// @param useMOABAdjacencies
    /// @param trMesh
    /// @return
    void ComputeAdjacencyRelations( std::vector< std::unordered_set< int > >& vecAdjFaces,
                                    int nrings,
                                    const Range& entities,
                                    bool useMOABAdjacencies = true,
                                    Mesh* trMesh            = nullptr );
 
#ifdef MOAB_HAVE_EIGEN3
 
    typedef Eigen::Matrix< double, 1, Eigen::Dynamic > WeightDRowVector;
    typedef Eigen::Matrix< double, Eigen::Dynamic, 1 > WeightDColVector;
    typedef Eigen::SparseVector< double > WeightSVector;
    typedef Eigen::SparseMatrix< double, Eigen::RowMajor > WeightRMatrix;
    typedef Eigen::SparseMatrix< double, Eigen::ColMajor > WeightCMatrix;
 
    typedef WeightDRowVector WeightRowVector;
    typedef WeightDColVector WeightColVector;
    typedef WeightRMatrix WeightMatrix;
 
    /// <summary>
    ///     Get the raw reference to the Eigen weight matrix representing the projection from source to
    /// destination mesh.
    /// </summary>
    WeightMatrix& GetWeightMatrix();
 
    /// <summary>
    ///     Get the row vector that is amenable for application of A*x operation.
    /// </summary>
    WeightRowVector& GetRowVector();
 
    /// <summary>
    ///     Get the column vector that is amenable for application of A^T*x operation.
    /// </summary>
    WeightColVector& GetColVector();
 
#endif
 
    /// <summary>
    ///     Get the number of total Degrees-Of-Freedom defined on the source mesh.
    /// </summary>
    int GetSourceGlobalNDofs();
 
    /// <summary>
    ///     Get the number of total Degrees-Of-Freedom defined on the destination mesh.
    /// </summary>
    int GetDestinationGlobalNDofs();
 
    /// <summary>
    ///     Get the number of local Degrees-Of-Freedom defined on the source mesh.
    /// </summary>
    int GetSourceLocalNDofs();
 
    /// <summary>
    ///     Get the number of local Degrees-Of-Freedom defined on the destination mesh.
    /// </summary>
    int GetDestinationLocalNDofs();
 
    /// <summary>
    ///     Get the number of Degrees-Of-Freedom per element on the source mesh.
    /// </summary>
    int GetSourceNDofsPerElement();
 
    /// <summary>
    ///     Get the number of Degrees-Of-Freedom per element on the destination mesh.
    /// </summary>
    int GetDestinationNDofsPerElement();
 
    /// <summary>
    ///     Set the number of Degrees-Of-Freedom per element on the source mesh.
    /// </summary>
    void SetSourceNDofsPerElement( int ns );
 
    /// <summary>
    ///     Get the number of Degrees-Of-Freedom per element on the destination mesh.
    /// </summary>
    void SetDestinationNDofsPerElement( int nt );
 
    /// <summary>
    ///     Get the global Degrees-Of-Freedom ID on the destination mesh.
    /// </summary>
    int GetRowGlobalDoF( int localID ) const;
 
    /// <summary>
    ///     Get the index of globaRowDoF.
    /// </summary>
    inline int GetIndexOfRowGlobalDoF( int globalRowDoF ) const;
 
    /// <summary>
    ///     Get the global Degrees-Of-Freedom ID on the source mesh.
    /// </summary>
    int GetColGlobalDoF( int localID ) const;
 
    /// <summary>
    ///     Get the index of globaColDoF.
    /// </summary>
    inline int GetIndexOfColGlobalDoF( int globalColDoF ) const;
 
    /// <summary>
    ///     Apply the weight matrix onto the source vector (tag) provided as input, and return the
    /// column vector (solution projection) in a tag, after the map application
    ///     Compute:        \p tgtVals = A(S->T) * \srcVals, or
    ///     if (transpose)  \p tgtVals = [A(T->S)]^T * \srcVals
    /// </summary>
    moab::ErrorCode ApplyWeights( moab::Tag srcSolutionTag,
                                  moab::Tag tgtSolutionTag,
                                  bool transpose            = false,
                                  CAASType caasType         = CAAS_NONE,
                                  double default_projection = 0.0 );
 
    typedef double ( *sample_function )( double, double );
 
    /// <summary>
    ///     Define an analytical solution over the given (source or target) mesh, as specificed in
    ///     the context. This routine will define a tag that is compatible with the specified
    ///     discretization method type and order and sample the solution exactly using the
    ///     analytical function provided by the user.
    /// </summary>
    moab::ErrorCode DefineAnalyticalSolution( moab::Tag& exactSolnTag,
                                              const std::string& solnName,
                                              Remapper::IntersectionContext ctx,
                                              sample_function testFunction,
                                              moab::Tag* clonedSolnTag  = NULL,
                                              std::string cloneSolnName = "" );
 
    /// <summary>
    ///     Compute the error between a sampled (exact) solution and a projected solution in various
    ///     error norms.
    /// </summary>
    moab::ErrorCode ComputeMetrics( Remapper::IntersectionContext ctx,
                                    moab::Tag& exactTag,
                                    moab::Tag& approxTag,
                                    std::map< std::string, double >& metrics,
                                    bool verbose = true );
 
    moab::ErrorCode fill_col_ids( std::vector< int >& ids_of_interest )
    {
        ids_of_interest.reserve( col_gdofmap.size() );
        // need to add 1
        for( auto it = col_gdofmap.begin(); it != col_gdofmap.end(); it++ )
            ids_of_interest.push_back( *it + 1 );
        return moab::MB_SUCCESS;
    }
 
    moab::ErrorCode set_col_dc_dofs( std::vector< int >& values_entities );
 
    moab::ErrorCode set_row_dc_dofs( std::vector< int >& values_entities );
 
    // hack
    void SetMeshInput( Mesh* imesh )
    {
        m_meshInput = imesh;
    };
 
  private:
    template < typename SparseMatrixType >
    void serializeSparseMatrix( const SparseMatrixType& mat, const std::string& filename );
 
    void setup_sizes_dimensions();
 
    void CAASLimiter( std::vector< double >& dataCorrectedField,
                      std::vector< double >& dataLowerBound,
                      std::vector< double >& dataUpperBound,
                      double& dMass );
    double QLTLimiter( int caasIteration,
                       std::vector< double >& dataCorrectedField,
                       std::vector< double >& dataLowerBound,
                       std::vector< double >& dataUpperBound,
                       std::vector< double >& dMassDefect );
 
    /// <summary>
    ///     Apply the weight matrix onto the source vector provided as input, and return the column
    /// vector (solution projection) after the map application
    ///     Compute:        \p tgtVals = A(S->T) * \srcVals, or
    ///     if (transpose)  \p tgtVals = [A(T->S)]^T * \srcVals
    /// </summary>
    moab::ErrorCode ApplyWeights( std::vector< double >& srcVals,
                                  std::vector< double >& tgtVals,
                                  bool transpose = false );
 
#ifdef MOAB_HAVE_MPI
    int rearrange_arrays_by_dofs( const std::vector< unsigned int >& gdofmap,
                                  DataArray1D< double >& vecFaceArea,
                                  DataArray1D< double >& dCenterLon,
                                  DataArray1D< double >& dCenterLat,
                                  DataArray2D< double >& dVertexLat,
                                  DataArray2D< double >& dVertexLon,
                                  std::vector< int >& masks,
                                  unsigned& N,  // this will be output too now
                                  int nv,
                                  int& maxdof );
#endif
 
    /// <summary>
    ///     The fundamental remapping operator object.
    /// </summary>
    moab::TempestRemapper* m_remapper;
 
#ifdef MOAB_HAVE_EIGEN3
 
    int num_rows, num_cols;
    WeightMatrix m_weightMatrix;
    WeightRowVector m_rowVector;
    WeightColVector m_colVector;
 
#endif
 
    /// <summary>
    ///     The reference to the moab::Core object that contains source/target and overlap sets.
    /// </summary>
    moab::Interface* m_interface;
 
#ifdef MOAB_HAVE_MPI
    /// <summary>
    ///     The reference to the parallel communicator object used by the Core object.
    /// </summary>
    moab::ParallelComm* m_pcomm;
#endif
 
    /// <summary>
    ///     The original tag data and local to global DoF mapping to associate matrix values to
    /// solution    <summary>
    moab::Tag m_dofTagSrc, m_dofTagDest;
    std::vector< unsigned > row_gdofmap, col_gdofmap, srccol_gdofmap;
 
    // make it int, because it can be -1 in new logic
    std::vector< int > row_dtoc_dofmap, col_dtoc_dofmap, srccol_dtoc_dofmap;
 
    std::map< int, int > rowMap, colMap;
    int m_input_order, m_output_order;
 
    DataArray3D< int > dataGLLNodesSrc, dataGLLNodesSrcCov, dataGLLNodesDest;
    DiscretizationType m_srcDiscType, m_destDiscType;
    int m_nTotDofs_Src, m_nTotDofs_SrcCov, m_nTotDofs_Dest;
 
    // Key details about the current map
    int m_nDofsPEl_Src, m_nDofsPEl_Dest;
    DiscretizationType m_eInputType, m_eOutputType;
    bool m_bConserved;
    int m_iMonotonicity;
 
    Mesh* m_meshInput;
    Mesh* m_meshInputCov;
    Mesh* m_meshOutput;
    Mesh* m_meshOverlap;
 
    bool is_parallel, is_root;
    int rank, size;
};
 
///////////////////////////////////////////////////////////////////////////////
 
inline int moab::TempestOnlineMap::GetRowGlobalDoF( int localRowID ) const
{
    return row_gdofmap[localRowID];
}
 
inline int moab::TempestOnlineMap::GetIndexOfRowGlobalDoF( int globalRowDoF ) const /* 0 based */
{
    return globalRowDoF + 1;
}
///////////////////////////////////////////////////////////////////////////////
 
inline int moab::TempestOnlineMap::GetColGlobalDoF( int localColID ) const
{
    return col_gdofmap[localColID];
}
 
inline int moab::TempestOnlineMap::GetIndexOfColGlobalDoF( int globalColDoF ) const /* 0 based */
{
    return globalColDoF + 1;  // temporary
}
///////////////////////////////////////////////////////////////////////////////
 
inline int moab::TempestOnlineMap::GetSourceNDofsPerElement()
{
    return m_nDofsPEl_Src;
}
 
///////////////////////////////////////////////////////////////////////////////
 
inline int moab::TempestOnlineMap::GetDestinationNDofsPerElement()
{
    return m_nDofsPEl_Dest;
}
 
// setters for m_nDofsPEl_Src, m_nDofsPEl_Dest
inline void moab::TempestOnlineMap::SetSourceNDofsPerElement( int ns )
{
    m_nDofsPEl_Src = ns;
}
 
inline void moab::TempestOnlineMap::SetDestinationNDofsPerElement( int nt )
{
    m_nDofsPEl_Dest = nt;
}
 
///////////////////////////////////////////////////////////////////////////////
#ifdef MOAB_HAVE_EIGEN3
 
inline int moab::TempestOnlineMap::GetSourceGlobalNDofs()
{
    return m_weightMatrix.cols();  // return the global number of rows from the weight matrix
}
 
// ///////////////////////////////////////////////////////////////////////////////
 
inline int moab::TempestOnlineMap::GetDestinationGlobalNDofs()
{
    return m_weightMatrix.rows();  // return the global number of columns from the weight matrix
}
 
///////////////////////////////////////////////////////////////////////////////
 
inline int moab::TempestOnlineMap::GetSourceLocalNDofs()
{
    return m_weightMatrix.cols();  // return the local number of rows from the weight matrix
}
 
///////////////////////////////////////////////////////////////////////////////
 
inline int moab::TempestOnlineMap::GetDestinationLocalNDofs()
{
    return m_weightMatrix.rows();  // return the local number of columns from the weight matrix
}
 
///////////////////////////////////////////////////////////////////////////////
 
inline moab::TempestOnlineMap::WeightMatrix& moab::TempestOnlineMap::GetWeightMatrix()
{
    assert( m_weightMatrix.rows() != 0 && m_weightMatrix.cols() != 0 );
    return m_weightMatrix;
}
 
///////////////////////////////////////////////////////////////////////////////
 
inline moab::TempestOnlineMap::WeightRowVector& moab::TempestOnlineMap::GetRowVector()
{
    assert( m_rowVector.size() != 0 );
    return m_rowVector;
}
 
///////////////////////////////////////////////////////////////////////////////
 
inline moab::TempestOnlineMap::WeightColVector& moab::TempestOnlineMap::GetColVector()
{
    assert( m_colVector.size() != 0 );
    return m_colVector;
}
 
///////////////////////////////////////////////////////////////////////////////
 
#endif
 
}  // namespace moab
 
#endif