DOFMatrix.h

// ============================================================================
// ==                                                                        ==
// == AMDiS - Adaptive multidimensional simulations                          ==
// ==                                                                        ==
// ==  http://www.amdis-fem.org                                              ==
// ==                                                                        ==
// ============================================================================
//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology 
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.



/** \file DOFMatrix.h */

#ifndef AMDIS_DOFMATRIX_H
#define AMDIS_DOFMATRIX_H

#include <vector>
#include <set>
#include <memory>
#include <list>
#include <boost/numeric/mtl/mtl.hpp>
#include "AMDiS_fwd.h"
#include "Global.h"
#include "Flag.h"
#include "RCNeighbourList.h"
#include "DOFAdmin.h"
#include "DOFIndexed.h"
#include "Boundary.h"
#include "Serializable.h"

namespace AMDiS {

  using namespace std;

  /** \ingroup DOFAdministration
   * \brief
   * A DOFMatrix is a sparse matrix representation for matrices that work
   * on DOFVectors. The underlying matrix type 
   * is a CRS matrix of double.
   */
  class DOFMatrix : public DOFIndexed<bool>,
                    public Serializable
  {
  public:
    /// Type of scalars in the underlying matrix
    typedef double value_type;

    typedef unsigned size_type;
    typedef mtl::matrix::parameters<mtl::row_major, mtl::index::c_index, mtl::non_fixed::dimensions, false, size_type> para;

    /// Type of underlying matrix
    typedef mtl::compressed2D<value_type, para> base_matrix_type;

    /// Type of inserter for the base matrix;
    typedef mtl::matrix::inserter<base_matrix_type, mtl::operations::update_plus<value_type> >  inserter_type;

  private:
    /// Symbolic constant for an unused matrix entry
    static const int UNUSED_ENTRY = -1;
    
    /// Symbolic constant for an unused entry which is not followed by any
    /// used entry in this row
    static const int NO_MORE_ENTRIES = -2;

  public:    
    DOFMatrix();

    /// Constructs a DOFMatrix with name n and the given row and olumn FeSpaces.
    DOFMatrix(const FiniteElemSpace* rowFeSpace, 
	      const FiniteElemSpace* colFeSpace,
	      string n = "");

    /// Copy-Constructor
    DOFMatrix(const DOFMatrix& rhs);

    /// Destructor
    virtual ~DOFMatrix();
  
    /// Assignment operator.
    DOFMatrix& operator=(const DOFMatrix& rhs);

    void copy(const DOFMatrix& rhs);

    /// Access underlying matrix directly
    base_matrix_type& getBaseMatrix()
    {
	return matrix;
    }

    /// Access underlying matrix directly (const)
    const base_matrix_type& getBaseMatrix() const
    {
	return matrix;
    }

    // Only to get rid of the abstract functions, I hope they are not used
    vector<bool>::iterator begin() 
    {
      ERROR_EXIT("Shouldn't be used, only fake."); vector<bool> v; 
      return v.begin();
    }
    
    vector<bool>::iterator end() 
    {
      ERROR_EXIT("Shouldn't be used, only fake."); vector<bool> v; 
      return v.end();
    }

    // Only to get rid of the abstract functions, I hope they are not used
    vector<bool>::const_iterator begin() const
    {
      ERROR_EXIT("Shouldn't be used, only fake."); vector<bool> v;
      return v.begin();
    }

    vector<bool>::const_iterator end() const
    {
      ERROR_EXIT("Shouldn't be used, only fake."); vector<bool> v;
      return v.end();
    }
    
    bool dummy; // Must be deleted later
    bool& operator[](int i) 
    {
      ERROR_EXIT("Shouldn't be used, only fake."); 
      return dummy;
    }

    const bool& operator[](int i) const 
    {
      ERROR_EXIT("Shouldn't be used, only fake."); 
      return dummy;
    }
 
    /// DOFMatrix does not need to be compressed before assembling, when using MTL4.
    void compressDOFIndexed(int first, int last, vector<DegreeOfFreedom> &newDOF) 
    {}

    /// Implements DOFIndexedBase::freeDOFContent()
    virtual void freeDOFContent(int index);

    /// Returns \ref coupleMatrix.
    inline bool isCoupleMatrix() 
    { 
      return coupleMatrix; 
    }

    /// Returns \ref coupleMatrix.
    inline void setCoupleMatrix(bool c) 
    { 
      coupleMatrix = c; 
    }

    /// a * x + y
    void axpy(double a, const DOFMatrix& x, const DOFMatrix& y);

    /// Multiplication with a scalar.
    void scal(double s);

    /// Adds an operator to the DOFMatrix. A factor, that is multipled to the 
    /// operator, and a multilier factor for the estimator may be also given.
    void addOperator(Operator *op, 
		     double* factor = NULL, 
		     double* estFactor = NULL);

    ///
    void clearOperators();

    inline vector<double*>::iterator getOperatorFactorBegin() 
    {
      return operatorFactor.begin();
    }

    inline vector<double*>::iterator getOperatorFactorEnd() 
    {
      return operatorFactor.end();
    }

    inline vector<double*>::iterator getOperatorEstFactorBegin() 
    {
      return operatorEstFactor.begin();
    }

    inline vector<double*>::iterator getOperatorEstFactorEnd() 
    {
      return operatorEstFactor.end();
    }

    inline vector<Operator*>::iterator getOperatorsBegin() 
    {
      return operators.begin();
    }

    inline vector<Operator*>::iterator getOperatorsEnd() 
    {
      return operators.end();
    }

    Flag getAssembleFlag();

    /** \brief
     * Updates the matrix matrix by traversing the underlying mesh and assembling
     * the element contributions into the matrix. Information about the 
     * computation of element matrices and connection of local and global DOFs is
     * stored in minfo; the flags for the mesh traversal are stored at 
     * minfo->fill_flags which specifies the elements to be visited and 
     * information that should be present on the elements for the calculation of 
     * the element matrices and boundary information (if minfo->boundBas is not
     * NULL). On the elements, information about the row DOFs is accessed by 
     * minfo->rowBas using info->row_admin; this vector is also used for the 
     * column DOFs if minfo->nCol is less or equal zero, or minfo->col_admin or 
     * minfo->colBas is a NULL pointer; if row and column DOFs are the same, the 
     * boundary type of the DOFs is accessed by minfo->boundBas if 
     * minfo->boundBas is not a NULL pointer; then the element matrix is 
     * computed by minfo->fillElementMatrix(el info, minfo->myFill); these 
     * contributions, multiplied by minfo->factor, are eventually added to matrix
     * by a call of addElementMatrix() with all information about row and column 
     * DOFs, the element matrix, and boundary types, if available;
     * updateMatrix() only adds element contributions; this makes several calls 
     * for the assemblage of one matrix possible; before the first call, the 
     * matrix should be cleared by calling clear dof matrix().
     */
  
    void assemble(double factor, ElInfo *elInfo, const BoundaryType *bound);

    void assemble(double factor, ElInfo *elInfo, const BoundaryType *bound,
		  Operator *op);

    void assemble(double factor, 
		  ElInfo *rowElInfo, ElInfo *colElInfo,
		  ElInfo *smallElInfo, ElInfo *largeElInfo,
		  const BoundaryType *bound,
		  Operator *op = NULL);

    void assemble2(double factor, 
		   ElInfo *mainElInfo, ElInfo *auxElInfo,
		   ElInfo *smallElInfo, ElInfo *largeElInfo,
		   const BoundaryType *bound, 
		   Operator *op = NULL);

    /// Adds an element matrix to \ref matrix
    void addElementMatrix(const ElementMatrix& elMat, 
			  const BoundaryType *bound,
			  ElInfo* rowElInfo,
			  ElInfo* colElInfo);

    ///
    void assembleOperator(Operator &op);

    /// That function must be called after the matrix assembling has been 
    /// finished. This makes it possible to start some cleanup or matrix 
    /// data compressing procedures.
    void finishAssembling();

    /// Enable insertion for assembly. You can optionally give an upper limit for
    /// entries per row (per column for CCS matrices).  Choosing this parameter
    /// too small can induce perceivable overhead for compressed matrices. Thus,
    /// it's better to choose a bit too large than too small.
    void startInsertion(int nnz_per_row = 10);

    /// Finishes insertion. For compressed matrix types, this is where the
    /// compression happens.
    void finishInsertion()
    {
      FUNCNAME("DOFMatrix::finishInsertion()");

      TEST_EXIT(inserter)("Inserter wasn't used or is already finished.\n");
      
      delete inserter;
      inserter= 0;
    }

#if 0
    /// Returns whether restriction should be performed after coarsening
    /// (false by default)
    virtual bool coarseRestrict() 
    {
      return false;
    }
#endif

    /// Returns const \ref rowFeSpace
    const FiniteElemSpace* getRowFeSpace() const 
    { 
      return rowFeSpace; 
    }

    /// Returns const \ref colFeSpace
    const FiniteElemSpace* getColFeSpace() const 
    { 
      return colFeSpace; 
    }

    /// Returns const \ref rowFeSpace
    const FiniteElemSpace* getFeSpace() const 
    { 
      return rowFeSpace; 
    }

    /// Returns number of rows (\ref matrix.size())
    inline int getSize() const 
    { 
      return num_rows(matrix);
    }

    /// Returns the number of used rows (equal to number of used DOFs in
    /// the row FE space).
    inline int getUsedSize() const 
    {
      return rowFeSpace->getAdmin()->getUsedSize();
    }

    std::set<DegreeOfFreedom>& getDirichletRows()
    {
      return dirichletDofs;
    }

    /// Returns \ref name
    inline string getName() const 
    { 
      return name; 
    }

    /// Resizes \ref matrix to n rows
    inline void resize(int n) 
    { 
      TEST_EXIT_DBG(n >= 0)("Can't resize DOFMatrix to negative size\n");
    }

    /// Returns value at logical indices a,b
    double logAcc(DegreeOfFreedom a, DegreeOfFreedom b) const;

    /// Changes col at logical indices a,b to c 
    void changeColOfEntry(DegreeOfFreedom a, DegreeOfFreedom b, DegreeOfFreedom c);

    /// Creates an entry with logical indices irow, icol if there is no entry
    /// yet. Than sign * entry is added to the value at this logical indices
    void addSparseDOFEntry(double sign,
			   int irow, int jcol, double entry,
			   bool add = true);

    void clearDirichletRows();

    /// Prints \ref matrix to stdout
    void print() const;

    /// Removes all matrix entries
    void clear()
    {
	set_to_zero(matrix);
    }

    /// Test whether \ref matrix is symmetric. Exits if not.
    void test();

    bool symmetric();

    inline vector<Operator*>& getOperators() 
    { 
      return operators; 
    }
    
    inline vector<double*>& getOperatorFactor() 
    { 
      return operatorFactor; 
    }

    inline vector<double*>& getOperatorEstFactor() 
    { 
      return operatorEstFactor; 
    }

    inline BoundaryManager* getBoundaryManager() const 
    { 
      return boundaryManager; 
    }

    inline void setBoundaryManager(BoundaryManager *bm) 
    {
      boundaryManager = bm;
    }

    /// Calculates the average of non zero entries per row in matrix.
    void calculateNnz()
    {
      nnzPerRow = 0;

      if (num_rows(matrix) != 0)
	nnzPerRow = int(double(matrix.nnz()) / num_rows(matrix) * 1.2); 
      if (nnzPerRow < 20) 
	nnzPerRow = 20;
    }

    /// Returns \ref nnzPerRow.
    int getNnz()
    {
      return nnzPerRow;
    }

    /// Writes the matrix to an output stream.
    void serialize(ostream &out);

    /// Reads a matrix from an input stream.
    void deserialize(istream &in);

    ///
    int memsize();

  protected:
    /// Pointer to a FiniteElemSpace with information about corresponding row DOFs
    /// and basis functions
    const FiniteElemSpace *rowFeSpace;

    /// Pointer to a FiniteElemSpace with information about corresponding 
    /// column DOFs and basis functions
    const FiniteElemSpace *colFeSpace;

    /// Name of the DOFMatrix
    string name;

    /// Sparse matrix, type is a template parameter by 
    /// default compressed2D<double>
    base_matrix_type matrix;

    /// Pointers to all operators of the equation systems. Are used in the
    /// assembling process.
    vector<Operator*> operators;
    
    /// Defines for each operator a factor which is used to scal the element
    /// matrix after the assembling process of the operator.
    vector<double*> operatorFactor;

    ///
    vector<double*> operatorEstFactor;

    ///
    BoundaryManager *boundaryManager;

    /// If false, the matrix is a diagonal matrix within a matrix of DOF matrices.
    /// Otherwise the value is true, and the matrix is an off-diagonal matrix.
    bool coupleMatrix;

    /// Temporary variable used in assemble()
    ElementMatrix elementMatrix;

    /// Number of basis functions in the row fe space.
    int nRow;

    /// Number of basis functions in the col fe space.
    int nCol;

    /// Maps local row indices of an element to global matrix indices.
    vector<DegreeOfFreedom> rowIndices;

    /// Maps local col indices of an element to global matrix indices.
    vector<DegreeOfFreedom> colIndices;

    /// A set of row indices. When assembling the DOF matrix, all rows, that
    /// correspond to a dof at a dirichlet boundary, are ignored and the row is
    /// left blank. After assembling, the diagonal element of the matrix must be
    /// set to 1. The indices of all rows, where this should be done, are stored
    /// in this set.
    std::set<DegreeOfFreedom> dirichletDofs;

    /// Number of non zero entries per row (average). For instationary problems this
    /// information may be used in the next timestep to accelerate insertion of
    /// elemnts during assembling.
    int nnzPerRow;

    /// Inserter object: implemented as pointer, allocated and deallocated as needed
    inserter_type *inserter;
      
    friend class DOFAdmin;
    friend class DOFVector<double>;
    friend class DOFVector<unsigned char>;
    friend class DOFVector<int>;
    friend class DOFVector<WorldVector<double> >;
  };

}

#endif  // AMDIS_DOFMATRIX_H