ProblemVec.h

// ============================================================================
// ==                                                                        ==
// == AMDiS - Adaptive multidimensional simulations                          ==
// ==                                                                        ==
// ============================================================================
// ==                                                                        ==
// ==  TU Dresden                                                            ==
// ==                                                                        ==
// ==  Institut fr Wissenschaftliches Rechnen                               ==
// ==  Zellescher Weg 12-14                                                  ==
// ==  01069 Dresden                                                         ==
// ==  germany                                                               ==
// ==                                                                        ==
// ============================================================================
// ==                                                                        ==
// ==  https://gforge.zih.tu-dresden.de/projects/amdis/                      ==
// ==                                                                        ==
// ============================================================================

/** \file ProblemVec.h */

#ifndef AMDIS_PROBLEMVEC_H
#define AMDIS_PROBLEMVEC_H

#include <vector>
#include <list>
#include "AMDiS_fwd.h"
#include "ProblemStatBase.h"
#include "Parameters.h"
#include "Boundary.h"
#include "MatrixVector.h"
#include "StandardProblemIteration.h"
#include "ElementFileWriter.h"
#include "ComponentTraverseInfo.h"
#include "AbstractFunction.h"
#include "SolverMatrix.h"

namespace AMDiS {

  class ProblemVec : public ProblemStatBase,
		     public StandardProblemIteration
  {
  private:
    // Defines a mapping type from dof indices to world coordinates.
    typedef std::map<DegreeOfFreedom, WorldVector<double> > DofToCoord;

    // Defines a mapping type from dof indices to world coordinates.
    typedef std::map<WorldVector<double>, DegreeOfFreedom> CoordToDof;

  public:
    /// Constructor
    ProblemVec(std::string nameStr,
	       ProblemIterationInterface *problemIteration = NULL)
      : StandardProblemIteration(this),
	name(nameStr),
	nComponents(-1),
	nMeshes(0),
	traverseInfo(0),
	solver(NULL),
	solution(NULL),
	rhs(NULL),
	systemMatrix(NULL),
	useGetBound(true),
	info(10),
	allowFirstRef(false),
	computeExactError(false)
    {
      GET_PARAMETER(0, name + "->components", "%d", &nComponents);
      TEST_EXIT(nComponents > 0)("components not set!\n");    
      estimator.resize(nComponents, NULL);
      marker.resize(nComponents, NULL);

      assembleMatrixOnlyOnce.resize(nComponents);
      assembledMatrix.resize(nComponents);
      for (int i = 0; i < nComponents; i++) {
	assembleMatrixOnlyOnce[i].resize(nComponents);
	assembledMatrix[i].resize(nComponents);
	for (int j = 0; j < nComponents; j++) {
	  assembleMatrixOnlyOnce[i][j] = false;
	  assembledMatrix[i][j] = false;
	}
      }

      exactSolutionFcts.resize(nComponents);
    }

    /// Destructor
    virtual ~ProblemVec() {}

    /// Initialisation of the problem.
    virtual void initialize(Flag initFlag,
			    ProblemVec *adoptProblem = NULL,
			    Flag adoptFlag = INIT_NOTHING);


    /// Used in \ref initialize().
    virtual void createMesh();

    /// Used in \ref initialize().
    virtual void createFESpace(DOFAdmin *admin);

    /// Used in \ref initialize().
    virtual void createMatricesAndVectors();

    /// Used in \ref initialize().
    virtual void createSolver();

    /// Used in \ref initialize().
    virtual void createEstimator();

    /// Used in \ref initialize().
    virtual void createMarker();

    /// Used in \ref initialize().
    virtual void createFileWriter();

    /// Used in \ref initialize().
    virtual void doOtherStuff();

    /** \brief
     * Implementation of ProblemStatBase::solve(). Deligates the solving
     * of problems system to \ref solver.
     */
    virtual void solve(AdaptInfo *adaptInfo, bool fixedMatrix = false);

    /** \brief
     * Implementation of ProblemStatBase::estimate(). Deligates the estimation
     * to \ref estimator.
     */
    virtual void estimate(AdaptInfo *adaptInfo);

    /** \brief
     * Implementation of ProblemStatBase::markElements().
     * Deligated to \ref adapt.
     */
    virtual Flag markElements(AdaptInfo *adaptInfo);

    /** \brief
     * Implementation of ProblemStatBase::refineMesh(). Deligated to the
     * RefinementManager of \ref adapt.
     */
    virtual Flag refineMesh(AdaptInfo *adaptInfo);

    /** \brief
     * Implementation of ProblemStatBase::coarsenMesh(). Deligated to the
     * CoarseningManager of \ref adapt.
     */
    virtual Flag coarsenMesh(AdaptInfo *adaptInfo);

    /** \brief
     * Implementation of ProblemStatBase::buildBeforeRefine().
     * Does nothing here.
     */
    virtual void buildBeforeRefine(AdaptInfo *adaptInfo, Flag) {}

    /** \brief
     * Implementation of ProblemStatBase::buildBeforeCoarsen().
     * Does nothing here.
     */
    virtual void buildBeforeCoarsen(AdaptInfo *adaptInfo, Flag) {}

    /** \brief
     * Implementation of ProblemStatBase::buildAfterCoarsen().
     * Assembles \ref A and \ref rhs. With the last two parameters, assembling
     * can be restricted to matrices or vectors only.
     */
    virtual void buildAfterCoarsen(AdaptInfo *adaptInfo, Flag flag,
				   bool assembleMatrix = true,
				   bool assembleVector = true);

    void createPrecon();


    /** \brief
     * Determines the execution order of the single adaption steps. If adapt is
     * true, mesh adaption will be performed. This allows to avoid mesh adaption,
     * e.g. in timestep adaption loops of timestep adaptive strategies.
     */
    virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION);

    /// Returns number of managed problems
    virtual int getNumProblems() 
    { 
      return 1; 
    }

    /// Implementation of ProblemStatBase::getNumComponents()
    virtual int getNumComponents() 
    { 
      return nComponents; 
    }

    /** \brief
     * Returns the problem with the given number. If only one problem
     * is managed by this master problem, the number hasn't to be given.
     */
    virtual ProblemStatBase *getProblem(int number = 0) 
    { 
      return this; 
    }

    /// Writes output files.
    void writeFiles(AdaptInfo *adaptInfo, bool force);

    /// Interpolates fct to \ref solution.
    void interpolInitialSolution(std::vector<AbstractFunction<double, WorldVector<double> >*> *fct);

    /// Adds an Operator to \ref A.
    void addMatrixOperator(Operator *op, int i, int j,
			   double *factor = NULL,
			   double *estFactor = NULL,
			   bool fake = false);

    /// Adds an Operator to \ref rhs.
    void addVectorOperator(Operator *op, int i,
			   double *factor = NULL,
			   double *estFactor = NULL,
			   bool fake = false);

    /// Adds dirichlet boundary conditions.
    virtual void addDirichletBC(BoundaryType type, int row, int col,
				AbstractFunction<double, WorldVector<double> > *b);

    /// Adds neumann boundary conditions.
    virtual void addNeumannBC(BoundaryType type, int row, int col, 
			      AbstractFunction<double, WorldVector<double> > *n);

    /// Adds robin boundary conditions.
    virtual void addRobinBC(BoundaryType type, int row, int col, 
			    AbstractFunction<double, WorldVector<double> > *n,
			    AbstractFunction<double, WorldVector<double> > *r);

    /// Adds periodic boundary conditions.
    virtual void addPeriodicBC(BoundaryType type, int row, int col);

    /// Implementation of ProblemStatBase::allowFirstRefinement().
    inline void allowFirstRefinement() 
    {
      allowFirstRef = true;
    }

    /** \brief
     * This function assembles a DOFMatrix and a DOFVector for the case,
     * the meshes from row and col FE-space are equal.
     */
    void assembleOnOneMesh(FiniteElemSpace *feSpace, 
			   Flag assembleFlag,
			   DOFMatrix *matrix, DOFVector<double> *vector);

    ///
    void assembleOnDifMeshes(FiniteElemSpace *rowFeSpace, 
			     FiniteElemSpace *colFeSpace,
			     Flag assembleFlag,
			     DOFMatrix *matrix, 
			     DOFVector<double> *vector);

    ///
    void assembleOnDifMeshes2(const FiniteElemSpace *mainFeSpace, 
			      const FiniteElemSpace *auxFeSpace,
			      Flag assembleFlag,
			      DOFMatrix *matrix,
			      DOFVector<double> *vector);

    ///
    void assembleBoundaryConditions(DOFVector<double> *rhs,
				    DOFVector<double> *solution,
				    Mesh *mesh,
				    Flag assembleFlag);
  
    /** \name getting methods
     * \{ 
     */

    /// Returns \ref solution.
    inline SystemVector* getSolution() 
    { 
      return solution; 
    }

    /// Returns \ref rhs.
    inline SystemVector* getRHS() 
    { 
      return rhs; 
    }

    /// Returns \ref systemMatrix.
    inline Matrix<DOFMatrix*> *getSystemMatrix() 
    { 
      return systemMatrix; 
    }

    /// Returns a pointer to the corresponding DOFMatrix.
    inline DOFMatrix* getSystemMatrix(int row, int col) 
    {
      return (*systemMatrix)[row][col];
    }

    /// Returns mesh of given component
    inline Mesh* getMesh(int comp) 
    {
      FUNCNAME("ProblemVec::getMesh()");
      TEST_EXIT(comp < static_cast<int>(componentMeshes.size()) && comp >= 0)
	("invalid component number\n");
      return componentMeshes[comp]; 
    }

    /// Returns \ref meshes
    inline std::vector<Mesh*> getMeshes() 
    {
      return meshes; 
    }

    /// Returns \ref feSpace_.
    inline FiniteElemSpace* getFESpace(int comp) 
    { 
      FUNCNAME("ProblemVec::getFESpace()");
      TEST_EXIT(comp < static_cast<int>(componentSpaces.size()) && comp >= 0)
	("invalid component number\n");
      return componentSpaces[comp]; 
    }

    /// Returns \ref feSpaces.
    inline std::vector<FiniteElemSpace*> getFESpaces() 
    { 
      return feSpaces; 
    }

    /// Returns \ref componentSpaces;
    inline std::vector<FiniteElemSpace*> getComponentFESpaces() 
    {
      return componentSpaces;
    }

    /// Returns \ref estimator.
    inline std::vector<Estimator*> getEstimator() 
    { 
      return estimator; 
    }

    /// Returns \ref estimator.
    inline Estimator* getEstimator(int comp) 
    { 
      return estimator[comp]; 
    }

    /// Returns \ref refinementManager.
    inline RefinementManager* getRefinementManager(int comp) 
    { 
      return refinementManager; 
    }

    /// Returns \ref refinementManager.
    inline CoarseningManager* getCoarseningManager(int comp) 
    { 
      return coarseningManager; 
    }

    /// Returns \ref solver.
    inline OEMSolver* getSolver() 
    { 
      return solver; 
    }

    /// Returns \ref marker.
    inline Marker *getMarker(int comp) 
    { 
      return marker[comp]; 
    }

    /// Returns \ref marker.
    inline std::vector<Marker*> getMarker() 
    { 
      return marker; 
    }

    /// Returns the name of the problem
    inline virtual std::string getName() 
    { 
      return name; 
    }

    /// Returns \ref useGetBound.
    inline bool getBoundUsed() 
    { 
      return useGetBound; 
    }

    /// Returns \ref info.
    int getInfo()
    {
      return info;
    }

    /** \} */

    /** \name setting methods
     * \{ 
     */

    /// Sets \ref estimator.
    inline void setEstimator(std::vector<Estimator*> est) 
    { 
      estimator = est; 
    }

    /// Sets the FE space for the given component.
    inline void setFESpace(FiniteElemSpace *feSpace, int comp) 
    {
      feSpaces[comp] = feSpace;
    }

    /// Sets \ref estimator.
    inline void setEstimator(Estimator* est, int comp) 
    { 
      estimator[comp] = est; 
    }

    /// Sets \ref marker.
    inline void setMarker(Marker* mark, int comp) 
    { 
      marker[comp] = mark; 
    }

    /// Sets \ref solver.
    inline void setSolver(OEMSolver* sol) 
    { 
      solver = sol; 
    }

    ///
    inline void setAssembleMatrixOnlyOnce(int i, int j, bool value = true) 
    {
      assembleMatrixOnlyOnce[i][j] = value;
    }

    ///
    void setExactSolutionFct(AbstractFunction<double, WorldVector<double> > *fct,
			     int component) 
    {
      exactSolutionFcts[component] = fct;
    }

    ///
    AbstractFunction<double, WorldVector<double> > *getExactSolutionFct(int component) 
    {
      return exactSolutionFcts[component];
    }

    ///
    void setComputeExactError(bool v) 
    {
      computeExactError = v;
    }

    /** \} */

    /** \brief
     * Outputs the mesh of the given component, but the values are taken from the 
     * residual error estimator. 
     */
    void writeResidualMesh(int comp, AdaptInfo *adaptInfo, std::string name);

    /// Function that implements the serialization procedure.
    virtual void serialize(std::ostream &out);

    /// Function that implements the deserialization procedure.
    virtual void deserialize(std::istream &in);


    /// Returns \ref fileWriters.
    std::vector<FileWriterInterface*>& getFileWriterList() 
    {
      return fileWriters;
    }

    /** \brief
     * This function writes the system matrix and the system vector to a file
     * for debugging. The entries of both, the matrix and the vector, are not
     * indicated by the dof indices, but by the world coordinates of the dofs.
     * This makes it possible to compare dof matrices, where the dof indices
     * are different, e.g., when using domain decomposition parallelization.
     */
    void writeDbgMatrix(std::string filename);

    /** \brief
     * Reads a file, that was created using the function \ref writeDbgMatrix, and
     * compares the date with the system matrix of this problem.
     */
    void readAndCompareDbgMatrix(std::vector<std::string> filenames);

  protected:
    /** \brief
     * If the exact solution is known, the problem can compute the exact
     * error instead of the error estimation. This is done in this function.
     */
    void computeError(AdaptInfo *adaptInfo);

    /** \brief
     * Create from the current problem a map from dof indices to world coordinates.
     * This function is used by the debugging function \ref writeDbgMatrix and \ref
     * readAndCompareDbgMatrix.
     */
    void createDofToCoordMap(DofToCoord &dofMap);

    /** \brief
     * Create from the current problem a map from world coordinates of all dofs to
     * the corresponding dof indices. This function is used by the debugging function 
     * \ref writeDbgMatrix and \ref readAndCompareDbgMatrix.
     */
    void createCoordToDofMap(CoordToDof &dofMap);

  protected:
    
    /// Name of this problem.
    std::string name;

    /// Number of problem components
    int nComponents;

    /** \brief
     * Number of problem meshes. If all components are defined on the same mesh,
     * this number is 1. Otherwise, this variable is the number of different meshes
     * within the problem.
     */
    int nMeshes;

    /// FE spaces of this problem.
    std::vector<FiniteElemSpace*> feSpaces;

    /// Meshes of this problem.
    std::vector<Mesh*> meshes;

    /// Pointer to the fe spaces for the different problem components
    std::vector<FiniteElemSpace*> componentSpaces;

    /// Pointer to the meshes for the different problem components
    std::vector<Mesh*> componentMeshes;

    /** \brief
     * Stores information about which meshes must be traversed to assemble the
     * specific components. I.e., it was implemented to make use of different
     * meshes for different components.
     */
    ComponentTraverseInfo traverseInfo;
    
    /// Responsible for element marking.
    std::vector<Marker*> marker;

    /// Estimator of this problem. Used in \ref estimate().
    std::vector<Estimator*> estimator;

    /// Linear solver of this problem. Used in \ref solve().
    OEMSolver *solver;

    /// System vector  storing the calculated solution of the problem.
    SystemVector *solution;

    /// System vector for the right hand side 
    SystemVector *rhs;

    /// System matrix
    Matrix<DOFMatrix*> *systemMatrix;

    /// Composed system matrix
    SolverMatrix<Matrix<DOFMatrix*> > solverMatrix;

    /** \brief
     * Some DOFMatrices of the systemMatrix may be assembled only once (for
     * example if they are independent of the time or older solutions). If
     * [i][j] of this field is set to true, the corresponding DOFMatrix will
     * be assembled only once. All other matrices will be assembled at every
     * time step.
     */
    std::vector< std::vector< bool > > assembleMatrixOnlyOnce;

    /** \brief
     * If [i][j] of this field is set to true, the corresponding DOFMatrix of
     * the systemMatrix has been assembled at least once. This field is used
     * to determine, if assembling of a matrix can be ommitted, if it is set
     * to be assembled only once.
     */
    std::vector< std::vector< bool > > assembledMatrix;

    /// Determines whether domain boundaries should be considered at assembling.
    bool useGetBound;

    /// Writes the meshes and solution after the adaption loop.
    std::vector<FileWriterInterface*> fileWriters;

    /** \brief
     * All actions of mesh refinement are performed by refinementManager.
     * If new refinement algorithms should be realized, one has to override
     * RefinementManager and give one instance of it to AdaptStationary.
     */
    RefinementManager *refinementManager;

    /** \brief
     * All actions of mesh coarsening are performed by coarseningManager.
     * If new coarsening algorithms should be realized, one has to override
     * CoarseningManager and give one instance of it to AdaptStationary.
     */
    CoarseningManager *coarseningManager;
  
    /// Info level.
    int info;

    /// Allows one refinement although the adapt tolerance is reached already.
    bool allowFirstRef;

    /** \brief
     * This vectors stores pointers to functions defining the exact solution of
     * the problem. This may be used to compute the real error of the computed
     * solution.
     */
    std::vector<AbstractFunction<double, WorldVector<double> >*> exactSolutionFcts;

    /** \brief
     * If true, the error is not estimated but computed from the exact solution
     * defined by \ref exactSolutionFcts.
     */
    bool computeExactError;
  };
}

#endif