ProblemScal.cc

#include "ProblemScal.h"
#include "AbstractFunction.h"
#include "DirichletBC.h"
#include "RobinBC.h"
#include "FixVec.h"
#include "Flag.h"
#include "Serializer.h"
#include "RecoveryEstimator.h"
#include "Operator.h"
#include "DOFMatrix.h"
#include "FiniteElemSpace.h"
#include "Estimator.h"
#include "OEMSolver.h"
#include "DOFVector.h"
#include "Marker.h"
#include "AdaptInfo.h"
#include "ElInfo.h"
#include "FileWriter.h"
#include "RefinementManager.h"
#include "CoarseningManager.h"
#include "Lagrange.h"
#include "PeriodicBC.h"
#include "ValueReader.h"
#include "ElementFileWriter.h"
#include "ProblemVec.h"

namespace AMDiS {

  ProblemScal::~ProblemScal()
  {
    FUNCNAME("ProblemScal::~ProblemScal()");

    for (int i = 0; i < static_cast<int>(fileWriters.size()); i++) {
      DELETE fileWriters[i];
    }

    if (systemMatrix)
      DELETE systemMatrix;
    if (rhs) 
      DELETE rhs;
    if (solution)
      DELETE solution;
    if (estimator)
      DELETE estimator;
    if (marker)
      DELETE marker;
    if (solver)
      DELETE solver;
    if (mesh)
      DELETE mesh;

    FiniteElemSpace::clear();
    Lagrange::clear();
  }

  void ProblemScal::writeFiles(AdaptInfo *adaptInfo, bool force) {
    for (int i = 0; i < static_cast<int>(fileWriters.size()); i++) {
      fileWriters[i]->writeFiles(adaptInfo, force);
    }
  }

  void ProblemScal::interpolInitialSolution(AbstractFunction<double, WorldVector<double> > *fct) 
  {
    solution->interpol(fct);
  }

  void ProblemScal::addMatrixOperator(Operator *op, 
				      double *factor,
				      double *estFactor) 
  {
    systemMatrix->addOperator(op, factor, estFactor);
  }

  void ProblemScal::addVectorOperator(Operator *op, 
				      double *factor,
				      double *estFactor) 
  {
    rhs->addOperator(op, factor, estFactor);
  }
  
  void ProblemScal::addDirichletBC(BoundaryType type, 
				   AbstractFunction<double, WorldVector<double> >* b) 
  {
    DirichletBC *dirichlet = new DirichletBC(type, b, feSpace);
    if (systemMatrix) 
      systemMatrix->getBoundaryManager()->addBoundaryCondition(dirichlet);
    if (rhs) 
      rhs->getBoundaryManager()->addBoundaryCondition(dirichlet);
    if (solution)
      solution->getBoundaryManager()->addBoundaryCondition(dirichlet);
  }

  void ProblemScal::addDirichletBC(BoundaryType type, 
				   DOFVector<double> *vec) 
  {
    DirichletBC *dirichlet = new DirichletBC(type, vec);
    if (systemMatrix) 
      systemMatrix->getBoundaryManager()->addBoundaryCondition(dirichlet);
    if (rhs) 
      rhs->getBoundaryManager()->addBoundaryCondition(dirichlet);
    if (solution)
      solution->getBoundaryManager()->addBoundaryCondition(dirichlet);
  }

  void ProblemScal::addRobinBC(BoundaryType type, 
			       AbstractFunction<double, WorldVector<double> > *n,
			       AbstractFunction<double, WorldVector<double> > *r)
  {
    RobinBC *robin = new RobinBC(type, n, r, feSpace);
    if (rhs) 
      rhs->getBoundaryManager()->addBoundaryCondition(robin);
    if (systemMatrix)
      systemMatrix->getBoundaryManager()->addBoundaryCondition(robin);
  }

  void ProblemScal::addNeumannBC(BoundaryType type, 
				 AbstractFunction<double, WorldVector<double> > *n)
  {
    NeumannBC *neumann = new NeumannBC(type, n, feSpace);
    if (rhs) 
      rhs->getBoundaryManager()->addBoundaryCondition(neumann);
  }

  void ProblemScal::addRobinBC(BoundaryType type, 
			       DOFVector<double> *n,
			       DOFVector<double> *r)
  {
    RobinBC *robin = new RobinBC(type, n, r, feSpace);
    if (rhs) 
      rhs->getBoundaryManager()->addBoundaryCondition(robin);
    if (systemMatrix)
      systemMatrix->getBoundaryManager()->addBoundaryCondition(robin);
  }

  void ProblemScal::addPeriodicBC(BoundaryType type) 
  {
    PeriodicBC *periodic = new PeriodicBC(type, feSpace);

    if (systemMatrix) 
      systemMatrix->getBoundaryManager()->addBoundaryCondition(periodic);
    if (rhs) 
      rhs->getBoundaryManager()->addBoundaryCondition(periodic);
  }

#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
  void ProblemScal::useApplicationOrdering(AO *ao) 
  {
    applicationOrdering = ao;
    systemMatrix->useApplicationOrdering(ao);
    rhs->useApplicationOrdering(ao);
  }
#endif


  void ProblemScal::createMesh()
  {
    TEST_EXIT(Parameters::initialized())("parameters not initialized\n");

    // === create problems mesh ===
    std::string meshName("");

    GET_PARAMETER(0, name + "->info", "%d", &info);
    GET_PARAMETER(0, name + "->mesh", &meshName);

    TEST_EXIT(meshName != "")("no mesh name specified\n");

    // get problem dimension
    int dim = 0;
    GET_PARAMETER(0, name + "->dim", "%d", &dim);
    TEST_EXIT(dim)("no problem dimension specified!\n");

    // create the mesh
    mesh = NEW Mesh(meshName, dim);

    switch (dim) {
    case 1:
      coarseningManager = NEW CoarseningManager1d();
      refinementManager = NEW RefinementManager1d();
      break;
    case 2:
      coarseningManager = NEW CoarseningManager2d();
      refinementManager = NEW RefinementManager2d();
      break;
    case 3:
      coarseningManager = NEW CoarseningManager3d();
      refinementManager = NEW RefinementManager3d();
      break;
    default:
      ERROR_EXIT("invalid dim!\n");
    }
  }

  void ProblemScal::setMeshFromProblemVec(ProblemVec* pv, int i) 
  { 
    mesh = pv->getMesh(i);
    coarseningManager = pv->getCoarseningManager(i);
    refinementManager = pv->getRefinementManager(i);
  }

  Flag ProblemScal::markElements(AdaptInfo *adaptInfo) 
  { 
    if (marker)
      return marker->markMesh(adaptInfo, mesh);
    else
      WARNING("no marker\n");

    return 0;
  }

  Flag ProblemScal::refineMesh(AdaptInfo *adaptInfo) 
  { 
    return refinementManager->refineMesh(mesh); 
  }

  Flag ProblemScal::coarsenMesh(AdaptInfo *adaptInfo) 
  {
    if (adaptInfo->isCoarseningAllowed(0)) {
      return coarseningManager->coarsenMesh(mesh);
    } else {
      WARNING("coarsening not allowed\n");
      return 0;
    }
  }

  void ProblemScal::solve(AdaptInfo *adaptInfo, bool fixedMatrix)
  {
    FUNCNAME("Problem::solve()");
    if (!solver) {
      WARNING("no solver\n");
      return;
    }

#ifdef _OPENMP
    double wtime = omp_get_wtime();
#endif

    clock_t first = clock();

    SolverMatrix<DOFMatrix> solverMatrix;
    solverMatrix.setMatrix(*systemMatrix);
    int iter = solver->solveSystem(solverMatrix, *solution, *rhs);

#ifdef _OPENMP
    INFO(info, 8)("solution of discrete system needed %.5f seconds system time / %.5f seconds wallclock time\n",
		   TIME_USED(first, clock()),
		   omp_get_wtime() - wtime);
#else
    INFO(info, 8)("solution of discrete system needed %.5f seconds\n",
		   TIME_USED(first, clock()));
#endif

    adaptInfo->setSolverIterations(iter);
    adaptInfo->setMaxSolverIterations(solver->getMaxIterations());
    adaptInfo->setSolverTolerance(solver->getTolerance());
    adaptInfo->setSolverResidual(solver->getResidual());
  }

  void ProblemScal::initialize(Flag initFlag,
			       ProblemScal *adoptProblem,
			       Flag adoptFlag) 
  {
    FUNCNAME("Problem::initialize()");

    // === create mesh ===
    if (mesh) { 
      WARNING("mesh already created\n");
    } else {
      if(initFlag.isSet(CREATE_MESH) || 
	 ((!adoptFlag.isSet(INIT_MESH))&&
	  (initFlag.isSet(INIT_SYSTEM)||initFlag.isSet(INIT_FE_SPACE)))) {
	createMesh();
      } 
      
      if(adoptProblem && 
	 (adoptFlag.isSet(INIT_MESH) || 
	  adoptFlag.isSet(INIT_SYSTEM) ||
	  adoptFlag.isSet(INIT_FE_SPACE))) {
	TEST_EXIT(!mesh)("mesh already created\n");
	mesh = adoptProblem->getMesh();
	refinementManager = adoptProblem->refinementManager;
	coarseningManager = adoptProblem->coarseningManager;
      }
    }

    if (!mesh) 
      WARNING("no mesh created\n");

    // === create fespace ===
    if (feSpace) {
      WARNING("feSpace already created\n");
    } else {
      if (initFlag.isSet(INIT_FE_SPACE) || 
	  (initFlag.isSet(INIT_SYSTEM) && !adoptFlag.isSet(INIT_FE_SPACE))) {
	createFESpace();
      } 

      if (adoptProblem && 
	  (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
	TEST_EXIT(!feSpace)("feSpace already created");
	feSpace = dynamic_cast<ProblemScal*>(adoptProblem)->getFESpace();
      }
    }

    if (!feSpace) 
      WARNING("no feSpace created\n");

    // === create system ===
    if (initFlag.isSet(INIT_SYSTEM)) {
      createMatricesAndVectors();
    } 
    if (adoptProblem && adoptFlag.isSet(INIT_SYSTEM)) {
      TEST_EXIT(!solution)("solution already created\n");
      TEST_EXIT(!rhs)("rhs already created\n");
      TEST_EXIT(!systemMatrix)("systemMatrix already created\n");
      solution = adoptProblem->getSolution();
      rhs = adoptProblem->getRHS();
      systemMatrix  = adoptProblem->getSystemMatrix();
    }

    // === create solver ===
    if (solver) {
      WARNING("solver already created\n");
    } else {
      if (initFlag.isSet(INIT_SOLVER)) {
	createSolver();
      } 
      if (adoptProblem && adoptFlag.isSet(INIT_SOLVER)) {
	TEST_EXIT(!solver)("solver already created\n");
	solver = adoptProblem->getSolver();
      }
    }

    if (!solver) 
      WARNING("no solver created\n");

    // === create estimator ===
    if (estimator) {
      WARNING("estimator already created\n");
    } else {
      if (initFlag.isSet(INIT_ESTIMATOR)) {
	createEstimator();
      } 
      if (adoptProblem && adoptFlag.isSet(INIT_ESTIMATOR)) {
	TEST_EXIT(!estimator)("estimator already created\n");
	estimator = adoptProblem->getEstimator();
      } 
    }

    if (!estimator) 
      WARNING("no estimator created\n");

    // === create marker ===
    if (marker) {
      WARNING("marker already created\n");
    } else {
      if(initFlag.isSet(INIT_MARKER)) {
	createMarker();
      } 
      if(adoptProblem && adoptFlag.isSet(INIT_MARKER)) {
	TEST_EXIT(!marker)("marker already created\n");
	marker = adoptProblem->getMarker();
      } 
    }

    if (!marker) 
      WARNING("no marker created\n");

    // === create file writer ===
    if(initFlag.isSet(INIT_FILEWRITER)) {
      createFileWriter();
    }

  

    // === read serialization and init mesh ===

    // There are two possiblities where the user can define a serialization
    // to be read from disk. Either by providing the parameter -rs when executing
    // the program or in the init file. The -rs parameter is always checked first,
    // because it can be added automatically when  rescheduling the program
    // before timeout of the runqueue.

    int readSerialization = 0;
    std::string serializationFilename = "";
    GET_PARAMETER(0, "argv->rs", &serializationFilename);

    // If the parameter -rs is set, we do nothing here, because the problem will be
    // deserialized in the constructor of a following AdaptInstationary initialization.
    if (!serializationFilename.compare("")) {
      GET_PARAMETER(0, name + "->input->read serialization", "%d", 
		    &readSerialization);
      if (readSerialization) {
	GET_PARAMETER(0, name + "->input->serialization filename", 
		      &serializationFilename);
	TEST_EXIT(serializationFilename != "")("no serialization file\n");

	MSG("Deserialization from file: %s\n", serializationFilename.c_str());
	std::ifstream in(serializationFilename.c_str());
	deserialize(in);
	in.close();
      } else {
	if (initFlag.isSet(INIT_MESH) && mesh && !mesh->isInitialized()) {
	  mesh->initialize();
	}
    
	// === read value file and use it for the mesh values ===
	std::string valueFilename("");
	GET_PARAMETER(0, mesh->getName() + "->value file name", &valueFilename);     
	if (valueFilename.length()) {     
	  ValueReader::readValue(valueFilename,
				 mesh,
				 solution,
				 mesh->getMacroFileInfo());
	  mesh->clearMacroFileInfo();
	}
	
	// === do global refinements ===
	if (initFlag.isSet(INIT_GLOBAL_REFINES)) {
	  int globalRefinements = 0;
	  GET_PARAMETER(0, mesh->getName() + "->global refinements", "%d", &globalRefinements);
	  refinementManager->globalRefine(mesh, globalRefinements);	
	}
      }
    }
  }

  void ProblemScal::createFESpace()
  {
    // create finite element space
    int degree = 1;
    GET_PARAMETER(0, name + "->polynomial degree" ,"%d", &degree);
    feSpace = FiniteElemSpace::provideFESpace(NULL,
					       Lagrange::getLagrange(mesh->getDim(), degree),
					       mesh,
					       name + "->feSpace");  

    // create dof admin for vertex dofs if neccessary
    if (mesh->getNumberOfDOFs(VERTEX) == 0) {
      DimVec<int> ln_dof(mesh->getDim(), DEFAULT_VALUE, 0);
      ln_dof[VERTEX]= 1;
      mesh->createDOFAdmin("vertex dofs", ln_dof);
    }
  }

  void ProblemScal::createMatricesAndVectors()
  {
    // === create vectors and system matrix ===
    systemMatrix = NEW DOFMatrix(feSpace, feSpace, "system matrix");
    rhs = NEW DOFVector<double>(feSpace, "rhs");
    solution = NEW DOFVector<double>(feSpace, "solution");

    solution->setCoarsenOperation(COARSE_INTERPOL);
    solution->set(0.0);      /*  initialize u_h  !                      */
  }

  void ProblemScal::createSolver()
  {
    // === create solver ===
    std::string solverType("0");
    GET_PARAMETER(0, name + "->solver", &solverType);
    OEMSolverCreator *solverCreator = 
      dynamic_cast<OEMSolverCreator*>(CreatorMap<OEMSolver>::getCreator(solverType));
    TEST_EXIT(solverCreator)("no solver type\n");
    solverCreator->setName(name + "->solver");
    solver = solverCreator->create();
    solver->initParameters();
  }

  void ProblemScal::createEstimator()
  {
    // create and set leaf data prototype
    mesh->setElementDataPrototype(NEW LeafDataEstimatable(NEW LeafDataCoarsenable));

    // === create estimator ===
    std::string estimatorType("0");
    GET_PARAMETER(0, name + "->estimator", &estimatorType);
    EstimatorCreator *estimatorCreator = 
      dynamic_cast<EstimatorCreator*>(
				      CreatorMap<Estimator>::getCreator(estimatorType));
    if (estimatorCreator) {
      estimatorCreator->setName(name + "->estimator");
      if (estimatorType == "recovery") {
	dynamic_cast<RecoveryEstimator::Creator*>(estimatorCreator)->setSolution(solution);
      }
      estimator = estimatorCreator->create();

      // init estimator
      estimator->addSystem(systemMatrix, solution, rhs);
    }
  }

  void ProblemScal::createMarker()
  {
    marker = dynamic_cast<Marker*>(Marker::createMarker(name + "->marker", -1));
  }

  void ProblemScal::createFileWriter()
  {
    fileWriters.push_back(NEW FileWriter(name + "->output", mesh, solution));
    int writeSerialization = 0;
    GET_PARAMETER(0, name + "->output->write serialization", "%d", 
		  &writeSerialization);
    if (writeSerialization) {
      fileWriters.push_back(NEW Serializer<ProblemScal>(this));
    }
  }

  void ProblemScal::estimate(AdaptInfo *adaptInfo) 
  {
    FUNCNAME("Problem::estimate()");

    if (estimator) {
      clock_t first = clock();
      estimator->estimate(adaptInfo->getTimestep());
      INFO(info,8)("estimation of the error needed %.5f seconds\n",
		    TIME_USED(first,clock()));

      adaptInfo->setEstSum(estimator->getErrorSum(), 0);

      adaptInfo->
	setTimeEstSum(estimator->getTimeEst(), 0);

      adaptInfo->
	setEstMax(estimator->getErrorMax(), 0);

      adaptInfo->
	setTimeEstMax(estimator->getTimeEstMax(), 0);

    } else {
      WARNING("no estimator\n");
    }
  }

  void ProblemScal::buildAfterCoarsen(AdaptInfo *adaptInfo, Flag flag,
				      bool assembleMatrix, bool assembleVector)
  {
    FUNCNAME("ProblemScal::buildAfterCoarsen()");

    clock_t first = clock();

#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
    mesh->dofCompress();
#endif

    MSG("%d DOFs for %s\n", 
	feSpace->getAdmin()->getUsedDOFs(), feSpace->getName().c_str());

    rhs->set(0.0);

    DOFMatrix::base_matrix_type& base_matrix= systemMatrix->getBaseMatrix(); 

    int nnz_per_row= 0;
    if (num_rows(base_matrix) != 0)
      nnz_per_row= int(double(base_matrix.nnz()) / num_rows(base_matrix) * 1.2); 
    if (nnz_per_row < 5) 
      nnz_per_row= 5;

    // Correct dimensionality of matrix
    base_matrix.change_dim(feSpace->getAdmin()->getUsedSize(), 
			   feSpace->getAdmin()->getUsedSize());
   
    // Reuse old sparsity information (if available) or default
    systemMatrix->startInsertion(nnz_per_row);

    // fill boundary conditions
    if (systemMatrix->getBoundaryManager())
      systemMatrix->getBoundaryManager()->initMatrix(systemMatrix);
    if (rhs->getBoundaryManager())
      rhs->getBoundaryManager()->initVector(rhs);
    if (solution->getBoundaryManager())
      solution->getBoundaryManager()->initVector(solution);

    BoundaryType *bound;
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL | 
					           Mesh::FILL_BOUND |
					           Mesh::FILL_COORDS |
					           Mesh::FILL_DET |
					           Mesh::FILL_GRD_LAMBDA |
					           Mesh::FILL_NEIGH);

    while (elInfo) {
      if (useGetBound) {
	bound = GET_MEMORY(BoundaryType, feSpace->getBasisFcts()->getNumber());
	feSpace->getBasisFcts()->getBound(elInfo, bound);
      } else {
	bound = NULL;
      }
      
      systemMatrix->assemble(1.0, elInfo, bound);
      rhs->assemble(1.0, elInfo, bound);
      
      if (useGetBound)
	FREE_MEMORY(bound, BoundaryType, feSpace->getBasisFcts()->getNumber());	    
      
      if (systemMatrix->getBoundaryManager()) 
	systemMatrix->getBoundaryManager()->fillBoundaryConditions(elInfo, systemMatrix);
      if (rhs->getBoundaryManager())
	rhs->getBoundaryManager()->fillBoundaryConditions(elInfo, rhs);
      if (solution->getBoundaryManager())
	solution->getBoundaryManager()->fillBoundaryConditions(elInfo, solution);
      elInfo = stack.traverseNext(elInfo);
    }

    systemMatrix->removeRowsWithDBC(systemMatrix->getApplyDBCs());

    // TODO: ExitMatrix should be called after finishInsertion!
    if (systemMatrix->getBoundaryManager())
      systemMatrix->getBoundaryManager()->exitMatrix(systemMatrix);
    if (rhs->getBoundaryManager())
      rhs->getBoundaryManager()->exitVector(rhs);
    if (solution->getBoundaryManager())
      solution->getBoundaryManager()->exitVector(solution);

    systemMatrix->finishInsertion();

    INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n", TIME_USED(first,clock()));

#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
//     PetscErrorCode ierr;
//     Mat A;

//     ierr = MatCreate(PETSC_COMM_WORLD, &A); CHKERRQ(ierr);
#endif
    
    createPrecon();
  }

  void ProblemScal::writeResidualMesh(AdaptInfo *adaptInfo, const std::string name)
  {
    FUNCNAME("ProblemScal::writeResidualMesh()");

    std::map<int, double> vec;    
    TraverseStack stack;
    ElInfo *elInfo = stack.traverseFirst(this->getMesh(),  -1, 
					 Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
    
    while (elInfo) {		  
      vec[elInfo->getElement()->getIndex()] = elInfo->getElement()->getEstimation(0);
      elInfo = stack.traverseNext(elInfo);
    }
    
    ElementFileWriter fw(name, this->getFESpace(), vec);
    fw.writeFiles(adaptInfo, true);    
  }

  void ProblemScal::createPrecon()
  {
    std::string preconType("no");
    GET_PARAMETER(0, name + "->solver->left precon", &preconType);

    CreatorInterface<ITL_BasePreconditioner> *preconCreator = 
      CreatorMap<ITL_BasePreconditioner>::getCreator(preconType);

    solver->setLeftPrecon( preconCreator->create(systemMatrix->getBaseMatrix()) );

    preconType= "no";
    GET_PARAMETER(0, name + "->solver->right precon", &preconType);

    preconCreator = CreatorMap<ITL_BasePreconditioner>::getCreator(preconType);
    solver->setRightPrecon( preconCreator->create(systemMatrix->getBaseMatrix()) );
  }

  void ProblemScal::serialize(std::ostream &out) 
  {
    FUNCNAME("ProblemScal::serialize()");

    mesh->serialize(out);
    solution->serialize(out);
  }

  void ProblemScal::deserialize(std::istream &in) 
  {
    FUNCNAME("ProblemScal::deserialize()");

    mesh->deserialize(in);    
    solution->deserialize(in);
  }

}