GenerateMesh.h

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/******************************************************************************
 * Copyright (c) 2021.                                                        *
 * The Regents of the University of Michigan and DFT-EFE developers.          *
 *                                                                            *
 * This file is part of the DFT-EFE code.                                     *
 *                                                                            *
 * DFT-EFE is free software: you can redistribute it and/or modify            *
 *   it under the terms of the Lesser GNU General Public License as           *
 *   published by the Free Software Foundation, either version 3 of           *
 *   the License, or (at your option) any later version.                      *
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 * DFT-EFE is distributed in the hope that it will be useful, but             *
 *   WITHOUT ANY WARRANTY; without even the implied warranty                  *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.                     *
 *   See the Lesser GNU General Public License for more details.              *
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 * You should have received a copy of the GNU Lesser General Public           *
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/*
 * @author Avirup Sircar
 * The GenerateMesh for adaptive mesh generation around atom is borrowed from
 * dftfe.
 */
 
#ifndef dftefeGenerateMesh_h
#define dftefeGenerateMesh_h
 
#include <utils/MPICommunicatorP2P.h>
#include <utils/ConditionalOStream.h>
#include <basis/TriangulationBase.h>
#include <basis/CellMappingBase.h>
#include <utils/Point.h>
#include <vector>
#include <string>
#include <memory>
namespace dftefe
{
  namespace basis
  {
    class GenerateMesh
    {
    public:
      GenerateMesh(
        const std::vector<utils::Point> &atomCoordinates,
        const std::vector<utils::Point> &domainBoundingVectors,
        double                           radiusAroundAtom,
        double                           meshSizeAroundAtom,
        const std::vector<bool> &        isPeriodicFlags,
        const basis::CellMappingBase &   cellMapping,
        const MPI_Comm &                 mpiDomainCommunicator,
        const MPI_Comm &mpiInterpoolCommunicator = utils::mpi::MPICommSelf);
 
      GenerateMesh(
        const std::vector<utils::Point> &atomCoordinates,
        const std::vector<utils::Point> &domainBoundingVectors,
        double                           radiusAtAtom,
        double                           meshSizeAtAtom,
        double                           radiusAroundAtom,
        double                           meshSizeAroundAtom,
        const std::vector<bool> &        isPeriodicFlags,
        const basis::CellMappingBase &   cellMapping,
        const MPI_Comm &                 mpiDomainCommunicator,
        const MPI_Comm &mpiInterpoolCommunicator = utils::mpi::MPICommSelf);
 
      ~GenerateMesh() = default;
 
      void
      createMesh(TriangulationBase &triangulation);
 
    private:
      void
      generateCoarseMesh(TriangulationBase &      triangulation,
                         const std::vector<bool> &isPeriodicFlags);
 
      bool
      refinementAlgorithm(
        TriangulationBase &             triangulation,
        std::vector<size_type> &        locallyOwnedCellsRefineFlags,
        std::map<size_type, size_type> &cellIdToCellRefineFlagMapLocal,
        const basis::CellMappingBase &  cellMapping);
 
      bool
      refineInsideSystemNonPeriodicAlgorithm(
        TriangulationBase &  triangulation,
        std::vector<double> &maxAtomCoordinates,
        std::vector<double> &minAtomCoordinates);
 
      bool                             d_adaptiveWithFineMesh;
      size_type                        d_dim;
      double                           d_radiusAtAtom;
      double                           d_radiusAroundAtom;
      double                           d_meshSizeAtAtom;
      double                           d_meshSizeAroundAtom;
      size_type                        d_maxRefinementSteps;
      const std::vector<utils::Point> &d_atomCoordinates;
      const std::vector<utils::Point> &d_domainBoundingVectors;
      const std::vector<bool> &        d_isPeriodicFlags;
      const MPI_Comm &                 d_mpiDomainCommunicator;
      const MPI_Comm &                 d_mpiInterpoolCommunicator;
      const basis::CellMappingBase &   d_cellMapping;
      utils::ConditionalOStream        d_rootCout;
      std::vector<std::vector<bool>>   d_triaCurrentRefinement;
 
    }; // end of GenerateMesh
  }    // end of namespace basis
} // end of namespace dftefe
#endif // dftefeGenerateMesh_h