SinglePhaseReactiveTransport.hpp

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/*
 * ------------------------------------------------------------------------------------------------------------
 * SPDX-License-Identifier: LGPL-2.1-only
 *
 * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
 * Copyright (c) 2018-2024 TotalEnergies
 * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
 * Copyright (c) 2023-2024 Chevron
 * Copyright (c) 2019-     GEOS/GEOSX Contributors
 * All rights reserved
 *
 * See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
 * ------------------------------------------------------------------------------------------------------------
 */
 
#ifndef GEOS_PHYSICSSOLVERS_FLUIDFLOW_SINGLEPHASEREACTIVETRANSPORT_HPP_
#define GEOS_PHYSICSSOLVERS_FLUIDFLOW_SINGLEPHASEREACTIVETRANSPORT_HPP_
 
#include "fieldSpecification/FieldSpecificationManager.hpp"
#include "physicsSolvers/fluidFlow/SinglePhaseBase.hpp"
#include "physicsSolvers/fluidFlow/SinglePhaseFVM.hpp"
#include "physicsSolvers/fluidFlow/SinglePhaseReactiveTransportFields.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/AccumulationKernels.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/DirichletFluxComputeKernel.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/FluidUpdateKernel.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/FluxComputeKernel.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/ResidualNormKernel.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/ReactionUpdateKernel.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/SourceFluxComputeKernel.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/ThermalAccumulationKernels.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/ThermalDirichletFluxComputeKernel.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/ThermalFluxComputeKernel.hpp"
#include "physicsSolvers/fluidFlow/kernels/singlePhase/reactive/ThermalSourceFluxComputeKernel.hpp"
#include "constitutive/fluid/reactivefluid/ReactiveSinglePhaseFluid.hpp"
 
 
namespace geos
{
 
class SinglePhaseReactiveTransport : public SinglePhaseBase
{
 
public:
 
  SinglePhaseReactiveTransport( const string & name,
                                dataRepository::Group * const parent );
 
  SinglePhaseReactiveTransport() = delete;
 
  SinglePhaseReactiveTransport( SinglePhaseReactiveTransport const & ) = delete;
 
  SinglePhaseReactiveTransport( SinglePhaseReactiveTransport && ) = default;
 
  SinglePhaseReactiveTransport & operator=( SinglePhaseReactiveTransport const & ) = delete;
 
  SinglePhaseReactiveTransport & operator=( SinglePhaseReactiveTransport && ) = delete;
 
  virtual ~SinglePhaseReactiveTransport() override = default;
 
  static string catalogName()
  {
    return "SinglePhaseReactiveTransport";
  }
 
  string getCatalogName() const override { return catalogName(); }
 
  virtual void registerDataOnMesh( dataRepository::Group & meshBodies ) override;
 
  virtual void
  setupDofs( DomainPartition const & domain,
             DofManager & dofManager ) const override;
 
  virtual void
  implicitStepSetup( real64 const & time_n,
                     real64 const & dt,
                     DomainPartition & domain ) override final;
 
  virtual void
  assembleSystem( real64 const time_n,
                  real64 const dt,
                  DomainPartition & domain,
                  DofManager const & dofManager,
                  CRSMatrixView< real64, globalIndex const > const & localMatrix,
                  arrayView1d< real64 > const & localRhs ) override;
 
  virtual void
  applyBoundaryConditions( real64 const time_n,
                           real64 const dt,
                           DomainPartition & domain,
                           DofManager const & dofManager,
                           CRSMatrixView< real64, globalIndex const > const & localMatrix,
                           arrayView1d< real64 > const & localRhs ) override;
 
  virtual real64
  calculateResidualNorm( real64 const & time_n,
                         real64 const & dt,
                         DomainPartition const & domain,
                         DofManager const & dofManager,
                         arrayView1d< real64 const > const & localRhs ) override;
 
  virtual void
  applySystemSolution( DofManager const & dofManager,
                       arrayView1d< real64 const > const & localSolution,
                       real64 const scalingFactor,
                       real64 const dt,
                       DomainPartition & domain ) override;
 
  virtual void
  resetStateToBeginningOfStep( DomainPartition & domain ) override;
 
  virtual void
  implicitStepComplete( real64 const & time,
                        real64 const & dt,
                        DomainPartition & domain ) override final;
 
  virtual void saveConvergedState( ElementSubRegionBase & subRegion ) const override final;
 
  virtual void
  updateState ( DomainPartition & domain ) override final;
 
  void updateMixedReactionSystem( ElementSubRegionBase & subRegion ) const;
 
  void updateSurfaceArea( ElementSubRegionBase & subRegion ) const;
 
  void updateSpeciesAmount( ElementSubRegionBase & subRegion ) const;
 
  void updateKineticReactionMolarIncrements( real64 const dt,
                                             ElementSubRegionBase & subRegion ) const;
 
  virtual void updateFluidModel( ObjectManagerBase & dataGroup ) const override;
 
  virtual void updatePorosityAndPermeability( CellElementSubRegion & subRegion ) const override;
 
  virtual void initializePostInitialConditionsPreSubGroups() override;
 
  virtual void initializeFluidState( MeshLevel & mesh, string_array const & regionNames ) override;
 
  void initializeEquilibriumReaction( ElementSubRegionBase & subRegion ) const;
 
  virtual void validateConstitutiveModels( DomainPartition & domain ) const override final;
 
  integer numPrimarySpecies() const { return m_numPrimarySpecies; }
 
  void assembleAccumulationTermsInMassBalanceAndSpeciesAmountEqs( real64 const dt,
                                                                  DomainPartition & domain,
                                                                  DofManager const & dofManager,
                                                                  CRSMatrixView< real64, globalIndex const > const & localMatrix,
                                                                  arrayView1d< real64 > const & localRhs ) const;
 
  virtual void
  assembleFluxTerms( real64 const dt,
                     DomainPartition const & domain,
                     DofManager const & dofManager,
                     CRSMatrixView< real64, globalIndex const > const & localMatrix,
                     arrayView1d< real64 > const & localRhs ) override;
 
  virtual void
  applySourceFluxBC( real64 const time_n,
                     real64 const dt,
                     DomainPartition & domain,
                     DofManager const & dofManager,
                     CRSMatrixView< real64, globalIndex const > const & localMatrix,
                     arrayView1d< real64 > const & localRhs ) const override;
 
  virtual void
  applyDirichletBC( real64 const time_n,
                    real64 const dt,
                    DomainPartition & domain,
                    DofManager const & dofManager,
                    CRSMatrixView< real64, globalIndex const > const & localMatrix,
                    arrayView1d< real64 > const & localRhs ) const override;
 
  template< typename OBJECT_TYPE >
  void applyFieldValue( real64 const & time_n,
                        real64 const & dt,
                        MeshLevel & mesh,
                        char const logMessage[],
                        string const fieldKey,
                        string const boundaryFieldKey ) const;
 
  virtual void
  applyAquiferBC( real64 const time,
                  real64 const dt,
                  DomainPartition & domain,
                  DofManager const & dofManager,
                  CRSMatrixView< real64, globalIndex const > const & localMatrix,
                  arrayView1d< real64 > const & localRhs ) const override;
 
  virtual void
  assembleEDFMFluxTerms( real64 const time_n,
                         real64 const dt,
                         DomainPartition const & domain,
                         DofManager const & dofManager,
                         CRSMatrixView< real64, globalIndex const > const & localMatrix,
                         arrayView1d< real64 > const & localRhs,
                         string const & jumpDofKey ) override final;
 
  virtual void
  assembleStabilizedFluxTerms( real64 const dt,
                               DomainPartition const & domain,
                               DofManager const & dofManager,
                               CRSMatrixView< real64, globalIndex const > const & localMatrix,
                               arrayView1d< real64 > const & localRhs ) override;
 
  struct viewKeyStruct : SinglePhaseBase::viewKeyStruct
  {
    static constexpr char const * diffusionNamesString() { return "diffusionNames"; }
    static constexpr char const * isUpdateReactivePorosityString() { return "isUpdateReactivePorosity"; }
    static constexpr char const * isUpdateSurfaceAreaString() { return "isUpdateSurfaceArea"; }
    static constexpr char const * immobilePrimarySpeciesIndicesString() { return "immobilePrimarySpeciesIndices"; }
  };
 
protected:
 
  integer m_numPrimarySpecies;
 
  integer m_numKineticReactions;
 
  string m_reactiveFluidModelName;
 
  integer m_hasDiffusion;
 
  integer m_isUpdateReactivePorosity;
 
  integer m_isUpdateSurfaceArea;
 
  array1d< integer > m_immobilePrimarySpeciesIndices;
 
private:
 
  void applyFaceDirichletBC( real64 const time_n,
                             real64 const dt,
                             DofManager const & faceSet,
                             DomainPartition & domain,
                             CRSMatrixView< real64, globalIndex const > const & localMatrix,
                             arrayView1d< real64 > const & localRhs );
 
};
 
template< typename OBJECT_TYPE >
void SinglePhaseReactiveTransport::applyFieldValue( real64 const & time_n,
                                                    real64 const & dt,
                                                    MeshLevel & mesh,
                                                    char const logMessage[],
                                                    string const fieldKey,
                                                    string const boundaryFieldKey ) const
{
  FieldSpecificationManager & fsManager = FieldSpecificationManager::getInstance();
 
  fsManager.apply< OBJECT_TYPE >( time_n + dt,
                                  mesh,
                                  fieldKey,
                                  [&]( FieldSpecificationBase const & fs,
                                       string const & setName,
                                       SortedArrayView< localIndex const > const & lset,
                                       OBJECT_TYPE & targetGroup,
                                       string const & )
  {
    if( fs.getLogLevel() >= 1 && m_nonlinearSolverParameters.m_numNewtonIterations == 0 )
    {
      globalIndex const numTargetElems = MpiWrapper::sum< globalIndex >( lset.size() );
      GEOS_LOG_RANK_0( GEOS_FMT( logMessage,
                                 getName(), time_n+dt, fs.getCatalogName(), fs.getName(),
                                 setName, targetGroup.getName(), fs.getScale(), numTargetElems ) );
    }
 
    // Specify the bc value of the field
    fs.applyFieldValue< FieldSpecificationEqual,
                        parallelDevicePolicy<> >( lset,
                                                  time_n + dt,
                                                  targetGroup,
                                                  boundaryFieldKey );
  } );
}
 
} /* namespace geos */
 
#endif //GEOS_PHYSICSSOLVERS_FLUIDFLOW_SINGLEPHASEREACTIVETRANSPORT_HPP_