reaction_term.hh

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/*!
 *
 * Copyright (C) 2015 Technical University of Liberec.  All rights reserved.
 * 
 * This program is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License version 3 as published by the
 * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
 * 
 * This program is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 *
 * 
 * @file    reaction_term.hh
 * @brief   Class ReactionTerm is an abstract class representing reaction term in transport.
 *
 * Descending classes implements different physical models - dual porosity, sorption, decays, 
 * chemical reactions.
 */
 
#ifndef REACTION_TERM_H
#define REACTION_TERM_H
 
#include <memory>                    // for shared_ptr
#include <string>                    // for string
#include "coupling/equation.hh"      // for EquationBase
#include "system/index_types.hh"     // for LongInt
#include "input/input_exception.hh"  // for DECLARE_INPUT_EXCEPTION, Exception
#include "system/exceptions.hh"      // for ExcStream, operator<<, EI, TYPED...
#include "transport/substance.hh"    // for SubstanceList
#include "fem/dofhandler.hh"         // for DOFHandlerMultiDim
#include "fields/field_fe.hh"        // for FieldFE
 
class Distribution;
class Mesh;
class OutputTime;
namespace Input {
    class Record;
    namespace Type {
        class Abstract;
    }
}
 
 
class ReactionTerm: public EquationBase
{
public:
    TYPEDEF_ERR_INFO( EI_Substance, std::string);
    TYPEDEF_ERR_INFO( EI_Model, std::string);
    DECLARE_INPUT_EXCEPTION( ExcUnknownSubstance, << "Unknown substance name: " << EI_Substance::qval);
    DECLARE_INPUT_EXCEPTION( ExcWrongDescendantModel, << "Impossible descendant model: " << EI_Model::qval);
    
    typedef std::vector<std::shared_ptr<FieldFE< 3, FieldValue<3>::Scalar>>> FieldFEScalarVec;
 
  /**
   * Static variable for definition of common input record in reaction term.
   */
  static Input::Type::Abstract & it_abstract_term();
  static Input::Type::Abstract & it_abstract_mobile_term();
  static Input::Type::Abstract & it_abstract_immobile_term();
  static Input::Type::Abstract & it_abstract_reaction();
  
  /// Constructor.
  /** @param init_mesh is the reference to the computational mesh
   *  @param in_rec is the input record
   */
  ReactionTerm(Mesh &init_mesh, Input::Record in_rec);
 
  /// Destructor.
  ~ReactionTerm(void);
  
 
  ///@name Setters
  //@{
  ///Sets the names of substances considered in transport.
  ReactionTerm &substances(SubstanceList &substances)
  {substances_.initialize(substances); return *this;}
 
  ///Sets the output stream which is given from transport class.
  ReactionTerm &output_stream(std::shared_ptr<OutputTime> ostream)
  {output_stream_=ostream; return *this;}
  
  /**
   * Sets the pointer to concentration matrix for the mobile zone, 
   * all substances and on all elements (given by transport).
   */
  ReactionTerm &concentration_fields(FieldFEScalarVec& conc_mobile)
  {
    conc_mobile_fe = conc_mobile;
    dof_handler_ = conc_mobile_fe[0]->get_dofhandler();
    return *this;
  }
  //@}
 
  /** @brief Output method.
   * 
   * Some reaction models have their own data to output (sorption, dual porosity) 
   * - this is where it must be reimplemented.
   * On the other hand, some do not have (linear reaction, pade approximant) 
   * - that is why it is not pure virtual.
   */
  virtual void output_data(void) override {};
 
  /// Disable changes in TimeGovernor by empty method.
  void choose_next_time(void) override;
 
protected:
  /// Compute reaction on a single element.
  virtual void compute_reaction(const DHCellAccessor& dh_cell) = 0;
 
  /// FieldFEs representing P0 interpolation of mobile concentration (passed from transport).
  FieldFEScalarVec conc_mobile_fe;
  
  /// Names belonging to substances.
  /**  
   * Must be same as in the transport.
   */
  SubstanceList substances_;
 
  /// Pointer to a transport output stream.
  std::shared_ptr<OutputTime> output_stream_;
 
  /// Pointer to DOF handler used through the reaction tree
  std::shared_ptr<DOFHandlerMultiDim> dof_handler_;
 
};
 
#endif  // REACTION_TERM_H