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 "mesh/long_idx.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

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);
    
  /**
   * 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;}

  /// Computes a constraint for time step.
  virtual bool evaluate_time_constraint(double &time_constraint) = 0;
  
  /**
   * Sets the pointer to concentration matrix for the mobile zone, 
   * all substances and on all elements (given by transport).
   */
  ReactionTerm &concentration_matrix(double **concentration, Distribution *conc_distr, 
                                     LongIdx *el_4_loc, LongIdx *row_4_el)
  {
    concentration_matrix_ = concentration;
    distribution_ = conc_distr;
    el_4_loc_ = el_4_loc;
    row_4_el_ = row_4_el;
    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:
  /**
   * Communicate parallel concentration vectors into sequential output vector.
   */
  virtual void output_vector_gather(void){};

  /**
   * Computation of reaction term on a single element.
   * Inputs should be loc_el and local copies of concentrations of the element, which is then returned.
   */
  virtual double **compute_reaction(double **concentrations, int loc_el) =0;

  /**
   * Pointer to two-dimensional array[species][elements] containing concentrations.
   */
  double **concentration_matrix_;
  
  /// Indices of elements belonging to local dofs.
  LongIdx *el_4_loc_;
  /// Indices of rows belonging to elements.
  LongIdx *row_4_el_;
  
  /// Pointer to reference to distribution of elements between processors.
  Distribution *distribution_;
  
  /// 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_;

};

#endif  // REACTION_TERM_H