GeochemistrySpatialReactor.h

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//* This file is part of the MOOSE framework
//* https://mooseframework.inl.gov
//*
//* All rights reserved, see COPYRIGHT for full restrictions
//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
//*
//* Licensed under LGPL 2.1, please see LICENSE for details
//* https://www.gnu.org/licenses/lgpl-2.1.html

#pragma once

#include "GeochemicalSolver.h"
#include "GeochemistryReactorBase.h"

class GeochemistrySpatialReactor : public GeochemistryReactorBase
{
public:
  static InputParameters sharedParams();

  static InputParameters validParams();
  GeochemistrySpatialReactor(const InputParameters & parameters);
  virtual void initialize() override;

  virtual void finalize() override;
  virtual void threadJoin(const UserObject & uo) override;

  virtual void initialSetup() override;
  virtual void execute() override;
  virtual void meshChanged() override;

  virtual const GeochemicalSystem & getGeochemicalSystem(dof_id_type node_id) const override;
  virtual const std::stringstream & getSolverOutput(dof_id_type node_id) const override;
  virtual unsigned getSolverIterations(dof_id_type node_id) const override;
  virtual Real getSolverResidual(dof_id_type node_id) const override;
  virtual const DenseVector<Real> & getMoleAdditions(dof_id_type node_id) const override;
  virtual Real getMolesDumped(dof_id_type node_id, const std::string & species) const override;

protected:
  const Real _initial_temperature;
  const VariableValue & _temperature;
  const unsigned _num_kin;
  std::vector<ModelGeochemicalDatabase> _mgd_at_node;
  std::vector<GeochemicalSystem> _egs_at_node;
  GeochemicalSystem _egs_copy;
  GeochemicalSolver _solver;
  const Real _close_system_at_time;
  bool _closed_system;
  const std::vector<std::string> _source_species_names;
  const unsigned _num_source_species;
  std::vector<const VariableValue *> _source_species_rates;
  const std::vector<std::string> _remove_fixed_activity_name;
  const std::vector<Real> _remove_fixed_activity_time;
  const unsigned _num_removed_fixed;
  std::vector<std::vector<bool>> _removed_fixed_activity;
  const std::vector<std::string> _controlled_activity_species_names;
  const unsigned _num_controlled_activity;
  std::vector<const VariableValue *> _controlled_activity_species_values;
  DenseVector<Real> _mole_rates;
  std::vector<DenseVector<Real>> _mole_additions;
  std::vector<DenseMatrix<Real>> _dmole_additions;
  const unsigned _ramp_subsequent;
  std::unordered_map<dof_id_type, unsigned> _my_node_number;
  std::vector<bool> _execute_done;
  const bool _adaptive_timestepping;
  const Real _dt_min;
  const Real _dt_dec;
  const Real _dt_inc;
  unsigned _nthreads;

  void buildMyNodeNumber();
};