GeochemicalDatabaseReader.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 "nlohmann/json.h"
#include "MooseTypes.h"
 
struct GeochemistryBasisSpecies
{
  GeochemistryBasisSpecies() {}
 
  std::string name;
  std::map<std::string, Real> elements;
  Real radius;
  Real charge;
  Real molecular_weight;
};
 
struct GeochemistryEquilibriumSpecies
{
  GeochemistryEquilibriumSpecies() {}
 
  std::string name;
  std::map<std::string, Real> basis_species;
  std::vector<Real> equilibrium_const;
  Real radius;
  Real charge;
  Real molecular_weight;
};
 
struct GeochemistryMineralSpecies
{
  GeochemistryMineralSpecies() {}
 
  std::string name;
  Real molecular_volume;
  std::map<std::string, Real> basis_species;
  std::vector<Real> equilibrium_const;
  Real molecular_weight;
  Real surface_area;
  std::map<std::string, Real> sorption_sites;
};
 
struct GeochemistryGasSpecies
{
  GeochemistryGasSpecies() {}
 
  std::string name;
  std::map<std::string, Real> basis_species;
  std::vector<Real> equilibrium_const;
  Real molecular_weight;
  std::vector<Real> chi;
  Real Pcrit;
  Real Tcrit;
  Real omega;
};
 
struct GeochemistryRedoxSpecies
{
  GeochemistryRedoxSpecies() {}
 
  std::string name;
  std::map<std::string, Real> basis_species;
  std::vector<Real> equilibrium_const;
  Real radius;
  Real charge;
  Real molecular_weight;
};
 
struct GeochemistryOxideSpecies
{
  GeochemistryOxideSpecies() {}
 
  std::string name;
  std::map<std::string, Real> basis_species;
  Real molecular_weight;
};
 
struct GeochemistrySurfaceSpecies
{
  GeochemistrySurfaceSpecies() {}
 
  std::string name;
  std::map<std::string, Real> basis_species;
  Real charge;
  Real molecular_weight;
  Real log10K;
  Real dlog10KdT;
};
 
struct GeochemistryDebyeHuckel
{
  GeochemistryDebyeHuckel() {}
 
  std::vector<Real> adh;
  std::vector<Real> bdh;
  std::vector<Real> bdot;
};
 
struct GeochemistryElements
{
  GeochemistryElements() {}
 
  std::string name;
  Real molecular_weight;
};
 
struct GeochemistryNeutralSpeciesActivity
{
  GeochemistryNeutralSpeciesActivity() {}
  GeochemistryNeutralSpeciesActivity(std::vector<std::vector<Real>> coeffs)
    : a(coeffs[0]), b(coeffs[1]), c(coeffs[2]), d(coeffs[3])
  {
  }
 
  std::vector<Real> a;
  std::vector<Real> b;
  std::vector<Real> c;
  std::vector<Real> d;
};
 
class GeochemicalDatabaseReader
{
public:
  GeochemicalDatabaseReader(const FileName filename,
                            const bool reexpress_free_electron = true,
                            const bool use_piecewise_interpolation = false,
                            const bool remove_all_extrapolated_secondary_species = false);
 
  void read(const FileName filename);
 
  void validate(const FileName filename, const nlohmann::json & db);
 
  void reexpressFreeElectron();
 
  std::string getActivityModel() const;
 
  std::string getFugacityModel() const;
 
  std::string getLogKModel() const;
 
  std::vector<std::string> getBasisSpeciesNames() const { return _bs_names; };
 
  std::vector<std::string> getEquilibriumSpeciesNames() const { return _es_names; };
 
  std::vector<std::string> getMineralSpeciesNames() const { return _ms_names; };
 
  const std::vector<Real> & getTemperatures() const;
 
  std::vector<Real> getPressures();
 
  const GeochemistryDebyeHuckel & getDebyeHuckel() const;
 
  std::map<std::string, GeochemistryBasisSpecies>
  getBasisSpecies(const std::vector<std::string> & names);
 
  std::map<std::string, GeochemistryEquilibriumSpecies>
  getEquilibriumSpecies(const std::vector<std::string> & names);
 
  std::map<std::string, GeochemistryMineralSpecies>
  getMineralSpecies(const std::vector<std::string> & names);
 
  std::map<std::string, GeochemistryElements> getElements();
 
  std::map<std::string, GeochemistryGasSpecies>
  getGasSpecies(const std::vector<std::string> & names);
 
  std::map<std::string, GeochemistryRedoxSpecies>
  getRedoxSpecies(const std::vector<std::string> & names);
 
  std::map<std::string, GeochemistryOxideSpecies>
  getOxideSpecies(const std::vector<std::string> & names);
 
  std::map<std::string, GeochemistrySurfaceSpecies>
  getSurfaceSpecies(const std::vector<std::string> & names);
 
  const std::map<std::string, GeochemistryNeutralSpeciesActivity> &
  getNeutralSpeciesActivity() const;
 
  std::vector<std::string> equilibriumReactions(const std::vector<std::string> & names) const;
 
  std::vector<std::string> mineralReactions(const std::vector<std::string> & names) const;
 
  std::vector<std::string> gasReactions(const std::vector<std::string> & names) const;
 
  std::vector<std::string> redoxReactions(const std::vector<std::string> & names) const;
 
  std::vector<std::string> oxideReactions(const std::vector<std::string> & names) const;
 
  std::string getSpeciesData(const std::string name) const;
 
  const FileName & filename() const;
 
  bool isSecondarySpecies(const std::string & name) const;
 
  bool isBasisSpecies(const std::string & name) const;
  bool isRedoxSpecies(const std::string & name) const;
  bool isGasSpecies(const std::string & name) const;
  bool isMineralSpecies(const std::string & name) const;
  bool isOxideSpecies(const std::string & name) const;
  bool isSurfaceSpecies(const std::string & name) const;
 
  bool isSorbingMineral(const std::string & name) const;
 
  std::vector<std::string> mineralSpeciesNames() const;
 
  std::vector<std::string> secondarySpeciesNames() const;
 
  std::vector<std::string> redoxCoupleNames() const;
 
  std::vector<std::string> surfaceSpeciesNames() const;
 
protected:
  void removeExtrapolatedSecondarySpecies();
 
  void setTemperatures();
 
  void setDebyeHuckel();
 
  void setNeutralSpeciesActivity();
 
  const FileName _filename;
  nlohmann::json _root;
  std::vector<std::string> _bs_names;
  std::vector<std::string> _es_names;
  std::vector<std::string> _ms_names;
  std::vector<Real> _temperature_points;
  std::vector<Real> _pressure_points;
  std::map<std::string, GeochemistryElements> _elements;
  std::map<std::string, GeochemistryBasisSpecies> _basis_species;
  std::map<std::string, GeochemistryEquilibriumSpecies> _equilibrium_species;
  std::map<std::string, GeochemistryMineralSpecies> _mineral_species;
  std::map<std::string, GeochemistryGasSpecies> _gas_species;
  std::map<std::string, GeochemistryRedoxSpecies> _redox_species;
  std::map<std::string, GeochemistryOxideSpecies> _oxide_species;
  std::map<std::string, GeochemistrySurfaceSpecies> _surface_species;
  GeochemistryDebyeHuckel _debye_huckel;
  std::map<std::string, GeochemistryNeutralSpeciesActivity> _neutral_species_activity;
  // Helper for converting json node to Real from string
  static Real getReal(const nlohmann::json & node);
 
private:
  std::vector<std::string>
  printReactions(const std::vector<std::string> & names,
                 const std::vector<std::map<std::string, Real>> & basis_species) const;
};