GeochemistrySpeciesSwapper.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 "DenseMatrix.h"
#include "PertinentGeochemicalSystem.h"
#include <libmesh/dense_vector.h>
 
class GeochemistrySpeciesSwapper
{
public:
  GeochemistrySpeciesSwapper(unsigned basis_size, Real stoi_tol);
 
  bool operator==(const GeochemistrySpeciesSwapper & rhs) const
  {
    return (_stoi_tol == rhs._stoi_tol) && (_swap_matrix.m() == rhs._swap_matrix.m());
  };
 
  void checkSwap(const ModelGeochemicalDatabase & mgd,
                 const std::string & replace_this,
                 const std::string & with_this);
 
  void checkSwap(const ModelGeochemicalDatabase & mgd,
                 unsigned basis_index_to_replace,
                 unsigned eqm_index_to_insert);
 
  void performSwap(ModelGeochemicalDatabase & mgd,
                   const std::string & replace_this,
                   const std::string & with_this);
 
  void performSwap(ModelGeochemicalDatabase & mgd,
                   unsigned basis_index_to_replace,
                   unsigned eqm_index_to_insert);
 
  void performSwap(ModelGeochemicalDatabase & mgd,
                   DenseVector<Real> & bulk_composition,
                   const std::string & replace_this,
                   const std::string & with_this);
 
  void performSwap(ModelGeochemicalDatabase & mgd,
                   DenseVector<Real> & bulk_composition,
                   unsigned basis_index_to_replace,
                   unsigned eqm_index_to_insert);
 
  bool findBestEqmSwap(unsigned basis_ind,
                       const ModelGeochemicalDatabase & mgd,
                       const std::vector<Real> & eqm_molality,
                       bool minerals_allowed,
                       bool gas_allowed,
                       bool sorption_allowed,
                       unsigned & best_eqm_species) const;
 
private:
  void constructInverseMatrix(const ModelGeochemicalDatabase & mgd,
                              unsigned basis_index_to_replace,
                              unsigned eqm_index_to_insert);
 
  void alterMGD(ModelGeochemicalDatabase & mgd,
                unsigned basis_index_to_replace,
                unsigned eqm_index_to_insert);
 
  void alterBulkComposition(unsigned basis_size, DenseVector<Real> & bulk_composition) const;
 
  Real _stoi_tol;
 
  DenseMatrix<Real> _swap_matrix;
 
  DenseMatrix<Real> _true_swap_matrix;
 
  DenseMatrix<Real> _inv_swap_matrix;
 
  DenseVector<Real> _swap_sigma;
 
  DenseMatrix<Real> _swap_U;
 
  DenseMatrix<Real> _swap_VT;
};