Line data    Source code

       1             : //* This file is part of the MOOSE framework
       2             : //* https://mooseframework.inl.gov
       3             : //*
       4             : //* All rights reserved, see COPYRIGHT for full restrictions
       5             : //* https://github.com/idaholab/moose/blob/master/COPYRIGHT
       6             : //*
       7             : //* Licensed under LGPL 2.1, please see LICENSE for details
       8             : //* https://www.gnu.org/licenses/lgpl-2.1.html
       9             : 
      10             : #include "GeochemicalModelDefinition.h"
      11             : #include "GeochemistryKineticRate.h"
      12             : 
      13             : registerMooseObject("GeochemistryApp", GeochemicalModelDefinition);
      14             : 
      15             : InputParameters
      16        1516 : GeochemicalModelDefinition::validParams()
      17             : {
      18        1516 :   InputParameters params = GeneralUserObject::validParams();
      19        3032 :   params.addRequiredParam<FileName>("database_file", "The name of the geochemical database file");
      20        3032 :   params.addParam<bool>(
      21             :       "reexpress_free_electron",
      22        3032 :       true,
      23             :       "If true then if: (1) the 'free electron' appears in the database file; and (2) its "
      24             :       "equilibrium reaction includes O2(g); and (3) O2(g) is a gas; and (4) O2(g)'s equilibrium "
      25             :       "reaction is O2(g)=O2(eq); and (5) O2(aq) exists as a basis species in the database file; "
      26             :       "then reexpress the free electron's equilibrium reaction in terms of O2(aq).  Note that if "
      27             :       "you choose 'reexpress_free_electron=false' and these other 5 conditions are true, then the "
      28             :       "'free electron' will not be available as a secondary species");
      29        3032 :   params.addParam<bool>(
      30             :       "piecewise_linear_interpolation",
      31        3032 :       false,
      32             :       "If true then use a piecewise-linear interpolation of logK and Debye-Huckel parameters, "
      33             :       "regardless of the interpolation type specified in the database file.  This can be useful "
      34             :       "for comparing with results using other geochemistry software");
      35        3032 :   params.addRequiredParam<std::vector<std::string>>(
      36             :       "basis_species",
      37             :       "A list of basis components relevant to the aqueous-equilibrium problem. H2O must appear "
      38             :       "first in this list.  These components must be chosen from the 'basis species' in the "
      39             :       "database, the sorbing sites (if any) and the decoupled redox states that are in "
      40             :       "disequilibrium (if any).");
      41        3032 :   params.addParam<std::vector<std::string>>(
      42             :       "equilibrium_minerals",
      43             :       {},
      44             :       "A list of minerals that are in equilibrium with the aqueous solution.  All members of this "
      45             :       "list must be in the 'minerals' section of the database file");
      46        3032 :   params.addParam<std::vector<std::string>>(
      47             :       "equilibrium_gases",
      48             :       {},
      49             :       "A list of gases that are in equilibrium with the aqueous solution and can have their "
      50             :       "fugacities fixed, at least for some time and spatial location.  All members of this list "
      51             :       "must be in the 'gas' section of the database file");
      52        3032 :   params.addParam<std::vector<std::string>>(
      53             :       "kinetic_minerals",
      54             :       {},
      55             :       "A list of minerals whose dynamics are governed by a rate law.  These are not in equilibrium "
      56             :       "with the aqueous solution.  All members of this list must be in the 'minerals' section of "
      57             :       "the database "
      58             :       "file.");
      59        3032 :   params.addParam<std::vector<std::string>>(
      60             :       "kinetic_redox",
      61             :       {},
      62             :       "A list alternative oxidation states (eg Fe+++) whose dynamics are governed by a rate law.  "
      63             :       "These are not in equilibrium with the aqueous solution.  All members of this list must be "
      64             :       "in the "
      65             :       "'redox couples' section of the database file.");
      66        3032 :   params.addParam<std::vector<std::string>>(
      67             :       "kinetic_surface_species",
      68             :       {},
      69             :       "A list surface sorbing species whose dynamics are governed by a rate law.  These are not in "
      70             :       "equilibrium with the aqueous solution.  All members of this list must be in the 'surface "
      71             :       "species' section of the database file.");
      72        3032 :   params.addParam<std::string>(
      73             :       "redox_oxygen",
      74             :       "O2(aq)",
      75             :       "The name of the oxygen species that appears in redox reactions.  For redox pairs that are "
      76             :       "in disequilibrium to be correctly recorded, and hence their Nernst potentials to be "
      77             :       "computed easily, redox_oxygen must be a basis species and it must appear in the reaction "
      78             :       "for each redox pair");
      79        3032 :   params.addParam<std::string>(
      80             :       "redox_electron",
      81             :       "e-",
      82             :       "The name of the free electron.  For redox pairs that are in disequilibrium to be correctly "
      83             :       "recorded, and hence their Nernst potentials to be computed eqsily, the equilibrium reaction "
      84             :       "for redox_electron must involve redox_oxygen, and the basis species must be chosen to that "
      85             :       "redox_electron is an equilibrium species");
      86        3032 :   params.addParam<std::vector<UserObjectName>>(
      87             :       "kinetic_rate_descriptions",
      88             :       {},
      89             :       "A list of GeochemistryKineticRate UserObject names that define the kinetic rates.  If a "
      90             :       "kinetic species has no rate prescribed to it, its reaction rate will be zero");
      91        3032 :   params.addParam<bool>(
      92             :       "remove_all_extrapolated_secondary_species",
      93        3032 :       false,
      94             :       "After reading the database file, immediately remove all secondary species that have "
      95             :       "extrapolated equilibrium constants.  Sometimes these extrapolations are completely crazy "
      96             :       "and those secondary species greatly impact the results");
      97             : 
      98        1516 :   params.addClassDescription("User object that parses a geochemical database file, and only "
      99             :                              "retains information relevant to the current geochemical model");
     100             : 
     101        1516 :   return params;
     102           0 : }
     103             : 
     104         758 : GeochemicalModelDefinition::GeochemicalModelDefinition(const InputParameters & parameters)
     105             :   : GeneralUserObject(parameters),
     106        1516 :     _db(getParam<FileName>("database_file"),
     107        1516 :         getParam<bool>("reexpress_free_electron"),
     108        1516 :         getParam<bool>("piecewise_linear_interpolation"),
     109         758 :         getParam<bool>("remove_all_extrapolated_secondary_species")),
     110        6064 :     _model(_db,
     111             :            getParam<std::vector<std::string>>("basis_species"),
     112             :            getParam<std::vector<std::string>>("equilibrium_minerals"),
     113             :            getParam<std::vector<std::string>>("equilibrium_gases"),
     114             :            getParam<std::vector<std::string>>("kinetic_minerals"),
     115             :            getParam<std::vector<std::string>>("kinetic_redox"),
     116             :            getParam<std::vector<std::string>>("kinetic_surface_species"),
     117        1516 :            getParam<std::string>("redox_oxygen"),
     118        1516 :            getParam<std::string>("redox_electron"))
     119             : {
     120        1597 :   for (const auto & kr : getParam<std::vector<UserObjectName>>("kinetic_rate_descriptions"))
     121          81 :     _model.addKineticRate(getUserObjectByName<GeochemistryKineticRate>(kr).getRateDescription());
     122         758 : }
     123             : 
     124             : void
     125        4692 : GeochemicalModelDefinition::initialize()
     126             : {
     127        4692 : }
     128             : 
     129             : void
     130        4692 : GeochemicalModelDefinition::execute()
     131             : {
     132        4692 : }
     133             : 
     134             : void
     135        4692 : GeochemicalModelDefinition::finalize()
     136             : {
     137        4692 : }
     138             : 
     139             : const ModelGeochemicalDatabase &
     140        1658 : GeochemicalModelDefinition::getDatabase() const
     141             : {
     142        1658 :   return _model.modelGeochemicalDatabase();
     143             : }
     144             : 
     145             : const PertinentGeochemicalSystem &
     146         933 : GeochemicalModelDefinition::getPertinentGeochemicalSystem() const
     147             : {
     148         933 :   return _model;
     149             : }
     150             : 
     151             : const GeochemicalDatabaseReader &
     152         933 : GeochemicalModelDefinition::getOriginalFullDatabase() const
     153             : {
     154         933 :   return _db;
     155             : }