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 "GeochemistryKineticRate.h"
11 :
12 : registerMooseObject("GeochemistryApp", GeochemistryKineticRate);
13 :
14 : InputParameters
15 162 : GeochemistryKineticRate::validParams()
16 : {
17 162 : InputParameters params = GeneralUserObject::validParams();
18 324 : params.addRequiredParam<std::string>(
19 : "kinetic_species_name",
20 : "The name of the kinetic species that will be controlled by this rate");
21 324 : params.addRequiredRangeCheckedParam<Real>("intrinsic_rate_constant",
22 : "intrinsic_rate_constant >= 0.0",
23 : "The intrinsic rate constant for the reaction");
24 486 : params.addRangeCheckedParam<Real>(
25 : "area_quantity",
26 324 : 1.0,
27 : "area_quantity > 0.0",
28 : "The surface area of the kinetic species in m^2 (if multiply_by_mass = false) or the "
29 : "specific surface area of the kinetic species in m^2/g (if multiply_by_mass = true)");
30 324 : params.addParam<bool>(
31 : "multiply_by_mass",
32 324 : false,
33 : "Whether the rate should be multiplied by the kinetic_species mass (in grams)");
34 324 : params.addParam<Real>("kinetic_molal_index",
35 324 : 0.0,
36 : "The rate is multiplied by kinetic_species_molality^kinetic_molal_index / "
37 : "(kinetic_species_molality^kinetic_molal_index + "
38 : "kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index");
39 324 : params.addParam<Real>("kinetic_monod_index",
40 324 : 0.0,
41 : "The rate is multiplied by kinetic_species_molality^kinetic_molal_index / "
42 : "(kinetic_species_molality^kinetic_molal_index + "
43 : "kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index");
44 324 : params.addParam<Real>("kinetic_half_saturation",
45 324 : 0.0,
46 : "The rate is multiplied by kinetic_species_molality^kinetic_molal_index / "
47 : "(kinetic_species_molality^kinetic_molal_index + "
48 : "kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index");
49 324 : params.addParam<std::vector<std::string>>(
50 : "promoting_species_names", {}, "Names of any promoting species");
51 324 : params.addParam<std::vector<Real>>("promoting_indices", {}, "Indices of the promoting species");
52 324 : params.addParam<std::vector<Real>>(
53 : "promoting_monod_indices",
54 : "Indices of the monod denominators of the promoting species. If not given, then the default "
55 : "is 0 for each promoting species, meaning that there is no monod form");
56 324 : params.addParam<std::vector<Real>>("promoting_half_saturation",
57 : "Half-saturation constants for the monod expression. If not "
58 : "given, then the default is 0 for each promoting species");
59 324 : params.addParam<Real>("theta", 1.0, "Theta parameter, which appears in |1 - (Q/K)^theta|^eta");
60 324 : params.addParam<Real>("eta", 1.0, "Eta parameter, which appears in |1 - (Q/K)^theta|^eta");
61 486 : params.addRangeCheckedParam<Real>(
62 : "activation_energy",
63 324 : 0.0,
64 : "activation_energy >= 0.0",
65 : "Activation energy, in J.mol^-1, which appears in exp(activation_energy / R * (1/T0 - 1/T))");
66 324 : params.addParam<Real>(
67 : "one_over_T0",
68 324 : 0.0,
69 : "1/T0, in 1/Kelvin, which appears in exp(activation_energy / R * (1/T0 - 1/T))");
70 324 : MooseEnum direction("both dissolution precipitation raw death", "both");
71 324 : params.addParam<MooseEnum>(
72 : "direction",
73 : direction,
74 : "Direction of reaction. Let Q = the activity product of the kinetic reaction, and K = the "
75 : "equilibrium constant of the reaction. Then direction means the following. both = "
76 : "dissolution and precipitation are allowed. (Specifically, if Q < K then dissolution will "
77 : "occur, that is, the kinetic species mass will decrease with time. If Q > K then "
78 : "precipitation will occur, that is, the kinetic species mass will increase with time.) "
79 : "dissolution = if Q < K then dissolution will occur, and when Q > K then the rate will be "
80 : "set to zero so that precipitation will be prevented. precipitation = if Q > K then "
81 : "precipitation will occur, and when Q < K then the rate will be set to zero so that "
82 : "dissolution will be prevented. raw = the rate will not depend on sgn(1 - (Q/K)), which "
83 : "means dissolution will occur if intrinsic_rate_constant > 0, and precipitation will occur "
84 : "when intrinsic_rate_constant < 0. death = the rate will not depend on sgn(1 - (Q/K)), "
85 : "which means dissolution will occur if intrinsic_rate_constant > 0, and precipitation will "
86 : "occur when intrinsic_rate_constant < 0, and, in addition, no reactants will be produced or "
87 : "consumed by this kinetic reaction (only the kinetic species mass will change).");
88 324 : params.addParam<std::string>(
89 : "non_kinetic_biological_catalyst",
90 : "H2O",
91 : "Name of the primary or equilibrium species that acts as a biological catalyst.");
92 324 : params.addParam<Real>(
93 : "non_kinetic_biological_efficiency",
94 324 : 0.0,
95 : "When one mole of the kinetic species dissolves, non_kinetic_biological_efficiency moles of "
96 : "the non_kinetic_biological_catalyst is created");
97 324 : params.addParam<Real>(
98 : "kinetic_biological_efficiency",
99 324 : -1,
100 : "This is used when modelling biologically-catalysed reactions, when the biomass is treated "
101 : "as a kinetic species, and the reactants and reactant-products are in equilibrium in the "
102 : "aqueous solution. When one mole of reaction is catalysed, the biomass increases by "
103 : "kinetic_biological_efficiency moles");
104 324 : params.addParam<Real>(
105 : "energy_captured",
106 324 : 0.0,
107 : "In biologically-catalysed kinetic reactions, this is the energy captured by the cell, per "
108 : "mol of reaction turnover. Specifically, for each mole of kinetic reaction, the microbe "
109 : "will produce m moles of ATP via a reaction such as ADP + PO4--- -> ATP + H2O, with "
110 : "free-energy change G (usually around 45 kJ/mol). Then, energy_captured = m * G. For "
111 : "non-biologically-catalysed reactions, this should be zero. The impact of energy_captured "
112 : "is that the reaction's equilibrium constant is K_database * exp(-energy_captured / R / "
113 : "T_in_Kelvin)");
114 162 : params.addClassDescription(
115 : "User object that defines a kinetic rate. Note that more than one rate can be prescribed to "
116 : "a single kinetic_species: the sum the individual rates defines the overall rate. "
117 : "GeochemistryKineticRate simply specifies the algebraic form for a kinetic rate: to actually "
118 : "use it in a calculation, you must use it in the GeochemicalModelDefinition. The rate is "
119 : "intrinsic_rate_constant * area_quantity * (optionally, mass of kinetic_species in "
120 : "grams) * kinetic_molality^kinetic_molal_index / (kinetic_molality^kinetic_molal_index + "
121 : "kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index * "
122 : "(product_over_promoting_species m^promoting_index / (m^promoting_index + "
123 : "promoting_half_saturation^promiting_index)^promoting_monod_index) * |1 - (Q/K)^theta|^eta * "
124 : "exp(activation_energy / R * (1/T0 - 1/T)) * Direction(1 - (Q/K)). Please see the markdown "
125 : "documentation for examples");
126 :
127 162 : return params;
128 162 : }
129 :
130 81 : GeochemistryKineticRate::GeochemistryKineticRate(const InputParameters & parameters)
131 : : GeneralUserObject(parameters),
132 81 : _promoting_names(getParam<std::vector<std::string>>("promoting_species_names")),
133 198 : _monod_ind(isParamValid("promoting_monod_indices")
134 81 : ? getParam<std::vector<Real>>("promoting_monod_indices")
135 81 : : std::vector<Real>(_promoting_names.size(), 0.0)),
136 198 : _half_sat(isParamValid("promoting_half_saturation")
137 81 : ? getParam<std::vector<Real>>("promoting_half_saturation")
138 81 : : std::vector<Real>(_promoting_names.size(), 0.0)),
139 567 : _rate_description(getParam<std::string>("kinetic_species_name"),
140 162 : getParam<Real>("intrinsic_rate_constant"),
141 81 : getParam<Real>("area_quantity"),
142 243 : getParam<bool>("multiply_by_mass"),
143 162 : getParam<Real>("kinetic_molal_index"),
144 162 : getParam<Real>("kinetic_monod_index"),
145 162 : getParam<Real>("kinetic_half_saturation"),
146 : _promoting_names,
147 : getParam<std::vector<Real>>("promoting_indices"),
148 81 : _monod_ind,
149 81 : _half_sat,
150 162 : getParam<Real>("theta"),
151 162 : getParam<Real>("eta"),
152 162 : getParam<Real>("activation_energy"),
153 162 : getParam<Real>("one_over_T0"),
154 162 : getParam<MooseEnum>("direction").getEnum<DirectionChoiceEnum>(),
155 : getParam<std::string>("non_kinetic_biological_catalyst"),
156 162 : getParam<Real>("non_kinetic_biological_efficiency"),
157 162 : getParam<Real>("kinetic_biological_efficiency"),
158 162 : getParam<Real>("energy_captured"))
159 : {
160 81 : }
161 :
162 : void
163 1539 : GeochemistryKineticRate::initialize()
164 : {
165 1539 : }
166 :
167 : void
168 1539 : GeochemistryKineticRate::execute()
169 : {
170 1539 : }
171 :
172 : void
173 1539 : GeochemistryKineticRate::finalize()
174 : {
175 1539 : }
176 :
177 : const KineticRateUserDescription &
178 81 : GeochemistryKineticRate::getRateDescription() const
179 : {
180 81 : return _rate_description;
181 : }
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