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f96e449094
limits the amount of static variable declarations
591 lines
24 KiB
C++
591 lines
24 KiB
C++
// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
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// vi: set et ts=4 sw=4 sts=4:
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/*
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This file is part of the Open Porous Media project (OPM).
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OPM is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 2 of the License, or
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(at your option) any later version.
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OPM is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with OPM. If not, see <http://www.gnu.org/licenses/>.
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Consult the COPYING file in the top-level source directory of this
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module for the precise wording of the license and the list of
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copyright holders.
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*/
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/*!
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* \file
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*
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* \brief Contains the classes required to extend the black-oil model by MICP.
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*/
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#ifndef EWOMS_BLACK_OIL_MICP_MODULE_HH
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#define EWOMS_BLACK_OIL_MICP_MODULE_HH
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#include "blackoilproperties.hh"
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#include <opm/models/blackoil/blackoilmicpparams.hh>
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#include <opm/models/io/vtkblackoilmicpmodule.hh>
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#if HAVE_ECL_INPUT
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#include <opm/input/eclipse/EclipseState/EclipseState.hpp>
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#include <opm/input/eclipse/EclipseState/MICPpara.hpp>
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#endif
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#include <dune/common/fvector.hh>
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#include <cmath>
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#include <cstddef>
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#include <stdexcept>
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#include <string>
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namespace Opm {
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/*!
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* \ingroup BlackOil
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* \brief Contains the high level supplements required to extend the black oil
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* model by MICP.
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*/
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template <class TypeTag, bool enableMICPV = getPropValue<TypeTag, Properties::EnableMICP>()>
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class BlackOilMICPModule
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{
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using Scalar = GetPropType<TypeTag, Properties::Scalar>;
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using Evaluation = GetPropType<TypeTag, Properties::Evaluation>;
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using PrimaryVariables = GetPropType<TypeTag, Properties::PrimaryVariables>;
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using IntensiveQuantities = GetPropType<TypeTag, Properties::IntensiveQuantities>;
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using ExtensiveQuantities = GetPropType<TypeTag, Properties::ExtensiveQuantities>;
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using ElementContext = GetPropType<TypeTag, Properties::ElementContext>;
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using FluidSystem = GetPropType<TypeTag, Properties::FluidSystem>;
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using Model = GetPropType<TypeTag, Properties::Model>;
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using Simulator = GetPropType<TypeTag, Properties::Simulator>;
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using EqVector = GetPropType<TypeTag, Properties::EqVector>;
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using RateVector = GetPropType<TypeTag, Properties::RateVector>;
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using Indices = GetPropType<TypeTag, Properties::Indices>;
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using Toolbox = MathToolbox<Evaluation>;
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static constexpr unsigned microbialConcentrationIdx = Indices::microbialConcentrationIdx;
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static constexpr unsigned oxygenConcentrationIdx = Indices::oxygenConcentrationIdx;
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static constexpr unsigned ureaConcentrationIdx = Indices::ureaConcentrationIdx;
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static constexpr unsigned biofilmConcentrationIdx = Indices::biofilmConcentrationIdx;
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static constexpr unsigned calciteConcentrationIdx = Indices::calciteConcentrationIdx;
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static constexpr unsigned contiMicrobialEqIdx = Indices::contiMicrobialEqIdx;
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static constexpr unsigned contiOxygenEqIdx = Indices::contiOxygenEqIdx;
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static constexpr unsigned contiUreaEqIdx = Indices::contiUreaEqIdx;
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static constexpr unsigned contiBiofilmEqIdx = Indices::contiBiofilmEqIdx;
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static constexpr unsigned contiCalciteEqIdx = Indices::contiCalciteEqIdx;
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static constexpr unsigned waterPhaseIdx = FluidSystem::waterPhaseIdx;
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static constexpr unsigned enableMICP = enableMICPV;
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static constexpr unsigned numEq = getPropValue<TypeTag, Properties::NumEq>();
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public:
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#if HAVE_ECL_INPUT
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//
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//* \brief Initialize all internal data structures needed by the MICP module
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//
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static void initFromState(const EclipseState& eclState)
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{
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// some sanity checks: if MICP is enabled, the MICP keyword must be
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// present, if MICP is disabled the keyword must not be present.
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if (enableMICP && !eclState.runspec().micp()) {
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throw std::runtime_error("Non-trivial MICP treatment requested at compile time, but "
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"the deck does not contain the MICP keyword");
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}
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else if (!enableMICP && eclState.runspec().micp()) {
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throw std::runtime_error("MICP treatment disabled at compile time, but the deck "
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"contains the MICP keyword");
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}
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if (!eclState.runspec().micp())
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return; // MICP treatment is supposed to be disabled*/
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// initialize the objects which deal with the MICPpara keyword
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const auto& MICPpara = eclState.getMICPpara();
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setMICPpara(MICPpara.getDensityBiofilm(),
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MICPpara.getDensityCalcite(),
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MICPpara.getDetachmentRate(),
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MICPpara.getCriticalPorosity(),
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MICPpara.getFittingFactor(),
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MICPpara.getHalfVelocityOxygen(),
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MICPpara.getHalfVelocityUrea(),
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MICPpara.getMaximumGrowthRate(),
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MICPpara.getMaximumUreaUtilization(),
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MICPpara.getMicrobialAttachmentRate(),
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MICPpara.getMicrobialDeathRate(),
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MICPpara.getMinimumPermeability(),
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MICPpara.getOxygenConsumptionFactor(),
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MICPpara.getYieldGrowthCoefficient(),
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MICPpara.getMaximumOxygenConcentration(),
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MICPpara.getMaximumUreaConcentration(),
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MICPpara.getToleranceBeforeClogging());
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// obtain the porosity for the clamp in the blackoilnewtonmethod
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params_.phi_ = eclState.fieldProps().get_double("PORO");
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}
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#endif
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/*!
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* \brief The simulator stops if "clogging" has been (almost) reached in any of the cells.
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*
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* I.e., porosity - biofilm - calcite < tol_clgg, where tol_clgg is a given tolerance. In the
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* implemented model a permebaility-porosity relatonship is used where a minimum
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* permeability value is reached if porosity - biofilm - calcite < phi_crit.
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*/
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static void checkCloggingMICP(const Model& model, const Scalar phi, unsigned dofIdx)
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{
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const PrimaryVariables& priVars = model.solution(/*timeIdx=*/1)[dofIdx];
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if (phi - priVars[biofilmConcentrationIdx] - priVars[calciteConcentrationIdx] < toleranceBeforeClogging())
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throw std::logic_error("Clogging has been (almost) reached in at least one cell\n");
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}
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/*!
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* \brief Specify the MICP properties a single region.
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*
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* The index of specified here must be in range [0, numSatRegions)
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*/
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static void setMICPpara(const Scalar& densityBiofilm,
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const Scalar& densityCalcite,
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const Scalar& detachmentRate,
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const Scalar& criticalPorosity,
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const Scalar& fittingFactor,
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const Scalar& halfVelocityOxygen,
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const Scalar& halfVelocityUrea,
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const Scalar& maximumGrowthRate,
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const Scalar& maximumUreaUtilization,
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const Scalar& microbialAttachmentRate,
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const Scalar& microbialDeathRate,
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const Scalar& minimumPermeability,
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const Scalar& oxygenConsumptionFactor,
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const Scalar& yieldGrowthCoefficient,
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const Scalar& maximumOxygenConcentration,
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const Scalar& maximumUreaConcentration,
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const Scalar& toleranceBeforeClogging)
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{
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params_.densityBiofilm_ = densityBiofilm;
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params_.densityCalcite_ = densityCalcite;
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params_.detachmentRate_ = detachmentRate;
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params_.criticalPorosity_ = criticalPorosity;
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params_.fittingFactor_ = fittingFactor;
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params_.halfVelocityOxygen_ = halfVelocityOxygen;
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params_.halfVelocityUrea_ = halfVelocityUrea;
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params_.maximumGrowthRate_ = maximumGrowthRate;
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params_.maximumUreaUtilization_ = maximumUreaUtilization;
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params_.microbialAttachmentRate_ = microbialAttachmentRate;
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params_.microbialDeathRate_ = microbialDeathRate;
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params_.minimumPermeability_ = minimumPermeability;
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params_.oxygenConsumptionFactor_ = oxygenConsumptionFactor;
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params_.yieldGrowthCoefficient_ = yieldGrowthCoefficient;
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params_.maximumOxygenConcentration_ = maximumOxygenConcentration;
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params_.maximumUreaConcentration_ = maximumUreaConcentration;
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params_.toleranceBeforeClogging_ = toleranceBeforeClogging;
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}
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/*!
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* \brief Register all run-time parameters for the black-oil MICP module.
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*/
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static void registerParameters()
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{
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if (!enableMICP)
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// MICP has been disabled at compile time
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return;
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VtkBlackOilMICPModule<TypeTag>::registerParameters();
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}
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/*!
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* \brief Register all MICP specific VTK and ECL output modules.
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*/
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static void registerOutputModules(Model& model,
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Simulator& simulator)
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{
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if (!enableMICP)
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// MICP has been disabled at compile time
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return;
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model.addOutputModule(new VtkBlackOilMICPModule<TypeTag>(simulator));
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}
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static bool eqApplies(unsigned eqIdx)
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{
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if (!enableMICP)
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return false;
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// All MICP components are true here
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return eqIdx == contiMicrobialEqIdx || eqIdx == contiOxygenEqIdx || eqIdx == contiUreaEqIdx || eqIdx == contiBiofilmEqIdx || eqIdx == contiCalciteEqIdx;
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}
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static Scalar eqWeight([[maybe_unused]] unsigned eqIdx)
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{
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assert(eqApplies(eqIdx));
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// TODO: it may be beneficial to chose this differently.
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return static_cast<Scalar>(1.0);
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}
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// must be called after water storage is computed
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template <class LhsEval>
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static void addStorage(Dune::FieldVector<LhsEval, numEq>& storage,
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const IntensiveQuantities& intQuants)
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{
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if (!enableMICP)
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return;
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LhsEval surfaceVolumeWater = Toolbox::template decay<LhsEval>(intQuants.porosity());
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// avoid singular matrix if no water is present.
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surfaceVolumeWater = max(surfaceVolumeWater, 1e-10);
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// Suspended microbes in water phase
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const LhsEval massMicrobes = surfaceVolumeWater * Toolbox::template decay<LhsEval>(intQuants.microbialConcentration());
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LhsEval accumulationMicrobes = massMicrobes;
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storage[contiMicrobialEqIdx] += accumulationMicrobes;
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// Oxygen in water phase
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const LhsEval massOxygen = surfaceVolumeWater * Toolbox::template decay<LhsEval>(intQuants.oxygenConcentration());
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LhsEval accumulationOxygen = massOxygen;
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storage[contiOxygenEqIdx] += accumulationOxygen;
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// Urea in water phase
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const LhsEval massUrea = surfaceVolumeWater * Toolbox::template decay<LhsEval>(intQuants.ureaConcentration());
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LhsEval accumulationUrea = massUrea;
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storage[contiUreaEqIdx] += accumulationUrea;
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// Biofilm
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const LhsEval massBiofilm = Toolbox::template decay<LhsEval>(intQuants.biofilmConcentration());
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LhsEval accumulationBiofilm = massBiofilm;
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storage[contiBiofilmEqIdx] += accumulationBiofilm;
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// Calcite
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const LhsEval massCalcite = Toolbox::template decay<LhsEval>(intQuants.calciteConcentration());
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LhsEval accumulationCalcite = massCalcite;
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storage[contiCalciteEqIdx] += accumulationCalcite;
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}
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static void computeFlux(RateVector& flux,
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const ElementContext& elemCtx,
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unsigned scvfIdx,
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unsigned timeIdx)
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{
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if (!enableMICP)
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return;
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const auto& extQuants = elemCtx.extensiveQuantities(scvfIdx, timeIdx);
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const unsigned upIdx = extQuants.upstreamIndex(waterPhaseIdx);
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const unsigned inIdx = extQuants.interiorIndex();
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const auto& up = elemCtx.intensiveQuantities(upIdx, timeIdx);
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if (upIdx == inIdx) {
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flux[contiMicrobialEqIdx] = extQuants.volumeFlux(waterPhaseIdx) * up.microbialConcentration();
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flux[contiOxygenEqIdx] = extQuants.volumeFlux(waterPhaseIdx) * up.oxygenConcentration();
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flux[contiUreaEqIdx] = extQuants.volumeFlux(waterPhaseIdx) * up.ureaConcentration();
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}
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else {
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flux[contiMicrobialEqIdx] = extQuants.volumeFlux(waterPhaseIdx) * decay<Scalar>(up.microbialConcentration());
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flux[contiOxygenEqIdx] = extQuants.volumeFlux(waterPhaseIdx) * decay<Scalar>(up.oxygenConcentration());
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flux[contiUreaEqIdx] = extQuants.volumeFlux(waterPhaseIdx) * decay<Scalar>(up.ureaConcentration());
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}
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}
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// See https://doi.org/10.1016/j.ijggc.2021.103256 for the micp processes in the model.
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static void addSource(RateVector& source,
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const ElementContext& elemCtx,
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unsigned dofIdx,
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unsigned timeIdx)
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{
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if (!enableMICP)
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return;
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// compute dpW (max norm of the pressure gradient in the cell center)
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const IntensiveQuantities& intQuants = elemCtx.intensiveQuantities(dofIdx, timeIdx);
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const auto& K = elemCtx.problem().intrinsicPermeability(elemCtx, dofIdx, 0);
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size_t numInteriorFaces = elemCtx.numInteriorFaces(timeIdx);
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Evaluation dpW = 0;
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for (unsigned scvfIdx = 0; scvfIdx < numInteriorFaces; scvfIdx++) {
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const auto& extQuants = elemCtx.extensiveQuantities(scvfIdx, timeIdx);
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unsigned upIdx = extQuants.upstreamIndex(waterPhaseIdx);
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const auto& up = elemCtx.intensiveQuantities(upIdx, timeIdx);
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const Evaluation& mobWater = up.mobility(waterPhaseIdx);
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// compute water velocity from flux
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Evaluation waterVolumeVelocity = extQuants.volumeFlux(waterPhaseIdx) / (K[0][0] * mobWater);
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dpW = std::max(dpW, abs(waterVolumeVelocity));
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}
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// get the model parameters
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Scalar k_a = microbialAttachmentRate();
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Scalar k_d = microbialDeathRate();
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Scalar rho_b = densityBiofilm();
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Scalar rho_c = densityCalcite();
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Scalar k_str = detachmentRate();
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Scalar k_o = halfVelocityOxygen();
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Scalar k_u = halfVelocityUrea() / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp)
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Scalar mu = maximumGrowthRate();
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Scalar mu_u = maximumUreaUtilization() / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp)
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Scalar Y_sb = yieldGrowthCoefficient();
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Scalar F = oxygenConsumptionFactor();
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Scalar Y_uc = 1.67 * 10; //Multiplying by scaling factor 10 (see WellInterface_impl.hpp)
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// compute the processes
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source[Indices::contiMicrobialEqIdx] += intQuants.microbialConcentration() * intQuants.porosity() *
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(Y_sb * mu * intQuants.oxygenConcentration() / (k_o + intQuants.oxygenConcentration()) - k_d - k_a)
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+ rho_b * intQuants.biofilmConcentration() * k_str * pow(intQuants.porosity() * dpW, 0.58);
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source[Indices::contiOxygenEqIdx] -= (intQuants.microbialConcentration() * intQuants.porosity() + rho_b * intQuants.biofilmConcentration()) *
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F * mu * intQuants.oxygenConcentration() / (k_o + intQuants.oxygenConcentration());
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source[Indices::contiUreaEqIdx] -= rho_b * intQuants.biofilmConcentration() * mu_u * intQuants.ureaConcentration() / (k_u + intQuants.ureaConcentration());
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source[Indices::contiBiofilmEqIdx] += intQuants.biofilmConcentration() * (Y_sb * mu * intQuants.oxygenConcentration() / (k_o + intQuants.oxygenConcentration()) - k_d
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- k_str * pow(intQuants.porosity() * dpW, 0.58) - Y_uc * (rho_b / rho_c) * intQuants.biofilmConcentration() * mu_u *
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(intQuants.ureaConcentration() / (k_u + intQuants.ureaConcentration())) / (intQuants.porosity() + intQuants.biofilmConcentration()))
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+ k_a * intQuants.microbialConcentration() * intQuants.porosity() / rho_b;
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source[Indices::contiCalciteEqIdx] += (rho_b / rho_c) * intQuants.biofilmConcentration() * Y_uc * mu_u * intQuants.ureaConcentration() / (k_u + intQuants.ureaConcentration());
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}
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static const Scalar densityBiofilm()
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{
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return params_.densityBiofilm_;
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}
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static const Scalar densityCalcite()
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{
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return params_.densityCalcite_;
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}
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static const Scalar detachmentRate()
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{
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return params_.detachmentRate_;
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}
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static const Scalar criticalPorosity()
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{
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return params_.criticalPorosity_;
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}
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static const Scalar fittingFactor()
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{
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return params_.fittingFactor_;
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}
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static const Scalar halfVelocityOxygen()
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{
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return params_.halfVelocityOxygen_;
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}
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static const Scalar halfVelocityUrea()
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{
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return params_.halfVelocityUrea_;
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}
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static const Scalar maximumGrowthRate()
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{
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return params_.maximumGrowthRate_;
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}
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static const Scalar maximumOxygenConcentration()
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{
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return params_.maximumOxygenConcentration_;
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}
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static const Scalar maximumUreaConcentration()
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{
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return params_.maximumUreaConcentration_ / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp);
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}
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static const Scalar maximumUreaUtilization()
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{
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return params_.maximumUreaUtilization_;
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}
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static const Scalar microbialAttachmentRate()
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{
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return params_.microbialAttachmentRate_;
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}
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static const Scalar microbialDeathRate()
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{
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return params_.microbialDeathRate_;
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}
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static const Scalar minimumPermeability()
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{
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return params_.minimumPermeability_;
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}
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static const Scalar oxygenConsumptionFactor()
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{
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return params_.oxygenConsumptionFactor_;
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}
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static const Scalar toleranceBeforeClogging()
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{
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return params_.toleranceBeforeClogging_;
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}
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static const Scalar yieldGrowthCoefficient()
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{
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return params_.yieldGrowthCoefficient_;
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}
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static const std::vector<Scalar> phi()
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{
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return params_.phi_;
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}
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private:
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static BlackOilMICPParams<Scalar> params_;
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};
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template <class TypeTag, bool enableMICPV>
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BlackOilMICPParams<typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar>
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BlackOilMICPModule<TypeTag, enableMICPV>::params_;
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/*!
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* \ingroup BlackOil
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* \class Opm::BlackOilMICPIntensiveQuantities
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*
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* \brief Provides the volumetric quantities required for the equations needed by the
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* MICP extension of the black-oil model.
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*/
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template <class TypeTag, bool enableMICPV = getPropValue<TypeTag, Properties::EnableMICP>()>
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class BlackOilMICPIntensiveQuantities
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{
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using Implementation = GetPropType<TypeTag, Properties::IntensiveQuantities>;
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using Scalar = GetPropType<TypeTag, Properties::Scalar>;
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using Evaluation = GetPropType<TypeTag, Properties::Evaluation>;
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using PrimaryVariables = GetPropType<TypeTag, Properties::PrimaryVariables>;
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using FluidSystem = GetPropType<TypeTag, Properties::FluidSystem>;
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using Indices = GetPropType<TypeTag, Properties::Indices>;
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using ElementContext = GetPropType<TypeTag, Properties::ElementContext>;
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using MICPModule = BlackOilMICPModule<TypeTag>;
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static constexpr int microbialConcentrationIdx = Indices::microbialConcentrationIdx;
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static constexpr int oxygenConcentrationIdx = Indices::oxygenConcentrationIdx;
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static constexpr int ureaConcentrationIdx = Indices::ureaConcentrationIdx;
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static constexpr int biofilmConcentrationIdx = Indices::biofilmConcentrationIdx;
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static constexpr int calciteConcentrationIdx = Indices::calciteConcentrationIdx;
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static constexpr int waterPhaseIdx = FluidSystem::waterPhaseIdx;
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public:
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/*!
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* \brief Update the intensive properties needed to handle MICP from the
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* primary variables
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*
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*/
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void MICPPropertiesUpdate_(const ElementContext& elemCtx,
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unsigned dofIdx,
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unsigned timeIdx)
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{
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const auto linearizationType = elemCtx.linearizationType();
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const PrimaryVariables& priVars = elemCtx.primaryVars(dofIdx, timeIdx);
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const auto& intQuants = elemCtx.intensiveQuantities(dofIdx, timeIdx);
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const auto& K = elemCtx.problem().intrinsicPermeability(elemCtx, dofIdx, timeIdx);
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Scalar referencePorosity_ = elemCtx.problem().porosity(elemCtx, dofIdx, timeIdx);
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Scalar eta = MICPModule::fittingFactor();
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Scalar k_min = MICPModule::minimumPermeability();
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Scalar phi_crit = MICPModule::criticalPorosity();
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microbialConcentration_ = priVars.makeEvaluation(microbialConcentrationIdx, timeIdx, linearizationType);
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oxygenConcentration_ = priVars.makeEvaluation(oxygenConcentrationIdx, timeIdx, linearizationType);
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ureaConcentration_ = priVars.makeEvaluation(ureaConcentrationIdx, timeIdx, linearizationType);
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biofilmConcentration_ = priVars.makeEvaluation(biofilmConcentrationIdx, timeIdx, linearizationType);
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calciteConcentration_ = priVars.makeEvaluation(calciteConcentrationIdx, timeIdx, linearizationType);
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// Permeability reduction due to MICP, by adjusting the water mobility
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asImp_().mobility_[waterPhaseIdx] *= max((pow((intQuants.porosity() - phi_crit) / (referencePorosity_ - phi_crit), eta) + k_min / K[0][0])/(1. + k_min / K[0][0]), k_min / K[0][0]);
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}
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const Evaluation& microbialConcentration() const
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{ return microbialConcentration_; }
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const Evaluation& oxygenConcentration() const
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{ return oxygenConcentration_; }
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const Evaluation& ureaConcentration() const
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{ return ureaConcentration_; }
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const Evaluation& biofilmConcentration() const
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{ return biofilmConcentration_; }
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const Evaluation& calciteConcentration() const
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{ return calciteConcentration_; }
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protected:
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Implementation& asImp_()
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{ return *static_cast<Implementation*>(this); }
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Evaluation microbialConcentration_;
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Evaluation oxygenConcentration_;
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Evaluation ureaConcentration_;
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Evaluation biofilmConcentration_;
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Evaluation calciteConcentration_;
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};
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template <class TypeTag>
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class BlackOilMICPIntensiveQuantities<TypeTag, false>
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{
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using Evaluation = GetPropType<TypeTag, Properties::Evaluation>;
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using ElementContext = GetPropType<TypeTag, Properties::ElementContext>;
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using Scalar = GetPropType<TypeTag, Properties::Scalar>;
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public:
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void MICPPropertiesUpdate_(const ElementContext&,
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unsigned,
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unsigned)
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{ }
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const Evaluation& microbialConcentration() const
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{ throw std::logic_error("microbialConcentration() called but MICP is disabled"); }
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const Evaluation& oxygenConcentration() const
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{ throw std::logic_error("oxygenConcentration() called but MICP is disabled"); }
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const Evaluation& ureaConcentration() const
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{ throw std::logic_error("ureaConcentration() called but MICP is disabled"); }
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const Evaluation& biofilmConcentration() const
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{ throw std::logic_error("biofilmConcentration() called but MICP is disabled"); }
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const Evaluation& calciteConcentration() const
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{ throw std::logic_error("calciteConcentration() called but MICP is disabled"); }
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};
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/*!
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* \ingroup BlackOil
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* \class Opm::BlackOilMICPExtensiveQuantities
|
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*
|
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* \brief Provides the MICP specific extensive quantities to the generic black-oil
|
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* module's extensive quantities.
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*/
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template <class TypeTag, bool enableMICPV = getPropValue<TypeTag, Properties::EnableMICP>()>
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class BlackOilMICPExtensiveQuantities
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{
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using Implementation = GetPropType<TypeTag, Properties::ExtensiveQuantities>;
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private:
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Implementation& asImp_()
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{ return *static_cast<Implementation*>(this); }
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};
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template <class TypeTag>
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class BlackOilMICPExtensiveQuantities<TypeTag, false>{};
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} // namespace Opm
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#endif
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