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Merge pull request #722 from akva2/micp_module_params

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blackoilmicpmodules: put parameters in separate class
This commit is contained in:
Markus Blatt 2022-09-20 11:42:23 +02:00 committed by GitHub
commit 453261d6ad
3 changed files with 158 additions and 180 deletions
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268
opm/models/blackoil/blackoilmicpmodules.hh
View File

@ -29,8 +29,9 @@
#define EWOMS_BLACK_OIL_MICP_MODULE_HH
#include "blackoilproperties.hh"
#include <opm/models/blackoil/blackoilmicpparams.hh>
#include <opm/models/io/vtkblackoilmicpmodule.hh>
#include <opm/models/common/quantitycallbacks.hh>
#if HAVE_ECL_INPUT
#include <opm/input/eclipse/EclipseState/EclipseState.hpp>
@ -39,6 +40,9 @@
#include <dune/common/fvector.hh>
#include <cmath>
#include <cstddef>
#include <stdexcept>
#include <string>
namespace Opm {
@ -123,7 +127,7 @@ public:
MICPpara.getMaximumUreaConcentration(),
MICPpara.getToleranceBeforeClogging());
// obtain the porosity for the clamp in the blackoilnewtonmethod
phi_ = eclState.fieldProps().get_double("PORO");
params_.phi_ = eclState.fieldProps().get_double("PORO");
}
#endif
@ -137,7 +141,7 @@ public:
static void checkCloggingMICP(const Model& model, const Scalar phi, unsigned dofIdx)
{
const PrimaryVariables& priVars = model.solution(/*timeIdx=*/1)[dofIdx];
if (phi - priVars[biofilmConcentrationIdx] - priVars[calciteConcentrationIdx] < MICPparaToleranceBeforeClogging())
if (phi - priVars[biofilmConcentrationIdx] - priVars[calciteConcentrationIdx] < toleranceBeforeClogging())
throw std::logic_error("Clogging has been (almost) reached in at least one cell\n");
}
@ -146,41 +150,41 @@ public:
*
* The index of specified here must be in range [0, numSatRegions)
*/
static void setMICPpara(const Scalar& MICPparaDensityBiofilm,
const Scalar& MICPparaDensityCalcite,
const Scalar& MICPparaDetachmentRate,
const Scalar& MICPparaCriticalPorosity,
const Scalar& MICPparaFittingFactor,
const Scalar& MICPparaHalfVelocityOxygen,
const Scalar& MICPparaHalfVelocityUrea,
const Scalar& MICPparaMaximumGrowthRate,
const Scalar& MICPparaMaximumUreaUtilization,
const Scalar& MICPparaMicrobialAttachmentRate,
const Scalar& MICPparaMicrobialDeathRate,
const Scalar& MICPparaMinimumPermeability,
const Scalar& MICPparaOxygenConsumptionFactor,
const Scalar& MICPparaYieldGrowthCoefficient,
const Scalar& MICPparaMaximumOxygenConcentration,
const Scalar& MICPparaMaximumUreaConcentration,
const Scalar& MICPparaToleranceBeforeClogging)
static void setMICPpara(const Scalar& densityBiofilm,
const Scalar& densityCalcite,
const Scalar& detachmentRate,
const Scalar& criticalPorosity,
const Scalar& fittingFactor,
const Scalar& halfVelocityOxygen,
const Scalar& halfVelocityUrea,
const Scalar& maximumGrowthRate,
const Scalar& maximumUreaUtilization,
const Scalar& microbialAttachmentRate,
const Scalar& microbialDeathRate,
const Scalar& minimumPermeability,
const Scalar& oxygenConsumptionFactor,
const Scalar& yieldGrowthCoefficient,
const Scalar& maximumOxygenConcentration,
const Scalar& maximumUreaConcentration,
const Scalar& toleranceBeforeClogging)
{
MICPparaDensityBiofilm_ = MICPparaDensityBiofilm;
MICPparaDensityCalcite_ = MICPparaDensityCalcite;
MICPparaDetachmentRate_ = MICPparaDetachmentRate;
MICPparaCriticalPorosity_ = MICPparaCriticalPorosity;
MICPparaFittingFactor_ = MICPparaFittingFactor;
MICPparaHalfVelocityOxygen_ = MICPparaHalfVelocityOxygen;
MICPparaHalfVelocityUrea_ = MICPparaHalfVelocityUrea;
MICPparaMaximumGrowthRate_ = MICPparaMaximumGrowthRate;
MICPparaMaximumUreaUtilization_ = MICPparaMaximumUreaUtilization;
MICPparaMicrobialAttachmentRate_ = MICPparaMicrobialAttachmentRate;
MICPparaMicrobialDeathRate_ = MICPparaMicrobialDeathRate;
MICPparaMinimumPermeability_ = MICPparaMinimumPermeability;
MICPparaOxygenConsumptionFactor_ = MICPparaOxygenConsumptionFactor;
MICPparaYieldGrowthCoefficient_ = MICPparaYieldGrowthCoefficient;
MICPparaMaximumOxygenConcentration_ = MICPparaMaximumOxygenConcentration;
MICPparaMaximumUreaConcentration_ = MICPparaMaximumUreaConcentration;
MICPparaToleranceBeforeClogging_ = MICPparaToleranceBeforeClogging;
params_.densityBiofilm_ = densityBiofilm;
params_.densityCalcite_ = densityCalcite;
params_.detachmentRate_ = detachmentRate;
params_.criticalPorosity_ = criticalPorosity;
params_.fittingFactor_ = fittingFactor;
params_.halfVelocityOxygen_ = halfVelocityOxygen;
params_.halfVelocityUrea_ = halfVelocityUrea;
params_.maximumGrowthRate_ = maximumGrowthRate;
params_.maximumUreaUtilization_ = maximumUreaUtilization;
params_.microbialAttachmentRate_ = microbialAttachmentRate;
params_.microbialDeathRate_ = microbialDeathRate;
params_.minimumPermeability_ = minimumPermeability;
params_.oxygenConsumptionFactor_ = oxygenConsumptionFactor;
params_.yieldGrowthCoefficient_ = yieldGrowthCoefficient;
params_.maximumOxygenConcentration_ = maximumOxygenConcentration;
params_.maximumUreaConcentration_ = maximumUreaConcentration;
params_.toleranceBeforeClogging_ = toleranceBeforeClogging;
}
/*!
@ -313,17 +317,17 @@ public:
}
// get the model parameters
Scalar k_a = MICPparaMicrobialAttachmentRate();
Scalar k_d = MICPparaMicrobialDeathRate();
Scalar rho_b = MICPparaDensityBiofilm();
Scalar rho_c = MICPparaDensityCalcite();
Scalar k_str = MICPparaDetachmentRate();
Scalar k_o = MICPparaHalfVelocityOxygen();
Scalar k_u = MICPparaHalfVelocityUrea() / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp)
Scalar mu = MICPparaMaximumGrowthRate();
Scalar mu_u = MICPparaMaximumUreaUtilization() / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp)
Scalar Y_sb = MICPparaYieldGrowthCoefficient();
Scalar F = MICPparaOxygenConsumptionFactor();
Scalar k_a = microbialAttachmentRate();
Scalar k_d = microbialDeathRate();
Scalar rho_b = densityBiofilm();
Scalar rho_c = densityCalcite();
Scalar k_str = detachmentRate();
Scalar k_o = halfVelocityOxygen();
Scalar k_u = halfVelocityUrea() / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp)
Scalar mu = maximumGrowthRate();
Scalar mu_u = maximumUreaUtilization() / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp)
Scalar Y_sb = yieldGrowthCoefficient();
Scalar F = oxygenConsumptionFactor();
Scalar Y_uc = 1.67 * 10; //Multiplying by scaling factor 10 (see WellInterface_impl.hpp)
// compute the processes
@ -344,190 +348,104 @@ public:
source[Indices::contiCalciteEqIdx] += (rho_b / rho_c) * intQuants.biofilmConcentration() * Y_uc * mu_u * intQuants.ureaConcentration() / (k_u + intQuants.ureaConcentration());
}
static const Scalar MICPparaDensityBiofilm()
static const Scalar densityBiofilm()
{
return MICPparaDensityBiofilm_;
return params_.densityBiofilm_;
}
static const Scalar MICPparaDensityCalcite()
static const Scalar densityCalcite()
{
return MICPparaDensityCalcite_;
return params_.densityCalcite_;
}
static const Scalar MICPparaDetachmentRate()
static const Scalar detachmentRate()
{
return MICPparaDetachmentRate_;
return params_.detachmentRate_;
}
static const Scalar MICPparaCriticalPorosity()
static const Scalar criticalPorosity()
{
return MICPparaCriticalPorosity_;
return params_.criticalPorosity_;
}
static const Scalar MICPparaFittingFactor()
static const Scalar fittingFactor()
{
return MICPparaFittingFactor_;
return params_.fittingFactor_;
}
static const Scalar MICPparaHalfVelocityOxygen()
static const Scalar halfVelocityOxygen()
{
return MICPparaHalfVelocityOxygen_;
return params_.halfVelocityOxygen_;
}
static const Scalar MICPparaHalfVelocityUrea()
static const Scalar halfVelocityUrea()
{
return MICPparaHalfVelocityUrea_;
return params_.halfVelocityUrea_;
}
static const Scalar MICPparaMaximumGrowthRate()
static const Scalar maximumGrowthRate()
{
return MICPparaMaximumGrowthRate_;
return params_.maximumGrowthRate_;
}
static const Scalar MICPparaMaximumOxygenConcentration()
static const Scalar maximumOxygenConcentration()
{
return MICPparaMaximumOxygenConcentration_;
return params_.maximumOxygenConcentration_;
}
static const Scalar MICPparaMaximumUreaConcentration()
static const Scalar maximumUreaConcentration()
{
return MICPparaMaximumUreaConcentration_ / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp);
return params_.maximumUreaConcentration_ / 10.0;//Dividing by scaling factor 10 (see WellInterface_impl.hpp);
}
static const Scalar MICPparaMaximumUreaUtilization()
static const Scalar maximumUreaUtilization()
{
return MICPparaMaximumUreaUtilization_;
return params_.maximumUreaUtilization_;
}
static const Scalar MICPparaMicrobialAttachmentRate()
static const Scalar microbialAttachmentRate()
{
return MICPparaMicrobialAttachmentRate_;
return params_.microbialAttachmentRate_;
}
static const Scalar MICPparaMicrobialDeathRate()
static const Scalar microbialDeathRate()
{
return MICPparaMicrobialDeathRate_;
return params_.microbialDeathRate_;
}
static const Scalar MICPparaMinimumPermeability()
static const Scalar minimumPermeability()
{
return MICPparaMinimumPermeability_;
return params_.minimumPermeability_;
}
static const Scalar MICPparaOxygenConsumptionFactor()
static const Scalar oxygenConsumptionFactor()
{
return MICPparaOxygenConsumptionFactor_;
return params_.oxygenConsumptionFactor_;
}
static const Scalar MICPparaToleranceBeforeClogging()
static const Scalar toleranceBeforeClogging()
{
return MICPparaToleranceBeforeClogging_;
return params_.toleranceBeforeClogging_;
}
static const Scalar MICPparaYieldGrowthCoefficient()
static const Scalar yieldGrowthCoefficient()
{
return MICPparaYieldGrowthCoefficient_;
return params_.yieldGrowthCoefficient_;
}
static const std::vector<Scalar> phi()
{
return phi_;
return params_.phi_;
}
private:
static Scalar MICPparaDensityBiofilm_;
static Scalar MICPparaDensityCalcite_;
static Scalar MICPparaDetachmentRate_;
static Scalar MICPparaCriticalPorosity_;
static Scalar MICPparaFittingFactor_;
static Scalar MICPparaHalfVelocityOxygen_;
static Scalar MICPparaHalfVelocityUrea_;
static Scalar MICPparaMaximumGrowthRate_;
static Scalar MICPparaMaximumUreaUtilization_;
static Scalar MICPparaMicrobialAttachmentRate_;
static Scalar MICPparaMicrobialDeathRate_;
static Scalar MICPparaMinimumPermeability_;
static Scalar MICPparaOxygenConsumptionFactor_;
static Scalar MICPparaYieldGrowthCoefficient_;
static Scalar MICPparaMaximumOxygenConcentration_;
static Scalar MICPparaMaximumUreaConcentration_;
static Scalar MICPparaToleranceBeforeClogging_;
static std::vector<Scalar> phi_;
static BlackOilMICPParams<Scalar> params_;
};
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaDensityBiofilm_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaDensityCalcite_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaDetachmentRate_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaCriticalPorosity_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaFittingFactor_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaHalfVelocityOxygen_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaHalfVelocityUrea_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaMaximumGrowthRate_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaMaximumUreaUtilization_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaMicrobialAttachmentRate_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaMicrobialDeathRate_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaMinimumPermeability_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaOxygenConsumptionFactor_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaYieldGrowthCoefficient_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaMaximumOxygenConcentration_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaMaximumUreaConcentration_;
template <class TypeTag, bool enableMICPV>
typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar
BlackOilMICPModule<TypeTag, enableMICPV>::MICPparaToleranceBeforeClogging_;
template <class TypeTag, bool enableMICPV>
std::vector<typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar>
BlackOilMICPModule<TypeTag, enableMICPV>::phi_;
BlackOilMICPParams<typename BlackOilMICPModule<TypeTag, enableMICPV>::Scalar>
BlackOilMICPModule<TypeTag, enableMICPV>::params_;
/*!
* \ingroup BlackOil
@ -574,9 +492,9 @@ public:
const auto& intQuants = elemCtx.intensiveQuantities(dofIdx, timeIdx);
const auto& K = elemCtx.problem().intrinsicPermeability(elemCtx, dofIdx, timeIdx);
Scalar referencePorosity_ = elemCtx.problem().porosity(elemCtx, dofIdx, timeIdx);
Scalar eta = MICPModule::MICPparaFittingFactor();
Scalar k_min = MICPModule::MICPparaMinimumPermeability();
Scalar phi_crit = MICPModule::MICPparaCriticalPorosity();
Scalar eta = MICPModule::fittingFactor();
Scalar k_min = MICPModule::minimumPermeability();
Scalar phi_crit = MICPModule::criticalPorosity();
microbialConcentration_ = priVars.makeEvaluation(microbialConcentrationIdx, timeIdx, linearizationType);
oxygenConcentration_ = priVars.makeEvaluation(oxygenConcentrationIdx, timeIdx, linearizationType);

60
opm/models/blackoil/blackoilmicpparams.hh Normal file
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@ -0,0 +1,60 @@
// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
// vi: set et ts=4 sw=4 sts=4:
/*
This file is part of the Open Porous Media project (OPM).
OPM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
OPM is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with OPM. If not, see <http://www.gnu.org/licenses/>.
Consult the COPYING file in the top-level source directory of this
module for the precise wording of the license and the list of
copyright holders.
*/
/*!
* \file
*
* \brief Contains the parameters required to extend the black-oil model by MICP.
*/
#ifndef EWOMS_BLACK_OIL_MICP_PARAMS_HH
#define EWOMS_BLACK_OIL_MICP_PARAMS_HH
#include <vector>
namespace Opm {
//! \brief Struct holding the parameters for the BlackOilMICPModule class.
template<class Scalar>
struct BlackOilMICPParams {
Scalar densityBiofilm_;
Scalar densityCalcite_;
Scalar detachmentRate_;
Scalar criticalPorosity_;
Scalar fittingFactor_;
Scalar halfVelocityOxygen_;
Scalar halfVelocityUrea_;
Scalar maximumGrowthRate_;
Scalar maximumUreaUtilization_;
Scalar microbialAttachmentRate_;
Scalar microbialDeathRate_;
Scalar minimumPermeability_;
Scalar oxygenConsumptionFactor_;
Scalar yieldGrowthCoefficient_;
Scalar maximumOxygenConcentration_;
Scalar maximumUreaConcentration_;
Scalar toleranceBeforeClogging_;
std::vector<Scalar> phi_;
};
} // namespace Opm
#endif

10
opm/models/blackoil/blackoilnewtonmethod.hh
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@ -404,15 +404,15 @@ protected:
// concentration (the urea concentration has been scaled by 10). For
// the biofilm and calcite, we set this value equal to the porosity minus the clogging tolerance.
if (enableMICP && pvIdx == Indices::microbialConcentrationIdx)
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::MICPparaDensityBiofilm());
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::densityBiofilm());
if (enableMICP && pvIdx == Indices::oxygenConcentrationIdx)
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::MICPparaMaximumOxygenConcentration());
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::maximumOxygenConcentration());
if (enableMICP && pvIdx == Indices::ureaConcentrationIdx)
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::MICPparaMaximumUreaConcentration());
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::maximumUreaConcentration());
if (enableMICP && pvIdx == Indices::biofilmConcentrationIdx)
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::phi()[globalDofIdx] - MICPModule::MICPparaToleranceBeforeClogging());
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::phi()[globalDofIdx] - MICPModule::toleranceBeforeClogging());
if (enableMICP && pvIdx == Indices::calciteConcentrationIdx)
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::phi()[globalDofIdx] - MICPModule::MICPparaToleranceBeforeClogging());
nextValue[pvIdx] = std::clamp(nextValue[pvIdx], 0.0, MICPModule::phi()[globalDofIdx] - MICPModule::toleranceBeforeClogging());
}
// switch the new primary variables to something which is physically meaningful.