From d3be24fdad7f56645bf8b86e5108336d12336e9d Mon Sep 17 00:00:00 2001
From: Simon Scholz <simon.scholz@iws.uni-stuttgart.de>
Date: Thu, 7 Dec 2017 15:19:02 +0100
Subject: [PATCH] [min] introduce mineralization folder with localresidual,
model (former properties), volVars and VTK output
---
dumux/porousmediumflow/CMakeLists.txt | 1 +
.../mineralization/CMakeLists.txt | 7 +
.../mineralization/localresidual.hh | 92 +++++++++++
.../porousmediumflow/mineralization/model.hh | 73 +++++++++
.../mineralization/volumevariables.hh | 152 ++++++++++++++++++
.../mineralization/vtkoutputfields.hh | 61 +++++++
6 files changed, 386 insertions(+)
create mode 100644 dumux/porousmediumflow/mineralization/CMakeLists.txt
create mode 100644 dumux/porousmediumflow/mineralization/localresidual.hh
create mode 100644 dumux/porousmediumflow/mineralization/model.hh
create mode 100644 dumux/porousmediumflow/mineralization/volumevariables.hh
create mode 100644 dumux/porousmediumflow/mineralization/vtkoutputfields.hh
diff --git a/dumux/porousmediumflow/CMakeLists.txt b/dumux/porousmediumflow/CMakeLists.txt
index 33c612c76a..602b161d2c 100644
--- a/dumux/porousmediumflow/CMakeLists.txt
+++ b/dumux/porousmediumflow/CMakeLists.txt
@@ -12,6 +12,7 @@ add_subdirectory("co2")
add_subdirectory("compositional")
add_subdirectory("immiscible")
add_subdirectory("implicit")
+add_subdirectory("mineralization")
add_subdirectory("mpnc")
add_subdirectory("nonisothermal")
add_subdirectory("richards")
diff --git a/dumux/porousmediumflow/mineralization/CMakeLists.txt b/dumux/porousmediumflow/mineralization/CMakeLists.txt
new file mode 100644
index 0000000000..783fba4a28
--- /dev/null
+++ b/dumux/porousmediumflow/mineralization/CMakeLists.txt
@@ -0,0 +1,7 @@
+#install headers
+install(FILES
+localresidual.hh
+model.hh
+volumevariables.hh
+vtkoutputfields.hh
+DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/dumux/porousmediumflow/mineralization)
\ No newline at end of file
diff --git a/dumux/porousmediumflow/mineralization/localresidual.hh b/dumux/porousmediumflow/mineralization/localresidual.hh
new file mode 100644
index 0000000000..af85e08c67
--- /dev/null
+++ b/dumux/porousmediumflow/mineralization/localresidual.hh
@@ -0,0 +1,92 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program 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. *
+ * *
+ * This program 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 this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+/*!
+ * \file
+ *
+ * \brief Element-wise calculation of the local residual for problems using a
+ * compositional fully implicit model that also considers solid phases.
+ */
+#ifndef DUMUX_COMPOSITIONAL_MINERALIZATION_LOCAL_RESIDUAL_HH
+#define DUMUX_COMPOSITIONAL_MINERALIZATION_LOCAL_RESIDUAL_HH
+
+#include <dumux/porousmediumflow/compositional/localresidual.hh>
+
+namespace Dumux
+{
+/*!
+ * \ingroup Mineralization
+ * \ingroup LocalResidual
+ * \brief Element-wise calculation of the local residual for problems
+ * using a one/two-phase n-component mineralization fully implicit model.
+ */
+template<class TypeTag>
+class MineralizationLocalResidual: public CompositionalLocalResidual<TypeTag>
+{
+ using ParentType = CompositionalLocalResidual<TypeTag>;
+ using ResidualVector = typename GET_PROP_TYPE(TypeTag, NumEqVector);
+ using SubControlVolume = typename GET_PROP_TYPE(TypeTag, SubControlVolume);
+ using VolumeVariables = typename GET_PROP_TYPE(TypeTag, VolumeVariables);
+ using Indices = typename GET_PROP_TYPE(TypeTag, Indices);
+ using Problem = typename GET_PROP_TYPE(TypeTag, Problem);
+
+ static constexpr int numPhases = GET_PROP_VALUE(TypeTag, NumPhases);
+ static constexpr int numSPhases = GET_PROP_VALUE(TypeTag, NumSPhases);
+ static constexpr int numComponents = GET_PROP_VALUE(TypeTag, NumComponents);
+ static constexpr bool useMoles = GET_PROP_VALUE(TypeTag, UseMoles);
+
+ enum { conti0EqIdx = Indices::conti0EqIdx };
+
+public:
+ using ParentType::ParentType;
+
+ /*!
+ * \brief Evaluate the amount of all conservation quantities
+ * (e.g. phase mass) within a sub-control volume.
+ *
+ * The result should be averaged over the volume (e.g. phase mass
+ * inside a sub control volume divided by the volume)
+ *
+ * \param storage The mass of the component within the sub-control volume
+ * \param scvIdx The SCV (sub-control-volume) index
+ * \param usePrevSol Evaluate function with solution of current or previous time step
+ */
+ ResidualVector computeStorage(const Problem& problem,
+ const SubControlVolume& scv,
+ const VolumeVariables& volVars) const
+ {
+ auto storage = ParentType::computeStorage(problem, scv, volVars);
+
+ const auto massOrMoleDensity = [](const auto& volVars, const int phaseIdx)
+ { return useMoles ? volVars.molarDensity(phaseIdx) : volVars.density(phaseIdx); };
+
+ // compute storage term of all components within all fluid phases
+ for (int phaseIdx = numPhases; phaseIdx < numPhases + numSPhases; ++phaseIdx)
+ {
+ auto eqIdx = conti0EqIdx + numComponents-numPhases + phaseIdx;
+ storage[eqIdx] += volVars.precipitateVolumeFraction(phaseIdx)
+ * massOrMoleDensity(volVars, phaseIdx);
+ }
+
+ return storage;
+ }
+};
+
+} // end namespace Dumux
+
+#endif
diff --git a/dumux/porousmediumflow/mineralization/model.hh b/dumux/porousmediumflow/mineralization/model.hh
new file mode 100644
index 0000000000..6ec7775ac4
--- /dev/null
+++ b/dumux/porousmediumflow/mineralization/model.hh
@@ -0,0 +1,73 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program 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. *
+ * *
+ * This program 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 this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+/*!
+ * \ingroup Mineralization
+ * \file
+ *
+ * \brief Defines the properties required for the
+ * implicit mineralization models.
+ */
+
+#ifndef DUMUX_MINERALIZATION_MODEL_HH
+#define DUMUX_MINERALIZATION_MODEL_HH
+
+#include <dumux/common/properties.hh>
+#include "localresidual.hh"
+#include "volumevariables.hh"
+#include "vtkoutputfields.hh"
+
+namespace Dumux {
+namespace Properties {
+//////////////////////////////////////////////////////////////////
+// Type tags
+//////////////////////////////////////////////////////////////////
+NEW_TYPE_TAG(Mineralization);
+
+//! Set the general mineralization volume variables
+SET_TYPE_PROP(Mineralization, VolumeVariables, MineralizationVolumeVariables<TypeTag>);
+
+//! Set the general mineralization compositional local residual
+SET_TYPE_PROP(Mineralization, LocalResidual, MineralizationLocalResidual<TypeTag>);
+
+//! VTK outputs for mineralization models
+SET_TYPE_PROP(Mineralization, VtkOutputFields, MineralizationVtkOutputFields<TypeTag>);
+
+//! Set the property for the number of solid phases, excluding the non-reactive matrix.
+SET_PROP(Mineralization, NumSPhases)
+{
+private:
+ using FluidSystem = typename GET_PROP_TYPE(TypeTag, PTAG(FluidSystem));
+public:
+ static const int value = FluidSystem::numSPhases;
+};
+
+//! Set the property for the number of equations. For each component and each
+//precipitated mineral/solid phase one equation has to be solved.
+SET_PROP(Mineralization, NumEq)
+{
+private:
+ using FluidSystem = typename GET_PROP_TYPE(TypeTag, PTAG(FluidSystem));
+public:
+ static const int value = FluidSystem::numComponents + FluidSystem::numSPhases;
+};
+
+} // end namespace Properties
+} // end namespace Dumux
+
+#endif
diff --git a/dumux/porousmediumflow/mineralization/volumevariables.hh b/dumux/porousmediumflow/mineralization/volumevariables.hh
new file mode 100644
index 0000000000..adc516930a
--- /dev/null
+++ b/dumux/porousmediumflow/mineralization/volumevariables.hh
@@ -0,0 +1,152 @@
+// -**- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program 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. *
+ * *
+ * This program 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 this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+/*!
+ * \file
+ *
+ * \brief Contains the quantities which are constant within a
+ * finite volume in the two-phase, n-component mineralization model.
+ */
+#ifndef DUMUX_MINERALIZATION_VOLUME_VARIABLES_HH
+#define DUMUX_MINERALIZATION_VOLUME_VARIABLES_HH
+
+#include <dumux/common/math.hh>
+
+#include <dumux/material/fluidstates/compositional.hh>
+#include <dumux/discretization/volumevariables.hh>
+
+#include "model.hh"
+
+namespace Dumux
+{
+
+/*!
+ * \ingroup Mineralization
+ * \ingroup ImplicitVolumeVariables
+ * \brief Contains the quantities which are are constant within a
+ * finite volume in a mineralization n-component model.
+ */
+template <class TypeTag>
+class MineralizationVolumeVariables : public GET_PROP_TYPE(TypeTag, NonMineralizationVolumeVariables)
+{
+ using ParentType = typename GET_PROP_TYPE(TypeTag, NonMineralizationVolumeVariables);
+ using Scalar = typename GET_PROP_TYPE(TypeTag, Scalar);
+ using GridView = typename GET_PROP_TYPE(TypeTag, GridView);
+ using Problem = typename GET_PROP_TYPE(TypeTag, Problem);
+ using SubControlVolume = typename GET_PROP_TYPE(TypeTag, SubControlVolume);
+ using ElementSolutionVector = typename GET_PROP_TYPE(TypeTag, ElementSolutionVector);
+ using FluidSystem = typename GET_PROP_TYPE(TypeTag, FluidSystem);
+ using MaterialLawParams = typename GET_PROP_TYPE(TypeTag, MaterialLaw)::Params;
+ using Element = typename GridView::template Codim<0>::Entity;
+
+ enum
+ {
+ dimWorld=GridView::dimensionworld,
+
+ numPhases = GET_PROP_VALUE(TypeTag, NumPhases),
+ numSPhases = GET_PROP_VALUE(TypeTag, NumSPhases),
+ numComponents = GET_PROP_VALUE(TypeTag, NumComponents),
+ };
+
+public:
+ using FluidState = typename GET_PROP_TYPE(TypeTag, FluidState);
+
+ /*!
+ * \copydoc ImplicitVolumeVariables::update
+ */
+ void update(const ElementSolutionVector &elemSol,
+ const Problem &problem,
+ const Element &element,
+ const SubControlVolume& scv)
+ {
+ // Update parent type (also completes the fluid state)
+ ParentType::update(elemSol, problem, element, scv);
+
+ /////////////
+ // calculate the remaining quantities
+ /////////////
+ auto&& priVars = elemSol[scv.indexInElement()];
+
+ sumPrecipitates_ = 0.0;
+ for(int sPhaseIdx = 0; sPhaseIdx < numSPhases; ++sPhaseIdx)
+ {
+ precipitateVolumeFraction_[sPhaseIdx] = priVars[numComponents + sPhaseIdx];
+ sumPrecipitates_+= precipitateVolumeFraction_[sPhaseIdx];
+ }
+ }
+
+ /*!
+ * \brief Returns the volume fraction of the precipitate (solid phase)
+ * for the given phaseIdx
+ *
+ * \param phaseIdx the index of the solid phase
+ */
+ Scalar precipitateVolumeFraction(int phaseIdx) const
+ { return precipitateVolumeFraction_[phaseIdx - numPhases]; }
+
+ /*!
+ * \brief Returns the density of the phase for all fluid and solid phases
+ *
+ * \param phaseIdx the index of the fluid phase
+ */
+ Scalar density(int phaseIdx) const
+ {
+ if (phaseIdx < numPhases)
+ return this->fluidState_.density(phaseIdx);
+ else
+ return FluidSystem::precipitateDensity(phaseIdx);
+ }
+
+ /*!
+ * \brief Returns the mass density of a given phase within the
+ * control volume.
+ *
+ * \param phaseIdx The phase index
+ */
+ Scalar molarDensity(int phaseIdx) const
+ {
+ if (phaseIdx < numPhases)
+ return this->fluidState_.molarDensity(phaseIdx);
+ else
+ return FluidSystem::precipitateMolarDensity(phaseIdx);
+ }
+
+ /*!
+ * \brief Returns the molality of a component in the phase
+ *
+ * \param phaseIdx the index of the fluid phase
+ * \param compIdx the index of the component
+ * \f$\mathrm{molality}=\frac{n_\mathrm{component}}{m_\mathrm{solvent}}
+ * =\frac{n_\mathrm{component}}{n_\mathrm{solvent}*M_\mathrm{solvent}}\f$
+ * compIdx of the main component (solvent) in the
+ * phase is equal to the phaseIdx
+ */
+ Scalar molality(int phaseIdx, int compIdx) const // [moles/Kg]
+ {
+ return this->fluidState_.moleFraction(phaseIdx, compIdx)
+ /(this->fluidState_.moleFraction(phaseIdx, phaseIdx)
+ * FluidSystem::molarMass(phaseIdx));
+ }
+
+protected:
+ Scalar precipitateVolumeFraction_[numSPhases];
+ Scalar sumPrecipitates_;
+};
+} // end namespace Dumux
+
+#endif
diff --git a/dumux/porousmediumflow/mineralization/vtkoutputfields.hh b/dumux/porousmediumflow/mineralization/vtkoutputfields.hh
new file mode 100644
index 0000000000..70e7a2acf5
--- /dev/null
+++ b/dumux/porousmediumflow/mineralization/vtkoutputfields.hh
@@ -0,0 +1,61 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program 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. *
+ * *
+ * This program 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 this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+/*!
+ * \file
+ * \brief Adds vtk output fields specific to the twop-nc-min model
+ */
+#ifndef DUMUX_MINERALIZATION_VTK_OUTPUT_FIELDS_HH
+#define DUMUX_MINERALIZATION_VTK_OUTPUT_FIELDS_HH
+
+#include <dumux/common/properties.hh>
+
+namespace Dumux
+{
+
+/*!
+ * \ingroup Mineralization, InputOutput
+ * \brief Adds vtk output fields specific to the a NCMin model
+ */
+template<class TypeTag>
+class MineralizationVtkOutputFields
+{
+ using NonMineralizationVtkOutputFields = typename GET_PROP_TYPE(TypeTag, NonMineralizationVtkOutputFields);
+ using VolumeVariables = typename GET_PROP_TYPE(TypeTag, VolumeVariables);
+ using FluidSystem = typename GET_PROP_TYPE(TypeTag, FluidSystem);
+
+ static constexpr int numPhases = GET_PROP_VALUE(TypeTag, NumPhases);
+ static constexpr int numSPhases = GET_PROP_VALUE(TypeTag, NumSPhases);
+
+public:
+ template <class VtkOutputModule>
+ static void init(VtkOutputModule& vtk)
+ {
+ NonMineralizationVtkOutputFields::init(vtk);
+
+ //additional output
+ for (int i = 0; i < numSPhases; ++i)
+ {
+ vtk.addVolumeVariable([i](const VolumeVariables& v){ return v.precipitateVolumeFraction(numPhases + i); },"precipVolFrac_"+ FluidSystem::phaseName(numPhases + i));
+ }
+ }
+};
+
+} // end namespace Dumux
+
+#endif
--
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