BIOFILM effects for gas-water systems

flow/flow_biofilm.cpp

@@ -0,0 +1,124 @@
+/*
+  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 3 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/>.
+*/
+#include "config.h"
+
+// Define making clear that the simulator supports AMG
+#define FLOW_SUPPORT_AMG 1
+
+#include <flow/flow_biofilm.hpp>
+
+#include <opm/material/common/ResetLocale.hpp>
+#include <opm/models/blackoil/blackoiltwophaseindices.hh>
+#include <opm/models/blackoil/blackoillocalresidualtpfa.hh>
+#include <opm/models/discretization/common/tpfalinearizer.hh>
+
+#include <opm/grid/CpGrid.hpp>
+#include <opm/simulators/flow/Main.hpp>
+#include <opm/simulators/flow/SimulatorFullyImplicitBlackoil.hpp>
+
+namespace Opm {
+/*!
+ * \brief Two-phase (gas+water) flow problem including biofilm effects (one transported
+ * quantity: suspended microbes and one solid phase: biofilm). 
+ */
+namespace Properties {
+namespace TTag {
+struct FlowBiofilmProblem {
+    using InheritsFrom = std::tuple<FlowProblem>;
+};
+}
+
+template<class TypeTag>
+struct EnableBioeffects<TypeTag, TTag::FlowBiofilmProblem> {
+    static constexpr bool value = true;
+};
+
+template<class TypeTag>
+struct EnableDiffusion<TypeTag, TTag::FlowBiofilmProblem> {
+    static constexpr bool value = true;
+};
+
+template<class TypeTag>
+struct EnableDispersion<TypeTag, TTag::FlowBiofilmProblem> {
+    static constexpr bool value = true;
+};
+
+template<class TypeTag>
+struct EnableDisgasInWater<TypeTag, TTag::FlowBiofilmProblem> {
+    static constexpr bool value = true;
+};
+
+template<class TypeTag>
+struct EnableVapwat<TypeTag, TTag::FlowBiofilmProblem> {
+    static constexpr bool value = true;
+};
+
+template<class TypeTag>
+struct Linearizer<TypeTag, TTag::FlowBiofilmProblem> { using type = TpfaLinearizer<TypeTag>; };
+template<class TypeTag>
+struct LocalResidual<TypeTag, TTag::FlowBiofilmProblem> { using type = BlackOilLocalResidualTPFA<TypeTag>; };
+
+//! The indices required by the model
+template<class TypeTag>
+struct Indices<TypeTag, TTag::FlowBiofilmProblem>
+{
+private:
+    // it is unfortunately not possible to simply use 'TypeTag' here because this leads
+    // to cyclic definitions of some properties. if this happens the compiler error
+    // messages unfortunately are *really* confusing and not really helpful.
+    using BaseTypeTag = TTag::FlowProblem;
+    using FluidSystem = GetPropType<BaseTypeTag, Properties::FluidSystem>;
+
+public:
+    using type = BlackOilTwoPhaseIndices<getPropValue<TypeTag, Properties::EnableSolvent>(),
+                                         getPropValue<TypeTag, Properties::EnableExtbo>(),
+                                         getPropValue<TypeTag, Properties::EnablePolymer>(),
+                                         getPropValue<TypeTag, Properties::EnableEnergy>(),
+                                         getPropValue<TypeTag, Properties::EnableFoam>(),
+                                         getPropValue<TypeTag, Properties::EnableBrine>(),
+                                         /*PVOffset=*/0,
+                                         /*disabledCompIdx=*/FluidSystem::oilCompIdx,
+                                         2>; //Two biocomponents (suspended microbes and biofilm)
+};
+}}
+
+namespace Opm {
+
+
+// ----------------- Main program -----------------
+int flowBiofilmMain(int argc, char** argv, bool outputCout, bool outputFiles)
+{
+    // we always want to use the default locale, and thus spare us the trouble
+    // with incorrect locale settings.
+    resetLocale();
+
+    FlowMain<Properties::TTag::FlowBiofilmProblem>
+        mainfunc {argc, argv, outputCout, outputFiles} ;
+    return mainfunc.execute();
+}
+
+int flowBiofilmMainStandalone(int argc, char** argv)
+{
+    using TypeTag = Properties::TTag::FlowBiofilmProblem;
+    auto mainObject = std::make_unique<Opm::Main>(argc, argv);
+    auto ret = mainObject->runStatic<TypeTag>();
+    // Destruct mainObject as the destructor calls MPI_Finalize!
+    mainObject.reset();
+    return ret;
+}
+
+} // namespace Opm

flow/flow_biofilm.hpp

@@ -0,0 +1,27 @@
+/*
+  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 3 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/>.
+*/
+#ifndef FLOW_BIOFILM_HPP
+#define FLOW_BIOFILM_HPP
+
+namespace Opm {
+
+//! \brief Main function used in flow binary.
+int flowBiofilmMain(int argc, char** argv, bool outputCout, bool outputFiles);
+
+//! \brief Main function used in flow_biofilm binary.
+int flowBiofilmMainStandalone(int argc, char** argv);
+
+}
+
+#endif // FLOW_BIOFILM_HPP

flow/flow_biofilm_main.cpp

@@ -0,0 +1,21 @@
+/*
+  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 3 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/>.
+*/
+#include "config.h"
+#include <flow/flow_biofilm.hpp>
+
+
+int main(int argc, char** argv)
+{
+    return Opm::flowBiofilmMainStandalone(argc, argv);
+}

flow/flow_gasoil.cpp

@@ -65,7 +65,7 @@ public:
                                        getPropValue<TypeTag, Properties::EnableBrine>(),
                                        /*PVOffset=*/0,
                                        /*disabledCompIdx=*/FluidSystem::waterCompIdx,
-                                       getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                       getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gasoil_energy.cpp

@@ -55,7 +55,7 @@ public:
                                        getPropValue<TypeTag, Properties::EnableBrine>(),
                                        /*PVOffset=*/0,
                                        /*disabledCompIdx=*/FluidSystem::waterCompIdx,
-                                       getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                       getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 template<class TypeTag>
 struct EnableEnergy<TypeTag, TTag::FlowGasOilEnergyProblem> {

flow/flow_gasoildiffuse.cpp

@@ -67,7 +67,7 @@ public:
                                        getPropValue<TypeTag, Properties::EnableBrine>(),
                                        /*PVOffset=*/0,
                                        /*disabledCompIdx=*/FluidSystem::waterCompIdx,
-                                       getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                       getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gaswater.cpp

@@ -63,7 +63,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::oilCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gaswater_brine.cpp

@@ -64,7 +64,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::oilCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gaswater_dissolution.cpp

@@ -78,7 +78,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::oilCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gaswater_dissolution_diffuse.cpp

@@ -81,7 +81,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::oilCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gaswater_energy.cpp

@@ -86,7 +86,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::oilCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gaswater_saltprec_energy.cpp

@@ -77,7 +77,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::oilCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gaswater_saltprec_vapwat.cpp

@@ -72,7 +72,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::oilCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_gaswater_solvent.cpp

@@ -61,7 +61,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::oilCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_micp.cpp

@@ -29,6 +29,11 @@
 #include <opm/simulators/flow/SimulatorFullyImplicitBlackoil.hpp>
 
 namespace Opm {
+/*!
+ * \brief Single-phase (water) flow problem including microbially induced calcite precipitation (MICP)
+ * effects (three transported quantities: suspended microbes, oxygen, and urea, and two solid phases:
+ * biofilm and calcite).
+ */
 namespace Properties {
 namespace TTag {
 struct FlowMICPProblem {
@@ -36,7 +41,7 @@ struct FlowMICPProblem {
 };
 }
 template<class TypeTag>
-struct EnableMICP<TypeTag, TTag::FlowMICPProblem> {
+struct EnableBioeffects<TypeTag, TTag::FlowMICPProblem> {
     static constexpr bool value = true;
 };
 template<class TypeTag>

flow/flow_oilwater.cpp

@@ -66,7 +66,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::gasCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_oilwater_brine.cpp

@@ -56,7 +56,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::gasCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_oilwater_polymer.cpp

@@ -56,7 +56,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::gasCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_oilwater_polymer_injectivity.cpp

@@ -63,7 +63,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*disabledCompIdx=*/FluidSystem::gasCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 }}
 

flow/flow_onephase.cpp

@@ -63,7 +63,7 @@ public:
                                          getPropValue<TypeTag, Properties::EnableBrine>(),
                                          /*PVOffset=*/0,
                                          /*enabledCompIdx=*/FluidSystem::waterCompIdx,
-                                         getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                         getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 
 } // namespace Opm::Properties

flow/flow_onephase_energy.cpp

@@ -58,7 +58,7 @@ public:
                                               getPropValue<TypeTag, Properties::EnableBrine>(),
                                               /*PVOffset=*/0,
                                               /*enebledCompIdx=*/FluidSystem::waterCompIdx,
-                                              getPropValue<TypeTag, Properties::EnableMICP>()>;
+                                              getPropValue<TypeTag, Properties::EnableBioeffects>()>;
 };
 
 } // namespace Opm::Properties