add MICPContainer, a container for MICP data output

start by moving data members into it

CMakeLists_files.cmake

@@ -108,6 +108,7 @@ list (APPEND MAIN_SOURCE_FILES
   opm/simulators/flow/Main.cpp
   opm/simulators/flow/MainDispatchDynamic.cpp
   opm/simulators/flow/MechContainer.cpp
+  opm/simulators/flow/MICPContainer.cpp
   opm/simulators/flow/MixingRateControls.cpp
   opm/simulators/flow/NonlinearSolver.cpp
   opm/simulators/flow/partitionCells.cpp
@@ -858,6 +859,7 @@ list (APPEND PUBLIC_HEADER_FILES
   opm/simulators/flow/LogOutputHelper.hpp
   opm/simulators/flow/Main.hpp
   opm/simulators/flow/MechContainer.hpp
+  opm/simulators/flow/MICPContainer.hpp
   opm/simulators/flow/MixingRateControls.hpp
   opm/simulators/flow/NewTranFluxModule.hpp
   opm/simulators/flow/NonlinearSolver.hpp

opm/simulators/flow/FlowProblemBlackoil.hpp

@@ -1180,11 +1180,11 @@ protected:
             if constexpr (enablePolymer)
                 this->polymer_.concentration[elemIdx] = this->eclWriter_->outputModule().getPolymerConcentration(elemIdx);
             if constexpr (enableMICP){
-                this->micp_.microbialConcentration[elemIdx] = this->eclWriter_->outputModule().getMicrobialConcentration(elemIdx);
+                this->micp_.microbialConcentration[elemIdx] = this->eclWriter_->outputModule().getMICP().getMicrobialConcentration(elemIdx);
-                this->micp_.oxygenConcentration[elemIdx] = this->eclWriter_->outputModule().getOxygenConcentration(elemIdx);
+                this->micp_.oxygenConcentration[elemIdx] = this->eclWriter_->outputModule().getMICP().getOxygenConcentration(elemIdx);
-                this->micp_.ureaConcentration[elemIdx] = this->eclWriter_->outputModule().getUreaConcentration(elemIdx);
+                this->micp_.ureaConcentration[elemIdx] = this->eclWriter_->outputModule().getMICP().getUreaConcentration(elemIdx);
-                this->micp_.biofilmConcentration[elemIdx] = this->eclWriter_->outputModule().getBiofilmConcentration(elemIdx);
+                this->micp_.biofilmConcentration[elemIdx] = this->eclWriter_->outputModule().getMICP().getBiofilmConcentration(elemIdx);
-                this->micp_.calciteConcentration[elemIdx] = this->eclWriter_->outputModule().getCalciteConcentration(elemIdx);
+                this->micp_.calciteConcentration[elemIdx] = this->eclWriter_->outputModule().getMICP().getCalciteConcentration(elemIdx);
             }
             // if we need to restart for polymer molecular weight simulation, we need to add related here
         }

opm/simulators/flow/GenericOutputBlackoilModule.cpp

@@ -514,11 +514,11 @@ assignToSolution(data::Solution& sol)
     addEntry(flowsSolutionVector, "FLRWATK-", UnitSystem::measure::rate,                flores_[FaceDir::ToIntersectionIndex(Dir::ZMinus)][waterCompIdx], waterCompIdx);
 
     auto extendedSolutionArrays = std::array {
-        DataEntry{"BIOFILM",  UnitSystem::measure::identity,           cBiofilm_},
+        DataEntry{"BIOFILM",  UnitSystem::measure::identity,           micpC_.cBiofilm_},
-        DataEntry{"CALCITE",  UnitSystem::measure::identity,           cCalcite_},
+        DataEntry{"CALCITE",  UnitSystem::measure::identity,           micpC_.cCalcite_},
         DataEntry{"DRSDTCON", UnitSystem::measure::gas_oil_ratio_rate, drsdtcon_},
-        DataEntry{"MICROBES", UnitSystem::measure::density,            cMicrobes_},
+        DataEntry{"MICROBES", UnitSystem::measure::density,            micpC_.cMicrobes_},
-        DataEntry{"OXYGEN",   UnitSystem::measure::density,            cOxygen_},
+        DataEntry{"OXYGEN",   UnitSystem::measure::density,            micpC_.cOxygen_},
         DataEntry{"PERMFACT", UnitSystem::measure::identity,           permFact_},
         DataEntry{"PORV_RC",  UnitSystem::measure::identity,           rockCompPorvMultiplier_},
         DataEntry{"PRES_OVB", UnitSystem::measure::pressure,           overburdenPressure_},
@@ -535,7 +535,7 @@ assignToSolution(data::Solution& sol)
         DataEntry{"STD_GAS",  UnitSystem::measure::identity,           mFracGas_},
         DataEntry{"STD_OIL",  UnitSystem::measure::identity,           mFracOil_},
         DataEntry{"TMULT_RC", UnitSystem::measure::identity,           rockCompTransMultiplier_},
-        DataEntry{"UREA",     UnitSystem::measure::density,            cUrea_},
+        DataEntry{"UREA",     UnitSystem::measure::density,            micpC_.cUrea_},
     };
 
     // basically, for compositional, we can not use std::array for this.  We need to generate the ZMF1, ZMF2, and so on
@@ -763,11 +763,11 @@ setRestart(const data::Solution& sol,
     };
 
     const auto fields = std::array{
-        std::pair{"BIOFILM",  &cBiofilm_},
+        std::pair{"BIOFILM",  &micpC_.cBiofilm_},
-        std::pair{"CALCITE",  &cCalcite_},
+        std::pair{"CALCITE",  &micpC_.cCalcite_},
         std::pair{"FOAM",     &cFoam_},
-        std::pair{"MICROBES", &cMicrobes_},
+        std::pair{"MICROBES", &micpC_.cMicrobes_},
-        std::pair{"OXYGEN",   &cOxygen_},
+        std::pair{"OXYGEN",   &micpC_.cOxygen_},
         std::pair{"PERMFACT", &permFact_},
         std::pair{"POLYMER",  &cPolymer_},
         std::pair{"PPCW",     &ppcw_},
@@ -785,7 +785,7 @@ setRestart(const data::Solution& sol,
         std::pair{"SWHY1",    &swmin_},
         std::pair{"SWMAX",    &swMax_},
         std::pair{"TEMP",     &temperature_},
-        std::pair{"UREA",     &cUrea_},
+        std::pair{"UREA",     &micpC_.cUrea_},
     };
 
     std::for_each(fields.begin(), fields.end(),
@@ -1036,11 +1036,11 @@ doAllocBuffers(const unsigned bufferSize,
     }
 
     if (enableMICP_) {
-        cMicrobes_.resize(bufferSize, 0.0);
+        micpC_.cMicrobes_.resize(bufferSize, 0.0);
-        cOxygen_.resize(bufferSize, 0.0);
+        micpC_.cOxygen_.resize(bufferSize, 0.0);
-        cUrea_.resize(bufferSize, 0.0);
+        micpC_.cUrea_.resize(bufferSize, 0.0);
-        cBiofilm_.resize(bufferSize, 0.0);
+        micpC_.cBiofilm_.resize(bufferSize, 0.0);
-        cCalcite_.resize(bufferSize, 0.0);
+        micpC_.cCalcite_.resize(bufferSize, 0.0);
     }
 
     if (vapparsActive) {

opm/simulators/flow/GenericOutputBlackoilModule.hpp

@@ -37,6 +37,7 @@
 #include <opm/simulators/flow/InterRegFlows.hpp>
 #include <opm/simulators/flow/LogOutputHelper.hpp>
 #include <opm/simulators/flow/MechContainer.hpp>
+#include <opm/simulators/flow/MICPContainer.hpp>
 #include <opm/simulators/flow/RegionPhasePVAverage.hpp>
 
 #include <opm/simulators/utils/ParallelCommunication.hpp>
@@ -198,45 +199,8 @@ public:
         return 0;
     }
 
-    Scalar getMicrobialConcentration(unsigned elemIdx) const
+    const MICPContainer<Scalar>& getMICP() const
-    {
+    { return this->micpC_; }
-        if (cMicrobes_.size() > elemIdx)
-            return cMicrobes_[elemIdx];
-
-        return 0;
-    }
-
-    Scalar getOxygenConcentration(unsigned elemIdx) const
-    {
-        if (cOxygen_.size() > elemIdx)
-            return cOxygen_[elemIdx];
-
-        return 0;
-    }
-
-    Scalar getUreaConcentration(unsigned elemIdx) const
-    {
-        if (cUrea_.size() > elemIdx)
-            return cUrea_[elemIdx];
-
-        return 0;
-    }
-
-    Scalar getBiofilmConcentration(unsigned elemIdx) const
-    {
-        if (cBiofilm_.size() > elemIdx)
-            return cBiofilm_[elemIdx];
-
-        return 0;
-    }
-
-    Scalar getCalciteConcentration(unsigned elemIdx) const
-    {
-        if (cCalcite_.size() > elemIdx)
-            return cCalcite_[elemIdx];
-
-        return 0;
-    }
 
     const std::array<FlowsData<double>, 3>& getFlowsn() const
     {
@@ -494,11 +458,7 @@ protected:
     ScalarBuffer minimumOilPressure_;
     ScalarBuffer saturatedOilFormationVolumeFactor_;
     ScalarBuffer rockCompTransMultiplier_;
-    ScalarBuffer cMicrobes_;
+    MICPContainer<Scalar> micpC_;
-    ScalarBuffer cOxygen_;
-    ScalarBuffer cUrea_;
-    ScalarBuffer cBiofilm_;
-    ScalarBuffer cCalcite_;
     ScalarBuffer pcgw_;
     ScalarBuffer pcow_;
     ScalarBuffer pcog_;

opm/simulators/flow/MICPContainer.cpp

@@ -0,0 +1,34 @@
+// -*- 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.
+*/
+
+#include <config.h>
+#include <opm/simulators/flow/MICPContainer.hpp>
+
+namespace Opm {
+
+template class MICPContainer<double>;
+
+#if FLOW_INSTANTIATE_FLOAT
+template class MICPContainer<float>;
+#endif
+
+} // namespace Opm

opm/simulators/flow/MICPContainer.hpp

@@ -0,0 +1,88 @@
+// -*- 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
+ * \copydoc Opm::OutputBlackOilModule
+ */
+#ifndef OPM_MICP_CONTAINER_HPP
+#define OPM_MICP_CONTAINER_HPP
+
+#include <vector>
+
+namespace Opm {
+
+template<class Scalar>
+class MICPContainer
+{
+    using ScalarBuffer = std::vector<Scalar>;
+
+public:
+    Scalar getMicrobialConcentration(unsigned elemIdx) const
+    {
+        if (cMicrobes_.size() > elemIdx)
+            return cMicrobes_[elemIdx];
+
+        return 0;
+    }
+
+    Scalar getOxygenConcentration(unsigned elemIdx) const
+    {
+        if (cOxygen_.size() > elemIdx)
+            return cOxygen_[elemIdx];
+
+        return 0;
+    }
+
+    Scalar getUreaConcentration(unsigned elemIdx) const
+    {
+        if (cUrea_.size() > elemIdx)
+            return cUrea_[elemIdx];
+
+        return 0;
+    }
+
+    Scalar getBiofilmConcentration(unsigned elemIdx) const
+    {
+        if (cBiofilm_.size() > elemIdx)
+            return cBiofilm_[elemIdx];
+
+        return 0;
+    }
+
+    Scalar getCalciteConcentration(unsigned elemIdx) const
+    {
+        if (cCalcite_.size() > elemIdx)
+            return cCalcite_[elemIdx];
+
+        return 0;
+    }
+
+    ScalarBuffer cMicrobes_;
+    ScalarBuffer cOxygen_;
+    ScalarBuffer cUrea_;
+    ScalarBuffer cBiofilm_;
+    ScalarBuffer cCalcite_;
+};
+
+} // namespace Opm
+
+#endif // OPM_MICP_CONTAINER_HPP

opm/simulators/flow/OutputBlackoilModule.hpp

@@ -475,26 +475,26 @@ public:
                 this->mFracCo2_[globalDofIdx] = stdVolCo2 * rhoCO2 / stdMassTotal;
             }
 
-            if (!this->cMicrobes_.empty()) {
+            if (!this->micpC_.cMicrobes_.empty()) {
-                this->cMicrobes_[globalDofIdx] = intQuants.microbialConcentration().value();
+                this->micpC_.cMicrobes_[globalDofIdx] = intQuants.microbialConcentration().value();
             }
 
-            if (!this->cOxygen_.empty()) {
+            if (!this->micpC_.cOxygen_.empty()) {
-                this->cOxygen_[globalDofIdx] = intQuants.oxygenConcentration().value();
+                this->micpC_.cOxygen_[globalDofIdx] = intQuants.oxygenConcentration().value();
             }
 
-            if (!this->cUrea_.empty()) {
+            if (!this->micpC_.cUrea_.empty()) {
-                this->cUrea_[globalDofIdx] = 10
+                this->micpC_.cUrea_[globalDofIdx] = 10
                     * intQuants.ureaConcentration()
                           .value(); // Reescaling back the urea concentration (see WellInterface_impl.hpp)
             }
 
-            if (!this->cBiofilm_.empty()) {
+            if (!this->micpC_.cBiofilm_.empty()) {
-                this->cBiofilm_[globalDofIdx] = intQuants.biofilmConcentration().value();
+                this->micpC_.cBiofilm_[globalDofIdx] = intQuants.biofilmConcentration().value();
             }
 
-            if (!this->cCalcite_.empty()) {
+            if (!this->micpC_.cCalcite_.empty()) {
-                this->cCalcite_[globalDofIdx] = intQuants.calciteConcentration().value();
+                this->micpC_.cCalcite_[globalDofIdx] = intQuants.calciteConcentration().value();
             }
 
             if (!this->bubblePointPressure_.empty()) {