[pnm][grid] Use PoreInscribedRadius and ThroatInscribedRadius consistently

dumux/discretization/porenetwork/gridgeometry.hh

@@ -140,9 +140,9 @@ public:
         {
             const int eIdx = gridView.indexSet().index(element);
             const auto& params = gridData.parameters(element);
-            static const auto throatRadiusIdx = gridData.parameterIndex("ThroatRadius");
+            static const auto throatInscribedRadiusIdx = gridData.parameterIndex("ThroatInscribedRadius");
             static const auto throatLengthIdx = gridData.parameterIndex("ThroatLength");
-            throatInscribedRadius_[eIdx] = params[throatRadiusIdx];
+            throatInscribedRadius_[eIdx] = params[throatInscribedRadiusIdx];
             throatLength_[eIdx] = params[throatLengthIdx];
 
             // use a default value if no throat label is given by the grid

dumux/io/grid/porenetwork/griddata.hh

@@ -247,7 +247,7 @@ public:
             else if (paramName.find("Pore") != std::string::npos)
                 msg = "Make sure to include it in the vector of parameter names VertexParameters = " + paramName + " ... ...";
 
-            DUNE_THROW(Dumux::ParameterException, paramName << " not set in the grid or input file. \n" << msg << "\n" << list.str());
+            DUNE_THROW(Dumux::ParameterException, paramName << " not set in the grid file. \n" << msg << "\n" << list.str());
         }
     }
 
@@ -317,7 +317,7 @@ private:
         if (!isDgfData_)
         {
             vertexParameterNames_ = StringVector{"PoreInscribedRadius", "PoreVolume", "PoreLabel"};
-            elementParameterNames_ = StringVector{"ThroatRadius", "ThroatLength", "ThroatLabel"};
+            elementParameterNames_ = StringVector{"ThroatInscribedRadius", "ThroatLength", "ThroatLabel"};
             if (numSubregions_ > 0)
             {
                 vertexParameterNames_.push_back("PoreRegionId");

dumux/io/grid/porenetwork/parametersforgeneratedgrid.hh

@@ -194,15 +194,15 @@ public:
         }
 
         // treat throat parameters
-        auto defaultThroatRadius = throatRadiusGenerator_(-1, getParameter);
+        auto defaultThroatInscribedRadius = throatInscribedRadiusGenerator_(-1, getParameter);
         auto defaultThroatLength = throatLengthGenerator_(-1, getParameter);
 
         // get helper functions for throat radii and lengths on subregions
-        std::vector<decltype(defaultThroatRadius)> subregionThroatRadius;
+        std::vector<decltype(defaultThroatInscribedRadius)> subregionThroatInscribedRadius;
         std::vector<decltype(defaultThroatLength)> subregionThroatLength;
         for (int i = 0; i < numSubregions; ++i)
         {
-            subregionThroatRadius.emplace_back(throatRadiusGenerator_(i, getParameter));
+            subregionThroatInscribedRadius.emplace_back(throatInscribedRadiusGenerator_(i, getParameter));
             subregionThroatLength.emplace_back(throatLengthGenerator_(i, getParameter));
         }
 
@@ -211,14 +211,14 @@ public:
         {
             if (numSubregions == 0) // assign values if no subregions are specified
             {
-                setParameter(element, "ThroatRadius", defaultThroatRadius(element));
+                setParameter(element, "ThroatInscribedRadius", defaultThroatInscribedRadius(element));
                 setParameter(element, "ThroatLength", defaultThroatLength(element));
             }
             else // assign values to throats if they are within a subregion
             {
                 // default value for elements not belonging to a subregion
                 setParameter(element, "ThroatRegionId", -1);
-                setParameter(element, "ThroatRadius", defaultThroatRadius(element));
+                setParameter(element, "ThroatInscribedRadius", defaultThroatInscribedRadius(element));
                 setParameter(element, "ThroatLength", defaultThroatLength(element));
 
                 for (int id = 0; id < numSubregions; ++id)
@@ -227,7 +227,7 @@ public:
                     if (intersectsPointGeometry(element.geometry().center(), subregion))
                     {
                         setParameter(element, "ThroatRegionId", id);
-                        setParameter(element, "ThroatRadius", subregionThroatRadius[id](element));
+                        setParameter(element, "ThroatInscribedRadius", subregionThroatInscribedRadius[id](element));
                         setParameter(element, "ThroatLength", subregionThroatLength[id](element));
                     }
                 }
@@ -435,7 +435,7 @@ private:
             };
         };
 
-        const Scalar fixedPoreRadius = getParamFromGroup<Scalar>(paramGroup_, prefix + "PoreRadius", -1.0);
+        const Scalar fixedPoreRadius = getParamFromGroup<Scalar>(paramGroup_, prefix + "PoreInscribedRadius", -1.0);
         // return random radius according to a user-specified distribution
         if (fixedPoreRadius <= 0.0)
         {
@@ -443,12 +443,13 @@ private:
             const auto seed = getParamFromGroup<unsigned int>(paramGroup_, prefix + "ParameterRandomNumberSeed", std::random_device{}());
             generator.seed(seed);
 
-            const auto type = getParamFromGroup<std::string>(paramGroup_, prefix + "ParameterType");
+            const auto type = getParamFromGroup<std::string>(paramGroup_, prefix + "ParameterType", "lognormal");
             if (type == "lognormal")
             {
                 // if we use a lognormal distribution, get the mean and standard deviation from input file
-                const Scalar meanPoreRadius = getParamFromGroup<Scalar>(paramGroup_, prefix + "MeanPoreRadius");
-                const Scalar stddevPoreRadius = getParamFromGroup<Scalar>(paramGroup_, prefix + "StandardDeviationPoreRadius");
+                const auto [meanPoreRadius, stddevPoreRadius] = getDistributionInputParams_("Lognormal", prefix,
+                                                                                            "MeanPoreInscribedRadius",
+                                                                                            "StandardDeviationPoreInscribedRadius");
                 const Scalar variance = stddevPoreRadius*stddevPoreRadius;
 
                 using std::log;
@@ -462,12 +463,11 @@ private:
             else if (type == "uniform")
             {
                 // if we use a uniform distribution, get the min and max from input file
-                const Scalar minPoreRadius = getParamFromGroup<Scalar>(paramGroup_, prefix + "MinPoreRadius");
-                const Scalar maxPoreRadius = getParamFromGroup<Scalar>(paramGroup_, prefix + "MaxPoreRadius");
-
+                const auto [minPoreRadius, maxPoreRadius] = getDistributionInputParams_("Uniform", prefix,
+                                                                                        "MinPoreInscribedRadius",
+                                                                                        "MaxPoreInscribedRadius");
                 Dumux::SimpleUniformDistribution<> poreRadiusDist(minPoreRadius, maxPoreRadius);
                 return generateFunction(poreRadiusDist);
-
             }
             else
                 DUNE_THROW(Dune::InvalidStateException, "Unknown parameter type " << type);
@@ -481,6 +481,26 @@ private:
         }
     }
 
+    // print helpful error message if params are not properly provided
+    std::array<Scalar, 2> getDistributionInputParams_(const std::string& distributionName,
+                                                      const std::string& prefix,
+                                                      const std::string& paramName0,
+                                                      const std::string& paramName1) const
+    {
+        try
+        {
+            return std::array{getParamFromGroup<Scalar>(paramGroup_, prefix + paramName0),
+                              getParamFromGroup<Scalar>(paramGroup_, prefix + paramName1)};
+        }
+        catch (const Dumux::ParameterException& e)
+        {
+            std::cout << "\n" << distributionName << " pore-size distribution needs input parameters "
+                      << prefix + paramName0 << " and " << prefix + paramName1 << ".\n"
+                      << "Alternatively, use " << prefix << "PoreInscribedRadius to set a fixed inscribed pore radius." << std::endl;
+            DUNE_THROW(Dumux::ParameterException, e.what());
+        }
+    }
+
     template <class GetParameter>
     auto poreVolumeGenerator_(const GetParameter& getParameter) const
     {
@@ -531,16 +551,16 @@ private:
 
     // returns a lambda taking a element and returning a radius
     template <class GetParameter>
-    auto throatRadiusGenerator_(const int subregionId, const GetParameter& getParameter) const
+    auto throatInscribedRadiusGenerator_(const int subregionId, const GetParameter& getParameter) const
     {
         // adapt the parameter name if there are subregions
         const std::string prefix = subregionId < 0 ? "Grid." : "Grid.Subregion" + std::to_string(subregionId) + ".";
 
         // check for a user-specified fixed throat radius
-        const Scalar inputThroatRadius = getParamFromGroup<Scalar>(paramGroup_, prefix + "ThroatRadius", -1.0);
+        const Scalar inputThroatInscribedRadius = getParamFromGroup<Scalar>(paramGroup_, prefix + "ThroatInscribedRadius", -1.0);
 
         // shape parameter for calculation of throat radius
-        const Scalar throatN = getParamFromGroup<Scalar>(paramGroup_, prefix + "ThroatRadiusN", 0.1);
+        const Scalar throatN = getParamFromGroup<Scalar>(paramGroup_, prefix + "ThroatInscribedRadiusN", 0.1);
 
         return [=](const Element& element)
         {
@@ -548,8 +568,8 @@ private:
             const std::array<Vertex, 2> vertices = {element.template subEntity<dim>(0), element.template subEntity<dim>(1)};
 
             // the element parameters (throat radius and length)
-            if (inputThroatRadius > 0.0)
-                return inputThroatRadius;
+            if (inputThroatInscribedRadius > 0.0)
+                return inputThroatInscribedRadius;
             else
             {
                 const Scalar poreRadius0 = getParameter(vertices[0], "PoreInscribedRadius");

examples/porenetwork_upscaling/params.input

@@ -10,8 +10,8 @@ UpperRight = 4e-4 4e-4 4e-4
 NumPores = 20 20 20
 
 ParameterType = lognormal
-MeanPoreRadius = 1e-5
-StandardDeviationPoreRadius = 4e-6
+MeanPoreInscribedRadius = 1e-5
+StandardDeviationPoreInscribedRadius = 4e-6
 PoreGeometry = Sphere
 ThroatCrossSectionShape = Square
 ParameterRandomNumberSeed = 1

test/io/gridmanager/test_pnm_gridmanager-constant-params.input

@@ -5,9 +5,9 @@ Name = constant-params
 UpperRight = 1e-3 1e-3 1e-3
 NumPores = 5 5 5
 
-PoreRadius = 1e-5
+PoreInscribedRadius = 1e-5
 PoreGeometry = Sphere
-ThroatRadius = 1e-6
+ThroatInscribedRadius = 1e-6
 ThroatLength = 1e-4
 
 BoundaryFaceMarker = 2 3 1 1 1 1
@@ -28,9 +28,9 @@ Sanitize = true
 UpperRight = 1e-3 1e-3
 NumPores = 5 5
 
-PoreRadius = 1e-5
+PoreInscribedRadius = 1e-5
 PoreGeometry = Cube
-ThroatRadius = 1e-6
+ThroatInscribedRadius = 1e-6
 ThroatLength = 1e-4
 
 BoundaryFaceMarker = 2 3 1 1
@@ -50,10 +50,10 @@ Sanitize = true
 UpperRight = 1e-3
 NumPores = 20
 
-PoreRadius = 1e-5
+PoreInscribedRadius = 1e-5
 PoreGeometry = Cylinder
 PoreHeight = 1e-5
-ThroatRadius = 1e-6
+ThroatInscribedRadius = 1e-6
 ThroatLength = 1e-4
 
 BoundaryFaceMarker = 1 1

test/io/gridmanager/test_pnm_gridmanager-random-params.input

@@ -6,8 +6,8 @@ UpperRight = 1e-3 1e-3 1e-3
 NumPores = 5 5 5
 
 ParameterType = lognormal
-MeanPoreRadius = 1e-5
-StandardDeviationPoreRadius = 3e-6
+MeanPoreInscribedRadius = 1e-5
+StandardDeviationPoreInscribedRadius = 3e-6
 PoreGeometry = Sphere
 
 BoundaryFaceMarker = 2 3 1 1 1 1
@@ -29,8 +29,8 @@ UpperRight = 1e-3 1e-3
 NumPores = 5 5
 
 ParameterType = lognormal
-MeanPoreRadius = 1e-5
-StandardDeviationPoreRadius = 3e-6
+MeanPoreInscribedRadius = 1e-5
+StandardDeviationPoreInscribedRadius = 3e-6
 PoreGeometry = Cube
 
 BoundaryFaceMarker = 2 3 1 1
@@ -52,8 +52,8 @@ UpperRight = 1e-3
 NumPores = 20
 
 ParameterType = lognormal
-MeanPoreRadius = 1e-5
-StandardDeviationPoreRadius = 3e-6
+MeanPoreInscribedRadius = 1e-5
+StandardDeviationPoreInscribedRadius = 3e-6
 PoreGeometry = Cylinder
 PoreHeight = 1e-5
 

test/io/gridmanager/test_pnm_subgriddata.input

@@ -3,10 +3,10 @@ NumPores = 10 10 10
 UpperRight = 1e-3 1e-3 1e-3
 NumSubregions = 1
 
-PoreRadius = 1e-5
+PoreInscribedRadius = 1e-5
 PoreGeometry = Sphere
 ThroatCrossSectionShape = Circle
 
 Subregion0.LowerLeft = 0 0 0
 Subregion0.UpperRight = 0.5e-3 0.5e-3 0.5e-3
-Subregion0.PoreRadius = 2e-5
+Subregion0.PoreInscribedRadius = 2e-5

test/io/gridmanager/test_remove-troats-on-boundary.input

@@ -6,7 +6,7 @@ WriteVTK = false
 UpperRight = 1e-3 1e-3
 NumPores = 5 5
 
-PoreRadius = 1e-4
+PoreInscribedRadius = 1e-4
 ThroatRadius = 1e-5
 PoreGeometry = Sphere
 

test/porenetwork/1p/grids/pnm_converted.dgf

 DGF
 % Vertex parameters: PoreInscribedRadius PoreLabel
-% Element parameters: ThroatRadius ThroatLength ThroatLabel
+% Element parameters: ThroatInscribedRadius ThroatLength ThroatLabel
 Vertex % Coordinates and volumes of the pore bodies
 parameters 2
 1 1 4 0.0002263 2.0

test/porenetwork/1p/params_hydrostatic_pressure.input

@@ -4,8 +4,8 @@ ThroatCrossSectionShape = Square
 
 UpperRight = 1e-3 1e-3 1e-3
 NumPores = 4 4 4
-PoreRadius = 2e-5
-ThroatRadius = 2e-6
+PoreInscribedRadius = 2e-5
+ThroatInscribedRadius = 2e-6
 BoundaryFaceMarker = 1 1 1 1 2 1
 PriorityList = 4 5 0 1 2 3
 

test/porenetwork/2p/static/params.input

@@ -4,8 +4,8 @@ NumPores = 10 10 10
 PoreGeometry = Cube
 ThroatCrossSectionShape = Square
 ParameterType = lognormal
-MeanPoreRadius = 4.5e-5
-StandardDeviationPoreRadius = 3e-6
+MeanPoreInscribedRadius = 4.5e-5
+StandardDeviationPoreInscribedRadius = 3e-6
 BoundaryFaceMarker = 2 3 1 1 1 1
 MinThroatLength = 1e-9
 DeletionProbability = 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9

test/references/pnm_gridmanager-1d-constant.vtp

@@ -16,8 +16,8 @@
           -1 -1 -1 -1 -1 -1 -1 1
         </DataArray>
       </PointData>
-      <CellData Scalars="throatRadius">
-        <DataArray type="Float32" Name="throatRadius" NumberOfComponents="1" format="ascii">
+      <CellData Scalars="throatInscribedRadius">
+        <DataArray type="Float32" Name="throatInscribedRadius" NumberOfComponents="1" format="ascii">
           1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06
           1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06
         </DataArray>

test/references/pnm_gridmanager-1d-random.vtp

@@ -16,8 +16,8 @@
           -1 -1 -1 -1 -1 -1 -1 1
         </DataArray>
       </PointData>
-      <CellData Scalars="throatRadius">
-        <DataArray type="Float32" Name="throatRadius" NumberOfComponents="1" format="ascii">
+      <CellData Scalars="throatInscribedRadius">
+        <DataArray type="Float32" Name="throatInscribedRadius" NumberOfComponents="1" format="ascii">
           4.14377e-06 4.74707e-06 4.78717e-06 5.06117e-06 4.85118e-06 5.15151e-06 5.76601e-06 4.33998e-06 4.34305e-06 5.23155e-06 5.23184e-06 9.47504e-06
           7.18404e-06 6.61131e-06 6.932e-06 7.54417e-06 4.15076e-06 4.13528e-06 5.6777e-06
         </DataArray>

test/references/pnm_gridmanager-2d-constant.vtp

@@ -16,8 +16,8 @@
           -1 -1 3 -1 -1 -1 3 1 2 1 1 3
         </DataArray>
       </PointData>
-      <CellData Scalars="throatRadius">
-        <DataArray type="Float32" Name="throatRadius" NumberOfComponents="1" format="ascii">
+      <CellData Scalars="throatInscribedRadius">
+        <DataArray type="Float32" Name="throatInscribedRadius" NumberOfComponents="1" format="ascii">
           1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06
           1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06
           1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06

test/references/pnm_gridmanager-2d-random.vtp

@@ -16,8 +16,8 @@
           -1 -1 3 -1 -1 -1 3 1 2 1 1 3
         </DataArray>
       </PointData>
-      <CellData Scalars="throatRadius">
-        <DataArray type="Float32" Name="throatRadius" NumberOfComponents="1" format="ascii">
+      <CellData Scalars="throatInscribedRadius">
+        <DataArray type="Float32" Name="throatInscribedRadius" NumberOfComponents="1" format="ascii">
           4.11658e-06 4.70756e-06 4.12337e-06 4.81161e-06 4.09397e-06 5.71113e-06 5.03676e-06 5.10376e-06 4.28953e-06 6.9563e-06 5.18869e-06 6.48355e-06
           9.31931e-06 5.8116e-06 6.58115e-06 7.10058e-06 5.25119e-06 6.98718e-06 6.5364e-06 5.18384e-06 8.64324e-06 6.8266e-06 4.12387e-06 7.58904e-06
           4.12097e-06 5.64464e-06 5.61358e-06 7.12156e-06 7.21317e-06 4.12475e-06 8.66678e-06 4.12122e-06 7.35925e-06 4.12238e-06 7.42437e-06

test/references/pnm_gridmanager-3d-constant.vtp

@@ -25,8 +25,8 @@
           1 1 2 1 3 1 1 2 3 1 1
         </DataArray>
       </PointData>
-      <CellData Scalars="throatRadius">
-        <DataArray type="Float32" Name="throatRadius" NumberOfComponents="1" format="ascii">
+      <CellData Scalars="throatInscribedRadius">
+        <DataArray type="Float32" Name="throatInscribedRadius" NumberOfComponents="1" format="ascii">
           1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06
           1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06
           1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06 1e-06

test/references/pnm_gridmanager-3d-random.vtp

@@ -25,8 +25,8 @@
           1 1 2 1 3 1 1 2 3 1 1
         </DataArray>
       </PointData>
-      <CellData Scalars="throatRadius">
-        <DataArray type="Float32" Name="throatRadius" NumberOfComponents="1" format="ascii">
+      <CellData Scalars="throatInscribedRadius">
+        <DataArray type="Float32" Name="throatInscribedRadius" NumberOfComponents="1" format="ascii">
           4.11658e-06 4.70756e-06 4.31042e-06 6.9563e-06 5.16132e-06 5.18517e-06 4.31144e-06 5.7185e-06 4.31344e-06 7.44744e-06 4.12163e-06 5.61949e-06
           7.21941e-06 7.20563e-06 8.31374e-06 7.59153e-06 7.33705e-06 6.99583e-06 5.75207e-06 7.54291e-06 4.31091e-06 4.10902e-06 5.81255e-06 8.10476e-06
           8.10679e-06 5.18072e-06 1.22845e-05 4.10978e-06 5.08512e-06 7.11641e-06 7.20984e-06 7.21875e-06 6.25225e-06 4.9708e-06 6.30755e-06 6.10565e-06