TUT: basic, IO, preProcessing, VV: clean up tutorials

- TUT: mesh: add missing SnakeRiverCanyon files
- TUT: mesh: add missing cp source in a foamyHexMesh tutorial

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/Allrun

@@ -3,8 +3,8 @@ cd "${0%/*}" || exit                                # Run from this directory
 . ${WM_PROJECT_DIR:?}/bin/tools/RunFunctions        # Tutorial run functions
 #------------------------------------------------------------------------------
 
-(cd precursor && foamRunTutorials)
+(cd precursor && ./Allrun)
 
-(cd successor && foamRunTutorials)
+(cd successor && ./Allrun)
 
 #------------------------------------------------------------------------------

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/Allclean

@@ -5,9 +5,10 @@ cd "${0%/*}" || exit                                # Run from this directory
 
 cleanCase0
 
-rm -f constant/fvOptions
-rm -f constant/turbulenceProperties
-rm -rf system/atm-Koblitz-2013
+rm -rf 0.orig
+rm -rf system
+rm -rf constant
+rm -rf results
 rm -rf plots
 
 #------------------------------------------------------------------------------

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/Allrun

@@ -4,33 +4,123 @@ cd "${0%/*}" || exit                                # Run from this directory
 . ${WM_PROJECT_DIR:?}/bin/tools/CleanFunctions      # Tutorial clean functions
 #------------------------------------------------------------------------------
 
-./Allrun.pre
+# settings
 
-# Settings
-RASmodel="kEpsilon"    # "kOmegaSST"
-stability="neutral"
-Lmax="41.8"
-qPlant="0.0"
+    # operand setups (only neutral stability)
+    setups="
+    kEpsilon
+    kOmegaSST
+    "
 
-echo "  # Computations for the atmopsheric stability = $stability:"
-echo "    ## Lmax = $Lmax [m], qPlant = $qPlant [-]"
+    # flag to enable computations in parallel mode
+    parallel=true
+
+
+#------------------------------------------------------------------------------
+#######################################
+# Collect results and mesh into a given path
+# and clean the case for the next run
+# Arguments:
+#    $1 = Path to move results
+# Outputs:
+#    Writes info to stdout
+#######################################
+collect() {
+
+    [ $# -eq 0 ] && { echo "Usage: $0 dir-model"; exit 1; }
+
+    collection="$1"
+
+    dirResult=results/"$collection"
+    dirSettings="$dirResult"/settings
+
+    if [ ! -d "$dirResult" ]
+    then
+
+        echo "      # Collecting results and settings into $dirResult"
+
+        mkdir -p "$dirResult"
+        mkdir -p "$dirSettings"
+
+        mv -f $(foamListTimes) "$dirResult"
+        [ -d postProcessing ] && mv -f postProcessing "$dirResult"
+        [ -d processor0 ] && mv -f processor* "$dirResult"
+        mv -f log.* "$dirResult"
+        cp -f system/{fv*,controlDict} constant/*Properties "$dirSettings"
+        mv -f 0/ "$dirSettings"
+        [ -d constant ] && mv -f constant "$dirResult"
+        [ -d system ] && mv -f system "$dirResult"
+
+        echo "      # Cleaning up the case"
+
+        cleanTimeDirectories
+        cleanPostProcessing
+
+    else
+
+        echo "      # Directory $dirResult already exists"
+        echo "      # Skipping the computation"
+
+    fi
+}
 
 
 #------------------------------------------------------------------------------
 
-sed -e "s|RAS_MODEL|$RASmodel|g" \
-    constant/turbulenceProperties.template \
-  > constant/turbulenceProperties
-sed -e "s|L_MAX|$Lmax|g" constant/fvOptions.template > constant/fvOptions
-sed -e "s|Q_PLANT|$qPlant|g" 0/qPlant.template > 0/qPlant
-rm -f 0/qPlant.template
+for setup in $setups
+do
 
-runApplication renumberMesh -overwrite
+    echo ""
+    echo "# Computations for the setup: $setup"
+    echo ""
 
-runApplication $(getApplication)
+    dirSetup="setups.orig/$setup"
+
+    if [ ! -d "$dirSetup" ]
+    then
+        echo "Setup directory: $dirSetup" \
+             "could not be found - skipping execution" 1>&2
+        exit 1
+    fi
+
+    cp -rfL "$dirSetup/0.orig" .
+    cp -rfL "$dirSetup/constant" .
+    cp -rfL "$dirSetup/system" .
+    cp -rf 0.orig/ 0/
+
+    if [ ! -d constant/polyMesh ]
+    then
+
+        runApplication blockMesh
+
+        runApplication renumberMesh -overwrite -constant
+
+        runApplication checkMesh -allTopology -allGeometry -constant
+
+    fi
+
+    if [ "$parallel" = true ]
+    then
+
+        runApplication decomposePar
+
+        runParallel $(getApplication)
+
+        runApplication reconstructPar
+
+    else
+
+        runApplication $(getApplication)
+
+    fi
+
+    # Scale up all the dimensions of the precursor computational domain
+    # to encapsulate the successor domain, so that mapFields can be used
+    runApplication transformPoints -scale '(10 10 1)' -translate '(0 0 20)'
+
+    collect "$setup"
+
+done
 
-# Scale up all the dimensions of the precursor computational domain
-# to encapsulate the successor domain, so that mapFields can be used
-runApplication transformPoints -scale '(10 10 1)' -translate '(0 0 20)'
 
 #------------------------------------------------------------------------------

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/Allrun.pre

@@ -1,10 +0,0 @@
-#!/bin/sh
-cd "${0%/*}" || exit                                # Run from this directory
-. ${WM_PROJECT_DIR:?}/bin/tools/RunFunctions        # Tutorial run functions
-#------------------------------------------------------------------------------
-
-restore0Dir
-
-runApplication blockMesh
-
-#------------------------------------------------------------------------------

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/plot

@@ -3,54 +3,65 @@ cd "${0%/*}" || exit                                # Run from this directory
 . ${WM_PROJECT_DIR:?}/bin/tools/RunFunctions        # Tutorial run functions
 #------------------------------------------------------------------------------
 
-# Benchmark dataset:
-#  Lettau, H. (1950).
-#  A re-examination of the "Leipzig wind profile" considering some
-#  relations between wind and turbulence in the frictional layer.
-#  Tellus, 2(2), 125-129.
-#  DOI:10.3402/tellusa.v2i2.8534
-#
-#  Koblitz, T. (2013).
-#  CFD Modeling of Non-Neutral Atmospheric Boundary Layer Conditions.
-#  DTU Wind Energy. DTU Wind Energy PhD, No. 0019(EN).
-#  Figure 4.1
+# settings
+
+    # operand setups
+    setups="
+    kEpsilon-neutral-stability
+    kOmegaSST-neutral-stability
+    "
+
+
 #------------------------------------------------------------------------------
 
-plotU() {
-    sample=$1
+plot_u_vs_z() {
 
-    echo "  Plotting the ground-normal streamwise flow speed profile."
+    echo "  # Plots for the ground-normal streamwise flow speed profile"
+
+    setup="$1"
+    endTime="$2"
+
+    benchmarkFile="$FOAM_TUTORIALS/resources/dataset/atm-Koblitz-2013/u-z-Leipzig.dat"
+    sampleFile="results/$setup/postProcessing/sampleLines/$endTime/lineZ1_U.xy"
+    image="plots/$setup/u_z.png"
 
-    outName="plots/u-z.png"
     gnuplot<<PLT_U
     set terminal pngcairo font "helvetica,20" size 600, 1000
-    set xrange [0:25]
-    set yrange [0:3000]
     set grid
     set key left top
+    set xrange [0:25]
+    set yrange [0:3000]
     set key samplen 2
     set key spacing 0.75
     set xlabel "u [m/s]"
     set ylabel "z [m]"
     set offset .05, .05
-    set output "$outName"
+    set output "$image"
 
-    bench="system/atm-Koblitz-2013/u-z-Leipzig.dat"
-    sample="$sample"
+    # Benchmark - experimental
+        benchmark="$benchmarkFile"
+
+    # OpenFOAM
+        samples="$sampleFile"
 
     plot \
-        bench every ::0::16 u 1:2 t "Leipzig" w p ps 2 pt 6 lc rgb "#000000", \
-        sample u 2:1 t "Neutral" w l lw 2 lc rgb "#D55E00"
+        benchmark every ::0::16 u 1:2 t "Leipzig" w p ps 2 pt 6 lc rgb "#000000", \
+        samples u 2:1 t "OpenFOAM" w l lw 2 lc rgb "#D55E00"
 PLT_U
 }
 
 
-plotV() {
-    sample=$1
+plot_v_vs_z() {
 
-    echo "  Plotting the ground-normal spanwise flow speed profile."
+    echo "  # Plots for the ground-normal spanwise flow speed profile"
+
+    setup="$1"
+    endTime="$2"
+
+    benchmarkFile="$FOAM_TUTORIALS/resources/dataset/atm-Koblitz-2013/u-z-Leipzig.dat"
+    sampleFile="results/$setup/postProcessing/sampleLines/$endTime/lineZ1_U.xy"
+    image="plots/$setup/v_z.png"
 
-    outName="plots/v-z.png"
     gnuplot<<PLT_V
     set terminal pngcairo font "helvetica,20" size 600, 1000
     set xrange [-1:6]
@@ -62,14 +73,17 @@ plotV() {
     set xlabel "v [m/s]"
     set ylabel "z [m]"
     set offset .2, .05
-    set output "$outName"
+    set output "$image"
 
-    bench="system/atm-Koblitz-2013/u-z-Leipzig.dat"
-    sample="$sample"
+    # Benchmark - experimental
+        benchmark="$benchmarkFile"
+
+    # OpenFOAM
+        samples="$sampleFile"
 
     plot \
-        bench every ::17::35 u 1:2 t "Leipzig" w p ps 2 pt 6 lc rgb "#000000", \
-        sample u 3:1 t "Neutral" w l lw 2 lc rgb "#D55E00"
+        benchmark every ::17::35 u 1:2 t "Leipzig" w p ps 2 pt 6 lc rgb "#000000", \
+        samples u 3:1 t "OpenFOAM" w l lw 2 lc rgb "#D55E00"
 PLT_V
 }
 
@@ -88,23 +102,29 @@ command -v awk >/dev/null || {
     exit 1
 }
 
-# The latestTime in postProcessing/samples
-timeDir=$(foamListTimes -case postProcessing/samples -latestTime 2>/dev/null)
-[ -n "$timeDir" ] || {
-    echo "No results found in postProcessing - skipping graph creation" 1>&2
-    exit 1
-}
-timeDir="postProcessing/samples/$timeDir"
 
-# Settings
-sample="$timeDir/lineZ1_U.xy"
-stability="neutral"
+#------------------------------------------------------------------------------
 
-# Postprocessing
-mkdir -p plots
-cp -rf $FOAM_TUTORIALS/resources/dataset/atm-Koblitz-2013 system/.
-plotU $sample
-plotV $sample
+for setup in $setups
+do
+
+    echo ""
+    echo "# Plots for the setup: $setup"
+    echo ""
+
+    dirPlots="plots/$setup"
+    [ -d "$dirPlots" ] || mkdir -p "$dirPlots"
+
+    endTime=$(\
+        foamDictionary results/$setup/settings/controlDict \
+            -disableFunctionEntries -entry endTime -value \
+        )
+
+    plot_u_vs_z "$setup" "$endTime"
+
+    plot_v_vs_z "$setup" "$endTime"
+
+done
 
 
 #------------------------------------------------------------------------------

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/common/0.orig/p_rgh

@@ -20,7 +20,7 @@ internalField   uniform 0.0;
 
 boundaryField
 {
-    "bottom|top"
+    "(bottom|top)"
     {
        type             fixedFluxPressure;
        rho              rhok;

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/common/system/controlDict

@@ -49,7 +49,7 @@ runTimeModifiable false;
 
 functions
 {
-    #includeFunc "samples"
+    #includeFunc "sampleLines"
 }
 
 

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/common/system/decomposeParDict

@@ -0,0 +1,22 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2012                                 |
+|   \\  /    A nd           | Website:  www.openfoam.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      decomposeParDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+numberOfSubdomains 2;
+
+method          scotch;
+
+
+// ************************************************************************* //

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/T

@@ -0,0 +1 @@
+../../common/0.orig/T

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/U

@@ -0,0 +1 @@
+../../common/0.orig/U

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/alphat

@@ -0,0 +1 @@
+../../common/0.orig/alphat

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/k

@@ -0,0 +1 @@
+../../common/0.orig/k

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/leafAreaDensity

@@ -0,0 +1 @@
+../../common/0.orig/leafAreaDensity

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/nut

@@ -0,0 +1 @@
+../../common/0.orig/nut

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/p_rgh

@@ -0,0 +1 @@
+../../common/0.orig/p_rgh

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/plantCd

@@ -0,0 +1 @@
+../../common/0.orig/plantCd

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/0.orig/qPlant

@@ -16,7 +16,7 @@ FoamFile
 
 dimensions      [0 2 -3 0 0 0 0];
 
-internalField  uniform  Q_PLANT;
+internalField   uniform 0;
 
 boundaryField
 {

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/constant/fvOptions

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  v2012                                 |
+|  \\    /   O peration     | Version:  com                                   |
 |   \\  /    A nd           | Website:  www.openfoam.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/
@@ -16,87 +16,80 @@ FoamFile
 
 pressureGradient
 {
-    type                vectorSemiImplicitSource;
-    volumeMode          specific;
-    selectionMode       all;
+    type            vectorSemiImplicitSource;
+    volumeMode      specific;
+    selectionMode   all;
     injectionRateSuSp
     {
-        U ((0 1.978046e-03  0) 0);
+        U               ( ( 0 0.00197805 0 ) 0 );
     }
 }
 
-
 atmCoriolisUSource1
 {
-    type                atmCoriolisUSource;
+    type            atmCoriolisUSource;
     atmCoriolisUSourceCoeffs
     {
         selectionMode   all;
-        Omega           (0 0 5.65156e-05);
+        Omega           ( 0 0 5.65156e-05 );
     }
 }
 
-
 atmAmbientTurbSource1
 {
-    type                atmAmbientTurbSource;
+    type            atmAmbientTurbSource;
     atmAmbientTurbSourceCoeffs
     {
         selectionMode   all;
-        kAmb            1.0e-04;
+        kAmb            0.0001;
         epsilonAmb      7.208e-08;
     }
 }
 
-
 atmBuoyancyTurbSource1
 {
-    type                atmBuoyancyTurbSource;
+    type            atmBuoyancyTurbSource;
     atmBuoyancyTurbSourceCoeffs
     {
         selectionMode   all;
         rho             rho;
-        Lmax            L_MAX;
-        beta            3.3e-03;
+        Lmax            41.8;
+        beta            0.0033;
     }
 }
 
-
 atmLengthScaleTurbSource1
 {
-    type                atmLengthScaleTurbSource;
+    type            atmLengthScaleTurbSource;
     atmLengthScaleTurbSourceCoeffs
     {
         selectionMode   all;
-        Lmax            L_MAX;
-        n               3.0;
+        Lmax            41.8;
+        n               3;
     }
 }
 
-
 atmPlantCanopyUSource1
 {
-    type                atmPlantCanopyUSource;
+    type            atmPlantCanopyUSource;
     atmPlantCanopyUSourceCoeffs
     {
         selectionMode   all;
     }
 }
 
-
 atmPlantCanopyTSource1
 {
-    type                atmPlantCanopyTSource;
+    type            atmPlantCanopyTSource;
     atmPlantCanopyTSourceCoeffs
     {
         selectionMode   all;
     }
 }
 
-
 atmPlantCanopyTurbSource1
 {
-    type             atmPlantCanopyTurbSource;
+    type            atmPlantCanopyTurbSource;
     atmPlantCanopyTurbSourceCoeffs
     {
         selectionMode   all;

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/constant/g

@@ -0,0 +1 @@
+../../common/constant/g

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/constant/transportProperties

@@ -0,0 +1 @@
+../../common/constant/transportProperties

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/constant/turbulenceProperties

@@ -18,14 +18,15 @@ simulationType      RAS;
 
 RAS
 {
-    RASModel        RAS_MODEL;
+    RASModel        kEpsilon;
+
     turbulence      on;
+
     printCoeffs     on;
 
-    RAS_MODELCoeffs
+    kEpsilonCoeffs
     {
         Cmu             0.09;
-        betaStar        0.09;
         sigmaEps        1.30;
         sigmaK          1;
         C1              1.44;

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kEpsilon/system

@@ -0,0 +1 @@
+../common/system

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/T

@@ -0,0 +1 @@
+../../common/0.orig/T

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/U

@@ -0,0 +1 @@
+../../common/0.orig/U

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/alphat

@@ -0,0 +1 @@
+../../common/0.orig/alphat

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/k

@@ -0,0 +1 @@
+../../common/0.orig/k

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/leafAreaDensity

@@ -0,0 +1 @@
+../../common/0.orig/leafAreaDensity

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/nut

@@ -0,0 +1 @@
+../../common/0.orig/nut

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/p_rgh

@@ -0,0 +1 @@
+../../common/0.orig/p_rgh

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/plantCd

@@ -0,0 +1 @@
+../../common/0.orig/plantCd

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/0.orig/qPlant

@@ -0,0 +1,36 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2012                                 |
+|   \\  /    A nd           | Website:  www.openfoam.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    object      qPlant;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -3 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    "(bottom|top)"
+    {
+        type            fixedValue;
+        value           uniform 0;
+    }
+
+    "(inlet|outlet|left|right)"
+    {
+        type            cyclic;
+    }
+}
+
+
+// ************************************************************************* //

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/constant/fvOptions

@@ -0,0 +1,101 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  com                                   |
+|   \\  /    A nd           | Website:  www.openfoam.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      fvOptions;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+pressureGradient
+{
+    type            vectorSemiImplicitSource;
+    volumeMode      specific;
+    selectionMode   all;
+    injectionRateSuSp
+    {
+        U               ( ( 0 0.00197805 0 ) 0 );
+    }
+}
+
+atmCoriolisUSource1
+{
+    type            atmCoriolisUSource;
+    atmCoriolisUSourceCoeffs
+    {
+        selectionMode   all;
+        Omega           ( 0 0 5.65156e-05 );
+    }
+}
+
+atmAmbientTurbSource1
+{
+    type            atmAmbientTurbSource;
+    atmAmbientTurbSourceCoeffs
+    {
+        selectionMode   all;
+        kAmb            0.0001;
+        epsilonAmb      7.208e-08;
+    }
+}
+
+atmBuoyancyTurbSource1
+{
+    type            atmBuoyancyTurbSource;
+    atmBuoyancyTurbSourceCoeffs
+    {
+        selectionMode   all;
+        rho             rho;
+        Lmax            41.8;
+        beta            0.0033;
+    }
+}
+
+atmLengthScaleTurbSource1
+{
+    type            atmLengthScaleTurbSource;
+    atmLengthScaleTurbSourceCoeffs
+    {
+        selectionMode   all;
+        Lmax            41.8;
+        n               3;
+    }
+}
+
+atmPlantCanopyUSource1
+{
+    type            atmPlantCanopyUSource;
+    atmPlantCanopyUSourceCoeffs
+    {
+        selectionMode   all;
+    }
+}
+
+atmPlantCanopyTSource1
+{
+    type            atmPlantCanopyTSource;
+    atmPlantCanopyTSourceCoeffs
+    {
+        selectionMode   all;
+    }
+}
+
+atmPlantCanopyTurbSource1
+{
+    type            atmPlantCanopyTurbSource;
+    atmPlantCanopyTurbSourceCoeffs
+    {
+        selectionMode   all;
+        rho             rho;
+    }
+}
+
+
+// ************************************************************************* //

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/constant/g

@@ -0,0 +1 @@
+../../common/constant/g

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/constant/transportProperties

@@ -0,0 +1 @@
+../../common/constant/transportProperties

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/constant/turbulenceProperties

@@ -0,0 +1,37 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2012                                 |
+|   \\  /    A nd           | Website:  www.openfoam.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      turbulenceProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+simulationType      RAS;
+
+RAS
+{
+    RASModel        kOmegaSST;
+
+    turbulence      on;
+
+    printCoeffs     on;
+
+    kOmegaSSTCoeffs
+    {
+        betaStar        0.09;
+        sigmaK          1;
+        C1              1.44;
+        C2              1.92;
+    }
+}
+
+
+// ************************************************************************* //

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/precursor/setups.orig/kOmegaSST/system

@@ -0,0 +1 @@
+../common/system

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/successor/Allclean

@@ -5,7 +5,10 @@ cd "${0%/*}" || exit                                # Run from this directory
 
 cleanCase0
 
-rm -rf constant/polyMesh
-rm -f constant/turbulenceProperties
+rm -rf 0.orig
+rm -rf system
+rm -rf constant
+rm -rf results
+rm -rf plots
 
-#------------------------------------------------------------------------------
+#------------------------------------------------------------------------------

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/successor/Allrun

@@ -1,26 +1,130 @@
 #!/bin/sh
 cd "${0%/*}" || exit                                # Run from this directory
 . ${WM_PROJECT_DIR:?}/bin/tools/RunFunctions        # Tutorial run functions
+. ${WM_PROJECT_DIR:?}/bin/tools/CleanFunctions      # Tutorial clean functions
 #------------------------------------------------------------------------------
 
-RASModel="kEpsilon"    # "kOmegaSST"
+# settings
 
-sed -e "s|RAS_MODEL|$RASModel|g" \
-    constant/turbulenceProperties.template \
-  > constant/turbulenceProperties
+    # operand setups (only neutral stability)
+    setups="
+    kEpsilon
+    kOmegaSST
+    "
 
-restore0Dir
+    # flag to enable computations in parallel mode
+    parallel=true
+
+
+#------------------------------------------------------------------------------
+
+#######################################
+# Collect results and mesh into a given path
+# and clean the case for the next run
+# Arguments:
+#    $1 = Path to move results
+# Outputs:
+#    Writes info to stdout
+#######################################
+collect() {
+
+    [ $# -eq 0 ] && { echo "Usage: $0 dir-model"; exit 1; }
+
+    collection="$1"
+
+    dirResult=results/"$collection"
+    dirSettings="$dirResult"/settings
+
+    if [ ! -d "$dirResult" ]
+    then
+
+        echo "      # Collecting results and settings into $dirResult"
+
+        mkdir -p "$dirResult"
+        mkdir -p "$dirSettings"
+
+        mv -f $(foamListTimes) "$dirResult"
+        [ -d postProcessing ] && mv -f postProcessing "$dirResult"
+        [ -d processor0 ] && mv -f processor* "$dirResult"
+        mv -f log.* "$dirResult"
+        cp -f system/{fv*,controlDict} constant/*Properties "$dirSettings"
+        mv -f 0/ "$dirSettings"
+        [ -d constant ] && mv -f constant "$dirResult"
+        [ -d system ] && mv -f system "$dirResult"
+
+        echo "      # Cleaning up the case"
+
+        cleanTimeDirectories
+        cleanPostProcessing
+
+    else
+
+        echo "      # Directory $dirResult already exists"
+        echo "      # Skipping the computation"
+
+    fi
+}
+
+
+#------------------------------------------------------------------------------
+
+for setup in $setups
+do
+
+    echo ""
+    echo "# Computations for the setup: $setup"
+    echo ""
+
+    dirSetup="setups.orig/$setup"
+
+    if [ ! -d "$dirSetup" ]
+    then
+        echo "Setup directory: $dirSetup" \
+             "could not be found - skipping execution" 1>&2
+        exit 1
+    fi
+
+    cp -rfL "$dirSetup/0.orig" .
+    cp -rfL "$dirSetup/constant" .
+    cp -rfL "$dirSetup/system" .
+    cp -rf 0.orig/ 0/
+
+    if [ ! -d constant/polyMesh ]
+    then
+
+        runApplication blockMesh
+
+        runApplication topoSet
+
+        runApplication createPatch -overwrite
+
+        runApplication renumberMesh -overwrite -constant
+
+        runApplication checkMesh -allTopology -allGeometry -constant
+
+    fi
+
+    runApplication mapFields \
+        ../precursor/results/"$setup" -sourceTime latestTime
+
+    if [ "$parallel" = true ]
+    then
+
+        runApplication decomposePar
+
+        runParallel $(getApplication)
+
+        runApplication reconstructPar
+
+    else
+
+        runApplication $(getApplication)
+
+    fi
+
+    collect "$setup"
+
+done
 
-cp -rf constant/polyMesh.orig constant/polyMesh
-
-runApplication mapFields ../precursor -sourceTime latestTime
-
-runApplication decomposePar -force
-
-runParallel renumberMesh -overwrite
-
-runParallel $(getApplication)
-
-runApplication reconstructPar -latestTime
 
 #------------------------------------------------------------------------------

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/successor/setups.orig/common/0.orig/T

@@ -48,12 +48,6 @@ boundaryField
     {
         type            slip;
     }
-
-    "(upperInterface|lowerInterface)"
-    {
-        type            cyclicAMI;
-        value           $internalField;
-    }
 }
 
 

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/successor/setups.orig/common/0.orig/U

@@ -44,12 +44,6 @@ boundaryField
     {
         type            slip;
     }
-
-    "(upperInterface|lowerInterface)"
-    {
-        type            cyclicAMI;
-        value           $internalField;
-    }
 }
 
 

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/successor/setups.orig/common/0.orig/alphat

@@ -49,12 +49,6 @@ boundaryField
     {
         type            slip;
     }
-
-    "(upperInterface|lowerInterface)"
-    {
-        type            cyclicAMI;
-        value           $internalField;
-    }
 }
 
 

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/successor/setups.orig/common/0.orig/k

@@ -44,12 +44,6 @@ boundaryField
     {
         type            slip;
     }
-
-    "(upperInterface|lowerInterface)"
-    {
-        type            cyclicAMI;
-        value           $internalField;
-    }
 }
 
 

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/successor/setups.orig/common/0.orig/nut

@@ -47,12 +47,6 @@ boundaryField
     {
         type            slip;
     }
-
-    "(upperInterface|lowerInterface)"
-    {
-        type            cyclicAMI;
-        value           $internalField;
-    }
 }
 
 

tutorials/verificationAndValidation/atmosphericModels/atmFlatTerrain/successor/setups.orig/common/0.orig/p_rgh

@@ -37,12 +37,6 @@ boundaryField
         type            fixedValue;
         value           uniform 10.123;
     }
-
-    "(upperInterface|lowerInterface)"
-    {
-        type            cyclicAMI;
-        value           $internalField;
-    }
 }