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/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)'
 
 #------------------------------------------------------------------------------