Tutorial case to create a recurrence matrix.

tutorials/rStatAnalysis/createRecurrenceMatrix/CFD/system/controlDict

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  2.3.0                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application     pisoFoam;
+
+startFrom       startTime;
+
+startTime       0;
+
+stopAt          endTime;
+
+endTime         0.00025;
+
+deltaT          0.00025;
+
+writeControl    timeStep;
+
+writeInterval   4000;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  6;
+
+writeCompression off;
+
+timeFormat      general;
+
+timePrecision   6;
+
+runTimeModifiable true;
+
+libs (
+ //     "libOpenFOAM.so"
+ //     "libsimpleSwakFunctionObjects.so"
+ //     "libswakFunctionObjects.so"
+ //     "libgroovyBC.so"
+ //     "libgroovyStandardBCs.so"
+     );
+
+functions
+{
+ 
+/*	probes1
+	{
+		type probes;
+
+		functionObjectLibs ("libsampling.so");
+
+		#include "probesDict";
+	}
+*/
+/*        temperatureSum
+        {
+            type patchExpression;
+	    outputControl   timeStep;
+	    outputInterval  40;
+            accumulations (
+                sum
+            );
+            patches (
+                outlet 
+            );
+            expression "phi*T";
+            verbose false;
+        }
+
+*/
+
+}
+
+// ************************************************************************* //

tutorials/rStatAnalysis/createRecurrenceMatrix/CFD/system/createPatchDict

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  2.3.0                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      createPatchDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// This application/dictionary controls:
+// - optional: create new patches from boundary faces (either given as
+//   a set of patches or as a faceSet)
+// - always: order faces on coupled patches such that they are opposite. This
+//   is done for all coupled faces, not just for any patches created.
+// - optional: synchronise points on coupled patches.
+
+// 1. Create cyclic:
+// - specify where the faces should come from
+// - specify the type of cyclic. If a rotational specify the rotationAxis
+//   and centre to make matching easier
+// - always create both halves in one invocation with correct 'neighbourPatch'
+//   setting.
+// - optionally pointSync true to guarantee points to line up.
+
+// 2. Correct incorrect cyclic:
+// This will usually fail upon loading:
+//  "face 0 area does not match neighbour 2 by 0.0100005%"
+//  " -- possible face ordering problem."
+// - in polyMesh/boundary file:
+//      - loosen matchTolerance of all cyclics to get case to load
+//      - or change patch type from 'cyclic' to 'patch'
+//        and regenerate cyclic as above
+
+
+// Do a synchronisation of coupled points after creation of any patches.
+// Note: this does not work with points that are on multiple coupled patches
+//       with transformations (i.e. cyclics).
+pointSync false;
+
+// Patches to create.
+patches
+(
+);
+
+// ************************************************************************* //

tutorials/rStatAnalysis/createRecurrenceMatrix/CFD/system/decomposeParDict

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+/*-------------------------------*- C++ -*---------------------------------*\
+|    =========                                                              |
+|    \\      /     OpenFOAM                                                 |
+|     \\    /                                                               |
+|      \\  /       The Open Source CFD Toolbox                              |
+|       \\/                                        http://www.OpenFOAM.org  |
+\*-------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    note        "mesh decomposition control dictionary";
+    location    "system";
+    object      decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+numberOfSubdomains  2;
+
+//- Keep owner and neighbour on same processor for faces in zones:
+// preserveFaceZones (heater solid1 solid3);
+
+//method          scotch;
+// method          hierarchical;
+ method          simple;
+// method          metis;
+// method          manual;
+
+simpleCoeffs
+{
+    n           (1 1 2);
+//    n           (2 1 4);
+    delta       0.001;
+}
+
+hierarchicalCoeffs
+{
+    n           (2 2 1);
+    delta       0.001;
+    order       xyz;
+}
+
+metisCoeffs
+{
+ /*
+    processorWeights
+    (
+        1
+        1
+        1
+        1
+    );
+  */
+}
+
+scotchCoeffs
+{
+    //processorWeights
+    //(
+    //    1
+    //    1
+    //    1
+    //    1
+    //);
+    //writeGraph  true;
+    //strategy "b";
+}
+
+manualCoeffs
+{
+    dataFile    "decompositionData";
+}
+
+
+//// Is the case distributed
+//distributed     yes;
+//// Per slave (so nProcs-1 entries) the directory above the case.
+//roots           
+//(
+//    "/tmp"
+//    "/tmp"
+//);
+
+
+// ************************************************************************* //

tutorials/rStatAnalysis/createRecurrenceMatrix/CFD/system/fvSchemes

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  2.3.0                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+    default         Euler;
+}
+
+gradSchemes
+{
+    default         Gauss linear;
+}
+
+divSchemes
+{
+    default         Gauss linear;
+    div(phi,U)      Gauss limitedLinearV 1;
+    div(phi,k)      Gauss limitedLinear 1;
+    div(phi,epsilon) Gauss limitedLinear 1;
+    div(phi,R)      Gauss limitedLinear 1;
+    div(R)          Gauss linear;
+    div(phi,nuTilda) Gauss limitedLinear 1;
+    div((nuEff*dev(T(grad(U))))) Gauss linear;
+    div(phi,T)      Gauss limitedLinear 1;
+ //   div(phi,T)      Gauss upwind;
+}
+
+laplacianSchemes
+{
+    default         Gauss linear corrected;
+}
+
+interpolationSchemes
+{
+    default         linear;
+}
+
+snGradSchemes
+{
+    default         corrected;
+}
+
+fluxRequired
+{
+    default         no;
+    p               ;
+    T               ;
+}
+
+
+// ************************************************************************* //

tutorials/rStatAnalysis/createRecurrenceMatrix/CFD/system/fvSolution

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  2.3.0                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSolution;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+solvers
+{
+    p
+    {
+        solver          GAMG;
+        tolerance       1e-06;
+        relTol          0.1;
+        smoother        GaussSeidel;
+        nPreSweeps      0;
+        nPostSweeps     2;
+        cacheAgglomeration on;
+        agglomerator    faceAreaPair;
+        nCellsInCoarsestLevel 10;
+        mergeLevels     1;
+    }
+
+    pFinal
+    {
+        $p;
+        tolerance       1e-06;
+        relTol          0;
+    }
+
+    "(U|k|epsilon|R|nuTilda|c)"
+    {
+        solver          smoothSolver;
+        smoother        GaussSeidel;
+        tolerance       1e-05;
+        relTol          0;
+    }
+
+    T
+    {
+        solver          PBiCG;
+        preconditioner  DILU;
+        tolerance       1e-8;
+        relTol          0;
+    }
+}
+
+PISO
+{
+    nCorrectors     2;
+    nNonOrthogonalCorrectors 0;
+    pRefCell        0;
+    pRefValue       0;
+}
+
+
+// ************************************************************************* //

tutorials/rStatAnalysis/createRecurrenceMatrix/CFD/system/probesDict

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+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \    /   O peration     | Version:  2.1.x                                 |
+|   \  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+	version		2.0;
+	format		ascii;
+	class		dictionary;
+	object		probesDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+
+fields
+(
+    voidfraction
+    UsRec
+    URec
+    pRec
+    rhoRec
+    voidfractionRec
+    addSource
+);
+
+outputControl   timeStep; //outputTime;
+
+outputInterval  40;
+
+
+// Locations to be probed.
+probeLocations
+(
+	(0.0 0.0 0.03)
+        (0.0 0.0 0.06)
+        (0.0 0.0 0.09)
+	(0.035 0.0 0.03)
+	(-0.035 0.0 0.03)
+	(0.02 0.0 0.001)
+	(-0.02 0.0 0.001)
+
+);
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //