TUT: added mixerVesselAMI2DRefined to show example of AMI with topology change

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/0/U

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volVectorField;
+    object      U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 1 -1 0 0 0 0];
+
+internalField   uniform (0 0 0);
+
+boundaryField
+{
+    rotor
+    {
+        type            movingWallVelocity;
+        value           uniform (0 0 0);
+    }
+
+    stator
+    {
+        type            movingWallVelocity;
+        value           uniform (0 0 0);
+    }
+
+    front
+    {
+        type            movingWallVelocity;
+        value           uniform (0 0 0);
+    }
+
+    back
+    {
+        type            movingWallVelocity;
+        value           uniform (0 0 0);
+    }
+
+    AMI1
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+
+    AMI2
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+}
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/0/epsilon

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      epsilon;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -3 0 0 0 0];
+
+internalField   uniform 20;
+
+boundaryField
+{
+    rotor
+    {
+        type            epsilonWallFunction;
+        value           $internalField;
+    }
+
+    stator
+    {
+        type            epsilonWallFunction;
+        value           $internalField;
+    }
+
+    front
+    {
+        type            epsilonWallFunction;
+        value           $internalField;
+    }
+
+    back
+    {
+        type            epsilonWallFunction;
+        value           $internalField;
+    }
+
+    AMI1
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+
+    AMI2
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+}
+
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/0/k

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      k;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -2 0 0 0 0];
+
+internalField   uniform 1;
+
+boundaryField
+{
+    rotor
+    {
+        type            kqRWallFunction;
+        value           uniform 0;
+    }
+
+    stator
+    {
+        type            kqRWallFunction;
+        value           uniform 0;
+    }
+
+    front
+    {
+        type            kqRWallFunction;
+        value           uniform 0;
+    }
+
+    back
+    {
+        type            kqRWallFunction;
+        value           uniform 0;
+    }
+
+    AMI1
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+
+    AMI2
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+}
+
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/0/nut

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    location    "0";
+    object      nut;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -1 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    rotor
+    {
+        type            nutkWallFunction;
+        value           uniform 0;
+    }
+
+    stator
+    {
+        type            nutkWallFunction;
+        value           uniform 0;
+    }
+
+    front
+    {
+        type            nutkWallFunction;
+        value           uniform 0;
+    }
+
+    back
+    {
+        type            nutkWallFunction;
+        value           uniform 0;
+    }
+
+    AMI1
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+
+    AMI2
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+}
+
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/0/p

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volScalarField;
+    object      p;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [0 2 -2 0 0 0 0];
+
+internalField   uniform 0;
+
+boundaryField
+{
+    rotor
+    {
+        type            zeroGradient;
+    }
+
+    stator
+    {
+        type            zeroGradient;
+    }
+
+    front
+    {
+        type            zeroGradient;
+    }
+
+    back
+    {
+        type            zeroGradient;
+    }
+
+    AMI1
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+
+    AMI2
+    {
+        type            cyclicAMI;
+        value           $internalField;
+    }
+}
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/Allrun

+#!/bin/sh
+cd ${0%/*} || exit 1                        # Run from this directory
+. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+
+./makeMesh
+
+#runApplication $(getApplication)
+runApplication decomposePar
+runParallel $(getApplication)
+runParallel redistributePar -reconstruct
+
+#------------------------------------------------------------------------------

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/README

+Refined version that includes wall layers.
+
+- this causes significant pressure spikes using the default AMI
+
+    dynamicFvMesh   dynamicMotionSolverFvMesh;
+
+- enabling topology change where a 1-to-1 connectivity is established across
+  the AMI leads to a much smoother pressure trace.  Ony change needed is to the
+  motion solver:
+
+    dynamicFvMesh   dynamicMotionSolverFvMeshAMI;

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/constant/dynamicMeshDict

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      dynamicMeshDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dynamicFvMesh   dynamicMotionSolverFvMeshAMI;
+//dynamicFvMesh   dynamicMotionSolverFvMesh;
+
+motionSolver    solidBody;
+
+cellZone        rotor;
+
+solidBodyMotionFunction  rotatingMotion;
+
+origin        (0 0 0);
+axis          (0 0 1);
+omega         6.2832; // rad/s
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/constant/transportProperties

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      transportProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+transportModel  Newtonian;
+
+nu              1e-05;
+
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/constant/turbulenceProperties

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      turbulenceProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+simulationType  laminar;
+
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/makeMesh

+#!/bin/sh
+cd ${0%/*} || exit 1                        # Run from this directory
+. $WM_PROJECT_DIR/bin/tools/RunFunctions    # Tutorial run functions
+
+m4 < system/blockMeshDict.m4 > system/blockMeshDict
+
+runApplication blockMesh
+
+runApplication topoSet
+
+#------------------------------------------------------------------------------

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/plot

+set terminal pngcairo
+set output "plot.png"
+set yrange [-0.001 : 0.001]
+plot "postProcessing/forces/0/moment.dat" u 1:4 w lines
+

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/system/controlDict

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application     pimpleFoam;
+
+startFrom       startTime;
+
+startTime       0;
+
+stopAt          endTime;
+
+endTime         0.2; // 5;
+
+deltaT          1e-3;
+
+writeControl    adjustableRunTime;
+
+writeInterval   0.1;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  6;
+
+writeCompression off;
+
+timeFormat      general;
+
+timePrecision   6;
+
+runTimeModifiable true;
+
+adjustTimeStep  yes;
+
+maxCo           0.5;
+
+functions
+{
+    AMI1
+    {
+        type            surfaceFieldValue;
+        functionObjectLibs ("libfieldFunctionObjects.so");
+	log		true;
+ 	executeControl      timeStep;
+        executeInterval     1;
+	writeFields	true;
+	regionType	patch;
+	name		AMI1;
+	operation	sum;
+	surfaceFormat	none;
+	fields		(phi);
+    }
+    AMI2
+    {
+         type            surfaceFieldValue;
+        functionObjectLibs ("libfieldFunctionObjects.so");
+	log		true;
+ 	executeControl      timeStep;
+        executeInterval     1;
+	writeFields	true;
+	regionType	patch;
+	name		AMI2;
+	operation	sum;
+	surfaceFormat	none;
+	fields		(phi);
+    }
+
+forces
+{
+    type        forces;
+
+    functionObjectLibs ( "libforces.so" );
+
+    outputControl   timeStep;
+    timeInterval    1;
+
+    log         yes;
+
+    patches     ( "rotor" );
+    pName       p;
+    UName       U;
+    rho     rhoInf;     // Indicates incompressible
+    log         true;
+    rhoInf      997;        // Redundant for incompressible
+
+    CofR        (0 0 0);    // Rotation around centre line of propeller
+    pitchAxis   (0 0 1);
+}
+
+
+}
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/system/decomposeParDict

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      decomposeParDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+//- Force AMI to be on single processor. Can cause imbalance with some
+//  decomposers.
+//singleProcessorFaceSets ((AMI -1));
+
+numberOfSubdomains 4;
+
+method          scotch;
+
+distributed     no;
+
+roots           ( );
+
+
+// ************************************************************************* //

tutorials/incompressible/pimpleFoam/laminar/mixerVesselAMI2D/mixerVesselAMI2D-topologyChange/system/fvSchemes

+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  v2006                                 |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |