diff --git a/etc/caseDicts/annotated/blockMeshDict b/etc/caseDicts/annotated/blockMeshDict
new file mode 100644
index 0000000000000000000000000000000000000000..c088a1fd168a98711120c5ce20d1173f80bcc460
--- /dev/null
+++ b/etc/caseDicts/annotated/blockMeshDict
@@ -0,0 +1,96 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object blockMeshDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+scale 1;
+
+
+x0 0;
+x1 #eval "$x0 + 1.0";
+y0 0;
+y1 1;
+z0 0;
+z1 1;
+
+nx 2;
+ny 2;
+nz 1;
+
+gr 40.0;
+grInv #eval "1/$gr";
+
+vertices
+(
+ ($x0 $y0 $z0)
+ ($x1 $y0 $z0)
+ ($x1 $y1 $z0)
+ ($x0 $y1 $z0)
+ ($x0 $y0 $z1)
+ ($x1 $y0 $z1)
+ ($x1 $y1 $z1)
+ ($x0 $y1 $z1)
+);
+
+blocks
+(
+ hex (0 1 2 3 4 5 6 7) ($nx $ny $nz) simpleGrading (1 $grInv 1)
+);
+
+edges
+(
+);
+
+boundary
+(
+ upperWall
+ {
+ type symmetry;
+ faces
+ (
+ (3 7 6 2)
+ );
+ }
+ lowerWall
+ {
+ type wall;
+ faces
+ (
+ (1 5 4 0)
+ );
+ }
+ inlet
+ {
+ type patch;
+ faces
+ (
+ (0 4 7 3)
+ );
+ }
+ outlet
+ {
+ type patch;
+ faces
+ (
+ (2 6 5 1)
+ );
+ }
+);
+
+mergePatchPairs
+(
+);
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/boxTurbDict b/etc/caseDicts/annotated/boxTurbDict
new file mode 100644
index 0000000000000000000000000000000000000000..b42bfc0388b9021f23da2dae93ce39bc2fcee086
--- /dev/null
+++ b/etc/caseDicts/annotated/boxTurbDict
@@ -0,0 +1,23 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object boxTurbDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+Ea 10;
+
+k0 5;
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/createBoxTurbDict b/etc/caseDicts/annotated/createBoxTurbDict
new file mode 100644
index 0000000000000000000000000000000000000000..35b426f065698815c96e300b12be29a98ea4413d
--- /dev/null
+++ b/etc/caseDicts/annotated/createBoxTurbDict
@@ -0,0 +1,52 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object createBoxTurbDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+N (64 64 64);
+
+// Suggested box size of 9*2*pi [cm]
+L (0.56548667765 0.56548667765 0.56548667765);
+
+nModes 5000;
+
+// Energy as a function of wave number
+// Here using Comte-Bellot and Corrsin data at t.U_0/M = 42 (see Ref. table 3)
+Ek table
+(
+ (15 0)
+ (20 0.000129)
+ (25 0.00023)
+ (30 0.000322)
+ (40 0.000435)
+ (50 0.000457)
+ (70 0.00038)
+ (100 0.00027)
+ (150 0.000168)
+ (200 0.00012)
+ (250 8.9e-05)
+ (300 7.03e-05)
+ (400 4.7e-05)
+ (600 2.47e-05)
+ (800 1.26e-05)
+ (1000 7.42e-06)
+ (1250 3.96e-06)
+ (1500 2.33e-06)
+ (1750 1.34e-06)
+ (2000 8e-07)
+);
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/dsmcInitialiseDict b/etc/caseDicts/annotated/dsmcInitialiseDict
new file mode 100644
index 0000000000000000000000000000000000000000..d37723266528be6c840d59a8cfa94e47f4a9f1a3
--- /dev/null
+++ b/etc/caseDicts/annotated/dsmcInitialiseDict
@@ -0,0 +1,29 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "system";
+ object dsmcInitialiseDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+numberDensities
+{
+ N2 0.777e20;
+ O2 0.223e20;
+};
+
+temperature 300;
+
+velocity (1325 -352 823);
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/extrudeMeshDict b/etc/caseDicts/annotated/extrudeMeshDict
index a5d944d885ec6fb7a9f993df4f6aec702cac668f..81742b86ab4a946eb0145a41d45799d71d144e6e 100644
--- a/etc/caseDicts/annotated/extrudeMeshDict
+++ b/etc/caseDicts/annotated/extrudeMeshDict
@@ -24,7 +24,7 @@ constructFrom patch;
//constructFrom surface;
// If construct from patch/mesh:
-sourceCase "../cavity";
+sourceCase "$FOAM_CASE";
sourcePatches (movingWall);
// If construct from patch: patch to use for back (can be same as sourcePatch)
diff --git a/etc/caseDicts/annotated/mdEquilibrationDict b/etc/caseDicts/annotated/mdEquilibrationDict
new file mode 100644
index 0000000000000000000000000000000000000000..6c2a3a4fc8c92958390ad3e81414d694fabc26c8
--- /dev/null
+++ b/etc/caseDicts/annotated/mdEquilibrationDict
@@ -0,0 +1,20 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+targetTemperature 298;
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/mdInitialiseDict b/etc/caseDicts/annotated/mdInitialiseDict
new file mode 100644
index 0000000000000000000000000000000000000000..f56f236ecfe1cebdf1ef3ab15d14941daba7ba50
--- /dev/null
+++ b/etc/caseDicts/annotated/mdInitialiseDict
@@ -0,0 +1,82 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object mdInitialiseDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+sectionA
+{
+ massDensity 1004;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+sectionB
+{
+ massDensity 1004;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ Ar
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+sectionC
+{
+ massDensity 1004;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water1
+ water2
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ (0 0.5 0.5)
+ (0.5 0 0.5)
+ (0.5 0.5 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/obstaclesDict b/etc/caseDicts/annotated/obstaclesDict
new file mode 100644
index 0000000000000000000000000000000000000000..87c2ee10d9f3f3875b33cbb74e8b886d67751a09
--- /dev/null
+++ b/etc/caseDicts/annotated/obstaclesDict
@@ -0,0 +1,39 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object obstaclesDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+scale 1.0;
+
+verbose 0;
+
+#include "groups/group4"
+
+_01
+{
+ groupId 1;
+
+ zpipe { direction z; length 0.947; diameter 0.026; }
+
+ obstacles
+ (
+ box { point (0 0 0); size (0.05 0.05 2); }
+ box { point (1 0 0); size (0.05 0.05 2); }
+ box { point (2 0 0); size (0.05 0.05 2); }
+ cyl { point (1.031 0.975 0.056); $zpipe; }
+ );
+}
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/optimisationDict b/etc/caseDicts/annotated/optimisationDict
new file mode 100644
index 0000000000000000000000000000000000000000..9887a5921bee194084b6a6a836b02d7444b8274c
--- /dev/null
+++ b/etc/caseDicts/annotated/optimisationDict
@@ -0,0 +1,393 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object optimisationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+optimisationManager steadyOptimisation; // singleRun;
+
+
+primalSolvers
+{
+ p1
+ {
+ active true;
+ type incompressible;
+ solver simple;
+
+ solutionControls
+ {
+ nIters 3000;
+ residualControl
+ {
+ "p.*" 1.e-7;
+ "U.*" 1.e-7;
+ }
+ }
+ }
+}
+
+
+adjointManagers
+{
+ am1
+ {
+ primalSolver p1;
+ adjointSolvers
+ {
+ as1
+ {
+ // choose adjoint solver
+ //----------------------
+ active true;
+ type incompressible;
+ solver adjointSimple;
+ useSolverNameForFields true;
+
+ // manage objectives
+ //------------------
+ objectives
+ {
+ type incompressible;
+ objectiveNames
+ {
+ losses
+ {
+ weight 1;
+ type PtLosses;
+ patches (Inlet Outlet);
+ }
+ }
+ }
+ // ATC treatment
+ //--------------
+ ATCModel
+ {
+ ATCModel standard;
+ }
+ // solution control
+ //------------------
+ solutionControls
+ {
+ nIters 3000;
+ residualControl
+ {
+ "pa.*" 1.e-7;
+ "Ua.*" 1.e-7;
+ }
+ }
+ }
+ vol
+ {
+ // choose adjoint solver
+ //----------------------
+ active true;
+ type incompressible;
+ solver adjointSimple;
+ useSolverNameForFields true;
+ isConstraint true;
+ // manage objectives
+ //------------------
+ objectives
+ {
+ type incompressible;
+
+ objectiveNames
+ {
+ vol
+ {
+ weight 1;
+ type partialVolume;
+ patches (lower upper);
+ }
+ }
+ }
+
+ // ATC treatment
+ //--------------
+ ATCModel
+ {
+ ATCModel standard;
+ }
+
+ // solution control
+ //------------------
+ solutionControls
+ {
+ nIters 3000;
+ residualControl
+ {
+ "pa.*" 1.e-7;
+ "Ua.*" 1.e-7;
+ }
+ }
+ }
+ }
+ }
+}
+
+
+optimisation
+{
+ optimisationType
+ {
+ type shapeOptimisation;
+ writeEachMesh true;
+ }
+
+ sensitivities
+ {
+ type volumetricBSplinesFI;
+ patches (lower upper);
+ }
+
+ updateMethod
+ {
+ method SQP;
+ SQP
+ {
+ etaHessian 0.8;
+ nSteepestDescent 1;
+ scaleFirstHessian true;
+ }
+ }
+
+ meshMovement
+ {
+ type volumetricBSplines;
+ maxAllowedDisplacement 2.e-3;
+ }
+
+/*
+ updateMethod
+ {
+ method BFGS;
+ BFGS
+ {
+ etaHessian 0.8;
+ nSteepestDescent 1;
+ scaleFirstHessian true;
+ activeDesignVariables
+ (
+ 141 142 144 145 147 148
+ );
+ }
+ }
+*/
+
+/*
+ sensitivities
+ {
+ type multiple; // used to compute many kinds of sensitivities at the same time
+ patches (lower upper);
+ sensTypes
+ {
+ FIVolSplines
+ {
+ type volumetricBSplinesFI;
+ patches (lower upper);
+ includeDistance true;
+ adjointEikonalSolver
+ {
+ iters 1000;
+ tolerance 1.e-6;
+ }
+ }
+ ESIVolSplines
+ {
+ type volumetricBSplines;
+ patches (lower upper);
+ includeObjectiveContribution true; // one of this or the equivalent flag in
+ // surfaceSensitivities has to be set to true
+ // with this being the prefered one
+ surfaceSensitivities
+ {
+ patches (lower upper);
+ includeSurfaceArea true;
+ includeMeshMovement true;
+ includeDistance true;
+ includeObjectiveContribution false;
+
+ // adjointEikonal and adjointMeshMovement solvers should be always nested
+ // within the dictionary of the sensitivity type they correspond to.
+ // For (E)SI based sensitivities, this means the surfaceSensitivities dict
+ // Default values are provided, so the dictionaries can be skipped
+ adjointEikonalSolver
+ {
+ iters 1000;
+ tolerance 1.e-6;
+ }
+ adjointMeshMovementSolver
+ {
+ iters 10000;
+ tolerance 1.e-6;
+ }
+ }
+ }
+ SIVolSplines
+ {
+ type volumetricBSplines;
+ patches (lower upper);
+ includeObjectiveContribution true; // same comment as above
+ surfaceSensitivities
+ {
+ patches (lower upper);
+ includeSurfaceArea true;
+ includeMeshMovement false;
+ includeDistance true;
+ includeObjectiveContribution false;
+ adjointEikonalSolver
+ {
+ iters 1000;
+ tolerance 1.e-6;
+ }
+ }
+ }
+ FIBezier
+ {
+ type BezierFI;
+ includeDistance true;
+ patches (lower upper);
+ dxdbSolver
+ {
+ iters 1000;
+ tolerance 1.e-6;
+ }
+ adjointEikonalSolver
+ {
+ iters 1000;
+ tolerance 1.e-6;
+ }
+ }
+ ESIBezier
+ {
+ type Bezier;
+ includeObjectiveContribution true; // same comment as above
+ surfaceSensitivities
+ {
+ patches (lower upper);
+ includeSurfaceArea true;
+ includeMeshMovement true;
+ includeDistance true;
+ includeObjectiveContribution false;
+ adjointEikonalSolver
+ {
+ iters 1000;
+ tolerance 1.e-6;
+ }
+ adjointMeshMovementSolver
+ {
+ iters 10000;
+ tolerance 1.e-6;
+ }
+ }
+ patches (lower upper);
+ }
+ SIBezier
+ {
+ type Bezier;
+ includeObjectiveContribution true; // same comment as above
+ surfaceSensitivities
+ {
+ patches (lower upper);
+ includeSurfaceArea true;
+ includeMeshMovement false;
+ includeDistance true;
+ includeObjectiveContribution false;
+ adjointEikonalSolver
+ {
+ iters 1000;
+ tolerance 1.e-6;
+ }
+ }
+ patches (lower upper);
+ }
+ }
+ }
+*/
+
+/*
+ sensitivities
+ {
+ type multiple; // used to compute many kinds of sensitivities at the same time
+ patches (lower upper);
+ sensTypes
+ {
+ FIVolSplines
+ {
+ type volumetricBSplinesFI;
+ patches (lower upper);
+ }
+ ESIVolSplines
+ {
+ type volumetricBSplines;
+ patches (lower upper);
+ }
+ SIVolSplines
+ {
+ type volumetricBSplines;
+ patches (lower upper);
+ surfaceSensitivities
+ {
+ includeMeshMovement false;
+ }
+ }
+ FIBezier
+ {
+ type BezierFI;
+ patches (lower upper);
+ }
+ ESIBezier
+ {
+ type Bezier;
+ patches (lower upper);
+ }
+ SIBezier
+ {
+ type Bezier;
+ patches (lower upper);
+ surfaceSensitivities
+ {
+ includeMeshMovement false;
+ }
+ }
+ }
+ }
+*/
+}
+
+
+/*
+Bezier
+{
+ nBezier 24;
+ confineXmovement
+ (
+ true false false false false false false false false false false true
+ true false false false false false false false false false false true
+ );
+ confineYmovement
+ (
+ true false false false false false false false false false false true
+ true false false false false false false false false false false true
+ );
+ confineZmovement
+ (
+ true true true true true true true true true true true true
+ true true true true true true true true true true true true
+ );
+}
+*/
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/potentialDict b/etc/caseDicts/annotated/potentialDict
new file mode 100644
index 0000000000000000000000000000000000000000..71552faf68331c3ca9b5fab5a9d218a0daa2fe4a
--- /dev/null
+++ b/etc/caseDicts/annotated/potentialDict
@@ -0,0 +1,118 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object potentialDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Subdictionaries specifying types of intermolecular potential.
+// Sub-sub dictionaries specify the potentials themselves.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Removal order
+
+// This is the order in which to remove overlapping pairs if more than one
+// type of molecule is present. The most valuable molecule type is at the
+// right hand end, the molecule that will be removed 1st is 1st on the list.
+// Not all types need to be present, a molecule that is not present is
+// automatically less valuable than any on the list. For molecules of the
+// same type there is no control over which is removed.
+
+removalOrder ( water );
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Potential Energy Limit
+
+// Maximum permissible pair energy allowed at startup. Used to remove
+// overlapping molecules created during preprocessing.
+
+potentialEnergyLimit 1e-18;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Pair potentials
+
+// If a pair are not present here it is assumed that they do not interact.
+
+// Electrostatic pair interactions are not listed here - they are handled
+// separately.
+
+// If there are r different type of molecules, and a pair force is required
+// between all combinations, then there are C = r(r+1)/2 combinations,
+// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
+
+// Pair potentials are specified by the combination of their ids,
+// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
+// (strictly OR, both or neither will throw an error)
+
+pair
+{
+ O-O
+ {
+ pairPotential lennardJones;
+ rCut 1.0e-9;
+ rMin 0.1e-9;
+ dr 1e-13;
+ lennardJonesCoeffs
+ {
+ sigma 3.154e-10;
+ epsilon 1.07690722e-21;
+ }
+ energyScalingFunction noScaling;
+ writeTables yes;
+ }
+
+ electrostatic
+ {
+ pairPotential dampedCoulomb;
+ rCut 1e-9;
+ rMin 2e-11;
+ dr 2e-12;
+ dampedCoulombCoeffs
+ {
+ alpha 2e9;
+ }
+ energyScalingFunction shiftedForce;
+ writeTables yes;
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Tethering Potentials
+
+tether
+{
+ O
+ {
+ tetherPotential restrainedHarmonicSpring;
+ restrainedHarmonicSpringCoeffs
+ {
+ springConstant 0.277;
+ rR 1.2e-9;
+ }
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// External Forces
+
+// Bulk external forces (namely gravity) will be specified as forces rather
+// than potentials to allow their direction to be controlled.
+
+external
+{
+ gravity (0 0 0);
+}
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/probesDict b/etc/caseDicts/annotated/probesDict
new file mode 100644
index 0000000000000000000000000000000000000000..81f8194456f6293d2f6f304aab97e8c2a04a97c3
--- /dev/null
+++ b/etc/caseDicts/annotated/probesDict
@@ -0,0 +1,31 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location system;
+ object probesDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Fields to be probed (runTime modifiable)
+fields
+(
+ T H2O p kT
+);
+
+// Locations to be probed (runTime modifiable)
+probeLocations
+(
+ (0.005 0.0 0.0)
+);
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
diff --git a/etc/caseDicts/annotated/sampleDict b/etc/caseDicts/annotated/sampleDict
new file mode 100644
index 0000000000000000000000000000000000000000..8695d9983a26e075b5caaa6010cd1fb4d1a0569e
--- /dev/null
+++ b/etc/caseDicts/annotated/sampleDict
@@ -0,0 +1,325 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object sampleDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Set output format : choice of
+// xmgr
+// jplot
+// gnuplot
+// raw
+// vtk
+// ensight
+// csv
+setFormat raw;
+
+// Surface output format. Choice of
+// null : suppress output
+// ensight : Ensight Gold format, one field per case file
+// foamFile : separate points, faces and values file
+// dx : DX scalar or vector format
+// vtk : VTK ascii format
+// raw : x y z value format for use with e.g. gnuplot 'splot'.
+//
+// Note:
+// other formats such as obj, stl, etc can also be written (by proxy)
+// but without any values!
+surfaceFormat vtk;
+
+// optionally define extra controls for the output formats
+formatOptions
+{
+ ensight
+ {
+ format ascii;
+ }
+}
+
+// interpolationScheme. choice of
+// cell : use cell-centre value only; constant over cells
+// (default)
+// cellPoint : use cell-centre and vertex values
+// cellPointFace : use cell-centre, vertex and face values.
+// pointMVC : use point values only (Mean Value Coordinates)
+// cellPatchConstrained : like 'cell' but uses cell-centre except on
+// boundary faces where it uses the boundary value.
+// For use with e.g. patchCloudSet.
+// 1] vertex values determined from neighbouring cell-centre values
+// 2] face values determined using the current face interpolation scheme
+// for the field (linear, gamma, etc.)
+interpolationScheme cellPoint;
+
+// Fields to sample.
+fields
+(
+ p
+ U
+);
+
+// Set sampling definition: choice of
+// uniform evenly distributed points on line
+// face one point per face intersection
+// midPoint one point per cell, inbetween two face intersections
+// midPointAndFace combination of face and midPoint
+//
+// polyLine specified points, not nessecary on line, uses
+// tracking
+// cloud specified points, uses findCell
+// triSurfaceMeshPointSet points of triSurface
+//
+// axis: how to write point coordinate. Choice of
+// - x/y/z: x/y/z coordinate only
+// - xyz: three columns
+// (probably does not make sense for anything but raw)
+// - distance: distance from start of sampling line (if uses line) or
+// distance from first specified sampling point
+//
+// type specific:
+// uniform, face, midPoint, midPointAndFace : start and end coordinate
+// uniform: extra number of sampling points
+// polyLine, cloud: list of coordinates
+// patchCloud: list of coordinates and set of patches to look for nearest
+// patchSeed: random sampling on set of patches. Points slightly off
+// face centre.
+sets
+(
+ lineX1
+ {
+ type uniform;
+ axis distance;
+
+ //- cavity. Slightly perturbed so not to align with face or edge.
+ start (0.0201 0.05101 0.00501);
+ end (0.0601 0.05101 0.00501);
+ nPoints 10;
+ }
+
+ lineX2
+ {
+ type face;
+ axis x;
+
+ //- cavity
+ start (0.0001 0.0525 0.00501);
+ end (0.0999 0.0525 0.00501);
+ }
+
+ somePoints
+ {
+ type cloud;
+ axis xyz;
+ points ((0.049 0.049 0.00501)(0.051 0.049 0.00501));
+ }
+
+ somePatchPoints
+ {
+ // Sample nearest points on selected patches. Looks only up to
+ // maxDistance away. Any sampling point not found will get value
+ // pTraits<Type>::max (usually VGREAT)
+ // Use with interpolations:
+ // - cell (cell value)
+ // - cellPatchConstrained (boundary value)
+ // - cellPoint (interpolated boundary value)
+ type patchCloud;
+ axis xyz;
+ points ((0.049 0.099 0.005)(0.051 0.054 0.005));
+ maxDistance 0.1; // maximum distance to search
+ patches (".*Wall.*");
+ }
+
+ patchSeed
+ {
+ type patchSeed;
+ axis xyz;
+ patches (".*Wall.*");
+ // Number of points to seed. Divided amongst all processors according
+ // to fraction of patches they hold.
+ maxPoints 100;
+ }
+
+);
+
+
+// Surface sampling definition
+//
+// 1] patches are not triangulated by default
+// 2] planes are always triangulated
+// 3] iso-surfaces are always triangulated
+surfaces
+(
+ constantPlane
+ {
+ type plane; // always triangulated
+ basePoint (0.0501 0.0501 0.005);
+ normalVector (0.1 0.1 1);
+
+ //- Optional: restrict to a particular zone
+ // zone zone1;
+
+ //- Optional: do not triangulate (only for surfaceFormats that support
+ // polygons)
+ //triangulate false;
+ }
+
+ interpolatedPlane
+ {
+ type plane; // always triangulated
+
+ // Make plane relative to the coordinateSystem (Cartesian)
+ coordinateSystem
+ {
+ origin (0.0501 0.0501 0.005);
+
+ // Add a coordinate rotation
+ // (required, so here one that doesn't change anything)
+ coordinateRotation
+ {
+ type axesRotation;
+ e1 (1 0 0);
+ e2 (0 1 0);
+ }
+ }
+ basePoint (0 0 0);
+ normalVector (0.1 0.1 1);
+ interpolate true;
+ }
+
+ walls_constant
+ {
+ type patch;
+ patches ( ".*Wall.*" );
+ // Optional: whether to leave as faces (=default) or triangulate
+ // triangulate false;
+ }
+
+ walls_interpolated
+ {
+ type patch;
+ patches ( ".*Wall.*" );
+ interpolate true;
+ // Optional: whether to leave as faces (=default) or triangulate
+ // triangulate false;
+ }
+
+ nearWalls_interpolated
+ {
+ // Sample cell values off patch. Does not need to be the near-wall
+ // cell, can be arbitrarily far away.
+ type patchInternalField;
+ patches ( ".*Wall.*" );
+ interpolate true;
+
+
+ // Optional: specify how to obtain sampling points from the patch
+ // face centres (default is 'normal')
+ //
+ // //- Specify distance to offset in normal direction
+ offsetMode normal;
+ distance 0.1;
+ //
+ // //- Specify single uniform offset
+ // offsetMode uniform;
+ // offset (0 0 0.0001);
+ //
+ // //- Specify offset per patch face
+ // offsetMode nonuniform;
+ // offsets ((0 0 0.0001) (0 0 0.0002));
+
+
+ // Optional: whether to leave as faces (=default) or triangulate
+ // triangulate false;
+ }
+
+ interpolatedIso
+ {
+ // Iso surface for interpolated values only
+ type isoSurface; // always triangulated
+ isoField rho;
+ isoValue 0.5;
+ interpolate true;
+
+ //zone ABC; // Optional: zone only
+ //exposedPatchName fixedWalls; // Optional: zone only
+
+ // regularise false; // Optional: do not simplify
+ // mergeTol 1e-10; // Optional: fraction of mesh bounding box
+ // to merge points (default=1e-6)
+ }
+ constantIso
+ {
+ // Iso surface for constant values.
+ // Triangles guaranteed not to cross cells.
+ type isoSurfaceCell; // always triangulated
+ isoField rho;
+ isoValue 0.5;
+ interpolate false;
+ regularise false; // do not simplify
+ // mergeTol 1e-10; // Optional: fraction of mesh bounding box
+ // to merge points (default=1e-6)
+ }
+
+ triangleCut
+ {
+ // Cutingplane using iso surface
+ type cuttingPlane;
+ planeType pointAndNormal;
+ pointAndNormalDict
+ {
+ basePoint (0.4 0 0.4);
+ normalVector (1 0.2 0.2);
+ }
+ interpolate true;
+
+ //zone ABC; // Optional: zone only
+ //exposedPatchName fixedWalls; // Optional: zone only
+
+ // regularise false; // Optional: do not simplify
+ // mergeTol 1e-10; // Optional: fraction of mesh bounding box
+ // to merge points (default=1e-6)
+ }
+
+ distance
+ {
+ // Isosurface from signed/unsigned distance to surface
+ type distanceSurface;
+ signed true;
+
+ // Definition of surface
+ surfaceType triSurfaceMesh;
+ surfaceName integrationPlane.stl;
+ // Distance to surface
+ distance 0.0;
+
+ //cell false;// optional: use isoSurface instead
+ // of isoSurfaceCell
+ interpolate false;
+ regularise false; // Optional: do not simplify
+ // mergeTol 1e-10; // Optional: fraction of mesh bounding box
+ // to merge points (default=1e-6)
+ }
+
+ triSurfaceSampling
+ {
+ // Sampling on triSurface
+ type sampledTriSurfaceMesh;
+ surface integrationPlane.stl;
+ source boundaryFaces; // What to sample: cells (nearest cell)
+ // insideCells (only triangles inside cell)
+ // boundaryFaces (nearest boundary face)
+ interpolate true;
+ }
+);
+
+
+// *********************************************************************** //
diff --git a/etc/caseDicts/annotated/setExprBoundaryFieldsDict b/etc/caseDicts/annotated/setExprBoundaryFieldsDict
new file mode 100644
index 0000000000000000000000000000000000000000..6412e4f64b29a30fd4887b49dc0b4e68119781e2
--- /dev/null
+++ b/etc/caseDicts/annotated/setExprBoundaryFieldsDict
@@ -0,0 +1,32 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object setExprBoundaryFieldsDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+pattern
+{
+ field T;
+
+ expressions
+ (
+ {
+ patch outlet2;
+ target something;
+ expression #{ (pos().x() < 1e-4 ? 60 : 120) #};
+ }
+ );
+}
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/setExprFieldsDict b/etc/caseDicts/annotated/setExprFieldsDict
new file mode 100644
index 0000000000000000000000000000000000000000..2e06d9a26e68afb3aa9611eb1ae267a712b10dd1
--- /dev/null
+++ b/etc/caseDicts/annotated/setExprFieldsDict
@@ -0,0 +1,52 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: v1912 |
+| \\ / A nd | Website: www.openfoam.com |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object setExprFieldsDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+expressions
+(
+ T
+ {
+ field T;
+ dimensions [0 0 0 1 0 0 0];
+
+ constants
+ {
+ centre (0.21 0 0.01);
+ }
+
+ variables
+ (
+ "radius = 0.1"
+ );
+
+ condition
+ #{
+ // Within the radius
+ (mag(pos() - $[(vector)constants.centre]) < radius)
+
+ // but only +ve y!
+ && pos((pos() - $[(vector)constants.centre]).y()) > 0
+ #};
+
+ expression
+ #{
+ 300
+ + 200 * (1 - mag(pos() - $[(vector)constants.centre]) / radius)
+ #};
+ }
+);
+
+
+// ************************************************************************* //
diff --git a/etc/caseDicts/annotated/topoSetSourcesDict b/etc/caseDicts/annotated/topoSetSourcesDict
index 8ba14c4bc9a5bb925ad7e8db64d1f30580b067d7..58bb81929da906a744762a0645df4af03a490f51 100644
--- a/etc/caseDicts/annotated/topoSetSourcesDict
+++ b/etc/caseDicts/annotated/topoSetSourcesDict
@@ -241,6 +241,12 @@ cellSet_doc
// name ".*Zone";
// }
}
+
+ //- Cells attached to the outside of the input cellSet
+ {
+ source haloToCell;
+ steps 3; // Number of grow/shrink steps to use
+ }
}