BUG: discrete tut tweaks and fixes to make them run.

src/OpenFOAM/meshes/primitiveMesh/primitiveMesh.H

@@ -686,8 +686,14 @@ public:
 
         // Useful derived info
 
-            //- Is the point in the cell bounding box
+            //- Is the point in the cell bounding box, option relative
-            bool pointInCellBB(const point& p, label celli) const;
+            //  tolerance to increase the effective size of the boundBox
+            bool pointInCellBB
+            (
+                const point& p,
+                label celli,
+                scalar tol = 0
+            ) const;
 
             //- Is the point in the cell
             bool pointInCell(const point& p, label celli) const;

src/OpenFOAM/meshes/primitiveMesh/primitiveMeshFindCell.C

@@ -30,16 +30,33 @@ License
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 // Is the point in the cell bounding box
-bool Foam::primitiveMesh::pointInCellBB(const point& p, label celli) const
+bool Foam::primitiveMesh::pointInCellBB
+(
+    const point& p,
+    label celli,
+    scalar tol
+) const
 {
-    return boundBox
+    boundBox bb
     (
         cells()[celli].points
         (
             faces(),
             points()
-        )
+        ),
-    ).contains(p);
+        false
+    );
+
+    if (tol > SMALL)
+    {
+        bb = boundBox
+        (
+            bb.min() - tol*bb.span(),
+            bb.max() + tol*bb.span()
+        );
+    }
+
+    return bb.contains(p);
 }
 
 

src/lagrangian/basic/Particle/ParticleI.H

@@ -970,11 +970,12 @@ inline void Foam::Particle<ParticleType>::initCellFacePt()
                 // number, but hasn't been able to find a cell to
                 // occupy.
 
-                if(!cloud_.polyMesh_.pointInCellBB(position_, oldCellI))
+                if(!cloud_.polyMesh_.pointInCellBB(position_, oldCellI, 0.1))
                 {
-                    // If the position is not inside the bound-box of
+                    // If the position is not inside the (slightly
-                    // the cell that it thought it should be in, then
+                    // extended) bound-box of the cell that it thought
-                    // this is considered an error.
+                    // it should be in, then this is considered an
+                    // error.
 
                     FatalErrorIn
                     (
@@ -985,18 +986,20 @@ inline void Foam::Particle<ParticleType>::initCellFacePt()
                         ")"
                     )   << "cell, tetFace and tetPt search failure at position "
                         << position_ << nl
+                        << "for requested cell " << oldCellI << nl
                         << abort(FatalError);
                 }
 
-                // The position is in the bound-box of the cell.  This
+                // The position is in the (slightly extended)
-                // situation may arise because the face decomposition
+                // bound-box of the cell.  This situation may arise
-                // of the cell is not the same as when the particle
+                // because the face decomposition of the cell is not
-                // acquired the cell index.  For example, it has been
+                // the same as when the particle acquired the cell
-                // read into a mesh that has made a different face
+                // index.  For example, it has been read into a mesh
-                // base-point decision for a boundary face and now
+                // that has made a different face base-point decision
-                // this particle is in a position that is not in the
+                // for a boundary face and now this particle is in a
-                // mesh.  Gradually move the particle towards the
+                // position that is not in the mesh.  Gradually move
-                // centre of the cell that it thought that it was in.
+                // the particle towards the centre of the cell that it
+                // thought that it was in.
 
                 cellI_ = oldCellI;
 

src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C

@@ -1108,7 +1108,7 @@ Foam::moleculeCloud::moleculeCloud
     mesh_(mesh),
     pot_(pot),
     cellOccupancy_(mesh_.nCells()),
-    il_(mesh_, pot_.pairPotentials().rCutMax(), true),
+    il_(mesh_, pot_.pairPotentials().rCutMax(), false),
     constPropList_(),
     rndGen_(clock::getTime())
 {

tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/Allclean

@@ -5,6 +5,6 @@ cd ${0%/*} || exit 1    # run from this directory
 . $WM_PROJECT_DIR/bin/tools/CleanFunctions
 
 cleanCase
-rm -rf 0/lagrangian 0/dsmcSigmaTcRMax
+rm -rf 0/lagrangian 0/dsmcSigmaTcRMax 0/uniform > /dev/null 2>&1
 
 # ----------------------------------------------------------------- end-of-file

tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/constant/polyMesh/blockMeshDict

@@ -34,29 +34,50 @@ blocks
     hex (0 1 2 3 4 5 6 7) (20 16 16) simpleGrading (1 1 1)
 );
 
-patches
+boundary
 (
-    cyclic
+    xPeriodic_half0
-    xPeriodic
+    {
-    (
+        type cyclic;
-        (1 2 6 5)
+        faces ((1 2 6 5));
-        (0 4 7 3)
+        neighbourPatch xPeriodic_half1;
-    )
+    }
 
-    cyclic
+    xPeriodic_half1
-    yPeriodic
+    {
-    (
+        type cyclic;
-        (2 3 7 6)
+        faces ((0 4 7 3));
-        (0 1 5 4)
+        neighbourPatch xPeriodic_half0;
-    )
+    }
 
-    cyclic
+    yPeriodic_half0
-    zPeriodic
+    {
-    (
+        type cyclic;
-        (4 5 6 7)
+        faces ((2 3 7 6));
-        (0 3 2 1)
+        neighbourPatch yPeriodic_half1;
-    )
+    }
-)
+
+    yPeriodic_half1
+    {
+        type cyclic;
+        faces ((0 1 5 4));
+        neighbourPatch yPeriodic_half0;
+    }
+
+    zPeriodic_half0
+    {
+        type cyclic;
+        faces ((4 5 6 7));
+        neighbourPatch zPeriodic_half1;
+    }
+
+    zPeriodic_half1
+    {
+        type cyclic;
+        faces ((0 3 2 1));
+        neighbourPatch zPeriodic_half0;
+    }
+);
 
 mergePatchPairs
 (

tutorials/discreteMethods/dsmcFoam/freeSpaceStream/Allclean

@@ -5,6 +5,6 @@ cd ${0%/*} || exit 1    # run from this directory
 . $WM_PROJECT_DIR/bin/tools/CleanFunctions
 
 cleanCase
-rm -rf 0/lagrangian 0/dsmcSigmaTcRMax
+rm -rf 0/lagrangian 0/dsmcSigmaTcRMax 0/uniform > /dev/null 2>&1
 
 # ----------------------------------------------------------------- end-of-file

tutorials/discreteMethods/dsmcFoam/supersonicCorner/Allclean

@@ -5,6 +5,6 @@ cd ${0%/*} || exit 1    # run from this directory
 . $WM_PROJECT_DIR/bin/tools/CleanFunctions
 
 cleanCase
-rm -rf 0/lagrangian 0/dsmcSigmaTcRMax
+rm -rf 0/lagrangian 0/dsmcSigmaTcRMax 0/uniform > /dev/null 2>&1
 
 # ----------------------------------------------------------------- end-of-file

tutorials/discreteMethods/dsmcFoam/wedge15Ma5/Allclean

@@ -5,6 +5,6 @@ cd ${0%/*} || exit 1    # run from this directory
 . $WM_PROJECT_DIR/bin/tools/CleanFunctions
 
 cleanCase
-rm -rf 0/lagrangian 0/dsmcSigmaTcRMax
+rm -rf 0/lagrangian 0/dsmcSigmaTcRMax 0/uniform > /dev/null 2>&1
 
 # ----------------------------------------------------------------- end-of-file

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean

@@ -7,7 +7,7 @@ cd ${0%/*} || exit 1    # run from this directory
 (
     cd periodicCubeArgon || exit
 
-    rm -rf 0/*
+    rm -rf 0/lagrangian 0/uniform
     rm -f Ar-Ar
     rm -f electrostatic
     rm -f constant/idList
@@ -19,7 +19,7 @@ cd ${0%/*} || exit 1    # run from this directory
 (
     cd periodicCubeWater || exit
 
-    rm -rf 0/*
+    rm -rf 0/lagrangian 0/uniform
     rm -f O-O
     rm -f electrostatic
     rm -f constant/idList

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/0/U

@@ -0,0 +1,51 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volVectorField;
+    location    "0";
+    object      U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [ 0 1 -1 0 0 0 0 ];
+
+internalField   uniform ( 0 0 0 );
+
+boundaryField
+{
+    periodicX_half0
+    {
+        type            cyclic;
+    }
+    periodicY_half0
+    {
+        type            cyclic;
+    }
+    periodicZ_half0
+    {
+        type            cyclic;
+    }
+    periodicY_half1
+    {
+        type            cyclic;
+    }
+    periodicZ_half1
+    {
+        type            cyclic;
+    }
+    periodicX_half1
+    {
+        type            cyclic;
+    }
+}
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict

@@ -34,29 +34,50 @@ blocks
     hex (0 1 2 3 4 5 6 7) liquid (12 12 12) simpleGrading (1 1 1)
 );
 
-patches
+boundary
 (
-    cyclic
+    periodicX_half0
-    periodicX
+    {
-    (
+        type cyclic;
-        (1 2 6 5)
+        faces ((1 2 6 5));
-        (0 4 7 3)
+        neighbourPatch periodicX_half1;
-    )
+    }
 
-    cyclic
+    periodicX_half1
-    periodicY
+    {
-    (
+        type cyclic;
-        (2 3 7 6)
+        faces ((0 4 7 3));
-        (0 1 5 4)
+        neighbourPatch periodicX_half0;
-    )
+    }
 
-    cyclic
+    periodicY_half0
-    periodicZ
+    {
-    (
+        type cyclic;
-        (0 3 2 1)
+        faces ((2 3 7 6));
-        (4 5 6 7)
+        neighbourPatch periodicY_half1;
-    )
+    }
-)
+
+    periodicY_half1
+    {
+        type cyclic;
+        faces ((0 1 5 4));
+        neighbourPatch periodicY_half0;
+    }
+
+    periodicZ_half0
+    {
+        type cyclic;
+        faces ((4 5 6 7));
+        neighbourPatch periodicZ_half1;
+    }
+
+    periodicZ_half1
+    {
+        type cyclic;
+        faces ((0 3 2 1));
+        neighbourPatch periodicZ_half0;
+    }
+);
 
 mergePatchPairs
 (

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict

@@ -22,7 +22,7 @@ startTime       0;
 
 stopAt          endTime;
 
-endTime         1e-10;
+endTime         5e-11;
 
 deltaT          1e-14;
 

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/0/U

@@ -0,0 +1,51 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       volVectorField;
+    location    "0";
+    object      U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions      [ 0 1 -1 0 0 0 0 ];
+
+internalField   uniform ( 0 0 0 );
+
+boundaryField
+{
+    periodicX_half0
+    {
+        type            cyclic;
+    }
+    periodicY_half0
+    {
+        type            cyclic;
+    }
+    periodicZ_half0
+    {
+        type            cyclic;
+    }
+    periodicY_half1
+    {
+        type            cyclic;
+    }
+    periodicZ_half1
+    {
+        type            cyclic;
+    }
+    periodicX_half1
+    {
+        type            cyclic;
+    }
+}
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict

@@ -34,29 +34,50 @@ blocks
     hex (0 1 2 3 4 5 6 7) liquid (12 12 11) simpleGrading (1 1 1)
 );
 
-patches
+boundary
 (
-    cyclic
+    periodicX_half0
-    periodicX
+    {
-    (
+        type cyclic;
-        (1 2 6 5)
+        faces ((1 2 6 5));
-        (0 4 7 3)
+        neighbourPatch periodicX_half1;
-    )
+    }
 
-    cyclic
+    periodicX_half1
-    periodicY
+    {
-    (
+        type cyclic;
-        (2 3 7 6)
+        faces ((0 4 7 3));
-        (0 1 5 4)
+        neighbourPatch periodicX_half0;
-    )
+    }
 
-    cyclic
+    periodicY_half0
-    periodicZ
+    {
-    (
+        type cyclic;
-        (0 3 2 1)
+        faces ((2 3 7 6));
-        (4 5 6 7)
+        neighbourPatch periodicY_half1;
-    )
+    }
-)
+
+    periodicY_half1
+    {
+        type cyclic;
+        faces ((0 1 5 4));
+        neighbourPatch periodicY_half0;
+    }
+
+    periodicZ_half0
+    {
+        type cyclic;
+        faces ((4 5 6 7));
+        neighbourPatch periodicZ_half1;
+    }
+
+    periodicZ_half1
+    {
+        type cyclic;
+        faces ((0 3 2 1));
+        neighbourPatch periodicZ_half0;
+    }
+);
 
 mergePatchPairs
 (

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict

@@ -22,13 +22,13 @@ startTime       0;
 
 stopAt          endTime;
 
-endTime         5e-12;
+endTime         2e-13;
 
 deltaT          1e-15;
 
 writeControl    runTime;
 
-writeInterval   2e-13;
+writeInterval   5e-14;
 
 purgeWrite      0;