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tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean

@@ -0,0 +1,30 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+
+# Source tutorial clean functions
+. $WM_PROJECT_DIR/bin/tools/CleanFunctions
+
+(
+    cd periodicCubeArgon || exit
+
+    rm -rf 0/lagrangian 0/uniform
+    rm -f Ar-Ar
+    rm -f electrostatic
+    rm -f constant/idList
+    rm -rf constant/polyMesh/sets
+    cleanCase
+)
+
+
+(
+    cd periodicCubeWater || exit
+
+    rm -rf 0/lagrangian 0/uniform
+    rm -f O-O
+    rm -f electrostatic
+    rm -f constant/idList
+    rm -rf constant/polyMesh/sets
+    cleanCase
+)
+
+# ----------------------------------------------------------------- end-of-file

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun

@@ -0,0 +1,18 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+
+
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+for caseName in periodicCubeArgon periodicCubeWater
+do
+(
+    cd $caseName || exit
+
+    runApplication blockMesh
+    runApplication mdInitialise
+    runApplication `getApplication`
+)
+done
+# ----------------------------------------------------------------- end-of-file

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.org                      |
+|    \\/     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/moleculeProperties

@@ -0,0 +1,36 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+Ar
+{
+    siteIds                     (Ar);
+    pairPotentialSiteIds        (Ar);
+    siteReferencePositions
+    (
+        (0 0 0)
+    );
+    siteMasses
+    (
+        6.63352033e-26
+    );
+    siteCharges
+    (
+        0
+    );
+}
+
+// ************************************************************************* //

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

@@ -0,0 +1,87 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      blockMeshDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 2.462491658e-9;
+
+vertices
+(
+    (-1 -1 -1)
+    (1 -1 -1)
+    (1 1 -1)
+    (-1 1 -1)
+    (-1 -1 1)
+    (1 -1 1)
+    (1 1 1)
+    (-1 1 1)
+);
+
+blocks
+(
+    hex (0 1 2 3 4 5 6 7) liquid (12 12 12) simpleGrading (1 1 1)
+);
+
+boundary
+(
+    periodicX_half0
+    {
+        type cyclic;
+        faces ((1 2 6 5));
+        neighbourPatch periodicX_half1;
+    }
+
+    periodicX_half1
+    {
+        type cyclic;
+        faces ((0 4 7 3));
+        neighbourPatch periodicX_half0;
+    }
+
+    periodicY_half0
+    {
+        type cyclic;
+        faces ((2 3 7 6));
+        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

@@ -0,0 +1,49 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application     mdEquilibrationFoam;
+
+startFrom       startTime;
+
+startTime       0;
+
+stopAt          endTime;
+
+endTime         5e-11;
+
+deltaT          1e-14;
+
+writeControl    runTime;
+
+writeInterval   5e-12;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  12;
+
+writeCompression off;
+
+timeFormat      general;
+
+timePrecision   6;
+
+runTimeModifiable true;
+
+adjustTimeStep  no;
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/decomposeParDict

@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 2;
+
+method              simple;
+
+simpleCoeffs
+{
+    n               (2 1 1);
+    delta           0.001;
+}
+
+hierarchicalCoeffs
+{
+    n               (1 1 1);
+    delta           0.001;
+    order           xyz;
+}
+
+manualCoeffs
+{
+    dataFile        "";
+}
+
+distributed     no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSchemes

@@ -0,0 +1,54 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+    default         none;
+}
+
+gradSchemes
+{
+    default         none;
+}
+
+divSchemes
+{
+    default         none;
+}
+
+laplacianSchemes
+{
+    default         none;
+}
+
+interpolationSchemes
+{
+    default         none;
+}
+
+snGradSchemes
+{
+    default         none;
+}
+
+fluxRequired
+{
+    default         no;
+}
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSolution

@@ -0,0 +1,22 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSolution;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+solvers
+{
+}
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdEquilibrationDict

@@ -0,0 +1,20 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+targetTemperature  300.0;
+
+// ************************************************************************* //
+

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdInitialiseDict

@@ -0,0 +1,37 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+liquid
+{
+    massDensity             1220;
+    temperature             300;
+    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);
+}
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/potentialDict

@@ -0,0 +1,121 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+n|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// 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 ( Ar );
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Potential Energy Limit
+
+// Maximum permissible pair energy allowed at startup.  Used to remove
+// overlapping molecules created during preprocessing.
+
+potentialEnergyLimit 1e-18;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Pair potentials
+
+// 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 combinaition of their ids,
+// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
+// (strictly OR, both or neither is an error)
+
+pair
+{
+    Ar-Ar
+    {
+        pairPotential   maitlandSmith;
+        rCut            1.0e-9;
+        rMin            0.15e-9;
+        dr              5e-14;
+        maitlandSmithCoeffs
+        {
+            m           13.0;
+            gamma       7.5;
+            rm          0.3756e-9;
+            epsilon     1.990108438e-21;
+        }
+        energyScalingFunction   doubleSigmoid;
+        doubleSigmoidCoeffs
+        {
+            shift1      0.9e-9;
+            scale1      0.3e11;
+            shift2      0.97e-9;
+            scale2      1.2e11;
+        }
+        writeTables     yes;
+    }
+
+    electrostatic
+    {
+        pairPotential   dampedCoulomb;
+        rCut            1.0e-9;
+        rMin            0.1e-9;
+        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);
+}
+
+
+// ************************************************************************* //

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.org                      |
+|    \\/     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/moleculeProperties

@@ -0,0 +1,72 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+water
+{
+    siteIds                     (H H O M);
+    pairPotentialSiteIds        (O);
+    siteReferencePositions
+    (
+        (7.56950327263661e-11 5.85882276618295e-11 0)
+        (-7.56950327263661e-11 5.85882276618295e-11 0)
+        (0 0 0)
+        (0 1.5e-11 0)
+    );
+    siteMasses
+    (
+        1.67353255e-27
+        1.67353255e-27
+        2.6560176e-26
+        0
+    );
+    siteCharges
+    (
+        8.3313177324e-20
+        8.3313177324e-20
+        0
+        -1.66626354648e-19
+    );
+}
+
+water2
+{
+    siteIds                     (H2 H2 O M2);
+    pairPotentialSiteIds        (O);
+    siteReferencePositions
+    (
+        (7.56950327263661e-11 5.85882276618295e-11 0)
+        (-7.56950327263661e-11 5.85882276618295e-11 0)
+        (0 0 0)
+        (0 1.5e-11 0)
+    );
+    siteMasses
+    (
+        1.67353255e-27
+        1.67353255e-27
+        2.6560176e-26
+        0
+    );
+    siteCharges
+    (
+        8.3313177324e-20
+        8.3313177324e-20
+        0
+        -1.66626354648e-19
+    );
+}
+
+// ************************************************************************* //

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

@@ -0,0 +1,87 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      blockMeshDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 2.10840e-9;
+
+vertices
+(
+    (-1 -1 -1)
+    (1 -1 -1)
+    (1 1 -1)
+    (-1 1 -1)
+    (-1 -1 1)
+    (1 -1 1)
+    (1 1 1)
+    (-1 1 1)
+);
+
+blocks
+(
+    hex (0 1 2 3 4 5 6 7) liquid (12 12 11) simpleGrading (1 1 1)
+);
+
+boundary
+(
+    periodicX_half0
+    {
+        type cyclic;
+        faces ((1 2 6 5));
+        neighbourPatch periodicX_half1;
+    }
+
+    periodicX_half1
+    {
+        type cyclic;
+        faces ((0 4 7 3));
+        neighbourPatch periodicX_half0;
+    }
+
+    periodicY_half0
+    {
+        type cyclic;
+        faces ((2 3 7 6));
+        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/periodicCubeWater/system/controlDict

@@ -0,0 +1,49 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application     mdEquilibrationFoam;
+
+startFrom       startTime;
+
+startTime       0;
+
+stopAt          endTime;
+
+endTime         5e-12;
+
+deltaT          1e-15;
+
+writeControl    runTime;
+
+writeInterval   2e-13;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  12;
+
+writeCompression off;
+
+timeFormat      general;
+
+timePrecision   6;
+
+runTimeModifiable true;
+
+adjustTimeStep  no;
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/decomposeParDict

@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 4;
+
+method              simple;
+
+simpleCoeffs
+{
+    n               (2 2 1);
+    delta           0.001;
+}
+
+hierarchicalCoeffs
+{
+    n               (1 1 1);
+    delta           0.001;
+    order           xyz;
+}
+
+manualCoeffs
+{
+    dataFile        "";
+}
+
+distributed     no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSchemes

@@ -0,0 +1,54 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+    default         none;
+}
+
+gradSchemes
+{
+    default         none;
+}
+
+divSchemes
+{
+    default         none;
+}
+
+laplacianSchemes
+{
+    default         none;
+}
+
+interpolationSchemes
+{
+    default         none;
+}
+
+snGradSchemes
+{
+    default         none;
+}
+
+fluxRequired
+{
+    default         no;
+}
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSolution

@@ -0,0 +1,22 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSolution;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+solvers
+{
+}
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdEquilibrationDict

@@ -0,0 +1,19 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+targetTemperature  298;
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdInitialiseDict

@@ -0,0 +1,46 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+liquid
+{
+    massDensity             980;
+    temperature             298;
+    bulkVelocity            (0.0 0.0 0.0);
+    latticeIds
+    (
+        water
+        water2
+        water
+        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);
+}
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/potentialDict

@@ -0,0 +1,118 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// 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 combinaition 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);
+}
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/0/U

@@ -0,0 +1,55 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     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
+{
+    sectionAEnd
+    {
+        type            fixedValue;
+        value           uniform (0 0 0);
+    }
+    sectionCEnd
+    {
+        type            fixedValue;
+        value           uniform (0 0 0);
+    }
+    front
+    {
+        type            fixedValue;
+        value           uniform (0 0 0);
+    }
+    back
+    {
+        type            fixedValue;
+        value           uniform (0 0 0);
+    }
+    top
+    {
+        type            fixedValue;
+        value           uniform (0 0 0);
+    }
+    bottom
+    {
+        type            fixedValue;
+        value           uniform (0 0 0);
+    }
+}
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/Allclean

@@ -0,0 +1,11 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+
+# Source tutorial clean functions
+. $WM_PROJECT_DIR/bin/tools/CleanFunctions
+
+rm -rf constant/polyMesh/sets
+rm -rf processor[0-9]
+cleanCase
+
+# ----------------------------------------------------------------- end-of-file

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/Allrun

@@ -0,0 +1,19 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+
+
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+application=`getApplication`
+
+runApplication blockMesh
+
+runApplication decomposePar
+
+runParallel mdInitialise 4
+runParallel $application 4
+
+runApplication reconstructPar
+
+# ----------------------------------------------------------------- end-of-file

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties

@@ -0,0 +1,45 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "constant";
+    object      moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+water
+{
+    siteIds                     (H H O M);
+    pairPotentialSiteIds        (O);
+    siteReferencePositions
+    (
+        (7.56950327263661e-11 5.85882276618295e-11 0)
+        (-7.56950327263661e-11 5.85882276618295e-11 0)
+        (0 0 0)
+        (0 1.5e-11 0)
+    );
+    siteMasses
+    (
+        1.67353255e-27
+        1.67353255e-27
+        2.6560176e-26
+        0
+    );
+    siteCharges
+    (
+        8.3313177324e-20
+        8.3313177324e-20
+        0
+        -1.66626354648e-19
+    );
+}
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict

@@ -0,0 +1,136 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      blockMeshDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 3.2e-9;
+
+vertices
+(
+    (0 0 0)
+    (3.5 0 0)
+    (3.5 3 0)
+    (0 3 0)
+    (0 0 3)
+    (3.5 0 3)
+    (3.5 3 3)
+    (0 3 3)
+    (7.5 1 0.5)
+    (7.5 2 0.5)
+    (7.5 1 2.5)
+    (7.5 2 2.5)
+    (10 1 0.5)
+    (10 2 0.5)
+    (10 1 2.5)
+    (10 2 2.5)
+    (11.5 0.5 -0.5)
+    (11.5 2.5 -0.5)
+    (11.5 0.5 3.5)
+    (11.5 2.5 3.5)
+    (16 0.5 -0.5)
+    (16 2.5 -0.5)
+    (16 0.5 3.5)
+    (16 2.5 3.5)
+);
+
+blocks
+(
+    hex (0 1 2 3 4 5 6 7) sectionA (20 16 16) simpleGrading (1 1 1)
+    hex (1 8 9 2 5 10 11 6) sectionA (20 16 16) simpleGrading (1 1 1)
+    hex (8 12 13 9 10 14 15 11) sectionB (29 16 16) simpleGrading (1 1 1)
+    hex (12 16 17 13 14 18 19 15) sectionC (17 16 16) simpleGrading (1 1 1)
+    hex (16 20 21 17 18 22 23 19) sectionC (20 16 16) simpleGrading (1 1 1)
+);
+
+edges
+();
+
+boundary
+(
+    sectionAEnd
+    {
+        type patch;
+        faces
+        (
+            (0 4 7 3)
+        );
+    }
+
+    sectionCEnd
+    {
+        type wall;
+        faces
+        (
+            (20 21 23 22)
+        );
+    }
+
+    front
+    {
+        type wall;
+        faces
+        (
+            (0 1 5 4)
+            (1 8 10 5)
+            (8 12 14 10)
+            (12 16 18 14)
+            (16 20 22 18)
+        );
+    }
+
+    back
+    {
+        type wall;
+        faces
+        (
+            (2 3 7 6)
+            (2 6 11 9)
+            (9 11 15 13)
+            (13 15 19 17)
+            (17 19 23 21)
+        );
+    }
+
+    top
+    {
+        type wall;
+        faces
+        (
+            (4 5 6 7)
+            (5 10 11 6)
+            (10 14 15 11)
+            (14 18 19 15)
+            (18 22 23 19)
+        );
+    }
+
+    bottom
+    {
+        type wall;
+        faces
+        (
+            (0 3 2 1)
+            (1 2 9 8)
+            (8 9 13 12)
+            (12 13 17 16)
+            (16 17 21 20)
+        );
+    }
+);
+
+mergePatchPairs
+(
+);
+
+// ************************************************************************* //

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

@@ -0,0 +1,49 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application     mdFoam;
+
+startFrom       startTime;
+
+startTime       0;
+
+stopAt          endTime;
+
+endTime         2e-13;
+
+deltaT          1e-15;
+
+writeControl    runTime;
+
+writeInterval   5e-14;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  12;
+
+writeCompression off;
+
+timeFormat      general;
+
+timePrecision   6;
+
+runTimeModifiable true;
+
+adjustTimeStep  no;
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/decomposeParDict

@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 4;
+
+method              scotch;
+
+simpleCoeffs
+{
+    n               (2 2 1);
+    delta           0.001;
+}
+
+hierarchicalCoeffs
+{
+    n               (1 1 1);
+    delta           0.001;
+    order           xyz;
+}
+
+manualCoeffs
+{
+    dataFile        "";
+}
+
+distributed     no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes

@@ -0,0 +1,54 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+    default         none;
+}
+
+gradSchemes
+{
+    default         none;
+}
+
+divSchemes
+{
+    default         none;
+}
+
+laplacianSchemes
+{
+    default         none;
+}
+
+interpolationSchemes
+{
+    default         none;
+}
+
+snGradSchemes
+{
+    default         none;
+}
+
+fluxRequired
+{
+    default         no;
+}
+
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution

@@ -0,0 +1,22 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSolution;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+solvers
+{
+}
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict

@@ -0,0 +1,19 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+targetTemperature  298;
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdInitialiseDict

@@ -0,0 +1,78 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// 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
+    (
+        water
+    );
+    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
+    (
+        water
+    );
+    tetherSiteIds           ();
+    latticePositions
+    (
+        (0 0 0)
+    );
+    anchor                  (0 0 0);
+    orientationAngles       (0 0 0);
+    latticeCellShape        (1 1 1);
+}
+
+// ************************************************************************* //

tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/potentialDict

@@ -0,0 +1,118 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// 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 combinaition 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);
+}
+
+
+// ************************************************************************* //