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New MD tutorials.

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This commit is contained in:
graham
2009-06-29 16:34:27 +01:00
parent c73fa61a97
commit 786a2621ad
46 changed files with 1088 additions and 917 deletions
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8
tutorials/compressible/rhoCentralFoam/LadenburgJet60psi/system/machines
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@ -1,8 +0,0 @@
borg1
borg2
borg3
borg4
borg5
borg6
borg7
borg8

163
tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict
View File

@ -1,163 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
object blockMeshDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
convertToMeters 0.25e-9;
vertices
(
(0 0 0) //0
(15 0 0)
(15 3 0)
(0 3 0)
(0 0 12)
(15 0 12)
(15 3 12)
(0 3 12) //7
(22 0 0)
(22 3 0)
(22 0 12)
(22 3 12) //11
(31 0 0)
(31 3 0)
(31 0 12)
(31 3 12) //15
(20 9 0)
(17 9 0)
(20 9 12)
(17 9 12) //19
(0 9 0)
(0 9 12) //21
(31 9 0)
(31 9 12) //23
(17 18 0)
(0 18 0)
(17 18 12)
(0 18 12) //27
(31 18 0)
(20 18 0)
(31 18 12)
(20 18 12) //31
(17 21 0)
(0 21 0)
(17 21 12)
(0 21 12) //35
(31 21 0)
(20 21 0)
(31 21 12)
(20 21 12) //39
(17 25 0)
(0 25 0)
(17 25 12)
(0 25 12) // 43
(31 25 0)
(20 25 0)
(31 25 12)
(20 25 12) // 47
);
blocks
(
hex (0 1 2 3 4 5 6 7) bottomWall (15 3 6) simpleGrading (1 1 1) //1
hex (1 8 9 2 5 10 11 6) bottomWall (3 3 6) simpleGrading (1 1 1) //2
hex (2 9 16 17 6 11 18 19) bottomWall (3 6 6) simpleGrading (1 1 1) //3
hex (8 12 13 9 10 14 15 11) bottomWall (9 3 6) simpleGrading (1 1 1) //4
hex (3 2 17 20 7 6 19 21) liquid (15 6 6) simpleGrading (1 1 1) //5
hex (20 17 24 25 21 19 26 27) liquid (15 9 6) simpleGrading (1 1 1) //6
hex (25 24 32 33 27 26 34 35) liquid (15 3 6) simpleGrading (1 1 1) //6A
hex (17 16 29 24 19 18 31 26) liquid (3 9 6) simpleGrading (1 1 1) //7
hex (16 22 28 29 18 23 30 31) liquid (9 9 6) simpleGrading (1 1 1) //8
hex (29 28 36 37 31 30 38 39) liquid (9 3 6) simpleGrading (1 1 1) //8A
hex (9 13 22 16 11 15 23 18) liquid (9 6 6) simpleGrading (1 1 1) //9
hex (33 32 40 41 35 34 42 43) topWall (15 3 6) simpleGrading (1 1 1) //10
hex (32 37 45 40 34 39 47 42) topWall (3 3 6) simpleGrading (1 1 1) //11
hex (24 29 37 32 26 31 39 34) topWall (3 3 6) simpleGrading (1 1 1) //12
hex (37 36 44 45 39 38 46 47) topWall (9 3 6) simpleGrading (1 1 1) //13
);
patches
(
cyclic
periodicX
(
(0 4 7 3)
(3 7 21 20)
(20 21 27 25)
(25 27 35 33)
(33 35 43 41)
(12 13 15 14)
(13 22 23 15)
(22 28 30 23)
(28 36 38 30)
(36 44 46 38)
)
cyclic
periodicZ
(
(0 3 2 1)
(1 2 9 8)
(8 9 13 12)
(2 17 16 9)
(2 3 20 17)
(9 16 22 13)
(17 20 25 24)
(16 29 28 22)
(16 17 24 29)
(24 25 33 32)
(28 29 37 36)
(32 33 41 40)
(36 37 45 44)
(32 40 45 37)
(24 32 37 29)
(4 5 6 7)
(5 10 11 6)
(10 14 15 11)
(6 11 18 19)
(7 6 19 21)
(11 15 23 18)
(19 26 27 21)
(18 23 30 31)
(18 31 26 19)
(26 34 35 27)
(30 38 39 31)
(34 42 43 35)
(38 46 47 39)
(34 39 47 42)
(26 31 39 34)
)
wall
outerBoundaryBottom
(
(0 1 5 4)
(1 8 10 5)
(8 12 14 10)
)
wall
outerBoundaryTop
(
(40 41 43 42)
(44 45 47 46)
(40 42 47 45)
)
);
mergePatchPairs
(
);
// ************************************************************************* //

46
tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSolution
View File

@ -1,46 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
solvers
{
p
{
solver PCG;
preconditioner DIC;
tolerance 1e-06;
relTol 0;
}
U
{
solver PBiCG;
preconditioner DILU;
tolerance 1e-05;
relTol 0;
}
}
PISO
{
nCorrectors 2;
nNonOrthogonalCorrectors 0;
pRefCell 0;
pRefValue 0;
}
// ************************************************************************* //

64
tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/molConfigDict
View File

@ -1,64 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object molConfigDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
bottomWall
{
massDensity 1220;
temperature 300;
velocityDistribution maxwellian;
bulkVelocity ( 0 0 0 );
id Ar;
mass 6.63352033e-26;
latticeStructure FCC;
anchor ( 1.05e-09 3.18e-09 2.87e-09 );
anchorSpecifies molecule;
tethered yes;
orientationAngles ( 30 0 0 );
}
liquid
{
massDensity 1100;
temperature 250;
velocityDistribution maxwellian;
bulkVelocity ( 245 0 0 );
id Ne;
mass 3.350996347e-26;
latticeStructure SC;
anchor ( 1.05e-09 3.18e-09 2.87e-09 );
anchorSpecifies molecule;
tethered no;
orientationAngles ( 45 0 0 );
}
topWall
{
massDensity 1220;
temperature 200;
velocityDistribution maxwellian;
bulkVelocity ( 0 0 0 );
id Ar;
mass 6.63352033e-26;
latticeStructure BCC;
anchor ( 1.05e-09 3.18e-09 2.87e-09 );
anchorSpecifies corner;
tethered yes;
orientationAngles ( 0 0 0 );
}
// ************************************************************************* //

104
tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/potentialDict
View File

@ -1,104 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object potentialDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
removalOrder 2 ( Ne Ar );
pair
{
Ar-Ar
{
pairPotential maitlandSmith;
rCut 1e-09;
rMin 1.5e-10;
dr 5e-14;
maitlandSmithCoeffs
{
m 13;
gamma 7.5;
rm 3.756e-10;
epsilon 1.990108438e-21;
}
energyScalingFunction doubleSigmoid;
doubleSigmoidCoeffs
{
shift1 9e-10;
scale1 -64771072;
shift2 9.7e-10;
scale2 -259084288;
}
writeTables yes;
}
Ar-Ne
{
pairPotential maitlandSmith;
rCut 9e-10;
rMin 1e-10;
dr 5e-14;
maitlandSmithCoeffs
{
m 13;
gamma 4;
rm 3.48e-10;
epsilon 8.765026657e-22;
}
energyScalingFunction shiftedForce;
writeTables yes;
}
Ne-Ne
{
pairPotential maitlandSmith;
rCut 8e-10;
rMin 1e-10;
dr 5e-14;
maitlandSmithCoeffs
{
m 13;
gamma 5;
rm 3.0739e-10;
epsilon 5.813260729e-22;
}
energyScalingFunction shiftedForce;
writeTables yes;
}
}
tether
{
Ar
{
tetherPotential restrainedHarmonicSpring;
restrainedHarmonicSpringCoeffs
{
springConstant 0.1;
rR 1.2e-09;
}
}
}
external
{
gravity ( 0 0 0 );
}
// ************************************************************************* //

46
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSolution
View File

@ -1,46 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
solvers
{
p
{
solver PCG;
preconditioner DIC;
tolerance 1e-06;
relTol 0;
}
U
{
solver PBiCG;
preconditioner DILU;
tolerance 1e-05;
relTol 0;
}
}
PISO
{
nCorrectors 2;
nNonOrthogonalCorrectors 0;
pRefCell 0;
pRefValue 0;
}
// ************************************************************************* //

64
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/molConfigDict
View File

@ -1,64 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object molConfigDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
sectionA
{
massDensity 1220;
temperature 300;
velocityDistribution maxwellian;
bulkVelocity ( -250 0 0 );
id Ar;
mass 6.63352033e-26;
latticeStructure SC;
anchor ( 0 0 0 );
anchorSpecifies molecule;
tethered no;
orientationAngles ( 0 0 0 );
}
sectionB
{
massDensity 1220;
temperature 300;
velocityDistribution maxwellian;
bulkVelocity ( -250 0 0 );
id Ne;
mass 3.350917e-26;
latticeStructure SC;
anchor ( 0 0 0 );
anchorSpecifies molecule;
tethered no;
orientationAngles ( 0 0 0 );
}
sectionC
{
massDensity 1220;
temperature 300;
velocityDistribution maxwellian;
bulkVelocity ( -250 0 0 );
id Ar;
mass 6.63352033e-26;
latticeStructure SC;
anchor ( 0 0 0 );
anchorSpecifies molecule;
tethered no;
orientationAngles ( 0 0 0 );
}
// ************************************************************************* //

86
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/potentialDict
View File

@ -1,86 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object potentialDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
removalOrder 1 ( Ar );
pair
{
Ar-Ar
{
pairPotential maitlandSmith;
rCut 1e-09;
rMin 1.5e-10;
dr 5e-14;
maitlandSmithCoeffs
{
m 13;
gamma 7.5;
rm 3.756e-10;
epsilon 1.990108438e-21;
}
energyScalingFunction doubleSigmoid;
doubleSigmoidCoeffs
{
shift1 9e-10;
scale1 -64771072;
shift2 9.7e-10;
scale2 -259084288;
}
writeTables no;
}
Ar-Ne
{
pairPotential maitlandSmith;
rCut 9e-10;
rMin 1e-10;
dr 5e-14;
maitlandSmithCoeffs
{
m 13;
gamma 4;
rm 3.48e-10;
epsilon 8.765026657e-22;
}
energyScalingFunction shiftedForce;
writeTables no;
}
Ne-Ne
{
pairPotential maitlandSmith;
rCut 8e-10;
rMin 1e-10;
dr 5e-14;
maitlandSmithCoeffs
{
m 13;
gamma 5;
rm 3.0739e-10;
epsilon 5.813260729e-22;
}
energyScalingFunction shiftedForce;
writeTables no;
}
}
// ************************************************************************* //

19
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
View File

@ -3,9 +3,20 @@
# Source tutorial clean functions # Source tutorial clean functions
. $WM_PROJECT_DIR/bin/tools/CleanFunctions . $WM_PROJECT_DIR/bin/tools/CleanFunctions
cd periodicCube cd periodicCubeArgon
rm -rf 0 rm -rf 0/*
rm -rf Ar-Ar rm -f Ar-Ar
rm -rf constant/idList rm -f electrostatic
rm -f constant/idList
rm -rf constant/polyMesh/sets
cleanCase
cd ..
cd periodicCubeWater
rm -rf 0/*
rm -f O-O
rm -f electrostatic
rm -f constant/idList
rm -rf constant/polyMesh/sets
cleanCase cleanCase
cd .. cd ..

11
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun
View File

@ -5,9 +5,14 @@
application="mdEquilibrationFoam" application="mdEquilibrationFoam"
cd periodicCube # cd periodicCubeArgon
# runApplication blockMesh
# runApplication mdInitialise
# runApplication $application
# cd ..
cd periodicCubeWater
runApplication blockMesh runApplication blockMesh
runApplication molConfig runApplication mdInitialise
runApplication $application runApplication $application
cd .. cd ..

46
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSolution
View File

@ -1,46 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
solvers
{
p
{
solver PCG;
preconditioner DIC;
tolerance 1e-06;
relTol 0;
}
U
{
solver PBiCG;
preconditioner DILU;
tolerance 1e-05;
relTol 0;
}
}
PISO
{
nCorrectors 2;
nNonOrthogonalCorrectors 0;
pRefCell 0;
pRefValue 0;
}
// ************************************************************************* //

34
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/molConfigDict
View File

@ -1,34 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object molConfigDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
liquid
{
massDensity 1220;
temperature 300;
velocityDistribution maxwellian;
bulkVelocity ( 0 0 0 );
id Ar;
mass 6.63352033e-26;
latticeStructure SC;
anchor ( 0 0 0 );
anchorSpecifies molecule;
tethered no;
orientationAngles ( 0 0 0 );
}
// ************************************************************************* //

65
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/potentialDict
View File

@ -1,65 +0,0 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object potentialDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
removalOrder 1 ( Ar );
pair
{
Ar-Ar
{
pairPotential azizChen;
rCut 1.2e-09;
rMin 1.5e-10;
dr 2e-14;
azizChenCoeffs
{
epsilon 1.97742255e-21;
rm 3.759e-10;
A 9502720;
alpha 16.345655;
C6 1.0914254;
C8 0.6002595;
C10 0.3700113;
D 1.4;
gamma 2;
}
energyScalingFunction noScaling;
writeTables yes;
}
}
tether
{
Ar
{
tetherPotential restrainedHarmonicSpring;
restrainedHarmonicSpringCoeffs
{
springConstant 0.0277;
rR 1.2e-09;
}
}
}
external
{
gravity ( 0 0 0 );
}
// ************************************************************************* //

36
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/moleculeProperties Normal file
View File

@ -0,0 +1,36 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: dev |
| \\ / A nd | Web: http://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
);
}
// ************************************************************************* //

15
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
View File

@ -1,17 +1,25 @@
/*--------------------------------*- C++ -*----------------------------------*\ /*---------------------------------------------------------------------------*\
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: 1.3 |
| \\ / A nd | Web: http://www.OpenFOAM.org | | \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile
{ {
version 2.0; version 2.0;
format ascii; format ascii;
root "";
case "";
instance "";
local "";
class dictionary; class dictionary;
object blockMeshDict; object blockMeshDict;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
convertToMeters 2.462491658e-9; convertToMeters 2.462491658e-9;
@ -61,4 +69,5 @@ mergePatchPairs
( (
); );
// ************************************************************************* // // ************************************************************************* //

4
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/boundary
View File

@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\ /*--------------------------------*- C++ -*----------------------------------*\
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: dev |
| \\ / A nd | Web: http://www.OpenFOAM.org | | \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile

4
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/controlDict → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
View File

@ -2,7 +2,7 @@
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org | | \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile
@ -10,7 +10,6 @@ FoamFile
version 2.0; version 2.0;
format ascii; format ascii;
class dictionary; class dictionary;
location "system";
object controlDict; object controlDict;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -45,5 +44,4 @@ runTimeModifiable yes;
adjustTimeStep no; adjustTimeStep no;
// ************************************************************************* // // ************************************************************************* //

64
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/decomposeParDict Normal file
View File

@ -0,0 +1,64 @@
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.3 |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
root "";
case "";
instance "";
local "";
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;
}
metisCoeffs
{
processorWeights
(
1
3
);
}
manualCoeffs
{
dataFile "";
}
distributed no;
roots
(
);
// ************************************************************************* //

14
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSchemes → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSchemes
View File

@ -17,43 +17,37 @@ FoamFile
ddtSchemes ddtSchemes
{ {
default Euler; default none;
} }
gradSchemes gradSchemes
{ {
default Gauss linear; default none;
grad(p) Gauss linear;
} }
divSchemes divSchemes
{ {
default none; default none;
div(phi,U) Gauss linear;
} }
laplacianSchemes laplacianSchemes
{ {
default none; default none;
laplacian(nu,U) Gauss linear corrected;
laplacian(1|A(U),p) Gauss linear corrected;
} }
interpolationSchemes interpolationSchemes
{ {
default linear; default none;
interpolate(HbyA) linear;
} }
snGradSchemes snGradSchemes
{ {
default corrected; default none;
} }
fluxRequired fluxRequired
{ {
default no; default no;
p ;
} }

7
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSolution
View File

@ -11,11 +11,12 @@ FoamFile
format ascii; format ascii;
class dictionary; class dictionary;
location "system"; location "system";
object mdEquilibrationDict; object fvSolution;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
equilibrationTargetTemperature 300; solvers
{
}
// ************************************************************************* // // ************************************************************************* //

19
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdEquilibrationDict Normal file
View File

@ -0,0 +1,19 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
object mdEquilibrationDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
equilibrationTargetTemperature 300.0;
// ************************************************************************* //

44
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdInitialiseDict Normal file
View File

@ -0,0 +1,44 @@
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.3 |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
root "";
case "";
instance "";
local "";
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);
}
// ************************************************************************* //

121
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/potentialDict Normal file
View File

@ -0,0 +1,121 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: http://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);
}
// ************************************************************************* //

72
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/moleculeProperties Normal file
View File

@ -0,0 +1,72 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: dev |
| \\ / A nd | Web: http://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
);
}
// ************************************************************************* //

73
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict Normal file
View File

@ -0,0 +1,73 @@
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.3 |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
root "";
case "";
instance "";
local "";
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)
);
patches
(
cyclic
periodicX
(
(1 2 6 5)
(0 4 7 3)
)
cyclic
periodicY
(
(2 3 7 6)
(0 1 5 4)
)
cyclic
periodicZ
(
(0 3 2 1)
(4 5 6 7)
)
)
mergePatchPairs
(
);
// ************************************************************************* //

33
tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/boundary → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/boundary
View File

@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\ /*--------------------------------*- C++ -*----------------------------------*\
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: dev |
| \\ / A nd | Web: http://www.OpenFOAM.org | | \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile
@ -15,34 +15,29 @@ FoamFile
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
4 3
( (
periodicX periodicX
{ {
type cyclic; type cyclic;
nFaces 288; nFaces 264;
startFace 10710; startFace 4344;
featureCos 0.9;
}
periodicY
{
type cyclic;
nFaces 264;
startFace 4608;
featureCos 0.9; featureCos 0.9;
} }
periodicZ periodicZ
{ {
type cyclic; type cyclic;
nFaces 1296; nFaces 288;
startFace 10998; startFace 4872;
featureCos 0.9; featureCos 0.9;
} }
outerBoundaryBottom
{
type wall;
nFaces 162;
startFace 12294;
}
outerBoundaryTop
{
type wall;
nFaces 162;
startFace 12456;
}
) )
// ************************************************************************* // // ************************************************************************* //

10
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/controlDict → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/controlDict
View File

@ -2,7 +2,7 @@
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org | | \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile
@ -10,7 +10,6 @@ FoamFile
version 2.0; version 2.0;
format ascii; format ascii;
class dictionary; class dictionary;
location "system";
object controlDict; object controlDict;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -21,13 +20,13 @@ startTime 0;
stopAt endTime; stopAt endTime;
endTime 3e-11; endTime 5e-12;
deltaT 1e-14; deltaT 1e-15;
writeControl runTime; writeControl runTime;
writeInterval 1e-12; writeInterval 2e-13;
purgeWrite 0; purgeWrite 0;
@ -45,5 +44,4 @@ runTimeModifiable yes;
adjustTimeStep no; adjustTimeStep no;
// ************************************************************************* // // ************************************************************************* //

30
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/decomposeParDict → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/decomposeParDict
View File

@ -1,27 +1,35 @@
/*--------------------------------*- C++ -*----------------------------------*\ /*---------------------------------------------------------------------------*\
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: 1.3 |
| \\ / A nd | Web: www.OpenFOAM.org | | \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile
{ {
version 2.0; version 2.0;
format ascii; format ascii;
root "";
case "";
instance "";
local "";
class dictionary; class dictionary;
location "system";
object decomposeParDict; object decomposeParDict;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
numberOfSubdomains 4; numberOfSubdomains 4;
method metis; method simple;
simpleCoeffs simpleCoeffs
{ {
n ( 4 1 1 ); n (2 2 1);
delta 0.001; delta 0.001;
} }
@ -34,7 +42,11 @@ hierarchicalCoeffs
metisCoeffs metisCoeffs
{ {
processorWeights ( 1 1 1 1 ); processorWeights
(
1
3
);
} }
manualCoeffs manualCoeffs
@ -44,7 +56,9 @@ manualCoeffs
distributed no; distributed no;
roots ( ); roots
(
);
// ************************************************************************* // // ************************************************************************* //

14
tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSchemes → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSchemes
View File

@ -17,43 +17,37 @@ FoamFile
ddtSchemes ddtSchemes
{ {
default Euler; default none;
} }
gradSchemes gradSchemes
{ {
default Gauss linear; default none;
grad(p) Gauss linear;
} }
divSchemes divSchemes
{ {
default none; default none;
div(phi,U) Gauss linear;
} }
laplacianSchemes laplacianSchemes
{ {
default none; default none;
laplacian(nu,U) Gauss linear corrected;
laplacian(1|A(U),p) Gauss linear corrected;
} }
interpolationSchemes interpolationSchemes
{ {
default linear; default none;
interpolate(HbyA) linear;
} }
snGradSchemes snGradSchemes
{ {
default corrected; default none;
} }
fluxRequired fluxRequired
{ {
default no; default no;
p ;
} }

9
tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/mdSolution → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSolution
View File

@ -11,13 +11,12 @@ FoamFile
format ascii; format ascii;
class dictionary; class dictionary;
location "system"; location "system";
object mdSolution; object fvSolution;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
integrationMethod verletLeapfrog; solvers
{
potentialEnergyLimit 5.256e-20; }
// ************************************************************************* // // ************************************************************************* //

10
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/mdSolution → tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdEquilibrationDict
View File

@ -2,7 +2,7 @@
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org | | \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile
@ -10,14 +10,10 @@ FoamFile
version 2.0; version 2.0;
format ascii; format ascii;
class dictionary; class dictionary;
location "system"; object mdEquilibrationDict;
object mdSolution;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
integrationMethod verletLeapfrog; targetTemperature 298;
potentialEnergyLimit 5.256e-20;
// ************************************************************************* // // ************************************************************************* //

53
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdInitialiseDict Normal file
View File

@ -0,0 +1,53 @@
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.3 |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
root "";
case "";
instance "";
local "";
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);
}
// ************************************************************************* //

118
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/potentialDict Normal file
View File

@ -0,0 +1,118 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: http://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);
}
// ************************************************************************* //

8
tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allclean → tutorials/discreteMethods/molecularDynamics/mdFoam/Allclean
View File

@ -3,14 +3,8 @@
# Source tutorial clean functions # Source tutorial clean functions
. $WM_PROJECT_DIR/bin/tools/CleanFunctions . $WM_PROJECT_DIR/bin/tools/CleanFunctions
cd constrictedChannel
rm -rf 0
rm -rf Ar-Ar Ar-Ne Ne-Ne
rm -rf constant/idList
cleanCase
cd ..
cd nanoNozzle cd nanoNozzle
rm -rf constant/polyMesh/sets
rm -rf processor[0-9] rm -rf processor[0-9]
cleanCase cleanCase
cd .. cd ..

10
tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allrun → tutorials/discreteMethods/molecularDynamics/mdFoam/Allrun
View File

@ -3,13 +3,7 @@
# Source tutorial run functions # Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions . $WM_PROJECT_DIR/bin/tools/RunFunctions
application="gnemdFoam" application="mdFoam"
cd constrictedChannel
runApplication blockMesh
runApplication molConfig
runApplication $application
cd ..
cd nanoNozzle cd nanoNozzle
runApplication blockMesh runApplication blockMesh
@ -17,7 +11,7 @@ cd nanoNozzle
runApplication decomposePar runApplication decomposePar
hostname > system/machines hostname > system/machines
runParallel molConfig 4 system/machines runParallel mdInitialise 4 system/machines
runParallel $application 4 system/machines runParallel $application 4 system/machines
runApplication reconstructPar runApplication reconstructPar

45
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties Normal file
View File

@ -0,0 +1,45 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: dev |
| \\ / A nd | Web: http://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
);
}
// ************************************************************************* //

44
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict → tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
View File

@ -14,7 +14,7 @@ FoamFile
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
convertToMeters 3e-9; convertToMeters 3.2e-9;
vertices vertices
( (
@ -46,43 +46,15 @@ vertices
blocks blocks
( (
hex (0 1 2 3 4 5 6 7) sectionA (16 15 15) simpleGrading (1 1 1) 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 (16 15 15) simpleGrading (0.4 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 (16 15 15) 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 (11 15 15) simpleGrading (2.8 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 (16 15 15) simpleGrading (1 1 1) hex (16 20 21 17 18 22 23 19) sectionC (20 16 16) simpleGrading (1 1 1)
); );
edges edges
( ();
simpleSpline 12 16
(
(10.375 0.875 0.4)
(10.75 0.75 0)
(11.125 0.625 -0.4)
)
simpleSpline 14 18
(
(10.375 0.875 2.6)
(10.75 0.75 3)
(11.125 0.625 3.4)
)
simpleSpline 15 19
(
(10.375 2.125 2.6)
(10.75 2.25 3)
(11.125 2.375 3.4)
)
simpleSpline 13 17
(
(10.375 2.125 0.4)
(10.75 2.25 0)
(11.125 2.375 -0.4)
)
);
patches patches
( (
@ -92,7 +64,7 @@ patches
(0 4 7 3) (0 4 7 3)
) )
patch wall
sectionCEnd sectionCEnd
( (
(20 21 23 22) (20 21 23 22)

30
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/boundary → tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/boundary
View File

@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\ /*--------------------------------*- C++ -*----------------------------------*\
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: dev |
| \\ / A nd | Web: http://www.OpenFOAM.org | | \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile
@ -20,38 +20,38 @@ FoamFile
sectionAEnd sectionAEnd
{ {
type patch; type patch;
nFaces 225; nFaces 256;
startFace 48150; startFace 77760;
} }
sectionCEnd sectionCEnd
{ {
type patch; type wall;
nFaces 225; nFaces 256;
startFace 48375; startFace 78016;
} }
front front
{ {
type wall; type wall;
nFaces 1125; nFaces 1696;
startFace 48600; startFace 78272;
} }
back back
{ {
type wall; type wall;
nFaces 1125; nFaces 1696;
startFace 49725; startFace 79968;
} }
top top
{ {
type wall; type wall;
nFaces 1125; nFaces 1696;
startFace 50850; startFace 81664;
} }
bottom bottom
{ {
type wall; type wall;
nFaces 1125; nFaces 1696;
startFace 51975; startFace 83360;
} }
) )

10
tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/controlDict → tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
View File

@ -2,7 +2,7 @@
| ========= | | | ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 | | \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: www.OpenFOAM.org | | \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | | | \\/ M anipulation | |
\*---------------------------------------------------------------------------*/ \*---------------------------------------------------------------------------*/
FoamFile FoamFile
@ -10,7 +10,6 @@ FoamFile
version 2.0; version 2.0;
format ascii; format ascii;
class dictionary; class dictionary;
location "system";
object controlDict; object controlDict;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -21,13 +20,13 @@ startTime 0;
stopAt endTime; stopAt endTime;
endTime 8e-11; endTime 1e-10;
deltaT 1e-14; deltaT 1e-15;
writeControl runTime; writeControl runTime;
writeInterval 2e-12; writeInterval 2e-13;
purgeWrite 0; purgeWrite 0;
@ -45,5 +44,4 @@ runTimeModifiable yes;
adjustTimeStep no; adjustTimeStep no;
// ************************************************************************* // // ************************************************************************* //

66
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/decomposeParDict Normal file
View File

@ -0,0 +1,66 @@
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.3 |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
root "";
case "";
instance "";
local "";
class dictionary;
object decomposeParDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
numberOfSubdomains 4;
method metis;
simpleCoeffs
{
n (2 2 1);
delta 0.001;
}
hierarchicalCoeffs
{
n (1 1 1);
delta 0.001;
order xyz;
}
metisCoeffs
{
processorWeights
(
1
1
1
1
);
}
manualCoeffs
{
dataFile "";
}
distributed no;
roots
(
);
// ************************************************************************* //

14
tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSchemes → tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes
View File

@ -17,43 +17,37 @@ FoamFile
ddtSchemes ddtSchemes
{ {
default Euler; default none;
} }
gradSchemes gradSchemes
{ {
default Gauss linear; default none;
grad(p) Gauss linear;
} }
divSchemes divSchemes
{ {
default none; default none;
div(phi,U) Gauss linear;
} }
laplacianSchemes laplacianSchemes
{ {
default none; default none;
laplacian(nu,U) Gauss linear corrected;
laplacian(1|A(U),p) Gauss linear corrected;
} }
interpolationSchemes interpolationSchemes
{ {
default linear; default none;
interpolate(HbyA) linear;
} }
snGradSchemes snGradSchemes
{ {
default corrected; default none;
} }
fluxRequired fluxRequired
{ {
default no; default no;
p ;
} }

9
tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdSolution → tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution
View File

@ -11,13 +11,12 @@ FoamFile
format ascii; format ascii;
class dictionary; class dictionary;
location "system"; location "system";
object mdSolution; object fvSolution;
} }
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
integrationMethod verletLeapfrog; solvers
{
potentialEnergyLimit 5.256e-20; }
// ************************************************************************* // // ************************************************************************* //

19
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict Normal file
View File

@ -0,0 +1,19 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
object mdEquilibrationDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
targetTemperature 298;
// ************************************************************************* //

85
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdInitialiseDict Normal file
View File

@ -0,0 +1,85 @@
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.3 |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
root "";
case "";
instance "";
local "";
class dictionary;
object molConfigDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Euler angles, expressed in degrees as phi, theta, psi, see
// http://mathworld.wolfram.com/EulerAngles.html
sectionA
{
massDensity 980;
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 980;
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 980;
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);
}
// ************************************************************************* //

118
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/potentialDict Normal file
View File

@ -0,0 +1,118 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: http://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);
}
// ************************************************************************* //

1
tutorials/multiphase/compressibleInterFoam/les/depthCharge3D/system/machines
View File

@ -1 +0,0 @@
noisy