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adding molecular dynamics sources/app/utility

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andy
2008-05-22 15:03:46 +01:00
parent b5a7c032c6
commit 4a9f21ba18
131 changed files with 15306 additions and 0 deletions
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13
tutorials/mdEquilibrationFoam/Allclean Executable file
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#!/bin/sh
currDir=`pwd`
application=`basename $currDir`
cases="periodicCube"
tutorialPath=`dirname $0`/..
. $tutorialPath/CleanFunctions
for case in $cases
do
cleanCase $case
done

19
tutorials/mdEquilibrationFoam/Allrun Executable file
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#!/bin/sh
currDir=`pwd`
application=`basename $currDir`
cases="periodicCube"
tutorialPath=`dirname $0`/..
. $tutorialPath/RunFunctions
. $tutorialPath/CleanFunctions
for case in $cases
do
runApplication blockMesh $case
runApplication molConfig $case
runApplication $application $case
done

73
tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / 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 2.462491658e-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)
);
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
(
);
// ************************************************************************* //

55
tutorials/mdEquilibrationFoam/periodicCube/system/controlDict Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.4 |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
root "";
case "";
instance "";
local "";
class dictionary;
object controlDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
startFrom startTime;
startTime 0;
stopAt endTime;
endTime 4e-10;
deltaT 1e-14;
writeControl runTime;
writeInterval 5e-11;
purgeWrite 0;
writeFormat ascii;
writePrecision 12;
writeCompression uncompressed;
timeFormat general;
timePrecision 6;
runTimeModifiable yes;
adjustTimeStep no;
// ************************************************************************* //

70
tutorials/mdEquilibrationFoam/periodicCube/system/decomposeParDict Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / 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
1
1
4
1
5
1
2
);
}
manualCoeffs
{
dataFile "";
}
distributed no;
roots
(
);
// ************************************************************************* //

67
tutorials/mdEquilibrationFoam/periodicCube/system/fvSchemes Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / 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 fvSchemes;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
ddtSchemes
{
default Euler;
}
gradSchemes
{
default Gauss linear;
grad(p) Gauss linear;
}
divSchemes
{
default none;
div(phi,U) Gauss linear;
}
laplacianSchemes
{
default none;
laplacian(nu,U) Gauss linear corrected;
laplacian(1|A(U),p) Gauss linear corrected;
}
interpolationSchemes
{
default linear;
interpolate(HbyA) linear;
}
snGradSchemes
{
default corrected;
}
fluxRequired
{
default no;
p;
}
// ************************************************************************* //

40
tutorials/mdEquilibrationFoam/periodicCube/system/fvSolution Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / 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 fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
solvers
{
p ICCG 1e-06 0;
U BICCG 1e-05 0;
}
PISO
{
nCorrectors 2;
nNonOrthogonalCorrectors 0;
pRefCell 0;
pRefValue 0;
}
// ************************************************************************* //

27
tutorials/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.4.1 |
| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
root "";
case "";
instance "";
local "";
class dictionary;
object mdEquilibrationDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
equilibrationTargetTemperature 300.0;
// ************************************************************************* //

31
tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / 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 mdSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
integrationMethod verletLeapfrog;
potentialEnergyLimit 5.256e-20;
guardRadius 0;
// ************************************************************************* //

43
tutorials/mdEquilibrationFoam/periodicCube/system/molConfigDict Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / 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 1220.0;
temperature 300.0;
velocityDistribution maxwellian;
bulkVelocity (0.0 0.0 0.0);
id Ar;
mass 6.63352033e-26;
latticeStructure SC;
anchor (0.0 0.0 0.0);
anchorSpecifies molecule;
tethered no;
orientationAngles (0 0 0);
}
// ************************************************************************* //

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tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict Normal file
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/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / 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 potentials;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Subdictionaries specifying types of intermoleular 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 1 (Ar);
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// 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 will thrown an error)
pair
{
Ar-Ar
{
potentialType maitlandSmithTabulated;
m 13.0;
gamma 7.5;
rm 0.3756e-9;
epsilon 1.990108438e-21;
rCut 1.0e-9;
rMin 0.15e-9;
dr 2e-14;
}
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Tethering Potentials
tether
{
Ar
{
potentialType harmonicSpring;
springConstant 0.0277;
}
}
// ************************************************************************* //
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// 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);
}