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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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10
tutorials/discreteMethods/molecularDynamics/mdFoam/Allclean Executable file
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#!/bin/sh
# Source tutorial clean functions
. $WM_PROJECT_DIR/bin/tools/CleanFunctions
cd nanoNozzle
rm -rf constant/polyMesh/sets
rm -rf processor[0-9]
cleanCase
cd ..

19
tutorials/discreteMethods/molecularDynamics/mdFoam/Allrun Executable file
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#!/bin/sh
# Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions
application="mdFoam"
cd nanoNozzle
runApplication blockMesh
runApplication decomposePar
hostname > system/machines
runParallel mdInitialise 4 system/machines
runParallel $application 4 system/machines
runApplication reconstructPar
cd ..

45
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties Normal file
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/*--------------------------------*- 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
);
}
// ************************************************************************* //

118
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict Normal file
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/*--------------------------------*- 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 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
();
patches
(
patch
sectionAEnd
(
(0 4 7 3)
)
wall
sectionCEnd
(
(20 21 23 22)
)
wall
front
(
(0 1 5 4)
(1 8 10 5)
(8 12 14 10)
(12 16 18 14)
(16 20 22 18)
)
wall
back
(
(2 3 7 6)
(2 6 11 9)
(9 11 15 13)
(13 15 19 17)
(17 19 23 21)
)
wall
top
(
(4 5 6 7)
(5 10 11 6)
(10 14 15 11)
(14 18 19 15)
(18 22 23 19)
)
wall
bottom
(
(0 3 2 1)
(1 2 9 8)
(8 9 13 12)
(12 13 17 16)
(16 17 21 20)
)
);
mergePatchPairs
(
);
// ************************************************************************* //

58
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/boundary Normal file
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/*--------------------------------*- 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 polyBoundaryMesh;
location "constant/polyMesh";
object boundary;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
6
(
sectionAEnd
{
type patch;
nFaces 256;
startFace 77760;
}
sectionCEnd
{
type wall;
nFaces 256;
startFace 78016;
}
front
{
type wall;
nFaces 1696;
startFace 78272;
}
back
{
type wall;
nFaces 1696;
startFace 79968;
}
top
{
type wall;
nFaces 1696;
startFace 81664;
}
bottom
{
type wall;
nFaces 1696;
startFace 83360;
}
)
// ************************************************************************* //

47
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict Normal file
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/*--------------------------------*- 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 controlDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
startFrom startTime;
startTime 0;
stopAt endTime;
endTime 1e-10;
deltaT 1e-15;
writeControl runTime;
writeInterval 2e-13;
purgeWrite 0;
writeFormat ascii;
writePrecision 12;
writeCompression uncompressed;
timeFormat general;
timePrecision 6;
runTimeModifiable yes;
adjustTimeStep no;
// ************************************************************************* //

66
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/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 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
(
);
// ************************************************************************* //

54
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes Normal file
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/*--------------------------------*- 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 fvSchemes;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
ddtSchemes
{
default none;
}
gradSchemes
{
default none;
}
divSchemes
{
default none;
}
laplacianSchemes
{
default none;
}
interpolationSchemes
{
default none;
}
snGradSchemes
{
default none;
}
fluxRequired
{
default no;
}
// ************************************************************************* //

22
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution Normal file
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/*--------------------------------*- 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
{
}
// ************************************************************************* //

19
tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict Normal file
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/*--------------------------------*- 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
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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
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
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/*--------------------------------*- 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);
}
// ************************************************************************* //