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Updated gnemdFoam, mdEquilibrationFoam and molConfig applications to use new separate potential and molecule libraries. Updated potentialDict description in mdEquilibrationFoam/periodicCube test case to new format.

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This commit is contained in:
graham
2008-06-17 16:08:28 +01:00
parent 1ebd73261e
commit 217f01e026
8 changed files with 67 additions and 27 deletions
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6
applications/solvers/molecularDynamics/gnemdFoam/Make/options
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@ -1,5 +1,6 @@
EXE_INC = \ EXE_INC = \
-I$(LIB_SRC)/lagrangian/molecule/lnInclude \ -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \ -I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \ -I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude -I$(LIB_SRC)/meshTools/lnInclude
@ -8,4 +9,5 @@ EXE_LIBS = \
-lmeshTools \ -lmeshTools \
-lfiniteVolume \ -lfiniteVolume \
-llagrangian \ -llagrangian \
-lmolecule -lmolecule \
-lpotential

6
applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options
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@ -1,5 +1,6 @@
EXE_INC = \ EXE_INC = \
-I$(LIB_SRC)/lagrangian/molecule/lnInclude \ -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \ -I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \ -I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude -I$(LIB_SRC)/meshTools/lnInclude
@ -8,4 +9,5 @@ EXE_LIBS = \
-lmeshTools \ -lmeshTools \
-lfiniteVolume \ -lfiniteVolume \
-llagrangian \ -llagrangian \
-lmolecule -lmolecule \
-lpotential

6
applications/utilities/preProcessing/molConfig/Make/options
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@ -3,7 +3,8 @@ EXE_INC = \
-I$(velocityDistributions) \ -I$(velocityDistributions) \
-I$(LIB_SRC)/meshTools/lnInclude \ -I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/dynamicMesh/lnInclude \ -I$(LIB_SRC)/dynamicMesh/lnInclude \
-I$(LIB_SRC)/lagrangian/molecule/lnInclude \ -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \ -I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude -I$(LIB_SRC)/finiteVolume/lnInclude
@ -12,4 +13,5 @@ EXE_LIBS = \
-ldynamicMesh \ -ldynamicMesh \
-lfiniteVolume \ -lfiniteVolume \
-llagrangian \ -llagrangian \
-lmolecule -lmolecule \
-lpotential

13
tutorials/mdEquilibrationFoam/Allclean Executable file
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@ -0,0 +1,13 @@
#!/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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@ -0,0 +1,19 @@
#!/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

10
tutorials/mdEquilibrationFoam/periodicCube/Allrun
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@ -1,10 +0,0 @@
#!/bin/sh
# Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions
# Get application name from directory
application=`basename $PWD`
runApplication blockMesh
runApplication molConfig
runApplication $application

2
tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
View File

@ -26,6 +26,4 @@ integrationMethod verletLeapfrog;
potentialEnergyLimit 5.256e-20; potentialEnergyLimit 5.256e-20;
guardRadius 0;
// ************************************************************************* // // ************************************************************************* //

32
tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
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@ -22,7 +22,7 @@ FoamFile
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Subdictionaries specifying types of intermoleular potential. // Subdictionaries specifying types of intermolecular potential.
// Sub-sub dictionaries specify the potentials themselves. // Sub-sub dictionaries specify the potentials themselves.
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -52,14 +52,24 @@ pair
{ {
Ar-Ar Ar-Ar
{ {
potentialType maitlandSmithTabulated; pairPotential azizChen;
m 13.0; rCut 1.2e-9;
gamma 7.5;
rm 0.3756e-9;
epsilon 1.990108438e-21;
rCut 1.0e-9;
rMin 0.15e-9; rMin 0.15e-9;
dr 2e-14; dr 2e-14;
azizChenCoeffs
{
epsilon 1.97742255e-21;
rm 3.759e-10;
A 0.9502720e7;
alpha 16.345655;
C6 1.0914254;
C8 0.6002595;
C10 0.3700113;
D 1.4;
gamma 2.0;
}
energyScalingFunction noScaling;
writeTables yes;
} }
} }
@ -70,8 +80,12 @@ tether
{ {
Ar Ar
{ {
potentialType harmonicSpring; tetherPotential restrainedHarmonicSpring;
springConstant 0.0277; restrainedHarmonicSpringCoeffs
{
springConstant 0.0277;
rR 1.2e-9;
}
} }
} }