From 217f01e02668db9e2b8fa44ba9f0652d3685d8a1 Mon Sep 17 00:00:00 2001
From: graham <graham.macpherson@strath.ac.uk>
Date: Tue, 17 Jun 2008 16:08:28 +0100
Subject: [PATCH] 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.
---
.../molecularDynamics/gnemdFoam/Make/options | 6 ++--
.../mdEquilibrationFoam/Make/options | 6 ++--
.../preProcessing/molConfig/Make/options | 6 ++--
tutorials/mdEquilibrationFoam/Allclean | 13 ++++++++
tutorials/mdEquilibrationFoam/Allrun | 19 +++++++++++
.../mdEquilibrationFoam/periodicCube/Allrun | 10 ------
.../periodicCube/system/mdSolution | 2 --
.../periodicCube/system/potentialDict | 32 +++++++++++++------
8 files changed, 67 insertions(+), 27 deletions(-)
create mode 100755 tutorials/mdEquilibrationFoam/Allclean
create mode 100755 tutorials/mdEquilibrationFoam/Allrun
delete mode 100755 tutorials/mdEquilibrationFoam/periodicCube/Allrun
diff --git a/applications/solvers/molecularDynamics/gnemdFoam/Make/options b/applications/solvers/molecularDynamics/gnemdFoam/Make/options
index 80f97734568..89431d06256 100755
--- a/applications/solvers/molecularDynamics/gnemdFoam/Make/options
+++ b/applications/solvers/molecularDynamics/gnemdFoam/Make/options
@@ -1,5 +1,6 @@
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$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude
@@ -8,4 +9,5 @@ EXE_LIBS = \
-lmeshTools \
-lfiniteVolume \
-llagrangian \
- -lmolecule
+ -lmolecule \
+ -lpotential
diff --git a/applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options b/applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options
index 80f97734568..89431d06256 100755
--- a/applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options
+++ b/applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options
@@ -1,5 +1,6 @@
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$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude
@@ -8,4 +9,5 @@ EXE_LIBS = \
-lmeshTools \
-lfiniteVolume \
-llagrangian \
- -lmolecule
+ -lmolecule \
+ -lpotential
diff --git a/applications/utilities/preProcessing/molConfig/Make/options b/applications/utilities/preProcessing/molConfig/Make/options
index 196a4d66ddb..aab9a2ca4f7 100755
--- a/applications/utilities/preProcessing/molConfig/Make/options
+++ b/applications/utilities/preProcessing/molConfig/Make/options
@@ -3,7 +3,8 @@ EXE_INC = \
-I$(velocityDistributions) \
-I$(LIB_SRC)/meshTools/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)/finiteVolume/lnInclude
@@ -12,4 +13,5 @@ EXE_LIBS = \
-ldynamicMesh \
-lfiniteVolume \
-llagrangian \
- -lmolecule
+ -lmolecule \
+ -lpotential
diff --git a/tutorials/mdEquilibrationFoam/Allclean b/tutorials/mdEquilibrationFoam/Allclean
new file mode 100755
index 00000000000..3d688adfb3e
--- /dev/null
+++ b/tutorials/mdEquilibrationFoam/Allclean
@@ -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
diff --git a/tutorials/mdEquilibrationFoam/Allrun b/tutorials/mdEquilibrationFoam/Allrun
new file mode 100755
index 00000000000..eefbf1aded0
--- /dev/null
+++ b/tutorials/mdEquilibrationFoam/Allrun
@@ -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
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/Allrun b/tutorials/mdEquilibrationFoam/periodicCube/Allrun
deleted file mode 100755
index 2121179f1cf..00000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/Allrun
+++ /dev/null
@@ -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
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution b/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
index 681963175de..c72bb260fac 100644
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
+++ b/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
@@ -26,6 +26,4 @@ integrationMethod verletLeapfrog;
potentialEnergyLimit 5.256e-20;
-guardRadius 0;
-
// ************************************************************************* //
\ No newline at end of file
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict b/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
index 78fa1c77465..f4d27d298b0 100644
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
+++ b/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
@@ -22,7 +22,7 @@ FoamFile
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// Subdictionaries specifying types of intermoleular potential.
+// Subdictionaries specifying types of intermolecular potential.
// Sub-sub dictionaries specify the potentials themselves.
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -52,14 +52,24 @@ pair
{
Ar-Ar
{
- potentialType maitlandSmithTabulated;
- m 13.0;
- gamma 7.5;
- rm 0.3756e-9;
- epsilon 1.990108438e-21;
- rCut 1.0e-9;
+ pairPotential azizChen;
+ rCut 1.2e-9;
rMin 0.15e-9;
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
{
- potentialType harmonicSpring;
- springConstant 0.0277;
+ tetherPotential restrainedHarmonicSpring;
+ restrainedHarmonicSpringCoeffs
+ {
+ springConstant 0.0277;
+ rR 1.2e-9;
+ }
}
}
--
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