From ba7d45228ac19c2c591e141b2bd6b59723ab6d08 Mon Sep 17 00:00:00 2001
From: graham <graham.macpherson@strath.ac.uk>
Date: Thu, 3 Jul 2008 17:49:51 +0100
Subject: [PATCH] Added Allrun and Allclean scripts to gnemdFoam and
mdEquilibrationFoam tutorials
---
tutorials/gnemdFoam/Allclean | 19 ++++++
tutorials/gnemdFoam/Allrun | 25 ++++++++
.../constant/polyMesh/boundary | 3 +-
.../constrictedChannel/system/potentialDict | 13 +----
.../nanoNozzle/constant/polyMesh/boundary | 58 +++++++++++++++++++
tutorials/mdEquilibrationFoam/Allclean | 13 +++++
tutorials/mdEquilibrationFoam/Allrun | 13 +++++
.../periodicCube/constant/polyMesh/boundary | 43 ++++++++++++++
8 files changed, 175 insertions(+), 12 deletions(-)
create mode 100755 tutorials/gnemdFoam/Allclean
create mode 100755 tutorials/gnemdFoam/Allrun
create mode 100644 tutorials/gnemdFoam/nanoNozzle/constant/polyMesh/boundary
create mode 100755 tutorials/mdEquilibrationFoam/Allclean
create mode 100755 tutorials/mdEquilibrationFoam/Allrun
create mode 100644 tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary
diff --git a/tutorials/gnemdFoam/Allclean b/tutorials/gnemdFoam/Allclean
new file mode 100755
index 00000000000..827eacb6ae5
--- /dev/null
+++ b/tutorials/gnemdFoam/Allclean
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+# Source tutorial clean functions
+. $WM_PROJECT_DIR/bin/tools/CleanFunctions
+
+cd constrictedChannel
+ rm -rf 0 > /dev/null 2>&1
+ rm Ar-Ar Ar-Ne Ne-Ne > /dev/null 2>&1
+ rm constant/idList
+
+ cleanCase
+cd ..
+
+cd nanoNozzle
+ rm -rf processor[0-9] > /dev/null 2>&1
+
+ cleanCase
+cd ..
+
diff --git a/tutorials/gnemdFoam/Allrun b/tutorials/gnemdFoam/Allrun
new file mode 100755
index 00000000000..640ecd9bdc1
--- /dev/null
+++ b/tutorials/gnemdFoam/Allrun
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+application="gnemdFoam"
+
+cd constrictedChannel
+ runApplication blockMesh
+ runApplication molConfig
+ runApplication $application
+cd ..
+
+cd nanoNozzle
+ runApplication blockMesh
+
+ runApplication decomposePar
+ hostname > system/machines
+
+ runParallel molConfig 4 system/machines
+ runParallel $application 4 system/machines
+
+ runApplication reconstructPar
+cd ..
+
diff --git a/tutorials/gnemdFoam/constrictedChannel/constant/polyMesh/boundary b/tutorials/gnemdFoam/constrictedChannel/constant/polyMesh/boundary
index e06cb6a7bc6..eaeb38f09e8 100644
--- a/tutorials/gnemdFoam/constrictedChannel/constant/polyMesh/boundary
+++ b/tutorials/gnemdFoam/constrictedChannel/constant/polyMesh/boundary
@@ -1,7 +1,7 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
+| \\ / O peration | Version: dev |
| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
@@ -10,6 +10,7 @@ FoamFile
version 2.0;
format ascii;
class polyBoundaryMesh;
+ location "constant/polyMesh";
object boundary;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
diff --git a/tutorials/gnemdFoam/constrictedChannel/system/potentialDict b/tutorials/gnemdFoam/constrictedChannel/system/potentialDict
index ce9f24b88a7..7f9346077fc 100644
--- a/tutorials/gnemdFoam/constrictedChannel/system/potentialDict
+++ b/tutorials/gnemdFoam/constrictedChannel/system/potentialDict
@@ -27,7 +27,7 @@ FoamFile
// 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);
+removalOrder 2 (Ne Ar);
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Pair potentials
@@ -111,19 +111,10 @@ tether
tetherPotential restrainedHarmonicSpring;
restrainedHarmonicSpringCoeffs
{
- springConstant 0.0277;
+ springConstant 0.1;
rR 1.2e-9;
}
}
-
- Ne
- {
- tetherPotential harmonicSpring;
- harmonicSpringCoeffs
- {
- springConstant 0.0277;
- }
- }
}
// ************************************************************************* //
diff --git a/tutorials/gnemdFoam/nanoNozzle/constant/polyMesh/boundary b/tutorials/gnemdFoam/nanoNozzle/constant/polyMesh/boundary
new file mode 100644
index 00000000000..b94dd10f195
--- /dev/null
+++ b/tutorials/gnemdFoam/nanoNozzle/constant/polyMesh/boundary
@@ -0,0 +1,58 @@
+/*--------------------------------*- 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 polyBoundaryMesh;
+ location "constant/polyMesh";
+ object boundary;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+6
+(
+ sectionAEnd
+ {
+ type patch;
+ nFaces 225;
+ startFace 48150;
+ }
+ sectionCEnd
+ {
+ type patch;
+ nFaces 225;
+ startFace 48375;
+ }
+ front
+ {
+ type wall;
+ nFaces 1125;
+ startFace 48600;
+ }
+ back
+ {
+ type wall;
+ nFaces 1125;
+ startFace 49725;
+ }
+ top
+ {
+ type wall;
+ nFaces 1125;
+ startFace 50850;
+ }
+ bottom
+ {
+ type wall;
+ nFaces 1125;
+ startFace 51975;
+ }
+)
+
+// ************************************************************************* //
diff --git a/tutorials/mdEquilibrationFoam/Allclean b/tutorials/mdEquilibrationFoam/Allclean
new file mode 100755
index 00000000000..7880b1387e0
--- /dev/null
+++ b/tutorials/mdEquilibrationFoam/Allclean
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+# Source tutorial clean functions
+. $WM_PROJECT_DIR/bin/tools/CleanFunctions
+
+cd periodicCube
+ rm -rf 0 > /dev/null 2>&1
+ rm Ar-Ar > /dev/null 2>&1
+ rm constant/idList
+
+ cleanCase
+cd ..
+
diff --git a/tutorials/mdEquilibrationFoam/Allrun b/tutorials/mdEquilibrationFoam/Allrun
new file mode 100755
index 00000000000..0c590da09a8
--- /dev/null
+++ b/tutorials/mdEquilibrationFoam/Allrun
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+application="mdEquilibrationFoam"
+
+cd periodicCube
+ runApplication blockMesh
+ runApplication molConfig
+ runApplication $application
+cd ..
+
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary b/tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary
new file mode 100644
index 00000000000..54dbb7ef4a6
--- /dev/null
+++ b/tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary
@@ -0,0 +1,43 @@
+/*--------------------------------*- 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 polyBoundaryMesh;
+ location "constant/polyMesh";
+ object boundary;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+3
+(
+ periodicX
+ {
+ type cyclic;
+ nFaces 288;
+ startFace 4752;
+ featureCos 0.9;
+ }
+ periodicY
+ {
+ type cyclic;
+ nFaces 288;
+ startFace 5040;
+ featureCos 0.9;
+ }
+ periodicZ
+ {
+ type cyclic;
+ nFaces 288;
+ startFace 5328;
+ featureCos 0.9;
+ }
+)
+
+// ************************************************************************* //
--
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