Updated gnemdFoam, mdEquilibrationFoam and molConfig applications to use new...

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.

applications/solvers/molecularDynamics/gnemdFoam/Make/options

 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

applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options

 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

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

tutorials/mdEquilibrationFoam/Allclean

+#!/bin/sh
+
+currDir=`pwd`
+application=`basename $currDir`
+cases="periodicCube"
+
+tutorialPath=`dirname $0`/..
+. $tutorialPath/CleanFunctions
+
+for case in $cases
+do
+    cleanCase $case
+done

tutorials/mdEquilibrationFoam/Allrun

+#!/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

tutorials/mdEquilibrationFoam/periodicCube/Allrun

-#!/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

tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution

@@ -26,6 +26,4 @@ integrationMethod               verletLeapfrog;
 
 potentialEnergyLimit            5.256e-20;
 
-guardRadius                     0;
-
 // ************************************************************************* //
\ No newline at end of file

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;
+        }
     }
 }