applying update from Graham

applications/solvers/molecularDynamics/gnemdFoam/Make/files

@@ -1,3 +0,0 @@
-gnemdFoam.C
-
-EXE = $(FOAM_APPBIN)/gnemdFoam

applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options

@@ -1,6 +1,7 @@
 EXE_INC = \
     -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
     -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
@@ -10,4 +11,6 @@ EXE_LIBS = \
     -lfiniteVolume \
     -llagrangian \
     -lmolecule \
-    -lpotential
+    -lpotential \
+    -lmolecularMeasurements
+

applications/solvers/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C

@@ -23,7 +23,7 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    mdEquilibrationFOAM
+    mdEquilibrationFoam
 
 Description
     Equilibrates and/or preconditions MD systems
@@ -40,9 +40,9 @@ int main(int argc, char *argv[])
 #   include "createTime.H"
 #   include "createMesh.H"
 
-    moleculeCloud molecules(mesh);
+    potential pot(mesh);
 
-    molecules.removeHighEnergyOverlaps();
+    moleculeCloud molecules(mesh, pot);
 
 #   include "temperatureAndPressureVariables.H"
 
@@ -60,7 +60,7 @@ int main(int argc, char *argv[])
 
         Info << "Time = " << runTime.timeName() << endl;
 
-        molecules.integrateEquationsOfMotion();
+        molecules.evolve();
 
 #       include "meanMomentumEnergyAndNMols.H"
 

applications/solvers/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H

@@ -1,4 +1,4 @@
-Info<< "Reading MD Equilibration Dictionary" << nl << endl;
+Info<< nl << "Reading MD Equilibration Dictionary" << nl << endl;
 
 IOdictionary mdEquilibrationDict
 (

applications/solvers/molecularDynamics/mdFoam/Make/files

@@ -0,0 +1,3 @@
+mdFoam.C
+
+EXE = $(FOAM_APPBIN)/mdFoam

applications/solvers/molecularDynamics/mdFoam/Make/options

@@ -1,6 +1,7 @@
 EXE_INC = \
     -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
     -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
@@ -10,4 +11,6 @@ EXE_LIBS = \
     -lfiniteVolume \
     -llagrangian \
     -lmolecule \
-    -lpotential
+    -lpotential \
+    -lmolecularMeasurements
+

applications/solvers/molecularDynamics/mdFoam/mdFoam.C

@@ -23,10 +23,10 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Application
-    gnemdFOAM
+    mdFoam
 
 Description
-    MD for Fluid Mechanics and hybridising with a continuum solver.
+    molecular dynamics solver for fluid dynamics
 
 \*---------------------------------------------------------------------------*/
 
@@ -40,11 +40,9 @@ int main(int argc, char *argv[])
 #   include "createTime.H"
 #   include "createMesh.H"
 
-    moleculeCloud molecules(mesh);
+    potential pot(mesh);
 
-#   include "createMDFields.H"
-
-    molecules.removeHighEnergyOverlaps();
+    moleculeCloud molecules(mesh, pot);
 
 #   include "temperatureAndPressureVariables.H"
 
@@ -60,20 +58,14 @@ int main(int argc, char *argv[])
 
         Info << "Time = " << runTime.timeName() << endl;
 
-        molecules.integrateEquationsOfMotion();
+        molecules.evolve();
 
 #       include "meanMomentumEnergyAndNMols.H"
 
 #       include "temperatureAndPressure.H"
 
-#       include "calculateMDFields.H"
-
-#       include "averageMDFields.H"
-
         runTime.write();
 
-#       include "resetMDFields.H"
-
         if (runTime.outputTime())
         {
             nAveragingSteps = 0;