Minor tweaks and comments.

examples/HelloSodiumChloride.cpp

@@ -187,9 +187,9 @@ struct MyOpenMMData {
 //                      INITIALIZE OpenMM DATA STRUCTURES
 // -----------------------------------------------------------------------------
 // We take these actions here:
-// (1) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
+// (1) Load any available OpenMM plugins, e.g. Cuda and Brook.
+// (2) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
 //     in a manner which is opaque to the caller.
-// (2) Allocate the OpenMM objects which persist from call to call.
 // (3) Fill the OpenMM::System with the force field parameters we want to
 //     use and the particular set of atoms to be simulated.
 // (4) Create an Integrator and a Context associating the Integrator with
@@ -232,7 +232,7 @@ myInitializeOpenMM( const MyAtomInfo    atoms[],
     //  (1) System needs to know the masses.
     //  (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
     //  (3) GBSA needs charge, radius, and scale factor.
-    //  (3) Collect default positions for initializing the simulation later.
+    //  (4) Collect default positions for initializing the simulation later.
     std::vector<Vec3> initialPosInNm;
     for (int n=0; *atoms[n].pdb; ++n) {
         const MyAtomInfo& atom = atoms[n];

examples/HelloSodiumChlorideInC.c

@@ -184,7 +184,7 @@ struct MyOpenMMData_s {
  *
  * Note that this function must understand the calling MD code's molecule and
  * force field data structures so will need to be customized for each MD code.
-*/
+ */
 static MyOpenMMData* 
 myInitializeOpenMM( const MyAtomInfo    atoms[],
                     double              temperature,
@@ -274,7 +274,7 @@ myGetOpenMMState(MyOpenMMData* omm, int wantEnergy,
                  MyAtomInfo atoms[])
 {
     OpenMM_State*           state;
-    const OpenMM_Vec3Array* posArray;
+    const OpenMM_Vec3Array* posArrayInNm;
     int                     infoMask;
     int n;
 
@@ -291,12 +291,11 @@ myGetOpenMMState(MyOpenMMData* omm, int wantEnergy,
 
     /* Positions are maintained as a Vec3Array inside the State. This will give
      * us access, but don't destroy it yourself -- it will go away with the State. */
-    posArray  = OpenMM_State_getPositions(state);
-    for (n=0; *atoms[n].pdb; ++n) {
-        double posInNm[3];
-        OpenMM_Vec3Array_get(posArray, n, posInNm);
-        OpenMM_Vec3_scale(posInNm, OpenMM_AngstromsPerNm, atoms[n].posInAng);
-    }
+    posArrayInNm = OpenMM_State_getPositions(state);
+    for (n=0; *atoms[n].pdb; ++n)
+        /* Sets atoms[n].pos = posArray[n] * Angstroms/nm. */
+        OpenMM_Vec3Array_getScaled(posArrayInNm, n, OpenMM_AngstromsPerNm, 
+                                   atoms[n].posInAng);
 
     /* If energy has been requested, obtain it and convert from kJ to kcal. */
     *energyInKcal = 0;

examples/wrappers/OpenMM_CWrapper.cpp

@@ -299,7 +299,7 @@ void OpenMM_GBSAOBCForce_destroy(OpenMM_GBSAOBCForce* doomed)
 void openmm_gbsaobcforce_destroy_(OpenMM_GBSAOBCForce*& doomed) 
 {   OpenMM_GBSAOBCForce_destroy(doomed); doomed = 0;}
 
-// Fortran only: recast NonbondedForce as a Force.
+// Fortran only: recast GBSAOBCForce as a Force.
 void openmm_gbsaobcforce_asforce_(OpenMM_GBSAOBCForce* const& gbsa,
 							      OpenMM_Force*&              force)
 {   force = (OpenMM_Force*)gbsa; }

examples/wrappers/OpenMM_CWrapper.h

@@ -129,7 +129,7 @@ extern void                 OpenMM_Vec3Array_get(const OpenMM_Vec3Array*, int i,
 extern void                 OpenMM_Vec3Array_getScaled(const OpenMM_Vec3Array*, int i, double s, double[3]);
 extern void                 OpenMM_Vec3Array_set(OpenMM_Vec3Array*, int i, const double[3]);
 extern void                 OpenMM_Vec3Array_setScaled(OpenMM_Vec3Array*, int i, const double[3], double s);
-extern void                 OpenMM_Vec3_scale(const double[3], double s, double[3]);
+extern void                 OpenMM_Vec3_scale(const double in[3], double s, double out[3]);
 
 /* OpenMM_String */
 extern OpenMM_String*       OpenMM_String_create(const char* init);