Minor tweaks and comments.

examples/HelloArgon.cpp

@@ -8,87 +8,87 @@
 // other visualization tool to produce an animation of the resulting trajectory.
 // -----------------------------------------------------------------------------
 
-#include "OpenMM.h"
-#include <cstdio>
-
-// Forward declaration of writePdb() subroutine for printing atomic 
-// coordinates, defined later in this source file.
-void writePdb(const OpenMM::OpenMMContext& context);
-
-void simulateArgon()
-{
-    // Load any shared libraries containing GPU implementations
-    OpenMM::Platform::loadPluginsFromDirectory(
-        OpenMM::Platform::getDefaultPluginsDirectory());
-
-    // Create a system with nonbonded forces
-    OpenMM::System system;
-    OpenMM::NonbondedForce* nonbond = new OpenMM::NonbondedForce(); 
-    system.addForce(nonbond);
-
-    // Create three atoms
-    std::vector<OpenMM::Vec3> initialPositions(3);
-    for (int a = 0; a < 3; ++a) 
-    {
-        system.addParticle(39.95); // mass, grams per mole
-
-        // charge, sigma, well depth
-        nonbond->addParticle(0.0, 0.3350, 0.996); 
-
-        initialPositions[a] = OpenMM::Vec3(0.5*a,0,0); // location, nanometers
-    }
-
-    OpenMM::VerletIntegrator integrator(0.004); // step size in picoseconds
-
-    // Let OpenMM Context choose best platform.
-    OpenMM::OpenMMContext context(system, integrator);
-    printf( "REMARK  Using OpenMM platform %s\n", 
-        context.getPlatform().getName().c_str() );
-
-    // Set the starting positions of the atoms. Velocities will be zero.
-    context.setPositions(initialPositions);
-
-    // Simulate
-    while(context.getTime() < 10.0) { // picoseconds
-        writePdb(context); // output coordinates
-        // Run 100 steps at a time, for efficient use of OpenMM
-        integrator.step(100);
-    }
-    writePdb(context); // output final coordinates
-}
-
-int main() 
-{
-    try {
-        simulateArgon();
-        return 0; // success!
-    }
+#include "OpenMM.h"
+#include <cstdio>
+
+// Forward declaration of writePdb() subroutine for printing atomic 
+// coordinates, defined later in this source file.
+void writePdb(const OpenMM::OpenMMContext& context);
+
+void simulateArgon()
+{
+    // Load any shared libraries containing GPU implementations
+    OpenMM::Platform::loadPluginsFromDirectory(
+        OpenMM::Platform::getDefaultPluginsDirectory());
+
+    // Create a system with nonbonded forces
+    OpenMM::System system;
+    OpenMM::NonbondedForce* nonbond = new OpenMM::NonbondedForce(); 
+    system.addForce(nonbond);
+
+    // Create three atoms
+    std::vector<OpenMM::Vec3> initialPositions(3);
+    for (int a = 0; a < 3; ++a) 
+    {
+        system.addParticle(39.95); // mass, grams per mole
+
+        // charge, sigma, well depth
+        nonbond->addParticle(0.0, 0.3350, 0.996); 
+
+        initialPositions[a] = OpenMM::Vec3(0.5*a,0,0); // location, nanometers
+    }
+
+    OpenMM::VerletIntegrator integrator(0.004); // step size in picoseconds
+
+    // Let OpenMM Context choose best platform.
+    OpenMM::OpenMMContext context(system, integrator);
+    printf( "REMARK  Using OpenMM platform %s\n", 
+        context.getPlatform().getName().c_str() );
+
+    // Set the starting positions of the atoms. Velocities will be zero.
+    context.setPositions(initialPositions);
+
+    // Simulate
+    while(context.getTime() < 10.0) { // picoseconds
+        writePdb(context); // output coordinates
+        // Run 100 steps at a time, for efficient use of OpenMM
+        integrator.step(100);
+    }
+    writePdb(context); // output final coordinates
+}
+
+int main() 
+{
+    try {
+        simulateArgon();
+        return 0; // success!
+    }
     // Catch and report usage and runtime errors detected by OpenMM and fail.
     catch(const std::exception& e) {
         printf("EXCEPTION: %s\n", e.what());
         return 1; // failure!
     }
-}
-
-// writePdb() subroutine for quick-and-dirty trajectory output.
-void writePdb(const OpenMM::OpenMMContext& context) 
-{
-    // Request atomic positions from OpenMM
-    const OpenMM::State state = context.getState(OpenMM::State::Positions);
-    const std::vector<OpenMM::Vec3>& pos = state.getPositions();
-
-    // write out in PDB format
-
-    // Use PDB MODEL cards to number trajectory frames
-    static int modelFrameNumber = 0; 
-    modelFrameNumber++;
-    printf("MODEL     %d\n", modelFrameNumber); // start of frame
-    for (int a = 0; a < context.getSystem().getNumParticles(); ++a)
-    {
-        printf("ATOM  %5d AR    AR     1    ", a+1); // atom number
-        printf("%8.3f%8.3f%8.3f  1.00  0.00          AR\n", // coordinates
-            // "*10" converts nanometers to Angstroms
-            pos[a][0]*10, pos[a][1]*10, pos[a][2]*10);
-    }
-    printf("ENDMDL\n"); // end of frame
-}
+}
+
+// writePdb() subroutine for quick-and-dirty trajectory output.
+void writePdb(const OpenMM::OpenMMContext& context) 
+{
+    // Request atomic positions from OpenMM
+    const OpenMM::State state = context.getState(OpenMM::State::Positions);
+    const std::vector<OpenMM::Vec3>& pos = state.getPositions();
+
+    // write out in PDB format
+
+    // Use PDB MODEL cards to number trajectory frames
+    static int modelFrameNumber = 0; 
+    modelFrameNumber++;
+    printf("MODEL     %d\n", modelFrameNumber); // start of frame
+    for (int a = 0; a < context.getSystem().getNumParticles(); ++a)
+    {
+        printf("ATOM  %5d AR    AR     1    ", a+1); // atom number
+        printf("%8.3f%8.3f%8.3f  1.00  0.00          AR\n", // coordinates
+            // "*10" converts nanometers to Angstroms
+            pos[a][0]*10, pos[a][1]*10, pos[a][2]*10);
+    }
+    printf("ENDMDL\n"); // end of frame
+}

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);