Reworked the NaCl example per dryrun feedback and fixed some warnings in ethane example.

examples/HelloSodiumChloride.cpp

+/* -----------------------------------------------------------------------------
+ *                OpenMM(tm) HelloSodiumChloride example (May 2009)
+ * -----------------------------------------------------------------------------
+ * This is a complete, self-contained "hello world" example demonstrating 
+ * GPU-accelerated constant energy simulation of a very simple system with just 
+ * nonbonded forces, consisting of several sodium (Na+) and chloride (Cl-) ions. 
+ * A multi-frame PDB file is written to stdout which can be read by VMD or other 
+ * visualization tool to produce an animation of the resulting trajectory.
+ *
+ * Pay particular attention to the handling of units in this example. Incorrect
+ * handling of units is a very common error; this example shows how you can
+ * continue to work with Amber-style units of Angstroms and kCals while correctly
+ * communicating with OpenMM in nanometers and kJoules.
+ * -------------------------------------------------------------------------- */
+
+// Suppress irrelevant warnings from Microsoft's compiler.
+#ifdef _MSC_VER
+    #pragma warning(disable:4996)   // sprintf is unsafe 
+    #pragma warning(disable:4251)   // no dll interface for some classes
+#endif
+
 #include "OpenMM.h"
 
 #include <iostream>
 #include <iomanip>
 #include <string>
 
-using namespace OpenMM;
-
-Vec3 operator*(const Vec3& v, double r) {
-    return Vec3(v[0]*r, v[1]*r, v[2]*r);
-}
-
-Vec3 operator*(double r, const Vec3& v) {
-    return Vec3(r*v[0], r*v[1], r*v[2]);
+using OpenMM::Vec3; // so we can just say "Vec3" below
+
+// -----------------------------------------------------------------------------
+//                   MODELING AND SIMULATION PARAMETERS
+// -----------------------------------------------------------------------------
+const double StepSizeInFs        = 2;       // integration step size (fs)
+const double ReportIntervalInFs  = 10;      // how often to generate PDB frame (fs)
+const double SimulationTimeInPs  = 100;     // total simulation time (ps)
+
+static void simulateNaCl();
+static void writePDB(const OpenMM::OpenMMContext&); // PDB file writer; see below.
+
+// -----------------------------------------------------------------------------
+//                                MAIN PROGRAM
+// -----------------------------------------------------------------------------
+int main() {
+    // ALWAYS enclose all OpenMM calls with a try/catch block to make sure that
+    // usage and runtime errors are caught and reported.
+    try {
+        // Load all available OpenMM plugins from their default location.
+        OpenMM::Platform::loadPluginsFromDirectory
+           (OpenMM::Platform::getDefaultPluginsDirectory());
+
+        simulateNaCl();
+
+        return 0; // Normal return from main.
+    }
+
+    // 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;
+    }
 }
 
+// -----------------------------------------------------------------------------
+//                          ATOM AND FORCE FIELD DATA
+// -----------------------------------------------------------------------------
 // This is not part of OpenMM; just a struct we can use to collect
 // atom parameters for this example. Normally atom parameters would
 // come from the force field's parameterization file.
 // We're going to use data in Angstrom and Kilocalorie units and
 // show how to safely convert to OpenMM's internal unit system
 // which uses nanometers and kilojoules.
-struct AtomInfo {
-    char*  symbol;
-    double mass, charge, vdwRadiusAng, vdwEnergyKcal;
-    Vec3   startPosAng;
-};
-
-static AtomInfo atoms[] = {
-    {"NA", 22.99,  1, 1.8680, 0.00277, Vec3(8,0,0)},
-    {"CL", 35.45, -1, 2.4700, 0.1000,  Vec3(-8,0,0)},
-    {"NA", 22.99,  1, 1.8680, 0.00277, Vec3(0,9,0)},
-    {"CL", 35.45, -1, 2.4700, 0.1000,  Vec3(0,-9,0)},
-    {"NA", 22.99,  1, 1.8680, 0.00277, Vec3(0,0,-10)},
-    {"CL", 35.45, -1, 2.4700, 0.1000,  Vec3( 0,0,10)},
+struct AtomInfo { 
+    const char* pdb; 
+    double      mass, charge, vdwRadiusInAng, vdwEnergyInKcal;
+    Vec3        initPosInAngstroms;
+} atoms[] = {
+    // pdb   mass   charge   vdwRadius  vdwEnergy   initPos
+    {" NA ", 22.99,   1,     1.8680,    0.00277,    Vec3(8,0,0)},
+    {" CL ", 35.45,  -1,     2.4700,    0.1000,     Vec3(-8,0,0)},
+    {" NA ", 22.99,   1,     1.8680,    0.00277,    Vec3(0,9,0)},
+    {" CL ", 35.45,  -1,     2.4700,    0.1000,     Vec3(0,-9,0)},
+    {" NA ", 22.99,   1,     1.8680,    0.00277,    Vec3(0,0,-10)},
+    {" CL ", 35.45,  -1,     2.4700,    0.1000,     Vec3( 0,0,10)},
     {""} // end of list
 };
 
-static const double Temperature         = 300;    // Kelvins
-static const double Friction            = 1./91.; // picoseconds between collisions
-static const double StepSizeFs          = 2;      // femtoseconds
-static const double ReportIntervalFs    = 10;
-static const double SimulationTimePs    = 100;    // total simulation time (ps)
-
-static const double SigmaPerVdwRadius = 2*std::pow(2., -1./6.);
-
-static void writePDB(const OpenMMContext&);
-
-int main() {
-  try {
-    // Load all available OpenMM plugins from their default location.
-    Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
-
-    // Create a System and a NonbondedForce object within the System. 
-    System system;
-    NonbondedForce* nonbond = new NonbondedForce();
+// Add missing scalar product operators for OpenMM::Vec3.
+Vec3 operator*(const Vec3& v, double r) {return Vec3(v[0]*r, v[1]*r, v[2]*r);}
+Vec3 operator*(double r, const Vec3& v) {return Vec3(r*v[0], r*v[1], r*v[2]);}
+// This is the conversion factor that takes you from a van der Waals radius
+// (defined as 1/2 the minimum energy separation) to the related Lennard Jones 
+// "sigma" parameter (defined as the zero crossing separation).
+static const double SigmaPerVdwRadius = 2*std::pow(2., -1./6.);
+
+// -----------------------------------------------------------------------------
+//                              NaCl SIMULATION
+// -----------------------------------------------------------------------------
+static void simulateNaCl() {
+    // -------------------------------------------------------------------------
+    // Create a System and Force objects within the System. Retain a reference
+    // to each force object so we can fill in the forces. Note: OpenMM owns
+    // the objects and will take care of deleting them; don't do it yourself!
+    // -------------------------------------------------------------------------
+    OpenMM::System system;
+    OpenMM::NonbondedForce* nonbond = new OpenMM::NonbondedForce();
     system.addForce(nonbond);
 
-    int numAtoms = 0;
-    for (; *atoms[numAtoms].symbol; ++numAtoms) {
-        const AtomInfo& atom = atoms[numAtoms];
+    nonbond->setNonbondedMethod(OpenMM::NonbondedForce::CutoffPeriodic);
+    nonbond->setCutoffDistance(2);
+    nonbond->setPeriodicBoxVectors(Vec3(5,0,0), Vec3(0,5,0), Vec3(0,0,5));
+
+    // -------------------------------------------------------------------------
+    // Specify the atoms and their properties:
+    //  (1) System needs to know the masses.
+    //  (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
+    //  (3) Collect default positions for initializing the simulation later.
+    // -------------------------------------------------------------------------
+    std::vector<Vec3> initialPositions;
+    for (int n=0; *atoms[n].pdb; ++n) {
+        const AtomInfo& atom = atoms[n];
         system.addParticle(atom.mass);
         nonbond->addParticle(atom.charge,
-                             atom.vdwRadiusAng  * NmPerAngstrom * SigmaPerVdwRadius,
-                             atom.vdwEnergyKcal * KJPerKcal);
+                             atom.vdwRadiusInAng  * OpenMM::NmPerAngstrom * SigmaPerVdwRadius,
+                             atom.vdwEnergyInKcal * OpenMM::KJPerKcal);
+        initialPositions.push_back(atoms[n].initPosInAngstroms * OpenMM::NmPerAngstrom);
     }
 
-    // Create an integrator object for advancing time.
-    LangevinIntegrator integrator(Temperature, Friction, StepSizeFs * PsPerFs);
-    //VerletIntegrator integrator(StepSizeFs * PsPerFs);
-
-    // Create an OpenMM Context for execution; let it choose best platform.
-    OpenMMContext context(system, integrator);
-
-    const std::string platformName = context.getPlatform().getName();
+    // -------------------------------------------------------------------------
+    // Choose an Integrator for advancing time, and a Context connecting the
+    // System with the Integrator for simulation. Let the Context choose the
+    // best available Platform. Initialize the configuration from the default
+    // positions we collected above. Initial velocities will be zero.
+    // -------------------------------------------------------------------------
+    OpenMM::VerletIntegrator integrator(StepSizeInFs * OpenMM::PsPerFs);
+    OpenMM::OpenMMContext    context(system, integrator);
+    context.setPositions(initialPositions);
+
+    // -------------------------------------------------------------------------
+    // Run the simulation:
+    //  (1) Write the first line of the PDB file and the initial configuration.
+    //  (2) Run silently entirely within OpenMM between reporting intervals.
+    //  (3) Write a PDB frame when the time comes.
+    // -------------------------------------------------------------------------
     printf( "REMARK  Using OpenMM platform %s\n", context.getPlatform().getName().c_str() );
-
-    // Fill in a vector of starting positions, one per atom.
-    std::vector<Vec3> positions(numAtoms);
-    for (int i=0; i < numAtoms; ++i)
-        positions[i] = atoms[i].startPosAng * NmPerAngstrom;
-
-    // Set the starting positions in the OpenMM context. Velocities will be zero.
-    context.setPositions(positions);
-
-    // Output the initial state.
     writePDB(context);
 
-    const int NumSilentSteps = (int)(ReportIntervalFs / StepSizeFs + 0.5);
+    const int NumSilentSteps = (int)(ReportIntervalInFs / StepSizeInFs + 0.5);
     do {
         integrator.step(NumSilentSteps);
         writePDB(context);
-    } while (context.getTime() < SimulationTimePs);
-
-    return 0;
-
-  } catch(const std::exception& e) {
-    std::cout << "EXCEPTION: " << e.what() << std::endl;
-    return 1;
-  }
-
+    } while (context.getTime() < SimulationTimeInPs);
 }
 
+// -----------------------------------------------------------------------------
+//                               PDB FILE WRITER
+// -----------------------------------------------------------------------------
 static void
-writePDB(const OpenMMContext& context) {
+writePDB(const OpenMM::OpenMMContext& context) {
     // Caution: at the moment asking for energy requires use of slow reference calculation.
-    const State                 state       = context.getState(State::Positions | State::Velocities | State::Energy);
-    const double                energy      = state.getPotentialEnergy() + state.getKineticEnergy();
-    const std::vector<Vec3>&    positions   = state.getPositions();
+    const OpenMM::State state = context.getState(  OpenMM::State::Positions 
+                                                 | OpenMM::State::Velocities 
+                                                 | OpenMM::State::Energy);
+    const double energy = state.getPotentialEnergy() + state.getKineticEnergy();
+    const std::vector<Vec3>& positions = state.getPositions();
     static int modelFrameNumber = 0; // numbering for MODEL records in pdb output
 
     // write out in PDB format -- printf is so much more compact than formatted cout
     modelFrameNumber++;
     printf("MODEL     %d\n", modelFrameNumber);
-    printf("REMARK 250 time=%.3f picoseconds; Energy = %.3f kilojoules/mole\n", state.getTime(), energy);
+    printf("REMARK 250 time=%.3f picoseconds; Energy = %.3f kilojoules/mole\n", 
+           state.getTime(), energy);
     for (unsigned i=0; i < positions.size(); ++i) {
-        const Vec3 pos = positions[i] * AngstromsPerNm;
-        printf("ATOM    %3d %2s   SLT     1    %8.3f%8.3f%8.3f  1.00  0.00          %2s\n", 
-            i+1, atoms[i].symbol, pos[0], pos[1], pos[2], atoms[i].symbol);
+        const Vec3 pos = positions[i] * OpenMM::AngstromsPerNm;
+        printf("ATOM  %5d %4s SLT     1    %8.3f%8.3f%8.3f  1.00  0.00            \n", 
+            i+1, atoms[i].pdb, pos[0], pos[1], pos[2]);
     }
     printf("ENDMDL\n");
 }