fix up ugly line endings

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
+/* -----------------------------------------------------------------------------
+ *                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"
 
@@ -26,41 +26,41 @@
 
 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)
+//                   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 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;
-    }
+// -----------------------------------------------------------------------------
+//                                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
+// -----------------------------------------------------------------------------
+//                          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
@@ -83,22 +83,22 @@ struct AtomInfo {
     {""} // end of list
 };
 
-// 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
+// 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!
+    // -------------------------------------------------------------------------
+    // 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();
@@ -108,11 +108,11 @@ static void simulateNaCl() {
     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.
+    // -------------------------------------------------------------------------
+    // 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) {
@@ -122,25 +122,25 @@ static void simulateNaCl() {
                              atom.vdwRadiusInAng  * OpenMM::NmPerAngstrom 
                                                   * SigmaPerVdwRadius,
                              atom.vdwEnergyInKcal * OpenMM::KJPerKcal);
-        initialPositions.push_back(atoms[n].initPosInAngstroms 
-                                                  * OpenMM::NmPerAngstrom);
+        initialPositions.push_back(atoms[n].initPosInAngstroms 
+                                                  * OpenMM::NmPerAngstrom);
     }
 
-    // -------------------------------------------------------------------------
-    // 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);
+    // -------------------------------------------------------------------------
+    // 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.
+    // -------------------------------------------------------------------------
+    // 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() );
     writePDB(context);
@@ -152,8 +152,8 @@ static void simulateNaCl() {
     } while (context.getTime() < SimulationTimeInPs);
 }
 
-// -----------------------------------------------------------------------------
-//                               PDB FILE WRITER
+// -----------------------------------------------------------------------------
+//                               PDB FILE WRITER
 // -----------------------------------------------------------------------------
 static void
 writePDB(const OpenMM::OpenMMContext& context) {