Merge pull request #827 from peastman/reference

Lots of cleanup to reference platform

openmmapi/include/openmm/GBVIForce.h

@@ -157,7 +157,7 @@ public:
      * 
      * @return number of bonds
      */
-    int getNumBonds( void ) const;
+    int getNumBonds() const;
 
     /**
      * Get the dielectric constant for the solvent.
@@ -208,7 +208,7 @@ public:
     /** 
      * Get Born radius scaling method
      */
-    BornRadiusScalingMethod getBornRadiusScalingMethod( void ) const;
+    BornRadiusScalingMethod getBornRadiusScalingMethod() const;
     /** 
      * Set Born radius scaling method
      */
@@ -216,7 +216,7 @@ public:
     /** 
      * Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
      */
-    double getQuinticLowerLimitFactor( void ) const;
+    double getQuinticLowerLimitFactor() const;
     /** 
      * Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
      */
@@ -224,7 +224,7 @@ public:
     /** 
      * Get the upper limit  used in the quintic spline scaling method, measured in nm (~5.0)
      */
-    double getQuinticUpperBornRadiusLimit( void ) const;
+    double getQuinticUpperBornRadiusLimit() const;
     /** 
      * Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
      */

openmmapi/src/GBVIForce.cpp

@@ -77,7 +77,7 @@ void GBVIForce::setCutoffDistance(double distance) {
     cutoffDistance = distance;
 }
 
-GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod( void ) const {
+GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod() const {
     return scalingMethod;
 }
 
@@ -85,7 +85,7 @@ void GBVIForce::setBornRadiusScalingMethod(BornRadiusScalingMethod method) {
     scalingMethod = method;
 }
 
-double GBVIForce::getQuinticLowerLimitFactor( void ) const {
+double GBVIForce::getQuinticLowerLimitFactor() const {
     return quinticLowerLimitFactor;
 }
 
@@ -93,7 +93,7 @@ void GBVIForce::setQuinticLowerLimitFactor(double inputQuinticLowerLimitFactor )
     quinticLowerLimitFactor = inputQuinticLowerLimitFactor;
 }
 
-double GBVIForce::getQuinticUpperBornRadiusLimit( void ) const {
+double GBVIForce::getQuinticUpperBornRadiusLimit() const {
     return quinticUpperBornRadiusLimit;
 }
 
@@ -113,7 +113,7 @@ void GBVIForce::setBondParameters( int index, int particle1, int particle2, doub
     bonds[index].bondLength = bondLength;
 }
 
-int GBVIForce::getNumBonds( void ) const {
+int GBVIForce::getNumBonds() const {
    return (int) bonds.size();
 }
 

openmmapi/src/GBVIForceImpl.cpp

@@ -145,8 +145,6 @@ int GBVIForceImpl::getBondsFromForces(ContextImpl& context) {
 }
 */
 
-#define GBVIDebug 0
-
 void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
                                      const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const {
 
@@ -219,26 +217,6 @@ void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<st
     if( errors ){
         throw OpenMMException("GBVIForceImpl::findScaledRadii errors -- aborting");
     }
-
-#if GBVIDebug
-    (void) fprintf( stderr, "                  R              q          gamma   scaled radii no. bnds\n" );
-    double totalQ = 0.0;
-    for( int i = 0; i < (int) scaledRadii.size(); i++ ){
-
-        double charge;
-        double gamma;
-        double radiusI;
-     
-        owner.getParticleParameters(i, charge, radiusI, gamma); 
-        totalQ += charge;
-        (void) fprintf( stderr, "%4d %14.5e %14.5e %14.5e %14.5e %d\n", i, radiusI, charge, gamma, scaledRadii[i], (int) bonded12[i].size() );
-    }
-    (void) fprintf( stderr, "Total charge=%e\n", totalQ );
-    (void) fflush( stderr );
-#endif
-
-#undef GBVIDebug
-
 }
 
 double GBVIForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {

platforms/cpu/include/CpuLangevinDynamics.h

@@ -31,7 +31,7 @@
 #include "openmm/internal/ThreadPool.h"
 #include "sfmt/SFMT.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class CpuLangevinDynamics : public ReferenceStochasticDynamics {
 public:
@@ -95,6 +95,6 @@ private:
     OpenMM::RealVec* xPrime;
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __CPU_LANGEVIN_DYNAMICS_H__

platforms/cpu/src/CpuCustomGBForce.cpp

@@ -25,8 +25,6 @@
 #include <string.h>
 #include <sstream>
 
-#include "SimTKOpenMMCommon.h"
-#include "SimTKOpenMMLog.h"
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "CpuCustomGBForce.h"

platforms/cpu/src/CpuCustomManyParticleForce.cpp

@@ -26,8 +26,6 @@
 #include <sstream>
 #include <utility>
 
-#include "SimTKOpenMMCommon.h"
-#include "SimTKOpenMMLog.h"
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "CpuCustomManyParticleForce.h"

platforms/cpu/src/CpuCustomNonbondedForce.cpp

@@ -25,8 +25,6 @@
 #include <string.h>
 #include <sstream>
 
-#include "SimTKOpenMMCommon.h"
-#include "SimTKOpenMMLog.h"
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "CpuCustomNonbondedForce.h"

platforms/cpu/src/CpuLangevinDynamics.cpp

@@ -23,8 +23,6 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include "SimTKOpenMMCommon.h"
-#include "SimTKOpenMMLog.h"
 #include "SimTKOpenMMUtilities.h"
 #include "CpuLangevinDynamics.h"
 

platforms/cpu/src/CpuNonbondedForce.cpp

@@ -24,7 +24,6 @@
 
 #include <complex>
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "CpuNonbondedForce.h"
 #include "ReferenceForce.h"

platforms/cpu/src/CpuNonbondedForceVec4.cpp

@@ -22,7 +22,6 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "CpuNonbondedForceVec4.h"
 

platforms/cpu/src/CpuNonbondedForceVec8.cpp

@@ -22,7 +22,6 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "CpuNonbondedForceVec8.h"
 #include "openmm/OpenMMException.h"

platforms/reference/include/GBVIParameters.h

@@ -25,9 +25,10 @@
 #ifndef __GBVIParameters_H__
 #define __GBVIParameters_H__
 
-#include "SimTKOpenMMCommon.h"
+#include "RealVec.h"
+#include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class GBVIParameters {
 
@@ -57,9 +58,9 @@ class GBVIParameters {
 
       // parameter vectors
 
-      RealOpenMMVector _atomicRadii;
-      RealOpenMMVector _scaledRadii;
-      RealOpenMMVector _gammaParameters;
+      std::vector<RealOpenMM> _atomicRadii;
+      std::vector<RealOpenMM> _scaledRadii;
+      std::vector<RealOpenMM> _gammaParameters;
 
       // cutoff and periodic boundary conditions
       
@@ -82,7 +83,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
       
-       GBVIParameters( int numberOfAtoms );
+       GBVIParameters(int numberOfAtoms);
 
       /**---------------------------------------------------------------------------------------
       
@@ -90,7 +91,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
       
-       ~GBVIParameters( );
+       ~GBVIParameters();
 
       /**---------------------------------------------------------------------------------------
       
@@ -100,7 +101,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      int getNumberOfAtoms( void ) const;
+      int getNumberOfAtoms() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -110,7 +111,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getElectricConstant( void ) const;
+      RealOpenMM getElectricConstant() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -120,7 +121,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getSolventDielectric( void ) const;
+      RealOpenMM getSolventDielectric() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -130,7 +131,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setSolventDielectric( RealOpenMM solventDielectric );
+      void setSolventDielectric(RealOpenMM solventDielectric);
 
       /**---------------------------------------------------------------------------------------
       
@@ -140,7 +141,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getSoluteDielectric( void ) const;
+      RealOpenMM getSoluteDielectric() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -150,7 +151,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setSoluteDielectric( RealOpenMM soluteDielectric );
+      void setSoluteDielectric(RealOpenMM soluteDielectric);
 
       /**---------------------------------------------------------------------------------------
       
@@ -160,7 +161,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      const RealOpenMMVector& getScaledRadii( void ) const;
+      const std::vector<RealOpenMM>& getScaledRadii() const;
         
       /**---------------------------------------------------------------------------------------
       
@@ -170,7 +171,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      void setScaledRadii( const RealOpenMMVector& scaledRadii );
+      void setScaledRadii(const std::vector<RealOpenMM>& scaledRadii);
         
       /**---------------------------------------------------------------------------------------
       
@@ -180,7 +181,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      const RealOpenMMVector& getAtomicRadii( void ) const;
+      const std::vector<RealOpenMM>& getAtomicRadii() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -190,7 +191,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setAtomicRadii( const RealOpenMMVector& atomicRadii );
+      void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
 
       /**---------------------------------------------------------------------------------------
       
@@ -200,7 +201,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      const RealOpenMMVector& getGammaParameters( void ) const;
+      const std::vector<RealOpenMM>& getGammaParameters() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -210,7 +211,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setGammaParameters( const RealOpenMMVector& gammaParameters );
+      void setGammaParameters(const std::vector<RealOpenMM>& gammaParameters);
 
       /**---------------------------------------------------------------------------------------
 
@@ -220,7 +221,7 @@ class GBVIParameters {
 
          --------------------------------------------------------------------------------------- */
 
-      void setUseCutoff( RealOpenMM distance );
+      void setUseCutoff(RealOpenMM distance);
 
       /**---------------------------------------------------------------------------------------
 
@@ -274,7 +275,7 @@ class GBVIParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM getTau( void ) const;
+      RealOpenMM getTau() const;
       
     /**---------------------------------------------------------------------------------------
     
@@ -284,7 +285,7 @@ class GBVIParameters {
     
        --------------------------------------------------------------------------------------- */
     
-    int getBornRadiusScalingMethod( void ) const;
+    int getBornRadiusScalingMethod() const;
     
     /**---------------------------------------------------------------------------------------
     
@@ -294,7 +295,7 @@ class GBVIParameters {
     
        --------------------------------------------------------------------------------------- */
     
-    void setBornRadiusScalingMethod( int bornRadiusScalingMethod );
+    void setBornRadiusScalingMethod(int bornRadiusScalingMethod);
     
     /**---------------------------------------------------------------------------------------
     
@@ -304,7 +305,7 @@ class GBVIParameters {
     
        --------------------------------------------------------------------------------------- */
     
-    RealOpenMM getQuinticLowerLimitFactor( void ) const;
+    RealOpenMM getQuinticLowerLimitFactor() const;
     
     /**---------------------------------------------------------------------------------------
     
@@ -314,7 +315,7 @@ class GBVIParameters {
     
        --------------------------------------------------------------------------------------- */
     
-    void setQuinticLowerLimitFactor( RealOpenMM quinticLowerLimitFactor );
+    void setQuinticLowerLimitFactor(RealOpenMM quinticLowerLimitFactor);
     
     /**---------------------------------------------------------------------------------------
     
@@ -324,7 +325,7 @@ class GBVIParameters {
     
        --------------------------------------------------------------------------------------- */
     
-    RealOpenMM getQuinticUpperBornRadiusLimit( void ) const;
+    RealOpenMM getQuinticUpperBornRadiusLimit() const;
     
     /**---------------------------------------------------------------------------------------
     
@@ -334,8 +335,10 @@ class GBVIParameters {
     
        --------------------------------------------------------------------------------------- */
     
-    void setQuinticUpperBornRadiusLimit( RealOpenMM quinticUpperSplineLimit );
+    void setQuinticUpperBornRadiusLimit(RealOpenMM quinticUpperSplineLimit);
 
 };
-   
+
+} // namespace OpenMM
+
 #endif // __GBVIParameters_H__

platforms/reference/include/ObcParameters.h

@@ -25,9 +25,10 @@
 #ifndef __ObcParameters_H__
 #define __ObcParameters_H__
 
-#include "SimTKOpenMMCommon.h"
+#include "RealVec.h"
+#include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ObcParameters {
 
@@ -57,8 +58,8 @@ class ObcParameters {
 
       // scaled radius factors (S_kk in HCT paper)
 
-      RealOpenMMVector _atomicRadii;
-      RealOpenMMVector _scaledRadiusFactors;
+      std::vector<RealOpenMM> _atomicRadii;
+      std::vector<RealOpenMM> _scaledRadiusFactors;
 
       // cutoff and periodic boundary conditions
       
@@ -75,7 +76,7 @@ class ObcParameters {
 
          --------------------------------------------------------------------------------------- */
       
-      void setDielectricOffset( RealOpenMM dielectricOffset );
+      void setDielectricOffset(RealOpenMM dielectricOffset);
 
    public:
 
@@ -87,7 +88,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-       ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType = ObcTypeII );
+       ObcParameters(int numberOfAtoms, ObcParameters::ObcType obcType = ObcTypeII);
 
       /**---------------------------------------------------------------------------------------
       
@@ -95,7 +96,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-       ~ObcParameters( );
+       ~ObcParameters();
 
       /**---------------------------------------------------------------------------------------
       
@@ -105,7 +106,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      int getNumberOfAtoms( void ) const;
+      int getNumberOfAtoms() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -115,7 +116,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getElectricConstant( void ) const;
+      RealOpenMM getElectricConstant() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -125,7 +126,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getProbeRadius( void ) const;
+      RealOpenMM getProbeRadius() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -135,7 +136,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setProbeRadius( RealOpenMM probeRadius );
+      void setProbeRadius(RealOpenMM probeRadius);
 
       /**---------------------------------------------------------------------------------------
       
@@ -146,7 +147,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getPi4Asolv( void ) const;
+      RealOpenMM getPi4Asolv() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -154,7 +155,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setPi4Asolv( RealOpenMM pi4Asolv );
+      void setPi4Asolv(RealOpenMM pi4Asolv);
 
       /**---------------------------------------------------------------------------------------
       
@@ -164,7 +165,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getSolventDielectric( void ) const;
+      RealOpenMM getSolventDielectric() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -174,7 +175,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setSolventDielectric( RealOpenMM solventDielectric );
+      void setSolventDielectric(RealOpenMM solventDielectric);
 
       /**---------------------------------------------------------------------------------------
       
@@ -184,7 +185,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getSoluteDielectric( void ) const;
+      RealOpenMM getSoluteDielectric() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -194,7 +195,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setSoluteDielectric( RealOpenMM soluteDielectric );
+      void setSoluteDielectric(RealOpenMM soluteDielectric);
 
       /**---------------------------------------------------------------------------------------
       
@@ -204,7 +205,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      ObcParameters::ObcType getObcType( void ) const;
+      ObcParameters::ObcType getObcType() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -214,7 +215,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      void setObcTypeParameters( ObcParameters::ObcType obcType );
+      void setObcTypeParameters(ObcParameters::ObcType obcType);
       
       /**---------------------------------------------------------------------------------------
       
@@ -224,7 +225,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM getAlphaObc( void ) const;
+      RealOpenMM getAlphaObc() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -234,7 +235,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM getBetaObc( void ) const;
+      RealOpenMM getBetaObc() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -244,7 +245,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM getGammaObc( void ) const;
+      RealOpenMM getGammaObc() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -254,7 +255,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM getDielectricOffset( void ) const;
+      RealOpenMM getDielectricOffset() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -264,7 +265,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      const RealOpenMMVector& getScaledRadiusFactors( void ) const;
+      const std::vector<RealOpenMM>& getScaledRadiusFactors() const;
         
       /**---------------------------------------------------------------------------------------
       
@@ -274,7 +275,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
       
-      void setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors );
+      void setScaledRadiusFactors(const std::vector<RealOpenMM>& scaledRadiusFactors);
         
       /**---------------------------------------------------------------------------------------
       
@@ -284,7 +285,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      const RealOpenMMVector& getAtomicRadii( void ) const;
+      const std::vector<RealOpenMM>& getAtomicRadii() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -294,7 +295,7 @@ class ObcParameters {
       
          --------------------------------------------------------------------------------------- */
 
-      void setAtomicRadii( const RealOpenMMVector& atomicRadii );
+      void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
 
 
       /**---------------------------------------------------------------------------------------
@@ -305,7 +306,7 @@ class ObcParameters {
 
          --------------------------------------------------------------------------------------- */
 
-      void setUseCutoff( RealOpenMM distance );
+      void setUseCutoff(RealOpenMM distance);
 
       /**---------------------------------------------------------------------------------------
 
@@ -352,7 +353,7 @@ class ObcParameters {
       const OpenMM::RealVec* getPeriodicBox();
 
 };
-   
-// ---------------------------------------------------------------------------------------
+
+} // namespace OpenMM
 
 #endif // __ObcParameters_H__

platforms/reference/include/ReferenceAndersenThermostat.h

@@ -25,10 +25,9 @@
 #ifndef __ReferenceAndersenThermostat_H__
 #define __ReferenceAndersenThermostat_H__
 
-#include "SimTKOpenMMCommon.h"
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceAndersenThermostat {
 
@@ -42,7 +41,7 @@ class ReferenceAndersenThermostat {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceAndersenThermostat( );
+       ReferenceAndersenThermostat();
 
       /**---------------------------------------------------------------------------------------
       
@@ -50,7 +49,7 @@ class ReferenceAndersenThermostat {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceAndersenThermostat( );
+       ~ReferenceAndersenThermostat();
 
       /**---------------------------------------------------------------------------------------
       
@@ -65,11 +64,11 @@ class ReferenceAndersenThermostat {
                   
          --------------------------------------------------------------------------------------- */
           
-      void applyThermostat( const std::vector<std::vector<int> >& atomGroups, std::vector<OpenMM::RealVec>& atomVelocities, std::vector<RealOpenMM>& atomMasses,
-              RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const;
+      void applyThermostat(const std::vector<std::vector<int> >& atomGroups, std::vector<OpenMM::RealVec>& atomVelocities, std::vector<RealOpenMM>& atomMasses,
+              RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize) const;
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceAndersenThermostat_H__

platforms/reference/include/ReferenceAngleBondIxn.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceBondIxn.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceAngleBondIxn : public ReferenceBondIxn {
 
@@ -41,7 +41,7 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceAngleBondIxn( );
+       ReferenceAngleBondIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -49,7 +49,7 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceAngleBondIxn( );
+       ~ReferenceAngleBondIxn();
 
       /**---------------------------------------------------------------------------------------
 
@@ -63,8 +63,8 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      void getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM* angleParameters,
-                                         RealOpenMM* dEdR, RealOpenMM* energyTerm ) const;
+      void getPrefactorsGivenAngleCosine(RealOpenMM cosine, RealOpenMM* angleParameters,
+                                         RealOpenMM* dEdR, RealOpenMM* energyTerm) const;
       
       /**---------------------------------------------------------------------------------------
 
@@ -79,13 +79,13 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
+      void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* totalEnergy ) const;
+                            RealOpenMM* totalEnergy) const;
       
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceAngleBondIxn_H__

platforms/reference/include/ReferenceBondForce.h

@@ -28,7 +28,7 @@
 #include "ReferenceForce.h"
 #include "ReferenceBondIxn.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
 
@@ -42,7 +42,7 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceBondForce( );
+       ReferenceBondForce();
 
       /**---------------------------------------------------------------------------------------
       
@@ -50,7 +50,7 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceBondForce( );
+       ~ReferenceBondForce();
 
       /**---------------------------------------------------------------------------------------
       
@@ -67,13 +67,13 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
       
          --------------------------------------------------------------------------------------- */
       
-       void calculateForce( int numberOfBonds, int** atomIndices,
+       void calculateForce(int numberOfBonds, int** atomIndices,
                            std::vector<OpenMM::RealVec>& atomCoordinates,
                            RealOpenMM** parameters, std::vector<OpenMM::RealVec>& forces, 
-                           RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn );
+                           RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn);
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceBondForce_H__

platforms/reference/include/ReferenceBondIxn.h

@@ -29,7 +29,7 @@
 #include "openmm/internal/windowsExport.h"
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferenceBondIxn {
 
@@ -43,7 +43,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceBondIxn( );
+       ReferenceBondIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -51,7 +51,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceBondIxn( );
+       ~ReferenceBondIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -65,9 +65,9 @@ class OPENMM_EXPORT ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      virtual void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
+      virtual void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
                                     RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
-                                    RealOpenMM* totalEnergy ) const;
+                                    RealOpenMM* totalEnergy) const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -82,7 +82,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry );
+      static RealOpenMM getNormedDotProduct(RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry);
       
       /**---------------------------------------------------------------------------------------
       
@@ -98,8 +98,8 @@ class OPENMM_EXPORT ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2, 
-                                                   RealOpenMM* outputDotProduct, int hasREntry );
+      static RealOpenMM getAngleBetweenTwoVectors(RealOpenMM* vector1, RealOpenMM* vector2, 
+                                                   RealOpenMM* outputDotProduct, int hasREntry);
       
       /**---------------------------------------------------------------------------------------
       
@@ -119,13 +119,13 @@ class OPENMM_EXPORT ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM getDihedralAngleBetweenThreeVectors( RealOpenMM* vector1, RealOpenMM* vector2, 
-                                                             RealOpenMM* vector3, RealOpenMM** outputCrossProduct, 
-                                                             RealOpenMM* cosineOfAngle, RealOpenMM* signVector, 
-                                                             RealOpenMM* signOfAngle, int hasREntry );
+      static RealOpenMM getDihedralAngleBetweenThreeVectors(RealOpenMM* vector1, RealOpenMM* vector2, 
+                                                            RealOpenMM* vector3, RealOpenMM** outputCrossProduct, 
+                                                            RealOpenMM* cosineOfAngle, RealOpenMM* signVector, 
+                                                            RealOpenMM* signOfAngle, int hasREntry);
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceBondIxn_H__

platforms/reference/include/ReferenceBrownianDynamics.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceDynamics.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceBrownianDynamics : public ReferenceDynamics {
 
@@ -50,7 +50,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceBrownianDynamics( int numberOfAtoms, RealOpenMM deltaT, RealOpenMM friction, RealOpenMM temperature );
+       ReferenceBrownianDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM friction, RealOpenMM temperature);
 
       /**---------------------------------------------------------------------------------------
       
@@ -58,7 +58,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceBrownianDynamics( );
+       ~ReferenceBrownianDynamics();
 
       /**---------------------------------------------------------------------------------------
       
@@ -68,7 +68,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM getFriction( void ) const;
+      RealOpenMM getFriction() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -88,6 +88,6 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceBrownianDynamics_H__

platforms/reference/include/ReferenceCCMAAlgorithm.h

@@ -30,7 +30,7 @@
 #include <vector>
 #include <set>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm {
 
@@ -69,22 +69,22 @@ public:
      */
     ReferenceCCMAAlgorithm(int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<RealOpenMM>& distance, std::vector<RealOpenMM>& masses, std::vector<AngleInfo>& angles);
 
-    ~ReferenceCCMAAlgorithm( );
+    ~ReferenceCCMAAlgorithm();
 
     /**
      * Get the number of constraints.
      */
-    int getNumberOfConstraints( void ) const;
+    int getNumberOfConstraints() const;
 
     /**
      * Get the maximum number of iterations to perform.
      */
-    int getMaximumNumberOfIterations( void ) const;
+    int getMaximumNumberOfIterations() const;
 
     /**
      * Set the maximum number of iterations to perform.
      */
-    void setMaximumNumberOfIterations( int maximumNumberOfIterations );
+    void setMaximumNumberOfIterations(int maximumNumberOfIterations);
 
     /**
      * Apply the constraint algorithm.
@@ -120,6 +120,6 @@ public:
     }
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceCCMAAlgorithm_H__

platforms/reference/include/ReferenceCMAPTorsionIxn.h

@@ -25,12 +25,11 @@
 #ifndef __ReferenceCMAPTorsionIxn_H__
 #define __ReferenceCMAPTorsionIxn_H__
 
-#include "SimTKOpenMMCommon.h"
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceBondIxn.h"
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCMAPTorsionIxn : public ReferenceBondIxn {
 
@@ -92,4 +91,6 @@ public:
 
 };
 
+} // namespace OpenMM
+
 #endif // __ReferenceCMAPTorsionIxn_H__