Merge remote-tracking branch 'upstream/master'

platforms/reference/include/ReferenceCustomDynamics.h

@@ -34,7 +34,7 @@
 #include <string>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomDynamics : public ReferenceDynamics {
 private:
@@ -121,6 +121,6 @@ public:
                                    std::map<std::string, RealOpenMM>& globals, std::vector<std::vector<OpenMM::RealVec> >& perDof, bool& forcesAreValid);
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceCustomDynamics_H__

platforms/reference/include/ReferenceCustomExternalIxn.h

@@ -28,7 +28,7 @@
 #include "ReferenceCustomExternalIxn.h"
 #include "lepton/CompiledExpression.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomExternalIxn {
 
@@ -65,7 +65,7 @@ class ReferenceCustomExternalIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceCustomExternalIxn( );
+       ~ReferenceCustomExternalIxn();
 
       /**---------------------------------------------------------------------------------------
 
@@ -79,12 +79,12 @@ class ReferenceCustomExternalIxn {
 
          --------------------------------------------------------------------------------------- */
 
-      void calculateForce( int atomIndex, std::vector<OpenMM::RealVec>& atomCoordinates,
-                            RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* energy ) const;
+      void calculateForce(int atomIndex, std::vector<OpenMM::RealVec>& atomCoordinates,
+                          RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces, RealOpenMM* energy) const;
 
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // _ReferenceCustomBondIxn___

platforms/reference/include/ReferenceCustomGBIxn.h

@@ -32,7 +32,7 @@
 #include <set>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomGBIxn {
 
@@ -244,7 +244,7 @@ class ReferenceCustomGBIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceCustomGBIxn( );
+       ~ReferenceCustomGBIxn();
 
       /**---------------------------------------------------------------------------------------
 
@@ -255,7 +255,7 @@ class ReferenceCustomGBIxn {
 
          --------------------------------------------------------------------------------------- */
 
-      void setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors );
+      void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors);
 
       /**---------------------------------------------------------------------------------------
 
@@ -290,4 +290,6 @@ class ReferenceCustomGBIxn {
 
 };
 
+} // namespace OpenMM
+
 #endif // __ReferenceCustomGBIxn_H__

platforms/reference/include/ReferenceCustomHbondIxn.h

@@ -32,7 +32,7 @@
 #include <set>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomHbondIxn : public ReferenceBondIxn {
 
@@ -198,4 +198,6 @@ public:
     }
 };
 
+} // namespace OpenMM
+
 #endif // __ReferenceCustomHbondIxn_H__

platforms/reference/include/ReferenceCustomManyParticleIxn.h

@@ -33,7 +33,7 @@
 #include <set>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomManyParticleIxn {
 
@@ -192,4 +192,6 @@ public:
     }
 };
 
+} // namespace OpenMM
+
 #endif // __ReferenceCustomManyParticleIxn_H__

platforms/reference/include/ReferenceCustomNonbondedIxn.h

@@ -33,7 +33,7 @@
 #include <utility>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomNonbondedIxn {
 
@@ -68,8 +68,8 @@ class ReferenceCustomNonbondedIxn {
 
          --------------------------------------------------------------------------------------- */
 
-      void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
+      void calculateOneIxn(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces,
+                           RealOpenMM* energyByAtom, RealOpenMM* totalEnergy);
 
 
    public:
@@ -89,7 +89,7 @@ class ReferenceCustomNonbondedIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceCustomNonbondedIxn( );
+       ~ReferenceCustomNonbondedIxn();
 
       /**---------------------------------------------------------------------------------------
 
@@ -100,7 +100,7 @@ class ReferenceCustomNonbondedIxn {
 
          --------------------------------------------------------------------------------------- */
 
-      void setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors );
+      void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors);
 
       /**---------------------------------------------------------------------------------------
 
@@ -121,7 +121,7 @@ class ReferenceCustomNonbondedIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      void setUseSwitchingFunction( RealOpenMM distance );
+      void setUseSwitchingFunction(RealOpenMM distance);
 
       /**---------------------------------------------------------------------------------------
 
@@ -152,13 +152,15 @@ class ReferenceCustomNonbondedIxn {
 
          --------------------------------------------------------------------------------------- */
 
-      void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
+      void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
                             RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
-                            std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy );
+                            std::vector<OpenMM::RealVec>& forces, RealOpenMM* energyByAtom, RealOpenMM* totalEnergy);
 
 // ---------------------------------------------------------------------------------------
 
 };
 
+} // namespace OpenMM
+
 #endif // __ReferenceCustomNonbondedxIxn_H__

platforms/reference/include/ReferenceCustomTorsionIxn.h

@@ -27,7 +27,7 @@
 #include "ReferenceBondIxn.h"
 #include "lepton/CompiledExpression.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
 
@@ -57,7 +57,7 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
 
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceCustomTorsionIxn( );
+       ~ReferenceCustomTorsionIxn();
 
       /**---------------------------------------------------------------------------------------
 
@@ -71,13 +71,13 @@ class ReferenceCustomTorsionIxn : 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 // _ReferenceCustomTorsionIxn___

platforms/reference/include/ReferenceDynamics.h

@@ -26,12 +26,11 @@
 #define __ReferenceDynamics_H__
 
 #include "ReferenceConstraintAlgorithm.h"
-#include "SimTKOpenMMCommon.h"
 #include "openmm/System.h"
 #include <cstddef>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 /**---------------------------------------------------------------------------------------
 
@@ -68,7 +67,7 @@ class OPENMM_EXPORT ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-       ReferenceDynamics( int numberOfAtoms, RealOpenMM _deltaT, RealOpenMM temperature );
+       ReferenceDynamics(int numberOfAtoms, RealOpenMM _deltaT, RealOpenMM temperature);
 
       /**---------------------------------------------------------------------------------------
       
@@ -76,7 +75,7 @@ class OPENMM_EXPORT ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
 
-       virtual ~ReferenceDynamics( );
+       virtual ~ReferenceDynamics();
 
       /**---------------------------------------------------------------------------------------
       
@@ -86,7 +85,7 @@ class OPENMM_EXPORT ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      int getNumberOfAtoms( void ) const;
+      int getNumberOfAtoms() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -96,7 +95,7 @@ class OPENMM_EXPORT ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      int getTimeStep( void ) const;
+      int getTimeStep() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -106,7 +105,7 @@ class OPENMM_EXPORT ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      int incrementTimeStep( void );
+      int incrementTimeStep();
       
       /**---------------------------------------------------------------------------------------
       
@@ -116,7 +115,7 @@ class OPENMM_EXPORT ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM getDeltaT( void ) const;
+      RealOpenMM getDeltaT() const;
 
       /**---------------------------------------------------------------------------------------
 
@@ -124,7 +123,7 @@ class OPENMM_EXPORT ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-      void setDeltaT( RealOpenMM deltaT );
+      void setDeltaT(RealOpenMM deltaT);
 
       /**---------------------------------------------------------------------------------------
       
@@ -134,7 +133,7 @@ class OPENMM_EXPORT ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
     
-      RealOpenMM getTemperature( void ) const;
+      RealOpenMM getTemperature() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -160,7 +159,7 @@ class OPENMM_EXPORT ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      ReferenceConstraintAlgorithm* getReferenceConstraintAlgorithm( void ) const;
+      ReferenceConstraintAlgorithm* getReferenceConstraintAlgorithm() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -170,9 +169,10 @@ class OPENMM_EXPORT ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      void setReferenceConstraintAlgorithm( ReferenceConstraintAlgorithm* referenceConstraint );
+      void setReferenceConstraintAlgorithm(ReferenceConstraintAlgorithm* referenceConstraint);
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
+
 
 #endif // __ReferenceDynamics_H__

platforms/reference/include/ReferenceForce.h

@@ -28,7 +28,7 @@
 #include "lepton/CompiledExpression.h"
 #include "openmm/internal/windowsExport.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT  ReferenceForce {
 
@@ -44,7 +44,7 @@ class OPENMM_EXPORT  ReferenceForce {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceForce( );
+       ReferenceForce();
 
       /**---------------------------------------------------------------------------------------
       
@@ -52,7 +52,7 @@ class OPENMM_EXPORT  ReferenceForce {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceForce( );
+       ~ReferenceForce();
 
       /**---------------------------------------------------------------------------------------
       
@@ -80,8 +80,8 @@ class OPENMM_EXPORT  ReferenceForce {
       
          --------------------------------------------------------------------------------------- */
       
-      static void getDeltaR( const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
-                            RealOpenMM* deltaR );
+      static void getDeltaR(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
+                            RealOpenMM* deltaR);
       
       /**---------------------------------------------------------------------------------------
 
@@ -95,8 +95,8 @@ class OPENMM_EXPORT  ReferenceForce {
 
          --------------------------------------------------------------------------------------- */
 
-      static void getDeltaRPeriodic( const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
-                                             const RealOpenMM* boxSize, RealOpenMM* deltaR );
+      static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
+                                    const RealOpenMM* boxSize, RealOpenMM* deltaR);
 
       /**---------------------------------------------------------------------------------------
 
@@ -110,8 +110,8 @@ class OPENMM_EXPORT  ReferenceForce {
 
          --------------------------------------------------------------------------------------- */
 
-      static void getDeltaRPeriodic( const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
-                                             const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR );
+      static void getDeltaRPeriodic(const OpenMM::RealVec& atomCoordinatesI, const OpenMM::RealVec& atomCoordinatesJ,
+                                    const OpenMM::RealVec* boxVectors, RealOpenMM* deltaR);
 
       /**
        * Get a pointer to the memory for setting a variable in a CompiledExpression.  If the expression
@@ -126,6 +126,6 @@ class OPENMM_EXPORT  ReferenceForce {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceForce_H__

platforms/reference/include/CpuGBVI.h → platforms/reference/include/ReferenceGBVI.h

@@ -22,24 +22,24 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#ifndef __CpuGBVI_H__
-#define __CpuGBVI_H__
+#ifndef __ReferenceGBVI_H__
+#define __ReferenceGBVI_H__
 
 #include <vector>
 
 #include "RealVec.h"
 #include "GBVIParameters.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
-class CpuGBVI {
+class ReferenceGBVI {
 
    private:
 
       // GB/VI parameters
 
       GBVIParameters* _gbviParameters;
-      RealOpenMMVector _switchDeriviative;
+      std::vector<RealOpenMM> _switchDeriviative;
 
    public:
 
@@ -53,7 +53,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
 
-       CpuGBVI( GBVIParameters* gbviParameters );
+       ReferenceGBVI(GBVIParameters* gbviParameters);
 
       /**---------------------------------------------------------------------------------------
       
@@ -61,7 +61,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
 
-       ~CpuGBVI( );
+       ~ReferenceGBVI();
 
       /**---------------------------------------------------------------------------------------
       
@@ -71,7 +71,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
 
-      GBVIParameters* getGBVIParameters( void ) const;
+      GBVIParameters* getGBVIParameters() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -81,7 +81,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
 
-      void setGBVIParameters( GBVIParameters* gbviParameters );
+      void setGBVIParameters(GBVIParameters* gbviParameters);
  
       /**---------------------------------------------------------------------------------------
       
@@ -93,7 +93,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      void computeBornRadii( const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii );
+      void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii);
       
       /**---------------------------------------------------------------------------------------
       
@@ -107,7 +107,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM getVolume( RealOpenMM r, RealOpenMM R, RealOpenMM S );
+      static RealOpenMM getVolume(RealOpenMM r, RealOpenMM R, RealOpenMM S);
       
       /**---------------------------------------------------------------------------------------
       
@@ -121,7 +121,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM getL( RealOpenMM r, RealOpenMM x, RealOpenMM S );
+      static RealOpenMM getL(RealOpenMM r, RealOpenMM x, RealOpenMM S);
 
       /**---------------------------------------------------------------------------------------
       
@@ -135,7 +135,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM dL_dr( RealOpenMM r, RealOpenMM x, RealOpenMM S );
+      static RealOpenMM dL_dr(RealOpenMM r, RealOpenMM x, RealOpenMM S);
 
       /**---------------------------------------------------------------------------------------
       
@@ -149,7 +149,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM dL_dx( RealOpenMM r, RealOpenMM x, RealOpenMM S );
+      static RealOpenMM dL_dx(RealOpenMM r, RealOpenMM x, RealOpenMM S);
 
       /**---------------------------------------------------------------------------------------
       
@@ -161,7 +161,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM Sgb( RealOpenMM t );
+      static RealOpenMM Sgb(RealOpenMM t);
       
       /**---------------------------------------------------------------------------------------
       
@@ -174,7 +174,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM computeBornEnergy( const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges );
+      RealOpenMM computeBornEnergy(const std::vector<OpenMM::RealVec>& atomCoordinates, const std::vector<RealOpenMM>& partialCharges);
       
       /**---------------------------------------------------------------------------------------
       
@@ -186,8 +186,8 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      void computeBornForces( std::vector<OpenMM::RealVec>& atomCoordinates,
-                              const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& inputForces );
+      void computeBornForces(std::vector<OpenMM::RealVec>& atomCoordinates,
+                             const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& inputForces);
       
       /**---------------------------------------------------------------------------------------
       
@@ -201,7 +201,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static double getVolumeD( double r, double R, double S );
+      static double getVolumeD(double r, double R, double S);
       
       /**---------------------------------------------------------------------------------------
       
@@ -215,7 +215,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static double getLD( double r, double x, double S );
+      static double getLD(double r, double x, double S);
 
       /**---------------------------------------------------------------------------------------
       
@@ -229,7 +229,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static double dL_drD( double r, double x, double S );
+      static double dL_drD(double r, double x, double S);
 
       /**---------------------------------------------------------------------------------------
       
@@ -243,7 +243,7 @@ class CpuGBVI {
       
          --------------------------------------------------------------------------------------- */
       
-      static double dL_dxD( double r, double x, double S );
+      static double dL_dxD(double r, double x, double S);
 
     /**---------------------------------------------------------------------------------------
     
@@ -254,7 +254,7 @@ class CpuGBVI {
     
        --------------------------------------------------------------------------------------- */
     
-      RealOpenMMVector& getSwitchDeriviative( void );
+      std::vector<RealOpenMM>& getSwitchDeriviative();
     
     /**---------------------------------------------------------------------------------------
     
@@ -268,8 +268,8 @@ class CpuGBVI {
     
        --------------------------------------------------------------------------------------- */
     
-    void quinticSpline( RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
-                        RealOpenMM* outValue, RealOpenMM* outDerivative );
+    void quinticSpline(RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
+                       RealOpenMM* outValue, RealOpenMM* outDerivative);
 
     /**---------------------------------------------------------------------------------------
     
@@ -285,32 +285,12 @@ class CpuGBVI {
     
        --------------------------------------------------------------------------------------- */
     
-    void computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius3, RealOpenMM bornSum,
-                                             GBVIParameters* gbviParameters,
-                                             RealOpenMM* bornRadius, RealOpenMM* switchDeriviative );
-
-    /**---------------------------------------------------------------------------------------
-    
-        Print GB/VI parameters, radii, forces, ...
-    
-        @param atomCoordinates     atomic coordinates
-        @param partialCharges      partial charges
-        @param bornRadii           Born radii (may be empty)
-        @param bornForces          Born forces (may be empty)
-        @param forces              forces (may be empty)
-        @param idString            id string (who is calling)
-        @param log                 log file
-    
-        --------------------------------------------------------------------------------------- */
-    
-    void printGbvi( const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
-                    const RealOpenMMVector& bornRadii,
-                    const RealOpenMMVector& bornForces,
-                    const std::vector<OpenMM::RealVec>& forces,
-                    const std::string& idString, FILE* log );
+    void computeBornRadiiUsingQuinticSpline(RealOpenMM atomicRadius3, RealOpenMM bornSum,
+                                            GBVIParameters* gbviParameters,
+                                            RealOpenMM* bornRadius, RealOpenMM* switchDeriviative);
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
-#endif // __CpuGBVI_H__
+#endif // __ReferenceGBVI_H__

platforms/reference/include/ReferenceHarmonicBondIxn.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceBondIxn.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
 
@@ -41,7 +41,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceHarmonicBondIxn( );
+       ReferenceHarmonicBondIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -49,7 +49,7 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceHarmonicBondIxn( );
+       ~ReferenceHarmonicBondIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -64,12 +64,12 @@ class ReferenceHarmonicBondIxn : 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 // _ReferenceHarmonicBondIxn___

platforms/reference/include/ReferenceKernels.h

@@ -39,8 +39,10 @@
 #include "lepton/CompiledExpression.h"
 #include "lepton/ExpressionProgram.h"
 
-class CpuObc;
-class CpuGBVI;
+namespace OpenMM {
+
+class ReferenceObc;
+class ReferenceGBVI;
 class ReferenceAndersenThermostat;
 class ReferenceCustomCompoundBondIxn;
 class ReferenceCustomHbondIxn;
@@ -54,8 +56,6 @@ class ReferenceVariableVerletDynamics;
 class ReferenceVerletDynamics;
 class ReferenceCustomDynamics;
 
-namespace OpenMM {
-
 /**
  * This kernel is invoked at the beginning and end of force and energy computations.  It gives the
  * Platform a chance to clear buffers and do other initialization at the beginning, and to do any
@@ -89,11 +89,13 @@ public:
      * @param includeForce  true if forces should be computed
      * @param includeEnergy true if potential energy should be computed
      * @param groups        a set of bit flags for which force groups to include
+     * @param valid         the method may set this to false to indicate the results are invalid and the force/energy
+     *                      calculation should be repeated
      * @return the potential energy of the system.  This value is added to all values returned by ForceImpls'
      * calcForcesAndEnergy() methods.  That is, each force kernel may <i>either</i> return its contribution to the
      * energy directly, <i>or</i> add it to an internal buffer so that it will be included here.
      */
-    double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups);
+    double finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid);
 private:
     std::vector<RealVec> savedForces;
 };
@@ -658,7 +660,7 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
 private:
-    CpuObc* obc;
+    ReferenceObc* obc;
     std::vector<RealOpenMM> charges;
     bool isPeriodic;
 };
@@ -689,7 +691,7 @@ public:
      */
     double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
 private:
-    CpuGBVI * gbvi;
+    ReferenceGBVI * gbvi;
     std::vector<RealOpenMM> charges;
     bool isPeriodic;
 };

platforms/reference/include/ReferenceLJCoulomb14.h

@@ -28,7 +28,7 @@
 #include "ReferenceBondIxn.h"
 #include "openmm/internal/windowsExport.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
 
@@ -40,7 +40,7 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceLJCoulomb14( );
+       ReferenceLJCoulomb14();
 
       /**---------------------------------------------------------------------------------------
       
@@ -48,7 +48,7 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceLJCoulomb14( );
+       ~ReferenceLJCoulomb14();
 
       /**---------------------------------------------------------------------------------------
       
@@ -62,12 +62,12 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : 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 // __ReferenceLJCoulomb14_H__

platforms/reference/include/ReferenceLJCoulombIxn.h

@@ -28,7 +28,7 @@
 #include "ReferencePairIxn.h"
 #include "ReferenceNeighborList.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceLJCoulombIxn {
 
@@ -67,9 +67,9 @@ class ReferenceLJCoulombIxn {
             
          --------------------------------------------------------------------------------------- */
           
-      void calculateOneIxn( int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates,
-                            RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
+      void calculateOneIxn(int atom1, int atom2, std::vector<OpenMM::RealVec>& atomCoordinates,
+                           RealOpenMM** atomParameters, std::vector<OpenMM::RealVec>& forces,
+                           RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const;
 
 
    public:
@@ -80,7 +80,7 @@ class ReferenceLJCoulombIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceLJCoulombIxn( );
+       ReferenceLJCoulombIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -88,7 +88,7 @@ class ReferenceLJCoulombIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceLJCoulombIxn( );
+       ~ReferenceLJCoulombIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -100,7 +100,7 @@ class ReferenceLJCoulombIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      void setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric );
+      void setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors, RealOpenMM solventDielectric);
 
       /**---------------------------------------------------------------------------------------
       
@@ -110,7 +110,7 @@ class ReferenceLJCoulombIxn {
       
          --------------------------------------------------------------------------------------- */
       
-      void setUseSwitchingFunction( RealOpenMM distance );
+      void setUseSwitchingFunction(RealOpenMM distance);
       
       /**---------------------------------------------------------------------------------------
       
@@ -197,6 +197,6 @@ private:
                             RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, bool includeDirect, bool includeReciprocal) const;
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceLJCoulombIxn_H__

platforms/reference/include/ReferenceLincsAlgorithm.h

@@ -28,7 +28,7 @@
 #include "SimTKOpenMMRealType.h"
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
 
@@ -92,7 +92,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
 
          --------------------------------------------------------------------------------------- */
 
-      ReferenceLincsAlgorithm( int numberOfConstraints, int** atomIndices, RealOpenMM* distance );
+      ReferenceLincsAlgorithm(int numberOfConstraints, int** atomIndices, RealOpenMM* distance);
 
       /**---------------------------------------------------------------------------------------
 
@@ -102,7 +102,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
 
          --------------------------------------------------------------------------------------- */
 
-      int getNumberOfConstraints( void ) const;
+      int getNumberOfConstraints() const;
 
       /**---------------------------------------------------------------------------------------
 
@@ -112,7 +112,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
 
          --------------------------------------------------------------------------------------- */
 
-      int getNumTerms( void ) const;
+      int getNumTerms() const;
 
       /**---------------------------------------------------------------------------------------
 
@@ -120,7 +120,7 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
 
          --------------------------------------------------------------------------------------- */
 
-      void setNumTerms( int terms );
+      void setNumTerms(int terms);
 
       /**---------------------------------------------------------------------------------------
 
@@ -131,13 +131,10 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
          @param atomCoordinatesP atom coordinates prime
          @param inverseMasses    1/mass
 
-         @return SimTKOpenMMCommon::DefaultReturn if converge; else
-          return SimTKOpenMMCommon::ErrorReturn
-
          --------------------------------------------------------------------------------------- */
 
-      int apply( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
-                       std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses );
+      void apply(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
+                       std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses);
 
       /**---------------------------------------------------------------------------------------
 
@@ -148,15 +145,12 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
          @param velocities       atom velocities
          @param inverseMasses    1/mass
 
-         @return SimTKOpenMMCommon::DefaultReturn if converge; else
-          return SimTKOpenMMCommon::ErrorReturn
-
          --------------------------------------------------------------------------------------- */
 
-      int applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
+      void applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
                      std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses);
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceLincsAlgorithm_H__

platforms/reference/include/ReferenceMonteCarloBarostat.h

@@ -25,11 +25,10 @@
 #ifndef __ReferenceMonteCarloBarostat_H__
 #define __ReferenceMonteCarloBarostat_H__
 
-#include "SimTKOpenMMCommon.h"
 #include <utility>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceMonteCarloBarostat {
 
@@ -82,6 +81,6 @@ class ReferenceMonteCarloBarostat {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceMonteCarloBarostat_H__

platforms/reference/include/ReferenceNeighborList.h

@@ -27,7 +27,7 @@ void OPENMM_EXPORT computeNeighborListNaive(
                               double maxDistance,
                               double minDistance = 0.0,
                               bool reportSymmetricPairs = false
-                             );
+                            );
 
 // O(n) neighbor list method using voxel hash data structure
 // parameter neighborList is automatically clear()ed before 
@@ -42,7 +42,7 @@ void OPENMM_EXPORT computeNeighborListVoxelHash(
                               double maxDistance,
                               double minDistance = 0.0,
                               bool reportSymmetricPairs = false
-                             );
+                            );
 
 } // namespace OpenMM
 

platforms/reference/include/CpuObc.h → platforms/reference/include/ReferenceObc.h

@@ -22,14 +22,14 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#ifndef __CpuObc_H__
-#define __CpuObc_H__
+#ifndef __ReferenceObc_H__
+#define __ReferenceObc_H__
 
 #include "ObcParameters.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
-class CpuObc {
+class ReferenceObc {
 
    private:
 
@@ -39,7 +39,7 @@ class CpuObc {
 
       // arrays containing OBC chain derivative 
 
-      RealOpenMMVector _obcChain;
+      std::vector<RealOpenMM> _obcChain;
 
       // flag to signal whether ACE approximation
       // is to be included
@@ -59,7 +59,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
 
-       CpuObc( ObcParameters* obcParameters );
+       ReferenceObc(ObcParameters* obcParameters);
 
       /**---------------------------------------------------------------------------------------
       
@@ -67,7 +67,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
 
-       ~CpuObc( );
+       ~ReferenceObc();
 
       /**---------------------------------------------------------------------------------------
       
@@ -77,7 +77,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
 
-      ObcParameters* getObcParameters( void ) const;
+      ObcParameters* getObcParameters() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -87,7 +87,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
 
-      void setObcParameters( ObcParameters* obcParameters );
+      void setObcParameters(ObcParameters* obcParameters);
  
       /**---------------------------------------------------------------------------------------
       
@@ -97,7 +97,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
 
-      int includeAceApproximation( void ) const;
+      int includeAceApproximation() const;
 
       /**---------------------------------------------------------------------------------------
       
@@ -107,7 +107,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
 
-      void setIncludeAceApproximation( int includeAceApproximation );
+      void setIncludeAceApproximation(int includeAceApproximation);
 
       /**---------------------------------------------------------------------------------------
       
@@ -117,7 +117,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMMVector& getObcChain( void );
+      std::vector<RealOpenMM>& getObcChain();
       
       /**---------------------------------------------------------------------------------------
       
@@ -128,7 +128,7 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
       
-      void computeBornRadii( const std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii );
+      void computeBornRadii(const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii);
       
       /**---------------------------------------------------------------------------------------
         
@@ -142,8 +142,8 @@ class CpuObc {
         
             --------------------------------------------------------------------------------------- */
         
-      void computeAceNonPolarForce( const ObcParameters* obcParameters, const RealOpenMMVector& bornRadii, 
-                                    RealOpenMM* energy, RealOpenMMVector& forces ) const;
+      void computeAceNonPolarForce(const ObcParameters* obcParameters, const std::vector<RealOpenMM>& bornRadii,
+                                   RealOpenMM* energy, std::vector<RealOpenMM>& forces) const;
         
       /**---------------------------------------------------------------------------------------
       
@@ -155,32 +155,11 @@ class CpuObc {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM computeBornEnergyForces( const std::vector<OpenMM::RealVec>& atomCoordinates,
-                                          const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& forces );
-      
-    /**---------------------------------------------------------------------------------------
-    
-        Print Obc parameters, radii, forces, ...
-    
-        @param atomCoordinates     atomic coordinates
-        @param partialCharges      partial charges
-        @param bornRadii           Born radii (may be empty)
-        @param bornForces          Born forces (may be empty)
-        @param forces              forces (may be empty)
-        @param idString            id string (who is calling)
-        @param log                 log file
-    
-        --------------------------------------------------------------------------------------- */
-    
-    void printObc( const std::vector<OpenMM::RealVec>& atomCoordinates,
-                   const RealOpenMMVector& partialCharges,
-                   const RealOpenMMVector& bornRadii,
-                   const RealOpenMMVector& bornForces,
-                   const std::vector<OpenMM::RealVec>& forces,
-                   const std::string& idString, FILE* log );
+      RealOpenMM computeBornEnergyForces(const std::vector<OpenMM::RealVec>& atomCoordinates,
+                                         const std::vector<RealOpenMM>& partialCharges, std::vector<OpenMM::RealVec>& forces);
     
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
-#endif // __CpuObc_H__
+#endif // __ReferenceObc_H__

platforms/reference/include/ReferencePME.h

@@ -29,10 +29,15 @@
  * POSSIBILITY OF SUCH DAMAGE.
  */
 
-#include "SimTKOpenMMCommon.h"
+#ifndef __ReferencePME_H__
+#define __ReferencePME_H__
+
+#include "RealVec.h"
 #include "openmm/internal/windowsExport.h"
 #include <vector>
 
+namespace OpenMM {
+
 typedef RealOpenMM rvec[3];
 
 
@@ -86,3 +91,7 @@ pme_exec(pme_t       pme,
 /* Release all memory in pme structure */
 int OPENMM_EXPORT
 pme_destroy(pme_t    pme);
+
+} // namespace OpenMM
+
+#endif // __ReferencePME_H__
\ No newline at end of file

platforms/reference/include/ReferencePairIxn.h

@@ -27,8 +27,9 @@
 
 #include "RealVec.h"
 #include "openmm/internal/windowsExport.h"
+#include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferencePairIxn {
 
@@ -42,7 +43,7 @@ class OPENMM_EXPORT ReferencePairIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferencePairIxn( );
+       ReferencePairIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -50,7 +51,7 @@ class OPENMM_EXPORT ReferencePairIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferencePairIxn( );
+       ~ReferencePairIxn();
 
       /**---------------------------------------------------------------------------------------
       
@@ -67,13 +68,13 @@ class OPENMM_EXPORT ReferencePairIxn {
             
          --------------------------------------------------------------------------------------- */
           
-      virtual void calculatePairIxn( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
+      virtual void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
                             RealOpenMM** atomParameters, int** exclusions,
                             RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces,
-                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const = 0;
+                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const = 0;
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferencePairIxn_H__