Merge pull request #827 from peastman/reference

Lots of cleanup to reference platform

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__

platforms/reference/include/ReferenceProperDihedralBond.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceBondIxn.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
 
@@ -41,7 +41,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceProperDihedralBond( );
+       ReferenceProperDihedralBond();
 
       /**---------------------------------------------------------------------------------------
       
@@ -49,7 +49,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceProperDihedralBond( );
+       ~ReferenceProperDihedralBond();
 
       /**---------------------------------------------------------------------------------------
       
@@ -65,12 +65,12 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : 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 // __ReferenceProperDihedralBond_H__

platforms/reference/include/ReferenceRbDihedralBond.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceBondIxn.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
 
@@ -41,7 +41,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceRbDihedralBond( );
+       ReferenceRbDihedralBond();
 
       /**---------------------------------------------------------------------------------------
       
@@ -49,7 +49,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceRbDihedralBond( );
+       ~ReferenceRbDihedralBond();
 
       /**---------------------------------------------------------------------------------------
       
@@ -63,12 +63,12 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : 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 // __ReferenceRbDihedralBond_H__

platforms/reference/include/ReferenceStochasticDynamics.h

@@ -28,7 +28,7 @@
 #include "ReferenceDynamics.h"
 #include "openmm/internal/windowsExport.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
 
@@ -51,7 +51,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceStochasticDynamics( int numberOfAtoms, RealOpenMM deltaT, RealOpenMM tau, RealOpenMM temperature );
+       ReferenceStochasticDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM tau, RealOpenMM temperature);
 
       /**---------------------------------------------------------------------------------------
       
@@ -59,7 +59,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceStochasticDynamics( );
+       ~ReferenceStochasticDynamics();
 
       /**---------------------------------------------------------------------------------------
       
@@ -69,7 +69,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      RealOpenMM getTau( void ) const;
+      RealOpenMM getTau() const;
       
       /**---------------------------------------------------------------------------------------
       
@@ -100,8 +100,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      virtual void updatePart1( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
-                       std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime );
+      virtual void updatePart1(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
+                       std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
       
       /**---------------------------------------------------------------------------------------
       
@@ -115,11 +115,11 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      virtual void updatePart2( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
-                       std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime );
+      virtual void updatePart2(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
+                       std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceStochasticDynamics_H__

platforms/reference/include/ReferenceVariableStochasticDynamics.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceDynamics.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
@@ -50,7 +50,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-       ReferenceVariableStochasticDynamics( int numberOfAtoms, RealOpenMM tau, RealOpenMM temperature, RealOpenMM accuracy );
+       ReferenceVariableStochasticDynamics(int numberOfAtoms, RealOpenMM tau, RealOpenMM temperature, RealOpenMM accuracy);
 
       /**---------------------------------------------------------------------------------------
 
@@ -58,7 +58,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceVariableStochasticDynamics( );
+       ~ReferenceVariableStochasticDynamics();
 
       /**---------------------------------------------------------------------------------------
 
@@ -68,7 +68,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getTau( void ) const;
+      RealOpenMM getTau() const;
       
       /**---------------------------------------------------------------------------------------
 
@@ -78,7 +78,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getAccuracy( void ) const;
+      RealOpenMM getAccuracy() const;
 
       /**---------------------------------------------------------------------------------------
 
@@ -86,7 +86,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-      void setAccuracy( RealOpenMM accuracy );
+      void setAccuracy(RealOpenMM accuracy);
 
       /**---------------------------------------------------------------------------------------
 
@@ -120,9 +120,9 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-      void updatePart1( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
+      void updatePart1(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
                        std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, std::vector<RealOpenMM>& inverseMasses,
-                       std::vector<OpenMM::RealVec>& xPrime, RealOpenMM maxStepSize );
+                       std::vector<OpenMM::RealVec>& xPrime, RealOpenMM maxStepSize);
 
       /**---------------------------------------------------------------------------------------
 
@@ -136,12 +136,12 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-      void updatePart2( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
+      void updatePart2(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
                        std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses,
-                       std::vector<OpenMM::RealVec>& xPrime );
+                       std::vector<OpenMM::RealVec>& xPrime);
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceVariableStochasticDynamics_H__

platforms/reference/include/ReferenceVariableVerletDynamics.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceDynamics.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceVariableVerletDynamics : public ReferenceDynamics {
 
@@ -48,7 +48,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-       ReferenceVariableVerletDynamics( int numberOfAtoms, RealOpenMM accuracy );
+       ReferenceVariableVerletDynamics(int numberOfAtoms, RealOpenMM accuracy);
 
       /**---------------------------------------------------------------------------------------
 
@@ -56,7 +56,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceVariableVerletDynamics( );
+       ~ReferenceVariableVerletDynamics();
 
       /**---------------------------------------------------------------------------------------
 
@@ -66,7 +66,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-      RealOpenMM getAccuracy( void ) const;
+      RealOpenMM getAccuracy() const;
 
       /**---------------------------------------------------------------------------------------
 
@@ -74,7 +74,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
 
          --------------------------------------------------------------------------------------- */
 
-      void setAccuracy( RealOpenMM accuracy );
+      void setAccuracy(RealOpenMM accuracy);
 
       /**---------------------------------------------------------------------------------------
 
@@ -95,6 +95,6 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceVariableVerletDynamics_H__

platforms/reference/include/ReferenceVerletDynamics.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceDynamics.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceVerletDynamics : public ReferenceDynamics {
 
@@ -49,7 +49,7 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceVerletDynamics( int numberOfAtoms, RealOpenMM deltaT );
+       ReferenceVerletDynamics(int numberOfAtoms, RealOpenMM deltaT);
 
       /**---------------------------------------------------------------------------------------
       
@@ -57,7 +57,7 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
 
-       ~ReferenceVerletDynamics( );
+       ~ReferenceVerletDynamics();
 
       /**---------------------------------------------------------------------------------------
       
@@ -77,6 +77,6 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceVerletDynamics_H__

platforms/reference/include/ReferenceVirtualSites.h

@@ -36,6 +36,8 @@
 #include "RealVec.h"
 #include <vector>
 
+namespace OpenMM {
+
 class OPENMM_EXPORT ReferenceVirtualSites {
 public:
     /**
@@ -48,4 +50,6 @@ public:
     static void distributeForces(const OpenMM::System& system, const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces);
 };
 
+} // namespace OpenMM
+
 #endif // __ReferenceVirtualSites_H__

platforms/reference/include/SimTKOpenMMCommon.h

-
-/* Portions copyright (c) 2006 Stanford University and Simbios.
- * Contributors: Pande Group
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject
- * to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included
- * in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
- * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
- * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
- * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-#ifndef __SimTKOpenMMCommon_H__
-#define __SimTKOpenMMCommon_H__
-
-// include file containing entries commonly used
-
-// STL includes
-
-#include <vector>
-#include <string>
-
-// ---------------------------------------------------------------------------------------
-
-#include "RealVec.h"
-
-// ---------------------------------------------------------------------------------------
-
-typedef std::vector<RealOpenMM> RealOpenMMVector;
-typedef RealOpenMMVector::iterator RealOpenMMVectorI;
-typedef RealOpenMMVector::const_iterator RealOpenMMVectorCI;
-
-// ---------------------------------------------------------------------------------------
-
-class SimTKOpenMMCommon {
-
-   public:
-
-      static const std::string NotSet;
-      static const RealOpenMM BigCutoffValue;
-      static const std::string Comment;
-      static const std::string Tab;
-      static const std::string YesU;
-      static const std::string YesUl;
-      static const std::string YesL;
-
-      // subroutine returns
-
-      static const int DefaultReturn;
-      static const int ErrorReturn;
-};
-
-#endif // __SimTKOpenMMCommon_H__

platforms/reference/include/SimTKOpenMMLog.h

-
-/* Portions copyright (c) 2006 Stanford University and Simbios.
- * Contributors: Pande Group
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject
- * to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included
- * in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
- * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
- * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
- * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
- * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-#ifndef __SimTKOpenMMLog_H__
-#define __SimTKOpenMMLog_H__
-
-#include <cstdio>
-#include <sstream>
-#include "SimTKOpenMMCommon.h"
-#include "openmm/internal/windowsExport.h"
-
-/** ---------------------------------------------------------------------------------------
-
-   SimTKOpenMMLog class used for logging
-
-   --------------------------------------------------------------------------------------- */
-
-class OPENMM_EXPORT SimTKOpenMMLog {
-
-   public:
-
-      // log levels
-
-      enum LogLevels { LogOff, LogLowLevel, LogHighLevel };
-
-   private:
-
-      // file to write to
-
-      FILE* _logFile;
-
-      // log level
-
-      LogLevels _logLevel;
-
-      // global reference
-
-      static SimTKOpenMMLog* _simTKOpenMMLog;
-
-   public:
-
-      /**---------------------------------------------------------------------------------------
-      
-         SimTKOpenMMLog constructor (Simbios)
-      
-         @param logFile file reference for logging
-      
-         --------------------------------------------------------------------------------------- */
-      
-      SimTKOpenMMLog( FILE* logFile = NULL );
-
-      /**---------------------------------------------------------------------------------------
-      
-         SimTKOpenMMLog destructor (Simbios)
-      
-         --------------------------------------------------------------------------------------- */
-      
-      ~SimTKOpenMMLog( );
-
-      /**---------------------------------------------------------------------------------------
-      
-         SimTKOpenMMLog log message to log (Simbios)
-      
-         @param message         message to log
-      
-         --------------------------------------------------------------------------------------- */
-      
-     void logMessage( const std::stringstream& message ) const;
-
-      /**---------------------------------------------------------------------------------------
-
-         Get LogFile
-
-         @return    logFile
-      
-         --------------------------------------------------------------------------------------- */
-
-      FILE* getLogFile( void ) const;
-
-      /**---------------------------------------------------------------------------------------
-
-         Set LogFile
-
-         @param    input logFile
-      
-         --------------------------------------------------------------------------------------- */
-
-      void setLogFile( FILE* logFile );
-
-      /**---------------------------------------------------------------------------------------
-
-         Set LogLevel
-
-         @param    input logLevel
-      
-         --------------------------------------------------------------------------------------- */
-
-      void setLogLevel( SimTKOpenMMLog::LogLevels logLevel );
-
-      /**---------------------------------------------------------------------------------------
-      
-         Set global simTKLog (Simbios)
-      
-         @param logFile         file to log to
-      
-         @return new SimTKOpenMMLog
-      
-         --------------------------------------------------------------------------------------- */
-      
-      static SimTKOpenMMLog* setSimTKOpenMMLog( FILE* logFile = NULL );
-      
-      /**---------------------------------------------------------------------------------------
-      
-         Get global simTKLog -- static method (Simbios)
-      
-         @return static member
-      
-         --------------------------------------------------------------------------------------- */
-      
-      static SimTKOpenMMLog* getSimTKOpenMMLog( void );
-      
-      /**---------------------------------------------------------------------------------------
-      
-         Get global simTKLog (Simbios)
-      
-         @return FILE reference
-      
-         --------------------------------------------------------------------------------------- */
-      
-      static FILE* getSimTKOpenMMLogFile( void );
-      
-      /**---------------------------------------------------------------------------------------
-      
-         Staitc method to print message (Simbios)
-      
-         @param message         message to log
-      
-         --------------------------------------------------------------------------------------- */
-      
-      static void printMessage( const std::stringstream& message );
-      
-      /**---------------------------------------------------------------------------------------
-      
-         Staitc method to print warning message (Simbios)
-      
-         @param message         message to log
-      
-         --------------------------------------------------------------------------------------- */
-      
-      static void printWarning( const std::stringstream& message );
-      
-      /**---------------------------------------------------------------------------------------
-      
-         Static method to print error message and exist program (Simbios)
-      
-         @param message         message to log
-      
-         --------------------------------------------------------------------------------------- */
-
-     static void printError( const std::stringstream& message );
-
-};
-
-#endif //__SimTKOpenMMLog_H__

platforms/reference/include/SimTKOpenMMUtilities.h

@@ -27,12 +27,14 @@
 
 // class of shared, static utility methods
 
-#include "SimTKOpenMMCommon.h" 
+#include "RealVec.h"
 #include "sfmt/SFMT.h"
 #include "openmm/internal/windowsExport.h"
 
 #include <string>
 
+namespace OpenMM {
+
 /**---------------------------------------------------------------------------------------
 
    Class of static methods to be shared
@@ -54,8 +56,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
 
       // dummy constructor/destructor
 
-       SimTKOpenMMUtilities(){};
-      ~SimTKOpenMMUtilities(){};
+       SimTKOpenMMUtilities() {};
+      ~SimTKOpenMMUtilities() {};
       
       /**---------------------------------------------------------------------------------------
       
@@ -73,9 +75,9 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM* allocateOneDRealOpenMMArray( int iSize, RealOpenMM* array1D, int initialize,
+      static RealOpenMM* allocateOneDRealOpenMMArray(int iSize, RealOpenMM* array1D, int initialize,
                                                       RealOpenMM initialValue,
-                                                      const std::string& idString = std::string( "1DArray" ) );
+                                                      const std::string& idString = std::string("1DArray"));
       
       /**---------------------------------------------------------------------------------------
       
@@ -94,10 +96,10 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM** allocateTwoDRealOpenMMArray( int iSize, int jSize,
+      static RealOpenMM** allocateTwoDRealOpenMMArray(int iSize, int jSize,
                                                        RealOpenMM** array2D, int initialize,
                                                        RealOpenMM initialValue,
-                                                       const std::string& idString = std::string( "2DArray" ) );
+                                                       const std::string& idString = std::string("2DArray"));
       
       /* ---------------------------------------------------------------------------------------
       
@@ -110,8 +112,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static void freeOneDRealOpenMMArray( RealOpenMM* array1D,
-                                          const std::string& idString = std::string( "1DArray" ) );
+      static void freeOneDRealOpenMMArray(RealOpenMM* array1D,
+                                          const std::string& idString = std::string("1DArray"));
       
       /* ---------------------------------------------------------------------------------------
       
@@ -124,8 +126,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static void freeTwoDRealOpenMMArray( RealOpenMM** array2D,
-                                          const std::string& idString = std::string( "2DArray" ) );
+      static void freeTwoDRealOpenMMArray(RealOpenMM** array2D,
+                                          const std::string& idString = std::string("2DArray"));
       
       /**---------------------------------------------------------------------------------------
       
@@ -140,8 +142,8 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static void initialize2DRealOpenMMArray( int iSize, int jSize,
-                                              RealOpenMM** array2D, RealOpenMM initialValue );
+      static void initialize2DRealOpenMMArray(int iSize, int jSize,
+                                              RealOpenMM** array2D, RealOpenMM initialValue);
 
       /**---------------------------------------------------------------------------------------
       
@@ -157,7 +159,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static void crossProductVector3( RealOpenMM* vectorX, RealOpenMM* vectorY, RealOpenMM* vectorZ );
+      static void crossProductVector3(RealOpenMM* vectorX, RealOpenMM* vectorY, RealOpenMM* vectorZ);
       
       /**---------------------------------------------------------------------------------------
       
@@ -167,7 +169,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM getNormallyDistributedRandomNumber( void );
+      static RealOpenMM getNormallyDistributedRandomNumber();
       
       /**---------------------------------------------------------------------------------------
       
@@ -177,7 +179,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static RealOpenMM getUniformlyDistributedRandomNumber( void );
+      static RealOpenMM getUniformlyDistributedRandomNumber();
 
       /**---------------------------------------------------------------------------------------
       
@@ -187,7 +189,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static uint32_t getRandomNumberSeed( void );
+      static uint32_t getRandomNumberSeed();
       
       /**---------------------------------------------------------------------------------------
       
@@ -197,7 +199,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static void setRandomNumberSeed( uint32_t seed );
+      static void setRandomNumberSeed(uint32_t seed);
       
       /**---------------------------------------------------------------------------------------
       
@@ -219,7 +221,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
 
       static void loadCheckpoint(std::istream& stream);
 };
-   
-// ---------------------------------------------------------------------------------------
+
+} // namespace OpenMM
 
 #endif // __SimTKOpenMMUtilities_H__

platforms/reference/include/fftpack.h

@@ -14,14 +14,13 @@
 * drop a line to lindahl@cbr.su.se and let me know about it!
 */
 
-#include "SimTKOpenMMCommon.h"
-
 #ifndef _FFTPACK_H_
 #define _FFTPACK_H_
 
 
 #include <stdio.h>
 
+#include "RealVec.h"
 #include "openmm/internal/windowsExport.h"
 
 #ifdef __cplusplus

platforms/reference/src/ReferenceKernelFactory.cpp

@@ -100,5 +100,5 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
         return new ReferenceApplyMonteCarloBarostatKernel(name, platform);
     if (name == RemoveCMMotionKernel::Name())
         return new ReferenceRemoveCMMotionKernel(name, platform, data);
-    throw OpenMMException( (std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str() );
+    throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str());
 }

platforms/reference/src/ReferenceKernels.cpp

@@ -30,8 +30,8 @@
  * -------------------------------------------------------------------------- */
 
 #include "ReferenceKernels.h"
-#include "CpuObc.h"
-#include "CpuGBVI.h"
+#include "ReferenceObc.h"
+#include "ReferenceGBVI.h"
 #include "ReferenceAndersenThermostat.h"
 #include "ReferenceAngleBondIxn.h"
 #include "ReferenceBondForce.h"
@@ -1105,13 +1105,13 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS
     ObcParameters* obcParameters = new ObcParameters(numParticles, ObcParameters::ObcTypeII);
     obcParameters->setAtomicRadii(atomicRadii);
     obcParameters->setScaledRadiusFactors(scaleFactors);
-    obcParameters->setSolventDielectric( static_cast<RealOpenMM>(force.getSolventDielectric()) );
-    obcParameters->setSoluteDielectric( static_cast<RealOpenMM>(force.getSoluteDielectric()) );
+    obcParameters->setSolventDielectric(static_cast<RealOpenMM>(force.getSolventDielectric()));
+    obcParameters->setSoluteDielectric(static_cast<RealOpenMM>(force.getSoluteDielectric()));
     obcParameters->setPi4Asolv(4*M_PI*force.getSurfaceAreaEnergy());
     if (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff)
         obcParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance()));
     isPeriodic = (force.getNonbondedMethod() == GBSAOBCForce::CutoffPeriodic);
-    obc = new CpuObc(obcParameters);
+    obc = new ReferenceObc(obcParameters);
     obc->setIncludeAceApproximation(true);
 }
 
@@ -1152,7 +1152,7 @@ ReferenceCalcGBVIForceKernel::~ReferenceCalcGBVIForceKernel() {
     }
 }
 
-void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIForce& force, const std::vector<double> & inputScaledRadii ) {
+void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIForce& force, const std::vector<double> & inputScaledRadii) {
 
     int numParticles = system.getNumParticles();
 
@@ -1185,7 +1185,7 @@ void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIFo
     if (force.getNonbondedMethod() != GBVIForce::NoCutoff)
         gBVIParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance()));
     isPeriodic = (force.getNonbondedMethod() == GBVIForce::CutoffPeriodic);
-    gbvi = new CpuGBVI(gBVIParameters);
+    gbvi = new ReferenceGBVI(gBVIParameters);
 }
 
 double ReferenceCalcGBVIForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
@@ -1201,7 +1201,7 @@ double ReferenceCalcGBVIForceKernel::execute(ContextImpl& context, bool includeF
         gbvi->computeBornForces(posData, charges, forceData);
         energy = 0.0;
     }
-    if( includeEnergy ){
+    if (includeEnergy) {
         energy = gbvi->computeBornEnergy(posData, charges);
     }
     return static_cast<double>(energy);
@@ -1710,7 +1710,7 @@ void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const Ver
         
         if (dynamics)
             delete dynamics;
-        dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) );
+        dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize));
         dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
         prevStepSize = stepSize;
     }
@@ -1748,12 +1748,12 @@ void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const L
         
         if (dynamics)
             delete dynamics;
-        RealOpenMM tau = static_cast<RealOpenMM>( friction == 0.0 ? 0.0 : 1.0/friction );
+        RealOpenMM tau = static_cast<RealOpenMM>(friction == 0.0 ? 0.0 : 1.0/friction);
         dynamics = new ReferenceStochasticDynamics(
                 context.getSystem().getNumParticles(), 
                 static_cast<RealOpenMM>(stepSize), 
                 static_cast<RealOpenMM>(tau), 
-                static_cast<RealOpenMM>(temperature) );
+                static_cast<RealOpenMM>(temperature));
         dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
         prevTemp = temperature;
         prevFriction = friction;
@@ -1797,7 +1797,7 @@ void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const B
                 context.getSystem().getNumParticles(), 
                 static_cast<RealOpenMM>(stepSize), 
                 static_cast<RealOpenMM>(friction), 
-                static_cast<RealOpenMM>(temperature) );
+                static_cast<RealOpenMM>(temperature));
         dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
         prevTemp = temperature;
         prevFriction = friction;
@@ -1837,7 +1837,7 @@ double ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& contex
 
         if (dynamics)
             delete dynamics;
-        RealOpenMM tau = static_cast<RealOpenMM>( friction == 0.0 ? 0.0 : 1.0/friction );
+        RealOpenMM tau = static_cast<RealOpenMM>(friction == 0.0 ? 0.0 : 1.0/friction);
         dynamics = new ReferenceVariableStochasticDynamics(context.getSystem().getNumParticles(), (RealOpenMM) tau, (RealOpenMM) temperature, (RealOpenMM) errorTol);
         dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
         prevTemp = temperature;

platforms/reference/src/gbsa/GBVIParameters.cpp → platforms/reference/src/SimTKReference/GBVIParameters.cpp

@@ -28,10 +28,9 @@
 
 #include "openmm/OpenMMException.h"
 #include "GBVIParameters.h"
-#include "SimTKOpenMMCommon.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 
@@ -41,19 +40,19 @@ using OpenMM::RealVec;
 
     --------------------------------------------------------------------------------------- */
 
-GBVIParameters::GBVIParameters( int numberOfAtoms ) : _numberOfAtoms(numberOfAtoms), 
-                                                      _soluteDielectric(1.0),
-                                                      _solventDielectric(78.3),
-                                                      _electricConstant(-0.5*ONE_4PI_EPS0),
-                                                      _cutoff(false),
-                                                      _periodic(false),
-                                                      _bornRadiusScalingMethod(0),
-                                                      _quinticLowerLimitFactor(0.8),
-                                                      _quinticUpperBornRadiusLimit(5.0) {
+GBVIParameters::GBVIParameters(int numberOfAtoms) : _numberOfAtoms(numberOfAtoms), 
+                                                    _soluteDielectric(1.0),
+                                                    _solventDielectric(78.3),
+                                                    _electricConstant(-0.5*ONE_4PI_EPS0),
+                                                    _cutoff(false),
+                                                    _periodic(false),
+                                                    _bornRadiusScalingMethod(0),
+                                                    _quinticLowerLimitFactor(0.8),
+                                                    _quinticUpperBornRadiusLimit(5.0) {
 
-    _atomicRadii.resize( numberOfAtoms );
-    _scaledRadii.resize( numberOfAtoms );
-    _gammaParameters.resize( numberOfAtoms ); 
+    _atomicRadii.resize(numberOfAtoms);
+    _scaledRadii.resize(numberOfAtoms);
+    _gammaParameters.resize(numberOfAtoms); 
 
 }
 
@@ -63,7 +62,7 @@ GBVIParameters::GBVIParameters( int numberOfAtoms ) : _numberOfAtoms(numberOfAto
 
     --------------------------------------------------------------------------------------- */
 
-GBVIParameters::~GBVIParameters( ){
+GBVIParameters::~GBVIParameters() {
 }
 
 /**---------------------------------------------------------------------------------------
@@ -74,7 +73,7 @@ GBVIParameters::~GBVIParameters( ){
 
    --------------------------------------------------------------------------------------- */
 
-int GBVIParameters::getNumberOfAtoms( void ) const {
+int GBVIParameters::getNumberOfAtoms() const {
     return _numberOfAtoms;
 }
 
@@ -86,7 +85,7 @@ int GBVIParameters::getNumberOfAtoms( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-RealOpenMM GBVIParameters::getElectricConstant( void ) const {
+RealOpenMM GBVIParameters::getElectricConstant() const {
     return _electricConstant;
 }
 
@@ -98,7 +97,7 @@ RealOpenMM GBVIParameters::getElectricConstant( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-RealOpenMM GBVIParameters::getSolventDielectric( void ) const {
+RealOpenMM GBVIParameters::getSolventDielectric() const {
     return _solventDielectric;
 }
 
@@ -110,7 +109,7 @@ RealOpenMM GBVIParameters::getSolventDielectric( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setSolventDielectric( RealOpenMM solventDielectric ){
+void GBVIParameters::setSolventDielectric(RealOpenMM solventDielectric) {
     _solventDielectric = solventDielectric;
 }
 
@@ -122,7 +121,7 @@ void GBVIParameters::setSolventDielectric( RealOpenMM solventDielectric ){
 
    --------------------------------------------------------------------------------------- */
 
-RealOpenMM GBVIParameters::getSoluteDielectric( void ) const {
+RealOpenMM GBVIParameters::getSoluteDielectric() const {
     return _soluteDielectric;
 }
 
@@ -134,7 +133,7 @@ RealOpenMM GBVIParameters::getSoluteDielectric( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
+void GBVIParameters::setSoluteDielectric(RealOpenMM soluteDielectric) {
     _soluteDielectric = soluteDielectric;
 }
 
@@ -146,7 +145,7 @@ void GBVIParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
 
     --------------------------------------------------------------------------------------- */
 
-const RealOpenMMVector& GBVIParameters::getAtomicRadii( void ) const {
+const vector<RealOpenMM>& GBVIParameters::getAtomicRadii() const {
     return _atomicRadii;
 }
 
@@ -158,10 +157,10 @@ const RealOpenMMVector& GBVIParameters::getAtomicRadii( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
+void GBVIParameters::setAtomicRadii(const vector<RealOpenMM>& atomicRadii) {
 
-    if( atomicRadii.size() == _atomicRadii.size() ){
-        for( unsigned int ii = 0; ii < atomicRadii.size(); ii++ ){
+    if (atomicRadii.size() == _atomicRadii.size()) {
+        for (unsigned int ii = 0; ii < atomicRadii.size(); ii++) {
             _atomicRadii[ii] = atomicRadii[ii];
         }   
     } else {
@@ -170,7 +169,7 @@ void GBVIParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
         msg << atomicRadii.size();
         msg << " current size=" << _atomicRadii.size();
         throw OpenMM::OpenMMException(msg.str());
-    }   
+    }
 
 }
 
@@ -181,7 +180,7 @@ void GBVIParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
 
     --------------------------------------------------------------------------------------- */
 
-const RealOpenMMVector& GBVIParameters::getScaledRadii( void ) const {
+const vector<RealOpenMM>& GBVIParameters::getScaledRadii() const {
     return _scaledRadii;
 }
 
@@ -193,10 +192,10 @@ const RealOpenMMVector& GBVIParameters::getScaledRadii( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setScaledRadii( const RealOpenMMVector& scaledRadii ){
+void GBVIParameters::setScaledRadii(const vector<RealOpenMM>& scaledRadii) {
 
-    if( scaledRadii.size() == _scaledRadii.size() ){
-        for( unsigned int ii = 0; ii < scaledRadii.size(); ii++ ){
+    if (scaledRadii.size() == _scaledRadii.size()) {
+        for (unsigned int ii = 0; ii < scaledRadii.size(); ii++) {
             _scaledRadii[ii] = scaledRadii[ii];
         }
     } else {
@@ -218,7 +217,7 @@ void GBVIParameters::setScaledRadii( const RealOpenMMVector& scaledRadii ){
 
     --------------------------------------------------------------------------------------- */
 
-const RealOpenMMVector& GBVIParameters::getGammaParameters( void ) const {
+const vector<RealOpenMM>& GBVIParameters::getGammaParameters() const {
     return _gammaParameters;
 }
 
@@ -230,10 +229,10 @@ const RealOpenMMVector& GBVIParameters::getGammaParameters( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setGammaParameters( const RealOpenMMVector& gammas ){
+void GBVIParameters::setGammaParameters(const vector<RealOpenMM>& gammas) {
 
-    if( gammas.size() == _gammaParameters.size() ){
-        for( unsigned int ii = 0; ii < gammas.size(); ii++ ){
+    if (gammas.size() == _gammaParameters.size()) {
+        for (unsigned int ii = 0; ii < gammas.size(); ii++) {
             _gammaParameters[ii] = gammas[ii];
         }
     } else {
@@ -254,7 +253,7 @@ void GBVIParameters::setGammaParameters( const RealOpenMMVector& gammas ){
 
       --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setUseCutoff( RealOpenMM distance ) {
+void GBVIParameters::setUseCutoff(RealOpenMM distance) {
 
      _cutoff          = true;
      _cutoffDistance = distance;
@@ -330,7 +329,7 @@ const OpenMM::RealVec* GBVIParameters::getPeriodicBox() {
 
     --------------------------------------------------------------------------------------- */
 
-RealOpenMM GBVIParameters::getTau( void ) const {
+RealOpenMM GBVIParameters::getTau() const {
 
     // ---------------------------------------------------------------------------------------
 
@@ -340,7 +339,7 @@ RealOpenMM GBVIParameters::getTau( void ) const {
     // ---------------------------------------------------------------------------------------
 
     RealOpenMM tau;
-    if( getSoluteDielectric() != zero && getSolventDielectric() != zero ){
+    if (getSoluteDielectric() != zero && getSolventDielectric() != zero) {
         tau = (one/getSoluteDielectric()) - (one/getSolventDielectric());
     } else {
         tau = zero;
@@ -357,7 +356,7 @@ RealOpenMM GBVIParameters::getTau( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-int GBVIParameters::getBornRadiusScalingMethod( void ) const {
+int GBVIParameters::getBornRadiusScalingMethod() const {
     return _bornRadiusScalingMethod;
 }
 
@@ -369,7 +368,7 @@ int GBVIParameters::getBornRadiusScalingMethod( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setBornRadiusScalingMethod( int bornRadiusScalingMethod ){
+void GBVIParameters::setBornRadiusScalingMethod(int bornRadiusScalingMethod) {
     _bornRadiusScalingMethod    = bornRadiusScalingMethod;
 }
 
@@ -381,7 +380,7 @@ void GBVIParameters::setBornRadiusScalingMethod( int bornRadiusScalingMethod ){
 
     --------------------------------------------------------------------------------------- */
 
-RealOpenMM GBVIParameters::getQuinticLowerLimitFactor( void ) const {
+RealOpenMM GBVIParameters::getQuinticLowerLimitFactor() const {
     return _quinticLowerLimitFactor;
 }
 
@@ -393,7 +392,7 @@ RealOpenMM GBVIParameters::getQuinticLowerLimitFactor( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setQuinticLowerLimitFactor( RealOpenMM quinticLowerLimitFactor ){
+void GBVIParameters::setQuinticLowerLimitFactor(RealOpenMM quinticLowerLimitFactor) {
     _quinticLowerLimitFactor    = quinticLowerLimitFactor;
 }
 
@@ -405,7 +404,7 @@ void GBVIParameters::setQuinticLowerLimitFactor( RealOpenMM quinticLowerLimitFac
 
     --------------------------------------------------------------------------------------- */
 
-RealOpenMM GBVIParameters::getQuinticUpperBornRadiusLimit( void ) const {
+RealOpenMM GBVIParameters::getQuinticUpperBornRadiusLimit() const {
     return _quinticUpperBornRadiusLimit;
 }
 
@@ -417,6 +416,6 @@ RealOpenMM GBVIParameters::getQuinticUpperBornRadiusLimit( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void GBVIParameters::setQuinticUpperBornRadiusLimit( RealOpenMM quinticUpperBornRadiusLimit ){
+void GBVIParameters::setQuinticUpperBornRadiusLimit(RealOpenMM quinticUpperBornRadiusLimit) {
     _quinticUpperBornRadiusLimit    = quinticUpperBornRadiusLimit;
 }

platforms/reference/src/gbsa/ObcParameters.cpp → platforms/reference/src/SimTKReference/ObcParameters.cpp

@@ -28,9 +28,9 @@
 
 #include "openmm/OpenMMException.h"
 #include "ObcParameters.h"
-#include "SimTKOpenMMCommon.h"
 
 using std::vector;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 
@@ -41,21 +41,21 @@ using std::vector;
 
     --------------------------------------------------------------------------------------- */
 
-ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType ) :
-                               _numberOfAtoms(numberOfAtoms),
-                               _solventDielectric( 78.3 ),
-                               _soluteDielectric( 1.0 ),
-                               _electricConstant(-0.5*ONE_4PI_EPS0),
-                               _probeRadius(0.14),
-                               _pi4Asolv( 28.3919551),
-                               _dielectricOffset( 0.009 ),
-                               _obcType( obcType ),
-                               _cutoff(false),
-                               _periodic(false) {
-
-    _atomicRadii.resize( numberOfAtoms );
-    _scaledRadiusFactors.resize( numberOfAtoms );
-    setObcTypeParameters( obcType );
+ObcParameters::ObcParameters(int numberOfAtoms, ObcParameters::ObcType obcType) :
+                              _numberOfAtoms(numberOfAtoms),
+                              _solventDielectric(78.3),
+                              _soluteDielectric(1.0),
+                              _electricConstant(-0.5*ONE_4PI_EPS0),
+                              _probeRadius(0.14),
+                              _pi4Asolv(28.3919551),
+                              _dielectricOffset(0.009),
+                              _obcType(obcType),
+                              _cutoff(false),
+                              _periodic(false) {
+
+    _atomicRadii.resize(numberOfAtoms);
+    _scaledRadiusFactors.resize(numberOfAtoms);
+    setObcTypeParameters(obcType);
 
 }
 
@@ -65,7 +65,7 @@ ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType
 
     --------------------------------------------------------------------------------------- */
 
-ObcParameters::~ObcParameters( ){
+ObcParameters::~ObcParameters() {
 }
 
 /**---------------------------------------------------------------------------------------
@@ -76,7 +76,7 @@ ObcParameters::~ObcParameters( ){
 
    --------------------------------------------------------------------------------------- */
 
-int ObcParameters::getNumberOfAtoms( void ) const {
+int ObcParameters::getNumberOfAtoms() const {
     return _numberOfAtoms;
 }
 
@@ -88,7 +88,7 @@ int ObcParameters::getNumberOfAtoms( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-ObcParameters::ObcType ObcParameters::getObcType( void ) const {
+ObcParameters::ObcType ObcParameters::getObcType() const {
     return _obcType;
 }
 
@@ -100,8 +100,8 @@ ObcParameters::ObcType ObcParameters::getObcType( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void ObcParameters::setObcTypeParameters( ObcParameters::ObcType obcType ){
-    if( obcType == ObcTypeI ){
+void ObcParameters::setObcTypeParameters(ObcParameters::ObcType obcType) {
+    if (obcType == ObcTypeI) {
         _alphaObc   = 0.8f;
         _betaObc    = 0.0f;
         _gammaObc   = 2.91f;
@@ -121,7 +121,7 @@ void ObcParameters::setObcTypeParameters( ObcParameters::ObcType obcType ){
 
     --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getDielectricOffset( void ) const {
+RealOpenMM ObcParameters::getDielectricOffset() const {
     return _dielectricOffset;
 }
 
@@ -133,7 +133,7 @@ RealOpenMM ObcParameters::getDielectricOffset( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getAlphaObc( void ) const {
+RealOpenMM ObcParameters::getAlphaObc() const {
     return _alphaObc;
 }
 
@@ -145,7 +145,7 @@ RealOpenMM ObcParameters::getAlphaObc( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getBetaObc( void ) const {
+RealOpenMM ObcParameters::getBetaObc() const {
     return _betaObc;
 }
 
@@ -157,7 +157,7 @@ RealOpenMM ObcParameters::getBetaObc( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getGammaObc( void ) const {
+RealOpenMM ObcParameters::getGammaObc() const {
     return _gammaObc;
 }
 
@@ -169,7 +169,7 @@ RealOpenMM ObcParameters::getGammaObc( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getSolventDielectric( void ) const {
+RealOpenMM ObcParameters::getSolventDielectric() const {
     return _solventDielectric;
 }
 
@@ -181,7 +181,7 @@ RealOpenMM ObcParameters::getSolventDielectric( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-void ObcParameters::setSolventDielectric( RealOpenMM solventDielectric ){
+void ObcParameters::setSolventDielectric(RealOpenMM solventDielectric) {
     _solventDielectric = solventDielectric;
 }
 /**---------------------------------------------------------------------------------------
@@ -192,7 +192,7 @@ void ObcParameters::setSolventDielectric( RealOpenMM solventDielectric ){
 
    --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getSoluteDielectric( void ) const {
+RealOpenMM ObcParameters::getSoluteDielectric() const {
     return _soluteDielectric;
 }
 
@@ -204,7 +204,7 @@ RealOpenMM ObcParameters::getSoluteDielectric( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-void ObcParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
+void ObcParameters::setSoluteDielectric(RealOpenMM soluteDielectric) {
     _soluteDielectric = soluteDielectric;
 }
 
@@ -216,7 +216,7 @@ void ObcParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
 
    --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getElectricConstant( void ) const {
+RealOpenMM ObcParameters::getElectricConstant() const {
     return _electricConstant;
 }
 
@@ -228,7 +228,7 @@ RealOpenMM ObcParameters::getElectricConstant( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getProbeRadius( void ) const {
+RealOpenMM ObcParameters::getProbeRadius() const {
     return _probeRadius;
 }
 
@@ -240,7 +240,7 @@ RealOpenMM ObcParameters::getProbeRadius( void ) const {
 
    --------------------------------------------------------------------------------------- */
 
-void ObcParameters::setProbeRadius( RealOpenMM probeRadius ){
+void ObcParameters::setProbeRadius(RealOpenMM probeRadius) {
     _probeRadius = probeRadius;
 }
 
@@ -254,7 +254,7 @@ void ObcParameters::setProbeRadius( RealOpenMM probeRadius ){
 
    --------------------------------------------------------------------------------------- */
 
-RealOpenMM ObcParameters::getPi4Asolv( void ) const {
+RealOpenMM ObcParameters::getPi4Asolv() const {
     return _pi4Asolv;
 }
 
@@ -270,7 +270,7 @@ void ObcParameters::setPi4Asolv(RealOpenMM pi4Asolv) {
 
     --------------------------------------------------------------------------------------- */
 
-const RealOpenMMVector& ObcParameters::getAtomicRadii( void ) const {
+const vector<RealOpenMM>& ObcParameters::getAtomicRadii() const {
     return _atomicRadii;
 }
 
@@ -282,10 +282,10 @@ const RealOpenMMVector& ObcParameters::getAtomicRadii( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
+void ObcParameters::setAtomicRadii(const vector<RealOpenMM>& atomicRadii) {
 
-    if( atomicRadii.size() == _atomicRadii.size() ){
-        for( unsigned int ii = 0; ii < atomicRadii.size(); ii++ ){
+    if (atomicRadii.size() == _atomicRadii.size()) {
+        for (unsigned int ii = 0; ii < atomicRadii.size(); ii++) {
             _atomicRadii[ii] = atomicRadii[ii];
         }   
     } else {
@@ -306,7 +306,7 @@ void ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
 
     --------------------------------------------------------------------------------------- */
 
-const RealOpenMMVector& ObcParameters::getScaledRadiusFactors( void ) const {
+const vector<RealOpenMM>& ObcParameters::getScaledRadiusFactors() const {
     return _scaledRadiusFactors;
 }
 
@@ -318,10 +318,10 @@ const RealOpenMMVector& ObcParameters::getScaledRadiusFactors( void ) const {
 
     --------------------------------------------------------------------------------------- */
 
-void ObcParameters::setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors ){
+void ObcParameters::setScaledRadiusFactors(const vector<RealOpenMM>& scaledRadiusFactors) {
 
-    if( scaledRadiusFactors.size() == _scaledRadiusFactors.size() ){
-        for( unsigned int ii = 0; ii < scaledRadiusFactors.size(); ii++ ){
+    if (scaledRadiusFactors.size() == _scaledRadiusFactors.size()) {
+        for (unsigned int ii = 0; ii < scaledRadiusFactors.size(); ii++) {
             _scaledRadiusFactors[ii] = scaledRadiusFactors[ii];
         }   
     } else {
@@ -342,7 +342,7 @@ void ObcParameters::setScaledRadiusFactors( const RealOpenMMVector& scaledRadius
 
       --------------------------------------------------------------------------------------- */
 
-void ObcParameters::setUseCutoff( RealOpenMM distance ) {
+void ObcParameters::setUseCutoff(RealOpenMM distance) {
 
      _cutoff         = true;
      _cutoffDistance = distance;

platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp

@@ -29,7 +29,7 @@
 #include "ReferenceAndersenThermostat.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
       /**---------------------------------------------------------------------------------------
       
@@ -37,7 +37,7 @@ using OpenMM::RealVec;
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceAndersenThermostat::ReferenceAndersenThermostat( ) {
+       ReferenceAndersenThermostat::ReferenceAndersenThermostat() {
        }
 
       /**---------------------------------------------------------------------------------------
@@ -46,7 +46,7 @@ using OpenMM::RealVec;
       
          --------------------------------------------------------------------------------------- */
 
-       ReferenceAndersenThermostat::~ReferenceAndersenThermostat( ) {
+       ReferenceAndersenThermostat::~ReferenceAndersenThermostat() {
        }
 
       /**---------------------------------------------------------------------------------------
@@ -61,8 +61,8 @@ using OpenMM::RealVec;
                   
          --------------------------------------------------------------------------------------- */
           
-      void ReferenceAndersenThermostat::applyThermostat( const vector<vector<int> >& atomGroups, vector<RealVec>& atomVelocities, vector<RealOpenMM>& atomMasses,
-              RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const {
+      void ReferenceAndersenThermostat::applyThermostat(const vector<vector<int> >& atomGroups, vector<RealVec>& atomVelocities, vector<RealOpenMM>& atomMasses,
+              RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize) const {
           
           const RealOpenMM collisionProbability = 1.0f - EXP(-collisionFrequency*stepSize);
           for (int i = 0; i < (int) atomGroups.size(); ++i) {