Merge remote-tracking branch 'upstream/master'

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/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());
 }