Moved reference platform classes into OpenMM namespace

platforms/reference/include/SimTKOpenMMCommon.h

@@ -25,18 +25,11 @@
 #ifndef __SimTKOpenMMCommon_H__
 #define __SimTKOpenMMCommon_H__
 
-// include file containing entries commonly used
-
-// STL includes
-
 #include <vector>
 #include <string>
-
-// ---------------------------------------------------------------------------------------
-
 #include "RealVec.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 typedef std::vector<RealOpenMM> RealOpenMMVector;
 typedef RealOpenMMVector::iterator RealOpenMMVectorI;
@@ -62,4 +55,6 @@ class SimTKOpenMMCommon {
       static const int ErrorReturn;
 };
 
+} // namespace OpenMM
+
 #endif // __SimTKOpenMMCommon_H__

platforms/reference/include/SimTKOpenMMLog.h

@@ -30,6 +30,8 @@
 #include "SimTKOpenMMCommon.h"
 #include "openmm/internal/windowsExport.h"
 
+namespace OpenMM {
+
 /** ---------------------------------------------------------------------------------------
 
    SimTKOpenMMLog class used for logging
@@ -182,4 +184,6 @@ class OPENMM_EXPORT SimTKOpenMMLog {
 
 };
 
+} // namespace OpenMM
+
 #endif //__SimTKOpenMMLog_H__

platforms/reference/include/SimTKOpenMMUtilities.h

@@ -33,6 +33,8 @@
 
 #include <string>
 
+namespace OpenMM {
+
 /**---------------------------------------------------------------------------------------
 
    Class of static methods to be shared
@@ -219,7 +221,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
 
       static void loadCheckpoint(std::istream& stream);
 };
-   
-// ---------------------------------------------------------------------------------------
+
+} // namespace OpenMM
 
 #endif // __SimTKOpenMMUtilities_H__

platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp

@@ -29,7 +29,7 @@
 #include "ReferenceAndersenThermostat.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
       /**---------------------------------------------------------------------------------------
       

platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp

@@ -32,7 +32,7 @@
 #include "ReferenceForce.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceBondForce.cpp

@@ -31,7 +31,7 @@
 #include "ReferenceBondForce.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp

@@ -32,7 +32,7 @@
 #include "ReferenceBondIxn.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp

@@ -34,7 +34,7 @@
 #include <cstdio>
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp

@@ -39,9 +39,7 @@ using std::map;
 using std::pair;
 using std::vector;
 using std::set;
-using OpenMM::OpenMMException;
-using OpenMM::Vec3;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
                                                   int numberOfConstraints,

platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.cpp

@@ -26,7 +26,7 @@
 #include "ReferenceForce.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp

@@ -37,7 +37,7 @@ using std::pair;
 using std::string;
 using std::stringstream;
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp

@@ -36,7 +36,7 @@ using std::set;
 using std::string;
 using std::stringstream;
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp

@@ -38,7 +38,7 @@ using std::set;
 using std::string;
 using std::stringstream;
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp

@@ -37,7 +37,7 @@ using std::string;
 using std::stringstream;
 using std::set;
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceDynamics.cpp

@@ -33,7 +33,7 @@
 #include <cstdio>
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 
 /**---------------------------------------------------------------------------------------

platforms/reference/src/SimTKReference/ReferenceForce.cpp

@@ -32,7 +32,7 @@
 
 #include <cstdio>
 
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp

@@ -32,7 +32,7 @@
 #include "ReferenceForce.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp

@@ -32,7 +32,7 @@
 #include "ReferenceForce.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp

@@ -40,7 +40,7 @@
 
 using std::set;
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp

@@ -32,7 +32,7 @@
 #include "openmm/OpenMMException.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------