Moved reference platform classes into OpenMM namespace

platforms/reference/src/SimTKReference/ReferencePME.cpp

@@ -37,10 +37,10 @@
 #include "fftpack.h"
 
 using std::vector;
-using OpenMM::RealVec;
 
 typedef int    ivec[3];
 
+namespace OpenMM {
 
 struct pme
 {
@@ -729,3 +729,5 @@ pme_destroy(pme_t    pme)
 
     return 0;
 }
+
+} // namespace OpenMM

platforms/reference/src/SimTKReference/ReferencePairIxn.cpp

@@ -31,6 +31,8 @@
 #include "ReferenceForce.h"
 #include "ReferencePairIxn.h"
 
+using namespace OpenMM;
+
 /**---------------------------------------------------------------------------------------
 
    ReferencePairIxn constructor

platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp

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

platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp

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

platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp

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

platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp

@@ -35,7 +35,7 @@
 #include <cstdio>
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp

@@ -33,7 +33,7 @@
 #include "ReferenceVirtualSites.h"
 
 using std::vector;
-using OpenMM::RealVec;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------
 

platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp

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

platforms/reference/src/SimTKUtilities/SimTKOpenMMCommon.cpp

@@ -24,6 +24,8 @@
 
 #include "SimTKOpenMMCommon.h"
 
+using namespace OpenMM;
+
 // static settings
 
 // initialization of static data members

platforms/reference/src/SimTKUtilities/SimTKOpenMMLog.cpp

@@ -26,6 +26,8 @@
 #include <stdlib.h>
 #include "openmm/OpenMMException.h"
 
+using namespace OpenMM;
+
 // static settings
 
 SimTKOpenMMLog* SimTKOpenMMLog::_simTKOpenMMLog = NULL;

platforms/reference/src/SimTKUtilities/SimTKOpenMMUtilities.cpp

@@ -36,6 +36,8 @@
 #include <string.h>
 #include <iostream>
 
+using namespace OpenMM;
+
 uint32_t SimTKOpenMMUtilities::_randomNumberSeed = 0;
 bool SimTKOpenMMUtilities::_randomInitialized = false;
 bool SimTKOpenMMUtilities::nextGaussianIsValid = false;

platforms/reference/src/gbsa/GBVIParameters.cpp

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

platforms/reference/src/gbsa/ObcParameters.cpp

@@ -31,6 +31,7 @@
 #include "SimTKOpenMMCommon.h"
 
 using std::vector;
+using namespace OpenMM;
 
 /**---------------------------------------------------------------------------------------