Moved reference platform classes into OpenMM namespace

platforms/reference/include/ReferenceCustomManyParticleIxn.h

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

platforms/reference/include/ReferenceCustomNonbondedIxn.h

@@ -33,7 +33,7 @@
 #include <utility>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomNonbondedIxn {
 
@@ -161,4 +161,6 @@ class ReferenceCustomNonbondedIxn {
 
 };
 
+} // namespace OpenMM
+
 #endif // __ReferenceCustomNonbondedxIxn_H__

platforms/reference/include/ReferenceCustomTorsionIxn.h

@@ -27,7 +27,7 @@
 #include "ReferenceBondIxn.h"
 #include "lepton/CompiledExpression.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
 
@@ -78,6 +78,6 @@ class ReferenceCustomTorsionIxn : public ReferenceBondIxn {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // _ReferenceCustomTorsionIxn___

platforms/reference/include/ReferenceDynamics.h

@@ -31,7 +31,7 @@
 #include <cstddef>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 /**---------------------------------------------------------------------------------------
 
@@ -173,6 +173,7 @@ class OPENMM_EXPORT ReferenceDynamics {
       void setReferenceConstraintAlgorithm( ReferenceConstraintAlgorithm* referenceConstraint );
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
+
 
 #endif // __ReferenceDynamics_H__

platforms/reference/include/ReferenceForce.h

@@ -28,7 +28,7 @@
 #include "lepton/CompiledExpression.h"
 #include "openmm/internal/windowsExport.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT  ReferenceForce {
 
@@ -126,6 +126,6 @@ class OPENMM_EXPORT  ReferenceForce {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceForce_H__

platforms/reference/include/ReferenceHarmonicBondIxn.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceBondIxn.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
 
@@ -70,6 +70,6 @@ class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // _ReferenceHarmonicBondIxn___

platforms/reference/include/ReferenceKernels.h

@@ -39,6 +39,8 @@
 #include "lepton/CompiledExpression.h"
 #include "lepton/ExpressionProgram.h"
 
+namespace OpenMM {
+
 class CpuObc;
 class CpuGBVI;
 class ReferenceAndersenThermostat;
@@ -54,8 +56,6 @@ class ReferenceVariableVerletDynamics;
 class ReferenceVerletDynamics;
 class ReferenceCustomDynamics;
 
-namespace OpenMM {
-
 /**
  * This kernel is invoked at the beginning and end of force and energy computations.  It gives the
  * Platform a chance to clear buffers and do other initialization at the beginning, and to do any

platforms/reference/include/ReferenceLJCoulomb14.h

@@ -28,7 +28,7 @@
 #include "ReferenceBondIxn.h"
 #include "openmm/internal/windowsExport.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
 
@@ -68,6 +68,6 @@ class OPENMM_EXPORT ReferenceLJCoulomb14 : public ReferenceBondIxn {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceLJCoulomb14_H__

platforms/reference/include/ReferenceLJCoulombIxn.h

@@ -28,7 +28,7 @@
 #include "ReferencePairIxn.h"
 #include "ReferenceNeighborList.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceLJCoulombIxn {
 
@@ -197,6 +197,6 @@ private:
                             RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, bool includeDirect, bool includeReciprocal) const;
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceLJCoulombIxn_H__

platforms/reference/include/ReferenceLincsAlgorithm.h

@@ -28,7 +28,7 @@
 #include "SimTKOpenMMRealType.h"
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
 
@@ -157,6 +157,6 @@ class ReferenceLincsAlgorithm : public ReferenceConstraintAlgorithm {
                      std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses);
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceLincsAlgorithm_H__

platforms/reference/include/ReferenceMonteCarloBarostat.h

@@ -29,7 +29,7 @@
 #include <utility>
 #include <vector>
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceMonteCarloBarostat {
 
@@ -82,6 +82,6 @@ class ReferenceMonteCarloBarostat {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceMonteCarloBarostat_H__

platforms/reference/include/ReferencePME.h

@@ -29,10 +29,15 @@
  * POSSIBILITY OF SUCH DAMAGE.
  */
 
+#ifndef __ReferencePME_H__
+#define __ReferencePME_H__
+
 #include "SimTKOpenMMCommon.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

@@ -28,7 +28,7 @@
 #include "RealVec.h"
 #include "openmm/internal/windowsExport.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class OPENMM_EXPORT ReferencePairIxn {
 
@@ -74,6 +74,6 @@ class OPENMM_EXPORT ReferencePairIxn {
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // 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 {
 
@@ -71,6 +71,6 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // 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 {
 
@@ -69,6 +69,6 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
 
 };
 
-// ---------------------------------------------------------------------------------------
+} // 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 {
 
@@ -120,6 +120,6 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceStochasticDynamics_H__

platforms/reference/include/ReferenceVariableStochasticDynamics.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceDynamics.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
 
@@ -142,6 +142,6 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
       
 };
 
-// ---------------------------------------------------------------------------------------
+} // namespace OpenMM
 
 #endif // __ReferenceVariableStochasticDynamics_H__

platforms/reference/include/ReferenceVariableVerletDynamics.h

@@ -27,7 +27,7 @@
 
 #include "ReferenceDynamics.h"
 
-// ---------------------------------------------------------------------------------------
+namespace OpenMM {
 
 class ReferenceVariableVerletDynamics : public ReferenceDynamics {
 
@@ -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 {
 
@@ -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__