Merge branch 'master' of github.com:SimTk/openmm

99ef4344 · Lee-Ping Wang · 471bea82 · 79fd69c3 · 99ef4344 · 99ef4344
Commit 99ef4344 authored Oct 24, 2013 by Lee-Ping Wang
20 changed files
--- a/platforms/reference/include/ReferenceCustomTorsionIxn.h
+++ b/platforms/reference/include/ReferenceCustomTorsionIxn.h
--- a/platforms/reference/include/ReferenceForce.h
+++ b/platforms/reference/include/ReferenceForce.h
--- a/platforms/reference/include/ReferenceKernels.h
+++ b/platforms/reference/include/ReferenceKernels.h
--- a/platforms/reference/src/SimTKReference/PME.h
+++ b/platforms/reference/src/SimTKReference/PME.h
@@ -77,7 +77,7 @@ int
 pme_exec(pme_t       pme,
         std::vector<OpenMM::RealVec>& atomCoordinates,
         std::vector<OpenMM::RealVec>& forces,
-         RealOpenMM **  atomParameters,
+         std::vector<RealOpenMM>& charges,
         const RealOpenMM  periodicBoxSize[3],
         RealOpenMM *    energy,
         RealOpenMM      pme_virial[3][3]);

--- a/platforms/reference/include/ReferencePairIxn.h
+++ b/platforms/reference/include/ReferencePairIxn.h
@@ -25,6 +25,7 @@
 #ifndef __ReferencePairIxn_H__
 #define __ReferencePairIxn_H__

+#include "RealVec.h"
 #include "openmm/internal/windowsExport.h"

 // ---------------------------------------------------------------------------------------

--- a/platforms/reference/include/ReferenceSETTLEAlgorithm.h
+++ b/platforms/reference/include/ReferenceSETTLEAlgorithm.h
--- a/platforms/reference/src/ReferenceKernels.cpp
+++ b/platforms/reference/src/ReferenceKernels.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceConstraint.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceConstraint.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceConstraints.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceConstraints.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceForce.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceForce.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceNeighborList.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceNeighborList.cpp