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

855ece90 · leeping · 471bea82 · a42c55ad · 855ece90 · 855ece90
Commit 855ece90 authored Oct 17, 2013 by leeping
20 changed files
--- 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
--- a/platforms/reference/src/SimTKReference/PME.cpp
+++ b/platforms/reference/src/SimTKReference/PME.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceSETTLEAlgorithm.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceSETTLEAlgorithm.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.cpp