Merge remote-tracking branch 'upstream/master'

eb232608 · John Chodera (MSKCC) · 62581e9c · 7f8c5089 · eb232608 · eb232608
Commit eb232608 authored Apr 22, 2015 by John Chodera (MSKCC)
20 changed files
--- a/platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.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/ReferenceCustomCompoundBondIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.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/ReferenceCustomGBIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.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/ReferenceDynamics.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceForce.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceForce.cpp
--- a/platforms/reference/src/gbsa/CpuGBVI.cpp
+++ b/platforms/reference/src/gbsa/CpuGBVI.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp
--- a/platforms/reference/src/SimTKReference/ReferenceMonteCarloBarostat.cpp
+++ b/platforms/reference/src/SimTKReference/ReferenceMonteCarloBarostat.cpp