Merge https://github.com/SimTk/openmm

CMakeLists.txt

@@ -417,9 +417,11 @@ ENDIF(OPENMM_BUILD_STATIC_LIB)
 FILE(GLOB CORE_HEADERS     include/*.h          */include/*.h)
 FILE(GLOB TOP_HEADERS      include/openmm/*.h          */include/openmm/*.h)
 FILE(GLOB INTERNAL_HEADERS include/openmm/internal/*.h */include/openmm/internal/*.h )
+FILE(GLOB REFERENCE_HEADERS platforms/reference/include/*.h)
 INSTALL_FILES(/include                 FILES ${CORE_HEADERS})
 INSTALL_FILES(/include/openmm          FILES ${TOP_HEADERS})
 INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS})
+INSTALL_FILES(/include/openmm/reference FILES ${REFERENCE_HEADERS})
 
 # Serialization support
 

openmmapi/src/Context.cpp

@@ -33,7 +33,7 @@
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ForceImpl.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <cmath>
 

platforms/cuda/CMakeLists.txt

@@ -102,4 +102,9 @@ SET(CUDA_KERNELS_H ${CMAKE_CURRENT_BINARY_DIR}/src/${CUDA_SOURCE_CLASS}.h)
 SET(SOURCE_FILES ${SOURCE_FILES} ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H})
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/src)
 
+# Install headers
+
+FILE(GLOB CORE_HEADERS include/*.h)
+INSTALL_FILES(/include/openmm/cuda FILES ${CORE_HEADERS})
+
 SUBDIRS (sharedTarget)

platforms/cuda/src/CudaContext.cpp

@@ -747,7 +747,8 @@ void CudaContext::findMoleculeGroups() {
             for (int j = 0; j < forces[i]->getNumParticleGroups(); j++) {
                 vector<int> particles;
                 forces[i]->getParticlesInGroup(j, particles);
-                molecules[atomMolecule[particles[0]]].groups[i].push_back(j);
+                if (particles.size() > 0)
+                    molecules[atomMolecule[particles[0]]].groups[i].push_back(j);
             }
     }
 

platforms/cuda/src/CudaKernels.cpp

@@ -44,8 +44,8 @@
 #include "lepton/Operation.h"
 #include "lepton/Parser.h"
 #include "lepton/ParsedExpression.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
-#include "../src/SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMRealType.h"
+#include "SimTKOpenMMUtilities.h"
 #include <cmath>
 #include <set>
 

platforms/cuda/tests/TestCudaAndersenThermostat.cpp

@@ -40,7 +40,7 @@
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

platforms/cuda/tests/TestCudaBrownianIntegrator.cpp

@@ -43,7 +43,7 @@
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
 #include "openmm/BrownianIntegrator.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

platforms/cuda/tests/TestCudaCMAPTorsionForce.cpp

@@ -40,7 +40,7 @@
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

platforms/cuda/tests/TestCudaCMMotionRemover.cpp

@@ -42,7 +42,7 @@
 #include "openmm/System.h"
 #include "openmm/LangevinIntegrator.h"
 #include "openmm/VerletIntegrator.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>