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

platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp

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

platforms/reference/tests/TestReferenceVerletIntegrator.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>

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp

@@ -778,6 +778,17 @@ public:
         }
         return true;
     }
+    int getNumParticleGroups() {
+        return 7*force.getNumMultipoles();
+    }
+    void getParticlesInGroup(int index, vector<int>& particles) {
+        int particle = index/7;
+        int type = index-7*particle;
+        force.getCovalentMap(particle, AmoebaMultipoleForce::CovalentType(type), particles);
+    }
+    bool areGroupsIdentical(int group1, int group2) {
+        return ((group1%7) == (group2%7));
+    }
 private:
     const AmoebaMultipoleForce& force;
 };

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h

@@ -31,8 +31,8 @@
 #include "openmm/amoebaKernels.h"
 #include "openmm/AmoebaMultipoleForce.h"
 #include "AmoebaReferenceMultipoleForce.h"
-#include "SimTKReference/ReferenceNeighborList.h"
-#include "SimTKUtilities/SimTKOpenMMRealType.h"
+#include "ReferenceNeighborList.h"
+#include "SimTKOpenMMRealType.h"
 
 namespace OpenMM {
 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceAngleForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceAngleForce_H__
 #define __AmoebaReferenceAngleForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include <vector>
 
 // ---------------------------------------------------------------------------------------

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceBondForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceBondForce_H__
 #define __AmoebaReferenceBondForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include <vector>
 
 // ---------------------------------------------------------------------------------------

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceForce_H__
 #define __AmoebaReferenceForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include "openmm/Vec3.h"
 #include <vector>
 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceGeneralizedKirkwoodForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceGeneralizedKirkwoodForce_H__
 #define __AmoebaReferenceGeneralizedKirkwoodForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include <vector>
 
 using namespace OpenMM;

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceInPlaneAngleForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceInPlaneAngleForce_H__
 #define __AmoebaReferenceInPlaneAngleForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include <vector>
 
 // ---------------------------------------------------------------------------------------

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h

@@ -24,7 +24,7 @@
 #ifndef __AmoebaReferenceMultipoleForce_H__
 #define __AmoebaReferenceMultipoleForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include "openmm/AmoebaMultipoleForce.h"
 #include "AmoebaReferenceGeneralizedKirkwoodForce.h"
 #include <map>

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceOutOfPlaneBendForce_H__
 #define __AmoebaReferenceOutOfPlaneBendForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include <vector>
 
 // ---------------------------------------------------------------------------------------

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferencePiTorsionForce_H__
 #define __AmoebaReferencePiTorsionForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include <vector>
 
 // ---------------------------------------------------------------------------------------

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceStretchBendForce_H__
 #define __AmoebaReferenceStretchBendForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include <vector>
 
 // ---------------------------------------------------------------------------------------

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceTorsionTorsionForce_H__
 #define __AmoebaReferenceTorsionTorsionForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include <vector>
 
 // ---------------------------------------------------------------------------------------

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceVdwForce.h

@@ -25,9 +25,9 @@
 #ifndef __AmoebaReferenceVdwForce_H__
 #define __AmoebaReferenceVdwForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include "openmm/Vec3.h"
-#include "SimTKReference/ReferenceNeighborList.h"
+#include "ReferenceNeighborList.h"
 #include <string>
 #include <vector>
 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceWcaDispersionForce.h

@@ -25,7 +25,7 @@
 #ifndef __AmoebaReferenceWcaDispersionForce_H__
 #define __AmoebaReferenceWcaDispersionForce_H__
 
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include "openmm/Vec3.h"
 #include <string>
 #include <vector>

plugins/cpupme/src/CpuPmeKernels.cpp

@@ -33,7 +33,7 @@
   #define _USE_MATH_DEFINES // Needed to get M_PI
 #endif
 #include "CpuPmeKernels.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include <cmath>
 #include <cstring>
 #include <smmintrin.h>

plugins/cpupme/tests/TestCpuPme.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VerletIntegrator.h"
 #include "openmm/internal/ContextImpl.h"
 #include "../src/CpuPmeKernels.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp

@@ -36,7 +36,7 @@
 #include "CudaForceInfo.h"
 #include "CudaIntegrationUtilities.h"
 #include "CudaKernelSources.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include <set>
 
 using namespace OpenMM;

plugins/drude/platforms/cuda/tests/TestCudaDrudeForce.cpp

@@ -40,7 +40,7 @@
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
 #include "openmm/DrudeForce.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>