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

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

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

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

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp

@@ -36,7 +36,7 @@
 #include "OpenCLForceInfo.h"
 #include "OpenCLIntegrationUtilities.h"
 #include "OpenCLKernelSources.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 #include <set>
 
 using namespace OpenMM;

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeForce.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>
 

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp

@@ -33,9 +33,9 @@
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
-#include "SimTKReference/ReferenceCCMAAlgorithm.h"
-#include "SimTKReference/ReferenceVirtualSites.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceCCMAAlgorithm.h"
+#include "ReferenceVirtualSites.h"
 #include <set>
 
 using namespace OpenMM;

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.h

@@ -34,7 +34,7 @@
 
 #include "ReferencePlatform.h"
 #include "openmm/DrudeKernels.h"
-#include "SimTKUtilities/RealVec.h"
+#include "RealVec.h"
 #include "lbfgs.h"
 #include <utility>
 #include <vector>

plugins/drude/platforms/reference/tests/TestReferenceDrudeForce.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>
 

plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/drude/platforms/reference/tests/TestReferenceDrudeSCFIntegrator.cpp

@@ -41,7 +41,7 @@
 #include "openmm/VirtualSite.h"
 #include "openmm/DrudeForce.h"
 #include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include <iostream>
 #include <vector>
 

plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp

@@ -36,7 +36,7 @@
 #include "CudaExpressionUtilities.h"
 #include "CudaKernelSources.h"
 #include "CudaNonbondedUtilities.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 
 using namespace OpenMM;
 using namespace std;

plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp

@@ -43,7 +43,7 @@
 #include "openmm/System.h"
 #include "openmm/RPMDIntegrator.h"
 #include "openmm/VirtualSite.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp

@@ -36,7 +36,7 @@
 #include "OpenCLExpressionUtilities.h"
 #include "OpenCLFFT3D.h"
 #include "OpenCLNonbondedUtilities.h"
-#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "SimTKOpenMMRealType.h"
 
 using namespace OpenMM;
 using namespace std;

plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp

@@ -43,7 +43,7 @@
 #include "openmm/System.h"
 #include "openmm/RPMDIntegrator.h"
 #include "openmm/VirtualSite.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp

@@ -32,7 +32,7 @@
 #include "ReferenceRpmdKernels.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 
 using namespace OpenMM;
 using namespace std;

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.h

@@ -34,8 +34,8 @@
 
 #include "ReferencePlatform.h"
 #include "openmm/RpmdKernels.h"
-#include "SimTKUtilities/RealVec.h"
-#include "SimTKReference/fftpack.h"
+#include "RealVec.h"
+#include "fftpack.h"
 
 namespace OpenMM {
 

plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp

@@ -42,7 +42,7 @@
 #include "openmm/System.h"
 #include "openmm/RPMDIntegrator.h"
 #include "openmm/VirtualSite.h"
-#include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "SimTKOpenMMUtilities.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
 #include <vector>

wrappers/python/simtk/openmm/app/data/hydrogens.xml

@@ -16,7 +16,7 @@
   <H name="HOP3" parent="OP3"/>
  </Residue>
  <Residue name="ACE">
-  <H name="H" parent="C"/>
+  <H name="H" parent="C" terminal="C"/>
   <H name="H1" parent="CH3"/>
   <H name="H2" parent="CH3"/>
   <H name="H3" parent="CH3"/>
@@ -313,7 +313,7 @@
   <H name="H1" parent="C"/>
   <H name="H2" parent="C"/>
   <H name="H3" parent="C"/>
-  <H name="HN2" parent="N"/>
+  <H name="HN2" parent="N" terminal="N"/>
  </Residue>
  <Residue name="ORN">
   <H name="H" parent="N"/>