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

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

@@ -34,10 +34,10 @@
 
 using namespace OpenMM;
 
-extern "C" void registerPlatforms() {
+extern "C" OPENMM_EXPORT void registerPlatforms() {
 }
 
-extern "C" void registerKernelFactories() {
+extern "C" OPENMM_EXPORT void registerKernelFactories() {
     try {
         Platform& platform = Platform::getPlatformByName("OpenCL");
         OpenCLDrudeKernelFactory* factory = new OpenCLDrudeKernelFactory();

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

@@ -34,10 +34,10 @@
 
 using namespace OpenMM;
 
-extern "C" void registerPlatforms() {
+extern "C" OPENMM_EXPORT void registerPlatforms() {
 }
 
-extern "C" void registerKernelFactories() {
+extern "C" OPENMM_EXPORT void registerKernelFactories() {
     try {
         Platform& platform = Platform::getPlatformByName("CUDA");
         CudaRpmdKernelFactory* factory = new CudaRpmdKernelFactory();

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

@@ -296,12 +296,25 @@ void CudaIntegrateRPMDStepKernel::setPositions(int copy, const vector<Vec3>& pos
         throw OpenMMException("RPMDIntegrator: Cannot set positions before the integrator is added to a Context");
     if (pos.size() != numParticles)
         throw OpenMMException("RPMDIntegrator: wrong number of values passed to setPositions()");
+
+    // Adjust the positions based on the current cell offsets.
+    
+    const vector<int>& order = cu.getAtomIndex();
+    double4 periodicBoxSize = cu.getPeriodicBoxSize();
+    vector<Vec3> offsetPos(numParticles);
+    for (int i = 0; i < numParticles; ++i) {
+        int4 offset = cu.getPosCellOffsets()[i];
+        offsetPos[order[i]] = pos[order[i]] + Vec3(offset.x*periodicBoxSize.x, offset.y*periodicBoxSize.y, offset.z*periodicBoxSize.z);
+    }
+
+    // Record the positions.
+
     CUresult result;
     if (cu.getUseDoublePrecision()) {
         vector<double4> posq(cu.getPaddedNumAtoms());
         cu.getPosq().download(posq);
         for (int i = 0; i < numParticles; i++)
-            posq[i] = make_double4(pos[i][0], pos[i][1], pos[i][2], posq[i].w);
+            posq[i] = make_double4(offsetPos[i][0], offsetPos[i][1], offsetPos[i][2], posq[i].w);
         result = cuMemcpyHtoD(positions->getDevicePointer()+copy*cu.getPaddedNumAtoms()*sizeof(double4), &posq[0], numParticles*sizeof(double4));
     }
     else if (cu.getUseMixedPrecision()) {
@@ -309,14 +322,14 @@ void CudaIntegrateRPMDStepKernel::setPositions(int copy, const vector<Vec3>& pos
         cu.getPosq().download(posqf);
         vector<double4> posq(cu.getPaddedNumAtoms());
         for (int i = 0; i < numParticles; i++)
-            posq[i] = make_double4(pos[i][0], pos[i][1], pos[i][2], posqf[i].w);
+            posq[i] = make_double4(offsetPos[i][0], offsetPos[i][1], offsetPos[i][2], posqf[i].w);
         result = cuMemcpyHtoD(positions->getDevicePointer()+copy*cu.getPaddedNumAtoms()*sizeof(double4), &posq[0], numParticles*sizeof(double4));
     }
     else {
         vector<float4> posq(cu.getPaddedNumAtoms());
         cu.getPosq().download(posq);
         for (int i = 0; i < numParticles; i++)
-            posq[i] = make_float4((float) pos[i][0], (float) pos[i][1], (float) pos[i][2], posq[i].w);
+            posq[i] = make_float4((float) offsetPos[i][0], (float) offsetPos[i][1], (float) offsetPos[i][2], posq[i].w);
         result = cuMemcpyHtoD(positions->getDevicePointer()+copy*cu.getPaddedNumAtoms()*sizeof(float4), &posq[0], numParticles*sizeof(float4));
     }
     if (result != CUDA_SUCCESS) {

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

@@ -28,16 +28,16 @@
 
 #include "OpenCLRpmdKernelFactory.h"
 #include "OpenCLRpmdKernels.h"
-#include "openmm/internal/windowsExport.h"
+#include "openmm/internal/windowsExportRpmd.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/OpenMMException.h"
 
 using namespace OpenMM;
 
-extern "C" void registerPlatforms() {
+extern "C" OPENMM_EXPORT void registerPlatforms() {
 }
 
-extern "C" void registerKernelFactories() {
+extern "C" OPENMM_EXPORT void registerKernelFactories() {
     try {
         Platform& platform = Platform::getPlatformByName("OpenCL");
         OpenCLRpmdKernelFactory* factory = new OpenCLRpmdKernelFactory();

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

@@ -312,11 +312,24 @@ void OpenCLIntegrateRPMDStepKernel::setPositions(int copy, const vector<Vec3>& p
         throw OpenMMException("RPMDIntegrator: Cannot set positions before the integrator is added to a Context");
     if (pos.size() != numParticles)
         throw OpenMMException("RPMDIntegrator: wrong number of values passed to setPositions()");
+
+    // Adjust the positions based on the current cell offsets.
+    
+    const vector<int>& order = cl.getAtomIndex();
+    mm_double4 periodicBoxSize = cl.getPeriodicBoxSizeDouble();
+    vector<Vec3> offsetPos(numParticles);
+    for (int i = 0; i < numParticles; ++i) {
+        mm_int4 offset = cl.getPosCellOffsets()[i];
+        offsetPos[order[i]] = pos[order[i]] + Vec3(offset.x*periodicBoxSize.x, offset.y*periodicBoxSize.y, offset.z*periodicBoxSize.z);
+    }
+
+    // Record the positions.
+
     if (cl.getUseDoublePrecision()) {
         vector<mm_double4> posq(cl.getPaddedNumAtoms());
         cl.getPosq().download(posq);
         for (int i = 0; i < numParticles; i++)
-            posq[i] = mm_double4(pos[i][0], pos[i][1], pos[i][2], posq[i].w);
+            posq[i] = mm_double4(offsetPos[i][0], offsetPos[i][1], offsetPos[i][2], posq[i].w);
         cl.getQueue().enqueueWriteBuffer(positions->getDeviceBuffer(), CL_TRUE, copy*cl.getPaddedNumAtoms()*sizeof(mm_double4), numParticles*sizeof(mm_double4), &posq[0]);
     }
     else if (cl.getUseMixedPrecision()) {
@@ -324,14 +337,14 @@ void OpenCLIntegrateRPMDStepKernel::setPositions(int copy, const vector<Vec3>& p
         cl.getPosq().download(posqf);
         vector<mm_double4> posq(cl.getPaddedNumAtoms());
         for (int i = 0; i < numParticles; i++)
-            posq[i] = mm_double4(pos[i][0], pos[i][1], pos[i][2], posqf[i].w);
+            posq[i] = mm_double4(offsetPos[i][0], offsetPos[i][1], offsetPos[i][2], posqf[i].w);
         cl.getQueue().enqueueWriteBuffer(positions->getDeviceBuffer(), CL_TRUE, copy*cl.getPaddedNumAtoms()*sizeof(mm_double4), numParticles*sizeof(mm_double4), &posq[0]);
     }
     else {
         vector<mm_float4> posq(cl.getPaddedNumAtoms());
         cl.getPosq().download(posq);
         for (int i = 0; i < numParticles; i++)
-            posq[i] = mm_float4((cl_float) pos[i][0], (cl_float) pos[i][1], (cl_float) pos[i][2], posq[i].w);
+            posq[i] = mm_float4((cl_float) offsetPos[i][0], (cl_float) offsetPos[i][1], (cl_float) offsetPos[i][2], posq[i].w);
         cl.getQueue().enqueueWriteBuffer(positions->getDeviceBuffer(), CL_TRUE, copy*cl.getPaddedNumAtoms()*sizeof(mm_float4), numParticles*sizeof(mm_float4), &posq[0]);
     }
 }

wrappers/python/simtk/openmm/app/amberprmtopfile.py

@@ -41,10 +41,25 @@ import simtk.openmm as mm
 
 # Enumerated values for implicit solvent model
 
-HCT = object()
-OBC1 = object()
-OBC2 = object()
-GBn = object()
+class HCT(object):
+    def __repr__(self):
+        return 'HCT'
+HCT = HCT()
+
+class OBC1(object):
+    def __repr__(self):
+        return 'OBC1'
+OBC1 = OBC1()
+
+class OBC2(object):
+    def __repr__(self):
+        return 'OBC2'
+OBC2 = OBC2()
+
+class GBn(object):
+    def __repr__(self):
+        return 'GBn'
+GBn = GBn()
 
 class AmberPrmtopFile(object):
     """AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it."""

wrappers/python/simtk/openmm/app/forcefield.py

@@ -42,17 +42,47 @@ from simtk.openmm.app import Topology
 
 # Enumerated values for nonbonded method
 
-NoCutoff = object()
-CutoffNonPeriodic = object()
-CutoffPeriodic = object()
-Ewald = object()
-PME = object()
+class NoCutoff(object):
+    def __repr__(self):
+        return 'NoCutoff'
+NoCutoff = NoCutoff()
+
+class CutoffNonPeriodic(object):
+    def __repr__(self):
+        return 'CutoffNonPeriodic'
+CutoffNonPeriodic = CutoffNonPeriodic()
+
+class CutoffPeriodic(object):
+    def __repr__(self):
+        return 'CutoffPeriodic'
+CutoffPeriodic = CutoffPeriodic()
+
+class Ewald(object):
+    def __repr__(self):
+        return 'Ewald'
+Ewald = Ewald()
+
+class PME(object):
+    def __repr__(self):
+        return 'PME'
+PME = PME()
 
 # Enumerated values for constraint type
 
-HBonds = object()
-AllBonds = object()
-HAngles = object()
+class HBonds(object):
+    def __repr__(self):
+        return 'HBonds'
+HBonds = HBonds()
+
+class AllBonds(object):
+    def __repr__(self):
+        return 'AllBonds'
+AllBonds = AllBonds()
+
+class HAngles(object):
+    def __repr__(self):
+        return 'HAngles'
+HAngles = HAngles()
 
 # A map of functions to parse elements of the XML file.
 

wrappers/python/simtk/openmm/vec3.py

@@ -40,6 +40,10 @@ class Vec3(tuple):
         """Create a new Vec3."""
         return tuple.__new__(cls, (x, y, z))
 
+    def __getnewargs__(self):
+        "Support for pickle protocol 2: http://docs.python.org/2/library/pickle.html#pickling-and-unpickling-normal-class-instances"
+        return self[0], self[1], self[2]
+
     def __add__(self, other):
         """Add two Vec3s."""
         return Vec3(self[0]+other[0], self[1]+other[1], self[2]+other[2])

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -218,6 +218,10 @@ class SwigInputBuilder:
         for name in sorted(integratorSubclassList):
             self.fOut.write(",\n         OpenMM::%s" % name)
         self.fOut.write(");\n\n")
+        self.fOut.write("%factory(OpenMM::Integrator& OpenMM::Context::getIntegrator")
+        for name in sorted(integratorSubclassList):
+            self.fOut.write(",\n         OpenMM::%s" % name)
+        self.fOut.write(");\n\n")
         self.fOut.write("%factory(OpenMM::VirtualSite& OpenMM::System::getVirtualSite, OpenMM::TwoParticleAverageSite, OpenMM::ThreeParticleAverageSite, OpenMM::OutOfPlaneSite);\n\n")
         self.fOut.write("\n")