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

Conflicts:
	wrappers/python/simtk/openmm/app/modeller.py

platforms/cuda/src/kernels/constraints.cu

-extern "C" __global__ void applyPositionDeltas(real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ posDelta) {
-    for (unsigned int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_ATOMS; index += blockDim.x*gridDim.x) {
+extern "C" __global__ void applyPositionDeltas(int numAtoms, real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ posDelta) {
+    for (unsigned int index = blockIdx.x*blockDim.x+threadIdx.x; index < numAtoms; index += blockDim.x*gridDim.x) {
 #ifdef USE_MIXED_PRECISION
         real4 pos1 = posq[index];
         real4 pos2 = posqCorrection[index];

platforms/cuda/src/kernels/langevin.cu

@@ -4,7 +4,7 @@ enum {VelScale, ForceScale, NoiseScale, MaxParams};
  * Perform the first step of Langevin integration.
  */
 
-extern "C" __global__ void integrateLangevinPart1(mixed4* __restrict__ velm, const long long* __restrict__ force, mixed4* __restrict__ posDelta,
+extern "C" __global__ void integrateLangevinPart1(int numAtoms, int paddedNumAtoms, mixed4* __restrict__ velm, const long long* __restrict__ force, mixed4* __restrict__ posDelta,
         const mixed* __restrict__ paramBuffer, const mixed2* __restrict__ dt, const float4* __restrict__ random, unsigned int randomIndex) {
     mixed vscale = paramBuffer[VelScale];
     mixed fscale = paramBuffer[ForceScale]/(mixed) 0x100000000;
@@ -12,13 +12,13 @@ extern "C" __global__ void integrateLangevinPart1(mixed4* __restrict__ velm, con
     mixed stepSize = dt[0].y;
     int index = blockIdx.x*blockDim.x+threadIdx.x;
     randomIndex += index;
-    while (index < NUM_ATOMS) {
+    while (index < numAtoms) {
         mixed4 velocity = velm[index];
         if (velocity.w != 0) {
             mixed sqrtInvMass = SQRT(velocity.w);
             velocity.x = vscale*velocity.x + fscale*velocity.w*force[index] + noisescale*sqrtInvMass*random[randomIndex].x;
-            velocity.y = vscale*velocity.y + fscale*velocity.w*force[index+PADDED_NUM_ATOMS] + noisescale*sqrtInvMass*random[randomIndex].y;
-            velocity.z = vscale*velocity.z + fscale*velocity.w*force[index+PADDED_NUM_ATOMS*2] + noisescale*sqrtInvMass*random[randomIndex].z;
+            velocity.y = vscale*velocity.y + fscale*velocity.w*force[index+paddedNumAtoms] + noisescale*sqrtInvMass*random[randomIndex].y;
+            velocity.z = vscale*velocity.z + fscale*velocity.w*force[index+paddedNumAtoms*2] + noisescale*sqrtInvMass*random[randomIndex].z;
             velm[index] = velocity;
             posDelta[index] = make_mixed4(stepSize*velocity.x, stepSize*velocity.y, stepSize*velocity.z, 0);
         }
@@ -31,7 +31,7 @@ extern "C" __global__ void integrateLangevinPart1(mixed4* __restrict__ velm, con
  * Perform the second step of Langevin integration.
  */
 
-extern "C" __global__ void integrateLangevinPart2(real4* __restrict__ posq, real4* __restrict__ posqCorrection, const mixed4* __restrict__ posDelta, mixed4* __restrict__ velm, const mixed2* __restrict__ dt) {
+extern "C" __global__ void integrateLangevinPart2(int numAtoms, real4* __restrict__ posq, real4* __restrict__ posqCorrection, const mixed4* __restrict__ posDelta, mixed4* __restrict__ velm, const mixed2* __restrict__ dt) {
 #if __CUDA_ARCH__ >= 130
     double invStepSize = 1.0/dt[0].y;
 #else
@@ -39,7 +39,7 @@ extern "C" __global__ void integrateLangevinPart2(real4* __restrict__ posq, real
     float correction = (1.0f-invStepSize*dt[0].y)/dt[0].y;
 #endif
     int index = blockIdx.x*blockDim.x+threadIdx.x;
-    while (index < NUM_ATOMS) {
+    while (index < numAtoms) {
         mixed4 vel = velm[index];
         if (vel.w != 0) {
 #ifdef USE_MIXED_PRECISION
@@ -78,7 +78,7 @@ extern "C" __global__ void integrateLangevinPart2(real4* __restrict__ posq, real
  * Select the step size to use for the next step.
  */
 
-extern "C" __global__ void selectLangevinStepSize(mixed maxStepSize, mixed errorTol, mixed tau, mixed kT, mixed2* __restrict__ dt,
+extern "C" __global__ void selectLangevinStepSize(int numAtoms, int paddedNumAtoms, mixed maxStepSize, mixed errorTol, mixed tau, mixed kT, mixed2* __restrict__ dt,
         const mixed4* __restrict__ velm, const long long* __restrict__ force, mixed* __restrict__ paramBuffer) {
     // Calculate the error.
 
@@ -87,8 +87,8 @@ extern "C" __global__ void selectLangevinStepSize(mixed maxStepSize, mixed error
     mixed err = 0;
     unsigned int index = threadIdx.x;
     const mixed scale = RECIP((mixed) 0x100000000);
-    while (index < NUM_ATOMS) {
-        mixed3 f = make_mixed3(scale*force[index], scale*force[index+PADDED_NUM_ATOMS], scale*force[index+PADDED_NUM_ATOMS*2]);
+    while (index < numAtoms) {
+        mixed3 f = make_mixed3(scale*force[index], scale*force[index+paddedNumAtoms], scale*force[index+paddedNumAtoms*2]);
         mixed invMass = velm[index].w;
         err += (f.x*f.x + f.y*f.y + f.z*f.z)*invMass;
         index += blockDim.x*gridDim.x;
@@ -106,7 +106,7 @@ extern "C" __global__ void selectLangevinStepSize(mixed maxStepSize, mixed error
     if (blockIdx.x*blockDim.x+threadIdx.x == 0) {
         // Select the new step size.
 
-        mixed totalError = SQRT(error[0]/(NUM_ATOMS*3));
+        mixed totalError = SQRT(error[0]/(numAtoms*3));
         mixed newStepSize = SQRT(errorTol/totalError);
         mixed oldStepSize = dt[0].y;
         if (oldStepSize > 0.0f)

platforms/cuda/src/kernels/verlet.cu

@@ -2,13 +2,13 @@
  * Perform the first step of Verlet integration.
  */
 
-extern "C" __global__ void integrateVerletPart1(const mixed2* __restrict__ dt, const real4* __restrict__ posq,
+extern "C" __global__ void integrateVerletPart1(int numAtoms, int paddedNumAtoms, const mixed2* __restrict__ dt, const real4* __restrict__ posq,
         const real4* __restrict__ posqCorrection, mixed4* __restrict__ velm, const long long* __restrict__ force, mixed4* __restrict__ posDelta) {
     const mixed2 stepSize = dt[0];
     const mixed dtPos = stepSize.y;
     const mixed dtVel = 0.5f*(stepSize.x+stepSize.y);
     const mixed scale = dtVel/(mixed) 0x100000000;
-    for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_ATOMS; index += blockDim.x*gridDim.x) {
+    for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < numAtoms; index += blockDim.x*gridDim.x) {
         mixed4 velocity = velm[index];
         if (velocity.w != 0.0) {
 #ifdef USE_MIXED_PRECISION
@@ -19,8 +19,8 @@ extern "C" __global__ void integrateVerletPart1(const mixed2* __restrict__ dt, c
             real4 pos = posq[index];
 #endif
             velocity.x += scale*force[index]*velocity.w;
-            velocity.y += scale*force[index+PADDED_NUM_ATOMS]*velocity.w;
-            velocity.z += scale*force[index+PADDED_NUM_ATOMS*2]*velocity.w;
+            velocity.y += scale*force[index+paddedNumAtoms]*velocity.w;
+            velocity.z += scale*force[index+paddedNumAtoms*2]*velocity.w;
             pos.x = velocity.x*dtPos;
             pos.y = velocity.y*dtPos;
             pos.z = velocity.z*dtPos;
@@ -34,7 +34,7 @@ extern "C" __global__ void integrateVerletPart1(const mixed2* __restrict__ dt, c
  * Perform the second step of Verlet integration.
  */
 
-extern "C" __global__ void integrateVerletPart2(mixed2* __restrict__ dt, real4* __restrict__ posq,
+extern "C" __global__ void integrateVerletPart2(int numAtoms, mixed2* __restrict__ dt, real4* __restrict__ posq,
         real4* __restrict__ posqCorrection, mixed4* __restrict__ velm, const mixed4* __restrict__ posDelta) {
     mixed2 stepSize = dt[0];
 #if __CUDA_ARCH__ >= 130
@@ -46,7 +46,7 @@ extern "C" __global__ void integrateVerletPart2(mixed2* __restrict__ dt, real4*
     int index = blockIdx.x*blockDim.x+threadIdx.x;
     if (index == 0)
         dt[0].x = stepSize.y;
-    for (; index < NUM_ATOMS; index += blockDim.x*gridDim.x) {
+    for (; index < numAtoms; index += blockDim.x*gridDim.x) {
         mixed4 velocity = velm[index];
         if (velocity.w != 0.0) {
 #ifdef USE_MIXED_PRECISION
@@ -80,14 +80,14 @@ extern "C" __global__ void integrateVerletPart2(mixed2* __restrict__ dt, real4*
  * Select the step size to use for the next step.
  */
 
-extern "C" __global__ void selectVerletStepSize(mixed maxStepSize, mixed errorTol, mixed2* __restrict__ dt, const mixed4* __restrict__ velm, const long long* __restrict__ force) {
+extern "C" __global__ void selectVerletStepSize(int numAtoms, int paddedNumAtoms, mixed maxStepSize, mixed errorTol, mixed2* __restrict__ dt, const mixed4* __restrict__ velm, const long long* __restrict__ force) {
     // Calculate the error.
 
     extern __shared__ mixed error[];
     mixed err = 0.0f;
     const mixed scale = RECIP((mixed) 0x100000000);
-    for (int index = threadIdx.x; index < NUM_ATOMS; index += blockDim.x*gridDim.x) {
-        mixed3 f = make_mixed3(scale*force[index], scale*force[index+PADDED_NUM_ATOMS], scale*force[index+PADDED_NUM_ATOMS*2]);
+    for (int index = threadIdx.x; index < numAtoms; index += blockDim.x*gridDim.x) {
+        mixed3 f = make_mixed3(scale*force[index], scale*force[index+paddedNumAtoms], scale*force[index+paddedNumAtoms*2]);
         mixed invMass = velm[index].w;
         err += (f.x*f.x + f.y*f.y + f.z*f.z)*invMass;
     }
@@ -102,7 +102,7 @@ extern "C" __global__ void selectVerletStepSize(mixed maxStepSize, mixed errorTo
         __syncthreads();
     }
     if (threadIdx.x == 0) {
-        mixed totalError = SQRT(error[0]/(NUM_ATOMS*3));
+        mixed totalError = SQRT(error[0]/(numAtoms*3));
         mixed newStepSize = SQRT(errorTol/totalError);
         mixed oldStepSize = dt[0].y;
         if (oldStepSize > 0.0f)

platforms/cuda/tests/TestCudaMonteCarloAnisotropicBarostat.cpp

@@ -53,44 +53,6 @@ using namespace std;
 
 CudaPlatform platform;
 
-void testChangingBoxSize() {
-    System system;
-    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 5, 0), Vec3(0, 0, 6));
-    system.addParticle(1.0);
-    NonbondedForce* nb = new NonbondedForce();
-    nb->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nb->setCutoffDistance(2.0);
-    nb->addParticle(1, 0.5, 0.5);
-    system.addForce(nb);
-    LangevinIntegrator integrator(300.0, 1.0, 0.01);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions;
-    positions.push_back(Vec3());
-    context.setPositions(positions);
-    Vec3 x, y, z;
-    context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-    ASSERT_EQUAL_VEC(Vec3(4, 0, 0), x, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 5, 0), y, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 6), z, 0);
-    context.setPeriodicBoxVectors(Vec3(7, 0, 0), Vec3(0, 8, 0), Vec3(0, 0, 9));
-    context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-    ASSERT_EQUAL_VEC(Vec3(7, 0, 0), x, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 8, 0), y, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 9), z, 0);
-    
-    // Shrinking the box too small should produce an exception.
-    
-    context.setPeriodicBoxVectors(Vec3(7, 0, 0), Vec3(0, 3.9, 0), Vec3(0, 0, 9));
-    bool ok = true;
-    try {
-        context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-        ok = false;
-    }
-    catch (exception& ex) {
-    }
-    ASSERT(ok);
-}
-
 void testIdealGas() {
     const int numParticles = 64;
     const int frequency = 10;
@@ -112,7 +74,7 @@ void testIdealGas() {
         system.addParticle(1.0);
         positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
     }
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], true, true, true, frequency);
     system.addForce(barostat);
     
     // Test it for three different temperatures.
@@ -170,7 +132,7 @@ void testIdealGasAxis(int axis) {
         system.addParticle(1.0);
         positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
     }
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency, scaleX, scaleY, scaleZ);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], scaleX, scaleY, scaleZ, frequency);
     system.addForce(barostat);
     
     // Test it for three different temperatures.
@@ -226,7 +188,7 @@ void testRandomSeed() {
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, 1);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, 1);
     system.addForce(barostat);
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
@@ -332,7 +294,7 @@ void testEinsteinCrystal() {
             system.addForce(force);
             system.addForce(nb);
             // Create the barostat.
-            MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pres3[p], pres3[p], pres3[p]), temp, frequency, (a==0||a==3), (a==1||a==3), (a==2||a==3));
+            MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pres3[p], pres3[p], pres3[p]), temp, (a==0||a==3), (a==1||a==3), (a==2||a==3), frequency);
             system.addForce(barostat);
             barostat->setTemperature(temp);
             LangevinIntegrator integrator(temp, 0.1, 0.01);
@@ -422,7 +384,6 @@ int main(int argc, char* argv[]) {
     try {
         if (argc > 1)
             platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
-        testChangingBoxSize();
         testIdealGas();
         testIdealGasAxis(0);
         testIdealGasAxis(1);

platforms/opencl/include/OpenCLContext.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2011 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -589,7 +589,6 @@ private:
     struct MoleculeGroup;
     class VirtualSiteInfo;
     void findMoleculeGroups();
-    static void tagAtomsInMolecule(int atom, int molecule, std::vector<int>& atomMolecule, std::vector<std::vector<int> >& atomBonds);
     /**
      * Ensure that all molecules marked as "identical" really are identical.  This should be
      * called whenever force field parameters change.  If necessary, it will rebuild the list

platforms/opencl/sharedTarget/CMakeLists.txt

@@ -19,6 +19,6 @@ ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
     SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
 ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_OPENCL_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-msse2 -DOPENMM_OPENCL_BUILDING_SHARED_LIBRARY")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

platforms/opencl/src/OpenCLContext.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -39,6 +39,7 @@
 #include "openmm/Platform.h"
 #include "openmm/System.h"
 #include "openmm/VirtualSite.h"
+#include "openmm/internal/ContextImpl.h"
 #include <algorithm>
 #include <fstream>
 #include <iostream>
@@ -618,15 +619,6 @@ void OpenCLContext::reduceBuffer(OpenCLArray& array, int numBuffers) {
     executeKernel(reduceReal4Kernel, bufferSize, 128);
 }
 
-void OpenCLContext::tagAtomsInMolecule(int atom, int molecule, vector<int>& atomMolecule, vector<vector<int> >& atomBonds) {
-    // Recursively tag atoms as belonging to a particular molecule.
-
-    atomMolecule[atom] = molecule;
-    for (int i = 0; i < (int) atomBonds[atom].size(); i++)
-        if (atomMolecule[atomBonds[atom][i]] == -1)
-            tagAtomsInMolecule(atomBonds[atom][i], molecule, atomMolecule, atomBonds);
-}
-
 /**
  * This class ensures that atom reordering doesn't break virtual sites.
  */
@@ -722,16 +714,14 @@ void OpenCLContext::findMoleculeGroups() {
             }
         }
 
-        // Now tag atoms by which molecule they belong to.
+        // Now identify atoms by which molecule they belong to.
 
-        vector<int> atomMolecule(numAtoms, -1);
-        int numMolecules = 0;
-        for (int i = 0; i < numAtoms; i++)
-            if (atomMolecule[i] == -1)
-                tagAtomsInMolecule(i, numMolecules++, atomMolecule, atomBonds);
-        vector<vector<int> > atomIndices(numMolecules);
-        for (int i = 0; i < numAtoms; i++)
-            atomIndices[atomMolecule[i]].push_back(i);
+        vector<vector<int> > atomIndices = ContextImpl::findMolecules(numAtoms, atomBonds);
+        int numMolecules = atomIndices.size();
+        vector<int> atomMolecule(numAtoms);
+        for (int i = 0; i < (int) atomIndices.size(); i++)
+            for (int j = 0; j < (int) atomIndices[i].size(); j++)
+                atomMolecule[atomIndices[i][j]] = i;
 
         // Construct a description of each molecule.
 

platforms/opencl/tests/CMakeLists.txt

@@ -39,13 +39,13 @@ FOREACH(TEST_PROG ${TEST_PROGS})
         SET(NONBOND_TEST "TestOpenCLNonbondedForce2")
         ADD_EXECUTABLE(${NONBOND_TEST} ${TEST_PROG})
 
-        SET_TARGET_PROPERTIES(${NONBOND_TEST} PROPERTIES COMPILE_FLAGS ${NONBOND_DEFINE_STRING} )
+        SET_TARGET_PROPERTIES(${NONBOND_TEST} PROPERTIES COMPILE_FLAGS "-msse2 ${NONBOND_DEFINE_STRING}" )
         ADD_TEST(${NONBOND_TEST} ${EXECUTABLE_OUTPUT_PATH}/${NONBOND_TEST})
 
         # OBC
 
         SET(DEFINE_STRING "${DEFINE_STRING} -DIMPLICIT_SOLVENT=1")
-        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES COMPILE_FLAGS ${DEFINE_STRING} )
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES COMPILE_FLAGS "-msse2 ${DEFINE_STRING}" )
 
         IF( INCLUDE_SERIALIZATION )
             TARGET_LINK_LIBRARIES(${NONBOND_TEST} ${SHARED_TARGET} ${SHARED_OPENMM_SERIALIZATION} )
@@ -54,6 +54,8 @@ FOREACH(TEST_PROG ${TEST_PROGS})
             TARGET_LINK_LIBRARIES(${NONBOND_TEST} ${SHARED_TARGET})
         ENDIF( INCLUDE_SERIALIZATION )
 
+    ELSE( ${TEST_ROOT} STREQUAL "TestOpenCLGBSAOBCForce2" )
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES COMPILE_FLAGS -msse2)
     ENDIF( ${TEST_ROOT} STREQUAL "TestOpenCLGBSAOBCForce2" )
     ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
     IF (OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)

platforms/opencl/tests/TestOpenCLMonteCarloAnisotropicBarostat.cpp

@@ -53,44 +53,6 @@ using namespace std;
 
 OpenCLPlatform platform;
 
-void testChangingBoxSize() {
-    System system;
-    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 5, 0), Vec3(0, 0, 6));
-    system.addParticle(1.0);
-    NonbondedForce* nb = new NonbondedForce();
-    nb->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nb->setCutoffDistance(2.0);
-    nb->addParticle(1, 0.5, 0.5);
-    system.addForce(nb);
-    LangevinIntegrator integrator(300.0, 1.0, 0.01);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions;
-    positions.push_back(Vec3());
-    context.setPositions(positions);
-    Vec3 x, y, z;
-    context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-    ASSERT_EQUAL_VEC(Vec3(4, 0, 0), x, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 5, 0), y, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 6), z, 0);
-    context.setPeriodicBoxVectors(Vec3(7, 0, 0), Vec3(0, 8, 0), Vec3(0, 0, 9));
-    context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-    ASSERT_EQUAL_VEC(Vec3(7, 0, 0), x, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 8, 0), y, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 9), z, 0);
-    
-    // Shrinking the box too small should produce an exception.
-    
-    context.setPeriodicBoxVectors(Vec3(7, 0, 0), Vec3(0, 3.9, 0), Vec3(0, 0, 9));
-    bool ok = true;
-    try {
-        context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-        ok = false;
-    }
-    catch (exception& ex) {
-    }
-    ASSERT(ok);
-}
-
 void testIdealGas() {
     const int numParticles = 64;
     const int frequency = 10;
@@ -112,7 +74,7 @@ void testIdealGas() {
         system.addParticle(1.0);
         positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
     }
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], true, true, true, frequency);
     system.addForce(barostat);
     
     // Test it for three different temperatures.
@@ -170,7 +132,7 @@ void testIdealGasAxis(int axis) {
         system.addParticle(1.0);
         positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
     }
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency, scaleX, scaleY, scaleZ);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], scaleX, scaleY, scaleZ, frequency);
     system.addForce(barostat);
     
     // Test it for three different temperatures.
@@ -226,7 +188,7 @@ void testRandomSeed() {
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, 1);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, 1);
     system.addForce(barostat);
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
@@ -332,7 +294,7 @@ void testEinsteinCrystal() {
             system.addForce(force);
             system.addForce(nb);
             // Create the barostat.
-            MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pres3[p], pres3[p], pres3[p]), temp, frequency, (a==0||a==3), (a==1||a==3), (a==2||a==3));
+            MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pres3[p], pres3[p], pres3[p]), temp, (a==0||a==3), (a==1||a==3), (a==2||a==3), frequency);
             system.addForce(barostat);
             barostat->setTemperature(temp);
             LangevinIntegrator integrator(temp, 0.1, 0.01);
@@ -422,7 +384,6 @@ int main(int argc, char* argv[]) {
     try {
         if (argc > 1)
             platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
-        testChangingBoxSize();
         testIdealGas();
         testIdealGasAxis(0);
         testIdealGasAxis(1);

platforms/reference/tests/TestReferenceMonteCarloAnisotropicBarostat.cpp

@@ -51,45 +51,6 @@
 using namespace OpenMM;
 using namespace std;
 
-void testChangingBoxSize() {
-    ReferencePlatform platform;
-    System system;
-    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 5, 0), Vec3(0, 0, 6));
-    system.addParticle(1.0);
-    NonbondedForce* nb = new NonbondedForce();
-    nb->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nb->setCutoffDistance(2.0);
-    nb->addParticle(1, 0.5, 0.5);
-    system.addForce(nb);
-    LangevinIntegrator integrator(300.0, 1.0, 0.01);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions;
-    positions.push_back(Vec3());
-    context.setPositions(positions);
-    Vec3 x, y, z;
-    context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-    ASSERT_EQUAL_VEC(Vec3(4, 0, 0), x, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 5, 0), y, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 6), z, 0);
-    context.setPeriodicBoxVectors(Vec3(7, 0, 0), Vec3(0, 8, 0), Vec3(0, 0, 9));
-    context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-    ASSERT_EQUAL_VEC(Vec3(7, 0, 0), x, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 8, 0), y, 0);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 9), z, 0);
-    
-    // Shrinking the box too small should produce an exception.
-    
-    context.setPeriodicBoxVectors(Vec3(7, 0, 0), Vec3(0, 3.9, 0), Vec3(0, 0, 9));
-    bool ok = true;
-    try {
-        context.getState(State::Forces).getPeriodicBoxVectors(x, y, z);
-        ok = false;
-    }
-    catch (exception& ex) {
-    }
-    ASSERT(ok);
-}
-
 void testIdealGas() {
     const int numParticles = 64;
     const int frequency = 10;
@@ -112,7 +73,7 @@ void testIdealGas() {
         system.addParticle(1.0);
         positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
     }
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], true, true, true, frequency);
     system.addForce(barostat);
     
     // Test it for three different temperatures.
@@ -171,7 +132,7 @@ void testIdealGasAxis(int axis) {
         system.addParticle(1.0);
         positions[i] = Vec3(initialLength*genrand_real2(sfmt), 0.5*initialLength*genrand_real2(sfmt), 2*initialLength*genrand_real2(sfmt));
     }
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], frequency, scaleX, scaleY, scaleZ);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], scaleX, scaleY, scaleZ, frequency);
     system.addForce(barostat);
     
     // Test it for three different temperatures.
@@ -228,7 +189,7 @@ void testRandomSeed() {
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
-    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, 1);
+    MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, 1);
     system.addForce(barostat);
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
@@ -335,7 +296,7 @@ void testEinsteinCrystal() {
             system.addForce(force);
             system.addForce(nb);
             // Create the barostat.
-            MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pres3[p], pres3[p], pres3[p]), temp, frequency, (a==0||a==3), (a==1||a==3), (a==2||a==3));
+            MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pres3[p], pres3[p], pres3[p]), temp, (a==0||a==3), (a==1||a==3), (a==2||a==3), frequency);
             system.addForce(barostat);
             barostat->setTemperature(temp);
             LangevinIntegrator integrator(temp, 0.1, 0.01);

plugins/drude/platforms/opencl/CMakeLists.txt

@@ -113,7 +113,7 @@ ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}OpenCL_d optimized ${OPENMM_LIBRARY_NAME}OpenCL)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_DRUDE_TARGET} optimized ${SHARED_DRUDE_TARGET})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-msse2 -DOPENMM_BUILDING_SHARED_LIBRARY")
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 # Ensure that links to the main OpenCL library will be resolved.

plugins/rpmd/platforms/opencl/CMakeLists.txt

@@ -112,7 +112,7 @@ ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${OPENMM_LIBRARY_NAME}OpenCL_d optimized ${OPENMM_LIBRARY_NAME}OpenCL)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_RPMD_TARGET} optimized ${SHARED_RPMD_TARGET})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-msse2 -DOPENMM_BUILDING_SHARED_LIBRARY")
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 # Ensure that links to the main OpenCL library will be resolved.

tests/TestFindMolecules.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/Platform.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+void testFindMolecules() {
+    const int numMolecules = 5;
+    const int moleculeSize[] = {1, 10, 100, 1000, 10000};
+    vector<int> particleMolecule;
+    System system;
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    system.addForce(bonds);
+    for (int i = 0; i < numMolecules; i++)
+        for (int j = 0; j < moleculeSize[i]; j++) {
+            int index = system.addParticle(1.0);
+            particleMolecule.push_back(i);
+            if (j > 0)
+                bonds->addBond(index, index-1, 1.0, 1.0);
+        }
+    VerletIntegrator integrator(1.0);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+    ContextImpl* contextImpl = *reinterpret_cast<ContextImpl**>(&context);
+    const vector<vector<int> >& molecules = contextImpl->getMolecules();
+    ASSERT_EQUAL(numMolecules, molecules.size());
+    for (int i = 0; i < numMolecules; i++) {
+        ASSERT_EQUAL(moleculeSize[i], molecules[i].size());
+        for (int j = 0; j < moleculeSize[i]; j++)
+            ASSERT_EQUAL(particleMolecule[molecules[i][j]], i);
+    }
+}
+
+int main() {
+    try {
+        testFindMolecules();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

wrappers/python/CMakeLists.txt

@@ -21,8 +21,25 @@ set(STAGING_OUTPUT_FILES "") # Will contain all required package files
 file(GLOB STAGING_INPUT_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}"
     "${CMAKE_CURRENT_SOURCE_DIR}/MANIFEST.in"
     "${CMAKE_CURRENT_SOURCE_DIR}/README.txt"
-    "${CMAKE_CURRENT_SOURCE_DIR}/*.py"
+    "${CMAKE_CURRENT_SOURCE_DIR}/filterPythonFiles.py"
 )
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup.py ${OPENMM_PYTHON_STAGING_DIR}/setup.py)
+
+###########################################################
+### Check the git revision of the source, and write it  ###
+### to a python file in the in the staging directory    ###
+###########################################################
+execute_process(
+  COMMAND git rev-parse HEAD
+  WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+  OUTPUT_VARIABLE rev_hash_str
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+  ERROR_QUIET
+)
+if(NOT rev_hash_str)
+  set(rev_hash_str "Unknown")
+endif()
+file(WRITE "${OPENMM_PYTHON_STAGING_DIR}/simtk/openmm/version.py" "git_revision = '${rev_hash_str}'\n")
 
 # file(GLOB_RECURSE temp RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}/src/*.i")
 # foreach(f ${temp})

wrappers/python/setup.py

@@ -6,15 +6,18 @@ setup.py: Used for building python wrappers for Simbios' OpenMM library.
 __author__ = "Randall J. Radmer"
 __version__ = "1.0"
 
-
-import os, sys, platform, glob, shutil
-import struct
-
+import ast
+import re
+import os
+import sys
+import platform
 from distutils.core import setup
 
-MAJOR_VERSION_NUM='5'
-MINOR_VERSION_NUM='1'
-BUILD_INFO='0'
+MAJOR_VERSION_NUM='@OPENMM_MAJOR_VERSION@'
+MINOR_VERSION_NUM='@OPENMM_MINOR_VERSION@'
+BUILD_INFO='@OPENMM_BUILD_VERSION@'
+IS_RELEASED = False
+
 
 def reportError(message):
     sys.stdout.write("ERROR: ")
@@ -64,6 +67,57 @@ def uninstall(verbose=True):
     sys.path=save_path
 
 
+def writeVersionPy(filename="simtk/openmm/version.py", major_version_num=MAJOR_VERSION_NUM,
+                     minor_version_num=MINOR_VERSION_NUM, build_info=BUILD_INFO):
+    """Write a version.py file into the python source directory before installation.
+    If a version.py file already exists, we assume that it contains only the git_revision
+    information, since from within this python session in the python staging directory, we're
+    not in the version controlled directory hierarchy.
+
+    When cmake is copying files into the PYTHON_STAGING_DIRECTORY, it will write the
+    git revision to version.py. We read that, and then overwrite it.
+    """
+
+    cnt = """
+# THIS FILE IS GENERATED FROM OPENMM SETUP.PY
+short_version = '%(version)s'
+version = '%(version)s'
+full_version = '%(full_version)s'
+git_revision = '%(git_revision)s'
+release = %(isrelease)s
+
+if not release:
+    version = full_version
+"""
+
+    if os.path.exists(filename):
+        # git_revision is written to the file by cmake
+        with open(filename) as f:
+            text = f.read()
+            match = re.search(r"git_revision\s+=\s+(.*)", text, re.MULTILINE)
+        try:
+            git_revision = ast.literal_eval(match.group(1))
+        except:
+            # except anything, including no re match or
+            # literal_eval failing
+            git_revision = 'Unknown'
+    else:
+        git_revision = 'Unknown'
+
+    version = full_version = '%s.%s.%s' % (major_version_num, minor_version_num, build_info)
+    if not IS_RELEASED:
+        full_version += '.dev-' + git_revision[:7]
+
+    a = open(filename, 'w')
+    try:
+        a.write(cnt % {'version': version,
+                       'full_version' : full_version,
+                       'git_revision' : git_revision,
+                       'isrelease': str(IS_RELEASED)})
+    finally:
+        a.close()
+
+
 def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                            minor_version_num=MINOR_VERSION_NUM,
                            build_info=BUILD_INFO):
@@ -184,6 +238,7 @@ def main():
         uninstall()
     except:
         pass
+    writeVersionPy()
     setupKeywords=buildKeywordDictionary()
     setup(**setupKeywords)
 

wrappers/python/simtk/openmm/app/data/swm4ndp.xml

+<ForceField>
+ <AtomTypes>
+  <Type name="swm4ndp-O" class="OW" element="O" mass="15.59943"/>
+  <Type name="swm4ndp-H" class="HW" element="H" mass="1.007947"/>
+  <Type name="swm4ndp-M" class="MW" mass="0"/>
+  <Type name="swm4ndp-OD" class="OWD" mass="0.4"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="HOH">
+   <Atom name="O" type="swm4ndp-O"/>
+   <Atom name="H1" type="swm4ndp-H"/>
+   <Atom name="H2" type="swm4ndp-H"/>
+   <Atom name="M" type="swm4ndp-M"/>
+   <Atom name="OD" type="swm4ndp-OD"/>
+   <VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
+   <Bond from="0" to="1"/>
+   <Bond from="0" to="2"/>
+  </Residue>
+ </Residues>
+ <HarmonicBondForce>
+  <Bond class1="OW" class2="HW" length="0.09572" k="462750.4"/>
+ </HarmonicBondForce>
+ <HarmonicAngleForce>
+  <Angle class1="HW" class2="OW" class3="HW" angle="1.82421813418" k="836.8"/>
+ </HarmonicAngleForce>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+  <Atom type="swm4ndp-O" charge="1.71636" sigma="0.318395" epsilon="0.882573"/>
+  <Atom type="swm4ndp-H" charge="0.55733" sigma="1" epsilon="0"/>
+  <Atom type="swm4ndp-M" charge="-1.11466" sigma="1" epsilon="0"/>
+  <Atom type="swm4ndp-OD" charge="-1.71636" sigma="1" epsilon="0"/>
+ </NonbondedForce>
+ <DrudeForce>
+  <Particle type1="swm4ndp-OD" type2="swm4ndp-O" charge="-1.71636" polarizability="7.040850e-6" thole="1.3"/>
+ </DrudeForce>
+</ForceField>
+

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

@@ -323,7 +323,7 @@ class ForceField(object):
                             template = t
                             break
                 if matches is None:
-                    raise ValueError('No template found for residue %d (%s).  This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.' % (res.index+1, res.name))
+                    raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
                 for atom, match in zip(res.atoms(), matches):
                     data.atomType[atom] = template.atoms[match].type
                     for site in template.virtualSites:
@@ -461,19 +461,24 @@ class ForceField(object):
         return sys
 
 
-def _createResidueSignature(elements):
-    """Create a signature for a residue based on the elements of the atoms it contains."""
+def _countResidueAtoms(elements):
+    """Count the number of atoms of each element in a residue."""
     counts = {}
     for element in elements:
-        if element is None:
-            pass # This residue contains "atoms" (probably virtual sites) that should match any element
-        elif element in counts:
+        if element in counts:
             counts[element] += 1
         else:
             counts[element] = 1
+    return counts
+
+
+def _createResidueSignature(elements):
+    """Create a signature for a residue based on the elements of the atoms it contains."""
+    counts = _countResidueAtoms(elements)
     sig = []
     for c in counts:
-        sig.append((c, counts[c]))
+        if c is not None:
+            sig.append((c, counts[c]))
     sig.sort(key=lambda x: -x[0].mass)
 
     # Convert it to a string.
@@ -539,6 +544,67 @@ def _findAtomMatches(atoms, template, bondedTo, externalBonds, matches, hasMatch
     return False
 
 
+def _findMatchErrors(forcefield, res):
+    """Try to guess why a residue failed to match any template and return an error message."""
+    residueCounts = _countResidueAtoms([atom.element for atom in res.atoms()])
+    numResidueAtoms = sum(residueCounts.itervalues())
+    numResidueHeavyAtoms = sum(residueCounts[element] for element in residueCounts if element not in (None, elem.hydrogen))
+    
+    # Loop over templates and see how closely each one might match.
+    
+    bestMatchName = None
+    numBestMatchAtoms = 3*numResidueAtoms
+    numBestMatchHeavyAtoms = 2*numResidueHeavyAtoms
+    for templateName in forcefield._templates:
+        template = forcefield._templates[templateName]
+        templateCounts = _countResidueAtoms([atom.element for atom in template.atoms])
+        
+        # Does the residue have any atoms that clearly aren't in the template?
+        
+        if any(element not in templateCounts or templateCounts[element] < residueCounts[element] for element in residueCounts):
+            continue
+        
+        # If there are too many missing atoms, discard this template.
+        
+        numTemplateAtoms = sum(templateCounts.itervalues())
+        numTemplateHeavyAtoms = sum(templateCounts[element] for element in templateCounts if element not in (None, elem.hydrogen))
+        if numTemplateAtoms > numBestMatchAtoms:
+            continue
+        if numTemplateHeavyAtoms > numBestMatchHeavyAtoms:
+            continue
+        
+        # If this template has the same number of missing atoms as our previous best one, look at the name
+        # to decide which one to use.
+        
+        if numTemplateAtoms == numBestMatchAtoms:
+            if bestMatchName == res.name or res.name not in templateName:
+                continue
+        
+        # Accept this as our new best match.
+        
+        bestMatchName = templateName
+        numBestMatchAtoms = numTemplateAtoms
+        numBestMatchHeavyAtoms = numTemplateHeavyAtoms
+        numBestMatchExtraParticles = len([atom for atom in template.atoms if atom.element is None])
+    
+    # Return an appropriate error message.
+    
+    if numBestMatchAtoms == numResidueAtoms:
+        chainLength = len(list(res.chain.residues()))
+        if chainLength > 1 and (res.index == 0 or res.index == chainLength-1):
+            return 'The set of atoms matches %s, but the bonds are different.  Perhaps the chain is missing a terminal group?' % bestMatchName
+        return 'The set of atoms matches %s, but the bonds are different.' % bestMatchName
+    if bestMatchName is not None:
+        if numBestMatchHeavyAtoms == numResidueHeavyAtoms:
+            numResidueExtraParticles = len([atom for atom in res.atoms() if atom.element is None])
+            if numResidueExtraParticles == 0 and numBestMatchExtraParticles == 0:
+                return 'The set of atoms is similar to %s, but it is missing %d hydrogen atoms.' % (bestMatchName, numBestMatchAtoms-numResidueAtoms)
+            if numBestMatchExtraParticles-numResidueExtraParticles == numBestMatchAtoms-numResidueAtoms:
+                return 'The set of atoms is similar to %s, but it is missing %d extra particles.  You can add them with Modeller.addExtraParticles().' % (bestMatchName, numBestMatchAtoms-numResidueAtoms)
+        return 'The set of atoms is similar to %s, but it is missing %d atoms.' % (bestMatchName, numBestMatchAtoms-numResidueAtoms)
+    return 'This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.'
+
+
 # The following classes are generators that know how to create Force subclasses and add them to a System that is being
 # created.  Each generator class must define two methods: 1) a static method that takes an etree Element and a ForceField,
 # and returns the corresponding generator object; 2) a createForce() method that constructs the Force object and adds it

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

@@ -462,6 +462,24 @@ class GromacsTopFile(object):
         topologyAtoms = list(self.topology.atoms())
         exceptions = []
         fudgeQQ = float(self._defaults[4])
+        
+        # Build a lookup table to let us process dihedrals more quickly.
+        
+        dihedralTypeTable = {}
+        for key in self._dihedralTypes:
+            if key[1] != 'X' and key[2] != 'X':
+                if (key[1], key[2]) not in dihedralTypeTable:
+                    dihedralTypeTable[(key[1], key[2])] = []
+                dihedralTypeTable[(key[1], key[2])].append(key)
+                if (key[2], key[1]) not in dihedralTypeTable:
+                    dihedralTypeTable[(key[2], key[1])] = []
+                dihedralTypeTable[(key[2], key[1])].append(key)
+        wildcardDihedralTypes = []
+        for key in self._dihedralTypes:
+            if key[1] == 'X' or key[2] == 'X':
+                wildcardDihedralTypes.append(key)
+                for types in dihedralTypeTable.itervalues():
+                    types.append(key)
 
         # Loop over molecules and create the specified number of each type.
 
@@ -584,7 +602,11 @@ class GromacsTopFile(object):
                     else:
                         # Look for a matching dihedral type.
                         paramsList = None
-                        for key in self._dihedralTypes:
+                        if (types[1], types[2]) in dihedralTypeTable:
+                            dihedralTypes = dihedralTypeTable[(types[1], types[2])]
+                        else:
+                            dihedralTypes = wildcardDihedralTypes
+                        for key in dihedralTypes:
                             if all(a == b or a == 'X' for a, b in zip(key, types)) or all(a == b or a == 'X' for a, b in zip(key, reversedTypes)):
                                 paramsList = self._dihedralTypes[key]
                                 if 'X' not in key:

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

@@ -176,6 +176,8 @@ class Modeller(object):
 
         Parameters:
          - model (string='tip3p') the water model to convert to.  Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
+        
+        @deprecated Use addExtraParticles() instead.  It performs the same function but in a more general way.
         """
         if model in ('tip3p', 'spce'):
             sites = 3
@@ -517,7 +519,7 @@ class Modeller(object):
                     terminal = hydrogen.attrib['terminal']
                 data.hydrogens.append(Modeller._Hydrogen(hydrogen.attrib['name'], hydrogen.attrib['parent'], maxph, atomVariants, terminal))
 
-    def addHydrogens(self, forcefield, pH=7.0, variants=None):
+    def addHydrogens(self, forcefield, pH=7.0, variants=None, platform=None):
         """Add missing hydrogens to the model.
 
         Some residues can exist in multiple forms depending on the pH and properties of the local environment.  These
@@ -564,6 +566,8 @@ class Modeller(object):
          - variants (list=None) an optional list of variants to use.  If this is specified, its length must equal the number
            of residues in the model.  variants[i] is the name of the variant to use for residue i (indexed starting at 0).
            If an element is None, the standard rules will be followed to select a variant for that residue.
+         - platform (Platform=None) the Platform to use when computing the hydrogen atom positions.  If this is None,
+           the default Platform will be used.
         Returns: a list of what variant was actually selected for each residue, in the same format as the variants parameter
         """
         # Check the list of variants.
@@ -757,9 +761,10 @@ class Modeller(object):
             if atoms[i].element != elem.hydrogen:
                 # This is a heavy atom, so make it immobile.
                 system.setParticleMass(i, 0)
-        from simtk.openmm import Platform
-        plt = Platform.getPlatformByName('Reference')
-        context = Context(system, VerletIntegrator(0.0), plt)
+        if platform is None:
+            context = Context(system, VerletIntegrator(0.0))
+        else:
+            context = Context(system, VerletIntegrator(0.0), platform)
         context.setPositions(newPositions)
         LocalEnergyMinimizer.minimize(context)
         self.topology = newTopology