Merge branch 'master' of github.com:pandegroup/openmm into genpt

plugins/amoeba/platforms/reference/CMakeLists.txt

@@ -75,6 +75,6 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
     SUBDIRS (tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)

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

@@ -6317,7 +6317,7 @@ RealOpenMM AmoebaReferencePmeMultipoleForce::calculatePmeSelfEnergy(const vector
         cii += particleI.charge*particleI.charge;
 
         RealVec dipole(particleI.sphericalDipole[1], particleI.sphericalDipole[2], particleI.sphericalDipole[0]);
-        dii += dipole.dot(dipole + (_inducedDipole[ii] + _inducedDipolePolar[ii])*0.5);
+        dii += dipole.dot(dipole + (_inducedDipole[ii]+_inducedDipolePolar[ii])*0.5);
 
         qii += (particleI.sphericalQuadrupole[0]*particleI.sphericalQuadrupole[0]
                +particleI.sphericalQuadrupole[1]*particleI.sphericalQuadrupole[1]

plugins/cpupme/src/CpuPmeKernels.cpp

@@ -49,7 +49,7 @@ static const int PME_ORDER = 5;
 bool CpuCalcPmeReciprocalForceKernel::hasInitializedThreads = false;
 int CpuCalcPmeReciprocalForceKernel::numThreads = 0;
 
-static void spreadCharge(int start, int end, float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
+static void spreadCharge(float* posq, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors, gmx_atomic_t& atomicCounter) {
     float temp[4];
     fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0);
     fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0);
@@ -64,7 +64,11 @@ static void spreadCharge(int start, int end, float* posq, float* grid, int gridx
     const float epsilonFactor = sqrt(ONE_4PI_EPS0);
     memset(grid, 0, sizeof(float)*gridx*gridy*gridz);
 
-    for (int i = start; i < end; i++) {
+    while (true) {
+        int i = gmx_atomic_fetch_add(&atomicCounter, 1);
+        if (i >= numParticles)
+            break;
+
         // Find the position relative to the nearest grid point.
 
         fvec4 pos(&posq[4*i]);
@@ -225,25 +229,15 @@ static double reciprocalEnergy(int start, int end, fftwf_complex* grid, int grid
     return 0.5*energy;
 }
 
-static void reciprocalConvolution(int start, int end, fftwf_complex* grid, int gridx, int gridy, int gridz, vector<float>& recipEterm) {
-    const unsigned int zsize = gridz/2+1;
-    const unsigned int yzsize = gridy*zsize;
-
-    int firstz = (start == 0 ? 1 : 0);
-    for (int kx = start; kx < end; kx++) {
-        for (int ky = 0; ky < gridy; ky++) {
-            for (int kz = firstz; kz < zsize; kz++) {
-                int index = kx*yzsize + ky*zsize + kz;
-                float eterm = recipEterm[index];
-                grid[index][0] *= eterm;
-                grid[index][1] *= eterm;
-            }
-            firstz = 0;
-        }
+static void reciprocalConvolution(int start, int end, fftwf_complex* grid, vector<float>& recipEterm) {
+    for (int index = start; index < end; index++) {
+        float eterm = recipEterm[index];
+        grid[index][0] *= eterm;
+        grid[index][1] *= eterm;
     }
 }
 
-static void interpolateForces(int start, int end, float* posq, float* force, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors) {
+static void interpolateForces(float* posq, float* force, float* grid, int gridx, int gridy, int gridz, int numParticles, Vec3* periodicBoxVectors, Vec3* recipBoxVectors, gmx_atomic_t& atomicCounter) {
     fvec4 boxSize((float) periodicBoxVectors[0][0], (float) periodicBoxVectors[1][1], (float) periodicBoxVectors[2][2], 0);
     fvec4 invBoxSize((float) recipBoxVectors[0][0], (float) recipBoxVectors[1][1], (float) recipBoxVectors[2][2], 0);
     fvec4 recipBoxVec0((float) recipBoxVectors[0][0], (float) recipBoxVectors[0][1], (float) recipBoxVectors[0][2], 0);
@@ -254,7 +248,11 @@ static void interpolateForces(int start, int end, float* posq, float* force, flo
     fvec4 one(1);
     fvec4 scale(1.0f/(PME_ORDER-1));
     const float epsilonFactor = sqrt(ONE_4PI_EPS0);
-    for (int i = start; i < end; i++) {
+    while (true) {
+        int i = gmx_atomic_fetch_add(&atomicCounter, 1);
+        if (i >= numParticles)
+            break;
+
         // Find the position relative to the nearest grid point.
         
         fvec4 pos(&posq[4*i]);
@@ -485,6 +483,7 @@ void CpuCalcPmeReciprocalForceKernel::runMainThread() {
             break;
         posq = io->getPosq();
         ComputeTask task(*this);
+        gmx_atomic_set(&atomicCounter, 0);
         threads.execute(task); // Signal threads to perform charge spreading.
         threads.waitForThreads();
         threads.resumeThreads(); // Signal threads to sum the charge grids.
@@ -503,6 +502,7 @@ void CpuCalcPmeReciprocalForceKernel::runMainThread() {
         threads.resumeThreads(); // Signal threads to perform reciprocal convolution.
         threads.waitForThreads();
         fftwf_execute_dft_c2r(backwardFFT, complexGrid, realGrid);
+        gmx_atomic_set(&atomicCounter, 0);
         threads.resumeThreads(); // Signal threads to interpolate forces.
         threads.waitForThreads();
         isFinished = true;
@@ -515,14 +515,15 @@ void CpuCalcPmeReciprocalForceKernel::runMainThread() {
 }
 
 void CpuCalcPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int index) {
-    int particleStart = (index*numParticles)/numThreads;
-    int particleEnd = ((index+1)*numParticles)/numThreads;
     int gridxStart = (index*gridx)/numThreads;
     int gridxEnd = ((index+1)*gridx)/numThreads;
     int gridSize = (gridx*gridy*gridz+3)/4;
     int gridStart = 4*((index*gridSize)/numThreads);
     int gridEnd = 4*(((index+1)*gridSize)/numThreads);
-    spreadCharge(particleStart, particleEnd, posq, tempGrid[index], gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors);
+    int complexSize = gridx*gridy*(gridz/2+1);
+    int complexStart = max(1, ((index*complexSize)/numThreads));
+    int complexEnd = (((index+1)*complexSize)/numThreads);
+    spreadCharge(posq, tempGrid[index], gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter);
     threads.syncThreads();
     int numGrids = tempGrid.size();
     for (int i = gridStart; i < gridEnd; i += 4) {
@@ -540,9 +541,9 @@ void CpuCalcPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int i
         threadEnergy[index] = reciprocalEnergy(gridxStart, gridxEnd, complexGrid, gridx, gridy, gridz, alpha, bsplineModuli, periodicBoxVectors, recipBoxVectors);
         threads.syncThreads();
     }
-    reciprocalConvolution(gridxStart, gridxEnd, complexGrid, gridx, gridy, gridz, recipEterm);
+    reciprocalConvolution(complexStart, complexEnd, complexGrid, recipEterm);
     threads.syncThreads();
-    interpolateForces(particleStart, particleEnd, posq, &force[0], realGrid, gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors);
+    interpolateForces(posq, &force[0], realGrid, gridx, gridy, gridz, numParticles, periodicBoxVectors, recipBoxVectors, atomicCounter);
 }
 
 void CpuCalcPmeReciprocalForceKernel::beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy) {

plugins/cpupme/src/CpuPmeKernels.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) 2013-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,6 +36,7 @@
 #include "internal/windowsExportPme.h"
 #include "openmm/kernels.h"
 #include "openmm/Vec3.h"
+#include "openmm/internal/gmx_atomic.h"
 #include "openmm/internal/ThreadPool.h"
 #include <fftw3.h>
 #include <pthread.h>
@@ -130,6 +131,7 @@ private:
     float* posq;
     Vec3 periodicBoxVectors[3], recipBoxVectors[3];
     bool includeEnergy;
+    gmx_atomic_t atomicCounter;
 };
 
 } // namespace OpenMM

plugins/drude/CMakeLists.txt

@@ -145,6 +145,6 @@ ENDIF (EXECUTABLE_OUTPUT_PATH)
 
 #INCLUDE(ApiDoxygen.cmake)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)
     ADD_SUBDIRECTORY(serialization/tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)

plugins/drude/openmmapi/include/openmm/DrudeForce.h

@@ -44,7 +44,7 @@ namespace OpenMM {
  * it applies: an anisotropic harmonic force connecting each Drude particle to its parent particle; and
  * a screened Coulomb interaction between specific pairs of dipoles.  The latter is typically used between
  * closely bonded particles whose Coulomb interaction would otherwise be fully excluded.
- * 
+ *
  * To use this class, create a DrudeForce object, then call addParticle() once for each Drude particle in the
  * System to define its parameters.  After a particle has been added, you can modify its force field parameters
  * by calling setParticleParameters().  This will have no effect on Contexts that already exist unless you
@@ -91,19 +91,19 @@ public:
     /**
      * Get the parameters for a Drude particle.
      *
-     * @param index           the index of the Drude particle for which to get parameters
-     * @param particle        the index within the System of the Drude particle
-     * @param particle1       the index within the System of the particle to which the Drude particle is attached
-     * @param particle2       the index within the System of the second particle used for defining anisotropic polarizability.
-     *                        This may be set to -1, in which case aniso12 will be ignored.
-     * @param particle3       the index within the System of the third particle used for defining anisotropic polarizability.
-     *                        This may be set to -1, in which case aniso34 will be ignored.
-     * @param particle4       the index within the System of the fourth particle used for defining anisotropic polarizability.
-     *                        This may be set to -1, in which case aniso34 will be ignored.
-     * @param charge          The charge on the Drude particle
-     * @param polarizability  The isotropic polarizability
-     * @param aniso12         The scale factor for the polarizability along the direction defined by particle1 and particle2
-     * @param aniso34         The scale factor for the polarizability along the direction defined by particle3 and particle4
+     * @param index                the index of the Drude particle for which to get parameters
+     * @param[out] particle        the index within the System of the Drude particle
+     * @param[out] particle1       the index within the System of the particle to which the Drude particle is attached
+     * @param[out] particle2       the index within the System of the second particle used for defining anisotropic polarizability.
+     *                             This may be set to -1, in which case aniso12 will be ignored.
+     * @param[out] particle3       the index within the System of the third particle used for defining anisotropic polarizability.
+     *                             This may be set to -1, in which case aniso34 will be ignored.
+     * @param[out] particle4       the index within the System of the fourth particle used for defining anisotropic polarizability.
+     *                             This may be set to -1, in which case aniso34 will be ignored.
+     * @param[out] charge          The charge on the Drude particle
+     * @param[out] polarizability  The isotropic polarizability
+     * @param[out] aniso12         The scale factor for the polarizability along the direction defined by particle1 and particle2
+     * @param[out] aniso34         The scale factor for the polarizability along the direction defined by particle3 and particle4
      */
     void getParticleParameters(int index, int& particle, int& particle1, int& particle2, int& particle3, int& particle4, double& charge, double& polarizability, double& aniso12, double& aniso34) const;
     /**
@@ -135,16 +135,16 @@ public:
     int addScreenedPair(int particle1, int particle2, double thole);
     /**
      * Get the force field parameters for screened pair.
-     * 
-     * @param index      the index of the pair for which to get parameters
-     * @param particle1  the index within this Force of the first particle involved in the interaction
-     * @param particle2  the index within this Force of the second particle involved in the interaction
-     * @param thole      the Thole screening factor
+     *
+     * @param index           the index of the pair for which to get parameters
+     * @param[out] particle1  the index within this Force of the first particle involved in the interaction
+     * @param[out] particle2  the index within this Force of the second particle involved in the interaction
+     * @param[out] thole      the Thole screening factor
      */
     void getScreenedPairParameters(int index, int& particle1, int& particle2, double& thole) const;
     /**
      * Set the force field parameters for screened pair.
-     * 
+     *
      * @param index      the index of the pair for which to get parameters
      * @param particle1  the index within this Force of the first particle involved in the interaction
      * @param particle2  the index within this Force of the second particle involved in the interaction
@@ -156,7 +156,7 @@ public:
      * provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
      * Simply call setParticleParameters() and setScreenedPairParameters() to modify this object's parameters, then call
      * updateParametersInContext() to copy them over to the Context.
-     * 
+     *
      * This method has several limitations.  It can be used to modify the numeric parameters associated with a particle or
      * screened pair (polarizability, thole, etc.), but not the identities of the particles they involve.  It also cannot
      * be used to add new particles or screenedPairs, only to change the parameters of existing ones.

plugins/drude/openmmapi/include/openmm/DrudeLangevinIntegrator.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) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -44,6 +44,10 @@ namespace OpenMM {
  * are not part of a Drude particle pair), as well as to the center of mass of each Drude particle pair.
  * A second thermostat, typically with a much lower temperature, is applied to the relative internal
  * displacement of each pair.
+ *
+ * This integrator can optionally set an upper limit on how far any Drude particle is ever allowed to
+ * get from its parent particle.  This can sometimes help to improve stability.  The limit is enforced
+ * with a hard wall constraint.
  * 
  * This Integrator requires the System to include a DrudeForce, which it uses to identify the Drude
  * particles.
@@ -129,6 +133,16 @@ public:
     void setDrudeFriction(double coeff) {
         drudeFriction = coeff;
     }
+    /**
+     * Get the maximum distance a Drude particle can ever move from its parent particle, measured in nm.  This is implemented
+     * with a hard wall constraint.  If this distance is set to 0 (the default), the hard wall constraint is omitted.
+     */
+    double getMaxDrudeDistance() const;
+    /**
+     * Set the maximum distance a Drude particle can ever move from its parent particle, measured in nm.  This is implemented
+     * with a hard wall constraint.  If this distance is set to 0 (the default), the hard wall constraint is omitted.
+     */
+    void setMaxDrudeDistance(double distance);
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */
@@ -181,7 +195,7 @@ protected:
      */
     double computeKineticEnergy();
 private:
-    double temperature, friction, drudeTemperature, drudeFriction;
+    double temperature, friction, drudeTemperature, drudeFriction, maxDrudeDistance;
     int randomNumberSeed;
     Kernel kernel;
 };

plugins/drude/openmmapi/src/DrudeLangevinIntegrator.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) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -46,11 +46,22 @@ DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double fric
     setFriction(frictionCoeff);
     setDrudeTemperature(drudeTemperature);
     setDrudeFriction(drudeFrictionCoeff);
+    setMaxDrudeDistance(0);
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
     setRandomNumberSeed(0);
 }
 
+double DrudeLangevinIntegrator::getMaxDrudeDistance() const {
+    return maxDrudeDistance;
+}
+
+void DrudeLangevinIntegrator::setMaxDrudeDistance(double distance) {
+    if (distance < 0)
+        throw OpenMMException("setMaxDrudeDistance: Distance cannot be negative");
+    maxDrudeDistance = distance;
+}
+
 void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {
     if (owner != NULL && &contextRef.getOwner() != owner)
         throw OpenMMException("This Integrator is already bound to a context");

plugins/drude/platforms/cuda/src/CudaDrudeKernels.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -279,6 +279,7 @@ void CudaIntegrateDrudeLangevinStepKernel::initialize(const System& system, cons
     CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaDrudeKernelSources::drudeLangevin, defines, "");
     kernel1 = cu.getKernel(module, "integrateDrudeLangevinPart1");
     kernel2 = cu.getKernel(module, "integrateDrudeLangevinPart2");
+    hardwallKernel = cu.getKernel(module, "applyHardWallConstraints");
     prevStepSize = -1.0;
 }
 
@@ -296,6 +297,8 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
     double vscaleDrude = exp(-stepSize*integrator.getDrudeFriction());
     double fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction()/(double) 0x100000000;
     double noisescaleDrude = sqrt(2*BOLTZ*integrator.getDrudeTemperature()*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
+    double maxDrudeDistance = integrator.getMaxDrudeDistance();
+    double hardwallscaleDrude = sqrt(BOLTZ*integrator.getDrudeTemperature());
     if (stepSize != prevStepSize) {
         if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
             double2 ss = make_double2(0, stepSize);
@@ -316,7 +319,9 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
     float vscaleDrudeFloat = (float) vscaleDrude;
     float fscaleDrudeFloat = (float) fscaleDrude;
     float noisescaleDrudeFloat = (float) noisescaleDrude;
-    void *vscalePtr, *fscalePtr, *noisescalePtr, *vscaleDrudePtr, *fscaleDrudePtr, *noisescaleDrudePtr;
+    float maxDrudeDistanceFloat =(float) maxDrudeDistance;
+    float hardwallscaleDrudeFloat = (float) hardwallscaleDrude;
+    void *vscalePtr, *fscalePtr, *noisescalePtr, *vscaleDrudePtr, *fscaleDrudePtr, *noisescaleDrudePtr, *maxDrudeDistancePtr, *hardwallscaleDrudePtr;
     if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
         vscalePtr = &vscale;
         fscalePtr = &fscale;
@@ -324,6 +329,8 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
         vscaleDrudePtr = &vscaleDrude;
         fscaleDrudePtr = &fscaleDrude;
         noisescaleDrudePtr = &noisescaleDrude;
+        maxDrudeDistancePtr = &maxDrudeDistance;
+        hardwallscaleDrudePtr = &hardwallscaleDrude;
     }
     else {
         vscalePtr = &vscaleFloat;
@@ -332,6 +339,8 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
         vscaleDrudePtr = &vscaleDrudeFloat;
         fscaleDrudePtr = &fscaleDrudeFloat;
         noisescaleDrudePtr = &noisescaleDrudeFloat;
+        maxDrudeDistancePtr = &maxDrudeDistanceFloat;
+        hardwallscaleDrudePtr = &hardwallscaleDrudeFloat;
     }
 
     // Call the first integration kernel.
@@ -352,6 +361,12 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
     void* args2[] = {&cu.getPosq().getDevicePointer(), &posCorrection, &integration.getPosDelta().getDevicePointer(),
             &cu.getVelm().getDevicePointer(), &integration.getStepSize().getDevicePointer()};
     cu.executeKernel(kernel2, args2, numAtoms);
+    
+    // Apply hard wall constraints.
+    
+    void* hardwallArgs[] = {&cu.getPosq().getDevicePointer(), &posCorrection, &cu.getVelm().getDevicePointer(),
+            &pairParticles->getDevicePointer(), &integration.getStepSize().getDevicePointer(), maxDrudeDistancePtr, hardwallscaleDrudePtr};
+    cu.executeKernel(hardwallKernel, hardwallArgs, pairParticles->getSize());
     integration.computeVirtualSites();
 
     // Update the time and step count.

plugins/drude/platforms/cuda/src/CudaDrudeKernels.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -113,7 +113,7 @@ private:
     double prevStepSize;
     CudaArray* normalParticles;
     CudaArray* pairParticles;
-    CUfunction kernel1, kernel2;
+    CUfunction kernel1, kernel2, hardwallKernel;
 };
 
 /**

plugins/drude/platforms/cuda/src/kernels/drudeLangevin.cu

@@ -101,3 +101,111 @@ extern "C" __global__ void integrateDrudeLangevinPart2(real4* __restrict__ posq,
         index += blockDim.x*gridDim.x;
     }
 }
+
+/**
+ * Apply hard wall constraints
+ */
+extern "C" __global__ void applyHardWallConstraints(real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ velm,
+        const int2* __restrict__ pairParticles, const mixed2* __restrict__ dt, mixed maxDrudeDistance, mixed hardwallscaleDrude) {
+    mixed stepSize = dt[0].y;
+    for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_PAIRS; i += blockDim.x*gridDim.x) {
+        int2 particles = pairParticles[i];
+#ifdef USE_MIXED_PRECISION
+        real4 posReal1 = posq[particles.x];
+        real4 posReal2 = posq[particles.y];
+        real4 posCorr1 = posqCorrection[particles.x];
+        real4 posCorr2 = posqCorrection[particles.y];
+        mixed4 pos1 = make_mixed4(posReal1.x+(mixed)posCorr1.x, posReal1.y+(mixed)posCorr1.y, posReal1.z+(mixed)posCorr1.z, posReal1.w);
+        mixed4 pos2 = make_mixed4(posReal2.x+(mixed)posCorr2.x, posReal2.y+(mixed)posCorr2.y, posReal2.z+(mixed)posCorr2.z, posReal2.w);
+#else
+        mixed4 pos1 = posq[particles.x];
+        mixed4 pos2 = posq[particles.y];
+#endif
+        mixed4 delta = pos1-pos2;
+        mixed r = SQRT(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
+        mixed rInv = RECIP(r);
+        if (rInv*maxDrudeDistance < 1) {
+            // The constraint has been violated, so make the inter-particle distance "bounce"
+            // off the hard wall.
+
+            mixed4 bondDir = delta*rInv;
+            mixed4 vel1 = velm[particles.x];
+            mixed4 vel2 = velm[particles.y];
+            mixed mass1 = RECIP(vel1.w);
+            mixed mass2 = RECIP(vel2.w);
+            mixed deltaR = r-maxDrudeDistance;
+            mixed deltaT = stepSize;
+            mixed dotvr1 = vel1.x*bondDir.x + vel1.y*bondDir.y + vel1.z*bondDir.z;
+            mixed4 vb1 = bondDir*dotvr1;
+            mixed4 vp1 = vel1-vb1;
+            if (vel2.w == 0) {
+                // The parent particle is massless, so move only the Drude particle.
+
+                if (dotvr1 != 0)
+                    deltaT = deltaR/fabs(dotvr1);
+                if (deltaT > stepSize)
+                    deltaT = stepSize;
+                dotvr1 = -dotvr1*hardwallscaleDrude/(fabs(dotvr1)*SQRT(mass1));
+                mixed dr = -deltaR + deltaT*dotvr1;
+                pos1.x += bondDir.x*dr;
+                pos1.y += bondDir.y*dr;
+                pos1.z += bondDir.z*dr;
+#ifdef USE_MIXED_PRECISION
+                posq[particles.x] = make_real4((real) pos1.x, (real) pos1.y, (real) pos1.z, (real) pos1.w);
+                posqCorrection[particles.x] = make_real4(pos1.x-(real) pos1.x, pos1.y-(real) pos1.y, pos1.z-(real) pos1.z, 0);
+#else
+                posq[particles.x] = pos1;
+#endif
+                vel1.x = vp1.x + bondDir.x*dotvr1;
+                vel1.y = vp1.y + bondDir.y*dotvr1;
+                vel1.z = vp1.z + bondDir.z*dotvr1;
+                velm[particles.x] = vel1;
+            }
+            else {
+                // Move both particles.
+
+                mixed invTotalMass = RECIP(mass1+mass2);
+                mixed dotvr2 = vel2.x*bondDir.x + vel2.y*bondDir.y + vel2.z*bondDir.z;
+                mixed4 vb2 = bondDir*dotvr2;
+                mixed4 vp2 = vel2-vb2;
+                mixed vbCMass = (mass1*dotvr1 + mass2*dotvr2)*invTotalMass;
+                dotvr1 -= vbCMass;
+                dotvr2 -= vbCMass;
+                if (dotvr1 != dotvr2)
+                    deltaT = deltaR/fabs(dotvr1-dotvr2);
+                if (deltaT > stepSize)
+                    deltaT = stepSize;
+                mixed vBond = hardwallscaleDrude/SQRT(mass1);
+                dotvr1 = -dotvr1*vBond*mass2*invTotalMass/fabs(dotvr1);
+                dotvr2 = -dotvr2*vBond*mass1*invTotalMass/fabs(dotvr2);
+                mixed dr1 = -deltaR*mass2*invTotalMass + deltaT*dotvr1;
+                mixed dr2 = deltaR*mass1*invTotalMass + deltaT*dotvr2;
+                dotvr1 += vbCMass;
+                dotvr2 += vbCMass;
+                pos1.x += bondDir.x*dr1;
+                pos1.y += bondDir.y*dr1;
+                pos1.z += bondDir.z*dr1;
+                pos2.x += bondDir.x*dr2;
+                pos2.y += bondDir.y*dr2;
+                pos2.z += bondDir.z*dr2;
+#ifdef USE_MIXED_PRECISION
+                posq[particles.x] = make_real4((real) pos1.x, (real) pos1.y, (real) pos1.z, (real) pos1.w);
+                posq[particles.y] = make_real4((real) pos2.x, (real) pos2.y, (real) pos2.z, (real) pos2.w);
+                posqCorrection[particles.x] = make_real4(pos1.x-(real) pos1.x, pos1.y-(real) pos1.y, pos1.z-(real) pos1.z, 0);
+                posqCorrection[particles.y] = make_real4(pos2.x-(real) pos2.x, pos2.y-(real) pos2.y, pos2.z-(real) pos2.z, 0);
+#else
+                posq[particles.x] = pos1;
+                posq[particles.y] = pos2;
+#endif
+                vel1.x = vp1.x + bondDir.x*dotvr1;
+                vel1.y = vp1.y + bondDir.y*dotvr1;
+                vel1.z = vp1.z + bondDir.z*dotvr1;
+                vel2.x = vp2.x + bondDir.x*dotvr2;
+                vel2.y = vp2.y + bondDir.y*dotvr2;
+                vel2.z = vp2.z + bondDir.z*dotvr2;
+                velm[particles.x] = vel1;
+                velm[particles.y] = vel2;
+            }
+        }
+    }
+}

plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -60,6 +60,7 @@ void testSinglePair() {
     const double mass2 = 0.1;
     const double totalMass = mass1+mass2;
     const double reducedMass = (mass1*mass2)/(mass1+mass2);
+    const double maxDistance = 0.05;
     System system;
     system.addParticle(mass1);
     system.addParticle(mass2);
@@ -70,6 +71,7 @@ void testSinglePair() {
     positions[0] = Vec3(0, 0, 0);
     positions[1] = Vec3(0, 0, 0);
     DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
+    integ.setMaxDrudeDistance(maxDistance);
     Platform& platform = Platform::getPlatformByName("CUDA");
     Context context(system, integ, platform);
     context.setPositions(positions);
@@ -84,12 +86,15 @@ void testSinglePair() {
     int numSteps = 10000;
     for (int i = 0; i < numSteps; i++) {
         integ.step(10);
-        State state = context.getState(State::Velocities);
+        State state = context.getState(State::Velocities | State::Positions);
         const vector<Vec3>& vel = state.getVelocities();
         Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
         keCM += 0.5*totalMass*velCM.dot(velCM);
         Vec3 velInternal = vel[0]-vel[1];
         keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
+        Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
+        double distance = sqrt(delta.dot(delta));
+        ASSERT(distance <= maxDistance*(1+1e-6));
     }
     ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
     ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);

plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -284,6 +284,7 @@ void OpenCLIntegrateDrudeLangevinStepKernel::initialize(const System& system, co
     cl::Program program = cl.createProgram(OpenCLDrudeKernelSources::drudeLangevin, defines, "");
     kernel1 = cl::Kernel(program, "integrateDrudeLangevinPart1");
     kernel2 = cl::Kernel(program, "integrateDrudeLangevinPart2");
+    hardwallKernel = cl::Kernel(program, "applyHardWallConstraints");
     prevStepSize = -1.0;
 }
 
@@ -307,6 +308,14 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
         kernel2.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
         kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
         kernel2.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
+        hardwallKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
+        if (cl.getUseMixedPrecision())
+            hardwallKernel.setArg<cl::Buffer>(1, cl.getPosqCorrection().getDeviceBuffer());
+        else
+            hardwallKernel.setArg<void*>(1, NULL);
+        hardwallKernel.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
+        hardwallKernel.setArg<cl::Buffer>(3, pairParticles->getDeviceBuffer());
+        hardwallKernel.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
     }
     
     // Compute integrator coefficients.
@@ -318,6 +327,8 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
     double vscaleDrude = exp(-stepSize*integrator.getDrudeFriction());
     double fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction();
     double noisescaleDrude = sqrt(2*BOLTZ*integrator.getDrudeTemperature()*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
+    double maxDrudeDistance = integrator.getMaxDrudeDistance();
+    double hardwallscaleDrude = sqrt(BOLTZ*integrator.getDrudeTemperature());
     if (stepSize != prevStepSize) {
         if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
             mm_double2 ss = mm_double2(0, stepSize);
@@ -336,6 +347,8 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
             kernel1.setArg<cl_double>(9, vscaleDrude);
             kernel1.setArg<cl_double>(10, fscaleDrude);
             kernel1.setArg<cl_double>(11, noisescaleDrude);
+            hardwallKernel.setArg<cl_double>(5, maxDrudeDistance);
+            hardwallKernel.setArg<cl_double>(6, hardwallscaleDrude);
     }
     else {
             kernel1.setArg<cl_float>(6, (cl_float) vscale);
@@ -344,6 +357,8 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
             kernel1.setArg<cl_float>(9, (cl_float) vscaleDrude);
             kernel1.setArg<cl_float>(10, (cl_float) fscaleDrude);
             kernel1.setArg<cl_float>(11, (cl_float) noisescaleDrude);
+            hardwallKernel.setArg<cl_float>(5, (cl_float) maxDrudeDistance);
+            hardwallKernel.setArg<cl_float>(6, (cl_float) hardwallscaleDrude);
     }
 
     // Call the first integration kernel.
@@ -358,6 +373,10 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
     // Call the second integration kernel.
 
     cl.executeKernel(kernel2, numAtoms);
+    
+    // Apply hard wall constraints.
+    
+    cl.executeKernel(hardwallKernel, pairParticles->getSize());
     integration.computeVirtualSites();
 
     // Update the time and step count.

plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -114,7 +114,7 @@ private:
     double prevStepSize;
     OpenCLArray* normalParticles;
     OpenCLArray* pairParticles;
-    cl::Kernel kernel1, kernel2;
+    cl::Kernel kernel1, kernel2, hardwallKernel;
 };
 
 /**

plugins/drude/platforms/opencl/src/kernels/drudeLangevin.cl

@@ -101,3 +101,99 @@ __kernel void integrateDrudeLangevinPart2(__global real4* restrict posq, __globa
         index += get_global_size(0);
     }
 }
+
+/**
+ * Apply hard wall constraints
+ */
+__kernel void applyHardWallConstraints(__global real4* restrict posq, __global real4* restrict posqCorrection, __global mixed4* restrict velm,
+        __global const int2* restrict pairParticles, __global const mixed2* restrict dt, mixed maxDrudeDistance, mixed hardwallscaleDrude) {
+    mixed stepSize = dt[0].y;
+    for (int i = get_global_id(0); i < NUM_PAIRS; i += get_global_size(0)) {
+        int2 particles = pairParticles[i];
+#ifdef USE_MIXED_PRECISION
+        real4 posReal1 = posq[particles.x];
+        real4 posReal2 = posq[particles.y];
+        real4 posCorr1 = posqCorrection[particles.x];
+        real4 posCorr2 = posqCorrection[particles.y];
+        mixed4 pos1 = (mixed4) (posReal1.x+(mixed)posCorr1.x, posReal1.y+(mixed)posCorr1.y, posReal1.z+(mixed)posCorr1.z, posReal1.w);
+        mixed4 pos2 = (mixed4) (posReal2.x+(mixed)posCorr2.x, posReal2.y+(mixed)posCorr2.y, posReal2.z+(mixed)posCorr2.z, posReal2.w);
+#else
+        mixed4 pos1 = posq[particles.x];
+        mixed4 pos2 = posq[particles.y];
+#endif
+        mixed4 delta = pos1-pos2;
+        mixed r = sqrt(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
+        mixed rInv = 1/r;
+        if (rInv*maxDrudeDistance < 1) {
+            // The constraint has been violated, so make the inter-particle distance "bounce"
+            // off the hard wall.
+
+            mixed4 bondDir = delta*rInv;
+            mixed4 vel1 = velm[particles.x];
+            mixed4 vel2 = velm[particles.y];
+            mixed mass1 = 1/vel1.w;
+            mixed mass2 = 1/vel2.w;
+            mixed deltaR = r-maxDrudeDistance;
+            mixed deltaT = stepSize;
+            mixed dotvr1 = vel1.x*bondDir.x + vel1.y*bondDir.y + vel1.z*bondDir.z;
+            mixed4 vb1 = bondDir*dotvr1;
+            mixed4 vp1 = vel1-vb1;
+            if (vel2.w == 0) {
+                // The parent particle is massless, so move only the Drude particle.
+
+                if (dotvr1 != 0)
+                    deltaT = deltaR/fabs(dotvr1);
+                if (deltaT > stepSize)
+                    deltaT = stepSize;
+                dotvr1 = -dotvr1*hardwallscaleDrude/(fabs(dotvr1)*sqrt(mass1));
+                mixed dr = -deltaR + deltaT*dotvr1;
+                pos1.xyz += bondDir.xyz*dr;
+#ifdef USE_MIXED_PRECISION
+                posq[particles.x] = (real4) ((real) pos1.x, (real) pos1.y, (real) pos1.z, (real) pos1.w);
+                posqCorrection[particles.x] = (real4) (pos1.x-(real) pos1.x, pos1.y-(real) pos1.y, pos1.z-(real) pos1.z, 0);
+#else
+                posq[particles.x] = pos1;
+#endif
+                vel1.xyz = vp1.xyz + bondDir.xyz*dotvr1;
+                velm[particles.x] = vel1;
+            }
+            else {
+                // Move both particles.
+
+                mixed invTotalMass = 1/(mass1+mass2);
+                mixed dotvr2 = vel2.x*bondDir.x + vel2.y*bondDir.y + vel2.z*bondDir.z;
+                mixed4 vb2 = bondDir*dotvr2;
+                mixed4 vp2 = vel2-vb2;
+                mixed vbCMass = (mass1*dotvr1 + mass2*dotvr2)*invTotalMass;
+                dotvr1 -= vbCMass;
+                dotvr2 -= vbCMass;
+                if (dotvr1 != dotvr2)
+                    deltaT = deltaR/fabs(dotvr1-dotvr2);
+                if (deltaT > stepSize)
+                    deltaT = stepSize;
+                mixed vBond = hardwallscaleDrude/sqrt(mass1);
+                dotvr1 = -dotvr1*vBond*mass2*invTotalMass/fabs(dotvr1);
+                dotvr2 = -dotvr2*vBond*mass1*invTotalMass/fabs(dotvr2);
+                mixed dr1 = -deltaR*mass2*invTotalMass + deltaT*dotvr1;
+                mixed dr2 = deltaR*mass1*invTotalMass + deltaT*dotvr2;
+                dotvr1 += vbCMass;
+                dotvr2 += vbCMass;
+                pos1.xyz += bondDir.xyz*dr1;
+                pos2.xyz += bondDir.xyz*dr2;
+#ifdef USE_MIXED_PRECISION
+                posq[particles.x] = (real4) ((real) pos1.x, (real) pos1.y, (real) pos1.z, (real) pos1.w);
+                posq[particles.y] = (real4) ((real) pos2.x, (real) pos2.y, (real) pos2.z, (real) pos2.w);
+                posqCorrection[particles.x] = (real4) (pos1.x-(real) pos1.x, pos1.y-(real) pos1.y, pos1.z-(real) pos1.z, 0);
+                posqCorrection[particles.y] = (real4) (pos2.x-(real) pos2.x, pos2.y-(real) pos2.y, pos2.z-(real) pos2.z, 0);
+#else
+                posq[particles.x] = pos1;
+                posq[particles.y] = pos2;
+#endif
+                vel1.xyz = vp1.xyz + bondDir.xyz*dotvr1;
+                vel2.xyz = vp2.xyz + bondDir.xyz*dotvr2;
+                velm[particles.x] = vel1;
+                velm[particles.y] = vel2;
+            }
+        }
+    }
+}

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -60,6 +60,7 @@ void testSinglePair() {
     const double mass2 = 0.1;
     const double totalMass = mass1+mass2;
     const double reducedMass = (mass1*mass2)/(mass1+mass2);
+    const double maxDistance = 0.05;
     System system;
     system.addParticle(mass1);
     system.addParticle(mass2);
@@ -70,6 +71,7 @@ void testSinglePair() {
     positions[0] = Vec3(0, 0, 0);
     positions[1] = Vec3(0, 0, 0);
     DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
+    integ.setMaxDrudeDistance(maxDistance);
     Platform& platform = Platform::getPlatformByName("OpenCL");
     Context context(system, integ, platform);
     context.setPositions(positions);
@@ -84,12 +86,15 @@ void testSinglePair() {
     int numSteps = 10000;
     for (int i = 0; i < numSteps; i++) {
         integ.step(10);
-        State state = context.getState(State::Velocities);
+        State state = context.getState(State::Velocities | State::Positions);
         const vector<Vec3>& vel = state.getVelocities();
         Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
         keCM += 0.5*totalMass*velCM.dot(velCM);
         Vec3 velInternal = vel[0]-vel[1];
         keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
+        Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
+        double distance = sqrt(delta.dot(delta));
+        ASSERT(distance <= maxDistance*(1+1e-6));
     }
     ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
     ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);

plugins/drude/platforms/reference/CMakeLists.txt

@@ -75,6 +75,6 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
     SUBDIRS (tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)

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

@@ -235,7 +235,6 @@ void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system,
     // Identify particle pairs and ordinary particles.
     
     set<int> particles;
-    vector<RealOpenMM> particleMass;
     for (int i = 0; i < system.getNumParticles(); i++) {
         particles.insert(i);
         double mass = system.getParticleMass(i);
@@ -325,6 +324,75 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
             pos[i] = xPrime[i];
         }
     }
+
+    // Apply hard wall constraints.
+
+    const RealOpenMM maxDrudeDistance = integrator.getMaxDrudeDistance();
+    if (maxDrudeDistance > 0) {
+        const RealOpenMM hardwallscaleDrude = sqrt(kTDrude);
+        for (int i = 0; i < (int) pairParticles.size(); i++) {
+            int p1 = pairParticles[i].first;
+            int p2 = pairParticles[i].second;
+            RealVec delta = pos[p1]-pos[p2];
+            RealOpenMM r = sqrt(delta.dot(delta));
+            RealOpenMM rInv = 1/r;
+            if (rInv*maxDrudeDistance < 1.0) {
+                // The constraint has been violated, so make the inter-particle distance "bounce"
+                // off the hard wall.
+                
+                if (rInv*maxDrudeDistance < 0.5)
+                    throw OpenMMException("Drude particle moved too far beyond hard wall constraint");
+                RealVec bondDir = delta*rInv;
+                RealVec vel1 = vel[p1];
+                RealVec vel2 = vel[p2];
+                RealOpenMM mass1 = particleMass[p1];
+                RealOpenMM mass2 = particleMass[p2];
+                RealOpenMM deltaR = r-maxDrudeDistance;
+                RealOpenMM deltaT = dt;
+                RealOpenMM dotvr1 = vel1.dot(bondDir);
+                RealVec vb1 = bondDir*dotvr1;
+                RealVec vp1 = vel1-vb1;
+                if (mass2 == 0) {
+                    // The parent particle is massless, so move only the Drude particle.
+
+                    if (dotvr1 != 0.0)
+                        deltaT = deltaR/abs(dotvr1);
+                    if (deltaT > dt)
+                        deltaT = dt;
+                    dotvr1 = -dotvr1*hardwallscaleDrude/(abs(dotvr1)*sqrt(mass1));
+                    RealOpenMM dr = -deltaR + deltaT*dotvr1;
+                    pos[p1] += bondDir*dr;
+                    vel[p1] = vp1 + bondDir*dotvr1;
+                }
+                else {
+                    // Move both particles.
+
+                    RealOpenMM invTotalMass = pairInvTotalMass[i];
+                    RealOpenMM dotvr2 = vel2.dot(bondDir);
+                    RealVec vb2 = bondDir*dotvr2;
+                    RealVec vp2 = vel2-vb2;
+                    RealOpenMM vbCMass = (mass1*dotvr1 + mass2*dotvr2)*invTotalMass;
+                    dotvr1 -= vbCMass;
+                    dotvr2 -= vbCMass;
+                    if (dotvr1 != dotvr2)
+                        deltaT = deltaR/abs(dotvr1-dotvr2);
+                    if (deltaT > dt)
+                        deltaT = dt;
+                    RealOpenMM vBond = hardwallscaleDrude/sqrt(mass1);
+                    dotvr1 = -dotvr1*vBond*mass2*invTotalMass/abs(dotvr1);
+                    dotvr2 = -dotvr2*vBond*mass1*invTotalMass/abs(dotvr2);
+                    RealOpenMM dr1 = -deltaR*mass2*invTotalMass + deltaT*dotvr1;
+                    RealOpenMM dr2 = deltaR*mass1*invTotalMass + deltaT*dotvr2;
+                    dotvr1 += vbCMass;
+                    dotvr2 += vbCMass;
+                    pos[p1] += bondDir*dr1;
+                    pos[p2] += bondDir*dr2;
+                    vel[p1] = vp1 + bondDir*dotvr1;
+                    vel[p2] = vp2 + bondDir*dotvr2;
+                }
+            }
+        }
+    }
     ReferenceVirtualSites::computePositions(context.getSystem(), pos);
     data.time += integrator.getStepSize();
     data.stepCount++;

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

@@ -115,6 +115,7 @@ private:
     ReferencePlatform::PlatformData& data;
     std::vector<int> normalParticles;
     std::vector<std::pair<int, int> > pairParticles;
+    std::vector<double> particleMass;
     std::vector<double> particleInvMass;
     std::vector<double> pairInvTotalMass;
     std::vector<double> pairInvReducedMass;
@@ -158,6 +159,7 @@ private:
     std::vector<double> particleInvMass;
     lbfgsfloatval_t *minimizerPos;
     lbfgs_parameter_t minimizerParams;
+    double maxDrudeDistance;
 };
 
 } // namespace OpenMM

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

@@ -60,6 +60,7 @@ void testSinglePair() {
     const double mass2 = 0.1;
     const double totalMass = mass1+mass2;
     const double reducedMass = (mass1*mass2)/(mass1+mass2);
+    const double maxDistance = 0.05;
     System system;
     system.addParticle(mass1);
     system.addParticle(mass2);
@@ -70,6 +71,7 @@ void testSinglePair() {
     positions[0] = Vec3(0, 0, 0);
     positions[1] = Vec3(0, 0, 0);
     DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
+    integ.setMaxDrudeDistance(maxDistance);
     Platform& platform = Platform::getPlatformByName("Reference");
     Context context(system, integ, platform);
     context.setPositions(positions);
@@ -84,12 +86,15 @@ void testSinglePair() {
     int numSteps = 10000;
     for (int i = 0; i < numSteps; i++) {
         integ.step(10);
-        State state = context.getState(State::Velocities);
+        State state = context.getState(State::Velocities | State::Positions);
         const vector<Vec3>& vel = state.getVelocities();
         Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
         keCM += 0.5*totalMass*velCM.dot(velCM);
         Vec3 velInternal = vel[0]-vel[1];
         keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
+        Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
+        double distance = sqrt(delta.dot(delta));
+        ASSERT(distance <= maxDistance*(1+1e-6));
     }
     ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
     ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);