CPU platform shares neighbor list between forces

platforms/cpu/include/CpuKernels.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) 2013-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -90,6 +90,7 @@ public:
 private:
     CpuPlatform::PlatformData& data;
     Kernel referenceKernel;
+    std::vector<RealVec> lastPositions;
 };
 
 /**
@@ -267,9 +268,7 @@ private:
     bool useSwitchingFunction, useOptimizedPme, hasInitializedPme;
     std::vector<std::set<int> > exclusions;
     std::vector<std::pair<float, float> > particleParams;
-    std::vector<RealVec> lastPositions;
     NonbondedMethod nonbondedMethod;
-    CpuNeighborList* neighborList;
     CpuNonbondedForce* nonbonded;
     Kernel optimizedPme;
     CpuBondForce bondForce;
@@ -317,7 +316,6 @@ private:
     std::vector<std::string> parameterNames, globalParameterNames;
     std::vector<std::pair<std::set<int>, std::set<int> > > interactionGroups;
     NonbondedMethod nonbondedMethod;
-    CpuNeighborList* neighborList;
     CpuCustomNonbondedForce* nonbonded;
 };
 
@@ -403,7 +401,6 @@ private:
     std::vector<OpenMM::CustomGBForce::ComputationType> valueTypes;
     std::vector<OpenMM::CustomGBForce::ComputationType> energyTypes;
     NonbondedMethod nonbondedMethod;
-    CpuNeighborList* neighborList;
 };
 
 /**

platforms/cpu/include/CpuNeighborList.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) 2013-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -51,6 +51,7 @@ public:
     void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
             const RealVec* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads);
     int getNumBlocks() const;
+    int getBlockSize() const;
     const std::vector<int>& getSortedAtoms() const;
     const std::vector<int>& getBlockNeighbors(int blockIndex) const;
     const std::vector<char>& getBlockExclusions(int blockIndex) const;

platforms/cpu/include/CpuPlatform.h

@@ -34,6 +34,7 @@
 
 #include "AlignedArray.h"
 #include "CpuRandom.h"
+#include "CpuNeighborList.h"
 #include "ReferencePlatform.h"
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/internal/ThreadPool.h"
@@ -80,12 +81,18 @@ private:
 class CpuPlatform::PlatformData {
 public:
     PlatformData(int numParticles, int numThreads);
+    ~PlatformData();
+    void requestNeighborList(double cutoffDistance, double padding, bool useExclusions, std::vector<std::set<int> >& exclusionList);
     AlignedArray<float> posq;
     std::vector<AlignedArray<float> > threadForce;
     ThreadPool threads;
     bool isPeriodic;
     CpuRandom random;
     std::map<std::string, std::string> propertyValues;
+    CpuNeighborList* neighborList;
+    double cutoff, paddedCutoff;
+    bool anyExclusions;
+    std::vector<std::set<int> > exclusions;
 };
 
 } // namespace OpenMM

platforms/cpu/src/CpuCustomGBForce.cpp

 
-/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -294,12 +294,13 @@ void CpuCustomGBForce::calculateParticlePairValue(int index, ThreadData& data, i
             int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
-            const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
+            const int blockSize = neighborList->getBlockSize();
+            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
                 int first = neighbors[i];
-                for (int k = 0; k < 4; k++) {
+                for (int k = 0; k < blockSize; k++) {
                     if ((blockExclusions[i] & (1<<k)) == 0) {
                         int second = blockAtom[k];
                         if (useExclusions && exclusions[first].find(second) != exclusions[first].end())
@@ -379,12 +380,13 @@ void CpuCustomGBForce::calculateParticlePairEnergyTerm(int index, ThreadData& da
             int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
-            const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
+            const int blockSize = neighborList->getBlockSize();
+            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
                 int first = neighbors[i];
-                for (int k = 0; k < 4; k++) {
+                for (int k = 0; k < blockSize; k++) {
                     if ((blockExclusions[i] & (1<<k)) == 0) {
                         int second = blockAtom[k];
                         if (useExclusions && exclusions[first].find(second) != exclusions[first].end())
@@ -460,12 +462,13 @@ void CpuCustomGBForce::calculateChainRuleForces(ThreadData& data, int numAtoms,
             int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
-            const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
+            const int blockSize = neighborList->getBlockSize();
+            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const vector<char>& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
                 int first = neighbors[i];
-                for (int k = 0; k < 4; k++) {
+                for (int k = 0; k < blockSize; k++) {
                     if ((blockExclusions[i] & (1<<k)) == 0) {
                         int second = blockAtom[k];
                         bool isExcluded = (exclusions[first].find(second) != exclusions[first].end());

platforms/cpu/src/CpuCustomNonbondedForce.cpp

 
-/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -190,7 +190,8 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
             int blockIndex = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), 1);
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
-            const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
+            const int blockSize = neighborList->getBlockSize();
+            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
@@ -199,7 +200,7 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
                     ReferenceForce::setVariable(data.energyParticleParams[j*2], atomParameters[first][j]);
                     ReferenceForce::setVariable(data.forceParticleParams[j*2], atomParameters[first][j]);
                 }
-                for (int k = 0; k < 4; k++) {
+                for (int k = 0; k < blockSize; k++) {
                     if ((exclusions[i] & (1<<k)) == 0) {
                         int second = blockAtom[k];
                         for (int j = 0; j < (int) paramNames.size(); j++) {

platforms/cpu/src/CpuKernels.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) 2013-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -230,6 +230,7 @@ CpuCalcForcesAndEnergyKernel::CpuCalcForcesAndEnergyKernel(std::string name, con
 
 void CpuCalcForcesAndEnergyKernel::initialize(const System& system) {
     referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().initialize(system);
+    lastPositions.resize(system.getNumParticles(), Vec3(1e10, 1e10, 1e10));
 }
 
 void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
@@ -237,11 +238,60 @@ void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool i
     
     // Convert positions to single precision and clear the forces.
 
-    InitForceTask task(context.getSystem().getNumParticles(), context, data);
+    int numParticles = context.getSystem().getNumParticles();
+    InitForceTask task(numParticles, context, data);
     data.threads.execute(task);
     data.threads.waitForThreads();
     if (!task.positionsValid)
         throw OpenMMException("Particle coordinate is nan");
+
+    // Determine whether we need to recompute the neighbor list.
+        
+    if (data.neighborList != NULL) {
+        double padding = data.paddedCutoff-data.cutoff;;
+        bool needRecompute = false;
+        double closeCutoff2 = 0.25*padding*padding;
+        double farCutoff2 = 0.5*padding*padding;
+        int maxNumMoved = numParticles/10;
+        vector<int> moved;
+        vector<RealVec>& posData = extractPositions(context);
+        for (int i = 0; i < numParticles; i++) {
+            RealVec delta = posData[i]-lastPositions[i];
+            double dist2 = delta.dot(delta);
+            if (dist2 > closeCutoff2) {
+                moved.push_back(i);
+                if (dist2 > farCutoff2 || moved.size() > maxNumMoved) {
+                    needRecompute = true;
+                    break;
+                }
+            }
+        }
+        if (!needRecompute && moved.size() > 0) {
+            // Some particles have moved further than half the padding distance.  Look for pairs
+            // that are missing from the neighbor list.
+
+            int numMoved = moved.size();
+            double cutoff2 = data.cutoff*data.cutoff;
+            double paddedCutoff2 = data.paddedCutoff*data.paddedCutoff;
+            for (int i = 1; i < numMoved && !needRecompute; i++)
+                for (int j = 0; j < i; j++) {
+                    RealVec delta = posData[moved[i]]-posData[moved[j]];
+                    if (delta.dot(delta) < cutoff2) {
+                        // These particles should interact.  See if they are in the neighbor list.
+                        
+                        RealVec oldDelta = lastPositions[moved[i]]-lastPositions[moved[j]];
+                        if (oldDelta.dot(oldDelta) > paddedCutoff2) {
+                            needRecompute = true;
+                            break;
+                        }
+                    }
+                }
+        }
+        if (needRecompute) {
+            data.neighborList->computeNeighborList(numParticles, data.posq, data.exclusions, extractBoxVectors(context), data.isPeriodic, data.paddedCutoff, data.threads);
+            lastPositions = posData;
+        }
+    }
 }
 
 double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups, bool& valid) {
@@ -473,15 +523,11 @@ CpuNonbondedForce* createCpuNonbondedForceVec4();
 CpuNonbondedForce* createCpuNonbondedForceVec8();
 
 CpuCalcNonbondedForceKernel::CpuCalcNonbondedForceKernel(string name, const Platform& platform, CpuPlatform::PlatformData& data) : CalcNonbondedForceKernel(name, platform),
-        data(data), bonded14IndexArray(NULL), bonded14ParamArray(NULL), hasInitializedPme(false), neighborList(NULL), nonbonded(NULL) {
-    if (isVec8Supported()) {
-        neighborList = new CpuNeighborList(8);
+        data(data), bonded14IndexArray(NULL), bonded14ParamArray(NULL), hasInitializedPme(false), nonbonded(NULL) {
+    if (isVec8Supported())
         nonbonded = createCpuNonbondedForceVec8();
-    }
-    else {
-        neighborList = new CpuNeighborList(4);
+    else
         nonbonded = createCpuNonbondedForceVec4();
-    }
 }
 
 CpuCalcNonbondedForceKernel::~CpuCalcNonbondedForceKernel() {
@@ -495,8 +541,6 @@ CpuCalcNonbondedForceKernel::~CpuCalcNonbondedForceKernel() {
     }
     if (nonbonded != NULL)
         delete nonbonded;
-    if (neighborList != NULL)
-        delete neighborList;
 }
 
 void CpuCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {
@@ -556,6 +600,7 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
     if (nonbondedMethod == NoCutoff)
         useSwitchingFunction = false;
     else {
+        data.requestNeighborList(nonbondedCutoff, 0.25*nonbondedCutoff, true, exclusions);
         useSwitchingFunction = force.getUseSwitchingFunction();
         switchingDistance = force.getSwitchingDistance();
     }
@@ -578,7 +623,6 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
         dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(system, force);
     else
         dispersionCoefficient = 0.0;
-    lastPositions.resize(numParticles, Vec3(1e10, 1e10, 1e10));
     data.isPeriodic = (nonbondedMethod == CutoffPeriodic || nonbondedMethod == Ewald || nonbondedMethod == PME);
 }
 
@@ -605,53 +649,8 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
     double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
     bool ewald  = (nonbondedMethod == Ewald);
     bool pme  = (nonbondedMethod == PME);
-    if (nonbondedMethod != NoCutoff) {
-        // Determine whether we need to recompute the neighbor list.
-        
-        double padding = 0.25*nonbondedCutoff;
-        bool needRecompute = false;
-        double closeCutoff2 = 0.25*padding*padding;
-        double farCutoff2 = 0.5*padding*padding;
-        int maxNumMoved = numParticles/10;
-        vector<int> moved;
-        for (int i = 0; i < numParticles; i++) {
-            RealVec delta = posData[i]-lastPositions[i];
-            double dist2 = delta.dot(delta);
-            if (dist2 > closeCutoff2) {
-                moved.push_back(i);
-                if (dist2 > farCutoff2 || moved.size() > maxNumMoved) {
-                    needRecompute = true;
-                    break;
-                }
-            }
-        }
-        if (!needRecompute && moved.size() > 0) {
-            // Some particles have moved further than half the padding distance.  Look for pairs
-            // that are missing from the neighbor list.
-
-            int numMoved = moved.size();
-            double cutoff2 = nonbondedCutoff*nonbondedCutoff;
-            double paddedCutoff2 = (nonbondedCutoff+padding)*(nonbondedCutoff+padding);
-            for (int i = 1; i < numMoved && !needRecompute; i++)
-                for (int j = 0; j < i; j++) {
-                    RealVec delta = posData[moved[i]]-posData[moved[j]];
-                    if (delta.dot(delta) < cutoff2) {
-                        // These particles should interact.  See if they are in the neighbor list.
-                        
-                        RealVec oldDelta = lastPositions[moved[i]]-lastPositions[moved[j]];
-                        if (oldDelta.dot(oldDelta) > paddedCutoff2) {
-                            needRecompute = true;
-                            break;
-                        }
-                    }
-                }
-        }
-        if (needRecompute) {
-            neighborList->computeNeighborList(numParticles, posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff+padding, data.threads);
-            lastPositions = posData;
-        }
-        nonbonded->setUseCutoff(nonbondedCutoff, *neighborList, rfDielectric);
-    }
+    if (nonbondedMethod != NoCutoff)
+        nonbonded->setUseCutoff(nonbondedCutoff, *data.neighborList, rfDielectric);
     if (data.isPeriodic) {
         RealVec* boxVectors = extractBoxVectors(context);
         double minAllowedSize = 1.999999*nonbondedCutoff;
@@ -748,7 +747,7 @@ void CpuCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int&
 }
 
 CpuCalcCustomNonbondedForceKernel::CpuCalcCustomNonbondedForceKernel(string name, const Platform& platform, CpuPlatform::PlatformData& data) :
-            CalcCustomNonbondedForceKernel(name, platform), data(data), forceCopy(NULL), neighborList(NULL), nonbonded(NULL) {
+            CalcCustomNonbondedForceKernel(name, platform), data(data), forceCopy(NULL), nonbonded(NULL) {
 }
 
 CpuCalcCustomNonbondedForceKernel::~CpuCalcCustomNonbondedForceKernel() {
@@ -757,8 +756,6 @@ CpuCalcCustomNonbondedForceKernel::~CpuCalcCustomNonbondedForceKernel() {
             delete[] particleParamArray[i];
         delete[] particleParamArray;
     }
-    if (neighborList != NULL)
-        delete neighborList;
     if (nonbonded != NULL)
         delete nonbonded;
     if (forceCopy != NULL)
@@ -795,7 +792,7 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
     if (nonbondedMethod == NoCutoff)
         useSwitchingFunction = false;
     else {
-        neighborList = new CpuNeighborList(4);
+        data.requestNeighborList(nonbondedCutoff, 0.25*nonbondedCutoff, true, exclusions);
         useSwitchingFunction = force.getUseSwitchingFunction();
         switchingDistance = force.getSwitchingDistance();
     }
@@ -861,10 +858,8 @@ double CpuCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool inc
     RealVec* boxVectors = extractBoxVectors(context);
     double energy = 0;
     bool periodic = (nonbondedMethod == CutoffPeriodic);
-    if (nonbondedMethod != NoCutoff) {
-        neighborList->computeNeighborList(numParticles, data.posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff, data.threads);
-        nonbonded->setUseCutoff(nonbondedCutoff, *neighborList);
-    }
+    if (nonbondedMethod != NoCutoff)
+        nonbonded->setUseCutoff(nonbondedCutoff, *data.neighborList);
     if (periodic) {
         double minAllowedSize = 2*nonbondedCutoff;
         if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize)
@@ -972,8 +967,6 @@ CpuCalcCustomGBForceKernel::~CpuCalcCustomGBForceKernel() {
             delete[] particleParamArray[i];
         delete[] particleParamArray;
     }
-    if (neighborList != NULL)
-        delete neighborList;
     if (ixn != NULL)
         delete ixn;
 }
@@ -1021,10 +1014,8 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
         globalParameterNames.push_back(force.getGlobalParameterName(i));
     nonbondedMethod = CalcCustomGBForceKernel::NonbondedMethod(force.getNonbondedMethod());
     nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
-    if (nonbondedMethod == NoCutoff)
-        neighborList = NULL;
-    else
-        neighborList = new CpuNeighborList(4);
+    if (nonbondedMethod != NoCutoff)
+        data.requestNeighborList(nonbondedCutoff, 0.25*nonbondedCutoff, true, exclusions);
 
     // Create custom functions for the tabulated functions.
 
@@ -1121,8 +1112,7 @@ double CpuCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeFor
         ixn->setPeriodic(extractBoxSize(context));
     if (nonbondedMethod != NoCutoff) {
         vector<set<int> > noExclusions(numParticles);
-        neighborList->computeNeighborList(numParticles, data.posq, exclusions, boxVectors, data.isPeriodic, nonbondedCutoff, data.threads);
-        ixn->setUseCutoff(nonbondedCutoff, *neighborList);
+        ixn->setUseCutoff(nonbondedCutoff, *data.neighborList);
     }
     map<string, double> globalParameters;
     for (int i = 0; i < (int) globalParameterNames.size(); i++)

platforms/cpu/src/CpuNeighborList.cpp

@@ -508,6 +508,10 @@ int CpuNeighborList::getNumBlocks() const {
     return sortedAtoms.size()/blockSize;
 }
 
+int CpuNeighborList::getBlockSize() const {
+    return blockSize;
+}
+
 const std::vector<int>& CpuNeighborList::getSortedAtoms() const {
     return sortedAtoms;
 }

platforms/cpu/src/CpuPlatform.cpp

@@ -34,6 +34,7 @@
 #include "CpuKernels.h"
 #include "CpuSETTLE.h"
 #include "ReferenceConstraints.h"
+#include "openmm/OpenMMException.h"
 #include "openmm/internal/hardware.h"
 #include "openmm/internal/vectorize.h"
 #include <sstream>
@@ -135,7 +136,8 @@ const CpuPlatform::PlatformData& CpuPlatform::getPlatformData(const ContextImpl&
     return *contextData[&context];
 }
 
-CpuPlatform::PlatformData::PlatformData(int numParticles, int numThreads) : posq(4*numParticles), threads(numThreads) {
+CpuPlatform::PlatformData::PlatformData(int numParticles, int numThreads) : posq(4*numParticles), threads(numThreads),
+        neighborList(NULL), cutoff(0.0), paddedCutoff(0.0), anyExclusions(false) {
     numThreads = threads.getNumThreads();
     threadForce.resize(numThreads);
     for (int i = 0; i < numThreads; i++)
@@ -145,3 +147,27 @@ CpuPlatform::PlatformData::PlatformData(int numParticles, int numThreads) : posq
     threadsProperty << numThreads;
     propertyValues[CpuThreads()] = threadsProperty.str();
 }
+
+CpuPlatform::PlatformData::~PlatformData() {
+    if (neighborList != NULL)
+        delete neighborList;
+}
+
+bool isVec8Supported();
+
+void CpuPlatform::PlatformData::requestNeighborList(double cutoffDistance, double padding, bool useExclusions, vector<set<int> >& exclusionList) {
+    if (neighborList == NULL)
+        neighborList = new CpuNeighborList(isVec8Supported() ? 8 : 4);
+    if (cutoffDistance > cutoff)
+        cutoff = cutoffDistance;
+    if (cutoffDistance+padding > paddedCutoff)
+        paddedCutoff = cutoffDistance+padding;
+    if (useExclusions) {
+        if (anyExclusions && exclusions != exclusionList)
+            throw OpenMMException("All Forces must have identical exclusions");
+        else {
+            exclusions = exclusionList;
+            anyExclusions = true;
+        }
+    }
+}