Implemented exclusions for CUDA version of CustomManyParticleForce

platforms/cuda/include/CudaKernels.h

@@ -931,7 +931,8 @@ private:
 class CudaCalcCustomManyParticleForceKernel : public CalcCustomManyParticleForceKernel {
 public:
     CudaCalcCustomManyParticleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomManyParticleForceKernel(name, platform),
-            hasInitializedKernel(false), cu(cu), params(NULL), globals(NULL), particleTypes(NULL), orderIndex(NULL), particleOrder(NULL), system(system) {
+            hasInitializedKernel(false), cu(cu), params(NULL), globals(NULL), particleTypes(NULL), orderIndex(NULL), particleOrder(NULL), exclusions(NULL),
+            exclusionStartIndex(NULL), system(system) {
     }
     ~CudaCalcCustomManyParticleForceKernel();
     /**
@@ -967,6 +968,8 @@ private:
     CudaArray* particleTypes;
     CudaArray* orderIndex;
     CudaArray* particleOrder;
+    CudaArray* exclusions;
+    CudaArray* exclusionStartIndex;
     std::vector<std::string> globalParamNames;
     std::vector<float> globalParamValues;
     std::vector<CudaArray*> tabulatedFunctions;

platforms/cuda/src/CudaKernels.cpp

@@ -4413,9 +4413,14 @@ public:
         return true;
     }
     int getNumParticleGroups() {
-        return 0;
+        return force.getNumExclusions();
     }
     void getParticlesInGroup(int index, vector<int>& particles) {
+        int particle1, particle2;
+        force.getExclusionParticles(index, particle1, particle2);
+        particles.resize(2);
+        particles[0] = particle1;
+        particles[1] = particle2;
     }
     bool areGroupsIdentical(int group1, int group2) {
         return true;
@@ -4436,6 +4441,10 @@ CudaCalcCustomManyParticleForceKernel::~CudaCalcCustomManyParticleForceKernel()
         delete particleOrder;
     if (particleTypes != NULL)
         delete particleTypes;
+    if (exclusions != NULL)
+        delete exclusions;
+    if (exclusionStartIndex != NULL)
+        delete exclusionStartIndex;
     for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
         delete tabulatedFunctions[i];
 }
@@ -4538,6 +4547,30 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
         particleOrder->upload(flattenedOrder);
     }
     
+    // Build data structures for exclusions.
+    
+    if (force.getNumExclusions() > 0) {
+        vector<vector<int> > particleExclusions(numParticles);
+        for (int i = 0; i < force.getNumExclusions(); i++) {
+            int p1, p2;
+            force.getExclusionParticles(i, p1, p2);
+            particleExclusions[p1].push_back(p2);
+            particleExclusions[p2].push_back(p1);
+        }
+        vector<int> exclusionsVec;
+        vector<int> exclusionStartIndexVec(numParticles+1);
+        exclusionStartIndexVec[0] = 0;
+        for (int i = 0; i < numParticles; i++) {
+            sort(particleExclusions[i].begin(), particleExclusions[i].end());
+            exclusionsVec.insert(exclusionsVec.end(), particleExclusions[i].begin(), particleExclusions[i].end());
+            exclusionStartIndexVec[i+1] = exclusionsVec.size();
+        }
+        exclusions = CudaArray::create<int>(cu, exclusionsVec.size(), "customManyParticleExclusions");
+        exclusionStartIndex = CudaArray::create<int>(cu, exclusionStartIndexVec.size(), "customManyParticleExclusionStart");
+        exclusions->upload(exclusionsVec);
+        exclusionStartIndex->upload(exclusionStartIndexVec);
+    }
+
     // Now to generate the kernel.  First, it needs to calculate all distances, angles,
     // and dihedrals the expression depends on.
 
@@ -4701,7 +4734,7 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
     
     // Create other replacements that depend on the number of particles per set.
     
-    stringstream numCombinations, atomsForCombination, isValidCombination, permute, loadData, verifyCutoff;
+    stringstream numCombinations, atomsForCombination, isValidCombination, permute, loadData, verifyCutoff, verifyExclusions;
     if (hasTypeFilters) {
         permute<<"int particleSet[] = {";
         for (int i = 0; i < particlesPerSet; i++) {
@@ -4741,6 +4774,12 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
             for (int j = i+1; j < particlesPerSet; j++)
                 verifyCutoff<<"includeInteraction &= (delta(pos"<<(i+1)<<", pos"<<(j+1)<<", periodicBoxSize, invPeriodicBoxSize).w < CUTOFF_SQUARED);\n";
     }
+    if (force.getNumExclusions() > 0) {
+        int startCheckFrom = 0;
+        for (int i = startCheckFrom; i < particlesPerSet; i++)
+            for (int j = i+1; j < particlesPerSet; j++)
+                verifyExclusions<<"includeInteraction &= !isInteractionExcluded(p"<<(i+1)<<", p"<<(j+1)<<", exclusions, exclusionStartIndex);\n";
+    }
     string computeTypeIndex = "particleTypes[p"+cu.intToString(particlesPerSet)+"]";
     for (int i = particlesPerSet-2; i >= 0; i--)
         computeTypeIndex = "particleTypes[p"+cu.intToString(i+1)+"]+"+cu.intToString(numTypes)+"*("+computeTypeIndex+")";
@@ -4763,6 +4802,7 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
     replacements["FIND_ATOMS_FOR_COMBINATION_INDEX"] = atomsForCombination.str();
     replacements["IS_VALID_COMBINATION"] = isValidCombination.str();
     replacements["VERIFY_CUTOFF"] = verifyCutoff.str();
+    replacements["VERIFY_EXCLUSIONS"] = verifyExclusions.str();
     replacements["PERMUTE_ATOMS"] = permute.str();
     replacements["LOAD_PARTICLE_DATA"] = loadData.str();
     replacements["COMPUTE_TYPE_INDEX"] = computeTypeIndex;
@@ -4774,6 +4814,8 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
         defines["USE_PERIODIC"] = "1";
     if (hasTypeFilters)
         defines["USE_FILTERS"] = "1";
+    if (force.getNumExclusions() > 0)
+        defines["USE_EXCLUSIONS"] = "1";
     defines["NUM_ATOMS"] = cu.intToString(cu.getNumAtoms());
     defines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
     defines["M_PI"] = cu.doubleToString(M_PI);
@@ -4797,6 +4839,10 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
             forceArgs.push_back(&orderIndex->getDevicePointer());
             forceArgs.push_back(&particleOrder->getDevicePointer());
         }
+        if (exclusions != NULL) {
+            forceArgs.push_back(&exclusions->getDevicePointer());
+            forceArgs.push_back(&exclusionStartIndex->getDevicePointer());
+        }
         if (globals != NULL)
             forceArgs.push_back(&globals->getDevicePointer());
         for (int i = 0; i < (int) params->getBuffers().size(); i++) {

platforms/cuda/src/kernels/customManyParticle.cu

@@ -58,6 +58,22 @@ inline __device__ real4 computeCross(real4 vec1, real4 vec2) {
     return make_real4(cp.x, cp.y, cp.z, cp.x*cp.x+cp.y*cp.y+cp.z*cp.z);
 }
 
+/**
+ * Determine whether a particular interaction is in the list of exclusions.
+ */
+inline __device__ bool isInteractionExcluded(int atom1, int atom2, int* __restrict__ exclusions, int* __restrict__ exclusionStartIndex) {
+    int first = exclusionStartIndex[atom1];
+    int last = exclusionStartIndex[atom1+1];
+    for (int i = last-1; i >= first; i--) {
+        int excluded = exclusions[i];
+        if (excluded == atom2)
+            return true;
+        if (excluded <= atom1)
+            return false;
+    }
+    return false;
+}
+
 /**
  * Compute the interaction.
  */
@@ -66,6 +82,9 @@ extern "C" __global__ void computeInteraction(
         real4 periodicBoxSize, real4 invPeriodicBoxSize
 #ifdef USE_FILTERS
         , int* __restrict__ particleTypes, int* __restrict__ orderIndex, int* __restrict__ particleOrder
+#endif
+#ifdef USE_EXCLUSIONS
+        , int* __restrict__ exclusions, int* __restrict__ exclusionStartIndex
 #endif
         PARAMETER_ARGUMENTS) {
     real energy = 0.0f;
@@ -87,6 +106,11 @@ extern "C" __global__ void computeInteraction(
             int order = orderIndex[COMPUTE_TYPE_INDEX];
             if (order == -1)
                 includeInteraction = false;
+#endif
+#ifdef USE_EXCLUSIONS
+            if (includeInteraction) {
+                VERIFY_EXCLUSIONS;
+            }
 #endif
             if (includeInteraction) {
                 PERMUTE_ATOMS;

platforms/cuda/tests/TestCudaCustomManyParticleForce.cpp

@@ -468,7 +468,7 @@ int main(int argc, char* argv[]) {
         testNoCutoff();
         testCutoff();
         testPeriodic();
-//        testExclusions();
+        testExclusions();
         testAllTerms();
         testParameters();
         testTabulatedFunctions();