Implemented type filters for CUDA version of CustomManyParticleForce

platforms/cuda/include/CudaKernels.h

@@ -931,7 +931,7 @@ 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), system(system) {
+            hasInitializedKernel(false), cu(cu), params(NULL), globals(NULL), particleTypes(NULL), orderIndex(NULL), particleOrder(NULL), system(system) {
     }
     ~CudaCalcCustomManyParticleForceKernel();
     /**
@@ -965,6 +965,8 @@ private:
     CudaParameterSet* params;
     CudaArray* globals;
     CudaArray* particleTypes;
+    CudaArray* orderIndex;
+    CudaArray* particleOrder;
     std::vector<std::string> globalParamNames;
     std::vector<float> globalParamValues;
     std::vector<CudaArray*> tabulatedFunctions;

platforms/cuda/src/CudaKernels.cpp

@@ -4430,6 +4430,10 @@ CudaCalcCustomManyParticleForceKernel::~CudaCalcCustomManyParticleForceKernel()
         delete params;
     if (globals != NULL)
         delete globals;
+    if (orderIndex != NULL)
+        delete orderIndex;
+    if (particleOrder != NULL)
+        delete particleOrder;
     if (particleTypes != NULL)
         delete particleTypes;
     for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
@@ -4513,6 +4517,27 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
         }
     }
     
+    // Build data structures for type filters.
+    
+    vector<int> particleTypesVec;
+    vector<int> orderIndexVec;
+    vector<std::vector<int> > particleOrderVec;
+    int numTypes;
+    CustomManyParticleForceImpl::buildFilterArrays(force, numTypes, particleTypesVec, orderIndexVec, particleOrderVec);
+    bool hasTypeFilters = (particleOrderVec.size() > 1);
+    if (hasTypeFilters) {
+        particleTypes = CudaArray::create<int>(cu, particleTypesVec.size(), "customManyParticleTypes");
+        orderIndex = CudaArray::create<int>(cu, orderIndexVec.size(), "customManyParticleOrderIndex");
+        particleOrder = CudaArray::create<int>(cu, particleOrderVec.size()*particlesPerSet, "customManyParticleOrder");
+        particleTypes->upload(particleTypesVec);
+        orderIndex->upload(orderIndexVec);
+        vector<int> flattenedOrder(particleOrder->getSize());
+        for (int i = 0; i < (int) particleOrderVec.size(); i++)
+            for (int j = 0; j < particlesPerSet; j++)
+                flattenedOrder[i*particlesPerSet+j] = particleOrderVec[i][j];
+        particleOrder->upload(flattenedOrder);
+    }
+
     // Now to generate the kernel.  First, it needs to calculate all distances, angles,
     // and dihedrals the expression depends on.
 
@@ -4677,7 +4702,19 @@ 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;
+    if (hasTypeFilters) {
+        permute<<"int particleSet[] = {";
+        for (int i = 0; i < particlesPerSet; i++) {
+            permute<<"p"<<(i+1);
+            if (i < particlesPerSet-1)
+                permute<<", ";
+        }
+        permute<<"};\n";
+    }
     for (int i = 0; i < particlesPerSet; i++) {
+        if (hasTypeFilters)
+            permute<<"int atom"<<(i+1)<<" = particleSet[particleOrder["<<numTypes<<"*order+"<<i<<"]];\n";
+        else
             permute<<"int atom"<<(i+1)<<" = p"<<(i+1)<<";\n";
         loadData<<"real4 pos"<<(i+1)<<" = posq[atom"<<(i+1)<<"];\n";
         for (int j = 0; j < (int) params->getBuffers().size(); j++)
@@ -4704,6 +4741,9 @@ 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";
     }
+    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+")";
     
     // Create replacements for extra arguments.
     
@@ -4725,12 +4765,15 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
     replacements["VERIFY_CUTOFF"] = verifyCutoff.str();
     replacements["PERMUTE_ATOMS"] = permute.str();
     replacements["LOAD_PARTICLE_DATA"] = loadData.str();
+    replacements["COMPUTE_TYPE_INDEX"] = computeTypeIndex;
     replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
     map<string, string> defines;
     if (nonbondedMethod != NoCutoff)
         defines["USE_CUTOFF"] = "1";
     if (nonbondedMethod == CutoffPeriodic)
         defines["USE_PERIODIC"] = "1";
+    if (hasTypeFilters)
+        defines["USE_FILTERS"] = "1";
     defines["NUM_ATOMS"] = cu.intToString(cu.getNumAtoms());
     defines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
     defines["M_PI"] = cu.doubleToString(M_PI);
@@ -4749,6 +4792,11 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
         forceArgs.push_back(&cu.getPosq().getDevicePointer());
         forceArgs.push_back(cu.getPeriodicBoxSizePointer());
         forceArgs.push_back(cu.getInvPeriodicBoxSizePointer());
+        if (particleTypes != NULL) {
+            forceArgs.push_back(&particleTypes->getDevicePointer());
+            forceArgs.push_back(&orderIndex->getDevicePointer());
+            forceArgs.push_back(&particleOrder->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

@@ -64,6 +64,9 @@ inline __device__ real4 computeCross(real4 vec1, real4 vec2) {
 extern "C" __global__ void computeInteraction(
         unsigned long long* __restrict__ forceBuffers, real* __restrict__ energyBuffer, const real4* __restrict__ posq,
         real4 periodicBoxSize, real4 invPeriodicBoxSize
+#ifdef USE_FILTERS
+        , int* __restrict__ particleTypes, int* __restrict__ orderIndex, int* __restrict__ particleOrder
+#endif
         PARAMETER_ARGUMENTS) {
     real energy = 0.0f;
     
@@ -79,6 +82,11 @@ extern "C" __global__ void computeInteraction(
             if (includeInteraction) {
                 VERIFY_CUTOFF;
             }
+#endif
+#ifdef USE_FILTERS
+            int order = orderIndex[COMPUTE_TYPE_INDEX];
+            if (order == -1)
+                includeInteraction = false;
 #endif
             if (includeInteraction) {
                 PERMUTE_ATOMS;

platforms/cuda/tests/TestCudaCustomManyParticleForce.cpp

@@ -469,10 +469,10 @@ int main(int argc, char* argv[]) {
         testCutoff();
         testPeriodic();
 //        testExclusions();
-//        testAllTerms();
+        testAllTerms();
         testParameters();
         testTabulatedFunctions();
-//        testTypeFilters();
+        testTypeFilters();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;