OpenCL allows different force groups to have different cutoffs

platforms/opencl/include/OpenCLKernels.h

@@ -732,7 +732,7 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force);
 private:
-    double prefactor, surfaceAreaFactor;
+    double prefactor, surfaceAreaFactor, cutoff;
     bool hasCreatedKernels;
     int maxTiles;
     OpenCLContext& cl;
@@ -783,6 +783,7 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
 private:
+    double cutoff;
     bool hasInitializedKernels, needParameterGradient;
     int maxTiles, numComputedValues;
     OpenCLContext& cl;

platforms/opencl/include/OpenCLNonbondedUtilities.h

@@ -135,31 +135,23 @@ public:
         return forceThreadBlockSize;
     }
     /**
-     * Get the cutoff distance.
+     * Get the maximum cutoff distance used by any force group.
      */
-    double getCutoffDistance() {
-        return cutoff;
-    }
+    double getMaxCutoffDistance();
     /**
      * Get whether any interactions have been added.
      */
     bool getHasInteractions() {
-        return cutoff != -1.0;
-    }
-    /**
-     * Get the force group in which nonbonded interactions should be computed.
-     */
-    int getForceGroup() {
-        return nonbondedForceGroup;
+        return (groupCutoff.size() > 0);
     }
     /**
      * Prepare to compute interactions.  This updates the neighbor list.
      */
-    void prepareInteractions();
+    void prepareInteractions(int forceGroups);
     /**
      * Compute the nonbonded interactions.
      */
-    void computeInteractions();
+    void computeInteractions(int forceGroups);
     /**
      * Check to see if the neighbor list arrays are large enough, and make them bigger if necessary.
      */
@@ -252,16 +244,20 @@ public:
      * @param arguments     arrays (other than per-atom parameters) that should be passed as arguments to the kernel
      * @param useExclusions specifies whether exclusions are applied to this interaction
      * @param isSymmetric   specifies whether the interaction is symmetric
+     * @param groups        the set of force groups this kernel is for
+     */
+    cl::Kernel createInteractionKernel(const std::string& source, const std::vector<ParameterInfo>& params, const std::vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups);
+    /**
+     * Create the set of kernels that will be needed for a particular combination of force groups.
+     * 
+     * @param groups    the set of force groups
      */
-    cl::Kernel createInteractionKernel(const std::string& source, const std::vector<ParameterInfo>& params, const std::vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric) const;
+    void createKernelsForGroups(int groups);
 private:
+    class KernelSet;
     class BlockSortTrait;
     OpenCLContext& context;
-    cl::Kernel forceKernel;
-    cl::Kernel findBlockBoundsKernel;
-    cl::Kernel sortBoxDataKernel;
-    cl::Kernel findInteractingBlocksKernel;
-    cl::Kernel findInteractionsWithinBlocksKernel;
+    std::map<int, KernelSet> groupKernels;
     OpenCLArray* exclusionTiles;
     OpenCLArray* exclusions;
     OpenCLArray* exclusionIndices;
@@ -280,12 +276,27 @@ private:
     std::vector<std::vector<int> > atomExclusions;
     std::vector<ParameterInfo> parameters;
     std::vector<ParameterInfo> arguments;
-    std::string kernelSource;
-    std::map<std::string, std::string> kernelDefines;
-    double cutoff;
-    bool useCutoff, usePeriodic, deviceIsCpu, anyExclusions, usePadding;
-    int numForceBuffers, startTileIndex, numTiles, startBlockIndex, numBlocks, numForceThreadBlocks;
-    int forceThreadBlockSize, interactingBlocksThreadBlockSize, nonbondedForceGroup;
+    std::map<int, double> groupCutoff;
+    std::map<int, std::string> groupKernelSource;
+    double lastCutoff;
+    bool useCutoff, usePeriodic, deviceIsCpu, anyExclusions, usePadding, forceRebuildNeighborList;
+    int numForceBuffers, startTileIndex, numTiles, startBlockIndex, numBlocks, maxExclusions, numForceThreadBlocks;
+    int forceThreadBlockSize, interactingBlocksThreadBlockSize, groupFlags;
+};
+
+/**
+ * This class stores the kernels to execute for a set of force groups.
+ */
+
+class OpenCLNonbondedUtilities::KernelSet {
+public:
+    bool hasForces;
+    double cutoffDistance;
+    cl::Kernel forceKernel;
+    cl::Kernel findBlockBoundsKernel;
+    cl::Kernel sortBoxDataKernel;
+    cl::Kernel findInteractingBlocksKernel;
+    cl::Kernel findInteractionsWithinBlocksKernel;
 };
 
 /**

platforms/opencl/src/OpenCLContext.cpp

@@ -43,6 +43,7 @@
 #include <algorithm>
 #include <fstream>
 #include <iostream>
+#include <set>
 #include <sstream>
 #include <typeinfo>
 
@@ -492,13 +493,32 @@ void OpenCLContext::addForce(OpenCLForceInfo* force) {
 }
 
 string OpenCLContext::replaceStrings(const string& input, const std::map<std::string, std::string>& replacements) const {
+    static set<char> symbolChars;
+    if (symbolChars.size() == 0) {
+        symbolChars.insert('_');
+        for (char c = 'a'; c <= 'z'; c++)
+            symbolChars.insert(c);
+        for (char c = 'A'; c <= 'Z'; c++)
+            symbolChars.insert(c);
+        for (char c = '0'; c <= '9'; c++)
+            symbolChars.insert(c);
+    }
     string result = input;
     for (map<string, string>::const_iterator iter = replacements.begin(); iter != replacements.end(); iter++) {
-        int index = -1;
+        int index = 0;
+        int size = iter->first.size();
         do {
-            index = result.find(iter->first);
-            if (index != result.npos)
-                result.replace(index, iter->first.size(), iter->second);
+            index = result.find(iter->first, index);
+            if (index != result.npos) {
+                if ((index == 0 || symbolChars.find(result[index-1]) == symbolChars.end()) && (index == result.size()-size || symbolChars.find(result[index+size]) == symbolChars.end())) {
+                    // We have found a complete symbol, not part of a longer symbol.
+                    
+                    result.replace(index, size, iter->second);
+                    index += iter->second.size();
+                }
+                else
+                    index++;
+            }
         } while (index != result.npos);
     }
     return result;
@@ -1130,7 +1150,7 @@ void OpenCLContext::reorderAtomsImpl() {
         if (useHilbert)
             binWidth = (Real) (max(max(maxx-minx, maxy-miny), maxz-minz)/255.0);
         else
-            binWidth = (Real) (0.2*nonbonded->getCutoffDistance());
+            binWidth = (Real) (0.2*nonbonded->getMaxCutoffDistance());
         Real invBinWidth = (Real) (1.0/binWidth);
         int xbins = 1 + (int) ((maxx-minx)*invBinWidth);
         int ybins = 1 + (int) ((maxy-miny)*invBinWidth);

platforms/opencl/src/OpenCLKernels.cpp

@@ -121,16 +121,13 @@ void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, boo
     for (vector<OpenCLContext::ForcePreComputation*>::iterator iter = cl.getPreComputations().begin(); iter != cl.getPreComputations().end(); ++iter)
         (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
     OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
-    bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
     cl.setComputeForceCount(cl.getComputeForceCount()+1);
-    if (includeNonbonded)
-        nb.prepareInteractions();
+    nb.prepareInteractions(groups);
 }
 
 double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
     cl.getBondedUtilities().computeInteractions(groups);
-    if ((groups&(1<<cl.getNonbondedUtilities().getForceGroup())) != 0)
-        cl.getNonbondedUtilities().computeInteractions();
+    cl.getNonbondedUtilities().computeInteractions(groups);
     double sum = 0.0;
     for (vector<OpenCLContext::ForcePostComputation*>::iterator iter = cl.getPostComputations().begin(); iter != cl.getPostComputations().end(); ++iter)
         sum += (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
@@ -2643,8 +2640,9 @@ void OpenCLCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOB
     surfaceAreaFactor = -6.0*4*M_PI*force.getSurfaceAreaEnergy();
     bool useCutoff = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff);
     bool usePeriodic = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff && force.getNonbondedMethod() != GBSAOBCForce::CutoffNonPeriodic);
+    cutoff = force.getCutoffDistance();
     string source = OpenCLKernelSources::gbsaObc2;
-    nb.addInteraction(useCutoff, usePeriodic, false, force.getCutoffDistance(), vector<vector<int> >(), source, force.getForceGroup());
+    nb.addInteraction(useCutoff, usePeriodic, false, cutoff, vector<vector<int> >(), source, force.getForceGroup());
     nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("obcParams", "float", 2, sizeof(cl_float2), params->getDeviceBuffer()));;
     nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("bornForce", "real", 1, elementSize, bornForce->getDeviceBuffer()));;
     cl.addForce(new OpenCLGBSAOBCForceInfo(nb.getNumForceBuffers(), force));
@@ -2663,8 +2661,8 @@ double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeF
             defines["USE_CUTOFF"] = "1";
         if (nb.getUsePeriodic())
             defines["USE_PERIODIC"] = "1";
-        defines["CUTOFF_SQUARED"] = cl.doubleToString(nb.getCutoffDistance()*nb.getCutoffDistance());
-        defines["CUTOFF"] = cl.doubleToString(nb.getCutoffDistance());
+        defines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
+        defines["CUTOFF"] = cl.doubleToString(cutoff);
         defines["PREFACTOR"] = cl.doubleToString(prefactor);
         defines["SURFACE_AREA_FACTOR"] = cl.doubleToString(surfaceAreaFactor);
         defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
@@ -2856,6 +2854,7 @@ OpenCLCalcCustomGBForceKernel::~OpenCLCalcCustomGBForceKernel() {
 void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const CustomGBForce& force) {
     if (cl.getPlatformData().contexts.size() > 1)
         throw OpenMMException("CustomGBForce does not support using multiple OpenCL devices");
+    cutoff = force.getCutoffDistance();
     bool useExclusionsForValue = false;
     numComputedValues = force.getNumComputedValues();
     vector<string> computedValueNames(force.getNumComputedValues());
@@ -3047,7 +3046,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
         if (useExclusionsForValue)
             pairValueDefines["USE_EXCLUSIONS"] = "1";
         pairValueDefines["FORCE_WORK_GROUP_SIZE"] = cl.intToString(cl.getNonbondedUtilities().getForceThreadBlockSize());
-        pairValueDefines["CUTOFF_SQUARED"] = cl.doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
+        pairValueDefines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
         pairValueDefines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
         pairValueDefines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
         pairValueDefines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
@@ -3240,7 +3239,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
         if (anyExclusions)
             pairEnergyDefines["USE_EXCLUSIONS"] = "1";
         pairEnergyDefines["FORCE_WORK_GROUP_SIZE"] = cl.intToString(cl.getNonbondedUtilities().getForceThreadBlockSize());
-        pairEnergyDefines["CUTOFF_SQUARED"] = cl.doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
+        pairEnergyDefines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
         pairEnergyDefines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
         pairEnergyDefines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
         pairEnergyDefines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
@@ -3492,7 +3491,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
             globals->upload(globalParamValues);
             arguments.push_back(OpenCLNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(cl_float), globals->getDeviceBuffer()));
         }
-        cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, force.getNumExclusions() > 0, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
+        cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, force.getNumExclusions() > 0, cutoff, exclusionList, source, force.getForceGroup());
         for (int i = 0; i < (int) parameters.size(); i++)
             cl.getNonbondedUtilities().addParameter(parameters[i]);
         for (int i = 0; i < (int) arguments.size(); i++)
@@ -3527,7 +3526,7 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
             int endExclusionIndex = (cl.getContextIndex()+1)*numExclusionTiles/numContexts;
             pairValueDefines["FIRST_EXCLUSION_TILE"] = cl.intToString(startExclusionIndex);
             pairValueDefines["LAST_EXCLUSION_TILE"] = cl.intToString(endExclusionIndex);
-            pairValueDefines["CUTOFF"] = cl.doubleToString(nb.getCutoffDistance());
+            pairValueDefines["CUTOFF"] = cl.doubleToString(cutoff);
             cl::Program program = cl.createProgram(pairValueSrc, pairValueDefines);
             pairValueKernel = cl::Kernel(program, "computeN2Value");
             pairValueSrc = "";
@@ -3541,7 +3540,7 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
             int endExclusionIndex = (cl.getContextIndex()+1)*numExclusionTiles/numContexts;
             pairEnergyDefines["FIRST_EXCLUSION_TILE"] = cl.intToString(startExclusionIndex);
             pairEnergyDefines["LAST_EXCLUSION_TILE"] = cl.intToString(endExclusionIndex);
-            pairEnergyDefines["CUTOFF"] = cl.doubleToString(nb.getCutoffDistance());
+            pairEnergyDefines["CUTOFF"] = cl.doubleToString(cutoff);
             cl::Program program = cl.createProgram(pairEnergySrc, pairEnergyDefines);
             pairEnergyKernel = cl::Kernel(program, "computeN2Energy");
             pairEnergySrc = "";

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -54,10 +54,10 @@ private:
     bool useDouble;
 };
 
-OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : context(context), cutoff(-1.0), useCutoff(false), usePeriodic(false), anyExclusions(false), usePadding(true),
+OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : context(context), useCutoff(false), usePeriodic(false), anyExclusions(false), usePadding(true),
         numForceBuffers(0), exclusionIndices(NULL), exclusionRowIndices(NULL), exclusionTiles(NULL), exclusions(NULL), interactingTiles(NULL), interactingAtoms(NULL),
         interactionCount(NULL), blockCenter(NULL), blockBoundingBox(NULL), sortedBlocks(NULL), sortedBlockCenter(NULL), sortedBlockBoundingBox(NULL),
-        oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), nonbondedForceGroup(0) {
+        oldPositions(NULL), rebuildNeighborList(NULL), blockSorter(NULL), forceRebuildNeighborList(true), lastCutoff(0.0), groupFlags(0) {
     // Decide how many thread blocks and force buffers to use.
 
     deviceIsCpu = (context.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
@@ -126,24 +126,28 @@ OpenCLNonbondedUtilities::~OpenCLNonbondedUtilities() {
 }
 
 void OpenCLNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic, bool usesExclusions, double cutoffDistance, const vector<vector<int> >& exclusionList, const string& kernel, int forceGroup) {
-    if (cutoff != -1.0) {
+    if (groupCutoff.size() > 0) {
         if (usesCutoff != useCutoff)
             throw OpenMMException("All Forces must agree on whether to use a cutoff");
         if (usesPeriodic != usePeriodic)
             throw OpenMMException("All Forces must agree on whether to use periodic boundary conditions");
-        if (cutoffDistance != cutoff)
-            throw OpenMMException("All Forces must use the same cutoff distance");
-        if (forceGroup != nonbondedForceGroup)
-            throw OpenMMException("All nonbonded forces must be in the same force group");
+        if (usesCutoff && groupCutoff.find(forceGroup) != groupCutoff.end() && groupCutoff[forceGroup] != cutoffDistance)
+            throw OpenMMException("All Forces in a single force group must use the same cutoff distance");
     }
     if (usesExclusions)
         requestExclusions(exclusionList);
     useCutoff = usesCutoff;
     usePeriodic = usesPeriodic;
-    cutoff = cutoffDistance;
-    if (kernel.size() > 0)
-        kernelSource += kernel+"\n";
-    nonbondedForceGroup = forceGroup;
+    groupCutoff[forceGroup] = cutoffDistance;
+    groupFlags |= 1<<forceGroup;
+    if (kernel.size() > 0) {
+        if (groupKernelSource.find(forceGroup) == groupKernelSource.end())
+            groupKernelSource[forceGroup] = "";
+        map<string, string> replacements;
+        replacements["CUTOFF"] = "CUTOFF_"+context.intToString(forceGroup);
+        replacements["CUTOFF_SQUARED"] = "CUTOFF_"+context.intToString(forceGroup)+"_SQUARED";
+        groupKernelSource[forceGroup] += context.replaceStrings(kernel, replacements)+"\n";
+    }
 }
 
 void OpenCLNonbondedUtilities::addParameter(const ParameterInfo& parameter) {
@@ -228,6 +232,9 @@ void OpenCLNonbondedUtilities::initialize(const System& system) {
         exclusionIndicesVec.insert(exclusionIndicesVec.end(), exclusionBlocksForBlock[i].begin(), exclusionBlocksForBlock[i].end());
         exclusionRowIndicesVec[i+1] = exclusionIndicesVec.size();
     }
+    maxExclusions = 0;
+    for (int i = 0; i < (int) exclusionBlocksForBlock.size(); i++)
+        maxExclusions = (maxExclusions > exclusionBlocksForBlock[i].size() ? maxExclusions : exclusionBlocksForBlock[i].size());
     exclusionIndices = OpenCLArray::create<cl_uint>(context, exclusionIndicesVec.size(), "exclusionIndices");
     exclusionRowIndices = OpenCLArray::create<cl_uint>(context, exclusionRowIndicesVec.size(), "exclusionRowIndices");
     exclusionIndices->upload(exclusionIndicesVec);
@@ -287,80 +294,6 @@ void OpenCLNonbondedUtilities::initialize(const System& system) {
         vector<cl_uint> count(1, 0);
         interactionCount->upload(count);
     }
-
-    // Create kernels.
-
-    if (kernelSource.size() > 0)
-        forceKernel = createInteractionKernel(kernelSource, parameters, arguments, true, true);
-    if (useCutoff) {
-        double padding = (usePadding ? 0.1*cutoff : 0.0);
-        double paddedCutoff = cutoff+padding;
-        map<string, string> defines;
-        defines["TILE_SIZE"] = context.intToString(OpenCLContext::TileSize);
-        defines["NUM_ATOMS"] = context.intToString(context.getNumAtoms());
-        defines["PADDING"] = context.doubleToString(padding);
-        defines["PADDED_CUTOFF"] = context.doubleToString(paddedCutoff);
-        defines["PADDED_CUTOFF_SQUARED"] = context.doubleToString(paddedCutoff*paddedCutoff);
-        defines["NUM_TILES_WITH_EXCLUSIONS"] = context.intToString(exclusionTiles->getSize());
-        defines["NUM_BLOCKS"] = context.intToString(context.getNumAtomBlocks());
-        defines["SIMD_WIDTH"] = context.intToString(context.getSIMDWidth());
-        if (usePeriodic)
-            defines["USE_PERIODIC"] = "1";
-        int maxExclusions = 0;
-        for (int i = 0; i < (int) exclusionBlocksForBlock.size(); i++)
-            maxExclusions = (maxExclusions > exclusionBlocksForBlock[i].size() ? maxExclusions : exclusionBlocksForBlock[i].size());
-        defines["MAX_EXCLUSIONS"] = context.intToString(maxExclusions);
-        defines["BUFFER_GROUPS"] = (deviceIsCpu ? "4" : "2");
-        string file = (deviceIsCpu ? OpenCLKernelSources::findInteractingBlocks_cpu : OpenCLKernelSources::findInteractingBlocks);
-        int groupSize = (deviceIsCpu || context.getSIMDWidth() < 32 ? 32 : 256);
-        while (true) {
-            defines["GROUP_SIZE"] = context.intToString(groupSize);
-            cl::Program interactingBlocksProgram = context.createProgram(file, defines);
-            findBlockBoundsKernel = cl::Kernel(interactingBlocksProgram, "findBlockBounds");
-            findBlockBoundsKernel.setArg<cl_int>(0, context.getNumAtoms());
-            findBlockBoundsKernel.setArg<cl::Buffer>(6, context.getPosq().getDeviceBuffer());
-            findBlockBoundsKernel.setArg<cl::Buffer>(7, blockCenter->getDeviceBuffer());
-            findBlockBoundsKernel.setArg<cl::Buffer>(8, blockBoundingBox->getDeviceBuffer());
-            findBlockBoundsKernel.setArg<cl::Buffer>(9, rebuildNeighborList->getDeviceBuffer());
-            findBlockBoundsKernel.setArg<cl::Buffer>(10, sortedBlocks->getDeviceBuffer());
-            sortBoxDataKernel = cl::Kernel(interactingBlocksProgram, "sortBoxData");
-            sortBoxDataKernel.setArg<cl::Buffer>(0, sortedBlocks->getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl::Buffer>(1, blockCenter->getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl::Buffer>(2, blockBoundingBox->getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl::Buffer>(3, sortedBlockCenter->getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl::Buffer>(4, sortedBlockBoundingBox->getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl::Buffer>(5, context.getPosq().getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl::Buffer>(6, oldPositions->getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl::Buffer>(7, interactionCount->getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl::Buffer>(8, rebuildNeighborList->getDeviceBuffer());
-            sortBoxDataKernel.setArg<cl_int>(9, true);
-            findInteractingBlocksKernel = cl::Kernel(interactingBlocksProgram, "findBlocksWithInteractions");
-            findInteractingBlocksKernel.setArg<cl::Buffer>(5, interactionCount->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(6, interactingTiles->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(7, interactingAtoms->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(8, context.getPosq().getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl_uint>(9, interactingTiles->getSize());
-            findInteractingBlocksKernel.setArg<cl_uint>(10, startBlockIndex);
-            findInteractingBlocksKernel.setArg<cl_uint>(11, numBlocks);
-            findInteractingBlocksKernel.setArg<cl::Buffer>(12, sortedBlocks->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(13, sortedBlockCenter->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(14, sortedBlockBoundingBox->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(15, exclusionIndices->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(16, exclusionRowIndices->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(17, oldPositions->getDeviceBuffer());
-            findInteractingBlocksKernel.setArg<cl::Buffer>(18, rebuildNeighborList->getDeviceBuffer());
-            if (findInteractingBlocksKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(context.getDevice()) < groupSize) {
-                // The device can't handle this block size, so reduce it.
-                
-                groupSize -= 32;
-                if (groupSize < 32)
-                    throw OpenMMException("Failed to create findInteractingBlocks kernel");
-                continue;
-            }
-            break;
-        }
-        interactingBlocksThreadBlockSize = (deviceIsCpu ? 1 : groupSize);
-    }
 }
 
 static void setPeriodicBoxArgs(OpenCLContext& cl, cl::Kernel& kernel, int index) {
@@ -380,34 +313,53 @@ static void setPeriodicBoxArgs(OpenCLContext& cl, cl::Kernel& kernel, int index)
     }
 }
 
-void OpenCLNonbondedUtilities::prepareInteractions() {
+double OpenCLNonbondedUtilities::getMaxCutoffDistance() {
+    double cutoff = 0.0;
+    for (map<int, double>::const_iterator iter = groupCutoff.begin(); iter != groupCutoff.end(); ++iter)
+        cutoff = max(cutoff, iter->second);
+    return cutoff;
+}
+
+void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
+    if ((forceGroups&groupFlags) == 0)
+        return;
+    if (groupKernels.find(forceGroups) == groupKernels.end())
+        createKernelsForGroups(forceGroups);
     if (!useCutoff)
         return;
     if (numTiles == 0)
         return;
+    KernelSet& kernels = groupKernels[forceGroups];
     if (usePeriodic) {
         mm_float4 box = context.getPeriodicBoxSize();
-        double minAllowedSize = 1.999999*cutoff;
+        double minAllowedSize = 1.999999*kernels.cutoffDistance;
         if (box.x < minAllowedSize || box.y < minAllowedSize || box.z < minAllowedSize)
             throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
     }
 
     // Compute the neighbor list.
 
-    setPeriodicBoxArgs(context, findBlockBoundsKernel, 1);
-    context.executeKernel(findBlockBoundsKernel, context.getNumAtoms());
+    if (lastCutoff != kernels.cutoffDistance)
+        forceRebuildNeighborList = true;
+    setPeriodicBoxArgs(context, kernels.findBlockBoundsKernel, 1);
+    context.executeKernel(kernels.findBlockBoundsKernel, context.getNumAtoms());
     blockSorter->sort(*sortedBlocks);
-    context.executeKernel(sortBoxDataKernel, context.getNumAtoms());
-    setPeriodicBoxArgs(context, findInteractingBlocksKernel, 0);
-    context.executeKernel(findInteractingBlocksKernel, context.getNumAtoms(), interactingBlocksThreadBlockSize);
-    sortBoxDataKernel.setArg<cl_int>(9, false);
+    kernels.sortBoxDataKernel.setArg<cl_int>(9, forceRebuildNeighborList);
+    context.executeKernel(kernels.sortBoxDataKernel, context.getNumAtoms());
+    setPeriodicBoxArgs(context, kernels.findInteractingBlocksKernel, 0);
+    context.executeKernel(kernels.findInteractingBlocksKernel, context.getNumAtoms(), interactingBlocksThreadBlockSize);
+    forceRebuildNeighborList = false;
+    lastCutoff = kernels.cutoffDistance;
 }
 
-void OpenCLNonbondedUtilities::computeInteractions() {
-    if (kernelSource.size() > 0) {
+void OpenCLNonbondedUtilities::computeInteractions(int forceGroups) {
+    if ((forceGroups&groupFlags) == 0)
+        return;
+    KernelSet& kernels = groupKernels[forceGroups];
+    if (kernels.hasForces) {
         if (useCutoff)
-            setPeriodicBoxArgs(context, forceKernel, 9);
-        context.executeKernel(forceKernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
+            setPeriodicBoxArgs(context, kernels.forceKernel, 9);
+        context.executeKernel(kernels.forceKernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
         if (context.getComputeForceCount() == 1)
             updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
     }
@@ -434,13 +386,15 @@ void OpenCLNonbondedUtilities::updateNeighborListSize() {
     interactingAtoms = NULL;
     interactingTiles = OpenCLArray::create<cl_int>(context, maxTiles, "interactingTiles");
     interactingAtoms = OpenCLArray::create<cl_int>(context, OpenCLContext::TileSize*maxTiles, "interactingAtoms");
-    forceKernel.setArg<cl::Buffer>(7, interactingTiles->getDeviceBuffer());
-    forceKernel.setArg<cl_uint>(14, maxTiles);
-    forceKernel.setArg<cl::Buffer>(17, interactingAtoms->getDeviceBuffer());
-    findInteractingBlocksKernel.setArg<cl::Buffer>(6, interactingTiles->getDeviceBuffer());
-    findInteractingBlocksKernel.setArg<cl::Buffer>(7, interactingAtoms->getDeviceBuffer());
-    findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
-    sortBoxDataKernel.setArg<cl_int>(9, true);
+    for (map<int, KernelSet>::iterator iter = groupKernels.begin(); iter != groupKernels.end(); ++iter) {
+        iter->second.forceKernel.setArg<cl::Buffer>(7, interactingTiles->getDeviceBuffer());
+        iter->second.forceKernel.setArg<cl_uint>(14, maxTiles);
+        iter->second.forceKernel.setArg<cl::Buffer>(17, interactingAtoms->getDeviceBuffer());
+        iter->second.findInteractingBlocksKernel.setArg<cl::Buffer>(6, interactingTiles->getDeviceBuffer());
+        iter->second.findInteractingBlocksKernel.setArg<cl::Buffer>(7, interactingAtoms->getDeviceBuffer());
+        iter->second.findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
+    }
+    forceRebuildNeighborList = true;
 }
 
 void OpenCLNonbondedUtilities::setUsePadding(bool padding) {
@@ -454,18 +408,103 @@ void OpenCLNonbondedUtilities::setAtomBlockRange(double startFraction, double en
     int totalTiles = context.getNumAtomBlocks()*(context.getNumAtomBlocks()+1)/2;
     startTileIndex = (int) (startFraction*totalTiles);;
     numTiles = (int) (endFraction*totalTiles)-startTileIndex;
-    if (useCutoff && interactingTiles != NULL) {
+    if (useCutoff) {
         // We are using a cutoff, and the kernels have already been created.
         
-        forceKernel.setArg<cl_uint>(5, startTileIndex);
-        forceKernel.setArg<cl_uint>(6, numTiles);
-        findInteractingBlocksKernel.setArg<cl_uint>(10, startBlockIndex);
-        findInteractingBlocksKernel.setArg<cl_uint>(11, numBlocks);
-        sortBoxDataKernel.setArg<cl_int>(9, true);
+        for (map<int, KernelSet>::iterator iter = groupKernels.begin(); iter != groupKernels.end(); ++iter) {
+            iter->second.forceKernel.setArg<cl_uint>(5, startTileIndex);
+            iter->second.forceKernel.setArg<cl_uint>(6, numTiles);
+            iter->second.findInteractingBlocksKernel.setArg<cl_uint>(10, startBlockIndex);
+            iter->second.findInteractingBlocksKernel.setArg<cl_uint>(11, numBlocks);
+        }
+        forceRebuildNeighborList = true;
+    }
+}
+
+void OpenCLNonbondedUtilities::createKernelsForGroups(int groups) {
+    KernelSet kernels;
+    double cutoff = 0.0;
+    string source;
+    for (int i = 0; i < 32; i++) {
+        if ((groups&(1<<i)) != 0) {
+            cutoff = max(cutoff, groupCutoff[i]);
+            source += groupKernelSource[i];
+        }
+    }
+    kernels.hasForces = (source.size() > 0);
+    kernels.cutoffDistance = cutoff;
+    if (kernels.hasForces)
+        kernels.forceKernel = createInteractionKernel(source, parameters, arguments, true, true, groups);
+    if (useCutoff && kernels.hasForces) {
+        double padding = (usePadding ? 0.1*cutoff : 0.0);
+        double paddedCutoff = cutoff+padding;
+        map<string, string> defines;
+        defines["TILE_SIZE"] = context.intToString(OpenCLContext::TileSize);
+        defines["NUM_ATOMS"] = context.intToString(context.getNumAtoms());
+        defines["PADDING"] = context.doubleToString(padding);
+        defines["PADDED_CUTOFF"] = context.doubleToString(paddedCutoff);
+        defines["PADDED_CUTOFF_SQUARED"] = context.doubleToString(paddedCutoff*paddedCutoff);
+        defines["NUM_TILES_WITH_EXCLUSIONS"] = context.intToString(exclusionTiles->getSize());
+        defines["NUM_BLOCKS"] = context.intToString(context.getNumAtomBlocks());
+        defines["SIMD_WIDTH"] = context.intToString(context.getSIMDWidth());
+        if (usePeriodic)
+            defines["USE_PERIODIC"] = "1";
+        defines["MAX_EXCLUSIONS"] = context.intToString(maxExclusions);
+        defines["BUFFER_GROUPS"] = (deviceIsCpu ? "4" : "2");
+        string file = (deviceIsCpu ? OpenCLKernelSources::findInteractingBlocks_cpu : OpenCLKernelSources::findInteractingBlocks);
+        int groupSize = (deviceIsCpu || context.getSIMDWidth() < 32 ? 32 : 256);
+        while (true) {
+            defines["GROUP_SIZE"] = context.intToString(groupSize);
+            cl::Program interactingBlocksProgram = context.createProgram(file, defines);
+            kernels.findBlockBoundsKernel = cl::Kernel(interactingBlocksProgram, "findBlockBounds");
+            kernels.findBlockBoundsKernel.setArg<cl_int>(0, context.getNumAtoms());
+            kernels.findBlockBoundsKernel.setArg<cl::Buffer>(6, context.getPosq().getDeviceBuffer());
+            kernels.findBlockBoundsKernel.setArg<cl::Buffer>(7, blockCenter->getDeviceBuffer());
+            kernels.findBlockBoundsKernel.setArg<cl::Buffer>(8, blockBoundingBox->getDeviceBuffer());
+            kernels.findBlockBoundsKernel.setArg<cl::Buffer>(9, rebuildNeighborList->getDeviceBuffer());
+            kernels.findBlockBoundsKernel.setArg<cl::Buffer>(10, sortedBlocks->getDeviceBuffer());
+            kernels.sortBoxDataKernel = cl::Kernel(interactingBlocksProgram, "sortBoxData");
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(0, sortedBlocks->getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(1, blockCenter->getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(2, blockBoundingBox->getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(3, sortedBlockCenter->getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(4, sortedBlockBoundingBox->getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(5, context.getPosq().getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(6, oldPositions->getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(7, interactionCount->getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl::Buffer>(8, rebuildNeighborList->getDeviceBuffer());
+            kernels.sortBoxDataKernel.setArg<cl_int>(9, true);
+            kernels.findInteractingBlocksKernel = cl::Kernel(interactingBlocksProgram, "findBlocksWithInteractions");
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(5, interactionCount->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(6, interactingTiles->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(7, interactingAtoms->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(8, context.getPosq().getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl_uint>(9, interactingTiles->getSize());
+            kernels.findInteractingBlocksKernel.setArg<cl_uint>(10, startBlockIndex);
+            kernels.findInteractingBlocksKernel.setArg<cl_uint>(11, numBlocks);
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(12, sortedBlocks->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(13, sortedBlockCenter->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(14, sortedBlockBoundingBox->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(15, exclusionIndices->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(16, exclusionRowIndices->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(17, oldPositions->getDeviceBuffer());
+            kernels.findInteractingBlocksKernel.setArg<cl::Buffer>(18, rebuildNeighborList->getDeviceBuffer());
+            if (kernels.findInteractingBlocksKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(context.getDevice()) < groupSize) {
+                // The device can't handle this block size, so reduce it.
+                
+                groupSize -= 32;
+                if (groupSize < 32)
+                    throw OpenMMException("Failed to create findInteractingBlocks kernel");
+                continue;
+            }
+            break;
+        }
+        interactingBlocksThreadBlockSize = (deviceIsCpu ? 1 : groupSize);
     }
+    groupKernels[groups] = kernels;
 }
 
-cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& source, const vector<ParameterInfo>& params, const vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric) const {
+cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& source, const vector<ParameterInfo>& params, const vector<ParameterInfo>& arguments, bool useExclusions, bool isSymmetric, int groups) {
     map<string, string> replacements;
     replacements["COMPUTE_INTERACTION"] = source;
     const string suffixes[] = {"x", "y", "z", "w"};
@@ -565,8 +604,16 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc
     if (useCutoff && context.getSIMDWidth() < 32)
         defines["PRUNE_BY_CUTOFF"] = "1";
     defines["FORCE_WORK_GROUP_SIZE"] = context.intToString(forceThreadBlockSize);
-    defines["CUTOFF_SQUARED"] = context.doubleToString(cutoff*cutoff);
-    defines["CUTOFF"] = context.doubleToString(cutoff);
+    double maxCutoff = 0.0;
+    for (int i = 0; i < 32; i++) {
+        if ((groups&(1<<i)) != 0) {
+            double cutoff = groupCutoff[i];
+            maxCutoff = max(maxCutoff, cutoff);
+            defines["CUTOFF_"+context.intToString(i)+"_SQUARED"] = context.doubleToString(cutoff*cutoff);
+            defines["CUTOFF_"+context.intToString(i)] = context.doubleToString(cutoff);
+        }
+    }
+    defines["MAX_CUTOFF"] = context.doubleToString(maxCutoff);
     defines["NUM_ATOMS"] = context.intToString(context.getNumAtoms());
     defines["PADDED_NUM_ATOMS"] = context.intToString(context.getPaddedNumAtoms());
     defines["NUM_BLOCKS"] = context.intToString(context.getNumAtomBlocks());

platforms/opencl/src/kernels/nonbonded.cl

@@ -220,9 +220,9 @@ __kernel void computeNonbonded(
         if (numTiles <= maxTiles) {
             x = tiles[pos];
             real4 blockSizeX = blockSize[x];
-            singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= CUTOFF &&
-                                  0.5f*periodicBoxSize.y-blockSizeX.y >= CUTOFF &&
-                                  0.5f*periodicBoxSize.z-blockSizeX.z >= CUTOFF);
+            singlePeriodicCopy = (0.5f*periodicBoxSize.x-blockSizeX.x >= MAX_CUTOFF &&
+                                  0.5f*periodicBoxSize.y-blockSizeX.y >= MAX_CUTOFF &&
+                                  0.5f*periodicBoxSize.z-blockSizeX.z >= MAX_CUTOFF);
         }
         else
 #endif

platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp

@@ -973,6 +973,62 @@ void testInteractionGroupLongRangeCorrection() {
     ASSERT_EQUAL_TOL(expected, energy2-energy1, 1e-4);
 }
 
+void testMultipleCutoffs() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    
+    // Add multiple nonbonded forces that have different cutoffs.
+    
+    CustomNonbondedForce* nonbonded1 = new CustomNonbondedForce("2*r");
+    nonbonded1->addParticle(vector<double>());
+    nonbonded1->addParticle(vector<double>());
+    nonbonded1->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
+    nonbonded1->setCutoffDistance(2.5);
+    system.addForce(nonbonded1);
+    CustomNonbondedForce* nonbonded2 = new CustomNonbondedForce("3*r");
+    nonbonded2->addParticle(vector<double>());
+    nonbonded2->addParticle(vector<double>());
+    nonbonded2->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
+    nonbonded2->setCutoffDistance(2.9);
+    nonbonded2->setForceGroup(1);
+    system.addForce(nonbonded2);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(0, 0, 0);
+    for (double r = 2.4; r < 3.2; r += 0.2) {
+        positions[1][1] = r;
+        context.setPositions(positions);
+        double e1 = (r < 2.5 ? 2.0*r : 0.0);
+        double e2 = (r < 2.9 ? 3.0*r : 0.0);
+        double f1 = (r < 2.5 ? 2.0 : 0.0);
+        double f2 = (r < 2.9 ? 3.0 : 0.0);
+        
+        // Check the first force.
+        
+        State state = context.getState(State::Forces | State::Energy, false, 1);
+        ASSERT_EQUAL_VEC(Vec3(0, f1, 0), state.getForces()[0], TOL);
+        ASSERT_EQUAL_VEC(Vec3(0, -f1, 0), state.getForces()[1], TOL);
+        ASSERT_EQUAL_TOL(e1, state.getPotentialEnergy(), TOL);
+        
+        // Check the second force.
+        
+        state = context.getState(State::Forces | State::Energy, false, 2);
+        ASSERT_EQUAL_VEC(Vec3(0, f2, 0), state.getForces()[0], TOL);
+        ASSERT_EQUAL_VEC(Vec3(0, -f2, 0), state.getForces()[1], TOL);
+        ASSERT_EQUAL_TOL(e2, state.getPotentialEnergy(), TOL);
+        
+        // Check the sum of both forces.
+
+        state = context.getState(State::Forces | State::Energy);
+        ASSERT_EQUAL_VEC(Vec3(0, f1+f2, 0), state.getForces()[0], TOL);
+        ASSERT_EQUAL_VEC(Vec3(0, -f1-f2, 0), state.getForces()[1], TOL);
+        ASSERT_EQUAL_TOL(e1+e2, state.getPotentialEnergy(), TOL);
+    }
+}
+
 int main(int argc, char* argv[]) {
     try {
         if (argc > 1)
@@ -997,6 +1053,7 @@ int main(int argc, char* argv[]) {
         testInteractionGroups();
         testLargeInteractionGroup();
         testInteractionGroupLongRangeCorrection();
+        testMultipleCutoffs();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;