OpenCLKernels.cpp 432 KB
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/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
 *                                                                            *
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 * Portions copyright (c) 2008-2017 Stanford University and the Authors.      *
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 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
 * This program is free software: you can redistribute it and/or modify       *
 * it under the terms of the GNU Lesser General Public License as published   *
 * by the Free Software Foundation, either version 3 of the License, or       *
 * (at your option) any later version.                                        *
 *                                                                            *
 * This program is distributed in the hope that it will be useful,            *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
 * GNU Lesser General Public License for more details.                        *
 *                                                                            *
 * You should have received a copy of the GNU Lesser General Public License   *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
 * -------------------------------------------------------------------------- */

#include "OpenCLKernels.h"
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#include "OpenCLForceInfo.h"
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#include "openmm/LangevinIntegrator.h"
#include "openmm/Context.h"
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#include "openmm/internal/AndersenThermostatImpl.h"
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#include "openmm/internal/CMAPTorsionForceImpl.h"
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#include "openmm/internal/ContextImpl.h"
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#include "openmm/internal/CustomCentroidBondForceImpl.h"
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#include "openmm/internal/CustomCompoundBondForceImpl.h"
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#include "openmm/internal/CustomHbondForceImpl.h"
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#include "openmm/internal/CustomManyParticleForceImpl.h"
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#include "openmm/internal/CustomNonbondedForceImpl.h"
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#include "openmm/internal/NonbondedForceImpl.h"
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#include "openmm/internal/OSRngSeed.h"
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#include "OpenCLBondedUtilities.h"
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#include "OpenCLExpressionUtilities.h"
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#include "OpenCLIntegrationUtilities.h"
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#include "OpenCLNonbondedUtilities.h"
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#include "OpenCLKernelSources.h"
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#include "lepton/CustomFunction.h"
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#include "lepton/ExpressionTreeNode.h"
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#include "lepton/Operation.h"
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#include "lepton/Parser.h"
#include "lepton/ParsedExpression.h"
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#include "SimTKOpenMMRealType.h"
#include "SimTKOpenMMUtilities.h"
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#include <algorithm>
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#include <cmath>
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#include <set>
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using namespace OpenMM;
using namespace std;
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using namespace Lepton;
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static void setPosqCorrectionArg(OpenCLContext& cl, cl::Kernel& kernel, int index) {
    if (cl.getUseMixedPrecision())
        kernel.setArg<cl::Buffer>(index, cl.getPosqCorrection().getDeviceBuffer());
    else
        kernel.setArg<void*>(index, NULL);
}

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static void setPeriodicBoxSizeArg(OpenCLContext& cl, cl::Kernel& kernel, int index) {
    if (cl.getUseDoublePrecision())
        kernel.setArg<mm_double4>(index, cl.getPeriodicBoxSizeDouble());
    else
        kernel.setArg<mm_float4>(index, cl.getPeriodicBoxSize());
}

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static void setPeriodicBoxArgs(OpenCLContext& cl, cl::Kernel& kernel, int index) {
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    if (cl.getUseDoublePrecision()) {
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        kernel.setArg<mm_double4>(index++, cl.getPeriodicBoxSizeDouble());
        kernel.setArg<mm_double4>(index++, cl.getInvPeriodicBoxSizeDouble());
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        kernel.setArg<mm_double4>(index++, cl.getPeriodicBoxVecXDouble());
        kernel.setArg<mm_double4>(index++, cl.getPeriodicBoxVecYDouble());
        kernel.setArg<mm_double4>(index, cl.getPeriodicBoxVecZDouble());
    }
    else {
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        kernel.setArg<mm_float4>(index++, cl.getPeriodicBoxSize());
        kernel.setArg<mm_float4>(index++, cl.getInvPeriodicBoxSize());
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        kernel.setArg<mm_float4>(index++, cl.getPeriodicBoxVecX());
        kernel.setArg<mm_float4>(index++, cl.getPeriodicBoxVecY());
        kernel.setArg<mm_float4>(index, cl.getPeriodicBoxVecZ());
    }
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}

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static bool isZeroExpression(const Lepton::ParsedExpression& expression) {
    const Lepton::Operation& op = expression.getRootNode().getOperation();
    if (op.getId() != Lepton::Operation::CONSTANT)
        return false;
    return (dynamic_cast<const Lepton::Operation::Constant&>(op).getValue() == 0.0);
}

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static bool usesVariable(const Lepton::ExpressionTreeNode& node, const string& variable) {
    const Lepton::Operation& op = node.getOperation();
    if (op.getId() == Lepton::Operation::VARIABLE && op.getName() == variable)
        return true;
    for (int i = 0; i < (int) node.getChildren().size(); i++)
        if (usesVariable(node.getChildren()[i], variable))
            return true;
    return false;
}

static bool usesVariable(const Lepton::ParsedExpression& expression, const string& variable) {
    return usesVariable(expression.getRootNode(), variable);
}

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static pair<ExpressionTreeNode, string> makeVariable(const string& name, const string& value) {
    return make_pair(ExpressionTreeNode(new Operation::Variable(name)), value);
}

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void OpenCLCalcForcesAndEnergyKernel::initialize(const System& system) {
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}

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void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
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    cl.setForcesValid(true);
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    cl.clearAutoclearBuffers();
    for (vector<OpenCLContext::ForcePreComputation*>::iterator iter = cl.getPreComputations().begin(); iter != cl.getPreComputations().end(); ++iter)
        (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
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    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
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    cl.setComputeForceCount(cl.getComputeForceCount()+1);
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    nb.prepareInteractions(groups);
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    map<string, double>& derivs = cl.getEnergyParamDerivWorkspace();
    for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter)
        derivs[iter->first] = 0;
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}

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double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
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    cl.getBondedUtilities().computeInteractions(groups);
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    cl.getNonbondedUtilities().computeInteractions(groups, includeForces, includeEnergy);
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    double sum = 0.0;
    for (vector<OpenCLContext::ForcePostComputation*>::iterator iter = cl.getPostComputations().begin(); iter != cl.getPostComputations().end(); ++iter)
        sum += (*iter)->computeForceAndEnergy(includeForces, includeEnergy, groups);
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    cl.reduceForces();
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    cl.getIntegrationUtilities().distributeForcesFromVirtualSites();
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    if (includeEnergy) {
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        OpenCLArray& energyArray = cl.getEnergyBuffer();
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        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
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            double* energy = (double*) cl.getPinnedBuffer();
            energyArray.download(energy);
            for (int i = 0; i < energyArray.getSize(); i++)
                sum += energy[i];
        }
        else {
            float* energy = (float*) cl.getPinnedBuffer();
            energyArray.download(energy);
            for (int i = 0; i < energyArray.getSize(); i++)
                sum += energy[i];
        }
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    }
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    if (!cl.getForcesValid())
        valid = false;
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    return sum;
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}

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void OpenCLUpdateStateDataKernel::initialize(const System& system) {
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}

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double OpenCLUpdateStateDataKernel::getTime(const ContextImpl& context) const {
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    return cl.getTime();
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}

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void OpenCLUpdateStateDataKernel::setTime(ContextImpl& context, double time) {
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    vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
    for (int i = 0; i < (int) contexts.size(); i++)
        contexts[i]->setTime(time);
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}

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void OpenCLUpdateStateDataKernel::getPositions(ContextImpl& context, vector<Vec3>& positions) {
    int numParticles = context.getSystem().getNumParticles();
    positions.resize(numParticles);
    vector<mm_float4> posCorrection;
    if (cl.getUseDoublePrecision()) {
        mm_double4* posq = (mm_double4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq);
    }
    else if (cl.getUseMixedPrecision()) {
        mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq, false);
        posCorrection.resize(numParticles);
        cl.getPosqCorrection().download(posCorrection);
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    }
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    else {
        mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq);
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    }
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    // Filling in the output array is done in parallel for speed.
    
    cl.getPlatformData().threads.execute([&] (ThreadPool& threads, int threadIndex) {
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        // Compute the position of each particle to return to the user.  This is done in parallel for speed.
        
        const vector<int>& order = cl.getAtomIndex();
        int numParticles = cl.getNumAtoms();
        Vec3 boxVectors[3];
        cl.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
        int numThreads = threads.getNumThreads();
        int start = threadIndex*numParticles/numThreads;
        int end = (threadIndex+1)*numParticles/numThreads;
        if (cl.getUseDoublePrecision()) {
            mm_double4* posq = (mm_double4*) cl.getPinnedBuffer();
            for (int i = start; i < end; ++i) {
                mm_double4 pos = posq[i];
                mm_int4 offset = cl.getPosCellOffsets()[i];
                positions[order[i]] = Vec3(pos.x, pos.y, pos.z)-boxVectors[0]*offset.x-boxVectors[1]*offset.y-boxVectors[2]*offset.z;
            }
        }
        else if (cl.getUseMixedPrecision()) {
            mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
            for (int i = start; i < end; ++i) {
                mm_float4 pos1 = posq[i];
                mm_float4 pos2 = posCorrection[i];
                mm_int4 offset = cl.getPosCellOffsets()[i];
                positions[order[i]] = Vec3((double)pos1.x+(double)pos2.x, (double)pos1.y+(double)pos2.y, (double)pos1.z+(double)pos2.z)-boxVectors[0]*offset.x-boxVectors[1]*offset.y-boxVectors[2]*offset.z;
            }
        }
        else {
            mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
            for (int i = start; i < end; ++i) {
                mm_float4 pos = posq[i];
                mm_int4 offset = cl.getPosCellOffsets()[i];
                positions[order[i]] = Vec3(pos.x, pos.y, pos.z)-boxVectors[0]*offset.x-boxVectors[1]*offset.y-boxVectors[2]*offset.z;
            }
        }
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    });
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    cl.getPlatformData().threads.waitForThreads();
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}

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void OpenCLUpdateStateDataKernel::setPositions(ContextImpl& context, const vector<Vec3>& positions) {
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    const vector<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
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    if (cl.getUseDoublePrecision()) {
        mm_double4* posq = (mm_double4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq);
        for (int i = 0; i < numParticles; ++i) {
            mm_double4& pos = posq[i];
            const Vec3& p = positions[order[i]];
            pos.x = p[0];
            pos.y = p[1];
            pos.z = p[2];
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            posq[i] = mm_double4(0.0, 0.0, 0.0, 0.0);
        cl.getPosq().upload(posq);
    }
    else {
        mm_float4* posq = (mm_float4*) cl.getPinnedBuffer();
        cl.getPosq().download(posq);
        for (int i = 0; i < numParticles; ++i) {
            mm_float4& pos = posq[i];
            const Vec3& p = positions[order[i]];
            pos.x = (cl_float) p[0];
            pos.y = (cl_float) p[1];
            pos.z = (cl_float) p[2];
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            posq[i] = mm_float4(0.0f, 0.0f, 0.0f, 0.0f);
        cl.getPosq().upload(posq);
    }
    if (cl.getUseMixedPrecision()) {
        mm_float4* posCorrection = (mm_float4*) cl.getPinnedBuffer();
        for (int i = 0; i < numParticles; ++i) {
            mm_float4& c = posCorrection[i];
            const Vec3& p = positions[order[i]];
            c.x = (cl_float) (p[0]-(cl_float)p[0]);
            c.y = (cl_float) (p[1]-(cl_float)p[1]);
            c.z = (cl_float) (p[2]-(cl_float)p[2]);
            c.w = 0;
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            posCorrection[i] = mm_float4(0.0f, 0.0f, 0.0f, 0.0f);
        cl.getPosqCorrection().upload(posCorrection);
    }
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    for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++)
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        cl.getPosCellOffsets()[i] = mm_int4(0, 0, 0, 0);
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    cl.reorderAtoms();
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}

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void OpenCLUpdateStateDataKernel::getVelocities(ContextImpl& context, vector<Vec3>& velocities) {
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    const vector<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
    velocities.resize(numParticles);
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    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        mm_double4* velm = (mm_double4*) cl.getPinnedBuffer();
        cl.getVelm().download(velm);
        for (int i = 0; i < numParticles; ++i) {
            mm_double4 vel = velm[i];
            mm_int4 offset = cl.getPosCellOffsets()[i];
            velocities[order[i]] = Vec3(vel.x, vel.y, vel.z);
        }
    }
    else {
        mm_float4* velm = (mm_float4*) cl.getPinnedBuffer();
        cl.getVelm().download(velm);
        for (int i = 0; i < numParticles; ++i) {
            mm_float4 vel = velm[i];
            mm_int4 offset = cl.getPosCellOffsets()[i];
            velocities[order[i]] = Vec3(vel.x, vel.y, vel.z);
        }
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    }
}

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void OpenCLUpdateStateDataKernel::setVelocities(ContextImpl& context, const vector<Vec3>& velocities) {
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    const vector<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
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    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        mm_double4* velm = (mm_double4*) cl.getPinnedBuffer();
        cl.getVelm().download(velm);
        for (int i = 0; i < numParticles; ++i) {
            mm_double4& vel = velm[i];
            const Vec3& p = velocities[order[i]];
            vel.x = p[0];
            vel.y = p[1];
            vel.z = p[2];
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            velm[i] = mm_double4(0.0, 0.0, 0.0, 0.0);
        cl.getVelm().upload(velm);
    }
    else {
        mm_float4* velm = (mm_float4*) cl.getPinnedBuffer();
        cl.getVelm().download(velm);
        for (int i = 0; i < numParticles; ++i) {
            mm_float4& vel = velm[i];
            const Vec3& p = velocities[order[i]];
            vel.x = p[0];
            vel.y = p[1];
            vel.z = p[2];
        }
        for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
            velm[i] = mm_float4(0.0f, 0.0f, 0.0f, 0.0f);
        cl.getVelm().upload(velm);
    }
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}

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void OpenCLUpdateStateDataKernel::getForces(ContextImpl& context, vector<Vec3>& forces) {
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    const vector<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
    forces.resize(numParticles);
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    if (cl.getUseDoublePrecision()) {
        mm_double4* force = (mm_double4*) cl.getPinnedBuffer();
        cl.getForce().download(force);
        for (int i = 0; i < numParticles; ++i) {
            mm_double4 f = force[i];
            forces[order[i]] = Vec3(f.x, f.y, f.z);
        }
    }
    else {
        mm_float4* force = (mm_float4*) cl.getPinnedBuffer();
        cl.getForce().download(force);
        for (int i = 0; i < numParticles; ++i) {
            mm_float4 f = force[i];
            forces[order[i]] = Vec3(f.x, f.y, f.z);
        }
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    }
}

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void OpenCLUpdateStateDataKernel::getEnergyParameterDerivatives(ContextImpl& context, map<string, double>& derivs) {
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    const vector<string>& paramDerivNames = cl.getEnergyParamDerivNames();
    int numDerivs = paramDerivNames.size();
    if (numDerivs == 0)
        return;
    derivs = cl.getEnergyParamDerivWorkspace();
    OpenCLArray& derivArray = cl.getEnergyParamDerivBuffer();
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        vector<double> derivBuffers;
        derivArray.download(derivBuffers);
        for (int i = numDerivs; i < derivArray.getSize(); i += numDerivs)
            for (int j = 0; j < numDerivs; j++)
                derivBuffers[j] += derivBuffers[i+j];
        for (int i = 0; i < numDerivs; i++)
            derivs[paramDerivNames[i]] += derivBuffers[i];
    }
    else {
        vector<float> derivBuffers;
        derivArray.download(derivBuffers);
        for (int i = numDerivs; i < derivArray.getSize(); i += numDerivs)
            for (int j = 0; j < numDerivs; j++)
                derivBuffers[j] += derivBuffers[i+j];
        for (int i = 0; i < numDerivs; i++)
            derivs[paramDerivNames[i]] += derivBuffers[i];
    }
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}

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void OpenCLUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const {
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    cl.getPeriodicBoxVectors(a, b, c);
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}

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void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
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    vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
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    // If any particles have been wrapped to the first periodic box, we need to unwrap them
    // to avoid changing their positions.

    vector<Vec3> positions;
    for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++) {
        mm_int4& offset = cl.getPosCellOffsets()[i];
        if (offset.x != 0 || offset.y != 0 || offset.z != 0) {
            getPositions(context, positions);
            break;
        }
    }
    
    // Update the vectors.

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    for (int i = 0; i < (int) contexts.size(); i++)
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        contexts[i]->setPeriodicBoxVectors(a, b, c);
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    if (positions.size() > 0)
        setPositions(context, positions);
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}

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void OpenCLUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream& stream) {
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    int version = 2;
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    stream.write((char*) &version, sizeof(int));
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    int precision = (cl.getUseDoublePrecision() ? 2 : cl.getUseMixedPrecision() ? 1 : 0);
    stream.write((char*) &precision, sizeof(int));
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    double time = cl.getTime();
    stream.write((char*) &time, sizeof(double));
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    int stepCount = cl.getStepCount();
    stream.write((char*) &stepCount, sizeof(int));
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    int stepsSinceReorder = cl.getStepsSinceReorder();
    stream.write((char*) &stepsSinceReorder, sizeof(int));
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    char* buffer = (char*) cl.getPinnedBuffer();
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    cl.getPosq().download(buffer);
    stream.write(buffer, cl.getPosq().getSize()*cl.getPosq().getElementSize());
    if (cl.getUseMixedPrecision()) {
        cl.getPosqCorrection().download(buffer);
        stream.write(buffer, cl.getPosqCorrection().getSize()*cl.getPosqCorrection().getElementSize());
    }
    cl.getVelm().download(buffer);
    stream.write(buffer, cl.getVelm().getSize()*cl.getVelm().getElementSize());
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    stream.write((char*) &cl.getAtomIndex()[0], sizeof(cl_int)*cl.getAtomIndex().size());
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    stream.write((char*) &cl.getPosCellOffsets()[0], sizeof(mm_int4)*cl.getPosCellOffsets().size());
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    Vec3 boxVectors[3];
    cl.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
    stream.write((char*) boxVectors, 3*sizeof(Vec3));
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    cl.getIntegrationUtilities().createCheckpoint(stream);
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    SimTKOpenMMUtilities::createCheckpoint(stream);
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}

void OpenCLUpdateStateDataKernel::loadCheckpoint(ContextImpl& context, istream& stream) {
    int version;
    stream.read((char*) &version, sizeof(int));
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    if (version != 2)
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        throw OpenMMException("Checkpoint was created with a different version of OpenMM");
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    int precision;
    stream.read((char*) &precision, sizeof(int));
    int expectedPrecision = (cl.getUseDoublePrecision() ? 2 : cl.getUseMixedPrecision() ? 1 : 0);
    if (precision != expectedPrecision)
        throw OpenMMException("Checkpoint was created with a different numeric precision");
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    double time;
    stream.read((char*) &time, sizeof(double));
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    int stepCount, stepsSinceReorder;
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    stream.read((char*) &stepCount, sizeof(int));
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    stream.read((char*) &stepsSinceReorder, sizeof(int));
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    vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
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    for (int i = 0; i < (int) contexts.size(); i++) {
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        contexts[i]->setTime(time);
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        contexts[i]->setStepCount(stepCount);
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        contexts[i]->setStepsSinceReorder(stepsSinceReorder);
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    }
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    char* buffer = (char*) cl.getPinnedBuffer();
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    stream.read(buffer, cl.getPosq().getSize()*cl.getPosq().getElementSize());
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    cl.getPosq().upload(buffer);
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    if (cl.getUseMixedPrecision()) {
        stream.read(buffer, cl.getPosqCorrection().getSize()*cl.getPosqCorrection().getElementSize());
        cl.getPosqCorrection().upload(buffer);
    }
    stream.read(buffer, cl.getVelm().getSize()*cl.getVelm().getElementSize());
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    cl.getVelm().upload(buffer);
    stream.read((char*) &cl.getAtomIndex()[0], sizeof(cl_int)*cl.getAtomIndex().size());
    cl.getAtomIndexArray().upload(cl.getAtomIndex());
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    stream.read((char*) &cl.getPosCellOffsets()[0], sizeof(mm_int4)*cl.getPosCellOffsets().size());
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    Vec3 boxVectors[3];
    stream.read((char*) &boxVectors, 3*sizeof(Vec3));
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    for (int i = 0; i < (int) contexts.size(); i++)
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        contexts[i]->setPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
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    cl.getIntegrationUtilities().loadCheckpoint(stream);
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    SimTKOpenMMUtilities::loadCheckpoint(stream);
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    for (int i = 0; i < (int) cl.getReorderListeners().size(); i++)
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        cl.getReorderListeners()[i]->execute();
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}

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void OpenCLApplyConstraintsKernel::initialize(const System& system) {
}

void OpenCLApplyConstraintsKernel::apply(ContextImpl& context, double tol) {
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    if (!hasInitializedKernel) {
        hasInitializedKernel = true;
        map<string, string> defines;
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        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
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        cl::Program program = cl.createProgram(OpenCLKernelSources::constraints, defines);
        applyDeltasKernel = cl::Kernel(program, "applyPositionDeltas");
        applyDeltasKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
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        setPosqCorrectionArg(cl, applyDeltasKernel, 1);
        applyDeltasKernel.setArg<cl::Buffer>(2, cl.getIntegrationUtilities().getPosDelta().getDeviceBuffer());
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    }
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    cl.clearBuffer(integration.getPosDelta());
    integration.applyConstraints(tol);
    cl.executeKernel(applyDeltasKernel, cl.getNumAtoms());
    integration.computeVirtualSites();
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}

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void OpenCLApplyConstraintsKernel::applyToVelocities(ContextImpl& context, double tol) {
    cl.getIntegrationUtilities().applyVelocityConstraints(tol);
}

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void OpenCLVirtualSitesKernel::initialize(const System& system) {
}

void OpenCLVirtualSitesKernel::computePositions(ContextImpl& context) {
    cl.getIntegrationUtilities().computeVirtualSites();
}

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class OpenCLCalcHarmonicBondForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const HarmonicBondForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumBonds();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2;
        double length, k;
        force.getBondParameters(index, particle1, particle2, length, k);
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2;
        double length1, length2, k1, k2;
        force.getBondParameters(group1, particle1, particle2, length1, k1);
        force.getBondParameters(group2, particle1, particle2, length2, k2);
        return (length1 == length2 && k1 == k2);
    }
private:
    const HarmonicBondForce& force;
};

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OpenCLCalcHarmonicBondForceKernel::~OpenCLCalcHarmonicBondForceKernel() {
    if (params != NULL)
        delete params;
}

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void OpenCLCalcHarmonicBondForceKernel::initialize(const System& system, const HarmonicBondForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    numBonds = endIndex-startIndex;
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    if (numBonds == 0)
        return;
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    vector<vector<int> > atoms(numBonds, vector<int>(2));
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    params = OpenCLArray::create<mm_float2>(cl, numBonds, "bondParams");
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    vector<mm_float2> paramVector(numBonds);
    for (int i = 0; i < numBonds; i++) {
        double length, k;
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        force.getBondParameters(startIndex+i, atoms[i][0], atoms[i][1], length, k);
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        paramVector[i] = mm_float2((cl_float) length, (cl_float) k);
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    }
    params->upload(paramVector);
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    map<string, string> replacements;
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    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
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    replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicBondForce;
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    replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
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    info = new ForceInfo(force);
    cl.addForce(info);
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}

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double OpenCLCalcHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    return 0.0;
}
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void OpenCLCalcHarmonicBondForceKernel::copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    if (numBonds != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of bonds has changed");
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    if (numBonds == 0)
        return;
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    // Record the per-bond parameters.
    
    vector<mm_float2> paramVector(numBonds);
    for (int i = 0; i < numBonds; i++) {
        int atom1, atom2;
        double length, k;
        force.getBondParameters(startIndex+i, atom1, atom2, length, k);
        paramVector[i] = mm_float2((cl_float) length, (cl_float) k);
    }
    params->upload(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcCustomBondForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const CustomBondForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumBonds();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2;
        vector<double> parameters;
        force.getBondParameters(index, particle1, particle2, parameters);
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2;
        vector<double> parameters1, parameters2;
        force.getBondParameters(group1, particle1, particle2, parameters1);
        force.getBondParameters(group2, particle1, particle2, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        return true;
    }
private:
    const CustomBondForce& force;
};

OpenCLCalcCustomBondForceKernel::~OpenCLCalcCustomBondForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
}

void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const CustomBondForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    numBonds = endIndex-startIndex;
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    if (numBonds == 0)
        return;
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    vector<vector<int> > atoms(numBonds, vector<int>(2));
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    params = new OpenCLParameterSet(cl, force.getNumPerBondParameters(), numBonds, "customBondParams");
    vector<vector<cl_float> > paramVector(numBonds);
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    for (int i = 0; i < numBonds; i++) {
        vector<double> parameters;
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        force.getBondParameters(startIndex+i, atoms[i][0], atoms[i][1], parameters);
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        paramVector[i].resize(parameters.size());
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        for (int j = 0; j < (int) parameters.size(); j++)
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            paramVector[i][j] = (cl_float) parameters[j];
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    }
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    params->setParameterValues(paramVector);
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    info = new ForceInfo(force);
    cl.addForce(info);
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    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
    Lepton::ParsedExpression forceExpression = energyExpression.differentiate("r").optimize();
    map<string, Lepton::ParsedExpression> expressions;
    expressions["energy += "] = energyExpression;
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    expressions["real dEdR = "] = forceExpression;
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    // Create the kernels.

    map<string, string> variables;
    variables["r"] = "r";
    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
        const string& name = force.getPerBondParameterName(i);
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        variables[name] = "bondParams"+params->getParameterSuffix(i);
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    }
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    if (force.getNumGlobalParameters() > 0) {
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        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customBondGlobals", CL_MEM_READ_ONLY);
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        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
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            string value = argName+"["+cl.intToString(i)+"]";
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            variables[name] = value;
        }
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    }
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    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        expressions[derivVariable+" += "] = derivExpression;
    }
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    stringstream compute;
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    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = "<<argName<<"[index];\n";
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    }
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    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
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    compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
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    map<string, string> replacements;
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    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
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    replacements["COMPUTE_FORCE"] = compute.str();
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::bondForce, replacements), force.getForceGroup());
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}

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double OpenCLCalcCustomBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    if (globals != NULL) {
        bool changed = false;
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        for (int i = 0; i < (int) globalParamNames.size(); i++) {
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            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
}

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void OpenCLCalcCustomBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomBondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    if (numBonds != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of bonds has changed");
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    if (numBonds == 0)
        return;
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    // Record the per-bond parameters.
    
    vector<vector<cl_float> > paramVector(numBonds);
    vector<double> parameters;
    for (int i = 0; i < numBonds; i++) {
        int atom1, atom2;
        force.getBondParameters(startIndex+i, atom1, atom2, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcHarmonicAngleForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const HarmonicAngleForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumAngles();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2, particle3;
        double angle, k;
        force.getAngleParameters(index, particle1, particle2, particle3, angle, k);
        particles.resize(3);
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3;
        double angle1, angle2, k1, k2;
        force.getAngleParameters(group1, particle1, particle2, particle3, angle1, k1);
        force.getAngleParameters(group2, particle1, particle2, particle3, angle2, k2);
        return (angle1 == angle2 && k1 == k2);
    }
private:
    const HarmonicAngleForce& force;
};

OpenCLCalcHarmonicAngleForceKernel::~OpenCLCalcHarmonicAngleForceKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLCalcHarmonicAngleForceKernel::initialize(const System& system, const HarmonicAngleForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumAngles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumAngles()/numContexts;
    numAngles = endIndex-startIndex;
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    if (numAngles == 0)
        return;
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    vector<vector<int> > atoms(numAngles, vector<int>(3));
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    params = OpenCLArray::create<mm_float2>(cl, numAngles, "angleParams");
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    vector<mm_float2> paramVector(numAngles);
    for (int i = 0; i < numAngles; i++) {
        double angle, k;
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        force.getAngleParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], angle, k);
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        paramVector[i] = mm_float2((cl_float) angle, (cl_float) k);
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    }
    params->upload(paramVector);
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    map<string, string> replacements;
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    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
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    replacements["COMPUTE_FORCE"] = OpenCLKernelSources::harmonicAngleForce;
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    replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float2");
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
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    info = new ForceInfo(force);
    cl.addForce(info);
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}

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double OpenCLCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    return 0.0;
}

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void OpenCLCalcHarmonicAngleForceKernel::copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumAngles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumAngles()/numContexts;
    if (numAngles != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of angles has changed");
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    if (numAngles == 0)
        return;
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    // Record the per-angle parameters.
    
    vector<mm_float2> paramVector(numAngles);
    for (int i = 0; i < numAngles; i++) {
        int atom1, atom2, atom3;
        double angle, k;
        force.getAngleParameters(startIndex+i, atom1, atom2, atom3, angle, k);
        paramVector[i] = mm_float2((cl_float) angle, (cl_float) k);
    }
    params->upload(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcCustomAngleForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const CustomAngleForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumAngles();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2, particle3;
        vector<double> parameters;
        force.getAngleParameters(index, particle1, particle2, particle3, parameters);
        particles.resize(3);
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3;
        vector<double> parameters1, parameters2;
        force.getAngleParameters(group1, particle1, particle2, particle3, parameters1);
        force.getAngleParameters(group2, particle1, particle2, particle3, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        return true;
    }
private:
    const CustomAngleForce& force;
};

OpenCLCalcCustomAngleForceKernel::~OpenCLCalcCustomAngleForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
}

void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const CustomAngleForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumAngles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumAngles()/numContexts;
    numAngles = endIndex-startIndex;
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    if (numAngles == 0)
        return;
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    vector<vector<int> > atoms(numAngles, vector<int>(3));
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    params = new OpenCLParameterSet(cl, force.getNumPerAngleParameters(), numAngles, "customAngleParams");
    vector<vector<cl_float> > paramVector(numAngles);
    for (int i = 0; i < numAngles; i++) {
        vector<double> parameters;
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        force.getAngleParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], parameters);
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        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
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    info = new ForceInfo(force);
    cl.addForce(info);
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    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
    Lepton::ParsedExpression forceExpression = energyExpression.differentiate("theta").optimize();
    map<string, Lepton::ParsedExpression> expressions;
    expressions["energy += "] = energyExpression;
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    expressions["real dEdAngle = "] = forceExpression;
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    // Create the kernels.

    map<string, string> variables;
    variables["theta"] = "theta";
    for (int i = 0; i < force.getNumPerAngleParameters(); i++) {
        const string& name = force.getPerAngleParameterName(i);
        variables[name] = "angleParams"+params->getParameterSuffix(i);
    }
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    if (force.getNumGlobalParameters() > 0) {
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        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customAngleGlobals", CL_MEM_READ_ONLY);
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        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
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            string value = argName+"["+cl.intToString(i)+"]";
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            variables[name] = value;
        }
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    }
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    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        expressions[derivVariable+" += "] = derivExpression;
    }
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    stringstream compute;
    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" angleParams"<<(i+1)<<" = "<<argName<<"[index];\n";
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    }
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    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
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    compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
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    map<string, string> replacements;
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    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
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    replacements["COMPUTE_FORCE"] = compute.str();
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::angleForce, replacements), force.getForceGroup());
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}

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double OpenCLCalcCustomAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
}

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void OpenCLCalcCustomAngleForceKernel::copyParametersToContext(ContextImpl& context, const CustomAngleForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumAngles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumAngles()/numContexts;
    if (numAngles != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of angles has changed");
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    if (numAngles == 0)
        return;
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    // Record the per-angle parameters.
    
    vector<vector<cl_float> > paramVector(numAngles);
    vector<double> parameters;
    for (int i = 0; i < numAngles; i++) {
        int atom1, atom2, atom3;
        force.getAngleParameters(startIndex+i, atom1, atom2, atom3, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcPeriodicTorsionForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const PeriodicTorsionForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumTorsions();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2, particle3, particle4, periodicity;
        double phase, k;
        force.getTorsionParameters(index, particle1, particle2, particle3, particle4, periodicity, phase, k);
        particles.resize(4);
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
        particles[3] = particle4;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3, particle4, periodicity1, periodicity2;
        double phase1, phase2, k1, k2;
        force.getTorsionParameters(group1, particle1, particle2, particle3, particle4, periodicity1, phase1, k1);
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        force.getTorsionParameters(group2, particle1, particle2, particle3, particle4, periodicity2, phase2, k2);
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        return (periodicity1 == periodicity2 && phase1 == phase2 && k1 == k2);
    }
private:
    const PeriodicTorsionForce& force;
};

OpenCLCalcPeriodicTorsionForceKernel::~OpenCLCalcPeriodicTorsionForceKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLCalcPeriodicTorsionForceKernel::initialize(const System& system, const PeriodicTorsionForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
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    if (numTorsions == 0)
        return;
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    vector<vector<int> > atoms(numTorsions, vector<int>(4));
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    params = OpenCLArray::create<mm_float4>(cl, numTorsions, "periodicTorsionParams");
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    vector<mm_float4> paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
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        int periodicity;
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        double phase, k;
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        force.getTorsionParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], periodicity, phase, k);
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        paramVector[i] = mm_float4((cl_float) k, (cl_float) phase, (cl_float) periodicity, 0.0f);
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    }
    params->upload(paramVector);
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    map<string, string> replacements;
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    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
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    replacements["COMPUTE_FORCE"] = OpenCLKernelSources::periodicTorsionForce;
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    replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float4");
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
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    info = new ForceInfo(force);
    cl.addForce(info);
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}

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double OpenCLCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    return 0.0;
}

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void OpenCLCalcPeriodicTorsionForceKernel::copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    if (numTorsions != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of torsions has changed");
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    if (numTorsions == 0)
        return;
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    // Record the per-torsion parameters.
    
    vector<mm_float4> paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        int atom1, atom2, atom3, atom4, periodicity;
        double phase, k;
        force.getTorsionParameters(startIndex+i, atom1, atom2, atom3, atom4, periodicity, phase, k);
        paramVector[i] = mm_float4((cl_float) k, (cl_float) phase, (cl_float) periodicity, 0.0f);
    }
    params->upload(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcRBTorsionForceKernel::ForceInfo : public OpenCLForceInfo {
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    ForceInfo(const RBTorsionForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumTorsions();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2, particle3, particle4;
        double c0, c1, c2, c3, c4, c5;
        force.getTorsionParameters(index, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
        particles.resize(4);
        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
        particles[3] = particle4;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3, particle4;
        double c0a, c0b, c1a, c1b, c2a, c2b, c3a, c3b, c4a, c4b, c5a, c5b;
        force.getTorsionParameters(group1, particle1, particle2, particle3, particle4, c0a, c1a, c2a, c3a, c4a, c5a);
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        force.getTorsionParameters(group2, particle1, particle2, particle3, particle4, c0b, c1b, c2b, c3b, c4b, c5b);
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        return (c0a == c0b && c1a == c1b && c2a == c2b && c3a == c3b && c4a == c4b && c5a == c5b);
    }
private:
    const RBTorsionForce& force;
};

OpenCLCalcRBTorsionForceKernel::~OpenCLCalcRBTorsionForceKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLCalcRBTorsionForceKernel::initialize(const System& system, const RBTorsionForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
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    if (numTorsions == 0)
        return;
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    vector<vector<int> > atoms(numTorsions, vector<int>(4));
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    params = OpenCLArray::create<mm_float8>(cl, numTorsions, "rbTorsionParams");
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    vector<mm_float8> paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        double c0, c1, c2, c3, c4, c5;
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        force.getTorsionParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], c0, c1, c2, c3, c4, c5);
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        paramVector[i] = mm_float8((cl_float) c0, (cl_float) c1, (cl_float) c2, (cl_float) c3, (cl_float) c4, (cl_float) c5, 0.0f, 0.0f);
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    }
    params->upload(paramVector);
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    map<string, string> replacements;
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    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
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    replacements["COMPUTE_FORCE"] = OpenCLKernelSources::rbTorsionForce;
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    replacements["PARAMS"] = cl.getBondedUtilities().addArgument(params->getDeviceBuffer(), "float8");
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
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    info = new ForceInfo(force);
    cl.addForce(info);
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}

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double OpenCLCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    return 0.0;
}

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void OpenCLCalcRBTorsionForceKernel::copyParametersToContext(ContextImpl& context, const RBTorsionForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    if (numTorsions != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of torsions has changed");
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    if (numTorsions == 0)
        return;
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    // Record the per-torsion parameters.
    
    vector<mm_float8> paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        int atom1, atom2, atom3, atom4;
        double c0, c1, c2, c3, c4, c5;
        force.getTorsionParameters(startIndex+i, atom1, atom2, atom3, atom4, c0, c1, c2, c3, c4, c5);
        paramVector[i] = mm_float8((cl_float) c0, (cl_float) c1, (cl_float) c2, (cl_float) c3, (cl_float) c4, (cl_float) c5, 0.0f, 0.0f);
    }
    params->upload(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcCMAPTorsionForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const CMAPTorsionForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumTorsions();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int map, a1, a2, a3, a4, b1, b2, b3, b4;
        force.getTorsionParameters(index, map, a1, a2, a3, a4, b1, b2, b3, b4);
        particles.resize(8);
        particles[0] = a1;
        particles[1] = a2;
        particles[2] = a3;
        particles[3] = a4;
        particles[4] = b1;
        particles[5] = b2;
        particles[6] = b3;
        particles[7] = b4;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int map1, map2, a1, a2, a3, a4, b1, b2, b3, b4;
        force.getTorsionParameters(group1, map1, a1, a2, a3, a4, b1, b2, b3, b4);
        force.getTorsionParameters(group2, map2, a1, a2, a3, a4, b1, b2, b3, b4);
        return (map1 == map2);
    }
private:
    const CMAPTorsionForce& force;
};

OpenCLCalcCMAPTorsionForceKernel::~OpenCLCalcCMAPTorsionForceKernel() {
    if (coefficients != NULL)
        delete coefficients;
    if (mapPositions != NULL)
        delete mapPositions;
    if (torsionMaps != NULL)
        delete torsionMaps;
}

void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CMAPTorsionForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
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    if (numTorsions == 0)
        return;
    int numMaps = force.getNumMaps();
    vector<mm_float4> coeffVec;
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    mapPositionsVec.resize(numMaps);
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    vector<double> energy;
    vector<vector<double> > c;
    int currentPosition = 0;
    for (int i = 0; i < numMaps; i++) {
        int size;
        force.getMapParameters(i, size, energy);
        CMAPTorsionForceImpl::calcMapDerivatives(size, energy, c);
        mapPositionsVec[i] = mm_int2(currentPosition, size);
        currentPosition += 4*size*size;
        for (int j = 0; j < size*size; j++) {
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            coeffVec.push_back(mm_float4((float) c[j][0], (float) c[j][1], (float) c[j][2], (float) c[j][3]));
            coeffVec.push_back(mm_float4((float) c[j][4], (float) c[j][5], (float) c[j][6], (float) c[j][7]));
            coeffVec.push_back(mm_float4((float) c[j][8], (float) c[j][9], (float) c[j][10], (float) c[j][11]));
            coeffVec.push_back(mm_float4((float) c[j][12], (float) c[j][13], (float) c[j][14], (float) c[j][15]));
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        }
    }
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    vector<vector<int> > atoms(numTorsions, vector<int>(8));
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    vector<cl_int> torsionMapsVec(numTorsions);
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    for (int i = 0; i < numTorsions; i++)
        force.getTorsionParameters(startIndex+i, torsionMapsVec[i], atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], atoms[i][4], atoms[i][5], atoms[i][6], atoms[i][7]);
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    coefficients = OpenCLArray::create<mm_float4>(cl, coeffVec.size(), "cmapTorsionCoefficients");
    mapPositions = OpenCLArray::create<mm_int2>(cl, numMaps, "cmapTorsionMapPositions");
    torsionMaps = OpenCLArray::create<cl_int>(cl, numTorsions, "cmapTorsionMaps");
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    coefficients->upload(coeffVec);
    mapPositions->upload(mapPositionsVec);
    torsionMaps->upload(torsionMapsVec);
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    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
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    replacements["COEFF"] = cl.getBondedUtilities().addArgument(coefficients->getDeviceBuffer(), "float4");
    replacements["MAP_POS"] = cl.getBondedUtilities().addArgument(mapPositions->getDeviceBuffer(), "int2");
    replacements["MAPS"] = cl.getBondedUtilities().addArgument(torsionMaps->getDeviceBuffer(), "int");
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::cmapTorsionForce, replacements), force.getForceGroup());
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    info = new ForceInfo(force);
    cl.addForce(info);
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}

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double OpenCLCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    return 0.0;
}

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void OpenCLCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) {
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    int numMaps = force.getNumMaps();
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
    if (mapPositions->getSize() != numMaps)
        throw OpenMMException("updateParametersInContext: The number of maps has changed");
    if (torsionMaps->getSize() != numTorsions)
        throw OpenMMException("updateParametersInContext: The number of CMAP torsions has changed");

    // Update the maps.

    vector<mm_float4> coeffVec;
    vector<double> energy;
    vector<vector<double> > c;
    int currentPosition = 0;
    for (int i = 0; i < numMaps; i++) {
        int size;
        force.getMapParameters(i, size, energy);
        if (size != mapPositionsVec[i].y)
            throw OpenMMException("updateParametersInContext: The size of a map has changed");
        CMAPTorsionForceImpl::calcMapDerivatives(size, energy, c);
        currentPosition += 4*size*size;
        for (int j = 0; j < size*size; j++) {
            coeffVec.push_back(mm_float4((float) c[j][0], (float) c[j][1], (float) c[j][2], (float) c[j][3]));
            coeffVec.push_back(mm_float4((float) c[j][4], (float) c[j][5], (float) c[j][6], (float) c[j][7]));
            coeffVec.push_back(mm_float4((float) c[j][8], (float) c[j][9], (float) c[j][10], (float) c[j][11]));
            coeffVec.push_back(mm_float4((float) c[j][12], (float) c[j][13], (float) c[j][14], (float) c[j][15]));
        }
    }
    coefficients->upload(coeffVec);

    // Update the indices.

    vector<int> torsionMapsVec(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        int index[8];
        force.getTorsionParameters(i, torsionMapsVec[i], index[0], index[1], index[2], index[3], index[4], index[5], index[6], index[7]);
    }
    torsionMaps->upload(torsionMapsVec);
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}

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class OpenCLCalcCustomTorsionForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const CustomTorsionForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumTorsions();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2, particle3, particle4;
        vector<double> parameters;
        force.getTorsionParameters(index, particle1, particle2, particle3, particle4, parameters);
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        particles.resize(4);
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        particles[0] = particle1;
        particles[1] = particle2;
        particles[2] = particle3;
        particles[3] = particle4;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2, particle3, particle4;
        vector<double> parameters1, parameters2;
        force.getTorsionParameters(group1, particle1, particle2, particle3, particle4, parameters1);
        force.getTorsionParameters(group2, particle1, particle2, particle3, particle4, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        return true;
    }
private:
    const CustomTorsionForce& force;
};

OpenCLCalcCustomTorsionForceKernel::~OpenCLCalcCustomTorsionForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
}

void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const CustomTorsionForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    numTorsions = endIndex-startIndex;
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    if (numTorsions == 0)
        return;
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    vector<vector<int> > atoms(numTorsions, vector<int>(4));
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    params = new OpenCLParameterSet(cl, force.getNumPerTorsionParameters(), numTorsions, "customTorsionParams");
    vector<vector<cl_float> > paramVector(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        vector<double> parameters;
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        force.getTorsionParameters(startIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], parameters);
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        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
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    info = new ForceInfo(force);
    cl.addForce(info);
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    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
    Lepton::ParsedExpression forceExpression = energyExpression.differentiate("theta").optimize();
    map<string, Lepton::ParsedExpression> expressions;
    expressions["energy += "] = energyExpression;
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    expressions["real dEdAngle = "] = forceExpression;
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    // Create the kernels.

    map<string, string> variables;
    variables["theta"] = "theta";
    for (int i = 0; i < force.getNumPerTorsionParameters(); i++) {
        const string& name = force.getPerTorsionParameterName(i);
        variables[name] = "torsionParams"+params->getParameterSuffix(i);
    }
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    if (force.getNumGlobalParameters() > 0) {
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        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customTorsionGlobals", CL_MEM_READ_ONLY);
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        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
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            string value = argName+"["+cl.intToString(i)+"]";
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            variables[name] = value;
        }
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    }
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    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        expressions[derivVariable+" += "] = derivExpression;
    }
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    stringstream compute;
    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" torsionParams"<<(i+1)<<" = "<<argName<<"[index];\n";
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    }
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    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
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    compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
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    map<string, string> replacements;
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    replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
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    replacements["COMPUTE_FORCE"] = compute.str();
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::torsionForce, replacements), force.getForceGroup());
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}

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double OpenCLCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
}

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void OpenCLCalcCustomTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
    if (numTorsions != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of torsions has changed");
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    if (numTorsions == 0)
        return;
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    // Record the per-torsion parameters.
    
    vector<vector<cl_float> > paramVector(numTorsions);
    vector<double> parameters;
    for (int i = 0; i < numTorsions; i++) {
        int atom1, atom2, atom3, atom4;
        force.getTorsionParameters(startIndex+i, atom1, atom2, atom3, atom4, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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}

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class OpenCLCalcNonbondedForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(int requiredBuffers, const NonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
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    }
    bool areParticlesIdentical(int particle1, int particle2) {
        double charge1, charge2, sigma1, sigma2, epsilon1, epsilon2;
        force.getParticleParameters(particle1, charge1, sigma1, epsilon1);
        force.getParticleParameters(particle2, charge2, sigma2, epsilon2);
        return (charge1 == charge2 && sigma1 == sigma2 && epsilon1 == epsilon2);
    }
    int getNumParticleGroups() {
        return force.getNumExceptions();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2;
        double chargeProd, sigma, epsilon;
        force.getExceptionParameters(index, particle1, particle2, chargeProd, sigma, epsilon);
        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        int particle1, particle2;
        double chargeProd1, chargeProd2, sigma1, sigma2, epsilon1, epsilon2;
        force.getExceptionParameters(group1, particle1, particle2, chargeProd1, sigma1, epsilon1);
        force.getExceptionParameters(group2, particle1, particle2, chargeProd2, sigma2, epsilon2);
        return (chargeProd1 == chargeProd2 && sigma1 == sigma2 && epsilon1 == epsilon2);
    }
private:
    const NonbondedForce& force;
};

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class OpenCLCalcNonbondedForceKernel::PmeIO : public CalcPmeReciprocalForceKernel::IO {
public:
    PmeIO(OpenCLContext& cl, cl::Kernel addForcesKernel) : cl(cl), addForcesKernel(addForcesKernel), forceTemp(NULL) {
        forceTemp = OpenCLArray::create<mm_float4>(cl, cl.getNumAtoms(), "PmeForce");
        addForcesKernel.setArg<cl::Buffer>(0, forceTemp->getDeviceBuffer());
    }
    ~PmeIO() {
        if (forceTemp != NULL)
            delete forceTemp;
    }
    float* getPosq() {
        cl.getPosq().download(posq);
        return (float*) &posq[0];
    }
    void setForce(float* force) {
        forceTemp->upload(force);
        addForcesKernel.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
        cl.executeKernel(addForcesKernel, cl.getNumAtoms());
    }
private:
    OpenCLContext& cl;
    vector<mm_float4> posq;
    OpenCLArray* forceTemp;
    cl::Kernel addForcesKernel;
};

class OpenCLCalcNonbondedForceKernel::PmePreComputation : public OpenCLContext::ForcePreComputation {
public:
    PmePreComputation(OpenCLContext& cl, Kernel& pme, CalcPmeReciprocalForceKernel::IO& io) : cl(cl), pme(pme), io(io) {
    }
    void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
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        Vec3 boxVectors[3] = {Vec3(cl.getPeriodicBoxSize().x, 0, 0), Vec3(0, cl.getPeriodicBoxSize().y, 0), Vec3(0, 0, cl.getPeriodicBoxSize().z)};
        pme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, boxVectors, includeEnergy);
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    }
private:
    OpenCLContext& cl;
    Kernel pme;
    CalcPmeReciprocalForceKernel::IO& io;
};

class OpenCLCalcNonbondedForceKernel::PmePostComputation : public OpenCLContext::ForcePostComputation {
public:
    PmePostComputation(Kernel& pme, CalcPmeReciprocalForceKernel::IO& io) : pme(pme), io(io) {
    }
    double computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
        return pme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
    }
private:
    Kernel pme;
    CalcPmeReciprocalForceKernel::IO& io;
};

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class OpenCLCalcNonbondedForceKernel::SyncQueuePreComputation : public OpenCLContext::ForcePreComputation {
public:
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    SyncQueuePreComputation(OpenCLContext& cl, cl::CommandQueue queue, int forceGroup) : cl(cl), queue(queue), forceGroup(forceGroup) {
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    }
    void computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
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        if ((groups&(1<<forceGroup)) != 0) {
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            vector<cl::Event> events(1);
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            cl.getQueue().enqueueMarker(&events[0]);
            queue.enqueueWaitForEvents(events);
        }
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    }
private:
    OpenCLContext& cl;
    cl::CommandQueue queue;
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    int forceGroup;
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};

class OpenCLCalcNonbondedForceKernel::SyncQueuePostComputation : public OpenCLContext::ForcePostComputation {
public:
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    SyncQueuePostComputation(OpenCLContext& cl, cl::Event& event, OpenCLArray& pmeEnergyBuffer, int forceGroup) : cl(cl), event(event),
            pmeEnergyBuffer(pmeEnergyBuffer), forceGroup(forceGroup) {
    }
    void setKernel(cl::Kernel kernel) {
        addEnergyKernel = kernel;
        addEnergyKernel.setArg<cl::Buffer>(0, pmeEnergyBuffer.getDeviceBuffer());
        addEnergyKernel.setArg<cl::Buffer>(1, cl.getEnergyBuffer().getDeviceBuffer());
        addEnergyKernel.setArg<cl_int>(2, pmeEnergyBuffer.getSize());
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    }
    double computeForceAndEnergy(bool includeForces, bool includeEnergy, int groups) {
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        if ((groups&(1<<forceGroup)) != 0) {
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            vector<cl::Event> events(1);
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            events[0] = event;
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            event = cl::Event();
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            cl.getQueue().enqueueWaitForEvents(events);
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            if (includeEnergy)
                cl.executeKernel(addEnergyKernel, pmeEnergyBuffer.getSize());
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        }
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        return 0.0;
    }
private:
    OpenCLContext& cl;
    cl::Event& event;
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    cl::Kernel addEnergyKernel;
    OpenCLArray& pmeEnergyBuffer;
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    int forceGroup;
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};

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OpenCLCalcNonbondedForceKernel::~OpenCLCalcNonbondedForceKernel() {
    if (sigmaEpsilon != NULL)
        delete sigmaEpsilon;
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    if (exceptionParams != NULL)
        delete exceptionParams;
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    if (cosSinSums != NULL)
        delete cosSinSums;
    if (pmeGrid != NULL)
        delete pmeGrid;
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    if (pmeGrid2 != NULL)
        delete pmeGrid2;
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    if (pmeBsplineModuliX != NULL)
        delete pmeBsplineModuliX;
    if (pmeBsplineModuliY != NULL)
        delete pmeBsplineModuliY;
    if (pmeBsplineModuliZ != NULL)
        delete pmeBsplineModuliZ;
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    if (pmeDispersionBsplineModuliX != NULL)
        delete pmeDispersionBsplineModuliX;
    if (pmeDispersionBsplineModuliY != NULL)
        delete pmeDispersionBsplineModuliY;
    if (pmeDispersionBsplineModuliZ != NULL)
        delete pmeDispersionBsplineModuliZ;
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    if (pmeBsplineTheta != NULL)
        delete pmeBsplineTheta;
    if (pmeAtomRange != NULL)
        delete pmeAtomRange;
    if (pmeAtomGridIndex != NULL)
        delete pmeAtomGridIndex;
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    if (pmeEnergyBuffer != NULL)
        delete pmeEnergyBuffer;
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    if (sort != NULL)
        delete sort;
    if (fft != NULL)
        delete fft;
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    if (dispersionFft != NULL)
        delete dispersionFft;
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    if (pmeio != NULL)
        delete pmeio;
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}

void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {

    // Identify which exceptions are 1-4 interactions.

    vector<pair<int, int> > exclusions;
    vector<int> exceptions;
    for (int i = 0; i < force.getNumExceptions(); i++) {
        int particle1, particle2;
        double chargeProd, sigma, epsilon;
        force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
        exclusions.push_back(pair<int, int>(particle1, particle2));
        if (chargeProd != 0.0 || epsilon != 0.0)
            exceptions.push_back(i);
    }

    // Initialize nonbonded interactions.

    int numParticles = force.getNumParticles();
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    sigmaEpsilon = OpenCLArray::create<mm_float2>(cl, cl.getPaddedNumAtoms(), "sigmaEpsilon");
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    vector<mm_float4> posqf(cl.getPaddedNumAtoms(), mm_float4(0,0,0,0));
    vector<mm_double4> posqd(cl.getPaddedNumAtoms(), mm_double4(0,0,0,0));
    vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms(), mm_float2(0,0));
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    vector<vector<int> > exclusionList(numParticles);
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    double sumSquaredCharges = 0.0;
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    double sumSquaredC6 = 0.0;
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    hasCoulomb = false;
    hasLJ = false;
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    for (int i = 0; i < numParticles; i++) {
        double charge, sigma, epsilon;
        force.getParticleParameters(i, charge, sigma, epsilon);
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        if (cl.getUseDoublePrecision())
            posqd[i] = mm_double4(0, 0, 0, charge);
        else
            posqf[i] = mm_float4(0, 0, 0, (float) charge);
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        double sig = 0.5*sigma;
        double eps = 2.0*sqrt(epsilon);
        sigmaEpsilonVector[i] = mm_float2((float) sig, (float) eps);
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        exclusionList[i].push_back(i);
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        sumSquaredCharges += charge*charge;
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        double C6 = 8.0*sig*sig*sig*eps;
        sumSquaredC6 += C6*C6;
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        if (charge != 0.0)
            hasCoulomb = true;
        if (epsilon != 0.0)
            hasLJ = true;
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    }
    for (int i = 0; i < (int) exclusions.size(); i++) {
        exclusionList[exclusions[i].first].push_back(exclusions[i].second);
        exclusionList[exclusions[i].second].push_back(exclusions[i].first);
    }
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    if (cl.getUseDoublePrecision())
        cl.getPosq().upload(posqd);
    else
        cl.getPosq().upload(posqf);
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    sigmaEpsilon->upload(sigmaEpsilonVector);
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    nonbondedMethod = CalcNonbondedForceKernel::NonbondedMethod(force.getNonbondedMethod());
    bool useCutoff = (nonbondedMethod != NoCutoff);
    bool usePeriodic = (nonbondedMethod != NoCutoff && nonbondedMethod != CutoffNonPeriodic);
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    doLJPME = (nonbondedMethod == LJPME);
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    map<string, string> defines;
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    defines["HAS_COULOMB"] = (hasCoulomb ? "1" : "0");
    defines["HAS_LENNARD_JONES"] = (hasLJ ? "1" : "0");
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    defines["USE_LJ_SWITCH"] = (useCutoff && force.getUseSwitchingFunction() ? "1" : "0");
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    if (useCutoff) {
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        // Compute the reaction field constants.

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        double reactionFieldK = pow(force.getCutoffDistance(), -3.0)*(force.getReactionFieldDielectric()-1.0)/(2.0*force.getReactionFieldDielectric()+1.0);
        double reactionFieldC = (1.0 / force.getCutoffDistance())*(3.0*force.getReactionFieldDielectric())/(2.0*force.getReactionFieldDielectric()+1.0);
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        defines["REACTION_FIELD_K"] = cl.doubleToString(reactionFieldK);
        defines["REACTION_FIELD_C"] = cl.doubleToString(reactionFieldC);
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        // Compute the switching coefficients.
        
        if (force.getUseSwitchingFunction()) {
            defines["LJ_SWITCH_CUTOFF"] = cl.doubleToString(force.getSwitchingDistance());
            defines["LJ_SWITCH_C3"] = cl.doubleToString(10/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 3.0));
            defines["LJ_SWITCH_C4"] = cl.doubleToString(15/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 4.0));
            defines["LJ_SWITCH_C5"] = cl.doubleToString(6/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 5.0));
        }
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    }
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    if (force.getUseDispersionCorrection() && cl.getContextIndex() == 0 && !doLJPME)
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        dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(system, force);
    else
        dispersionCoefficient = 0.0;
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    alpha = 0;
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    ewaldSelfEnergy = 0.0;
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    if (nonbondedMethod == Ewald) {
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        // Compute the Ewald parameters.

        int kmaxx, kmaxy, kmaxz;
        NonbondedForceImpl::calcEwaldParameters(system, force, alpha, kmaxx, kmaxy, kmaxz);
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        defines["EWALD_ALPHA"] = cl.doubleToString(alpha);
        defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
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        defines["USE_EWALD"] = "1";
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        if (cl.getContextIndex() == 0) {
            ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);

            // Create the reciprocal space kernels.

            map<string, string> replacements;
            replacements["NUM_ATOMS"] = cl.intToString(numParticles);
            replacements["KMAX_X"] = cl.intToString(kmaxx);
            replacements["KMAX_Y"] = cl.intToString(kmaxy);
            replacements["KMAX_Z"] = cl.intToString(kmaxz);
            replacements["EXP_COEFFICIENT"] = cl.doubleToString(-1.0/(4.0*alpha*alpha));
            cl::Program program = cl.createProgram(OpenCLKernelSources::ewald, replacements);
            ewaldSumsKernel = cl::Kernel(program, "calculateEwaldCosSinSums");
            ewaldForcesKernel = cl::Kernel(program, "calculateEwaldForces");
            int elementSize = (cl.getUseDoublePrecision() ? sizeof(mm_double2) : sizeof(mm_float2));
            cosSinSums = new OpenCLArray(cl, (2*kmaxx-1)*(2*kmaxy-1)*(2*kmaxz-1), elementSize, "cosSinSums");
        }
    }
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    else if (nonbondedMethod == PME || nonbondedMethod == LJPME) {
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        // Compute the PME parameters.

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        NonbondedForceImpl::calcPMEParameters(system, force, alpha, gridSizeX, gridSizeY, gridSizeZ, false);
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        gridSizeX = OpenCLFFT3D::findLegalDimension(gridSizeX);
        gridSizeY = OpenCLFFT3D::findLegalDimension(gridSizeY);
        gridSizeZ = OpenCLFFT3D::findLegalDimension(gridSizeZ);
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        if (doLJPME) {
            NonbondedForceImpl::calcPMEParameters(system, force, dispersionAlpha, dispersionGridSizeX,
                                                  dispersionGridSizeY, dispersionGridSizeZ, true);
            dispersionGridSizeX = OpenCLFFT3D::findLegalDimension(dispersionGridSizeX);
            dispersionGridSizeY = OpenCLFFT3D::findLegalDimension(dispersionGridSizeY);
            dispersionGridSizeZ = OpenCLFFT3D::findLegalDimension(dispersionGridSizeZ);
        }
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        defines["EWALD_ALPHA"] = cl.doubleToString(alpha);
        defines["TWO_OVER_SQRT_PI"] = cl.doubleToString(2.0/sqrt(M_PI));
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        defines["USE_EWALD"] = "1";
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        defines["DO_LJPME"] = doLJPME ? "1" : "0";
        if (doLJPME)
            defines["EWALD_DISPERSION_ALPHA"] = cl.doubleToString(dispersionAlpha);
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        if (cl.getContextIndex() == 0) {
            ewaldSelfEnergy = -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI);
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            if (doLJPME)
                ewaldSelfEnergy += pow(dispersionAlpha, 6)*sumSquaredC6/12.0;
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            pmeDefines["PME_ORDER"] = cl.intToString(PmeOrder);
            pmeDefines["NUM_ATOMS"] = cl.intToString(numParticles);
            pmeDefines["RECIP_EXP_FACTOR"] = cl.doubleToString(M_PI*M_PI/(alpha*alpha));
            pmeDefines["GRID_SIZE_X"] = cl.intToString(gridSizeX);
            pmeDefines["GRID_SIZE_Y"] = cl.intToString(gridSizeY);
            pmeDefines["GRID_SIZE_Z"] = cl.intToString(gridSizeZ);
            pmeDefines["EPSILON_FACTOR"] = cl.doubleToString(sqrt(ONE_4PI_EPS0));
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            pmeDefines["M_PI"] = cl.doubleToString(M_PI);
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            bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
            if (deviceIsCpu)
                pmeDefines["DEVICE_IS_CPU"] = "1";
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            if (cl.getPlatformData().useCpuPme && !doLJPME) {
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                // Create the CPU PME kernel.

                try {
                    cpuPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), *cl.getPlatformData().context);
                    cpuPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSizeX, gridSizeY, gridSizeZ, numParticles, alpha);
                    cl::Program program = cl.createProgram(OpenCLKernelSources::pme, pmeDefines);
                    cl::Kernel addForcesKernel = cl::Kernel(program, "addForces");
                    pmeio = new PmeIO(cl, addForcesKernel);
                    cl.addPreComputation(new PmePreComputation(cl, cpuPme, *pmeio));
                    cl.addPostComputation(new PmePostComputation(cpuPme, *pmeio));
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                }
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                catch (OpenMMException& ex) {
                    // The CPU PME plugin isn't available.
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                }
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            }
            if (pmeio == NULL) {
                // Create required data structures.

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                if (doLJPME) {
                    double invRCut6 = pow(force.getCutoffDistance(), -6);
                    double dalphaR = dispersionAlpha * force.getCutoffDistance();
                    double dar2 = dalphaR*dalphaR;
                    double dar4 = dar2*dar2;
                    double multShift6 = -invRCut6*(1.0 - exp(-dar2) * (1.0 + dar2 + 0.5*dar4));
                    defines["INVCUT6"] = cl.doubleToString(invRCut6);
                    defines["MULTSHIFT6"] = cl.doubleToString(multShift6);
                }
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                int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
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                int gridElements = gridSizeX*gridSizeY*gridSizeZ;
                if (doLJPME)
                    gridElements = max(gridElements, dispersionGridSizeX*dispersionGridSizeY*dispersionGridSizeZ);
                pmeGrid = new OpenCLArray(cl, gridElements, 2*elementSize, "pmeGrid");
                pmeGrid2 = new OpenCLArray(cl, gridElements, 2*elementSize, "pmeGrid2");
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                if (cl.getSupports64BitGlobalAtomics())
                    cl.addAutoclearBuffer(*pmeGrid2);
                else
                    cl.addAutoclearBuffer(*pmeGrid);
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                pmeBsplineModuliX = new OpenCLArray(cl, gridSizeX, elementSize, "pmeBsplineModuliX");
                pmeBsplineModuliY = new OpenCLArray(cl, gridSizeY, elementSize, "pmeBsplineModuliY");
                pmeBsplineModuliZ = new OpenCLArray(cl, gridSizeZ, elementSize, "pmeBsplineModuliZ");
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                if (doLJPME) {
                    pmeDispersionBsplineModuliX = new OpenCLArray(cl, dispersionGridSizeX, elementSize, "pmeDispersionBsplineModuliX");
                    pmeDispersionBsplineModuliY = new OpenCLArray(cl, dispersionGridSizeY, elementSize, "pmeDispersionBsplineModuliY");
                    pmeDispersionBsplineModuliZ = new OpenCLArray(cl, dispersionGridSizeZ, elementSize, "pmeDispersionBsplineModuliZ");
                }
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                pmeBsplineTheta = new OpenCLArray(cl, PmeOrder*numParticles, 4*elementSize, "pmeBsplineTheta");
                pmeAtomRange = OpenCLArray::create<cl_int>(cl, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
                pmeAtomGridIndex = OpenCLArray::create<mm_int2>(cl, numParticles, "pmeAtomGridIndex");
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                int energyElementSize = (cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
                pmeEnergyBuffer = new OpenCLArray(cl, cl.getNumThreadBlocks()*OpenCLContext::ThreadBlockSize, energyElementSize, "pmeEnergyBuffer");
                cl.clearBuffer(*pmeEnergyBuffer);
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                sort = new OpenCLSort(cl, new SortTrait(), cl.getNumAtoms());
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                fft = new OpenCLFFT3D(cl, gridSizeX, gridSizeY, gridSizeZ, true);
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                if (doLJPME)
                    dispersionFft = new OpenCLFFT3D(cl, dispersionGridSizeX, dispersionGridSizeY, dispersionGridSizeZ, true);
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                string vendor = cl.getDevice().getInfo<CL_DEVICE_VENDOR>();
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                bool isNvidia = (vendor.size() >= 6 && vendor.substr(0, 6) == "NVIDIA");
                if (isNvidia)
                    pmeDefines["USE_ALTERNATE_MEMORY_ACCESS_PATTERN"] = "1";
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                usePmeQueue = (!cl.getPlatformData().disablePmeStream && isNvidia);
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                if (usePmeQueue) {
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                    pmeDefines["USE_PME_STREAM"] = "1";
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                    pmeQueue = cl::CommandQueue(cl.getContext(), cl.getDevice());
                    int recipForceGroup = force.getReciprocalSpaceForceGroup();
                    if (recipForceGroup < 0)
                        recipForceGroup = force.getForceGroup();
                    cl.addPreComputation(new SyncQueuePreComputation(cl, pmeQueue, recipForceGroup));
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                    cl.addPostComputation(syncQueue = new SyncQueuePostComputation(cl, pmeSyncEvent, *pmeEnergyBuffer, recipForceGroup));
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                }
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                // Initialize the b-spline moduli.

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                for (int grid = 0; grid < 2; grid++) {
                    int xsize, ysize, zsize;
                    OpenCLArray *xmoduli, *ymoduli, *zmoduli;
                    if (grid == 0) {
                        xsize = gridSizeX;
                        ysize = gridSizeY;
                        zsize = gridSizeZ;
                        xmoduli = pmeBsplineModuliX;
                        ymoduli = pmeBsplineModuliY;
                        zmoduli = pmeBsplineModuliZ;
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                    }
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                    else {
                        if (!doLJPME)
                            continue;
                        xsize = dispersionGridSizeX;
                        ysize = dispersionGridSizeY;
                        zsize = dispersionGridSizeZ;
                        xmoduli = pmeDispersionBsplineModuliX;
                        ymoduli = pmeDispersionBsplineModuliY;
                        zmoduli = pmeDispersionBsplineModuliZ;
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                    }
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                    int maxSize = max(max(xsize, ysize), zsize);
                    vector<double> data(PmeOrder);
                    vector<double> ddata(PmeOrder);
                    vector<double> bsplines_data(maxSize);
                    data[PmeOrder-1] = 0.0;
                    data[1] = 0.0;
                    data[0] = 1.0;
                    for (int i = 3; i < PmeOrder; i++) {
                        double div = 1.0/(i-1.0);
                        data[i-1] = 0.0;
                        for (int j = 1; j < (i-1); j++)
                            data[i-j-1] = div*(j*data[i-j-2]+(i-j)*data[i-j-1]);
                        data[0] = div*data[0];
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                    }
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                    // Differentiate.

                    ddata[0] = -data[0];
                    for (int i = 1; i < PmeOrder; i++)
                        ddata[i] = data[i-1]-data[i];
                    double div = 1.0/(PmeOrder-1);
                    data[PmeOrder-1] = 0.0;
                    for (int i = 1; i < (PmeOrder-1); i++)
                        data[PmeOrder-i-1] = div*(i*data[PmeOrder-i-2]+(PmeOrder-i)*data[PmeOrder-i-1]);
                    data[0] = div*data[0];
                    for (int i = 0; i < maxSize; i++)
                        bsplines_data[i] = 0.0;
                    for (int i = 1; i <= PmeOrder; i++)
                        bsplines_data[i] = data[i-1];

                    // Evaluate the actual bspline moduli for X/Y/Z.

                    for(int dim = 0; dim < 3; dim++) {
                        int ndata = (dim == 0 ? xsize : dim == 1 ? ysize : zsize);
                        vector<cl_double> moduli(ndata);
                        for (int i = 0; i < ndata; i++) {
                            double sc = 0.0;
                            double ss = 0.0;
                            for (int j = 0; j < ndata; j++) {
                                double arg = (2.0*M_PI*i*j)/ndata;
                                sc += bsplines_data[j]*cos(arg);
                                ss += bsplines_data[j]*sin(arg);
                            }
                            moduli[i] = (float) (sc*sc+ss*ss);
                        }
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                        for (int i = 0; i < ndata; i++)
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                        {
                            if (moduli[i] < 1.0e-7)
                                moduli[i] = (moduli[i-1]+moduli[i+1])*0.5f;
                        }
                        if (cl.getUseDoublePrecision()) {
                            if (dim == 0)
                                xmoduli->upload(moduli);
                            else if (dim == 1)
                                ymoduli->upload(moduli);
                            else
                                zmoduli->upload(moduli);
                        }
                        else {
                            vector<float> modulif(ndata);
                            for (int i = 0; i < ndata; i++)
                                modulif[i] = (float) moduli[i];
                            if (dim == 0)
                                xmoduli->upload(modulif);
                            else if (dim == 1)
                                ymoduli->upload(modulif);
                            else
                                zmoduli->upload(modulif);
                        }
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                    }
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                }
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            }
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        }
    }
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    // Add the interaction to the default nonbonded kernel.
    
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    string source = cl.replaceStrings(OpenCLKernelSources::coulombLennardJones, defines);
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    cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
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    if (hasLJ)
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        cl.getNonbondedUtilities().addParameter(OpenCLNonbondedUtilities::ParameterInfo("sigmaEpsilon", "float", 2, sizeof(cl_float2), sigmaEpsilon->getDeviceBuffer()));
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    // Initialize the exceptions.
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*exceptions.size()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*exceptions.size()/numContexts;
    int numExceptions = endIndex-startIndex;
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    if (numExceptions > 0) {
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        exceptionAtoms.resize(numExceptions);
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        vector<vector<int> > atoms(numExceptions, vector<int>(2));
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        exceptionParams = OpenCLArray::create<mm_float4>(cl, numExceptions, "exceptionParams");
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        vector<mm_float4> exceptionParamsVector(numExceptions);
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        for (int i = 0; i < numExceptions; i++) {
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            double chargeProd, sigma, epsilon;
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            force.getExceptionParameters(exceptions[startIndex+i], atoms[i][0], atoms[i][1], chargeProd, sigma, epsilon);
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            exceptionParamsVector[i] = mm_float4((float) (ONE_4PI_EPS0*chargeProd), (float) sigma, (float) (4.0*epsilon), 0.0f);
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            exceptionAtoms[i] = make_pair(atoms[i][0], atoms[i][1]);
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        }
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        exceptionParams->upload(exceptionParamsVector);
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        map<string, string> replacements;
        replacements["PARAMS"] = cl.getBondedUtilities().addArgument(exceptionParams->getDeviceBuffer(), "float4");
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        cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::nonbondedExceptions, replacements), force.getForceGroup());
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    }
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    info = new ForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force);
    cl.addForce(info);
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}

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double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal) {
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    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
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    if (!hasInitializedKernel) {
        hasInitializedKernel = true;
        if (cosSinSums != NULL) {
            ewaldSumsKernel.setArg<cl::Buffer>(0, cl.getEnergyBuffer().getDeviceBuffer());
            ewaldSumsKernel.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
            ewaldSumsKernel.setArg<cl::Buffer>(2, cosSinSums->getDeviceBuffer());
            ewaldForcesKernel.setArg<cl::Buffer>(0, cl.getForceBuffers().getDeviceBuffer());
            ewaldForcesKernel.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
            ewaldForcesKernel.setArg<cl::Buffer>(2, cosSinSums->getDeviceBuffer());
        }
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        if (pmeGrid != NULL) {
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            // Create kernels for Coulomb PME.
            
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            cl::Program program = cl.createProgram(OpenCLKernelSources::pme, pmeDefines);
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            pmeUpdateBsplinesKernel = cl::Kernel(program, "updateBsplines");
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            pmeAtomRangeKernel = cl::Kernel(program, "findAtomRangeForGrid");
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            pmeZIndexKernel = cl::Kernel(program, "recordZIndex");
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            pmeSpreadChargeKernel = cl::Kernel(program, "gridSpreadCharge");
            pmeConvolutionKernel = cl::Kernel(program, "reciprocalConvolution");
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            pmeEvalEnergyKernel = cl::Kernel(program, "gridEvaluateEnergy");
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            pmeInterpolateForceKernel = cl::Kernel(program, "gridInterpolateForce");
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            int elementSize = (cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4));
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            pmeUpdateBsplinesKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
            pmeUpdateBsplinesKernel.setArg<cl::Buffer>(1, pmeBsplineTheta->getDeviceBuffer());
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            pmeUpdateBsplinesKernel.setArg(2, OpenCLContext::ThreadBlockSize*PmeOrder*elementSize, NULL);
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            pmeUpdateBsplinesKernel.setArg<cl::Buffer>(3, pmeAtomGridIndex->getDeviceBuffer());
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            pmeAtomRangeKernel.setArg<cl::Buffer>(0, pmeAtomGridIndex->getDeviceBuffer());
            pmeAtomRangeKernel.setArg<cl::Buffer>(1, pmeAtomRange->getDeviceBuffer());
            pmeAtomRangeKernel.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
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            pmeZIndexKernel.setArg<cl::Buffer>(0, pmeAtomGridIndex->getDeviceBuffer());
            pmeZIndexKernel.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
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            pmeSpreadChargeKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
            pmeSpreadChargeKernel.setArg<cl::Buffer>(1, pmeAtomGridIndex->getDeviceBuffer());
            pmeSpreadChargeKernel.setArg<cl::Buffer>(2, pmeAtomRange->getDeviceBuffer());
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            if (cl.getSupports64BitGlobalAtomics())
                pmeSpreadChargeKernel.setArg<cl::Buffer>(3, pmeGrid2->getDeviceBuffer());
            else
                pmeSpreadChargeKernel.setArg<cl::Buffer>(3, pmeGrid->getDeviceBuffer());
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            pmeSpreadChargeKernel.setArg<cl::Buffer>(4, pmeBsplineTheta->getDeviceBuffer());
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            pmeConvolutionKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
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            pmeConvolutionKernel.setArg<cl::Buffer>(1, pmeBsplineModuliX->getDeviceBuffer());
            pmeConvolutionKernel.setArg<cl::Buffer>(2, pmeBsplineModuliY->getDeviceBuffer());
            pmeConvolutionKernel.setArg<cl::Buffer>(3, pmeBsplineModuliZ->getDeviceBuffer());
            pmeEvalEnergyKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
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            pmeEvalEnergyKernel.setArg<cl::Buffer>(1, usePmeQueue ? pmeEnergyBuffer->getDeviceBuffer() : cl.getEnergyBuffer().getDeviceBuffer());
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            pmeEvalEnergyKernel.setArg<cl::Buffer>(2, pmeBsplineModuliX->getDeviceBuffer());
            pmeEvalEnergyKernel.setArg<cl::Buffer>(3, pmeBsplineModuliY->getDeviceBuffer());
            pmeEvalEnergyKernel.setArg<cl::Buffer>(4, pmeBsplineModuliZ->getDeviceBuffer());
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            pmeInterpolateForceKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
            pmeInterpolateForceKernel.setArg<cl::Buffer>(1, cl.getForceBuffers().getDeviceBuffer());
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            pmeInterpolateForceKernel.setArg<cl::Buffer>(2, pmeGrid->getDeviceBuffer());
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            pmeInterpolateForceKernel.setArg<cl::Buffer>(11, pmeAtomGridIndex->getDeviceBuffer());
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            if (cl.getSupports64BitGlobalAtomics()) {
                pmeFinishSpreadChargeKernel = cl::Kernel(program, "finishSpreadCharge");
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                pmeFinishSpreadChargeKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
                pmeFinishSpreadChargeKernel.setArg<cl::Buffer>(1, pmeGrid->getDeviceBuffer());
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            }
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            if (usePmeQueue)
                syncQueue->setKernel(cl::Kernel(program, "addEnergy"));
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            if (doLJPME) {
                // Create kernels for LJ PME.

                pmeDefines["EWALD_ALPHA"] = cl.doubleToString(dispersionAlpha);
                pmeDefines["GRID_SIZE_X"] = cl.intToString(dispersionGridSizeX);
                pmeDefines["GRID_SIZE_Y"] = cl.intToString(dispersionGridSizeY);
                pmeDefines["GRID_SIZE_Z"] = cl.intToString(dispersionGridSizeZ);
                pmeDefines["EPSILON_FACTOR"] = "1";
                pmeDefines["RECIP_EXP_FACTOR"] = cl.doubleToString(M_PI*M_PI/(dispersionAlpha*dispersionAlpha));
                pmeDefines["USE_LJPME"] = "1";
                program = cl.createProgram(OpenCLKernelSources::pme, pmeDefines);
                pmeDispersionUpdateBsplinesKernel = cl::Kernel(program, "updateBsplines");
                pmeDispersionAtomRangeKernel = cl::Kernel(program, "findAtomRangeForGrid");
                pmeDispersionZIndexKernel = cl::Kernel(program, "recordZIndex");
                pmeDispersionSpreadChargeKernel = cl::Kernel(program, "gridSpreadCharge");
                pmeDispersionConvolutionKernel = cl::Kernel(program, "reciprocalConvolution");
                pmeDispersionEvalEnergyKernel = cl::Kernel(program, "gridEvaluateEnergy");
                pmeDispersionInterpolateForceKernel = cl::Kernel(program, "gridInterpolateForce");
                int elementSize = (cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4));
                pmeDispersionUpdateBsplinesKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
                pmeDispersionUpdateBsplinesKernel.setArg<cl::Buffer>(1, pmeBsplineTheta->getDeviceBuffer());
                pmeDispersionUpdateBsplinesKernel.setArg(2, OpenCLContext::ThreadBlockSize*PmeOrder*elementSize, NULL);
                pmeDispersionUpdateBsplinesKernel.setArg<cl::Buffer>(3, pmeAtomGridIndex->getDeviceBuffer());
                pmeDispersionUpdateBsplinesKernel.setArg<cl::Buffer>(12, sigmaEpsilon->getDeviceBuffer());
                pmeDispersionAtomRangeKernel.setArg<cl::Buffer>(0, pmeAtomGridIndex->getDeviceBuffer());
                pmeDispersionAtomRangeKernel.setArg<cl::Buffer>(1, pmeAtomRange->getDeviceBuffer());
                pmeDispersionAtomRangeKernel.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
                pmeDispersionZIndexKernel.setArg<cl::Buffer>(0, pmeAtomGridIndex->getDeviceBuffer());
                pmeDispersionZIndexKernel.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
                pmeDispersionSpreadChargeKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
                pmeDispersionSpreadChargeKernel.setArg<cl::Buffer>(1, pmeAtomGridIndex->getDeviceBuffer());
                pmeDispersionSpreadChargeKernel.setArg<cl::Buffer>(2, pmeAtomRange->getDeviceBuffer());
                if (cl.getSupports64BitGlobalAtomics())
                    pmeDispersionSpreadChargeKernel.setArg<cl::Buffer>(3, pmeGrid2->getDeviceBuffer());
                else
                    pmeDispersionSpreadChargeKernel.setArg<cl::Buffer>(3, pmeGrid->getDeviceBuffer());
                pmeDispersionSpreadChargeKernel.setArg<cl::Buffer>(4, pmeBsplineTheta->getDeviceBuffer());
                pmeDispersionSpreadChargeKernel.setArg<cl::Buffer>(13, sigmaEpsilon->getDeviceBuffer());
                pmeDispersionConvolutionKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
                pmeDispersionConvolutionKernel.setArg<cl::Buffer>(1, pmeDispersionBsplineModuliX->getDeviceBuffer());
                pmeDispersionConvolutionKernel.setArg<cl::Buffer>(2, pmeDispersionBsplineModuliY->getDeviceBuffer());
                pmeDispersionConvolutionKernel.setArg<cl::Buffer>(3, pmeDispersionBsplineModuliZ->getDeviceBuffer());
                pmeDispersionEvalEnergyKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
                pmeDispersionEvalEnergyKernel.setArg<cl::Buffer>(1, usePmeQueue ? pmeEnergyBuffer->getDeviceBuffer() : cl.getEnergyBuffer().getDeviceBuffer());
                pmeDispersionEvalEnergyKernel.setArg<cl::Buffer>(2, pmeDispersionBsplineModuliX->getDeviceBuffer());
                pmeDispersionEvalEnergyKernel.setArg<cl::Buffer>(3, pmeDispersionBsplineModuliY->getDeviceBuffer());
                pmeDispersionEvalEnergyKernel.setArg<cl::Buffer>(4, pmeDispersionBsplineModuliZ->getDeviceBuffer());
                pmeDispersionInterpolateForceKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
                pmeDispersionInterpolateForceKernel.setArg<cl::Buffer>(1, cl.getForceBuffers().getDeviceBuffer());
                pmeDispersionInterpolateForceKernel.setArg<cl::Buffer>(2, pmeGrid->getDeviceBuffer());
                pmeDispersionInterpolateForceKernel.setArg<cl::Buffer>(11, pmeAtomGridIndex->getDeviceBuffer());
                pmeDispersionInterpolateForceKernel.setArg<cl::Buffer>(12, sigmaEpsilon->getDeviceBuffer());
                if (cl.getSupports64BitGlobalAtomics()) {
                    pmeDispersionFinishSpreadChargeKernel = cl::Kernel(program, "finishSpreadCharge");
                    pmeDispersionFinishSpreadChargeKernel.setArg<cl::Buffer>(0, pmeGrid2->getDeviceBuffer());
                    pmeDispersionFinishSpreadChargeKernel.setArg<cl::Buffer>(1, pmeGrid->getDeviceBuffer());
                }
            }
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       }
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    }
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    if (cosSinSums != NULL && includeReciprocal) {
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        mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
        mm_double4 recipBoxSize = mm_double4(2*M_PI/boxSize.x, 2*M_PI/boxSize.y, 2*M_PI/boxSize.z, 0.0);
        double recipCoefficient = ONE_4PI_EPS0*4*M_PI/(boxSize.x*boxSize.y*boxSize.z);
        if (cl.getUseDoublePrecision()) {
            ewaldSumsKernel.setArg<mm_double4>(3, recipBoxSize);
            ewaldSumsKernel.setArg<cl_double>(4, recipCoefficient);
            ewaldForcesKernel.setArg<mm_double4>(3, recipBoxSize);
            ewaldForcesKernel.setArg<cl_double>(4, recipCoefficient);
        }
        else {
            ewaldSumsKernel.setArg<mm_float4>(3, mm_float4((float) recipBoxSize.x, (float) recipBoxSize.y, (float) recipBoxSize.z, 0));
            ewaldSumsKernel.setArg<cl_float>(4, (cl_float) recipCoefficient);
            ewaldForcesKernel.setArg<mm_float4>(3, mm_float4((float) recipBoxSize.x, (float) recipBoxSize.y, (float) recipBoxSize.z, 0));
            ewaldForcesKernel.setArg<cl_float>(4, (cl_float) recipCoefficient);
        }
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        cl.executeKernel(ewaldSumsKernel, cosSinSums->getSize());
        cl.executeKernel(ewaldForcesKernel, cl.getNumAtoms());
    }
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    if (pmeGrid != NULL && includeReciprocal) {
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        if (usePmeQueue && !includeEnergy)
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            cl.setQueue(pmeQueue);
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        // Invert the periodic box vectors.
        
        Vec3 boxVectors[3];
        cl.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
        double determinant = boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2];
        double scale = 1.0/determinant;
        mm_double4 recipBoxVectors[3];
        recipBoxVectors[0] = mm_double4(boxVectors[1][1]*boxVectors[2][2]*scale, 0, 0, 0);
        recipBoxVectors[1] = mm_double4(-boxVectors[1][0]*boxVectors[2][2]*scale, boxVectors[0][0]*boxVectors[2][2]*scale, 0, 0);
        recipBoxVectors[2] = mm_double4((boxVectors[1][0]*boxVectors[2][1]-boxVectors[1][1]*boxVectors[2][0])*scale, -boxVectors[0][0]*boxVectors[2][1]*scale, boxVectors[0][0]*boxVectors[1][1]*scale, 0);
        mm_float4 recipBoxVectorsFloat[3];
        for (int i = 0; i < 3; i++)
            recipBoxVectorsFloat[i] = mm_float4((float) recipBoxVectors[i].x, (float) recipBoxVectors[i].y, (float) recipBoxVectors[i].z, 0);
        
        // Execute the reciprocal space kernels.

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        setPeriodicBoxArgs(cl, pmeUpdateBsplinesKernel, 4);
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        if (cl.getUseDoublePrecision()) {
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            pmeUpdateBsplinesKernel.setArg<mm_double4>(9, recipBoxVectors[0]);
            pmeUpdateBsplinesKernel.setArg<mm_double4>(10, recipBoxVectors[1]);
            pmeUpdateBsplinesKernel.setArg<mm_double4>(11, recipBoxVectors[2]);
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        }
        else {
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            pmeUpdateBsplinesKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[0]);
            pmeUpdateBsplinesKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[1]);
            pmeUpdateBsplinesKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[2]);
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        }
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        cl.executeKernel(pmeUpdateBsplinesKernel, cl.getNumAtoms());
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        if (deviceIsCpu && !cl.getSupports64BitGlobalAtomics()) {
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            setPeriodicBoxArgs(cl, pmeSpreadChargeKernel, 5);
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            if (cl.getUseDoublePrecision()) {
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                pmeSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
                pmeSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
                pmeSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
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            }
            else {
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                pmeSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
                pmeSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
                pmeSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
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            }
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            cl.executeKernel(pmeSpreadChargeKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
        }
        else {
            sort->sort(*pmeAtomGridIndex);
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            if (cl.getSupports64BitGlobalAtomics()) {
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                setPeriodicBoxArgs(cl, pmeSpreadChargeKernel, 5);
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                if (cl.getUseDoublePrecision()) {
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                    pmeSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
                    pmeSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
                    pmeSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
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                }
                else {
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                    pmeSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
                    pmeSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
                    pmeSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
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                }
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                cl.executeKernel(pmeSpreadChargeKernel, cl.getNumAtoms());
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                cl.executeKernel(pmeFinishSpreadChargeKernel, gridSizeX*gridSizeY*gridSizeZ);
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            }
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            else {
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                cl.executeKernel(pmeAtomRangeKernel, cl.getNumAtoms());
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                setPeriodicBoxSizeArg(cl, pmeZIndexKernel, 2);
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                if (cl.getUseDoublePrecision())
                    pmeZIndexKernel.setArg<mm_double4>(3, recipBoxVectors[2]);
                else
                    pmeZIndexKernel.setArg<mm_float4>(3, recipBoxVectorsFloat[2]);
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                cl.executeKernel(pmeZIndexKernel, cl.getNumAtoms());
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                cl.executeKernel(pmeSpreadChargeKernel, cl.getNumAtoms());
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            }
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        }
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        fft->execFFT(*pmeGrid, *pmeGrid2, true);
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        mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
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        if (cl.getUseDoublePrecision()) {
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            pmeConvolutionKernel.setArg<mm_double4>(4, recipBoxVectors[0]);
            pmeConvolutionKernel.setArg<mm_double4>(5, recipBoxVectors[1]);
            pmeConvolutionKernel.setArg<mm_double4>(6, recipBoxVectors[2]);
            pmeEvalEnergyKernel.setArg<mm_double4>(5, recipBoxVectors[0]);
            pmeEvalEnergyKernel.setArg<mm_double4>(6, recipBoxVectors[1]);
            pmeEvalEnergyKernel.setArg<mm_double4>(7, recipBoxVectors[2]);
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        }
        else {
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            pmeConvolutionKernel.setArg<mm_float4>(4, recipBoxVectorsFloat[0]);
            pmeConvolutionKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[1]);
            pmeConvolutionKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[2]);
            pmeEvalEnergyKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[0]);
            pmeEvalEnergyKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[1]);
            pmeEvalEnergyKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[2]);
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        }
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        if (includeEnergy)
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            cl.executeKernel(pmeEvalEnergyKernel, gridSizeX*gridSizeY*gridSizeZ);
        cl.executeKernel(pmeConvolutionKernel, gridSizeX*gridSizeY*gridSizeZ);
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        fft->execFFT(*pmeGrid2, *pmeGrid, false);
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        setPeriodicBoxArgs(cl, pmeInterpolateForceKernel, 3);
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        if (cl.getUseDoublePrecision()) {
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            pmeInterpolateForceKernel.setArg<mm_double4>(8, recipBoxVectors[0]);
            pmeInterpolateForceKernel.setArg<mm_double4>(9, recipBoxVectors[1]);
            pmeInterpolateForceKernel.setArg<mm_double4>(10, recipBoxVectors[2]);
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        }
        else {
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            pmeInterpolateForceKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[0]);
            pmeInterpolateForceKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[1]);
            pmeInterpolateForceKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[2]);
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        }
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        if (deviceIsCpu)
            cl.executeKernel(pmeInterpolateForceKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
        else
            cl.executeKernel(pmeInterpolateForceKernel, cl.getNumAtoms());
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        if (doLJPME) {
            setPeriodicBoxArgs(cl, pmeDispersionUpdateBsplinesKernel, 4);
            if (cl.getUseDoublePrecision()) {
                pmeDispersionUpdateBsplinesKernel.setArg<mm_double4>(9, recipBoxVectors[0]);
                pmeDispersionUpdateBsplinesKernel.setArg<mm_double4>(10, recipBoxVectors[1]);
                pmeDispersionUpdateBsplinesKernel.setArg<mm_double4>(11, recipBoxVectors[2]);
            }
            else {
                pmeDispersionUpdateBsplinesKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[0]);
                pmeDispersionUpdateBsplinesKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[1]);
                pmeDispersionUpdateBsplinesKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[2]);
            }
            cl.executeKernel(pmeDispersionUpdateBsplinesKernel, cl.getNumAtoms());
            if (deviceIsCpu && !cl.getSupports64BitGlobalAtomics()) {
                cl.clearBuffer(*pmeGrid);
                setPeriodicBoxArgs(cl, pmeDispersionSpreadChargeKernel, 5);
                if (cl.getUseDoublePrecision()) {
                    pmeDispersionSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
                    pmeDispersionSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
                    pmeDispersionSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
                }
                else {
                    pmeDispersionSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
                    pmeDispersionSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
                    pmeDispersionSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
                }
                cl.executeKernel(pmeDispersionSpreadChargeKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
            }
            else {
                sort->sort(*pmeAtomGridIndex);
                if (cl.getSupports64BitGlobalAtomics()) {
                    cl.clearBuffer(*pmeGrid2);
                    setPeriodicBoxArgs(cl, pmeDispersionSpreadChargeKernel, 5);
                    if (cl.getUseDoublePrecision()) {
                        pmeDispersionSpreadChargeKernel.setArg<mm_double4>(10, recipBoxVectors[0]);
                        pmeDispersionSpreadChargeKernel.setArg<mm_double4>(11, recipBoxVectors[1]);
                        pmeDispersionSpreadChargeKernel.setArg<mm_double4>(12, recipBoxVectors[2]);
                    }
                    else {
                        pmeDispersionSpreadChargeKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[0]);
                        pmeDispersionSpreadChargeKernel.setArg<mm_float4>(11, recipBoxVectorsFloat[1]);
                        pmeDispersionSpreadChargeKernel.setArg<mm_float4>(12, recipBoxVectorsFloat[2]);
                    }
                    cl.executeKernel(pmeDispersionSpreadChargeKernel, cl.getNumAtoms());
                    cl.executeKernel(pmeDispersionFinishSpreadChargeKernel, gridSizeX*gridSizeY*gridSizeZ);
                }
                else {
                    cl.clearBuffer(*pmeGrid);
                    cl.executeKernel(pmeDispersionAtomRangeKernel, cl.getNumAtoms());
                    setPeriodicBoxSizeArg(cl, pmeDispersionZIndexKernel, 2);
                    if (cl.getUseDoublePrecision())
                        pmeDispersionZIndexKernel.setArg<mm_double4>(3, recipBoxVectors[2]);
                    else
                        pmeDispersionZIndexKernel.setArg<mm_float4>(3, recipBoxVectorsFloat[2]);
                    cl.executeKernel(pmeDispersionZIndexKernel, cl.getNumAtoms());
                    cl.executeKernel(pmeDispersionSpreadChargeKernel, cl.getNumAtoms());
                }
            }
            dispersionFft->execFFT(*pmeGrid, *pmeGrid2, true);
            mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
            if (cl.getUseDoublePrecision()) {
                pmeDispersionConvolutionKernel.setArg<mm_double4>(4, recipBoxVectors[0]);
                pmeDispersionConvolutionKernel.setArg<mm_double4>(5, recipBoxVectors[1]);
                pmeDispersionConvolutionKernel.setArg<mm_double4>(6, recipBoxVectors[2]);
                pmeDispersionEvalEnergyKernel.setArg<mm_double4>(5, recipBoxVectors[0]);
                pmeDispersionEvalEnergyKernel.setArg<mm_double4>(6, recipBoxVectors[1]);
                pmeDispersionEvalEnergyKernel.setArg<mm_double4>(7, recipBoxVectors[2]);
            }
            else {
                pmeDispersionConvolutionKernel.setArg<mm_float4>(4, recipBoxVectorsFloat[0]);
                pmeDispersionConvolutionKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[1]);
                pmeDispersionConvolutionKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[2]);
                pmeDispersionEvalEnergyKernel.setArg<mm_float4>(5, recipBoxVectorsFloat[0]);
                pmeDispersionEvalEnergyKernel.setArg<mm_float4>(6, recipBoxVectorsFloat[1]);
                pmeDispersionEvalEnergyKernel.setArg<mm_float4>(7, recipBoxVectorsFloat[2]);
            }
            if (includeEnergy)
                cl.executeKernel(pmeDispersionEvalEnergyKernel, gridSizeX*gridSizeY*gridSizeZ);
            cl.executeKernel(pmeDispersionConvolutionKernel, gridSizeX*gridSizeY*gridSizeZ);
            fft->execFFT(*pmeGrid2, *pmeGrid, false);
            setPeriodicBoxArgs(cl, pmeDispersionInterpolateForceKernel, 3);
            if (cl.getUseDoublePrecision()) {
                pmeDispersionInterpolateForceKernel.setArg<mm_double4>(8, recipBoxVectors[0]);
                pmeDispersionInterpolateForceKernel.setArg<mm_double4>(9, recipBoxVectors[1]);
                pmeDispersionInterpolateForceKernel.setArg<mm_double4>(10, recipBoxVectors[2]);
            }
            else {
                pmeDispersionInterpolateForceKernel.setArg<mm_float4>(8, recipBoxVectorsFloat[0]);
                pmeDispersionInterpolateForceKernel.setArg<mm_float4>(9, recipBoxVectorsFloat[1]);
                pmeDispersionInterpolateForceKernel.setArg<mm_float4>(10, recipBoxVectorsFloat[2]);
            }
            if (deviceIsCpu)
                cl.executeKernel(pmeDispersionInterpolateForceKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
            else
                cl.executeKernel(pmeDispersionInterpolateForceKernel, cl.getNumAtoms());
        }
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        if (usePmeQueue) {
            pmeQueue.enqueueMarker(&pmeSyncEvent);
            cl.restoreDefaultQueue();
        }
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    }
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    double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
    if (dispersionCoefficient != 0.0 && includeDirect) {
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        mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
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        energy += dispersionCoefficient/(boxSize.x*boxSize.y*boxSize.z);
    }
    return energy;
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}

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void OpenCLCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const NonbondedForce& force) {
    // Make sure the new parameters are acceptable.
    
    if (force.getNumParticles() != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    if (!hasCoulomb || !hasLJ) {
        for (int i = 0; i < force.getNumParticles(); i++) {
            double charge, sigma, epsilon;
            force.getParticleParameters(i, charge, sigma, epsilon);
            if (!hasCoulomb && charge != 0.0)
                throw OpenMMException("updateParametersInContext: The nonbonded force kernel does not include Coulomb interactions, because all charges were originally 0");
            if (!hasLJ && epsilon != 0.0)
                throw OpenMMException("updateParametersInContext: The nonbonded force kernel does not include Lennard-Jones interactions, because all epsilons were originally 0");
        }
    }
    vector<int> exceptions;
    for (int i = 0; i < force.getNumExceptions(); i++) {
        int particle1, particle2;
        double chargeProd, sigma, epsilon;
        force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
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        if (exceptionAtoms.size() > exceptions.size() && make_pair(particle1, particle2) == exceptionAtoms[exceptions.size()])
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            exceptions.push_back(i);
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        else if (chargeProd != 0.0 || epsilon != 0.0)
            throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
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    }
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*exceptions.size()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*exceptions.size()/numContexts;
    int numExceptions = endIndex-startIndex;
    
    // Record the per-particle parameters.
    
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    vector<double> chargeVector(cl.getNumAtoms());
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    vector<mm_float2> sigmaEpsilonVector(cl.getPaddedNumAtoms(), mm_float2(0,0));
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    double sumSquaredCharges = 0.0;
    for (int i = 0; i < force.getNumParticles(); i++) {
        double charge, sigma, epsilon;
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        force.getParticleParameters(i, charge, sigma, epsilon);
        chargeVector[i] = charge;
        sigmaEpsilonVector[i] = mm_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
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        sumSquaredCharges += charge*charge;
    }
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    cl.setCharges(chargeVector);
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    sigmaEpsilon->upload(sigmaEpsilonVector);
    
    // Record the exceptions.
    
    if (numExceptions > 0) {
        vector<vector<int> > atoms(numExceptions, vector<int>(2));
        vector<mm_float4> exceptionParamsVector(numExceptions);
        for (int i = 0; i < numExceptions; i++) {
            double chargeProd, sigma, epsilon;
            force.getExceptionParameters(exceptions[startIndex+i], atoms[i][0], atoms[i][1], chargeProd, sigma, epsilon);
            exceptionParamsVector[i] = mm_float4((float) (ONE_4PI_EPS0*chargeProd), (float) sigma, (float) (4.0*epsilon), 0.0f);
        }
        exceptionParams->upload(exceptionParamsVector);
    }
    
    // Compute other values.
    
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    if (nonbondedMethod == Ewald || nonbondedMethod == PME)
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        ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
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    if (force.getUseDispersionCorrection() && cl.getContextIndex() == 0 && (nonbondedMethod == CutoffPeriodic || nonbondedMethod == Ewald || nonbondedMethod == PME))
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        dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
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    cl.invalidateMolecules(info);
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}

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void OpenCLCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
    if (nonbondedMethod != PME)
        throw OpenMMException("getPMEParametersInContext: This Context is not using PME");
    if (cl.getPlatformData().useCpuPme)
        cpuPme.getAs<CalcPmeReciprocalForceKernel>().getPMEParameters(alpha, nx, ny, nz);
    else {
        alpha = this->alpha;
        nx = gridSizeX;
        ny = gridSizeY;
        nz = gridSizeZ;
    }
}

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void OpenCLCalcNonbondedForceKernel::getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
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    if (nonbondedMethod != LJPME)
        throw OpenMMException("getPMEParametersInContext: This Context is not using PME");
    if (cl.getPlatformData().useCpuPme)
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        //cpuPme.getAs<CalcPmeReciprocalForceKernel>().getLJPMEParameters(alpha, nx, ny, nz);
        throw OpenMMException("getPMEParametersInContext: CPUPME has not been implemented for LJPME yet.");
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    else {
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        alpha = this->dispersionAlpha;
        nx = dispersionGridSizeX;
        ny = dispersionGridSizeY;
        nz = dispersionGridSizeZ;
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    }
}

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class OpenCLCalcCustomNonbondedForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(int requiredBuffers, const CustomNonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
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        if (force.getNumInteractionGroups() > 0) {
            groupsForParticle.resize(force.getNumParticles());
            for (int i = 0; i < force.getNumInteractionGroups(); i++) {
                set<int> set1, set2;
                force.getInteractionGroupParameters(i, set1, set2);
                for (set<int>::const_iterator iter = set1.begin(); iter != set1.end(); ++iter)
                    groupsForParticle[*iter].insert(2*i);
                for (set<int>::const_iterator iter = set2.begin(); iter != set2.end(); ++iter)
                    groupsForParticle[*iter].insert(2*i+1);
            }
        }
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    }
    bool areParticlesIdentical(int particle1, int particle2) {
        vector<double> params1;
        vector<double> params2;
        force.getParticleParameters(particle1, params1);
        force.getParticleParameters(particle2, params2);
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        for (int i = 0; i < (int) params1.size(); i++)
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            if (params1[i] != params2[i])
                return false;
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        if (groupsForParticle.size() > 0 && groupsForParticle[particle1] != groupsForParticle[particle2])
            return false;
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        return true;
    }
    int getNumParticleGroups() {
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        return force.getNumExclusions();
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    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int particle1, particle2;
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        force.getExclusionParticles(index, particle1, particle2);
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        particles.resize(2);
        particles[0] = particle1;
        particles[1] = particle2;
    }
    bool areGroupsIdentical(int group1, int group2) {
        return true;
    }
private:
    const CustomNonbondedForce& force;
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    vector<set<int> > groupsForParticle;
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};

OpenCLCalcCustomNonbondedForceKernel::~OpenCLCalcCustomNonbondedForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
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    if (interactionGroupData != NULL)
        delete interactionGroupData;
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    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
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    if (forceCopy != NULL)
        delete forceCopy;
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}

void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, const CustomNonbondedForce& force) {
    int forceIndex;
    for (forceIndex = 0; forceIndex < system.getNumForces() && &system.getForce(forceIndex) != &force; ++forceIndex)
        ;
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    string prefix = (force.getNumInteractionGroups() == 0 ? "custom"+cl.intToString(forceIndex)+"_" : "");
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    // Record parameters and exclusions.

    int numParticles = force.getNumParticles();
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    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), numParticles, "customNonbondedParameters");
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    if (force.getNumGlobalParameters() > 0)
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        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customNonbondedGlobals", CL_MEM_READ_ONLY);
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    vector<vector<cl_float> > paramVector(numParticles);
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    vector<vector<int> > exclusionList(numParticles);
    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
        force.getParticleParameters(i, parameters);
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        paramVector[i].resize(parameters.size());
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        for (int j = 0; j < (int) parameters.size(); j++)
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            paramVector[i][j] = (cl_float) parameters[j];
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        exclusionList[i].push_back(i);
    }
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    for (int i = 0; i < force.getNumExclusions(); i++) {
        int particle1, particle2;
        force.getExclusionParticles(i, particle1, particle2);
        exclusionList[particle1].push_back(particle2);
        exclusionList[particle2].push_back(particle1);
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    }
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    params->setParameterValues(paramVector);
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    // Record the tabulated functions.

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    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
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    vector<const TabulatedFunction*> functionList;
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    vector<string> tableTypes;
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    for (int i = 0; i < force.getNumFunctions(); i++) {
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        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
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        string arrayName = prefix+"table"+cl.intToString(i);
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        functionDefinitions.push_back(make_pair(name, arrayName));
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        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
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        int width;
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        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
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        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
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        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
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        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
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        if (width == 1)
            tableTypes.push_back("float");
        else
            tableTypes.push_back("float"+cl.intToString(width));
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    }

    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    if (globals != NULL)
        globals->upload(globalParamValues);
    bool useCutoff = (force.getNonbondedMethod() != CustomNonbondedForce::NoCutoff);
    bool usePeriodic = (force.getNonbondedMethod() != CustomNonbondedForce::NoCutoff && force.getNonbondedMethod() != CustomNonbondedForce::CutoffNonPeriodic);
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    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction(), functions).optimize();
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    Lepton::ParsedExpression forceExpression = energyExpression.differentiate("r").optimize();
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    map<string, Lepton::ParsedExpression> forceExpressions;
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    forceExpressions["real customEnergy = "] = energyExpression;
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    forceExpressions["tempForce -= "] = forceExpression;
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    // Create the kernels.

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    vector<pair<ExpressionTreeNode, string> > variables;
    ExpressionTreeNode rnode(new Operation::Variable("r"));
    variables.push_back(make_pair(rnode, "r"));
    variables.push_back(make_pair(ExpressionTreeNode(new Operation::Square(), rnode), "r2"));
    variables.push_back(make_pair(ExpressionTreeNode(new Operation::Reciprocal(), rnode), "invR"));
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    for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
        const string& name = force.getPerParticleParameterName(i);
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        variables.push_back(makeVariable(name+"1", prefix+"params"+params->getParameterSuffix(i, "1")));
        variables.push_back(makeVariable(name+"2", prefix+"params"+params->getParameterSuffix(i, "2")));
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    }
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        const string& name = force.getGlobalParameterName(i);
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        string value = "globals["+cl.intToString(i)+"]";
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        variables.push_back(makeVariable(name, prefix+value));
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    }
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    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getNonbondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        forceExpressions[derivVariable+" += interactionScale*switchValue*"] = derivExpression;
    }
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    stringstream compute;
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    compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, prefix+"temp");
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    map<string, string> replacements;
    replacements["COMPUTE_FORCE"] = compute.str();
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    replacements["USE_SWITCH"] = (useCutoff && force.getUseSwitchingFunction() ? "1" : "0");
    if (force.getUseSwitchingFunction()) {
        // Compute the switching coefficients.
        
        replacements["SWITCH_CUTOFF"] = cl.doubleToString(force.getSwitchingDistance());
        replacements["SWITCH_C3"] = cl.doubleToString(10/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 3.0));
        replacements["SWITCH_C4"] = cl.doubleToString(15/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 4.0));
        replacements["SWITCH_C5"] = cl.doubleToString(6/pow(force.getSwitchingDistance()-force.getCutoffDistance(), 5.0));
    }
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    string source = cl.replaceStrings(OpenCLKernelSources::customNonbonded, replacements);
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    if (force.getNumInteractionGroups() > 0)
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        initInteractionGroups(force, source, tableTypes);
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    else {
        cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
            cl.getNonbondedUtilities().addParameter(OpenCLNonbondedUtilities::ParameterInfo(prefix+"params"+cl.intToString(i+1), buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
        }
        if (globals != NULL) {
            globals->upload(globalParamValues);
            cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(cl_float), globals->getDeviceBuffer()));
        }
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    }
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    info = new ForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force);
    cl.addForce(info);
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    // Record information for the long range correction.
    
    if (force.getNonbondedMethod() == CustomNonbondedForce::CutoffPeriodic && force.getUseLongRangeCorrection() && cl.getContextIndex() == 0) {
        forceCopy = new CustomNonbondedForce(force);
        hasInitializedLongRangeCorrection = false;
    }
    else {
        longRangeCoefficient = 0.0;
        hasInitializedLongRangeCorrection = true;
    }
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}

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void OpenCLCalcCustomNonbondedForceKernel::initInteractionGroups(const CustomNonbondedForce& force, const string& interactionSource, const vector<string>& tableTypes) {
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    // Process groups to form tiles.
    
    vector<vector<int> > atomLists;
    vector<pair<int, int> > tiles;
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    map<pair<int, int>, int> duplicateInteractions;
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    for (int group = 0; group < force.getNumInteractionGroups(); group++) {
        // Get the list of atoms in this group and sort them.
        
        set<int> set1, set2;
        force.getInteractionGroupParameters(group, set1, set2);
        vector<int> atoms1, atoms2;
        atoms1.insert(atoms1.begin(), set1.begin(), set1.end());
        atoms2.insert(atoms2.begin(), set2.begin(), set2.end());
        sort(atoms1.begin(), atoms1.end());
        sort(atoms2.begin(), atoms2.end());
        
        // Find how many tiles we will create for this group.
        
        int tileWidth = min(min(32, (int) atoms1.size()), (int) atoms2.size());
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        if (tileWidth == 0)
            continue;
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        int numBlocks1 = (atoms1.size()+tileWidth-1)/tileWidth;
        int numBlocks2 = (atoms2.size()+tileWidth-1)/tileWidth;
        
        // Add the tiles.
        
        for (int i = 0; i < numBlocks1; i++)
            for (int j = 0; j < numBlocks2; j++)
                tiles.push_back(make_pair(atomLists.size()+i, atomLists.size()+numBlocks1+j));
        
        // Add the atom lists.
        
        for (int i = 0; i < numBlocks1; i++) {
            vector<int> atoms;
            int first = i*tileWidth;
            int last = min((i+1)*tileWidth, (int) atoms1.size());
            for (int j = first; j < last; j++)
                atoms.push_back(atoms1[j]);
            atomLists.push_back(atoms);
        }
        for (int i = 0; i < numBlocks2; i++) {
            vector<int> atoms;
            int first = i*tileWidth;
            int last = min((i+1)*tileWidth, (int) atoms2.size());
            for (int j = first; j < last; j++)
                atoms.push_back(atoms2[j]);
            atomLists.push_back(atoms);
        }
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        // If this group contains duplicate interactions, record that we need to skip them once.
        
        for (int i = 0; i < (int) atoms1.size(); i++) {
            int a1 = atoms1[i];
            if (set2.find(a1) == set2.end())
                continue;
            for (int j = 0; j < (int) atoms2.size() && atoms2[j] < a1; j++) {
                int a2 = atoms2[j];
                if (set1.find(a2) != set1.end()) {
                    pair<int, int> key = make_pair(a2, a1);
                    if (duplicateInteractions.find(key) == duplicateInteractions.end())
                        duplicateInteractions[key] = 0;
                    duplicateInteractions[key]++;
                }
            }
        }
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    }
    
    // Build a lookup table for quickly identifying excluded interactions.
    
    set<pair<int, int> > exclusions;
    for (int i = 0; i < force.getNumExclusions(); i++) {
        int p1, p2;
        force.getExclusionParticles(i, p1, p2);
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        exclusions.insert(make_pair(min(p1, p2), max(p1, p2)));
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    }
    
    // Build the exclusion flags for each tile.  While we're at it, filter out tiles
    // where all interactions are excluded, and sort the tiles by size.

    vector<vector<int> > exclusionFlags(tiles.size());
    vector<pair<int, int> > tileOrder;
    for (int tile = 0; tile < tiles.size(); tile++) {
        if (atomLists[tiles[tile].first].size() < atomLists[tiles[tile].second].size()) {
            // For efficiency, we want the first axis to be the larger one.
            
            int swap = tiles[tile].first;
            tiles[tile].first = tiles[tile].second;
            tiles[tile].second = swap;
        }
        vector<int>& atoms1 = atomLists[tiles[tile].first];
        vector<int>& atoms2 = atomLists[tiles[tile].second];
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        vector<int> flags(atoms1.size(), (int) (1LL<<atoms2.size())-1);
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        int numExcluded = 0;
        for (int i = 0; i < (int) atoms1.size(); i++)
            for (int j = 0; j < (int) atoms2.size(); j++) {
                int a1 = atoms1[i];
                int a2 = atoms2[j];
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                bool isExcluded = false;
                pair<int, int> key = make_pair(min(a1, a2), max(a1, a2));
                if (a1 == a2 || exclusions.find(key) != exclusions.end())
                    isExcluded = true; // This is an excluded interaction.
                else if (duplicateInteractions.find(key) != duplicateInteractions.end() && duplicateInteractions[key] > 0) {
                    // Both atoms are in both sets, so skip duplicate interactions.
                    
                    isExcluded = true;
                    duplicateInteractions[key]--;
                }
                if (isExcluded) {
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                    flags[i] &= -1-(1<<j);
                    numExcluded++;
                }
            }
        if (numExcluded == atoms1.size()*atoms2.size())
            continue; // All interactions are excluded.
        tileOrder.push_back(make_pair((int) -atoms2.size(), tile));
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        exclusionFlags[tile] = flags;
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    }
    sort(tileOrder.begin(), tileOrder.end());
    
    // Merge tiles to get as close as possible to 32 along the first axis of each one.
    
    vector<int> tileSetStart;
    tileSetStart.push_back(0);
    int tileSetSize = 0;
    for (int i = 0; i < tileOrder.size(); i++) {
        int tile = tileOrder[i].second;
        int size = atomLists[tiles[tile].first].size();
        if (tileSetSize+size > 32) {
            tileSetStart.push_back(i);
            tileSetSize = 0;
        }
        tileSetSize += size;
    }
    tileSetStart.push_back(tileOrder.size());
    
    // Build the data structures.
    
    int numTileSets = tileSetStart.size()-1;
    vector<mm_int4> groupData;
    for (int tileSet = 0; tileSet < numTileSets; tileSet++) {
        int indexInTileSet = 0;
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        int minSize = 0;
        if (cl.getSIMDWidth() < 32) {
            // We need to include a barrier inside the inner loop, so ensure that all
            // threads will loop the same number of times.
            
            for (int i = tileSetStart[tileSet]; i < tileSetStart[tileSet+1]; i++)
                minSize = max(minSize, (int) atomLists[tiles[tileOrder[i].second].first].size());
        }
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        for (int i = tileSetStart[tileSet]; i < tileSetStart[tileSet+1]; i++) {
            int tile = tileOrder[i].second;
            vector<int>& atoms1 = atomLists[tiles[tile].first];
            vector<int>& atoms2 = atomLists[tiles[tile].second];
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            int range = indexInTileSet + ((indexInTileSet+max(minSize, (int) atoms1.size()))<<16);
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            int allFlags = (1<<atoms2.size())-1;
            for (int j = 0; j < (int) atoms1.size(); j++) {
                int a1 = atoms1[j];
                int a2 = (j < atoms2.size() ? atoms2[j] : 0);
                int flags = (exclusionFlags[tile].size() > 0 ? exclusionFlags[tile][j] : allFlags);
                groupData.push_back(mm_int4(a1, a2, range, flags<<indexInTileSet));
            }
            indexInTileSet += atoms1.size();
        }
        for (; indexInTileSet < 32; indexInTileSet++)
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            groupData.push_back(mm_int4(0, 0, minSize<<16, 0));
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    }
    interactionGroupData = OpenCLArray::create<mm_int4>(cl, groupData.size(), "interactionGroupData");
    interactionGroupData->upload(groupData);
    
    // Create the kernel.
    
    map<string, string> replacements;
    replacements["COMPUTE_INTERACTION"] = interactionSource;
    const string suffixes[] = {"x", "y", "z", "w"};
    stringstream localData;
    int localDataSize = 0;
    vector<OpenCLNonbondedUtilities::ParameterInfo>& buffers = params->getBuffers(); 
    for (int i = 0; i < (int) buffers.size(); i++) {
        if (buffers[i].getNumComponents() == 1)
            localData<<buffers[i].getComponentType()<<" params"<<(i+1)<<";\n";
        else {
            for (int j = 0; j < buffers[i].getNumComponents(); ++j)
                localData<<buffers[i].getComponentType()<<" params"<<(i+1)<<"_"<<suffixes[j]<<";\n";
        }
        localDataSize += buffers[i].getSize();
    }
    replacements["ATOM_PARAMETER_DATA"] = localData.str();
    stringstream args;
    for (int i = 0; i < (int) buffers.size(); i++)
        args<<", __global const "<<buffers[i].getType()<<"* restrict global_params"<<(i+1);
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    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        args << ", __global const " << tableTypes[i]<< "* restrict table" << i;
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    if (globals != NULL)
        args<<", __global const float* restrict globals";
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    replacements["PARAMETER_ARGUMENTS"] = args.str();
    stringstream load1;
    for (int i = 0; i < (int) buffers.size(); i++)
        load1<<buffers[i].getType()<<" params"<<(i+1)<<"1 = global_params"<<(i+1)<<"[atom1];\n";
    replacements["LOAD_ATOM1_PARAMETERS"] = load1.str();
    stringstream loadLocal2;
    for (int i = 0; i < (int) buffers.size(); i++) {
        if (buffers[i].getNumComponents() == 1)
            loadLocal2<<"localData[get_local_id(0)].params"<<(i+1)<<" = global_params"<<(i+1)<<"[atom2];\n";
        else {
            loadLocal2<<buffers[i].getType()<<" temp_params"<<(i+1)<<" = global_params"<<(i+1)<<"[atom2];\n";
            for (int j = 0; j < buffers[i].getNumComponents(); ++j)
                loadLocal2<<"localData[get_local_id(0)].params"<<(i+1)<<"_"<<suffixes[j]<<" = temp_params"<<(i+1)<<"."<<suffixes[j]<<";\n";
        }
    }
    replacements["LOAD_LOCAL_PARAMETERS"] = loadLocal2.str();
    stringstream load2;
    for (int i = 0; i < (int) buffers.size(); i++) {
        if (buffers[i].getNumComponents() == 1)
            load2<<buffers[i].getType()<<" params"<<(i+1)<<"2 = localData[localIndex].params"<<(i+1)<<";\n";
        else {
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            load2<<buffers[i].getType()<<" params"<<(i+1)<<"2 = ("<<buffers[i].getType()<<") (";
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            for (int j = 0; j < buffers[i].getNumComponents(); ++j) {
                if (j > 0)
                    load2<<", ";
                load2<<"localData[localIndex].params"<<(i+1)<<"_"<<suffixes[j];
            }
            load2<<");\n";
        }
    }
    replacements["LOAD_ATOM2_PARAMETERS"] = load2.str();
    map<string, string> defines;
    if (force.getNonbondedMethod() != CustomNonbondedForce::NoCutoff)
        defines["USE_CUTOFF"] = "1";
    if (force.getNonbondedMethod() == CustomNonbondedForce::CutoffPeriodic)
        defines["USE_PERIODIC"] = "1";
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    defines["LOCAL_MEMORY_SIZE"] = cl.intToString(max(32, cl.getNonbondedUtilities().getForceThreadBlockSize()));
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    double cutoff = force.getCutoffDistance();
    defines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
    defines["TILE_SIZE"] = "32";
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*numTileSets/numContexts;
    int endIndex = (cl.getContextIndex()+1)*numTileSets/numContexts;
    defines["FIRST_TILE"] = cl.intToString(startIndex);
    defines["LAST_TILE"] = cl.intToString(endIndex);
    if ((localDataSize/4)%2 == 0 && !cl.getUseDoublePrecision())
        defines["PARAMETER_SIZE_IS_EVEN"] = "1";
    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customNonbondedGroups, replacements), defines);
    interactionGroupKernel = cl::Kernel(program, "computeInteractionGroups");
    numGroupThreadBlocks = cl.getNonbondedUtilities().getNumForceThreadBlocks();
}

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double OpenCLCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    if (globals != NULL) {
        bool changed = false;
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        for (int i = 0; i < (int) globalParamNames.size(); i++) {
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            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
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        if (changed) {
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            globals->upload(globalParamValues);
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            if (forceCopy != NULL) {
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                CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner(), longRangeCoefficient, longRangeCoefficientDerivs);
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                hasInitializedLongRangeCorrection = true;
            }
        }
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    }
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    if (!hasInitializedLongRangeCorrection) {
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        CustomNonbondedForceImpl::calcLongRangeCorrection(*forceCopy, context.getOwner(), longRangeCoefficient, longRangeCoefficientDerivs);
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        hasInitializedLongRangeCorrection = true;
    }
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    if (interactionGroupData != NULL) {
        if (!hasInitializedKernel) {
            hasInitializedKernel = true;
            int index = 0;
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            bool useLong = cl.getSupports64BitGlobalAtomics();
            interactionGroupKernel.setArg<cl::Buffer>(index++, (useLong ? cl.getLongForceBuffer() : cl.getForceBuffers()).getDeviceBuffer());
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            interactionGroupKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
            interactionGroupKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
            interactionGroupKernel.setArg<cl::Buffer>(index++, interactionGroupData->getDeviceBuffer());
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            index += 5;
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            for (int i = 0; i < (int) params->getBuffers().size(); i++)
                interactionGroupKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
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            for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
                interactionGroupKernel.setArg<cl::Memory>(index++, tabulatedFunctions[i]->getDeviceBuffer());
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            if (globals != NULL)
                interactionGroupKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        }
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        setPeriodicBoxArgs(cl, interactionGroupKernel, 4);
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        int forceThreadBlockSize = max(32, cl.getNonbondedUtilities().getForceThreadBlockSize());
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        cl.executeKernel(interactionGroupKernel, numGroupThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
    }
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    mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
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    double volume = boxSize.x*boxSize.y*boxSize.z;
    map<string, double>& derivs = cl.getEnergyParamDerivWorkspace();
    for (int i = 0; i < longRangeCoefficientDerivs.size(); i++)
        derivs[forceCopy->getEnergyParameterDerivativeName(i)] += longRangeCoefficientDerivs[i]/volume;
    return longRangeCoefficient/volume;
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}
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void OpenCLCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {
    int numParticles = force.getNumParticles();
    if (numParticles != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    
    // Record the per-particle parameters.
    
    vector<vector<cl_float> > paramVector(numParticles);
    vector<double> parameters;
    for (int i = 0; i < numParticles; i++) {
        force.getParticleParameters(i, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
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    // If necessary, recompute the long range correction.
    
    if (forceCopy != NULL) {
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        CustomNonbondedForceImpl::calcLongRangeCorrection(force, context.getOwner(), longRangeCoefficient, longRangeCoefficientDerivs);
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        hasInitializedLongRangeCorrection = true;
        *forceCopy = force;
    }
    
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    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcGBSAOBCForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(int requiredBuffers, const GBSAOBCForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
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    }
    bool areParticlesIdentical(int particle1, int particle2) {
        double charge1, charge2, radius1, radius2, scale1, scale2;
        force.getParticleParameters(particle1, charge1, radius1, scale1);
        force.getParticleParameters(particle2, charge2, radius2, scale2);
        return (charge1 == charge2 && radius1 == radius2 && scale1 == scale2);
    }
private:
    const GBSAOBCForce& force;
};

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OpenCLCalcGBSAOBCForceKernel::~OpenCLCalcGBSAOBCForceKernel() {
    if (params != NULL)
        delete params;
    if (bornSum != NULL)
        delete bornSum;
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    if (longBornSum != NULL)
        delete longBornSum;
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    if (bornRadii != NULL)
        delete bornRadii;
    if (bornForce != NULL)
        delete bornForce;
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    if (longBornForce != NULL)
        delete longBornForce;
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    if (obcChain != NULL)
        delete obcChain;
}

void OpenCLCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCForce& force) {
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    if (cl.getPlatformData().contexts.size() > 1)
        throw OpenMMException("GBSAOBCForce does not support using multiple OpenCL devices");
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    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
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    params = OpenCLArray::create<mm_float2>(cl, cl.getPaddedNumAtoms(), "gbsaObcParams");
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    int elementSize = (cl.getUseDoublePrecision() ? sizeof(cl_double) : sizeof(cl_float));
    bornRadii = new OpenCLArray(cl, cl.getPaddedNumAtoms(), elementSize, "bornRadii");
    obcChain = new OpenCLArray(cl, cl.getPaddedNumAtoms(), elementSize, "obcChain");
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    if (cl.getSupports64BitGlobalAtomics()) {
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        longBornSum = OpenCLArray::create<cl_long>(cl, cl.getPaddedNumAtoms(), "longBornSum");
        longBornForce = OpenCLArray::create<cl_long>(cl, cl.getPaddedNumAtoms(), "longBornForce");
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        bornForce = new OpenCLArray(cl, cl.getPaddedNumAtoms(), elementSize, "bornForce");
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        cl.addAutoclearBuffer(*longBornSum);
        cl.addAutoclearBuffer(*longBornForce);
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    }
    else {
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        bornSum = new OpenCLArray(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), elementSize, "bornSum");
        bornForce = new OpenCLArray(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), elementSize, "bornForce");
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        cl.addAutoclearBuffer(*bornSum);
        cl.addAutoclearBuffer(*bornForce);
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    }
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    vector<mm_float4> posqf(cl.getPaddedNumAtoms());
    vector<mm_double4> posqd(cl.getPaddedNumAtoms());
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    vector<mm_float2> paramsVector(cl.getPaddedNumAtoms(), mm_float2(1,1));
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    const double dielectricOffset = 0.009;
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    for (int i = 0; i < force.getNumParticles(); i++) {
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        double charge, radius, scalingFactor;
        force.getParticleParameters(i, charge, radius, scalingFactor);
        radius -= dielectricOffset;
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        paramsVector[i] = mm_float2((float) radius, (float) (scalingFactor*radius));
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        if (cl.getUseDoublePrecision())
            posqd[i] = mm_double4(0, 0, 0, charge);
        else
            posqf[i] = mm_float4(0, 0, 0, (float) charge);
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    }
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    if (cl.getUseDoublePrecision())
        cl.getPosq().upload(posqd);
    else
        cl.getPosq().upload(posqf);
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    params->upload(paramsVector);
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    prefactor = -ONE_4PI_EPS0*((1.0/force.getSoluteDielectric())-(1.0/force.getSolventDielectric()));
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    surfaceAreaFactor = -6.0*4*M_PI*force.getSurfaceAreaEnergy();
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    bool useCutoff = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff);
    bool usePeriodic = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff && force.getNonbondedMethod() != GBSAOBCForce::CutoffNonPeriodic);
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    cutoff = force.getCutoffDistance();
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    string source = OpenCLKernelSources::gbsaObc2;
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    nb.addInteraction(useCutoff, usePeriodic, false, cutoff, vector<vector<int> >(), source, force.getForceGroup());
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    nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("obcParams", "float", 2, sizeof(cl_float2), params->getDeviceBuffer()));;
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    nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("bornForce", "real", 1, elementSize, bornForce->getDeviceBuffer()));;
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    info = new ForceInfo(nb.getNumForceBuffers(), force);
    cl.addForce(info);
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}

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double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
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    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
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    if (!hasCreatedKernels) {
        // These Kernels cannot be created in initialize(), because the OpenCLNonbondedUtilities has not been initialized yet then.

        hasCreatedKernels = true;
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        maxTiles = (nb.getUseCutoff() ? nb.getInteractingTiles().getSize() : 0);
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        map<string, string> defines;
        if (nb.getUseCutoff())
            defines["USE_CUTOFF"] = "1";
        if (nb.getUsePeriodic())
            defines["USE_PERIODIC"] = "1";
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        defines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
        defines["CUTOFF"] = cl.doubleToString(cutoff);
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        defines["PREFACTOR"] = cl.doubleToString(prefactor);
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        defines["SURFACE_AREA_FACTOR"] = cl.doubleToString(surfaceAreaFactor);
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        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
        defines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
        defines["FORCE_WORK_GROUP_SIZE"] = cl.intToString(nb.getForceThreadBlockSize());
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        defines["TILE_SIZE"] = cl.intToString(OpenCLContext::TileSize);
        int numExclusionTiles = nb.getExclusionTiles().getSize();
        defines["NUM_TILES_WITH_EXCLUSIONS"] = cl.intToString(numExclusionTiles);
        int numContexts = cl.getPlatformData().contexts.size();
        int startExclusionIndex = cl.getContextIndex()*numExclusionTiles/numContexts;
        int endExclusionIndex = (cl.getContextIndex()+1)*numExclusionTiles/numContexts;
        defines["FIRST_EXCLUSION_TILE"] = cl.intToString(startExclusionIndex);
        defines["LAST_EXCLUSION_TILE"] = cl.intToString(endExclusionIndex);
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        string platformVendor = cl::Platform(cl.getDevice().getInfo<CL_DEVICE_PLATFORM>()).getInfo<CL_PLATFORM_VENDOR>();
        if (platformVendor == "Apple")
            defines["USE_APPLE_WORKAROUND"] = "1";
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        string file;
        if (deviceIsCpu)
            file = OpenCLKernelSources::gbsaObc_cpu;
        else
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            file = OpenCLKernelSources::gbsaObc;
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        cl::Program program = cl.createProgram(file, defines);
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        bool useLong = cl.getSupports64BitGlobalAtomics();
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        int index = 0;
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        computeBornSumKernel = cl::Kernel(program, "computeBornSum");
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        computeBornSumKernel.setArg<cl::Buffer>(index++, (useLong ? longBornSum->getDeviceBuffer() : bornSum->getDeviceBuffer()));
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        computeBornSumKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
        computeBornSumKernel.setArg<cl::Buffer>(index++, params->getDeviceBuffer());
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        if (nb.getUseCutoff()) {
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            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
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            index += 5; // The periodic box size arguments are set when the kernel is executed.
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            computeBornSumKernel.setArg<cl_uint>(index++, maxTiles);
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            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getBlockCenters().getDeviceBuffer());
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            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getBlockBoundingBoxes().getDeviceBuffer());
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            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractingAtoms().getDeviceBuffer());
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        }
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        else
            computeBornSumKernel.setArg<cl_uint>(index++, cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2);
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        computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getExclusionTiles().getDeviceBuffer());
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        force1Kernel = cl::Kernel(program, "computeGBSAForce1");
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        index = 0;
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        force1Kernel.setArg<cl::Buffer>(index++, (useLong ? cl.getLongForceBuffer().getDeviceBuffer() : cl.getForceBuffers().getDeviceBuffer()));
        force1Kernel.setArg<cl::Buffer>(index++, (useLong ? longBornForce->getDeviceBuffer() : bornForce->getDeviceBuffer()));
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        force1Kernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        force1Kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
        force1Kernel.setArg<cl::Buffer>(index++, bornRadii->getDeviceBuffer());
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        index++; // Whether to include energy.
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        if (nb.getUseCutoff()) {
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            force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
            force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
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            index += 5; // The periodic box size arguments are set when the kernel is executed.
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            force1Kernel.setArg<cl_uint>(index++, maxTiles);
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            force1Kernel.setArg<cl::Buffer>(index++, nb.getBlockCenters().getDeviceBuffer());
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            force1Kernel.setArg<cl::Buffer>(index++, nb.getBlockBoundingBoxes().getDeviceBuffer());
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            force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractingAtoms().getDeviceBuffer());
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        }
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        else
            force1Kernel.setArg<cl_uint>(index++, cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2);
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        force1Kernel.setArg<cl::Buffer>(index++, nb.getExclusionTiles().getDeviceBuffer());
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        program = cl.createProgram(OpenCLKernelSources::gbsaObcReductions, defines);
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        reduceBornSumKernel = cl::Kernel(program, "reduceBornSum");
        reduceBornSumKernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
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        reduceBornSumKernel.setArg<cl_int>(1, nb.getNumForceBuffers());
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        reduceBornSumKernel.setArg<cl_float>(2, 1.0f);
        reduceBornSumKernel.setArg<cl_float>(3, 0.8f);
        reduceBornSumKernel.setArg<cl_float>(4, 4.85f);
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        reduceBornSumKernel.setArg<cl::Buffer>(5, (useLong ? longBornSum->getDeviceBuffer() : bornSum->getDeviceBuffer()));
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        reduceBornSumKernel.setArg<cl::Buffer>(6, params->getDeviceBuffer());
        reduceBornSumKernel.setArg<cl::Buffer>(7, bornRadii->getDeviceBuffer());
        reduceBornSumKernel.setArg<cl::Buffer>(8, obcChain->getDeviceBuffer());
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        reduceBornForceKernel = cl::Kernel(program, "reduceBornForce");
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        index = 0;
        reduceBornForceKernel.setArg<cl_int>(index++, cl.getPaddedNumAtoms());
        reduceBornForceKernel.setArg<cl_int>(index++, nb.getNumForceBuffers());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, bornForce->getDeviceBuffer());
        if (useLong)
            reduceBornForceKernel.setArg<cl::Buffer>(index++, longBornForce->getDeviceBuffer());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, params->getDeviceBuffer());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, bornRadii->getDeviceBuffer());
        reduceBornForceKernel.setArg<cl::Buffer>(index++, obcChain->getDeviceBuffer());
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    }
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    force1Kernel.setArg<cl_int>(5, includeEnergy);
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    if (nb.getUseCutoff()) {
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        setPeriodicBoxArgs(cl, computeBornSumKernel, 5);
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        setPeriodicBoxArgs(cl, force1Kernel, 8);
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        if (maxTiles < nb.getInteractingTiles().getSize()) {
            maxTiles = nb.getInteractingTiles().getSize();
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            computeBornSumKernel.setArg<cl::Buffer>(3, nb.getInteractingTiles().getDeviceBuffer());
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            computeBornSumKernel.setArg<cl_uint>(10, maxTiles);
            computeBornSumKernel.setArg<cl::Buffer>(13, nb.getInteractingAtoms().getDeviceBuffer());
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            force1Kernel.setArg<cl::Buffer>(6, nb.getInteractingTiles().getDeviceBuffer());
            force1Kernel.setArg<cl_uint>(13, maxTiles);
            force1Kernel.setArg<cl::Buffer>(16, nb.getInteractingAtoms().getDeviceBuffer());
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        }
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    }
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    cl.executeKernel(computeBornSumKernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
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    cl.executeKernel(reduceBornSumKernel, cl.getPaddedNumAtoms());
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    cl.executeKernel(force1Kernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
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    cl.executeKernel(reduceBornForceKernel, cl.getPaddedNumAtoms());
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    return 0.0;
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}
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void OpenCLCalcGBSAOBCForceKernel::copyParametersToContext(ContextImpl& context, const GBSAOBCForce& force) {
    // Make sure the new parameters are acceptable.
    
    int numParticles = force.getNumParticles();
    if (numParticles != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    
    // Record the per-particle parameters.
    
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    vector<double> chargeVector(cl.getNumAtoms());
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    vector<mm_float2> paramsVector(cl.getPaddedNumAtoms(), mm_float2(1,1));
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    const double dielectricOffset = 0.009;
    for (int i = 0; i < numParticles; i++) {
        double charge, radius, scalingFactor;
        force.getParticleParameters(i, charge, radius, scalingFactor);
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        chargeVector[i] = charge;
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        radius -= dielectricOffset;
        paramsVector[i] = mm_float2((float) radius, (float) (scalingFactor*radius));
    }
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    cl.setCharges(chargeVector);
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    params->upload(paramsVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcCustomGBForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(int requiredBuffers, const CustomGBForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
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    }
    bool areParticlesIdentical(int particle1, int particle2) {
        vector<double> params1;
        vector<double> params2;
        force.getParticleParameters(particle1, params1);
        force.getParticleParameters(particle2, params2);
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        for (int i = 0; i < (int) params1.size(); i++)
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            if (params1[i] != params2[i])
                return false;
        return true;
    }
    int getNumParticleGroups() {
        return force.getNumExclusions();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        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;
    }
private:
    const CustomGBForce& force;
};

OpenCLCalcCustomGBForceKernel::~OpenCLCalcCustomGBForceKernel() {
    if (params != NULL)
        delete params;
    if (computedValues != NULL)
        delete computedValues;
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    if (energyDerivs != NULL)
        delete energyDerivs;
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    if (energyDerivChain != NULL)
        delete energyDerivChain;
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    if (longEnergyDerivs != NULL)
        delete longEnergyDerivs;
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    if (globals != NULL)
        delete globals;
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    if (valueBuffers != NULL)
        delete valueBuffers;
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    if (longValueBuffers != NULL)
        delete longValueBuffers;
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    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
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    for (int i = 0; i < dValue0dParam.size(); i++)
        delete dValue0dParam[i];
    for (int i = 0; i < dValuedParam.size(); i++)
        delete dValuedParam[i];
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}

void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const CustomGBForce& force) {
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    if (cl.getPlatformData().contexts.size() > 1)
        throw OpenMMException("CustomGBForce does not support using multiple OpenCL devices");
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    cutoff = force.getCutoffDistance();
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    bool useExclusionsForValue = false;
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    numComputedValues = force.getNumComputedValues();
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    vector<string> computedValueNames(force.getNumComputedValues());
    vector<string> computedValueExpressions(force.getNumComputedValues());
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    if (force.getNumComputedValues() > 0) {
        CustomGBForce::ComputationType type;
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        force.getComputedValueParameters(0, computedValueNames[0], computedValueExpressions[0], type);
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        if (type == CustomGBForce::SingleParticle)
            throw OpenMMException("OpenCLPlatform requires that the first computed value for a CustomGBForce be of type ParticlePair or ParticlePairNoExclusions.");
        useExclusionsForValue = (type == CustomGBForce::ParticlePair);
        for (int i = 1; i < force.getNumComputedValues(); i++) {
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            force.getComputedValueParameters(i, computedValueNames[i], computedValueExpressions[i], type);
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            if (type != CustomGBForce::SingleParticle)
                throw OpenMMException("OpenCLPlatform requires that a CustomGBForce only have one computed value of type ParticlePair or ParticlePairNoExclusions.");
        }
    }
    int forceIndex;
    for (forceIndex = 0; forceIndex < system.getNumForces() && &system.getForce(forceIndex) != &force; ++forceIndex)
        ;
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    string prefix = "custom"+cl.intToString(forceIndex)+"_";
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    // Record parameters and exclusions.

    int numParticles = force.getNumParticles();
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    int paddedNumParticles = cl.getPaddedNumAtoms();
    int numParams = force.getNumPerParticleParameters();
    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), paddedNumParticles, "customGBParameters", true);
    computedValues = new OpenCLParameterSet(cl, force.getNumComputedValues(), paddedNumParticles, "customGBComputedValues", true, cl.getUseDoublePrecision());
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    if (force.getNumGlobalParameters() > 0)
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        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customGBGlobals", CL_MEM_READ_ONLY);
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    vector<vector<cl_float> > paramVector(paddedNumParticles, vector<cl_float>(numParams, 0));
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    vector<vector<int> > exclusionList(numParticles);
    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
        force.getParticleParameters(i, parameters);
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        for (int j = 0; j < (int) parameters.size(); j++)
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            paramVector[i][j] = (cl_float) parameters[j];
        exclusionList[i].push_back(i);
    }
    for (int i = 0; i < force.getNumExclusions(); i++) {
        int particle1, particle2;
        force.getExclusionParticles(i, particle1, particle2);
        exclusionList[particle1].push_back(particle2);
        exclusionList[particle2].push_back(particle1);
    }
    params->setParameterValues(paramVector);

    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
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    vector<const TabulatedFunction*> functionList;
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    stringstream tableArgs;
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    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
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        string arrayName = prefix+"table"+cl.intToString(i);
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        functionDefinitions.push_back(make_pair(name, arrayName));
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        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
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        int width;
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        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
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        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
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        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
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        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", width, width*sizeof(float), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
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        tableArgs << ", __global const float";
        if (width > 1)
            tableArgs << width;
        tableArgs << "* restrict " << arrayName;
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    }

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    // Record the global parameters.
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    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    if (globals != NULL)
        globals->upload(globalParamValues);
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    // Record derivatives of expressions needed for the chain rule terms.

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    vector<vector<Lepton::ParsedExpression> > valueGradientExpressions(force.getNumComputedValues());
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    vector<vector<Lepton::ParsedExpression> > valueDerivExpressions(force.getNumComputedValues());
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    vector<vector<Lepton::ParsedExpression> > valueParamDerivExpressions(force.getNumComputedValues());
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    needParameterGradient = false;
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    for (int i = 0; i < force.getNumComputedValues(); i++) {
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        Lepton::ParsedExpression ex = Lepton::Parser::parse(computedValueExpressions[i], functions).optimize();
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        if (i > 0) {
            valueGradientExpressions[i].push_back(ex.differentiate("x").optimize());
            valueGradientExpressions[i].push_back(ex.differentiate("y").optimize());
            valueGradientExpressions[i].push_back(ex.differentiate("z").optimize());
            if (!isZeroExpression(valueGradientExpressions[i][0]) || !isZeroExpression(valueGradientExpressions[i][1]) || !isZeroExpression(valueGradientExpressions[i][2]))
                needParameterGradient = true;
             for (int j = 0; j < i; j++)
                valueDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]).optimize());
        }
        for (int j = 0; j < force.getNumEnergyParameterDerivatives(); j++)
            valueParamDerivExpressions[i].push_back(ex.differentiate(force.getEnergyParameterDerivativeName(j)).optimize());
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    }
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    vector<vector<Lepton::ParsedExpression> > energyDerivExpressions(force.getNumEnergyTerms());
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    vector<vector<Lepton::ParsedExpression> > energyParamDerivExpressions(force.getNumEnergyTerms());
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    vector<bool> needChainForValue(force.getNumComputedValues(), false);
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    for (int i = 0; i < force.getNumEnergyTerms(); i++) {
        string expression;
        CustomGBForce::ComputationType type;
        force.getEnergyTermParameters(i, expression, type);
        Lepton::ParsedExpression ex = Lepton::Parser::parse(expression, functions).optimize();
        for (int j = 0; j < force.getNumComputedValues(); j++) {
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            if (type == CustomGBForce::SingleParticle) {
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                energyDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]).optimize());
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                if (!isZeroExpression(energyDerivExpressions[i].back()))
                    needChainForValue[j] = true;
            }
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            else {
                energyDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]+"1").optimize());
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                if (!isZeroExpression(energyDerivExpressions[i].back()))
                    needChainForValue[j] = true;
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                energyDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]+"2").optimize());
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                if (!isZeroExpression(energyDerivExpressions[i].back()))
                    needChainForValue[j] = true;
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            }
        }
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        for (int j = 0; j < force.getNumEnergyParameterDerivatives(); j++)
            energyParamDerivExpressions[i].push_back(ex.differentiate(force.getEnergyParameterDerivativeName(j)).optimize());
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    }
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    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
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    bool useLong = cl.getSupports64BitGlobalAtomics();
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    if (useLong) {
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        longEnergyDerivs = OpenCLArray::create<cl_long>(cl, force.getNumComputedValues()*cl.getPaddedNumAtoms(), "customGBLongEnergyDerivatives");
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        energyDerivs = new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms(), "customGBEnergyDerivatives", true);
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    }
    else
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        energyDerivs = new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms()*cl.getNonbondedUtilities().getNumForceBuffers(), "customGBEnergyDerivatives", true);
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    energyDerivChain = new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms(), "customGBEnergyDerivativeChain", true);
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    int elementSize = (cl.getUseDoublePrecision() ? sizeof(cl_double) : sizeof(cl_float));
    needEnergyParamDerivs = (force.getNumEnergyParameterDerivatives() > 0);
    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
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        dValuedParam.push_back(new OpenCLParameterSet(cl, force.getNumComputedValues(), cl.getPaddedNumAtoms(), "dValuedParam", true, cl.getUseDoublePrecision()));
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        if (useLong)
            dValue0dParam.push_back(OpenCLArray::create<cl_long>(cl, cl.getPaddedNumAtoms(), "dValue0dParam"));
        else
            dValue0dParam.push_back(new OpenCLArray(cl, cl.getPaddedNumAtoms()*cl.getNonbondedUtilities().getNumForceBuffers(), elementSize, "dValue0dParam"));
        cl.addAutoclearBuffer(*dValue0dParam.back());
        string name = force.getEnergyParameterDerivativeName(i);
        cl.addEnergyParameterDerivative(name);
    }
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    // Create the kernels.

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    bool useCutoff = (force.getNonbondedMethod() != CustomGBForce::NoCutoff);
    bool usePeriodic = (force.getNonbondedMethod() != CustomGBForce::NoCutoff && force.getNonbondedMethod() != CustomGBForce::CutoffNonPeriodic);
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    {
        // Create the N2 value kernel.

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        vector<pair<ExpressionTreeNode, string> > variables;
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        map<string, string> rename;
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        ExpressionTreeNode rnode(new Operation::Variable("r"));
        variables.push_back(make_pair(rnode, "r"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Square(), rnode), "r2"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Reciprocal(), rnode), "invR"));
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        for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
            const string& name = force.getPerParticleParameterName(i);
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            variables.push_back(makeVariable(name+"1", "params"+params->getParameterSuffix(i, "1")));
            variables.push_back(makeVariable(name+"2", "params"+params->getParameterSuffix(i, "2")));
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            rename[name+"1"] = name+"2";
            rename[name+"2"] = name+"1";
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        }
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
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            string value = "globals["+cl.intToString(i)+"]";
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            variables.push_back(makeVariable(name, value));
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        }
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        map<string, Lepton::ParsedExpression> n2ValueExpressions;
        stringstream n2ValueSource;
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        Lepton::ParsedExpression ex = Lepton::Parser::parse(computedValueExpressions[0], functions).optimize();
        n2ValueExpressions["tempValue1 = "] = ex;
        n2ValueExpressions["tempValue2 = "] = ex.renameVariables(rename);
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        for (int i = 0; i < valueParamDerivExpressions[0].size(); i++) {
            string variableBase = "temp_dValue0dParam"+cl.intToString(i+1);
            if (!isZeroExpression(valueParamDerivExpressions[0][i])) {
                n2ValueExpressions[variableBase+"_1 = "] = valueParamDerivExpressions[0][i];
                n2ValueExpressions[variableBase+"_2 = "] = valueParamDerivExpressions[0][i].renameVariables(rename);
            }
        }
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        n2ValueSource << cl.getExpressionUtilities().createExpressions(n2ValueExpressions, variables, functionList, functionDefinitions, "temp");
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        map<string, string> replacements;
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        string n2ValueStr = n2ValueSource.str();
        replacements["COMPUTE_VALUE"] = n2ValueStr;
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        stringstream extraArgs, loadLocal1, loadLocal2, load1, load2, tempDerivs1, tempDerivs2, storeDeriv1, storeDeriv2;
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        if (force.getNumGlobalParameters() > 0)
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            extraArgs << ", __global const float* globals";
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        pairValueUsesParam.resize(params->getBuffers().size(), false);
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        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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            string paramName = "params"+cl.intToString(i+1);
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            if (n2ValueStr.find(paramName+"1") != n2ValueStr.npos || n2ValueStr.find(paramName+"2") != n2ValueStr.npos) {
                extraArgs << ", __global const " << buffer.getType() << "* restrict global_" << paramName << ", __local " << buffer.getType() << "* restrict local_" << paramName;
                loadLocal1 << "local_" << paramName << "[localAtomIndex] = " << paramName << "1;\n";
                loadLocal2 << "local_" << paramName << "[localAtomIndex] = global_" << paramName << "[j];\n";
                load1 << buffer.getType() << " " << paramName << "1 = global_" << paramName << "[atom1];\n";
                load2 << buffer.getType() << " " << paramName << "2 = local_" << paramName << "[atom2];\n";
                pairValueUsesParam[i] = true;
            }
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        }
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        for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
            string derivName = "dValue0dParam"+cl.intToString(i+1);
            if (useLong)
                extraArgs << ", __global long* restrict global_" << derivName;
            else
                extraArgs << ", __global real* restrict global_" << derivName;
            extraArgs << ", __local real* restrict local_" << derivName;
            loadLocal2 << "local_" << derivName << "[localAtomIndex] = 0;\n";
            load1 << "real " << derivName << " = 0;\n";
            if (!isZeroExpression(valueParamDerivExpressions[0][i])) {
                load2 << "real temp_" << derivName << "_1 = 0;\n";
                load2 << "real temp_" << derivName << "_2 = 0;\n";
                tempDerivs1 << derivName << " += temp_" << derivName << "_1;\n";
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                if (deviceIsCpu)
                    tempDerivs2 << "local_" << derivName << "[j] += temp_" << derivName << "_2;\n";
                else
                    tempDerivs2 << "local_" << derivName << "[tbx+tj] += temp_" << derivName << "_2;\n";
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                if (useLong) {
                    storeDeriv1 << "atom_add(&global_" << derivName << "[offset1], (long) (" << derivName << "*0x100000000));\n";
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                    if (deviceIsCpu)
                        storeDeriv2 << "atom_add(&global_" << derivName << "[offset2], (long) (local_" << derivName << "[tgx]*0x100000000));\n";
                    else
                        storeDeriv2 << "atom_add(&global_" << derivName << "[offset2], (long) (local_" << derivName << "[get_local_id(0)]*0x100000000));\n";
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                }
                else {
                    storeDeriv1 << "global_" << derivName << "[offset1] += " << derivName << ";\n";
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                    if (deviceIsCpu)
                        storeDeriv2 << "global_" << derivName << "[offset2] += local_" << derivName << "[tgx];\n";
                    else
                        storeDeriv2 << "global_" << derivName << "[offset2] += local_" << derivName << "[get_local_id(0)];\n";
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                }
            }
        }
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        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
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        replacements["LOAD_LOCAL_PARAMETERS_FROM_1"] = loadLocal1.str();
        replacements["LOAD_LOCAL_PARAMETERS_FROM_GLOBAL"] = loadLocal2.str();
        replacements["LOAD_ATOM1_PARAMETERS"] = load1.str();
        replacements["LOAD_ATOM2_PARAMETERS"] = load2.str();
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        replacements["ADD_TEMP_DERIVS1"] = tempDerivs1.str();
        replacements["ADD_TEMP_DERIVS2"] = tempDerivs2.str();
        replacements["STORE_PARAM_DERIVS1"] = storeDeriv1.str();
        replacements["STORE_PARAM_DERIVS2"] = storeDeriv2.str();
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        if (useCutoff)
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            pairValueDefines["USE_CUTOFF"] = "1";
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        if (usePeriodic)
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            pairValueDefines["USE_PERIODIC"] = "1";
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        if (useExclusionsForValue)
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            pairValueDefines["USE_EXCLUSIONS"] = "1";
        pairValueDefines["FORCE_WORK_GROUP_SIZE"] = cl.intToString(cl.getNonbondedUtilities().getForceThreadBlockSize());
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        pairValueDefines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
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        pairValueDefines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        pairValueDefines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
        pairValueDefines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
        pairValueDefines["TILE_SIZE"] = cl.intToString(OpenCLContext::TileSize);
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        string file;
        if (deviceIsCpu)
            file = OpenCLKernelSources::customGBValueN2_cpu;
        else
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            file = OpenCLKernelSources::customGBValueN2;
        pairValueSrc = cl.replaceStrings(file, replacements);
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        if (useExclusionsForValue)
            cl.getNonbondedUtilities().requestExclusions(exclusionList);
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    }
    {
        // Create the kernel to reduce the N2 value and calculate other values.

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        stringstream reductionSource, extraArgs, deriv0;
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        if (force.getNumGlobalParameters() > 0)
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            extraArgs << ", __global const float* globals";
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        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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            string paramName = "params"+cl.intToString(i+1);
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            extraArgs << ", __global const " << buffer.getType() << "* restrict " << paramName;
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        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
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            string valueName = "values"+cl.intToString(i+1);
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            extraArgs << ", __global " << buffer.getType() << "* restrict global_" << valueName;
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            reductionSource << buffer.getType() << " local_" << valueName << ";\n";
        }
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        for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
            string variableName = "dValuedParam_0_"+cl.intToString(i);
            if (useLong) {
                extraArgs << ", __global const long* restrict dValue0dParam" << i;
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                deriv0 << "real " << variableName << " = (1.0f/0x100000000)*dValue0dParam" << i << "[index];\n";
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            }
            else {
                extraArgs << ", __global const real* restrict dValue0dParam" << i;
                deriv0 << "real " << variableName << " = dValue0dParam" << i << "[index];\n";
                deriv0 << "for (int i = index+bufferSize; i < totalSize; i += bufferSize)\n";
                deriv0 << "    " << variableName << " += dValue0dParam" << i << "[i];\n";
            }
            for (int j = 0; j < dValuedParam[i]->getBuffers().size(); j++)
                extraArgs << ", __global real* restrict global_dValuedParam_" << j << "_" << i;
            deriv0 << "global_dValuedParam_0_" << i << "[index] = dValuedParam_0_" << i << ";\n";
        }
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        reductionSource << "local_values" << computedValues->getParameterSuffix(0) << " = sum;\n";
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        map<string, string> variables;
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        variables["x"] = "pos.x";
        variables["y"] = "pos.y";
        variables["z"] = "pos.z";
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        for (int i = 0; i < force.getNumPerParticleParameters(); i++)
            variables[force.getPerParticleParameterName(i)] = "params"+params->getParameterSuffix(i, "[index]");
        for (int i = 0; i < force.getNumGlobalParameters(); i++)
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            variables[force.getGlobalParameterName(i)] = "globals["+cl.intToString(i)+"]";
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        for (int i = 1; i < force.getNumComputedValues(); i++) {
            variables[computedValueNames[i-1]] = "local_values"+computedValues->getParameterSuffix(i-1);
            map<string, Lepton::ParsedExpression> valueExpressions;
            valueExpressions["local_values"+computedValues->getParameterSuffix(i)+" = "] = Lepton::Parser::parse(computedValueExpressions[i], functions).optimize();
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            reductionSource << cl.getExpressionUtilities().createExpressions(valueExpressions, variables, functionList, functionDefinitions, "value"+cl.intToString(i)+"_temp");
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        }
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        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
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            string valueName = "values"+cl.intToString(i+1);
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            reductionSource << "global_" << valueName << "[index] = local_" << valueName << ";\n";
        }
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        if (needEnergyParamDerivs) {
            map<string, Lepton::ParsedExpression> derivExpressions;
            for (int i = 1; i < force.getNumComputedValues(); i++) {
                for (int j = 0; j < valueParamDerivExpressions[i].size(); j++)
                    derivExpressions["real dValuedParam_"+cl.intToString(i)+"_"+cl.intToString(j)+" = "] = valueParamDerivExpressions[i][j];
                for (int j = 0; j < i; j++)
                    derivExpressions["real dVdV_"+cl.intToString(i)+"_"+cl.intToString(j)+" = "] = valueDerivExpressions[i][j];
            }
            reductionSource << cl.getExpressionUtilities().createExpressions(derivExpressions, variables, functionList, functionDefinitions, "derivChain_temp");
            for (int i = 1; i < force.getNumComputedValues(); i++) {
                for (int j = 0; j < i; j++)
                    for (int k = 0; k < valueParamDerivExpressions[i].size(); k++)
                        reductionSource << "dValuedParam_" << i << "_" << k << " += dVdV_" << i << "_" << j << "*dValuedParam_" << j <<"_" << k << ";\n";
                for (int j = 0; j < valueParamDerivExpressions[i].size(); j++)
                    reductionSource << "global_dValuedParam_" << i << "_" << j << "[index] = dValuedParam_" << i << "_" << j << ";\n";
            }
        }
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        map<string, string> replacements;
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        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
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        replacements["REDUCE_PARAM0_DERIV"] = deriv0.str();
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        replacements["COMPUTE_VALUES"] = reductionSource.str();
        map<string, string> defines;
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        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
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        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBValuePerParticle, replacements), defines);
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        perParticleValueKernel = cl::Kernel(program, "computePerParticleValues");
    }
    {
        // Create the N2 energy kernel.

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        vector<pair<ExpressionTreeNode, string> > variables;
        ExpressionTreeNode rnode(new Operation::Variable("r"));
        variables.push_back(make_pair(rnode, "r"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Square(), rnode), "r2"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Reciprocal(), rnode), "invR"));
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        for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
            const string& name = force.getPerParticleParameterName(i);
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            variables.push_back(makeVariable(name+"1", "params"+params->getParameterSuffix(i, "1")));
            variables.push_back(makeVariable(name+"2", "params"+params->getParameterSuffix(i, "2")));
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        }
        for (int i = 0; i < force.getNumComputedValues(); i++) {
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            variables.push_back(makeVariable(computedValueNames[i]+"1", "values"+computedValues->getParameterSuffix(i, "1")));
            variables.push_back(makeVariable(computedValueNames[i]+"2", "values"+computedValues->getParameterSuffix(i, "2")));
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        }
        for (int i = 0; i < force.getNumGlobalParameters(); i++)
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            variables.push_back(makeVariable(force.getGlobalParameterName(i), "globals["+cl.intToString(i)+"]"));
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        stringstream n2EnergySource;
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        bool anyExclusions = (force.getNumExclusions() > 0);
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        for (int i = 0; i < force.getNumEnergyTerms(); i++) {
            string expression;
            CustomGBForce::ComputationType type;
            force.getEnergyTermParameters(i, expression, type);
            if (type == CustomGBForce::SingleParticle)
                continue;
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            bool exclude = (anyExclusions && type == CustomGBForce::ParticlePair);
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            map<string, Lepton::ParsedExpression> n2EnergyExpressions;
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            n2EnergyExpressions["tempEnergy += "] = Lepton::Parser::parse(expression, functions).optimize();
            n2EnergyExpressions["dEdR += "] = Lepton::Parser::parse(expression, functions).differentiate("r").optimize();
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            if (useLong) {
                for (int j = 0; j < force.getNumComputedValues(); j++) {
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                    if (needChainForValue[j]) {
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                        string index = cl.intToString(j+1);
                        n2EnergyExpressions["/*"+cl.intToString(i+1)+"*/ deriv"+index+"_1 += "] = energyDerivExpressions[i][2*j];
                        n2EnergyExpressions["/*"+cl.intToString(i+1)+"*/ deriv"+index+"_2 += "] = energyDerivExpressions[i][2*j+1];
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                    }
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                }
            }
            else {
                for (int j = 0; j < force.getNumComputedValues(); j++) {
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                    if (needChainForValue[j]) {
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                        n2EnergyExpressions["/*"+cl.intToString(i+1)+"*/ deriv"+energyDerivs->getParameterSuffix(j, "_1")+" += "] = energyDerivExpressions[i][2*j];
                        n2EnergyExpressions["/*"+cl.intToString(i+1)+"*/ deriv"+energyDerivs->getParameterSuffix(j, "_2")+" += "] = energyDerivExpressions[i][2*j+1];
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                    }
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                }
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            }
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            for (int j = 0; j < force.getNumEnergyParameterDerivatives(); j++)
                n2EnergyExpressions["energyParamDeriv"+cl.intToString(j)+" += interactionScale*"] = energyParamDerivExpressions[i][j];
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            if (exclude)
                n2EnergySource << "if (!isExcluded) {\n";
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            n2EnergySource << cl.getExpressionUtilities().createExpressions(n2EnergyExpressions, variables, functionList, functionDefinitions, "temp");
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            if (exclude)
                n2EnergySource << "}\n";
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        }
        map<string, string> replacements;
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        string n2EnergyStr = n2EnergySource.str();
        replacements["COMPUTE_INTERACTION"] = n2EnergyStr;
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        stringstream extraArgs, loadLocal1, loadLocal2, clearLocal, load1, load2, declare1, recordDeriv, storeDerivs1, storeDerivs2, declareTemps, setTemps, initParamDerivs, saveParamDerivs;
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        if (force.getNumGlobalParameters() > 0)
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            extraArgs << ", __global const float* globals";
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        pairEnergyUsesParam.resize(params->getBuffers().size(), false);
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        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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            string paramName = "params"+cl.intToString(i+1);
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            if (n2EnergyStr.find(paramName+"1") != n2EnergyStr.npos || n2EnergyStr.find(paramName+"2") != n2EnergyStr.npos) {
                extraArgs << ", __global const " << buffer.getType() << "* restrict global_" << paramName << ", __local " << buffer.getType() << "* restrict local_" << paramName;
                loadLocal1 << "local_" << paramName << "[localAtomIndex] = " << paramName << "1;\n";
                loadLocal2 << "local_" << paramName << "[localAtomIndex] = global_" << paramName << "[j];\n";
                load1 << buffer.getType() << " " << paramName << "1 = global_" << paramName << "[atom1];\n";
                load2 << buffer.getType() << " " << paramName << "2 = local_" << paramName << "[atom2];\n";
                pairEnergyUsesParam[i] = true;
            }
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        }
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        pairEnergyUsesValue.resize(computedValues->getBuffers().size(), false);
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        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
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            string valueName = "values"+cl.intToString(i+1);
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            if (n2EnergyStr.find(valueName+"1") != n2EnergyStr.npos || n2EnergyStr.find(valueName+"2") != n2EnergyStr.npos) {
                extraArgs << ", __global const " << buffer.getType() << "* restrict global_" << valueName << ", __local " << buffer.getType() << "* restrict local_" << valueName;
                loadLocal1 << "local_" << valueName << "[localAtomIndex] = " << valueName << "1;\n";
                loadLocal2 << "local_" << valueName << "[localAtomIndex] = global_" << valueName << "[j];\n";
                load1 << buffer.getType() << " " << valueName << "1 = global_" << valueName << "[atom1];\n";
                load2 << buffer.getType() << " " << valueName << "2 = local_" << valueName << "[atom2];\n";
                pairEnergyUsesValue[i] = true;
            }
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        }
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        if (useLong) {
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            extraArgs << ", __global long* restrict derivBuffers";
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            for (int i = 0; i < force.getNumComputedValues(); i++) {
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                string index = cl.intToString(i+1);
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                extraArgs << ", __local real* restrict local_deriv" << index;
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                clearLocal << "local_deriv" << index << "[localAtomIndex] = 0.0f;\n";
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                declare1 << "real deriv" << index << "_1 = 0;\n";
                load2 << "real deriv" << index << "_2 = 0;\n";
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                recordDeriv << "local_deriv" << index << "[atom2] += deriv" << index << "_2;\n";
                storeDerivs1 << "STORE_DERIVATIVE_1(" << index << ")\n";
                storeDerivs2 << "STORE_DERIVATIVE_2(" << index << ")\n";
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                declareTemps << "__local real tempDerivBuffer" << index << "[64];\n";
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                setTemps << "tempDerivBuffer" << index << "[get_local_id(0)] = deriv" << index << "_1;\n";
            }
        }
        else {
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
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                string index = cl.intToString(i+1);
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                extraArgs << ", __global " << buffer.getType() << "* restrict derivBuffers" << index << ", __local " << buffer.getType() << "* restrict local_deriv" << index;
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                clearLocal << "local_deriv" << index << "[localAtomIndex] = 0.0f;\n";
                declare1 << buffer.getType() << " deriv" << index << "_1 = 0.0f;\n";
                load2 << buffer.getType() << " deriv" << index << "_2 = 0.0f;\n";
                recordDeriv << "local_deriv" << index << "[atom2] += deriv" << index << "_2;\n";
                storeDerivs1 << "STORE_DERIVATIVE_1(" << index << ")\n";
                storeDerivs2 << "STORE_DERIVATIVE_2(" << index << ")\n";
                declareTemps << "__local " << buffer.getType() << " tempDerivBuffer" << index << "[64];\n";
                setTemps << "tempDerivBuffer" << index << "[get_local_id(0)] = deriv" << index << "_1;\n";
            }
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        }
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        if (needEnergyParamDerivs) {
            extraArgs << ", __global mixed* restrict energyParamDerivs";
            const vector<string>& allParamDerivNames = cl.getEnergyParamDerivNames();
            int numDerivs = allParamDerivNames.size();
            for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
                initParamDerivs << "mixed energyParamDeriv" << i << " = 0;\n";
                for (int index = 0; index < numDerivs; index++)
                    if (allParamDerivNames[index] == force.getEnergyParameterDerivativeName(i))
                        saveParamDerivs << "energyParamDerivs[get_global_id(0)*" << numDerivs << "+" << index << "] += energyParamDeriv" << i << ";\n";
            }
        }
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        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
        replacements["LOAD_LOCAL_PARAMETERS_FROM_1"] = loadLocal1.str();
        replacements["LOAD_LOCAL_PARAMETERS_FROM_GLOBAL"] = loadLocal2.str();
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        replacements["CLEAR_LOCAL_DERIVATIVES"] = clearLocal.str();
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        replacements["LOAD_ATOM1_PARAMETERS"] = load1.str();
        replacements["LOAD_ATOM2_PARAMETERS"] = load2.str();
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        replacements["DECLARE_ATOM1_DERIVATIVES"] = declare1.str();
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        replacements["RECORD_DERIVATIVE_2"] = recordDeriv.str();
        replacements["STORE_DERIVATIVES_1"] = storeDerivs1.str();
        replacements["STORE_DERIVATIVES_2"] = storeDerivs2.str();
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        replacements["DECLARE_TEMP_BUFFERS"] = declareTemps.str();
        replacements["SET_TEMP_BUFFERS"] = setTemps.str();
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        replacements["INIT_PARAM_DERIVS"] = initParamDerivs.str();
        replacements["SAVE_PARAM_DERIVS"] = saveParamDerivs.str();
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        if (useCutoff)
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            pairEnergyDefines["USE_CUTOFF"] = "1";
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        if (usePeriodic)
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            pairEnergyDefines["USE_PERIODIC"] = "1";
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        if (anyExclusions)
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            pairEnergyDefines["USE_EXCLUSIONS"] = "1";
        pairEnergyDefines["FORCE_WORK_GROUP_SIZE"] = cl.intToString(cl.getNonbondedUtilities().getForceThreadBlockSize());
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        pairEnergyDefines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
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        pairEnergyDefines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        pairEnergyDefines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
        pairEnergyDefines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
        pairEnergyDefines["TILE_SIZE"] = cl.intToString(OpenCLContext::TileSize);
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        string file;
        if (deviceIsCpu)
            file = OpenCLKernelSources::customGBEnergyN2_cpu;
        else
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            file = OpenCLKernelSources::customGBEnergyN2;
        pairEnergySrc = cl.replaceStrings(file, replacements);
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    }
    {
        // Create the kernel to reduce the derivatives and calculate per-particle energy terms.

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        stringstream compute, extraArgs, reduce, initParamDerivs, saveParamDerivs;
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        if (force.getNumGlobalParameters() > 0)
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            extraArgs << ", __global const float* globals";
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        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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            string paramName = "params"+cl.intToString(i+1);
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            extraArgs << ", __global const " << buffer.getType() << "* restrict " << paramName;
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        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
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            string valueName = "values"+cl.intToString(i+1);
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            extraArgs << ", __global const " << buffer.getType() << "* restrict " << valueName;
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        }
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        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
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            string index = cl.intToString(i+1);
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            extraArgs << ", __global " << buffer.getType() << "* restrict derivBuffers" << index;
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            compute << buffer.getType() << " deriv" << index << " = derivBuffers" << index << "[index];\n";
        }
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        for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivChain->getBuffers()[i];
            string index = cl.intToString(i+1);
            extraArgs << ", __global " << buffer.getType() << "* restrict derivChain" << index;
        }
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        if (useLong) {
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            extraArgs << ", __global const long* restrict derivBuffersIn";
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            for (int i = 0; i < energyDerivs->getNumParameters(); ++i)
                reduce << "derivBuffers" << energyDerivs->getParameterSuffix(i, "[index]") <<
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                        " = (1.0f/0x100000000)*derivBuffersIn[index+PADDED_NUM_ATOMS*" << cl.intToString(i) << "];\n";
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        }
        else {
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
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                reduce << "REDUCE_VALUE(derivBuffers" << cl.intToString(i+1) << ", " << energyDerivs->getBuffers()[i].getType() << ")\n";
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        }
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        if (needEnergyParamDerivs) {
            extraArgs << ", __global mixed* restrict energyParamDerivs";
            const vector<string>& allParamDerivNames = cl.getEnergyParamDerivNames();
            int numDerivs = allParamDerivNames.size();
            for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
                initParamDerivs << "mixed energyParamDeriv" << i << " = 0;\n";
                for (int index = 0; index < numDerivs; index++)
                    if (allParamDerivNames[index] == force.getEnergyParameterDerivativeName(i))
                        saveParamDerivs << "energyParamDerivs[get_global_id(0)*" << numDerivs << "+" << index << "] += energyParamDeriv" << i << ";\n";
            }
        }
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        // Compute the various expressions.
        
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        map<string, string> variables;
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        variables["x"] = "pos.x";
        variables["y"] = "pos.y";
        variables["z"] = "pos.z";
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        for (int i = 0; i < force.getNumPerParticleParameters(); i++)
            variables[force.getPerParticleParameterName(i)] = "params"+params->getParameterSuffix(i, "[index]");
        for (int i = 0; i < force.getNumGlobalParameters(); i++)
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            variables[force.getGlobalParameterName(i)] = "globals["+cl.intToString(i)+"]";
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        for (int i = 0; i < force.getNumComputedValues(); i++)
            variables[computedValueNames[i]] = "values"+computedValues->getParameterSuffix(i, "[index]");
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        map<string, Lepton::ParsedExpression> expressions;
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        for (int i = 0; i < force.getNumEnergyTerms(); i++) {
            string expression;
            CustomGBForce::ComputationType type;
            force.getEnergyTermParameters(i, expression, type);
            if (type != CustomGBForce::SingleParticle)
                continue;
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            Lepton::ParsedExpression parsed = Lepton::Parser::parse(expression, functions).optimize();
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            expressions["/*"+cl.intToString(i+1)+"*/ energy += "] = parsed;
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            for (int j = 0; j < force.getNumComputedValues(); j++)
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                expressions["/*"+cl.intToString(i+1)+"*/ deriv"+energyDerivs->getParameterSuffix(j)+" += "] = energyDerivExpressions[i][j];
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            Lepton::ParsedExpression gradx = parsed.differentiate("x").optimize();
            Lepton::ParsedExpression grady = parsed.differentiate("y").optimize();
            Lepton::ParsedExpression gradz = parsed.differentiate("z").optimize();
            if (!isZeroExpression(gradx))
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                expressions["/*"+cl.intToString(i+1)+"*/ force.x -= "] = gradx;
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            if (!isZeroExpression(grady))
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                expressions["/*"+cl.intToString(i+1)+"*/ force.y -= "] = grady;
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            if (!isZeroExpression(gradz))
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                expressions["/*"+cl.intToString(i+1)+"*/ force.z -= "] = gradz;
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            for (int j = 0; j < force.getNumEnergyParameterDerivatives(); j++)
                expressions["/*"+cl.intToString(i+1)+"*/ energyParamDeriv"+cl.intToString(j)+" += "] = energyParamDerivExpressions[i][j];
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        }
        for (int i = 1; i < force.getNumComputedValues(); i++)
            for (int j = 0; j < i; j++)
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                expressions["real dV"+cl.intToString(i)+"dV"+cl.intToString(j)+" = "] = valueDerivExpressions[i][j];
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        compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "temp");
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        // Record values.
        
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        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            string index = cl.intToString(i+1);
            compute << "derivBuffers" << index << "[index] = deriv" << index << ";\n";
        }
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        compute << "forceBuffers[index] = forceBuffers[index]+force;\n";
        for (int i = 1; i < force.getNumComputedValues(); i++) {
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            compute << "real totalDeriv"<<i<<" = dV"<<i<<"dV0";
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            for (int j = 1; j < i; j++)
                compute << " + totalDeriv"<<j<<"*dV"<<i<<"dV"<<j;
            compute << ";\n";
            compute << "deriv"<<(i+1)<<" *= totalDeriv"<<i<<";\n";
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        }
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
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            string index = cl.intToString(i+1);
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            compute << "derivChain" << index << "[index] = deriv" << index << ";\n";
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        }
        map<string, string> replacements;
        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
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        replacements["REDUCE_DERIVATIVES"] = reduce.str();
        replacements["COMPUTE_ENERGY"] = compute.str();
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        replacements["INIT_PARAM_DERIVS"] = initParamDerivs.str();
        replacements["SAVE_PARAM_DERIVS"] = saveParamDerivs.str();
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        map<string, string> defines;
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        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
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        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBEnergyPerParticle, replacements), defines);
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        perParticleEnergyKernel = cl::Kernel(program, "computePerParticleEnergy");
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    }
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    if (needParameterGradient || needEnergyParamDerivs) {
        // Create the kernel to compute chain rule terms for computed values that depend explicitly on particle coordinates, and for
        // derivatives with respect to global parameters.
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        stringstream compute, extraArgs, initParamDerivs, saveParamDerivs;
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        if (force.getNumGlobalParameters() > 0)
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            extraArgs << ", __global const float* globals";
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        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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            string paramName = "params"+cl.intToString(i+1);
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            extraArgs << ", __global const " << buffer.getType() << "* restrict " << paramName;
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        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
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            string valueName = "values"+cl.intToString(i+1);
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            extraArgs << ", __global const " << buffer.getType() << "* restrict " << valueName;
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        }
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
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            string index = cl.intToString(i+1);
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            extraArgs << ", __global " << buffer.getType() << "* restrict derivBuffers" << index;
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            compute << buffer.getType() << " deriv" << index << " = derivBuffers" << index << "[index];\n";
        }
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        if (needEnergyParamDerivs) {
            extraArgs << ", __global mixed* restrict energyParamDerivs";
            const vector<string>& allParamDerivNames = cl.getEnergyParamDerivNames();
            int numDerivs = allParamDerivNames.size();
            for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
                for (int j = 0; j < dValuedParam[i]->getBuffers().size(); j++)
                    extraArgs << ", __global real* restrict dValuedParam_" << j << "_" << i;
                initParamDerivs << "mixed energyParamDeriv" << i << " = 0;\n";
                for (int index = 0; index < numDerivs; index++)
                    if (allParamDerivNames[index] == force.getEnergyParameterDerivativeName(i))
                        saveParamDerivs << "energyParamDerivs[get_global_id(0)*" << numDerivs << "+" << index << "] += energyParamDeriv" << i << ";\n";
            }
        }
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        map<string, string> variables;
        variables["x"] = "pos.x";
        variables["y"] = "pos.y";
        variables["z"] = "pos.z";
        for (int i = 0; i < force.getNumPerParticleParameters(); i++)
            variables[force.getPerParticleParameterName(i)] = "params"+params->getParameterSuffix(i, "[index]");
        for (int i = 0; i < force.getNumGlobalParameters(); i++)
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            variables[force.getGlobalParameterName(i)] = "globals["+cl.intToString(i)+"]";
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        for (int i = 0; i < force.getNumComputedValues(); i++)
            variables[computedValueNames[i]] = "values"+computedValues->getParameterSuffix(i, "[index]");
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        if (needParameterGradient) {
            for (int i = 1; i < force.getNumComputedValues(); i++) {
                string is = cl.intToString(i);
                compute << "real4 dV"<<is<<"dR = (real4) 0;\n";
                for (int j = 1; j < i; j++) {
                    if (!isZeroExpression(valueDerivExpressions[i][j])) {
                        map<string, Lepton::ParsedExpression> derivExpressions;
                        string js = cl.intToString(j);
                        derivExpressions["real dV"+is+"dV"+js+" = "] = valueDerivExpressions[i][j];
                        compute << cl.getExpressionUtilities().createExpressions(derivExpressions, variables, functionList, functionDefinitions, "temp_"+is+"_"+js);
                        compute << "dV"<<is<<"dR += dV"<<is<<"dV"<<js<<"*dV"<<js<<"dR;\n";
                    }
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                }
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                map<string, Lepton::ParsedExpression> gradientExpressions;
                if (!isZeroExpression(valueGradientExpressions[i][0]))
                    gradientExpressions["dV"+is+"dR.x += "] = valueGradientExpressions[i][0];
                if (!isZeroExpression(valueGradientExpressions[i][1]))
                    gradientExpressions["dV"+is+"dR.y += "] = valueGradientExpressions[i][1];
                if (!isZeroExpression(valueGradientExpressions[i][2]))
                    gradientExpressions["dV"+is+"dR.z += "] = valueGradientExpressions[i][2];
                compute << cl.getExpressionUtilities().createExpressions(gradientExpressions, variables, functionList, functionDefinitions, "temp");
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            }
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            for (int i = 1; i < force.getNumComputedValues(); i++)
                compute << "force -= deriv"<<energyDerivs->getParameterSuffix(i)<<"*dV"<<i<<"dR;\n";
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        }
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        if (needEnergyParamDerivs)
            for (int i = 0; i < force.getNumComputedValues(); i++)
                for (int j = 0; j < dValuedParam.size(); j++)
                    compute << "energyParamDeriv"<<j<<" += deriv"<<energyDerivs->getParameterSuffix(i)<<"*dValuedParam_"<<i<<"_"<<j<<"[index];\n";
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        map<string, string> replacements;
        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
        replacements["COMPUTE_FORCES"] = compute.str();
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        replacements["INIT_PARAM_DERIVS"] = initParamDerivs.str();
        replacements["SAVE_PARAM_DERIVS"] = saveParamDerivs.str();
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        map<string, string> defines;
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        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
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        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBGradientChainRule, replacements), defines);
        gradientChainRuleKernel = cl::Kernel(program, "computeGradientChainRuleTerms");
    }
3963
    {
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        // Create the code to calculate chain rules terms as part of the default nonbonded kernel.
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        vector<pair<ExpressionTreeNode, string> > globalVariables;
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        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
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            string value = "globals["+cl.intToString(i)+"]";
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            globalVariables.push_back(makeVariable(name, prefix+value));
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        }
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        vector<pair<ExpressionTreeNode, string> > variables = globalVariables;
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        map<string, string> rename;
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        ExpressionTreeNode rnode(new Operation::Variable("r"));
        variables.push_back(make_pair(rnode, "r"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Square(), rnode), "r2"));
        variables.push_back(make_pair(ExpressionTreeNode(new Operation::Reciprocal(), rnode), "invR"));
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        for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
            const string& name = force.getPerParticleParameterName(i);
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            variables.push_back(makeVariable(name+"1", prefix+"params"+params->getParameterSuffix(i, "1")));
            variables.push_back(makeVariable(name+"2", prefix+"params"+params->getParameterSuffix(i, "2")));
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            rename[name+"1"] = name+"2";
            rename[name+"2"] = name+"1";
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        }
        map<string, Lepton::ParsedExpression> derivExpressions;
        stringstream chainSource;
        Lepton::ParsedExpression dVdR = Lepton::Parser::parse(computedValueExpressions[0], functions).differentiate("r").optimize();
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        derivExpressions["real dV0dR1 = "] = dVdR;
        derivExpressions["real dV0dR2 = "] = dVdR.renameVariables(rename);
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        chainSource << cl.getExpressionUtilities().createExpressions(derivExpressions, variables, functionList, functionDefinitions, prefix+"temp0_");
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        if (needChainForValue[0]) {
            if (useExclusionsForValue)
                chainSource << "if (!isExcluded) {\n";
            chainSource << "tempForce -= dV0dR1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "1") << ";\n";
            chainSource << "tempForce -= dV0dR2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(0, "2") << ";\n";
            if (useExclusionsForValue)
                chainSource << "}\n";
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        }
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        for (int i = 1; i < force.getNumComputedValues(); i++) {
            if (needChainForValue[i]) {
                chainSource << "tempForce -= dV0dR1*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(i, "1") << ";\n";
                chainSource << "tempForce -= dV0dR2*" << prefix << "dEdV" << energyDerivs->getParameterSuffix(i, "2") << ";\n";
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            }
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        }
        map<string, string> replacements;
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        string chainStr = chainSource.str();
        replacements["COMPUTE_FORCE"] = chainStr;
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        string source = cl.replaceStrings(OpenCLKernelSources::customGBChainRule, replacements);
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        vector<OpenCLNonbondedUtilities::ParameterInfo> parameters;
        vector<OpenCLNonbondedUtilities::ParameterInfo> arguments;
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        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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            string paramName = prefix+"params"+cl.intToString(i+1);
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            if (chainStr.find(paramName+"1") != chainStr.npos || chainStr.find(paramName+"2") != chainStr.npos)
                parameters.push_back(OpenCLNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
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        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
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            string paramName = prefix+"values"+cl.intToString(i+1);
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            if (chainStr.find(paramName+"1") != chainStr.npos || chainStr.find(paramName+"2") != chainStr.npos)
                parameters.push_back(OpenCLNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
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        }
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        for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++) {
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            if (needChainForValue[i]) { 
4025
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivChain->getBuffers()[i];
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                string paramName = prefix+"dEdV"+cl.intToString(i+1);
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                parameters.push_back(OpenCLNonbondedUtilities::ParameterInfo(paramName, buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
            }
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        }
        if (globals != NULL) {
            globals->upload(globalParamValues);
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            arguments.push_back(OpenCLNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(cl_float), globals->getDeviceBuffer()));
        }
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        cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, force.getNumExclusions() > 0, cutoff, exclusionList, source, force.getForceGroup());
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        for (int i = 0; i < (int) parameters.size(); i++)
            cl.getNonbondedUtilities().addParameter(parameters[i]);
        for (int i = 0; i < (int) arguments.size(); i++)
            cl.getNonbondedUtilities().addArgument(arguments[i]);
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    }
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    info = new ForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force);
    cl.addForce(info);
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    if (useLong)
4043
        cl.addAutoclearBuffer(*longEnergyDerivs);
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    else {
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
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            cl.addAutoclearBuffer(buffer.getMemory(), buffer.getSize()*energyDerivs->getNumObjects());
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        }
    }
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}

4052
double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
4053
    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
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    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
4055
    int elementSize = (cl.getUseDoublePrecision() ? sizeof(cl_double) : sizeof(cl_float));
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    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
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        // These two kernels can't be compiled in initialize(), because the nonbonded utilities object
        // has not yet been initialized then.

        {
            int numExclusionTiles = nb.getExclusionTiles().getSize();
            pairValueDefines["NUM_TILES_WITH_EXCLUSIONS"] = cl.intToString(numExclusionTiles);
            int numContexts = cl.getPlatformData().contexts.size();
            int startExclusionIndex = cl.getContextIndex()*numExclusionTiles/numContexts;
            int endExclusionIndex = (cl.getContextIndex()+1)*numExclusionTiles/numContexts;
            pairValueDefines["FIRST_EXCLUSION_TILE"] = cl.intToString(startExclusionIndex);
            pairValueDefines["LAST_EXCLUSION_TILE"] = cl.intToString(endExclusionIndex);
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            pairValueDefines["CUTOFF"] = cl.doubleToString(cutoff);
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            cl::Program program = cl.createProgram(pairValueSrc, pairValueDefines);
            pairValueKernel = cl::Kernel(program, "computeN2Value");
            pairValueSrc = "";
            pairValueDefines.clear();
        }
        {
            int numExclusionTiles = nb.getExclusionTiles().getSize();
            pairEnergyDefines["NUM_TILES_WITH_EXCLUSIONS"] = cl.intToString(numExclusionTiles);
            int numContexts = cl.getPlatformData().contexts.size();
            int startExclusionIndex = cl.getContextIndex()*numExclusionTiles/numContexts;
            int endExclusionIndex = (cl.getContextIndex()+1)*numExclusionTiles/numContexts;
            pairEnergyDefines["FIRST_EXCLUSION_TILE"] = cl.intToString(startExclusionIndex);
            pairEnergyDefines["LAST_EXCLUSION_TILE"] = cl.intToString(endExclusionIndex);
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            pairEnergyDefines["CUTOFF"] = cl.doubleToString(cutoff);
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            cl::Program program = cl.createProgram(pairEnergySrc, pairEnergyDefines);
            pairEnergyKernel = cl::Kernel(program, "computeN2Energy");
            pairEnergySrc = "";
            pairEnergyDefines.clear();
        }

        // Set arguments for kernels.
        
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        maxTiles = (nb.getUseCutoff() ? nb.getInteractingTiles().getSize() : 0);
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        bool useLong = cl.getSupports64BitGlobalAtomics();
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        if (useLong) {
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            longValueBuffers = OpenCLArray::create<cl_long>(cl, cl.getPaddedNumAtoms(), "customGBLongValueBuffers");
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            cl.addAutoclearBuffer(*longValueBuffers);
            cl.clearBuffer(*longValueBuffers);
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        }
        else {
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            valueBuffers = new OpenCLArray(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), elementSize, "customGBValueBuffers");
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            cl.addAutoclearBuffer(*valueBuffers);
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            cl.clearBuffer(*valueBuffers);
        }
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        int index = 0;
        pairValueKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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        pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*4*elementSize, NULL);
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        pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusions().getDeviceBuffer());
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        pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionTiles().getDeviceBuffer());
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        pairValueKernel.setArg<cl::Buffer>(index++, useLong ? longValueBuffers->getDeviceBuffer() : valueBuffers->getDeviceBuffer());
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        pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*elementSize, NULL);
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        if (nb.getUseCutoff()) {
            pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
            pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
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            index += 5; // Periodic box size arguments are set when the kernel is executed.
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            pairValueKernel.setArg<cl_uint>(index++, maxTiles);
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            pairValueKernel.setArg<cl::Buffer>(index++, nb.getBlockCenters().getDeviceBuffer());
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            pairValueKernel.setArg<cl::Buffer>(index++, nb.getBlockBoundingBoxes().getDeviceBuffer());
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            pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractingAtoms().getDeviceBuffer());
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        }
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        else
            pairValueKernel.setArg<cl_uint>(index++, cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2);
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        if (globals != NULL)
            pairValueKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
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            if (pairValueUsesParam[i]) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
                pairValueKernel.setArg<cl::Memory>(index++, buffer.getMemory());
                pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*buffer.getSize(), NULL);
            }
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        }
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        for (int i = 0; i < dValue0dParam.size(); i++) {
            pairValueKernel.setArg<cl::Buffer>(index++, dValue0dParam[i]->getDeviceBuffer());
            pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*dValue0dParam[i]->getElementSize(), NULL);
        }
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        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            pairValueKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
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        index = 0;
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        perParticleValueKernel.setArg<cl_int>(index++, cl.getPaddedNumAtoms());
        perParticleValueKernel.setArg<cl_int>(index++, nb.getNumForceBuffers());
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        perParticleValueKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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        perParticleValueKernel.setArg<cl::Buffer>(index++, useLong ? longValueBuffers->getDeviceBuffer() : valueBuffers->getDeviceBuffer());
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        if (globals != NULL)
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            perParticleValueKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
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        for (int i = 0; i < (int) params->getBuffers().size(); i++)
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            perParticleValueKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
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        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++)
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            perParticleValueKernel.setArg<cl::Memory>(index++, computedValues->getBuffers()[i].getMemory());
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        for (int i = 0; i < dValuedParam.size(); i++) {
            perParticleValueKernel.setArg<cl::Memory>(index++, dValue0dParam[i]->getDeviceBuffer());
            for (int j = 0; j < dValuedParam[i]->getBuffers().size(); j++)
                perParticleValueKernel.setArg<cl::Memory>(index++, dValuedParam[i]->getBuffers()[j].getMemory());
        }
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        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            perParticleValueKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
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        index = 0;
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        pairEnergyKernel.setArg<cl::Buffer>(index++, useLong ? cl.getLongForceBuffer().getDeviceBuffer() : cl.getForceBuffers().getDeviceBuffer());
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        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
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        pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*4*elementSize, NULL);
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        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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        pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*4*elementSize, NULL);
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        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusions().getDeviceBuffer());
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        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionTiles().getDeviceBuffer());
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        index++; // Whether to include energy.
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        if (nb.getUseCutoff()) {
            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractingTiles().getDeviceBuffer());
            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractionCount().getDeviceBuffer());
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            index += 5; // Periodic box size arguments are set when the kernel is executed.
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            pairEnergyKernel.setArg<cl_uint>(index++, maxTiles);
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            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getBlockCenters().getDeviceBuffer());
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            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getBlockBoundingBoxes().getDeviceBuffer());
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            pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractingAtoms().getDeviceBuffer());
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        }
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        else
            pairEnergyKernel.setArg<cl_uint>(index++, cl.getNumAtomBlocks()*(cl.getNumAtomBlocks()+1)/2);
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        if (globals != NULL)
            pairEnergyKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
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            if (pairEnergyUsesParam[i]) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
                pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
                pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*buffer.getSize(), NULL);
            }
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        }
        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++) {
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            if (pairEnergyUsesValue[i]) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = computedValues->getBuffers()[i];
                pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
                pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*buffer.getSize(), NULL);
            }
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        }
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        if (useLong) {
            pairEnergyKernel.setArg<cl::Memory>(index++, longEnergyDerivs->getDeviceBuffer());
            for (int i = 0; i < numComputedValues; ++i)
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                pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*elementSize, NULL);
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        }
        else {
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
                pairEnergyKernel.setArg<cl::Memory>(index++, buffer.getMemory());
                pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*buffer.getSize(), NULL);
            }
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        }
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        if (needEnergyParamDerivs)
            pairEnergyKernel.setArg<cl::Memory>(index++, cl.getEnergyParamDerivBuffer().getDeviceBuffer());
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        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            pairEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
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        index = 0;
        perParticleEnergyKernel.setArg<cl_int>(index++, cl.getPaddedNumAtoms());
        perParticleEnergyKernel.setArg<cl_int>(index++, nb.getNumForceBuffers());
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        perParticleEnergyKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
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        perParticleEnergyKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
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        perParticleEnergyKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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        if (globals != NULL)
            perParticleEnergyKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) params->getBuffers().size(); i++)
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            perParticleEnergyKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
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        for (int i = 0; i < (int) computedValues->getBuffers().size(); i++)
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            perParticleEnergyKernel.setArg<cl::Memory>(index++, computedValues->getBuffers()[i].getMemory());
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        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
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            perParticleEnergyKernel.setArg<cl::Memory>(index++, energyDerivs->getBuffers()[i].getMemory());
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        for (int i = 0; i < (int) energyDerivChain->getBuffers().size(); i++)
            perParticleEnergyKernel.setArg<cl::Memory>(index++, energyDerivChain->getBuffers()[i].getMemory());
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        if (useLong)
            perParticleEnergyKernel.setArg<cl::Memory>(index++, longEnergyDerivs->getDeviceBuffer());
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        if (needEnergyParamDerivs)
            perParticleEnergyKernel.setArg<cl::Memory>(index++, cl.getEnergyParamDerivBuffer().getDeviceBuffer());
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        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            perParticleEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
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        if (needParameterGradient || needEnergyParamDerivs) {
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            index = 0;
            gradientChainRuleKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
            gradientChainRuleKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
            if (globals != NULL)
                gradientChainRuleKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
            for (int i = 0; i < (int) params->getBuffers().size(); i++)
                gradientChainRuleKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
            for (int i = 0; i < (int) computedValues->getBuffers().size(); i++)
                gradientChainRuleKernel.setArg<cl::Memory>(index++, computedValues->getBuffers()[i].getMemory());
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
                gradientChainRuleKernel.setArg<cl::Memory>(index++, energyDerivs->getBuffers()[i].getMemory());
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            if (needEnergyParamDerivs) {
                gradientChainRuleKernel.setArg<cl::Buffer>(index++, cl.getEnergyParamDerivBuffer().getDeviceBuffer());
                for (int i = 0; i < dValuedParam.size(); i++)
                    for (int j = 0; j < dValuedParam[i]->getBuffers().size(); j++)
                        gradientChainRuleKernel.setArg<cl::Memory>(index++, dValuedParam[i]->getBuffers()[j].getMemory());
            }
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        }
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    }
    if (globals != NULL) {
        bool changed = false;
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        for (int i = 0; i < (int) globalParamNames.size(); i++) {
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            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
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    pairEnergyKernel.setArg<cl_int>(7, includeEnergy);
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    if (nb.getUseCutoff()) {
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        setPeriodicBoxArgs(cl, pairValueKernel, 8);
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        setPeriodicBoxArgs(cl, pairEnergyKernel, 10);
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        if (maxTiles < nb.getInteractingTiles().getSize()) {
            maxTiles = nb.getInteractingTiles().getSize();
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            pairValueKernel.setArg<cl::Buffer>(6, nb.getInteractingTiles().getDeviceBuffer());
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            pairValueKernel.setArg<cl_uint>(13, maxTiles);
            pairValueKernel.setArg<cl::Buffer>(16, nb.getInteractingAtoms().getDeviceBuffer());
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            pairEnergyKernel.setArg<cl::Buffer>(8, nb.getInteractingTiles().getDeviceBuffer());
            pairEnergyKernel.setArg<cl_uint>(15, maxTiles);
            pairEnergyKernel.setArg<cl::Buffer>(18, nb.getInteractingAtoms().getDeviceBuffer());
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        }
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    }
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    cl.executeKernel(pairValueKernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
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    cl.executeKernel(perParticleValueKernel, cl.getPaddedNumAtoms());
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    cl.executeKernel(pairEnergyKernel, nb.getNumForceThreadBlocks()*nb.getForceThreadBlockSize(), nb.getForceThreadBlockSize());
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    cl.executeKernel(perParticleEnergyKernel, cl.getPaddedNumAtoms());
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    if (needParameterGradient || needEnergyParamDerivs)
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        cl.executeKernel(gradientChainRuleKernel, cl.getPaddedNumAtoms());
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    return 0.0;
}

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void OpenCLCalcCustomGBForceKernel::copyParametersToContext(ContextImpl& context, const CustomGBForce& force) {
    int numParticles = force.getNumParticles();
    if (numParticles != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    
    // Record the per-particle parameters.
    
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    vector<vector<cl_float> > paramVector(cl.getPaddedNumAtoms(), vector<cl_float>(force.getNumPerParticleParameters(), 0));
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    vector<double> parameters;
    for (int i = 0; i < numParticles; i++) {
        force.getParticleParameters(i, parameters);
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcCustomExternalForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const CustomExternalForce& force, int numParticles) : OpenCLForceInfo(0), force(force), indices(numParticles, -1) {
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        vector<double> params;
        for (int i = 0; i < force.getNumParticles(); i++) {
            int particle;
            force.getParticleParameters(i, particle, params);
            indices[particle] = i;
        }
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        particle1 = indices[particle1];
        particle2 = indices[particle2];
        if (particle1 == -1 && particle2 == -1)
            return true;
        if (particle1 == -1 || particle2 == -1)
            return false;
        int temp;
        vector<double> params1;
        vector<double> params2;
        force.getParticleParameters(particle1, temp, params1);
        force.getParticleParameters(particle2, temp, params2);
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        for (int i = 0; i < (int) params1.size(); i++)
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            if (params1[i] != params2[i])
                return false;
        return true;
    }
private:
    const CustomExternalForce& force;
    vector<int> indices;
};

OpenCLCalcCustomExternalForceKernel::~OpenCLCalcCustomExternalForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
}

void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const CustomExternalForce& force) {
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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumParticles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumParticles()/numContexts;
    numParticles = endIndex-startIndex;
    if (numParticles == 0)
        return;
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    vector<vector<int> > atoms(numParticles, vector<int>(1));
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    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), numParticles, "customExternalParams");
    vector<vector<cl_float> > paramVector(numParticles);
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    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
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        force.getParticleParameters(startIndex+i, atoms[i][0], parameters);
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        paramVector[i].resize(parameters.size());
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        for (int j = 0; j < (int) parameters.size(); j++)
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            paramVector[i][j] = (cl_float) parameters[j];
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    }
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    params->setParameterValues(paramVector);
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    info = new ForceInfo(force, system.getNumParticles());
    cl.addForce(info);
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    // Record information for the expressions.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
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    map<string, Lepton::CustomFunction*> customFunctions;
    customFunctions["periodicdistance"] = cl.getExpressionUtilities().getPeriodicDistancePlaceholder();
    Lepton::ParsedExpression energyExpression = Lepton::Parser::parse(force.getEnergyFunction(), customFunctions).optimize();
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    Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x").optimize();
    Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y").optimize();
    Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z").optimize();
    map<string, Lepton::ParsedExpression> expressions;
    expressions["energy += "] = energyExpression;
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    expressions["real dEdX = "] = forceExpressionX;
    expressions["real dEdY = "] = forceExpressionY;
    expressions["real dEdZ = "] = forceExpressionZ;
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    // Create the kernels.

    map<string, string> variables;
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    variables["x"] = "pos1.x";
    variables["y"] = "pos1.y";
    variables["z"] = "pos1.z";
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    for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
        const string& name = force.getPerParticleParameterName(i);
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        variables[name] = "particleParams"+params->getParameterSuffix(i);
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    }
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    if (force.getNumGlobalParameters() > 0) {
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        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customExternalGlobals", CL_MEM_READ_ONLY);
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        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
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            string value = argName+"["+cl.intToString(i)+"]";
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            variables[name] = value;
        }
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    }
    stringstream compute;
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    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
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        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" particleParams"<<(i+1)<<" = "<<argName<<"[index];\n";
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    }
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    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
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    compute << cl.getExpressionUtilities().createExpressions(expressions, variables, functions, functionNames, "temp");
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    map<string, string> replacements;
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    replacements["COMPUTE_FORCE"] = compute.str();
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    cl.getBondedUtilities().addInteraction(atoms, cl.replaceStrings(OpenCLKernelSources::customExternalForce, replacements), force.getForceGroup());
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}

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double OpenCLCalcCustomExternalForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    if (globals != NULL) {
        bool changed = false;
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        for (int i = 0; i < (int) globalParamNames.size(); i++) {
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            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
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}
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void OpenCLCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl& context, const CustomExternalForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumParticles()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumParticles()/numContexts;
    if (numParticles != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
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    if (numParticles == 0)
        return;
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    // Record the per-particle parameters.
    
    vector<vector<cl_float> > paramVector(numParticles);
    vector<double> parameters;
    for (int i = 0; i < numParticles; i++) {
        int particle;
        force.getParticleParameters(startIndex+i, particle, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcCustomHbondForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(int requiredBuffers, const CustomHbondForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
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    }
    bool areParticlesIdentical(int particle1, int particle2) {
        return true;
    }
    int getNumParticleGroups() {
        return force.getNumDonors()+force.getNumAcceptors()+force.getNumExclusions();
    }
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    void getParticlesInGroup(int index, vector<int>& particles) {
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        int p1, p2, p3;
        vector<double> parameters;
        if (index < force.getNumDonors()) {
            force.getDonorParameters(index, p1, p2, p3, parameters);
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            particles.clear();
            particles.push_back(p1);
            if (p2 > -1)
                particles.push_back(p2);
            if (p3 > -1)
                particles.push_back(p3);
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            return;
        }
        index -= force.getNumDonors();
        if (index < force.getNumAcceptors()) {
            force.getAcceptorParameters(index, p1, p2, p3, parameters);
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            particles.clear();
            particles.push_back(p1);
            if (p2 > -1)
                particles.push_back(p2);
            if (p3 > -1)
                particles.push_back(p3);
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            return;
        }
        index -= force.getNumAcceptors();
        int donor, acceptor;
        force.getExclusionParticles(index, donor, acceptor);
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        particles.clear();
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        force.getDonorParameters(donor, p1, p2, p3, parameters);
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        particles.push_back(p1);
        if (p2 > -1)
            particles.push_back(p2);
        if (p3 > -1)
            particles.push_back(p3);
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        force.getAcceptorParameters(acceptor, p1, p2, p3, parameters);
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        particles.push_back(p1);
        if (p2 > -1)
            particles.push_back(p2);
        if (p3 > -1)
            particles.push_back(p3);
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    }
    bool areGroupsIdentical(int group1, int group2) {
        int p1, p2, p3;
        vector<double> params1, params2;
        if (group1 < force.getNumDonors() && group2 < force.getNumDonors()) {
            force.getDonorParameters(group1, p1, p2, p3, params1);
            force.getDonorParameters(group2, p1, p2, p3, params2);
            return (params1 == params2 && params1 == params2);
        }
        if (group1 < force.getNumDonors() || group2 < force.getNumDonors())
            return false;
        group1 -= force.getNumDonors();
        group2 -= force.getNumDonors();
        if (group1 < force.getNumAcceptors() && group2 < force.getNumAcceptors()) {
            force.getAcceptorParameters(group1, p1, p2, p3, params1);
            force.getAcceptorParameters(group2, p1, p2, p3, params2);
            return (params1 == params2 && params1 == params2);
        }
        if (group1 < force.getNumAcceptors() || group2 < force.getNumAcceptors())
            return false;
        return true;
    }
private:
    const CustomHbondForce& force;
};

OpenCLCalcCustomHbondForceKernel::~OpenCLCalcCustomHbondForceKernel() {
    if (donorParams != NULL)
        delete donorParams;
    if (acceptorParams != NULL)
        delete acceptorParams;
    if (donors != NULL)
        delete donors;
    if (acceptors != NULL)
        delete acceptors;
    if (donorBufferIndices != NULL)
        delete donorBufferIndices;
    if (acceptorBufferIndices != NULL)
        delete acceptorBufferIndices;
    if (globals != NULL)
        delete globals;
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    if (donorExclusions != NULL)
        delete donorExclusions;
    if (acceptorExclusions != NULL)
        delete acceptorExclusions;
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    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

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static void addDonorAndAcceptorCode(stringstream& computeDonor, stringstream& computeAcceptor, const string& value) {
    computeDonor << value;
    computeAcceptor << value;
}

static void applyDonorAndAcceptorForces(stringstream& applyToDonor, stringstream& applyToAcceptor, int atom, const string& value) {
    string forceNames[] = {"f1", "f2", "f3"};
    if (atom < 3)
        applyToAcceptor << forceNames[atom]<<".xyz += "<<value<<";\n";
    else
        applyToDonor << forceNames[atom-3]<<".xyz += "<<value<<";\n";
}
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void OpenCLCalcCustomHbondForceKernel::initialize(const System& system, const CustomHbondForce& force) {
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    // Record the lists of donors and acceptors, and the parameters for each one.

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    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumDonors()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumDonors()/numContexts;
    numDonors = endIndex-startIndex;
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    numAcceptors = force.getNumAcceptors();
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    if (numDonors == 0 || numAcceptors == 0)
        return;
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    int numParticles = system.getNumParticles();
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    donors = OpenCLArray::create<mm_int4>(cl, numDonors, "customHbondDonors");
    acceptors = OpenCLArray::create<mm_int4>(cl, numAcceptors, "customHbondAcceptors");
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    donorParams = new OpenCLParameterSet(cl, force.getNumPerDonorParameters(), numDonors, "customHbondDonorParameters");
    acceptorParams = new OpenCLParameterSet(cl, force.getNumPerAcceptorParameters(), numAcceptors, "customHbondAcceptorParameters");
    if (force.getNumGlobalParameters() > 0)
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        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customHbondGlobals", CL_MEM_READ_ONLY);
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    vector<vector<cl_float> > donorParamVector(numDonors);
    vector<mm_int4> donorVector(numDonors);
    for (int i = 0; i < numDonors; i++) {
        vector<double> parameters;
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        force.getDonorParameters(startIndex+i, donorVector[i].x, donorVector[i].y, donorVector[i].z, parameters);
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        donorParamVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            donorParamVector[i][j] = (cl_float) parameters[j];
    }
    donors->upload(donorVector);
    donorParams->setParameterValues(donorParamVector);
    vector<vector<cl_float> > acceptorParamVector(numAcceptors);
    vector<mm_int4> acceptorVector(numAcceptors);
    for (int i = 0; i < numAcceptors; i++) {
        vector<double> parameters;
        force.getAcceptorParameters(i, acceptorVector[i].x, acceptorVector[i].y, acceptorVector[i].z, parameters);
        acceptorParamVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            acceptorParamVector[i][j] = (cl_float) parameters[j];
    }
    acceptors->upload(acceptorVector);
    acceptorParams->setParameterValues(acceptorParamVector);

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    // Select an output buffer index for each donor and acceptor.
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    donorBufferIndices = OpenCLArray::create<mm_int4>(cl, numDonors, "customHbondDonorBuffers");
    acceptorBufferIndices = OpenCLArray::create<mm_int4>(cl, numAcceptors, "customHbondAcceptorBuffers");
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    vector<mm_int4> donorBufferVector(numDonors);
    vector<mm_int4> acceptorBufferVector(numAcceptors);
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    vector<int> donorBufferCounter(numParticles, 0);
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    for (int i = 0; i < numDonors; i++)
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        donorBufferVector[i] = mm_int4(donorVector[i].x > -1 ? donorBufferCounter[donorVector[i].x]++ : 0,
                                       donorVector[i].y > -1 ? donorBufferCounter[donorVector[i].y]++ : 0,
                                       donorVector[i].z > -1 ? donorBufferCounter[donorVector[i].z]++ : 0, 0);
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    vector<int> acceptorBufferCounter(numParticles, 0);
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    for (int i = 0; i < numAcceptors; i++)
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        acceptorBufferVector[i] = mm_int4(acceptorVector[i].x > -1 ? acceptorBufferCounter[acceptorVector[i].x]++ : 0,
                                       acceptorVector[i].y > -1 ? acceptorBufferCounter[acceptorVector[i].y]++ : 0,
                                       acceptorVector[i].z > -1 ? acceptorBufferCounter[acceptorVector[i].z]++ : 0, 0);
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    donorBufferIndices->upload(donorBufferVector);
    acceptorBufferIndices->upload(acceptorBufferVector);
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    int maxBuffers = 1;
    for (int i = 0; i < (int) donorBufferCounter.size(); i++)
        maxBuffers = max(maxBuffers, donorBufferCounter[i]);
    for (int i = 0; i < (int) acceptorBufferCounter.size(); i++)
        maxBuffers = max(maxBuffers, acceptorBufferCounter[i]);
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    info = new ForceInfo(maxBuffers, force);
    cl.addForce(info);
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    // Record exclusions.

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    vector<mm_int4> donorExclusionVector(numDonors, mm_int4(-1, -1, -1, -1));
    vector<mm_int4> acceptorExclusionVector(numAcceptors, mm_int4(-1, -1, -1, -1));
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    for (int i = 0; i < force.getNumExclusions(); i++) {
        int donor, acceptor;
        force.getExclusionParticles(i, donor, acceptor);
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        if (donor < startIndex || donor >= endIndex)
            continue;
        donor -= startIndex;
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        if (donorExclusionVector[donor].x == -1)
            donorExclusionVector[donor].x = acceptor;
        else if (donorExclusionVector[donor].y == -1)
            donorExclusionVector[donor].y = acceptor;
        else if (donorExclusionVector[donor].z == -1)
            donorExclusionVector[donor].z = acceptor;
        else if (donorExclusionVector[donor].w == -1)
            donorExclusionVector[donor].w = acceptor;
        else
            throw OpenMMException("CustomHbondForce: OpenCLPlatform does not support more than four exclusions per donor");
        if (acceptorExclusionVector[acceptor].x == -1)
            acceptorExclusionVector[acceptor].x = donor;
        else if (acceptorExclusionVector[acceptor].y == -1)
            acceptorExclusionVector[acceptor].y = donor;
        else if (acceptorExclusionVector[acceptor].z == -1)
            acceptorExclusionVector[acceptor].z = donor;
        else if (acceptorExclusionVector[acceptor].w == -1)
            acceptorExclusionVector[acceptor].w = donor;
        else
            throw OpenMMException("CustomHbondForce: OpenCLPlatform does not support more than four exclusions per acceptor");
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    }
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    donorExclusions = OpenCLArray::create<mm_int4>(cl, numDonors, "customHbondDonorExclusions");
    acceptorExclusions = OpenCLArray::create<mm_int4>(cl, numAcceptors, "customHbondAcceptorExclusions");
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    donorExclusions->upload(donorExclusionVector);
    acceptorExclusions->upload(acceptorExclusionVector);
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    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
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    vector<const TabulatedFunction*> functionList;
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    stringstream tableArgs;
    for (int i = 0; i < force.getNumFunctions(); i++) {
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        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
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        string arrayName = "table"+cl.intToString(i);
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        functionDefinitions.push_back(make_pair(name, arrayName));
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        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
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        int width;
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        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
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        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
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        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
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        tableArgs << ", __global const float";
        if (width > 1)
            tableArgs << width;
        tableArgs << "* restrict " << arrayName;
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    }

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    // Record information about parameters.
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    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    if (globals != NULL)
        globals->upload(globalParamValues);
    map<string, string> variables;
    for (int i = 0; i < force.getNumPerDonorParameters(); i++) {
        const string& name = force.getPerDonorParameterName(i);
        variables[name] = "donorParams"+donorParams->getParameterSuffix(i);
    }
    for (int i = 0; i < force.getNumPerAcceptorParameters(); i++) {
        const string& name = force.getPerAcceptorParameterName(i);
        variables[name] = "acceptorParams"+acceptorParams->getParameterSuffix(i);
    }
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        const string& name = force.getGlobalParameterName(i);
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        variables[name] = "globals["+cl.intToString(i)+"]";
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    }
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    // Now to generate the kernel.  First, it needs to calculate all distances, angles,
    // and dihedrals the expression depends on.

    map<string, vector<int> > distances;
    map<string, vector<int> > angles;
    map<string, vector<int> > dihedrals;
    Lepton::ParsedExpression energyExpression = CustomHbondForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
    map<string, Lepton::ParsedExpression> forceExpressions;
    set<string> computedDeltas;
    computedDeltas.insert("D1A1");
    string atomNames[] = {"A1", "A2", "A3", "D1", "D2", "D3"};
    string atomNamesLower[] = {"a1", "a2", "a3", "d1", "d2", "d3"};
    stringstream computeDonor, computeAcceptor, extraArgs;
    int index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
        if (computedDeltas.count(deltaName) == 0) {
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            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName+" = delta("+atomNamesLower[atoms[0]]+", "+atomNamesLower[atoms[1]]+");\n");
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            computedDeltas.insert(deltaName);
        }
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real r_"+deltaName+" = SQRT(delta"+deltaName+".w);\n");
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        variables[iter->first] = "r_"+deltaName;
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        forceExpressions["real dEdDistance"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
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    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
        if (computedDeltas.count(deltaName1) == 0) {
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            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName1+" = delta("+atomNamesLower[atoms[1]]+", "+atomNamesLower[atoms[0]]+");\n");
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            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
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            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName2+" = delta("+atomNamesLower[atoms[1]]+", "+atomNamesLower[atoms[2]]+");\n");
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            computedDeltas.insert(deltaName2);
        }
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real "+angleName+" = computeAngle(delta"+deltaName1+", delta"+deltaName2+");\n");
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        variables[iter->first] = angleName;
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        forceExpressions["real dEdAngle"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
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    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
        if (computedDeltas.count(deltaName1) == 0) {
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            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName1+" = delta("+atomNamesLower[atoms[0]]+", "+atomNamesLower[atoms[1]]+");\n");
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            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
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            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName2+" = delta("+atomNamesLower[atoms[2]]+", "+atomNamesLower[atoms[1]]+");\n");
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            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
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            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 delta"+deltaName3+" = delta("+atomNamesLower[atoms[2]]+", "+atomNamesLower[atoms[3]]+");\n");
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            computedDeltas.insert(deltaName3);
        }
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 "+crossName1+" = computeCross(delta"+deltaName1+", delta"+deltaName2+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 "+crossName2+" = computeCross(delta"+deltaName2+", delta"+deltaName3+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real "+dihedralName+" = computeAngle("+crossName1+", "+crossName2+");\n");
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, dihedralName+" *= (delta"+deltaName1+".x*"+crossName2+".x + delta"+deltaName1+".y*"+crossName2+".y + delta"+deltaName1+".z*"+crossName2+".z < 0 ? -1 : 1);\n");
        variables[iter->first] = dihedralName;
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        forceExpressions["real dEdDihedral"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
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    }

    // Next it needs to load parameters from global memory.

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    if (force.getNumGlobalParameters() > 0)
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        extraArgs << ", __global const float* restrict globals";
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    for (int i = 0; i < (int) donorParams->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = donorParams->getBuffers()[i];
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        extraArgs << ", __global const "+buffer.getType()+"* restrict donor"+buffer.getName();
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, buffer.getType()+" donorParams"+cl.intToString(i+1)+" = donor"+buffer.getName()+"[index];\n");
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    }
    for (int i = 0; i < (int) acceptorParams->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = acceptorParams->getBuffers()[i];
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        extraArgs << ", __global const "+buffer.getType()+"* restrict acceptor"+buffer.getName();
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, buffer.getType()+" acceptorParams"+cl.intToString(i+1)+" = acceptor"+buffer.getName()+"[index];\n");
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    }
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    // Now evaluate the expressions.

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    computeAcceptor << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");
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    forceExpressions["energy += "] = energyExpression;
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    computeDonor << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");
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    // Finally, apply forces to atoms.

    index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
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        string value = "(dEdDistance"+cl.intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
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        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[0], "-"+value);
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[1], value);
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "{\n");
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 crossProd = cross(delta"+deltaName2+", delta"+deltaName1+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real lengthCross = max(length(crossProd), (real) 1e-6f);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 deltaCross0 = -cross(delta"+deltaName1+", crossProd)*dEdAngle"+cl.intToString(index)+"/(delta"+deltaName1+".w*lengthCross);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 deltaCross2 = cross(delta"+deltaName2+", crossProd)*dEdAngle"+cl.intToString(index)+"/(delta"+deltaName2+".w*lengthCross);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 deltaCross1 = -(deltaCross0+deltaCross2);\n");
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        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[0], "deltaCross0.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[1], "deltaCross1.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[2], "deltaCross2.xyz");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "}\n");
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "{\n");
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real r = SQRT(delta"+deltaName2+".w);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 ff;\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.x = (-dEdDihedral"+cl.intToString(index)+"*r)/"+crossName1+".w;\n");
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.y = (delta"+deltaName1+".x*delta"+deltaName2+".x + delta"+deltaName1+".y*delta"+deltaName2+".y + delta"+deltaName1+".z*delta"+deltaName2+".z)/delta"+deltaName2+".w;\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.z = (delta"+deltaName3+".x*delta"+deltaName2+".x + delta"+deltaName3+".y*delta"+deltaName2+".y + delta"+deltaName3+".z*delta"+deltaName2+".z)/delta"+deltaName2+".w;\n");
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        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.w = (dEdDihedral"+cl.intToString(index)+"*r)/"+crossName2+".w;\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 internalF0 = ff.x*"+crossName1+";\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 internalF3 = ff.w*"+crossName2+";\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "real4 s = ff.y*internalF0 - ff.z*internalF3;\n");
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        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[0], "internalF0.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[1], "s.xyz-internalF0.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[2], "-s.xyz-internalF3.xyz");
        applyDonorAndAcceptorForces(computeDonor, computeAcceptor, atoms[3], "internalF3.xyz");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "}\n");
    }

    // Generate the kernels.

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    map<string, string> replacements;
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    replacements["COMPUTE_DONOR_FORCE"] = computeDonor.str();
    replacements["COMPUTE_ACCEPTOR_FORCE"] = computeAcceptor.str();
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    replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
    map<string, string> defines;
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    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
    defines["NUM_DONORS"] = cl.intToString(numDonors);
    defines["NUM_ACCEPTORS"] = cl.intToString(numAcceptors);
    defines["PI"] = cl.doubleToString(M_PI);
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    if (force.getNonbondedMethod() != CustomHbondForce::NoCutoff) {
        defines["USE_CUTOFF"] = "1";
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        defines["CUTOFF_SQUARED"] = cl.doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
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    }
    if (force.getNonbondedMethod() != CustomHbondForce::NoCutoff && force.getNonbondedMethod() != CustomHbondForce::CutoffNonPeriodic)
        defines["USE_PERIODIC"] = "1";
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    if (force.getNumExclusions() > 0)
        defines["USE_EXCLUSIONS"] = "1";
4884
    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customHbondForce, replacements), defines);
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    donorKernel = cl::Kernel(program, "computeDonorForces");
    acceptorKernel = cl::Kernel(program, "computeAcceptorForces");
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}

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double OpenCLCalcCustomHbondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    if (numDonors == 0 || numAcceptors == 0)
        return 0.0;
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    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    if (!hasInitializedKernel) {
        hasInitializedKernel = true;
        int index = 0;
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        donorKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
        donorKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        donorKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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        donorKernel.setArg<cl::Buffer>(index++, donorExclusions->getDeviceBuffer());
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        donorKernel.setArg<cl::Buffer>(index++, donors->getDeviceBuffer());
        donorKernel.setArg<cl::Buffer>(index++, acceptors->getDeviceBuffer());
        donorKernel.setArg<cl::Buffer>(index++, donorBufferIndices->getDeviceBuffer());
        donorKernel.setArg(index++, 3*OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
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        index += 5; // Periodic box size arguments are set when the kernel is executed.
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        if (globals != NULL)
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            donorKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
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        for (int i = 0; i < (int) donorParams->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = donorParams->getBuffers()[i];
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            donorKernel.setArg<cl::Memory>(index++, buffer.getMemory());
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        }
        for (int i = 0; i < (int) acceptorParams->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = acceptorParams->getBuffers()[i];
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            donorKernel.setArg<cl::Memory>(index++, buffer.getMemory());
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        }
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        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            donorKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
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        index = 0;
        acceptorKernel.setArg<cl::Buffer>(index++, cl.getForceBuffers().getDeviceBuffer());
        acceptorKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        acceptorKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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        acceptorKernel.setArg<cl::Buffer>(index++, acceptorExclusions->getDeviceBuffer());
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        acceptorKernel.setArg<cl::Buffer>(index++, donors->getDeviceBuffer());
        acceptorKernel.setArg<cl::Buffer>(index++, acceptors->getDeviceBuffer());
        acceptorKernel.setArg<cl::Buffer>(index++, acceptorBufferIndices->getDeviceBuffer());
        acceptorKernel.setArg(index++, 3*OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
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        index += 5; // Periodic box size arguments are set when the kernel is executed.
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        if (globals != NULL)
            acceptorKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) donorParams->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = donorParams->getBuffers()[i];
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            acceptorKernel.setArg<cl::Memory>(index++, buffer.getMemory());
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        }
        for (int i = 0; i < (int) acceptorParams->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = acceptorParams->getBuffers()[i];
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            acceptorKernel.setArg<cl::Memory>(index++, buffer.getMemory());
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        }
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        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            acceptorKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
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    }
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    setPeriodicBoxArgs(cl, donorKernel, 8);
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    cl.executeKernel(donorKernel, max(numDonors, numAcceptors));
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    setPeriodicBoxArgs(cl, acceptorKernel, 8);
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    cl.executeKernel(acceptorKernel, max(numDonors, numAcceptors));
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    return 0.0;
}

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void OpenCLCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& context, const CustomHbondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumDonors()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumDonors()/numContexts;
    if (numDonors != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of donors has changed");
    if (numAcceptors != force.getNumAcceptors())
        throw OpenMMException("updateParametersInContext: The number of acceptors has changed");
    
    // Record the per-donor parameters.
    
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    if (numDonors > 0) {
        vector<vector<cl_float> > donorParamVector(numDonors);
        vector<double> parameters;
        for (int i = 0; i < numDonors; i++) {
            int d1, d2, d3;
            force.getDonorParameters(startIndex+i, d1, d2, d3, parameters);
            donorParamVector[i].resize(parameters.size());
            for (int j = 0; j < (int) parameters.size(); j++)
                donorParamVector[i][j] = (cl_float) parameters[j];
        }
        donorParams->setParameterValues(donorParamVector);
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    }
    
    // Record the per-acceptor parameters.
    
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    if (numAcceptors > 0) {
        vector<vector<cl_float> > acceptorParamVector(numAcceptors);
        vector<double> parameters;
        for (int i = 0; i < numAcceptors; i++) {
            int a1, a2, a3;
            force.getAcceptorParameters(i, a1, a2, a3, parameters);
            acceptorParamVector[i].resize(parameters.size());
            for (int j = 0; j < (int) parameters.size(); j++)
                acceptorParamVector[i][j] = (cl_float) parameters[j];
        }
        acceptorParams->setParameterValues(acceptorParamVector);
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    }
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcCustomCentroidBondForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const CustomCentroidBondForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumBonds();
    }
    void getParticlesInGroup(int index, vector<int>& particles) {
        vector<double> parameters;
        vector<int> groups;
        force.getBondParameters(index, groups, parameters);
        for (int i = 0; i < groups.size(); i++) {
            vector<int> groupParticles;
            vector<double> weights;
            force.getGroupParameters(groups[i], groupParticles, weights);
            particles.insert(particles.end(), groupParticles.begin(), groupParticles.end());
        }
    }
    bool areGroupsIdentical(int group1, int group2) {
        vector<int> groups1, groups2;
        vector<double> parameters1, parameters2;
        force.getBondParameters(group1, groups1, parameters1);
        force.getBondParameters(group2, groups2, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        for (int i = 0; i < groups1.size(); i++) {
            vector<int> groupParticles;
            vector<double> weights1, weights2;
            force.getGroupParameters(groups1[i], groupParticles, weights1);
            force.getGroupParameters(groups2[i], groupParticles, weights2);
            if (weights1.size() != weights2.size())
                return false;
            for (int j = 0; j < weights1.size(); j++)
                if (weights1[j] != weights2[j])
                    return false;
        }
        return true;
    }
private:
    const CustomCentroidBondForce& force;
};

OpenCLCalcCustomCentroidBondForceKernel::~OpenCLCalcCustomCentroidBondForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
    if (groupParticles != NULL)
        delete groupParticles;
    if (groupWeights != NULL)
        delete groupWeights;
    if (groupOffsets != NULL)
        delete groupOffsets;
    if (groupForces != NULL)
        delete groupForces;
    if (bondGroups != NULL)
        delete bondGroups;
    if (centerPositions != NULL)
        delete centerPositions;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

void OpenCLCalcCustomCentroidBondForceKernel::initialize(const System& system, const CustomCentroidBondForce& force) {
    numBonds = force.getNumBonds();
    if (numBonds == 0)
        return;
    if (!cl.getSupports64BitGlobalAtomics())
        throw OpenMMException("CustomCentroidBondForce requires a device that supports 64 bit atomic operations");
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    info = new ForceInfo(force);
    cl.addForce(info);
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    // Record the groups.
    
    numGroups = force.getNumGroups();
    vector<cl_int> groupParticleVec;
    vector<cl_float> groupWeightVecFloat;
    vector<cl_double> groupWeightVecDouble;
    vector<cl_int> groupOffsetVec;
    groupOffsetVec.push_back(0);
    for (int i = 0; i < numGroups; i++) {
        vector<int> particles;
        vector<double> weights;
        force.getGroupParameters(i, particles, weights);
        groupParticleVec.insert(groupParticleVec.end(), particles.begin(), particles.end());
        groupOffsetVec.push_back(groupParticleVec.size());
    }
    vector<vector<double> > normalizedWeights;
    CustomCentroidBondForceImpl::computeNormalizedWeights(force, system, normalizedWeights);
    if (cl.getUseDoublePrecision()) {
        for (int i = 0; i < numGroups; i++)
            groupWeightVecDouble.insert(groupWeightVecDouble.end(), normalizedWeights[i].begin(), normalizedWeights[i].end());
    }
    else {
        for (int i = 0; i < numGroups; i++)
            for (int j = 0; j < normalizedWeights[i].size(); j++)
                groupWeightVecFloat.push_back((float) normalizedWeights[i][j]);
    }
    groupParticles = OpenCLArray::create<int>(cl, groupParticleVec.size(), "groupParticles");
    groupParticles->upload(groupParticleVec);
    if (cl.getUseDoublePrecision()) {
        groupWeights = OpenCLArray::create<double>(cl, groupParticleVec.size(), "groupWeights");
        groupWeights->upload(groupWeightVecDouble);
        centerPositions = OpenCLArray::create<mm_double4>(cl, numGroups, "centerPositions");
    }
    else {
        groupWeights = OpenCLArray::create<float>(cl, groupParticleVec.size(), "groupWeights");
        groupWeights->upload(groupWeightVecFloat);
        centerPositions = OpenCLArray::create<mm_float4>(cl, numGroups, "centerPositions");
    }
    groupOffsets = OpenCLArray::create<int>(cl, groupOffsetVec.size(), "groupOffsets");
    groupOffsets->upload(groupOffsetVec);
    groupForces = OpenCLArray::create<long long>(cl, numGroups*3, "groupForces");
    cl.addAutoclearBuffer(*groupForces);
    
    // Record the bonds.
    
    int groupsPerBond = force.getNumGroupsPerBond();
    vector<cl_int> bondGroupVec(numBonds*groupsPerBond);
    params = new OpenCLParameterSet(cl, force.getNumPerBondParameters(), numBonds, "customCentroidBondParams");
    vector<vector<float> > paramVector(numBonds);
    for (int i = 0; i < numBonds; i++) {
        vector<int> groups;
        vector<double> parameters;
        force.getBondParameters(i, groups, parameters);
        for (int j = 0; j < groups.size(); j++)
            bondGroupVec[i+j*numBonds] = groups[j];
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (float) parameters[j];
    }
    params->setParameterValues(paramVector);
    bondGroups = OpenCLArray::create<int>(cl, bondGroupVec.size(), "bondGroups");
    bondGroups->upload(bondGroupVec);

    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
    vector<const TabulatedFunction*> functionList;
    stringstream extraArgs;
    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
        string arrayName = "table"+cl.intToString(i);
        functionDefinitions.push_back(make_pair(name, arrayName));
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
        int width;
        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
        tabulatedFunctions.back()->upload(f);
        extraArgs << ", __global const float";
        if (width > 1)
            extraArgs << width;
        extraArgs << "* restrict " << arrayName;
    }
    
    // Record information about parameters.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (float) force.getGlobalParameterDefaultValue(i);
    }
    map<string, string> variables;
    for (int i = 0; i < groupsPerBond; i++) {
        string index = cl.intToString(i+1);
        variables["x"+index] = "pos"+index+".x";
        variables["y"+index] = "pos"+index+".y";
        variables["z"+index] = "pos"+index+".z";
    }
    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
        const string& name = force.getPerBondParameterName(i);
        variables[name] = "bondParams"+params->getParameterSuffix(i);
    }
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    needEnergyParamDerivs = (force.getNumEnergyParameterDerivatives() > 0);
    if (needEnergyParamDerivs)
        extraArgs << ", __global mixed* restrict energyParamDerivs";
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    if (force.getNumGlobalParameters() > 0) {
        globals = OpenCLArray::create<float>(cl, force.getNumGlobalParameters(), "customCentroidBondGlobals");
        globals->upload(globalParamValues);
        extraArgs << ", __global const float* restrict globals";
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
            string value = "globals["+cl.intToString(i)+"]";
            variables[name] = value;
        }
    }

    // Now to generate the kernel.  First, it needs to calculate all distances, angles,
    // and dihedrals the expression depends on.

    map<string, vector<int> > distances;
    map<string, vector<int> > angles;
    map<string, vector<int> > dihedrals;
    Lepton::ParsedExpression energyExpression = CustomCentroidBondForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
    map<string, Lepton::ParsedExpression> forceExpressions;
    set<string> computedDeltas;
    vector<string> atomNames, posNames;
    for (int i = 0; i < groupsPerBond; i++) {
        string index = cl.intToString(i+1);
        atomNames.push_back("P"+index);
        posNames.push_back("pos"+index);
    }
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    stringstream compute, initParamDerivs, saveParamDerivs;
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    for (int i = 0; i < groupsPerBond; i++) {
        compute<<"int group"<<(i+1)<<" = bondGroups[index+"<<(i*numBonds)<<"];\n";
        compute<<"real4 pos"<<(i+1)<<" = centerPositions[group"<<(i+1)<<"];\n";
    }
    int index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName = atomNames[groups[0]]+atomNames[groups[1]];
        if (computedDeltas.count(deltaName) == 0) {
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            compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName);
        }
        compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
        variables[iter->first] = "r_"+deltaName;
        forceExpressions["real dEdDistance"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName1 = atomNames[groups[1]]+atomNames[groups[0]];
        string deltaName2 = atomNames[groups[1]]+atomNames[groups[2]];
        string angleName = "angle_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]];
        if (computedDeltas.count(deltaName1) == 0) {
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            compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[0]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
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            compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[1]]<<", "<<posNames[groups[2]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName2);
        }
        compute<<"real "<<angleName<<" = computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        variables[iter->first] = angleName;
        forceExpressions["real dEdAngle"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName1 = atomNames[groups[0]]+atomNames[groups[1]];
        string deltaName2 = atomNames[groups[2]]+atomNames[groups[1]];
        string deltaName3 = atomNames[groups[2]]+atomNames[groups[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        string dihedralName = "dihedral_"+atomNames[groups[0]]+atomNames[groups[1]]+atomNames[groups[2]]+atomNames[groups[3]];
        if (computedDeltas.count(deltaName1) == 0) {
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            compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[groups[0]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
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            compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
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            compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[groups[2]]<<", "<<posNames[groups[3]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName3);
        }
        compute<<"real4 "<<crossName1<<" = computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        compute<<"real4 "<<crossName2<<" = computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
        compute<<"real "<<dihedralName<<" = computeAngle("<<crossName1<<", "<<crossName2<<");\n";
        compute<<dihedralName<<" *= (delta"<<deltaName1<<".x*"<<crossName2<<".x + delta"<<deltaName1<<".y*"<<crossName2<<".y + delta"<<deltaName1<<".z*"<<crossName2<<".z < 0 ? -1 : 1);\n";
        variables[iter->first] = dihedralName;
        forceExpressions["real dEdDihedral"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }

    // Now evaluate the expressions.

    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
        extraArgs<<", __global const "<<buffer.getType()<<"* restrict globalParams"<<i;
        compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = globalParams"<<i<<"[index];\n";
    }
    forceExpressions["energy += "] = energyExpression;
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    if (needEnergyParamDerivs) {
        for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
            string paramName = force.getEnergyParameterDerivativeName(i);
            cl.addEnergyParameterDerivative(paramName);
            Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
            forceExpressions[string("energyParamDeriv")+cl.intToString(i)+" += "] = derivExpression;
            initParamDerivs << "mixed energyParamDeriv" << i << " = 0;\n";
        }
        const vector<string>& allParamDerivNames = cl.getEnergyParamDerivNames();
        int numDerivs = allParamDerivNames.size();
        for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
            for (int index = 0; index < numDerivs; index++)
                if (allParamDerivNames[index] == force.getEnergyParameterDerivativeName(i))
                    saveParamDerivs << "energyParamDerivs[get_global_id(0)*" << numDerivs << "+" << index << "] += energyParamDeriv" << i << ";\n";
    }
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    compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");

    // Finally, apply forces to groups.

    vector<string> forceNames;
    for (int i = 0; i < groupsPerBond; i++) {
        string istr = cl.intToString(i+1);
        string forceName = "force"+istr;
        forceNames.push_back(forceName);
        compute<<"real3 "<<forceName<<" = (real3) 0;\n";
        compute<<"{\n";
        Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x"+istr).optimize();
        Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y"+istr).optimize();
        Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z"+istr).optimize();
        map<string, Lepton::ParsedExpression> expressions;
        if (!isZeroExpression(forceExpressionX))
            expressions[forceName+".x -= "] = forceExpressionX;
        if (!isZeroExpression(forceExpressionY))
            expressions[forceName+".y -= "] = forceExpressionY;
        if (!isZeroExpression(forceExpressionZ))
            expressions[forceName+".z -= "] = forceExpressionZ;
        if (expressions.size() > 0)
            compute<<cl.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "coordtemp");
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName = atomNames[groups[0]]+atomNames[groups[1]];
        string value = "(dEdDistance"+cl.intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
        compute<<forceNames[groups[0]]<<" += "<<"-"<<value<<";\n";
        compute<<forceNames[groups[1]]<<" += "<<value<<";\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName1 = atomNames[groups[1]]+atomNames[groups[0]];
        string deltaName2 = atomNames[groups[1]]+atomNames[groups[2]];
        compute<<"{\n";
        compute<<"real4 crossProd = cross(delta"<<deltaName2<<", delta"<<deltaName1<<");\n";
        compute<<"real lengthCross = max(length(crossProd), (real) 1e-6f);\n";
        compute<<"real4 deltaCross0 = -cross(delta"<<deltaName1<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName1<<".w*lengthCross);\n";
        compute<<"real4 deltaCross2 = cross(delta"<<deltaName2<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName2<<".w*lengthCross);\n";
        compute<<"real4 deltaCross1 = -(deltaCross0+deltaCross2);\n";
        compute<<forceNames[groups[0]]<<".xyz += deltaCross0.xyz;\n";
        compute<<forceNames[groups[1]]<<".xyz += deltaCross1.xyz;\n";
        compute<<forceNames[groups[2]]<<".xyz += deltaCross2.xyz;\n";
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& groups = iter->second;
        string deltaName1 = atomNames[groups[0]]+atomNames[groups[1]];
        string deltaName2 = atomNames[groups[2]]+atomNames[groups[1]];
        string deltaName3 = atomNames[groups[2]]+atomNames[groups[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        compute<<"{\n";
        compute<<"real r = sqrt(delta"<<deltaName2<<".w);\n";
        compute<<"real4 ff;\n";
        compute<<"ff.x = (-dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName1<<".w;\n";
        compute<<"ff.y = (delta"<<deltaName1<<".x*delta"<<deltaName2<<".x + delta"<<deltaName1<<".y*delta"<<deltaName2<<".y + delta"<<deltaName1<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.z = (delta"<<deltaName3<<".x*delta"<<deltaName2<<".x + delta"<<deltaName3<<".y*delta"<<deltaName2<<".y + delta"<<deltaName3<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.w = (dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName2<<".w;\n";
        compute<<"real4 internalF0 = ff.x*"<<crossName1<<";\n";
        compute<<"real4 internalF3 = ff.w*"<<crossName2<<";\n";
        compute<<"real4 s = ff.y*internalF0 - ff.z*internalF3;\n";
        compute<<forceNames[groups[0]]<<".xyz += internalF0.xyz;\n";
        compute<<forceNames[groups[1]]<<".xyz += s.xyz-internalF0.xyz;\n";
        compute<<forceNames[groups[2]]<<".xyz += -s.xyz-internalF3.xyz;\n";
        compute<<forceNames[groups[3]]<<".xyz += internalF3.xyz;\n";
        compute<<"}\n";
    }
    
    // Save the forces to global memory.
    
    for (int i = 0; i < groupsPerBond; i++) {
        compute<<"atom_add(&groupForce[group"<<(i+1)<<"], (long) (force"<<(i+1)<<".x*0x100000000));\n";
        compute<<"atom_add(&groupForce[group"<<(i+1)<<"+NUM_GROUPS], (long) (force"<<(i+1)<<".y*0x100000000));\n";
        compute<<"atom_add(&groupForce[group"<<(i+1)<<"+NUM_GROUPS*2], (long) (force"<<(i+1)<<".z*0x100000000));\n";
    }
    map<string, string> replacements;
    replacements["M_PI"] = cl.doubleToString(M_PI);
    replacements["NUM_GROUPS"] = cl.intToString(numGroups);
    replacements["NUM_BONDS"] = cl.intToString(numBonds);
    replacements["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
    replacements["EXTRA_ARGS"] = extraArgs.str();
    replacements["COMPUTE_FORCE"] = compute.str();
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    replacements["INIT_PARAM_DERIVS"] = initParamDerivs.str();
    replacements["SAVE_PARAM_DERIVS"] = saveParamDerivs.str();
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    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customCentroidBond, replacements));
    index = 0;
    computeCentersKernel = cl::Kernel(program, "computeGroupCenters");
    computeCentersKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
    computeCentersKernel.setArg<cl::Buffer>(index++, groupParticles->getDeviceBuffer());
    computeCentersKernel.setArg<cl::Buffer>(index++, groupWeights->getDeviceBuffer());
    computeCentersKernel.setArg<cl::Buffer>(index++, groupOffsets->getDeviceBuffer());
    computeCentersKernel.setArg<cl::Buffer>(index++, centerPositions->getDeviceBuffer());
    index = 0;
    groupForcesKernel = cl::Kernel(program, "computeGroupForces");
    groupForcesKernel.setArg<cl::Buffer>(index++, groupForces->getDeviceBuffer());
    index++; // Energy buffer hasn't been created yet
    groupForcesKernel.setArg<cl::Buffer>(index++, centerPositions->getDeviceBuffer());
    groupForcesKernel.setArg<cl::Buffer>(index++, bondGroups->getDeviceBuffer());
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    index += 5; // Periodic box information
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    if (needEnergyParamDerivs)
        index++; // Deriv buffer hasn't been created yet.
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    for (int i = 0; i < tabulatedFunctions.size(); i++)
        groupForcesKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
    if (globals != NULL)
        groupForcesKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
    for (int i = 0; i < (int) params->getBuffers().size(); i++)
        groupForcesKernel.setArg<cl::Memory>(index++, params->getBuffers()[i].getMemory());
    index = 0;
    applyForcesKernel = cl::Kernel(program, "applyForcesToAtoms");
    applyForcesKernel.setArg<cl::Buffer>(index++, groupParticles->getDeviceBuffer());
    applyForcesKernel.setArg<cl::Buffer>(index++, groupWeights->getDeviceBuffer());
    applyForcesKernel.setArg<cl::Buffer>(index++, groupOffsets->getDeviceBuffer());
    applyForcesKernel.setArg<cl::Buffer>(index++, groupForces->getDeviceBuffer());
}

double OpenCLCalcCustomCentroidBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    if (numBonds == 0)
        return 0.0;
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    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            float value = (float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    cl.executeKernel(computeCentersKernel, OpenCLContext::TileSize*numGroups);
    groupForcesKernel.setArg<cl::Buffer>(1, cl.getEnergyBuffer().getDeviceBuffer());
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    setPeriodicBoxArgs(cl, groupForcesKernel, 4);
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    if (needEnergyParamDerivs)
        groupForcesKernel.setArg<cl::Memory>(9, cl.getEnergyParamDerivBuffer().getDeviceBuffer());
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    cl.executeKernel(groupForcesKernel, numBonds);
    applyForcesKernel.setArg<cl::Buffer>(4, cl.getLongForceBuffer().getDeviceBuffer());
    cl.executeKernel(applyForcesKernel, OpenCLContext::TileSize*numGroups);
    return 0.0;
}

void OpenCLCalcCustomCentroidBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force) {
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    if (numBonds != force.getNumBonds())
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        throw OpenMMException("updateParametersInContext: The number of bonds has changed");
    if (numBonds == 0)
        return;
    
    // Record the per-bond parameters.
    
    vector<vector<float> > paramVector(numBonds);
    vector<int> particles;
    vector<double> parameters;
    for (int i = 0; i < numBonds; i++) {
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        force.getBondParameters(i, particles, parameters);
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        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
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    cl.invalidateMolecules(info);
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}

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class OpenCLCalcCustomCompoundBondForceKernel::ForceInfo : public OpenCLForceInfo {
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public:
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    ForceInfo(const CustomCompoundBondForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    int getNumParticleGroups() {
        return force.getNumBonds();
    }
    void getParticlesInGroup(int index, vector<int>& particles) {
        vector<double> parameters;
        force.getBondParameters(index, particles, parameters);
    }
    bool areGroupsIdentical(int group1, int group2) {
        vector<int> particles;
        vector<double> parameters1, parameters2;
        force.getBondParameters(group1, particles, parameters1);
        force.getBondParameters(group2, particles, parameters2);
        for (int i = 0; i < (int) parameters1.size(); i++)
            if (parameters1[i] != parameters2[i])
                return false;
        return true;
    }
private:
    const CustomCompoundBondForce& force;
};

OpenCLCalcCustomCompoundBondForceKernel::~OpenCLCalcCustomCompoundBondForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

void OpenCLCalcCustomCompoundBondForceKernel::initialize(const System& system, const CustomCompoundBondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    numBonds = endIndex-startIndex;
    if (numBonds == 0)
        return;
    int particlesPerBond = force.getNumParticlesPerBond();
    vector<vector<int> > atoms(numBonds, vector<int>(particlesPerBond));
    params = new OpenCLParameterSet(cl, force.getNumPerBondParameters(), numBonds, "customCompoundBondParams");
    vector<vector<cl_float> > paramVector(numBonds);
    for (int i = 0; i < numBonds; i++) {
        vector<double> parameters;
        force.getBondParameters(startIndex+i, atoms[i], parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
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    info = new ForceInfo(force);
    cl.addForce(info);
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    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
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    vector<const TabulatedFunction*> functionList;
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    stringstream tableArgs;
    for (int i = 0; i < force.getNumFunctions(); i++) {
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        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
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        int width;
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        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
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        OpenCLArray* array = OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction");
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        tabulatedFunctions.push_back(array);
        array->upload(f);
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        string arrayName = cl.getBondedUtilities().addArgument(array->getDeviceBuffer(), width == 1 ? "float" : "float"+cl.intToString(width));
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        functionDefinitions.push_back(make_pair(name, arrayName));
    }
    
    // Record information about parameters.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (cl_float) force.getGlobalParameterDefaultValue(i);
    }
    map<string, string> variables;
    for (int i = 0; i < particlesPerBond; i++) {
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        string index = cl.intToString(i+1);
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        variables["x"+index] = "pos"+index+".x";
        variables["y"+index] = "pos"+index+".y";
        variables["z"+index] = "pos"+index+".z";
    }
    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
        const string& name = force.getPerBondParameterName(i);
        variables[name] = "bondParams"+params->getParameterSuffix(i);
    }
    if (force.getNumGlobalParameters() > 0) {
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        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customCompoundBondGlobals", CL_MEM_READ_ONLY);
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        globals->upload(globalParamValues);
        string argName = cl.getBondedUtilities().addArgument(globals->getDeviceBuffer(), "float");
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
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            string value = argName+"["+cl.intToString(i)+"]";
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            variables[name] = value;
        }
    }

    // Now to generate the kernel.  First, it needs to calculate all distances, angles,
    // and dihedrals the expression depends on.

    map<string, vector<int> > distances;
    map<string, vector<int> > angles;
    map<string, vector<int> > dihedrals;
    Lepton::ParsedExpression energyExpression = CustomCompoundBondForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
    map<string, Lepton::ParsedExpression> forceExpressions;
    set<string> computedDeltas;
    vector<string> atomNames, posNames;
    for (int i = 0; i < particlesPerBond; i++) {
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        string index = cl.intToString(i+1);
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        atomNames.push_back("P"+index);
        posNames.push_back("pos"+index);
    }
    stringstream compute;
    int index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
        if (computedDeltas.count(deltaName) == 0) {
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            compute<<"real4 delta"<<deltaName<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName);
        }
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        compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
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        variables[iter->first] = "r_"+deltaName;
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        forceExpressions["real dEdDistance"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
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    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
        if (computedDeltas.count(deltaName1) == 0) {
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            compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
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            compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName2);
        }
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        compute<<"real "<<angleName<<" = ccb_computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
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        variables[iter->first] = angleName;
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        forceExpressions["real dEdAngle"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
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    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
        if (computedDeltas.count(deltaName1) == 0) {
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            compute<<"real4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
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            compute<<"real4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
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            compute<<"real4 delta"<<deltaName3<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<", "<<force.usesPeriodicBoundaryConditions()<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName3);
        }
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        compute<<"real4 "<<crossName1<<" = ccb_computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        compute<<"real4 "<<crossName2<<" = ccb_computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
        compute<<"real "<<dihedralName<<" = ccb_computeAngle("<<crossName1<<", "<<crossName2<<");\n";
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        compute<<dihedralName<<" *= (delta"<<deltaName1<<".x*"<<crossName2<<".x + delta"<<deltaName1<<".y*"<<crossName2<<".y + delta"<<deltaName1<<".z*"<<crossName2<<".z < 0 ? -1 : 1);\n";
        variables[iter->first] = dihedralName;
5641
        forceExpressions["real dEdDihedral"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
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    }

    // Now evaluate the expressions.

    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
        string argName = cl.getBondedUtilities().addArgument(buffer.getMemory(), buffer.getType());
        compute<<buffer.getType()<<" bondParams"<<(i+1)<<" = "<<argName<<"[index];\n";
    }
    forceExpressions["energy += "] = energyExpression;
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    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
        string paramName = force.getEnergyParameterDerivativeName(i);
        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
        forceExpressions[derivVariable+" += "] = derivExpression;
    }
5658
    compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");
5659
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5663

    // Finally, apply forces to atoms.

    vector<string> forceNames;
    for (int i = 0; i < particlesPerBond; i++) {
5664
        string istr = cl.intToString(i+1);
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        string forceName = "force"+istr;
        forceNames.push_back(forceName);
5667
        compute<<"real4 "<<forceName<<" = (real4) 0;\n";
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        compute<<"{\n";
        Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x"+istr).optimize();
        Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y"+istr).optimize();
        Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z"+istr).optimize();
        map<string, Lepton::ParsedExpression> expressions;
        if (!isZeroExpression(forceExpressionX))
            expressions[forceName+".x -= "] = forceExpressionX;
        if (!isZeroExpression(forceExpressionY))
            expressions[forceName+".y -= "] = forceExpressionY;
        if (!isZeroExpression(forceExpressionZ))
            expressions[forceName+".z -= "] = forceExpressionZ;
        if (expressions.size() > 0)
5680
            compute<<cl.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "coordtemp");
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        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
5687
        string value = "(dEdDistance"+cl.intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
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        compute<<forceNames[atoms[0]]<<".xyz += "<<"-"<<value<<";\n";
        compute<<forceNames[atoms[1]]<<".xyz += "<<value<<";\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        compute<<"{\n";
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        compute<<"real4 crossProd = cross(delta"<<deltaName2<<", delta"<<deltaName1<<");\n";
        compute<<"real lengthCross = max(length(crossProd), (real) 1e-6f);\n";
        compute<<"real4 deltaCross0 = -cross(delta"<<deltaName1<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName1<<".w*lengthCross);\n";
        compute<<"real4 deltaCross2 = cross(delta"<<deltaName2<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName2<<".w*lengthCross);\n";
        compute<<"real4 deltaCross1 = -(deltaCross0+deltaCross2);\n";
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        compute<<forceNames[atoms[0]]<<".xyz += deltaCross0.xyz;\n";
        compute<<forceNames[atoms[1]]<<".xyz += deltaCross1.xyz;\n";
        compute<<forceNames[atoms[2]]<<".xyz += deltaCross2.xyz;\n";
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        compute<<"{\n";
5716
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        compute<<"real r = SQRT(delta"<<deltaName2<<".w);\n";
        compute<<"real4 ff;\n";
        compute<<"ff.x = (-dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName1<<".w;\n";
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        compute<<"ff.y = (delta"<<deltaName1<<".x*delta"<<deltaName2<<".x + delta"<<deltaName1<<".y*delta"<<deltaName2<<".y + delta"<<deltaName1<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.z = (delta"<<deltaName3<<".x*delta"<<deltaName2<<".x + delta"<<deltaName3<<".y*delta"<<deltaName2<<".y + delta"<<deltaName3<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
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        compute<<"ff.w = (dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName2<<".w;\n";
        compute<<"real4 internalF0 = ff.x*"<<crossName1<<";\n";
        compute<<"real4 internalF3 = ff.w*"<<crossName2<<";\n";
        compute<<"real4 s = ff.y*internalF0 - ff.z*internalF3;\n";
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        compute<<forceNames[atoms[0]]<<".xyz += internalF0.xyz;\n";
        compute<<forceNames[atoms[1]]<<".xyz += s.xyz-internalF0.xyz;\n";
        compute<<forceNames[atoms[2]]<<".xyz += -s.xyz-internalF3.xyz;\n";
        compute<<forceNames[atoms[3]]<<".xyz += internalF3.xyz;\n";
        compute<<"}\n";
    }
    cl.getBondedUtilities().addInteraction(atoms, compute.str(), force.getForceGroup());
    map<string, string> replacements;
5733
    replacements["M_PI"] = cl.doubleToString(M_PI);
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    cl.getBondedUtilities().addPrefixCode(cl.replaceStrings(OpenCLKernelSources::customCompoundBond, replacements));;
}

double OpenCLCalcCustomCompoundBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    return 0.0;
}

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void OpenCLCalcCustomCompoundBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force) {
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
    if (numBonds != endIndex-startIndex)
        throw OpenMMException("updateParametersInContext: The number of bonds has changed");
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    if (numBonds == 0)
        return;
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    // Record the per-bond parameters.
    
    vector<vector<cl_float> > paramVector(numBonds);
    vector<int> particles;
    vector<double> parameters;
    for (int i = 0; i < numBonds; i++) {
        force.getBondParameters(startIndex+i, particles, parameters);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (cl_float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
5776
    cl.invalidateMolecules(info);
5777
5778
}

5779
class OpenCLCalcCustomManyParticleForceKernel::ForceInfo : public OpenCLForceInfo {
5780
public:
5781
    ForceInfo(const CustomManyParticleForce& force) : OpenCLForceInfo(0), force(force) {
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    }
    bool areParticlesIdentical(int particle1, int particle2) {
        vector<double> params1, params2;
        int type1, type2;
        force.getParticleParameters(particle1, params1, type1);
        force.getParticleParameters(particle2, params2, type2);
        if (type1 != type2)
            return false;
        for (int i = 0; i < (int) params1.size(); i++)
            if (params1[i] != params2[i])
                return false;
        return true;
    }
    int getNumParticleGroups() {
        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;
    }
private:
    const CustomManyParticleForce& force;
};

OpenCLCalcCustomManyParticleForceKernel::~OpenCLCalcCustomManyParticleForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
    if (orderIndex != NULL)
        delete orderIndex;
    if (particleOrder != NULL)
        delete particleOrder;
    if (particleTypes != NULL)
        delete particleTypes;
    if (exclusions != NULL)
        delete exclusions;
    if (exclusionStartIndex != NULL)
        delete exclusionStartIndex;
    if (blockCenter != NULL)
        delete blockCenter;
    if (blockBoundingBox != NULL)
        delete blockBoundingBox;
    if (neighborPairs != NULL)
        delete neighborPairs;
    if (numNeighborPairs != NULL)
        delete numNeighborPairs;
    if (neighborStartIndex != NULL)
        delete neighborStartIndex;
    if (neighbors != NULL)
        delete neighbors;
    if (numNeighborsForAtom != NULL)
        delete numNeighborsForAtom;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

void OpenCLCalcCustomManyParticleForceKernel::initialize(const System& system, const CustomManyParticleForce& force) {
    if (!cl.getSupports64BitGlobalAtomics())
        throw OpenMMException("CustomManyParticleForce requires a device that supports 64 bit atomic operations");
    int numParticles = force.getNumParticles();
    int particlesPerSet = force.getNumParticlesPerSet();
    bool centralParticleMode = (force.getPermutationMode() == CustomManyParticleForce::UniqueCentralParticle);
    nonbondedMethod = CalcCustomManyParticleForceKernel::NonbondedMethod(force.getNonbondedMethod());
    forceWorkgroupSize = 128;
    findNeighborsWorkgroupSize = (cl.getSIMDWidth() >= 32 ? 128 : 32);
    
    // Record parameter values.
    
    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), numParticles, "customManyParticleParameters");
    vector<vector<float> > paramVector(numParticles);
    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
        int type;
        force.getParticleParameters(i, parameters, type);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (float) parameters[j];
    }
    params->setParameterValues(paramVector);
5868
5869
    info = new ForceInfo(force);
    cl.addForce(info);
5870
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6009

    // Record the tabulated functions.

    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
    vector<const TabulatedFunction*> functionList;
    stringstream tableArgs;
    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
        functionList.push_back(&force.getTabulatedFunction(i));
        string name = force.getTabulatedFunctionName(i);
        string arrayName = "table"+cl.intToString(i);
        functionDefinitions.push_back(make_pair(name, arrayName));
        functions[name] = cl.getExpressionUtilities().getFunctionPlaceholder(force.getTabulatedFunction(i));
        int width;
        vector<float> f = cl.getExpressionUtilities().computeFunctionCoefficients(force.getTabulatedFunction(i), width);
        tabulatedFunctions.push_back(OpenCLArray::create<float>(cl, f.size(), "TabulatedFunction"));
        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
        tableArgs << ", __global const float";
        if (width > 1)
            tableArgs << width;
        tableArgs << "* restrict " << arrayName;
    }
    
    // Record information about parameters.

    globalParamNames.resize(force.getNumGlobalParameters());
    globalParamValues.resize(force.getNumGlobalParameters());
    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
        globalParamNames[i] = force.getGlobalParameterName(i);
        globalParamValues[i] = (float) force.getGlobalParameterDefaultValue(i);
    }
    vector<pair<ExpressionTreeNode, string> > variables;
    for (int i = 0; i < particlesPerSet; i++) {
        string index = cl.intToString(i+1);
        variables.push_back(makeVariable("x"+index, "pos"+index+".x"));
        variables.push_back(makeVariable("y"+index, "pos"+index+".y"));
        variables.push_back(makeVariable("z"+index, "pos"+index+".z"));
    }
    for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
        const string& name = force.getPerParticleParameterName(i);
        for (int j = 0; j < particlesPerSet; j++) {
            string index = cl.intToString(j+1);
            variables.push_back(makeVariable(name+index, "params"+params->getParameterSuffix(i, index)));
        }
    }
    if (force.getNumGlobalParameters() > 0) {
        globals = OpenCLArray::create<cl_float>(cl, force.getNumGlobalParameters(), "customManyParticleGlobals", CL_MEM_READ_ONLY);
        globals->upload(globalParamValues);
        for (int i = 0; i < force.getNumGlobalParameters(); i++) {
            const string& name = force.getGlobalParameterName(i);
            string value = "globals["+cl.intToString(i)+"]";
            variables.push_back(makeVariable(name, value));
        }
    }
    
    // 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 = OpenCLArray::create<int>(cl, particleTypesVec.size(), "customManyParticleTypes");
        orderIndex = OpenCLArray::create<int>(cl, orderIndexVec.size(), "customManyParticleOrderIndex");
        particleOrder = OpenCLArray::create<int>(cl, 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);
    }
    
    // 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 = OpenCLArray::create<int>(cl, exclusionsVec.size(), "customManyParticleExclusions");
        exclusionStartIndex = OpenCLArray::create<int>(cl, exclusionStartIndexVec.size(), "customManyParticleExclusionStart");
        exclusions->upload(exclusionsVec);
        exclusionStartIndex->upload(exclusionStartIndexVec);
    }
    
    // Build data structures for the neighbor list.
    
    if (nonbondedMethod != NoCutoff) {
        int numAtomBlocks = cl.getNumAtomBlocks();
        int elementSize = (cl.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
        blockCenter = new OpenCLArray(cl, numAtomBlocks, 4*elementSize, "blockCenter");
        blockBoundingBox = new OpenCLArray(cl, numAtomBlocks, 4*elementSize, "blockBoundingBox");
        numNeighborPairs = OpenCLArray::create<int>(cl, 1, "customManyParticleNumNeighborPairs");
        neighborStartIndex = OpenCLArray::create<int>(cl, numParticles+1, "customManyParticleNeighborStartIndex");
        numNeighborsForAtom = OpenCLArray::create<int>(cl, numParticles, "customManyParticleNumNeighborsForAtom");

        // Select a size for the array that holds the neighbor list.  We have to make a fairly
        // arbitrary guess, but if this turns out to be too small we'll increase it later.

        maxNeighborPairs = 150*numParticles;
        neighborPairs = OpenCLArray::create<mm_int2>(cl, maxNeighborPairs, "customManyParticleNeighborPairs");
        neighbors = OpenCLArray::create<int>(cl, maxNeighborPairs, "customManyParticleNeighbors");
    }

    // Now to generate the kernel.  First, it needs to calculate all distances, angles,
    // and dihedrals the expression depends on.

    map<string, vector<int> > distances;
    map<string, vector<int> > angles;
    map<string, vector<int> > dihedrals;
    Lepton::ParsedExpression energyExpression = CustomManyParticleForceImpl::prepareExpression(force, functions, distances, angles, dihedrals);
    map<string, Lepton::ParsedExpression> forceExpressions;
    set<string> computedDeltas;
    vector<string> atomNames, posNames;
    for (int i = 0; i < particlesPerSet; i++) {
        string index = cl.intToString(i+1);
        atomNames.push_back("P"+index);
        posNames.push_back("pos"+index);
    }
    stringstream compute;
    int index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
        if (computedDeltas.count(deltaName) == 0) {
6010
            compute<<"real4 delta"<<deltaName<<" = delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName);
        }
        compute<<"real r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
        variables.push_back(makeVariable(iter->first, "r_"+deltaName));
        forceExpressions["real dEdDistance"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        string angleName = "angle_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]];
        if (computedDeltas.count(deltaName1) == 0) {
6024
            compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
6025
6026
6027
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
6028
            compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName2);
        }
        compute<<"real "<<angleName<<" = computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        variables.push_back(makeVariable(iter->first, angleName));
        forceExpressions["real dEdAngle"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        string dihedralName = "dihedral_"+atomNames[atoms[0]]+atomNames[atoms[1]]+atomNames[atoms[2]]+atomNames[atoms[3]];
        if (computedDeltas.count(deltaName1) == 0) {
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            compute<<"real4 delta"<<deltaName1<<" = delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
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            compute<<"real4 delta"<<deltaName2<<" = delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
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            compute<<"real4 delta"<<deltaName3<<" = delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ);\n";
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            computedDeltas.insert(deltaName3);
        }
        compute<<"real4 "<<crossName1<<" = computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        compute<<"real4 "<<crossName2<<" = computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
        compute<<"real "<<dihedralName<<" = computeAngle("<<crossName1<<", "<<crossName2<<");\n";
        compute<<dihedralName<<" *= (delta"<<deltaName1<<".x*"<<crossName2<<".x + delta"<<deltaName1<<".y*"<<crossName2<<".y + delta"<<deltaName1<<".z*"<<crossName2<<".z < 0 ? -1 : 1);\n";
        variables.push_back(makeVariable(iter->first, dihedralName));
        forceExpressions["real dEdDihedral"+cl.intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }

    // Now evaluate the expressions.

    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
        compute<<buffer.getType()<<" params"<<(i+1)<<" = global_params"<<(i+1)<<"[index];\n";
    }
    forceExpressions["energy += "] = energyExpression;
    compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, "temp");

    // Apply forces to atoms.

    vector<string> forceNames;
    for (int i = 0; i < particlesPerSet; i++) {
        string istr = cl.intToString(i+1);
        string forceName = "force"+istr;
        forceNames.push_back(forceName);
        compute<<"real4 "<<forceName<<" = (real4) 0;\n";
        compute<<"{\n";
        Lepton::ParsedExpression forceExpressionX = energyExpression.differentiate("x"+istr).optimize();
        Lepton::ParsedExpression forceExpressionY = energyExpression.differentiate("y"+istr).optimize();
        Lepton::ParsedExpression forceExpressionZ = energyExpression.differentiate("z"+istr).optimize();
        map<string, Lepton::ParsedExpression> expressions;
        if (!isZeroExpression(forceExpressionX))
            expressions[forceName+".x -= "] = forceExpressionX;
        if (!isZeroExpression(forceExpressionY))
            expressions[forceName+".y -= "] = forceExpressionY;
        if (!isZeroExpression(forceExpressionZ))
            expressions[forceName+".z -= "] = forceExpressionZ;
        if (expressions.size() > 0)
            compute<<cl.getExpressionUtilities().createExpressions(expressions, variables, functionList, functionDefinitions, "coordtemp");
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = distances.begin(); iter != distances.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName = atomNames[atoms[0]]+atomNames[atoms[1]];
        string value = "(dEdDistance"+cl.intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
        compute<<forceNames[atoms[0]]<<".xyz += "<<"-"<<value<<";\n";
        compute<<forceNames[atoms[1]]<<".xyz += "<<value<<";\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = angles.begin(); iter != angles.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[1]]+atomNames[atoms[0]];
        string deltaName2 = atomNames[atoms[1]]+atomNames[atoms[2]];
        compute<<"{\n";
        compute<<"real4 crossProd = cross(delta"<<deltaName2<<", delta"<<deltaName1<<");\n";
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        compute<<"real lengthCross = max(SQRT(dot(crossProd, crossProd)), (real) 1e-6f);\n";
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        compute<<"real4 deltaCross0 = -cross(delta"<<deltaName1<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName1<<".w*lengthCross);\n";
        compute<<"real4 deltaCross2 = cross(delta"<<deltaName2<<", crossProd)*dEdAngle"<<cl.intToString(index)<<"/(delta"<<deltaName2<<".w*lengthCross);\n";
        compute<<"real4 deltaCross1 = -(deltaCross0+deltaCross2);\n";
        compute<<forceNames[atoms[0]]<<".xyz += deltaCross0.xyz;\n";
        compute<<forceNames[atoms[1]]<<".xyz += deltaCross1.xyz;\n";
        compute<<forceNames[atoms[2]]<<".xyz += deltaCross2.xyz;\n";
        compute<<"}\n";
    }
    index = 0;
    for (map<string, vector<int> >::const_iterator iter = dihedrals.begin(); iter != dihedrals.end(); ++iter, ++index) {
        const vector<int>& atoms = iter->second;
        string deltaName1 = atomNames[atoms[0]]+atomNames[atoms[1]];
        string deltaName2 = atomNames[atoms[2]]+atomNames[atoms[1]];
        string deltaName3 = atomNames[atoms[2]]+atomNames[atoms[3]];
        string crossName1 = "cross_"+deltaName1+"_"+deltaName2;
        string crossName2 = "cross_"+deltaName2+"_"+deltaName3;
        compute<<"{\n";
        compute<<"real r = sqrt(delta"<<deltaName2<<".w);\n";
        compute<<"real4 ff;\n";
        compute<<"ff.x = (-dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName1<<".w;\n";
        compute<<"ff.y = (delta"<<deltaName1<<".x*delta"<<deltaName2<<".x + delta"<<deltaName1<<".y*delta"<<deltaName2<<".y + delta"<<deltaName1<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.z = (delta"<<deltaName3<<".x*delta"<<deltaName2<<".x + delta"<<deltaName3<<".y*delta"<<deltaName2<<".y + delta"<<deltaName3<<".z*delta"<<deltaName2<<".z)/delta"<<deltaName2<<".w;\n";
        compute<<"ff.w = (dEdDihedral"<<cl.intToString(index)<<"*r)/"<<crossName2<<".w;\n";
        compute<<"real4 internalF0 = ff.x*"<<crossName1<<";\n";
        compute<<"real4 internalF3 = ff.w*"<<crossName2<<";\n";
        compute<<"real4 s = ff.y*internalF0 - ff.z*internalF3;\n";
        compute<<forceNames[atoms[0]]<<".xyz += internalF0.xyz;\n";
        compute<<forceNames[atoms[1]]<<".xyz += s.xyz-internalF0.xyz;\n";
        compute<<forceNames[atoms[2]]<<".xyz += -s.xyz-internalF3.xyz;\n";
        compute<<forceNames[atoms[3]]<<".xyz += internalF3.xyz;\n";
        compute<<"}\n";
    }
    
    // Store forces to global memory.
    
    for (int i = 0; i < particlesPerSet; i++)
        compute<<"storeForce(atom"<<(i+1)<<", "<<forceNames[i]<<", forceBuffers);\n";
    
    // Create other replacements that depend on the number of particles per set.
    
    stringstream numCombinations, atomsForCombination, isValidCombination, permute, loadData, verifyCutoff, verifyExclusions;
    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)
peastman's avatar
Bug fix  
peastman committed
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            permute<<"int atom"<<(i+1)<<" = particleSet[particleOrder["<<particlesPerSet<<"*order+"<<i<<"]];\n";
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        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++)
            loadData<<params->getBuffers()[j].getType()<<" params"<<(j+1)<<(i+1)<<" = global_params"<<(j+1)<<"[atom"<<(i+1)<<"];\n";
    }
    if (centralParticleMode) {
        for (int i = 1; i < particlesPerSet; i++) {
            if (i > 1)
                isValidCombination<<" && p"<<(i+1)<<">p"<<i<<" && ";
            isValidCombination<<"p"<<(i+1)<<"!=p1";
        }
    }
    else {
        for (int i = 2; i < particlesPerSet; i++) {
            if (i > 2)
                isValidCombination<<" && ";
            isValidCombination<<"a"<<(i+1)<<">a"<<i;
        }
    }
    atomsForCombination<<"int tempIndex = index;\n";
    for (int i = 1; i < particlesPerSet; i++) {
        if (i > 1)
            numCombinations<<"*";
        numCombinations<<"numNeighbors";
        if (centralParticleMode)
            atomsForCombination<<"int a"<<(i+1)<<" = tempIndex%numNeighbors;\n";
        else
            atomsForCombination<<"int a"<<(i+1)<<" = 1+tempIndex%numNeighbors;\n";
        if (i < particlesPerSet-1)
            atomsForCombination<<"tempIndex /= numNeighbors;\n";
    }
    if (particlesPerSet > 2) {
        if (centralParticleMode)
            atomsForCombination<<"a2 = (a3%2 == 0 ? a2 : numNeighbors-a2-1);\n";
        else
            atomsForCombination<<"a2 = (a3%2 == 0 ? a2 : numNeighbors-a2+1);\n";
    }
    for (int i = 1; i < particlesPerSet; i++) {
        if (nonbondedMethod == NoCutoff) {
            if (centralParticleMode)
                atomsForCombination<<"int p"<<(i+1)<<" = a"<<(i+1)<<";\n";
            else
                atomsForCombination<<"int p"<<(i+1)<<" = p1+a"<<(i+1)<<";\n";
        }
        else {
            if (centralParticleMode)
                atomsForCombination<<"int p"<<(i+1)<<" = neighbors[firstNeighbor+a"<<(i+1)<<"];\n";
            else
                atomsForCombination<<"int p"<<(i+1)<<" = neighbors[firstNeighbor-1+a"<<(i+1)<<"];\n";
        }
    }
    if (nonbondedMethod != NoCutoff) {
        for (int i = 1; i < particlesPerSet; i++)
            verifyCutoff<<"real4 pos"<<(i+1)<<" = posq[p"<<(i+1)<<"];\n";
        if (!centralParticleMode) {
            for (int i = 1; i < particlesPerSet; i++) {
                for (int j = i+1; j < particlesPerSet; j++)
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                    verifyCutoff<<"includeInteraction &= (delta(pos"<<(i+1)<<", pos"<<(j+1)<<", periodicBoxSize, invPeriodicBoxSize, periodicBoxVecX, periodicBoxVecY, periodicBoxVecZ).w < CUTOFF_SQUARED);\n";
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            }
        }
    }
    if (force.getNumExclusions() > 0) {
        int startCheckFrom = (nonbondedMethod == NoCutoff ? 0 : 1);
        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"+cl.intToString(particlesPerSet)+"]";
    for (int i = particlesPerSet-2; i >= 0; i--)
        computeTypeIndex = "particleTypes[p"+cl.intToString(i+1)+"]+"+cl.intToString(numTypes)+"*("+computeTypeIndex+")";
    
    // Create replacements for extra arguments.
    
    stringstream extraArgs;
    if (force.getNumGlobalParameters() > 0)
        extraArgs << ", __global const float* globals";
    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
        OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
        extraArgs<<", __global const "<<buffer.getType()<<"* restrict global_params"<<(i+1);
    }

    // Create the kernels.

    map<string, string> replacements;
    replacements["COMPUTE_INTERACTION"] = compute.str();
    replacements["NUM_CANDIDATE_COMBINATIONS"] = numCombinations.str();
    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;
    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 (centralParticleMode)
        defines["USE_CENTRAL_PARTICLE"] = "1";
    if (hasTypeFilters)
        defines["USE_FILTERS"] = "1";
    if (force.getNumExclusions() > 0)
        defines["USE_EXCLUSIONS"] = "1";
    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
    defines["M_PI"] = cl.doubleToString(M_PI);
    defines["CUTOFF_SQUARED"] = cl.doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
    defines["TILE_SIZE"] = cl.intToString(OpenCLContext::TileSize);
    defines["NUM_BLOCKS"] = cl.intToString(cl.getNumAtomBlocks());
    defines["FIND_NEIGHBORS_WORKGROUP_SIZE"] = cl.intToString(findNeighborsWorkgroupSize);
    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customManyParticle, replacements), defines);
    forceKernel = cl::Kernel(program, "computeInteraction");
    blockBoundsKernel = cl::Kernel(program, "findBlockBounds");
    neighborsKernel = cl::Kernel(program, "findNeighbors");
    startIndicesKernel = cl::Kernel(program, "computeNeighborStartIndices");
    copyPairsKernel = cl::Kernel(program, "copyPairsToNeighborList");
}

double OpenCLCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
    if (!hasInitializedKernel) {
        hasInitializedKernel = true;
        
        // Set arguments for the force kernel.
        
        int index = 0;
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        forceKernel.setArg<cl::Buffer>(index++, cl.getLongForceBuffer().getDeviceBuffer());
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        forceKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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        setPeriodicBoxArgs(cl, forceKernel, index);
        index += 5;
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        if (nonbondedMethod != NoCutoff) {
            forceKernel.setArg<cl::Buffer>(index++, neighbors->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, neighborStartIndex->getDeviceBuffer());
        }
        if (particleTypes != NULL) {
            forceKernel.setArg<cl::Buffer>(index++, particleTypes->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, orderIndex->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, particleOrder->getDeviceBuffer());
        }
        if (exclusions != NULL) {
            forceKernel.setArg<cl::Buffer>(index++, exclusions->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, exclusionStartIndex->getDeviceBuffer());
        }
        if (globals != NULL)
            forceKernel.setArg<cl::Buffer>(index++, globals->getDeviceBuffer());
        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
            OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
            forceKernel.setArg<cl::Memory>(index++, buffer.getMemory());
        }
        for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
            forceKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
        
        if (nonbondedMethod != NoCutoff) {
            // Set arguments for the block bounds kernel.

            index = 0;
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            setPeriodicBoxArgs(cl, blockBoundsKernel, index);
            index += 5;
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            blockBoundsKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
            blockBoundsKernel.setArg<cl::Buffer>(index++, blockCenter->getDeviceBuffer());
            blockBoundsKernel.setArg<cl::Buffer>(index++, blockBoundingBox->getDeviceBuffer());
            blockBoundsKernel.setArg<cl::Buffer>(index++, numNeighborPairs->getDeviceBuffer());

            // Set arguments for the neighbor list kernel.

            index = 0;
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            setPeriodicBoxArgs(cl, neighborsKernel, index);
            index += 5;
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            neighborsKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, blockCenter->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, blockBoundingBox->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, neighborPairs->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, numNeighborPairs->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(index++, numNeighborsForAtom->getDeviceBuffer());
            index++;
            if (exclusions != NULL) {
                neighborsKernel.setArg<cl::Buffer>(index++, exclusions->getDeviceBuffer());
                neighborsKernel.setArg<cl::Buffer>(index++, exclusionStartIndex->getDeviceBuffer());
            }
            
            // Set arguments for the kernel to find neighbor list start indices.
            
            index = 0;
            startIndicesKernel.setArg<cl::Buffer>(index++, numNeighborsForAtom->getDeviceBuffer());
            startIndicesKernel.setArg<cl::Buffer>(index++, neighborStartIndex->getDeviceBuffer());
            startIndicesKernel.setArg<cl::Buffer>(index++, numNeighborPairs->getDeviceBuffer());

            // Set arguments for the kernel to assemble the final neighbor list.
            
            index = 0;
            copyPairsKernel.setArg<cl::Buffer>(index++, neighborPairs->getDeviceBuffer());
            copyPairsKernel.setArg<cl::Buffer>(index++, neighbors->getDeviceBuffer());
            copyPairsKernel.setArg<cl::Buffer>(index++, numNeighborPairs->getDeviceBuffer());
            index++;
            copyPairsKernel.setArg<cl::Buffer>(index++, numNeighborsForAtom->getDeviceBuffer());
            copyPairsKernel.setArg<cl::Buffer>(index++, neighborStartIndex->getDeviceBuffer());
       }
    }
    if (globals != NULL) {
        bool changed = false;
        for (int i = 0; i < (int) globalParamNames.size(); i++) {
            cl_float value = (cl_float) context.getParameter(globalParamNames[i]);
            if (value != globalParamValues[i])
                changed = true;
            globalParamValues[i] = value;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
    while (true) {
        int* numPairs = (int*) cl.getPinnedBuffer();
        cl::Event event;
        if (nonbondedMethod != NoCutoff) {
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            neighborsKernel.setArg<int>(11, maxNeighborPairs);
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            startIndicesKernel.setArg<int>(3, maxNeighborPairs);
            copyPairsKernel.setArg<int>(3, maxNeighborPairs);
            cl.executeKernel(blockBoundsKernel, cl.getNumAtomBlocks());
            cl.executeKernel(neighborsKernel, cl.getNumAtoms(), findNeighborsWorkgroupSize);

            // We need to make sure there was enough memory for the neighbor list.  Download the
            // information asynchronously so kernels can be running at the same time.

            numNeighborPairs->download(numPairs, false);
            cl.getQueue().enqueueMarker(&event);
            cl.executeKernel(startIndicesKernel, 256, 256);
            cl.executeKernel(copyPairsKernel, maxNeighborPairs);
        }
6395
6396
        int maxThreads = min(cl.getNumAtoms()*forceWorkgroupSize, cl.getEnergyBuffer().getSize());
        cl.executeKernel(forceKernel, maxThreads, forceWorkgroupSize);
6397
6398
6399
6400
6401
6402
6403
6404
6405
6406
6407
6408
6409
6410
        if (nonbondedMethod != NoCutoff) {
            // Make sure there was enough memory for the neighbor list.

            event.wait();
            if (*numPairs > maxNeighborPairs) {
                // Resize the arrays and run the calculation again.

                delete neighborPairs;
                neighborPairs = NULL;
                delete neighbors;
                neighbors = NULL;
                maxNeighborPairs = (int) (1.1*(*numPairs));
                neighborPairs = OpenCLArray::create<mm_int2>(cl, maxNeighborPairs, "customManyParticleNeighborPairs");
                neighbors = OpenCLArray::create<int>(cl, maxNeighborPairs, "customManyParticleNeighbors");
6411
6412
                forceKernel.setArg<cl::Buffer>(8, neighbors->getDeviceBuffer());
                neighborsKernel.setArg<cl::Buffer>(8, neighborPairs->getDeviceBuffer());
6413
6414
                copyPairsKernel.setArg<cl::Buffer>(0, neighborPairs->getDeviceBuffer());
                copyPairsKernel.setArg<cl::Buffer>(1, neighbors->getDeviceBuffer());
6415
6416
6417
6418
6419
6420
6421
6422
6423
6424
6425
6426
6427
6428
6429
6430
6431
6432
6433
6434
6435
6436
6437
6438
6439
6440
6441
6442
                continue;
            }
        }
        break;
    }
    return 0.0;
}

void OpenCLCalcCustomManyParticleForceKernel::copyParametersToContext(ContextImpl& context, const CustomManyParticleForce& force) {
    int numParticles = force.getNumParticles();
    if (numParticles != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    
    // Record the per-particle parameters.
    
    vector<vector<float> > paramVector(numParticles);
    vector<double> parameters;
    int type;
    for (int i = 0; i < numParticles; i++) {
        force.getParticleParameters(i, parameters, type);
        paramVector[i].resize(parameters.size());
        for (int j = 0; j < (int) parameters.size(); j++)
            paramVector[i][j] = (float) parameters[j];
    }
    params->setParameterValues(paramVector);
    
    // Mark that the current reordering may be invalid.
    
6443
    cl.invalidateMolecules(info);
6444
6445
}

6446
class OpenCLCalcGayBerneForceKernel::ForceInfo : public OpenCLForceInfo {
6447
public:
6448
    ForceInfo(int requiredBuffers, const GayBerneForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
6449
6450
6451
6452
6453
6454
6455
6456
6457
6458
6459
6460
6461
6462
6463
6464
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6466
6467
6468
6469
6470
6471
6472
6473
6474
6475
6476
6477
6478
6479
6480
6481
6482
6483
6484
6485
6486
6487
6488
6489
6490
6491
6492
6493
6494
6495
6496
6497
6498
6499
6500
6501
6502
6503
6504
6505
6506
6507
6508
6509
6510
6511
6512
6513
6514
6515
6516
6517
6518
6519
6520
6521
6522
6523
6524
6525
6526
6527
6528
6529
6530
6531
6532
6533
6534
6535
6536
6537
    }
    bool areParticlesIdentical(int particle1, int particle2) {
        int xparticle1, yparticle1;
        double sigma1, epsilon1, sx1, sy1, sz1, ex1, ey1, ez1;
        int xparticle2, yparticle2;
        double sigma2, epsilon2, sx2, sy2, sz2, ex2, ey2, ez2;
        force.getParticleParameters(particle1, sigma1, epsilon1, xparticle1, yparticle1, sx1, sy1, sz1, ex1, ey1, ez1);
        force.getParticleParameters(particle2, sigma2, epsilon2, xparticle2, yparticle2, sx2, sy2, sz2, ex2, ey2, ez2);
        return (sigma1 == sigma2 && epsilon1 == epsilon2 && sx1 == sx2 && sy1 == sy2 && sz1 == sz2 && ex1 == ex2 && ey1 == ey2 && ez1 == ez2);
    }
    int getNumParticleGroups() {
        return force.getNumExceptions()+force.getNumParticles();
    }
    void getParticlesInGroup(int index, vector<int>& particles) {
        if (index < force.getNumExceptions()) {
            int particle1, particle2;
            double sigma, epsilon;
            force.getExceptionParameters(index, particle1, particle2, sigma, epsilon);
            particles.resize(2);
            particles[0] = particle1;
            particles[1] = particle2;
        }
        else {
            int particle = index-force.getNumExceptions();
            int xparticle, yparticle;
            double sigma, epsilon, sx, sy, sz, ex, ey, ez;
            force.getParticleParameters(particle, sigma, epsilon, xparticle, yparticle, sx, sy, sz, ex, ey, ez);
            particles.clear();
            particles.push_back(particle);
            if (xparticle > -1)
                particles.push_back(xparticle);
            if (yparticle > -1)
                particles.push_back(yparticle);
        }
    }
    bool areGroupsIdentical(int group1, int group2) {
        if (group1 < force.getNumExceptions() && group2 < force.getNumExceptions()) {
            int particle1, particle2;
            double sigma1, sigma2, epsilon1, epsilon2;
            force.getExceptionParameters(group1, particle1, particle2, sigma1, epsilon1);
            force.getExceptionParameters(group2, particle1, particle2, sigma2, epsilon2);
            return (sigma1 == sigma2 && epsilon1 == epsilon2);
        }
        return true;
    }
private:
    const GayBerneForce& force;
};

class OpenCLCalcGayBerneForceKernel::ReorderListener : public OpenCLContext::ReorderListener {
public:
    ReorderListener(OpenCLCalcGayBerneForceKernel& owner) : owner(owner) {
    }
    void execute() {
        owner.sortAtoms();
    }
private:
    OpenCLCalcGayBerneForceKernel& owner;
};

OpenCLCalcGayBerneForceKernel::~OpenCLCalcGayBerneForceKernel() {
    if (sortedParticles != NULL)
        delete sortedParticles;
    if (axisParticleIndices != NULL)
        delete axisParticleIndices;
    if (sigParams != NULL)
        delete sigParams;
    if (epsParams != NULL)
        delete epsParams;
    if (scale != NULL)
        delete scale;
    if (exceptionParticles != NULL)
        delete exceptionParticles;
    if (exceptionParams != NULL)
        delete exceptionParams;
    if (aMatrix != NULL)
        delete aMatrix;
    if (bMatrix != NULL)
        delete bMatrix;
    if (gMatrix != NULL)
        delete gMatrix;
    if (exclusions != NULL)
        delete exclusions;
    if (exclusionStartIndex != NULL)
        delete exclusionStartIndex;
    if (blockCenter != NULL)
        delete blockCenter;
    if (blockBoundingBox != NULL)
        delete blockBoundingBox;
6538
6539
6540
6541
6542
6543
    if (neighbors != NULL)
        delete neighbors;
    if (neighborIndex != NULL)
        delete neighborIndex;
    if (neighborBlockCount != NULL)
        delete neighborBlockCount;
6544
6545
6546
6547
6548
6549
6550
    if (sortedPos != NULL)
        delete sortedPos;
    if (torque != NULL)
        delete torque;
}

void OpenCLCalcGayBerneForceKernel::initialize(const System& system, const GayBerneForce& force) {
6551
6552
    if (!cl.getSupports64BitGlobalAtomics())
        throw OpenMMException("GayBerneForce requires a device that supports 64 bit atomic operations");
6553
6554
6555
6556
6557
6558
6559
6560
6561
6562
6563
6564
6565
6566
6567
6568
6569
6570
6571
6572
6573
6574
6575
6576
6577

    // Initialize interactions.

    int numParticles = force.getNumParticles();
    sigParams = OpenCLArray::create<mm_float4>(cl, cl.getPaddedNumAtoms(), "sigParams");
    epsParams = OpenCLArray::create<mm_float2>(cl, cl.getPaddedNumAtoms(), "epsParams");
    scale = OpenCLArray::create<mm_float4>(cl, cl.getPaddedNumAtoms(), "scale");
    axisParticleIndices = OpenCLArray::create<mm_int2>(cl, cl.getPaddedNumAtoms(), "axisParticleIndices");
    sortedParticles = OpenCLArray::create<cl_int>(cl, cl.getPaddedNumAtoms(), "sortedParticles");
    aMatrix = OpenCLArray::create<cl_float>(cl, 9*cl.getPaddedNumAtoms(), "aMatrix");
    bMatrix = OpenCLArray::create<cl_float>(cl, 9*cl.getPaddedNumAtoms(), "bMatrix");
    gMatrix = OpenCLArray::create<cl_float>(cl, 9*cl.getPaddedNumAtoms(), "gMatrix");
    vector<mm_float4> sigParamsVector(cl.getPaddedNumAtoms(), mm_float4(0, 0, 0, 0));
    vector<mm_float2> epsParamsVector(cl.getPaddedNumAtoms(), mm_float2(0, 0));
    vector<mm_float4> scaleVector(cl.getPaddedNumAtoms(), mm_float4(0, 0, 0, 0));
    vector<mm_int2> axisParticleVector(cl.getPaddedNumAtoms(), mm_int2(0, 0));
    isRealParticle.resize(cl.getPaddedNumAtoms());
    for (int i = 0; i < numParticles; i++) {
        int xparticle, yparticle;
        double sigma, epsilon, sx, sy, sz, ex, ey, ez;
        force.getParticleParameters(i, sigma, epsilon, xparticle, yparticle, sx, sy, sz, ex, ey, ez);
        axisParticleVector[i] = mm_int2(xparticle, yparticle);
        sigParamsVector[i] = mm_float4((float) (0.5*sigma), (float) (0.25*sx*sx), (float) (0.25*sy*sy), (float) (0.25*sz*sz));
        epsParamsVector[i] = mm_float2((float) sqrt(epsilon), (float) (0.125*(sx*sy + sz*sz)*sqrt(sx*sy)));
        scaleVector[i] = mm_float4((float) (1/sqrt(ex)), (float) (1/sqrt(ey)), (float) (1/sqrt(ez)), 0);
6578
        isRealParticle[i] = (epsilon != 0.0);
6579
6580
6581
6582
6583
6584
    }
    sigParams->upload(sigParamsVector);
    epsParams->upload(epsParamsVector);
    scale->upload(scaleVector);
    axisParticleIndices->upload(axisParticleVector);
    
6585
6586
6587
6588
6589
6590
6591
6592
6593
6594
6595
6596
6597
6598
6599
6600
6601
6602
6603
6604
6605
6606
6607
6608
6609
6610
6611
6612
    // Record exceptions and exclusions.

    vector<mm_float2> exceptionParamsVec;
    for (int i = 0; i < force.getNumExceptions(); i++) {
        int particle1, particle2;
        double sigma, epsilon;
        force.getExceptionParameters(i, particle1, particle2, sigma, epsilon);
        if (epsilon != 0.0) {
            exceptionParamsVec.push_back(mm_float2((float) sigma, (float) epsilon));
            exceptionAtoms.push_back(make_pair(particle1, particle2));
            isRealParticle[particle1] = true;
            isRealParticle[particle2] = true;
        }
        if (isRealParticle[particle1] && isRealParticle[particle2])
            excludedPairs.push_back(pair<int, int>(particle1, particle2));
    }
    numRealParticles = 0;
    for (int i = 0; i < isRealParticle.size(); i++)
        if (isRealParticle[i])
            numRealParticles++;
    int numExceptions = exceptionParamsVec.size();
    exclusions = OpenCLArray::create<cl_int>(cl, max(1, (int) excludedPairs.size()), "exclusions");
    exclusionStartIndex = OpenCLArray::create<cl_int>(cl, numRealParticles+1, "exclusionStartIndex");
    exceptionParticles = OpenCLArray::create<mm_int4>(cl, max(1, numExceptions), "exceptionParticles");
    exceptionParams = OpenCLArray::create<mm_float2>(cl, max(1, numExceptions), "exceptionParams");
    if (numExceptions > 0)
        exceptionParams->upload(exceptionParamsVec);
    
6613
6614
6615
6616
6617
6618
6619
    // Create data structures used for the neighbor list.

    int numAtomBlocks = (numRealParticles+31)/32;
    int elementSize = (cl.getUseDoublePrecision() ? sizeof(cl_double) : sizeof(cl_float));
    blockCenter = new OpenCLArray(cl, numAtomBlocks, 4*elementSize, "blockCenter");
    blockBoundingBox = new OpenCLArray(cl, numAtomBlocks, 4*elementSize, "blockBoundingBox");
    sortedPos = new OpenCLArray(cl, numRealParticles, 4*elementSize, "sortedPos");
6620
6621
    maxNeighborBlocks = numRealParticles*2;
    neighbors = OpenCLArray::create<cl_int>(cl, maxNeighborBlocks*32, "neighbors");
6622
    neighborIndex = OpenCLArray::create<cl_int>(cl, maxNeighborBlocks, "neighborIndex");
6623
    neighborBlockCount = OpenCLArray::create<cl_int>(cl, 1, "neighborBlockCount");
6624

6625
    // Create array for accumulating torques.
6626
    
6627
    torque = OpenCLArray::create<cl_long>(cl, 3*cl.getPaddedNumAtoms(), "torque");
6628
6629
6630
6631
6632
6633
6634
6635
6636
    cl.addAutoclearBuffer(*torque);

    // Create the kernels.
    
    nonbondedMethod = force.getNonbondedMethod();
    bool useCutoff = (nonbondedMethod != GayBerneForce::NoCutoff);
    bool usePeriodic = (nonbondedMethod == GayBerneForce::CutoffPeriodic);
    map<string, string> defines;
    defines["USE_SWITCH"] = (useCutoff && force.getUseSwitchingFunction() ? "1" : "0");
6637
6638
    double cutoff = force.getCutoffDistance();
    defines["CUTOFF_SQUARED"] = cl.doubleToString(cutoff*cutoff);
6639
    if (useCutoff) {
6640
6641
6642
6643
        defines["USE_CUTOFF"] = 1;
        if (usePeriodic)
            defines["USE_PERIODIC"] = "1";
        
6644
6645
6646
6647
        // Compute the switching coefficients.
        
        if (force.getUseSwitchingFunction()) {
            defines["SWITCH_CUTOFF"] = cl.doubleToString(force.getSwitchingDistance());
6648
6649
6650
            defines["SWITCH_C3"] = cl.doubleToString(10/pow(force.getSwitchingDistance()-cutoff, 3.0));
            defines["SWITCH_C4"] = cl.doubleToString(15/pow(force.getSwitchingDistance()-cutoff, 4.0));
            defines["SWITCH_C5"] = cl.doubleToString(6/pow(force.getSwitchingDistance()-cutoff, 5.0));
6651
6652
        }
    }
6653
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
6654
6655
6656
6657
6658
    cl::Program program = cl.createProgram(OpenCLKernelSources::gayBerne, defines);
    framesKernel = cl::Kernel(program, "computeEllipsoidFrames");
    blockBoundsKernel = cl::Kernel(program, "findBlockBounds");
    neighborsKernel = cl::Kernel(program, "findNeighbors");
    forceKernel = cl::Kernel(program, "computeForce");
6659
    torqueKernel = cl::Kernel(program, "applyTorques");
6660
6661
    info = new ForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force);
    cl.addForce(info);
6662
6663
6664
6665
6666
6667
6668
6669
6670
6671
6672
6673
6674
6675
6676
6677
6678
6679
6680
6681
6682
6683
    cl.addReorderListener(new ReorderListener(*this));
}

double OpenCLCalcGayBerneForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        sortAtoms();
        framesKernel.setArg<cl_int>(0, numRealParticles);
        framesKernel.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
        framesKernel.setArg<cl::Buffer>(2, axisParticleIndices->getDeviceBuffer());
        framesKernel.setArg<cl::Buffer>(3, sigParams->getDeviceBuffer());
        framesKernel.setArg<cl::Buffer>(4, scale->getDeviceBuffer());
        framesKernel.setArg<cl::Buffer>(5, aMatrix->getDeviceBuffer());
        framesKernel.setArg<cl::Buffer>(6, bMatrix->getDeviceBuffer());
        framesKernel.setArg<cl::Buffer>(7, gMatrix->getDeviceBuffer());
        framesKernel.setArg<cl::Buffer>(8, sortedParticles->getDeviceBuffer());
        blockBoundsKernel.setArg<cl_int>(0, numRealParticles);
        blockBoundsKernel.setArg<cl::Buffer>(6, sortedParticles->getDeviceBuffer());
        blockBoundsKernel.setArg<cl::Buffer>(7, cl.getPosq().getDeviceBuffer());
        blockBoundsKernel.setArg<cl::Buffer>(8, sortedPos->getDeviceBuffer());
        blockBoundsKernel.setArg<cl::Buffer>(9, blockCenter->getDeviceBuffer());
        blockBoundsKernel.setArg<cl::Buffer>(10, blockBoundingBox->getDeviceBuffer());
6684
6685
6686
6687
6688
6689
6690
6691
6692
        blockBoundsKernel.setArg<cl::Buffer>(11, neighborBlockCount->getDeviceBuffer());
        neighborsKernel.setArg<cl_int>(0, numRealParticles);
        neighborsKernel.setArg<cl_int>(1, maxNeighborBlocks);
        neighborsKernel.setArg<cl::Buffer>(7, sortedPos->getDeviceBuffer());
        neighborsKernel.setArg<cl::Buffer>(8, blockCenter->getDeviceBuffer());
        neighborsKernel.setArg<cl::Buffer>(9, blockBoundingBox->getDeviceBuffer());
        neighborsKernel.setArg<cl::Buffer>(10, neighbors->getDeviceBuffer());
        neighborsKernel.setArg<cl::Buffer>(11, neighborIndex->getDeviceBuffer());
        neighborsKernel.setArg<cl::Buffer>(12, neighborBlockCount->getDeviceBuffer());
6693
6694
        neighborsKernel.setArg<cl::Buffer>(13, exclusions->getDeviceBuffer());
        neighborsKernel.setArg<cl::Buffer>(14, exclusionStartIndex->getDeviceBuffer());
6695
        int index = 0;
6696
        forceKernel.setArg<cl::Buffer>(index++, cl.getLongForceBuffer().getDeviceBuffer());
6697
6698
        forceKernel.setArg<cl::Buffer>(index++, torque->getDeviceBuffer());
        forceKernel.setArg<cl_int>(index++, numRealParticles);
6699
        forceKernel.setArg<cl_int>(index++, exceptionAtoms.size());
6700
6701
6702
6703
6704
6705
6706
6707
6708
6709
        forceKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, sortedPos->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, sigParams->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, epsParams->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, sortedParticles->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, aMatrix->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, bMatrix->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, gMatrix->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, exclusions->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, exclusionStartIndex->getDeviceBuffer());
6710
6711
        forceKernel.setArg<cl::Buffer>(index++, exceptionParticles->getDeviceBuffer());
        forceKernel.setArg<cl::Buffer>(index++, exceptionParams->getDeviceBuffer());
6712
6713
6714
6715
6716
6717
        if (nonbondedMethod != GayBerneForce::NoCutoff) {
            forceKernel.setArg<cl_int>(index++, maxNeighborBlocks);
            forceKernel.setArg<cl::Buffer>(index++, neighbors->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, neighborIndex->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(index++, neighborBlockCount->getDeviceBuffer());
        }
6718
        index = 0;
6719
        torqueKernel.setArg<cl::Buffer>(index++, cl.getLongForceBuffer().getDeviceBuffer());
6720
6721
6722
6723
6724
6725
6726
        torqueKernel.setArg<cl::Buffer>(index++, torque->getDeviceBuffer());
        torqueKernel.setArg<cl_int>(index++, numRealParticles);
        torqueKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
        torqueKernel.setArg<cl::Buffer>(index++, axisParticleIndices->getDeviceBuffer());
        torqueKernel.setArg<cl::Buffer>(index++, sortedParticles->getDeviceBuffer());
    }
    cl.executeKernel(framesKernel, numRealParticles);
6727
6728
    setPeriodicBoxArgs(cl, blockBoundsKernel, 1);
    cl.executeKernel(blockBoundsKernel, (numRealParticles+31)/32);
6729
6730
6731
6732
6733
6734
6735
6736
6737
6738
6739
6740
6741
6742
6743
6744
6745
6746
6747
6748
6749
6750
6751
6752
    if (nonbondedMethod == GayBerneForce::NoCutoff) {
        cl.executeKernel(forceKernel, cl.getNonbondedUtilities().getNumForceThreadBlocks()*cl.getNonbondedUtilities().getForceThreadBlockSize());
    }
    else {
        while (true) {
            setPeriodicBoxArgs(cl, neighborsKernel, 2);
            cl.executeKernel(neighborsKernel, numRealParticles);
            cl_int* count = (cl_int*) cl.getPinnedBuffer();
            cl::Event event;
            cl.getQueue().enqueueReadBuffer(neighborBlockCount->getDeviceBuffer(), CL_FALSE, 0, neighborBlockCount->getSize()*neighborBlockCount->getElementSize(), count, NULL, &event);
            setPeriodicBoxArgs(cl, forceKernel, 20);
            cl.executeKernel(forceKernel, cl.getNonbondedUtilities().getNumForceThreadBlocks()*cl.getNonbondedUtilities().getForceThreadBlockSize());
            event.wait();
            if (*count <= maxNeighborBlocks)
                break;
            
            // There wasn't enough room for the neighbor list, so we need to recreate it.

            delete neighbors;
            neighbors = NULL;
            delete neighborIndex;
            neighborIndex = NULL;
            maxNeighborBlocks = (int) ceil((*count)*1.1);
            neighbors = OpenCLArray::create<cl_int>(cl, maxNeighborBlocks*32, "neighbors");
6753
            neighborIndex = OpenCLArray::create<cl_int>(cl, maxNeighborBlocks, "neighborIndex");
6754
6755
6756
6757
6758
            neighborsKernel.setArg<cl::Buffer>(10, neighbors->getDeviceBuffer());
            neighborsKernel.setArg<cl::Buffer>(11, neighborIndex->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(17, neighbors->getDeviceBuffer());
            forceKernel.setArg<cl::Buffer>(18, neighborIndex->getDeviceBuffer());
        }
6759
    }
6760
    cl.executeKernel(torqueKernel, numRealParticles);
6761
6762
6763
6764
6765
6766
6767
6768
6769
6770
6771
6772
6773
6774
6775
6776
6777
6778
    return 0.0;
}

void OpenCLCalcGayBerneForceKernel::copyParametersToContext(ContextImpl& context, const GayBerneForce& force) {
    // Make sure the new parameters are acceptable.
    
    if (force.getNumParticles() != cl.getNumAtoms())
        throw OpenMMException("updateParametersInContext: The number of particles has changed");
    vector<int> exceptions;
    for (int i = 0; i < force.getNumExceptions(); i++) {
        int particle1, particle2;
        double sigma, epsilon;
        force.getExceptionParameters(i, particle1, particle2, sigma, epsilon);
        if (exceptionAtoms.size() > exceptions.size() && make_pair(particle1, particle2) == exceptionAtoms[exceptions.size()])
            exceptions.push_back(i);
        else if (epsilon != 0.0)
            throw OpenMMException("updateParametersInContext: The set of non-excluded exceptions has changed");
    }
6779
    int numExceptions = exceptionAtoms.size();
6780
6781
6782
6783
6784
6785
6786
6787
6788
6789
    
    // Record the per-particle parameters.
    
    vector<mm_float4> sigParamsVector(cl.getPaddedNumAtoms(), mm_float4(0, 0, 0, 0));
    vector<mm_float2> epsParamsVector(cl.getPaddedNumAtoms(), mm_float2(0, 0));
    vector<mm_float4> scaleVector(cl.getPaddedNumAtoms(), mm_float4(0, 0, 0, 0));
    for (int i = 0; i < force.getNumParticles(); i++) {
        int xparticle, yparticle;
        double sigma, epsilon, sx, sy, sz, ex, ey, ez;
        force.getParticleParameters(i, sigma, epsilon, xparticle, yparticle, sx, sy, sz, ex, ey, ez);
6790
        sigParamsVector[i] = mm_float4((float) (0.5*sigma), (float) (0.25*sx*sx), (float) (0.25*sy*sy), (float) (0.25*sz*sz));
6791
6792
        epsParamsVector[i] = mm_float2((float) sqrt(epsilon), (float) (0.125*(sx*sy + sz*sz)*sqrt(sx*sy)));
        scaleVector[i] = mm_float4((float) (1/sqrt(ex)), (float) (1/sqrt(ey)), (float) (1/sqrt(ez)), 0);
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        if (epsilon != 0.0 && !isRealParticle[i])
            throw OpenMMException("updateParametersInContext: The set of ignored particles (ones with epsilon=0) has changed");
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    }
    sigParams->upload(sigParamsVector);
    epsParams->upload(epsParamsVector);
    scale->upload(scaleVector);
    
    // Record the exceptions.
    
    if (numExceptions > 0) {
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        vector<mm_float2> exceptionParamsVec(numExceptions);
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        for (int i = 0; i < numExceptions; i++) {
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            int atom1, atom2;
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            double sigma, epsilon;
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            force.getExceptionParameters(exceptions[i], atom1, atom2, sigma, epsilon);
            exceptionParamsVec[i] = mm_float2((float) sigma, (float) epsilon);
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        }
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        exceptionParams->upload(exceptionParamsVec);
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    }
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    cl.invalidateMolecules(info);
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    sortAtoms();
}

void OpenCLCalcGayBerneForceKernel::sortAtoms() {
    // Sort the list of atoms by type to avoid thread divergence.  This is executed every time
    // the atoms are reordered.
    
    int nextIndex = 0;
    vector<cl_int> particles(cl.getPaddedNumAtoms(), 0);
    const vector<int>& order = cl.getAtomIndex();
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    vector<int> inverseOrder(order.size(), -1);
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    for (int i = 0; i < cl.getNumAtoms(); i++) {
        int atom = order[i];
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        if (isRealParticle[atom]) {
            inverseOrder[atom] = nextIndex;
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            particles[nextIndex++] = atom;
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        }
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    }
    sortedParticles->upload(particles);
    
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    // Update the list of exception particles.
    
    int numExceptions = exceptionAtoms.size();
    if (numExceptions > 0) {
        vector<mm_int4> exceptionParticlesVec(numExceptions);
        for (int i = 0; i < numExceptions; i++)
            exceptionParticlesVec[i] = mm_int4(exceptionAtoms[i].first, exceptionAtoms[i].second, inverseOrder[exceptionAtoms[i].first], inverseOrder[exceptionAtoms[i].second]);
        exceptionParticles->upload(exceptionParticlesVec);
    }
    
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    // Rebuild the list of exclusions.
    
    vector<vector<int> > excludedAtoms(numRealParticles);
    for (int i = 0; i < excludedPairs.size(); i++) {
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        int first = inverseOrder[min(excludedPairs[i].first, excludedPairs[i].second)];
        int second = inverseOrder[max(excludedPairs[i].first, excludedPairs[i].second)];
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        excludedAtoms[first].push_back(second);
    }
    int index = 0;
    vector<int> exclusionVec(exclusions->getSize());
    vector<int> startIndexVec(exclusionStartIndex->getSize());
    for (int i = 0; i < numRealParticles; i++) {
        startIndexVec[i] = index;
        for (int j = 0; j < excludedAtoms[i].size(); j++)
            exclusionVec[index++] = excludedAtoms[i][j];
    }
    startIndexVec[numRealParticles] = index;
    exclusions->upload(exclusionVec);
    exclusionStartIndex->upload(startIndexVec);
}

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OpenCLIntegrateVerletStepKernel::~OpenCLIntegrateVerletStepKernel() {
}

void OpenCLIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) {
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    cl.getPlatformData().initializeContexts(system);
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    cl::Program program = cl.createProgram(OpenCLKernelSources::verlet, "");
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    kernel1 = cl::Kernel(program, "integrateVerletPart1");
    kernel2 = cl::Kernel(program, "integrateVerletPart2");
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}

void OpenCLIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
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    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
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    int numAtoms = cl.getNumAtoms();
    double dt = integrator.getStepSize();
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    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        kernel1.setArg<cl_int>(0, numAtoms);
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        kernel1.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
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        kernel1.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
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        setPosqCorrectionArg(cl, kernel1, 3);
        kernel1.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(6, integration.getPosDelta().getDeviceBuffer());
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        kernel2.setArg<cl_int>(0, numAtoms);
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        kernel2.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
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        kernel2.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
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        setPosqCorrectionArg(cl, kernel2, 3);
        kernel2.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
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    }
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    cl.getIntegrationUtilities().setNextStepSize(dt);
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    // Call the first integration kernel.

    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

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    integration.applyConstraints(integrator.getConstraintTolerance());
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    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
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    integration.computeVirtualSites();
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    // Update the time and step count.

    cl.setTime(cl.getTime()+dt);
    cl.setStepCount(cl.getStepCount()+1);
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    cl.reorderAtoms();
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    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
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}

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double OpenCLIntegrateVerletStepKernel::computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}

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OpenCLIntegrateLangevinStepKernel::~OpenCLIntegrateLangevinStepKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
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    cl.getPlatformData().initializeContexts(system);
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    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    map<string, string> defines;
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    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
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    cl::Program program = cl.createProgram(OpenCLKernelSources::langevin, defines, "");
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    kernel1 = cl::Kernel(program, "integrateLangevinPart1");
    kernel2 = cl::Kernel(program, "integrateLangevinPart2");
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    params = new OpenCLArray(cl, 3, cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(cl_double) : sizeof(cl_float), "langevinParams");
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    prevStepSize = -1.0;
}

void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const LangevinIntegrator& integrator) {
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    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
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    int numAtoms = cl.getNumAtoms();
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    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
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        kernel1.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(3, params->getDeviceBuffer());
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        kernel1.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, integration.getRandom().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
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        setPosqCorrectionArg(cl, kernel2, 1);
        kernel2.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
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    }
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    double temperature = integrator.getTemperature();
    double friction = integrator.getFriction();
    double stepSize = integrator.getStepSize();
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    cl.getIntegrationUtilities().setNextStepSize(stepSize);
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    if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
        // Calculate the integration parameters.

        double kT = BOLTZ*temperature;
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        double vscale = exp(-stepSize*friction);
        double fscale = (friction == 0 ? stepSize : (1-vscale)/friction);
        double noisescale = sqrt(kT*(1-vscale*vscale));
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        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
            vector<cl_double> p(params->getSize());
            p[0] = vscale;
            p[1] = fscale;
            p[2] = noisescale;
            params->upload(p);
        }
        else {
            vector<cl_float> p(params->getSize());
            p[0] = (cl_float) vscale;
            p[1] = (cl_float) fscale;
            p[2] = (cl_float) noisescale;
            params->upload(p);
        }
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        prevTemp = temperature;
        prevFriction = friction;
        prevStepSize = stepSize;
    }

    // Call the first integration kernel.

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    kernel1.setArg<cl_uint>(6, integration.prepareRandomNumbers(cl.getPaddedNumAtoms()));
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    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

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    integration.applyConstraints(integrator.getConstraintTolerance());
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    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
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    integration.computeVirtualSites();
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    // Update the time and step count.

    cl.setTime(cl.getTime()+stepSize);
    cl.setStepCount(cl.getStepCount()+1);
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    cl.reorderAtoms();
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    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
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}
7017

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double OpenCLIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}

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OpenCLIntegrateBrownianStepKernel::~OpenCLIntegrateBrownianStepKernel() {
}

void OpenCLIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
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    cl.getPlatformData().initializeContexts(system);
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    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    map<string, string> defines;
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    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
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    cl::Program program = cl.createProgram(OpenCLKernelSources::brownian, defines, "");
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    kernel1 = cl::Kernel(program, "integrateBrownianPart1");
    kernel2 = cl::Kernel(program, "integrateBrownianPart2");
    prevStepSize = -1.0;
}

void OpenCLIntegrateBrownianStepKernel::execute(ContextImpl& context, const BrownianIntegrator& integrator) {
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    int numAtoms = cl.getNumAtoms();
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        kernel1.setArg<cl::Buffer>(2, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(3, integration.getPosDelta().getDeviceBuffer());
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        kernel1.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, integration.getRandom().getDeviceBuffer());
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        kernel2.setArg<cl::Buffer>(1, cl.getPosq().getDeviceBuffer());
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        setPosqCorrectionArg(cl, kernel2, 2);
        kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(4, integration.getPosDelta().getDeviceBuffer());
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    }
    double temperature = integrator.getTemperature();
    double friction = integrator.getFriction();
    double stepSize = integrator.getStepSize();
    if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
        double tau = (friction == 0.0 ? 0.0 : 1.0/friction);
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        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
            kernel1.setArg<cl_double>(0, tau*stepSize);
            kernel1.setArg<cl_double>(1, sqrt(2.0f*BOLTZ*temperature*stepSize*tau));
            kernel2.setArg<cl_double>(0, 1.0/stepSize);
        }
        else {
            kernel1.setArg<cl_float>(0, (cl_float) (tau*stepSize));
            kernel1.setArg<cl_float>(1, (cl_float) (sqrt(2.0f*BOLTZ*temperature*stepSize*tau)));
            kernel2.setArg<cl_float>(0, (cl_float) (1.0/stepSize));
        }
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        prevTemp = temperature;
        prevFriction = friction;
        prevStepSize = stepSize;
    }

    // Call the first integration kernel.

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    kernel1.setArg<cl_uint>(6, integration.prepareRandomNumbers(cl.getPaddedNumAtoms()));
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    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

    integration.applyConstraints(integrator.getConstraintTolerance());

    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
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    integration.computeVirtualSites();
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    // Update the time and step count.

    cl.setTime(cl.getTime()+stepSize);
    cl.setStepCount(cl.getStepCount()+1);
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    cl.reorderAtoms();
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    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
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}
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double OpenCLIntegrateBrownianStepKernel::computeKineticEnergy(ContextImpl& context, const BrownianIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0);
}

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OpenCLIntegrateVariableVerletStepKernel::~OpenCLIntegrateVariableVerletStepKernel() {
}

void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, const VariableVerletIntegrator& integrator) {
7105
    cl.getPlatformData().initializeContexts(system);
7106
    cl::Program program = cl.createProgram(OpenCLKernelSources::verlet, "");
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    kernel1 = cl::Kernel(program, "integrateVerletPart1");
    kernel2 = cl::Kernel(program, "integrateVerletPart2");
    selectSizeKernel = cl::Kernel(program, "selectVerletStepSize");
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    blockSize = min(min(256, system.getNumParticles()), (int) selectSizeKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(cl.getDevice()));
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}

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double OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
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    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
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    int numAtoms = cl.getNumAtoms();
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    bool useDouble = cl.getUseDoublePrecision() || cl.getUseMixedPrecision();
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    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        kernel1.setArg<cl_int>(0, numAtoms);
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        kernel1.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
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        kernel1.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
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        setPosqCorrectionArg(cl, kernel1, 3);
        kernel1.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(6, integration.getPosDelta().getDeviceBuffer());
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        kernel2.setArg<cl_int>(0, numAtoms);
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        kernel2.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
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        kernel2.setArg<cl::Buffer>(2, cl.getPosq().getDeviceBuffer());
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        setPosqCorrectionArg(cl, kernel2, 3);
        kernel2.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
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        selectSizeKernel.setArg<cl_int>(0, numAtoms);
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        selectSizeKernel.setArg<cl::Buffer>(3, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
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        selectSizeKernel.setArg<cl::Buffer>(4, cl.getVelm().getDeviceBuffer());
        selectSizeKernel.setArg<cl::Buffer>(5, cl.getForce().getDeviceBuffer());
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        int elementSize = (useDouble ? sizeof(cl_double) : sizeof(cl_float));
        selectSizeKernel.setArg(6, blockSize*elementSize, NULL);
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    }

    // Select the step size to use.

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    double maxStepSize = maxTime-cl.getTime();
    float maxStepSizeFloat = (float) maxStepSize;
    if (useDouble) {
        selectSizeKernel.setArg<cl_double>(1, maxStepSize);
        selectSizeKernel.setArg<cl_double>(2, integrator.getErrorTolerance());
    }
    else {
        selectSizeKernel.setArg<cl_float>(1, maxStepSizeFloat);
        selectSizeKernel.setArg<cl_float>(2, (cl_float) integrator.getErrorTolerance());
    }
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    cl.executeKernel(selectSizeKernel, blockSize, blockSize);

    // Call the first integration kernel.

    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

    integration.applyConstraints(integrator.getConstraintTolerance());

    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
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    integration.computeVirtualSites();
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    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
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    // Update the time and step count.

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    double dt = cl.getIntegrationUtilities().getLastStepSize();
    double time = cl.getTime()+dt;
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    if (useDouble) {
        if (dt == maxStepSize)
            time = maxTime; // Avoid round-off error
    }
    else {
        if (dt == maxStepSizeFloat)
            time = maxTime; // Avoid round-off error
    }
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    cl.setTime(time);
    cl.setStepCount(cl.getStepCount()+1);
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    cl.reorderAtoms();
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    return dt;
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}

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double OpenCLIntegrateVariableVerletStepKernel::computeKineticEnergy(ContextImpl& context, const VariableVerletIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}

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OpenCLIntegrateVariableLangevinStepKernel::~OpenCLIntegrateVariableLangevinStepKernel() {
    if (params != NULL)
        delete params;
}

void OpenCLIntegrateVariableLangevinStepKernel::initialize(const System& system, const VariableLangevinIntegrator& integrator) {
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    cl.getPlatformData().initializeContexts(system);
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    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    map<string, string> defines;
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    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = cl.intToString(cl.getPaddedNumAtoms());
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    cl::Program program = cl.createProgram(OpenCLKernelSources::langevin, defines, "");
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    kernel1 = cl::Kernel(program, "integrateLangevinPart1");
    kernel2 = cl::Kernel(program, "integrateLangevinPart2");
    selectSizeKernel = cl::Kernel(program, "selectLangevinStepSize");
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    params = new OpenCLArray(cl, 3, cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(cl_double) : sizeof(cl_float), "langevinParams");
Peter Eastman's avatar
Peter Eastman committed
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    blockSize = min(256, system.getNumParticles());
    blockSize = max(blockSize, params->getSize());
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    blockSize = min(blockSize, (int) selectSizeKernel.getWorkGroupInfo<CL_KERNEL_WORK_GROUP_SIZE>(cl.getDevice()));
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}

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double OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
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    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
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    int numAtoms = cl.getNumAtoms();
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    bool useDouble = cl.getUseDoublePrecision() || cl.getUseMixedPrecision();
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    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
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        kernel1.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(3, params->getDeviceBuffer());
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        kernel1.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, integration.getRandom().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
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        setPosqCorrectionArg(cl, kernel2, 1);
        kernel2.setArg<cl::Buffer>(2, integration.getPosDelta().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
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        selectSizeKernel.setArg<cl::Buffer>(4, integration.getStepSize().getDeviceBuffer());
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        selectSizeKernel.setArg<cl::Buffer>(5, cl.getVelm().getDeviceBuffer());
        selectSizeKernel.setArg<cl::Buffer>(6, cl.getForce().getDeviceBuffer());
        selectSizeKernel.setArg<cl::Buffer>(7, params->getDeviceBuffer());
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        int elementSize = (useDouble ? sizeof(cl_double) : sizeof(cl_float));
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        selectSizeKernel.setArg(8, params->getSize()*elementSize, NULL);
        selectSizeKernel.setArg(9, blockSize*elementSize, NULL);
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    }

    // Select the step size to use.

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    double maxStepSize = maxTime-cl.getTime();
    float maxStepSizeFloat = (float) maxStepSize;
    if (useDouble) {
        selectSizeKernel.setArg<cl_double>(0, maxStepSize);
        selectSizeKernel.setArg<cl_double>(1, integrator.getErrorTolerance());
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        selectSizeKernel.setArg<cl_double>(2, integrator.getFriction());
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        selectSizeKernel.setArg<cl_double>(3, BOLTZ*integrator.getTemperature());
    }
    else {
        selectSizeKernel.setArg<cl_float>(0, maxStepSizeFloat);
        selectSizeKernel.setArg<cl_float>(1, (cl_float) integrator.getErrorTolerance());
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        selectSizeKernel.setArg<cl_float>(2, (cl_float) integrator.getFriction());
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        selectSizeKernel.setArg<cl_float>(3, (cl_float) (BOLTZ*integrator.getTemperature()));
    }
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    cl.executeKernel(selectSizeKernel, blockSize, blockSize);

    // Call the first integration kernel.

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    kernel1.setArg<cl_uint>(6, integration.prepareRandomNumbers(cl.getPaddedNumAtoms()));
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    cl.executeKernel(kernel1, numAtoms);

    // Apply constraints.

    integration.applyConstraints(integrator.getConstraintTolerance());

    // Call the second integration kernel.

    cl.executeKernel(kernel2, numAtoms);
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    integration.computeVirtualSites();
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    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
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    // Update the time and step count.

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    double dt = cl.getIntegrationUtilities().getLastStepSize();
    double time = cl.getTime()+dt;
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    if (useDouble) {
        if (dt == maxStepSize)
            time = maxTime; // Avoid round-off error
    }
    else {
        if (dt == maxStepSizeFloat)
            time = maxTime; // Avoid round-off error
    }
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    cl.setTime(time);
    cl.setStepCount(cl.getStepCount()+1);
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    cl.reorderAtoms();
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    return dt;
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}

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double OpenCLIntegrateVariableLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const VariableLangevinIntegrator& integrator) {
    return cl.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}

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class OpenCLIntegrateCustomStepKernel::ReorderListener : public OpenCLContext::ReorderListener {
public:
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    ReorderListener(OpenCLContext& cl, OpenCLParameterSet& perDofValues, vector<vector<cl_float> >& localPerDofValuesFloat, vector<vector<cl_double> >& localPerDofValuesDouble, bool& deviceValuesAreCurrent) :
            cl(cl), perDofValues(perDofValues), localPerDofValuesFloat(localPerDofValuesFloat), localPerDofValuesDouble(localPerDofValuesDouble), deviceValuesAreCurrent(deviceValuesAreCurrent) {
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        int numAtoms = cl.getNumAtoms();
        lastAtomOrder.resize(numAtoms);
        for (int i = 0; i < numAtoms; i++)
            lastAtomOrder[i] = cl.getAtomIndex()[i];
    }
    void execute() {
        // Reorder the per-DOF variables to reflect the new atom order.

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        if (perDofValues.getNumParameters() == 0)
            return;
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        int numAtoms = cl.getNumAtoms();
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        const vector<int>& order = cl.getAtomIndex();
        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
            if (deviceValuesAreCurrent)
                perDofValues.getParameterValues(localPerDofValuesDouble);
            vector<vector<cl_double> > swap(3*numAtoms);
            for (int i = 0; i < numAtoms; i++) {
                swap[3*lastAtomOrder[i]] = localPerDofValuesDouble[3*i];
                swap[3*lastAtomOrder[i]+1] = localPerDofValuesDouble[3*i+1];
                swap[3*lastAtomOrder[i]+2] = localPerDofValuesDouble[3*i+2];
            }
            for (int i = 0; i < numAtoms; i++) {
                localPerDofValuesDouble[3*i] = swap[3*order[i]];
                localPerDofValuesDouble[3*i+1] = swap[3*order[i]+1];
                localPerDofValuesDouble[3*i+2] = swap[3*order[i]+2];
            }
            perDofValues.setParameterValues(localPerDofValuesDouble);
        }
        else {
            if (deviceValuesAreCurrent)
                perDofValues.getParameterValues(localPerDofValuesFloat);
            vector<vector<cl_float> > swap(3*numAtoms);
            for (int i = 0; i < numAtoms; i++) {
                swap[3*lastAtomOrder[i]] = localPerDofValuesFloat[3*i];
                swap[3*lastAtomOrder[i]+1] = localPerDofValuesFloat[3*i+1];
                swap[3*lastAtomOrder[i]+2] = localPerDofValuesFloat[3*i+2];
            }
            for (int i = 0; i < numAtoms; i++) {
                localPerDofValuesFloat[3*i] = swap[3*order[i]];
                localPerDofValuesFloat[3*i+1] = swap[3*order[i]+1];
                localPerDofValuesFloat[3*i+2] = swap[3*order[i]+2];
            }
            perDofValues.setParameterValues(localPerDofValuesFloat);
        }
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        for (int i = 0; i < numAtoms; i++)
            lastAtomOrder[i] = order[i];
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        deviceValuesAreCurrent = true;
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    }
private:
    OpenCLContext& cl;
    OpenCLParameterSet& perDofValues;
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    vector<vector<cl_float> >& localPerDofValuesFloat;
    vector<vector<cl_double> >& localPerDofValuesDouble;
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    bool& deviceValuesAreCurrent;
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    vector<int> lastAtomOrder;
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};

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class OpenCLIntegrateCustomStepKernel::DerivFunction : public CustomFunction {
public:
    DerivFunction(map<string, double>& energyParamDerivs, const string& param) : energyParamDerivs(energyParamDerivs), param(param) {
    }
    int getNumArguments() const {
        return 0;
    }
    double evaluate(const double* arguments) const {
        return energyParamDerivs[param];
    }
    double evaluateDerivative(const double* arguments, const int* derivOrder) const {
        return 0;
    }
    CustomFunction* clone() const {
        return new DerivFunction(energyParamDerivs, param);
    }
private:
    map<string, double>& energyParamDerivs;
    string param;
};

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OpenCLIntegrateCustomStepKernel::~OpenCLIntegrateCustomStepKernel() {
    if (globalValues != NULL)
        delete globalValues;
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    if (sumBuffer != NULL)
        delete sumBuffer;
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    if (summedValue != NULL)
        delete summedValue;
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    if (uniformRandoms != NULL)
        delete uniformRandoms;
    if (randomSeed != NULL)
        delete randomSeed;
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    if (perDofEnergyParamDerivs != NULL)
        delete perDofEnergyParamDerivs;
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    if (perDofValues != NULL)
        delete perDofValues;
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    for (map<int, OpenCLArray*>::iterator iter = savedForces.begin(); iter != savedForces.end(); ++iter)
        delete iter->second;
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}

void OpenCLIntegrateCustomStepKernel::initialize(const System& system, const CustomIntegrator& integrator) {
    cl.getPlatformData().initializeContexts(system);
    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    numGlobalVariables = integrator.getNumGlobalVariables();
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    int elementSize = (cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
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    sumBuffer = new OpenCLArray(cl, ((3*system.getNumParticles()+3)/4)*4, elementSize, "sumBuffer");
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    summedValue = new OpenCLArray(cl, 1, elementSize, "summedValue");
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    perDofValues = new OpenCLParameterSet(cl, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables", false, cl.getUseDoublePrecision() || cl.getUseMixedPrecision());
    cl.addReorderListener(new ReorderListener(cl, *perDofValues, localPerDofValuesFloat, localPerDofValuesDouble, deviceValuesAreCurrent));
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    SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
}

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string OpenCLIntegrateCustomStepKernel::createPerDofComputation(const string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator, const string& forceName, const string& energyName) {
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    const string suffixes[] = {".x", ".y", ".z"};
    string suffix = suffixes[component];
    map<string, Lepton::ParsedExpression> expressions;
    if (variable == "x")
        expressions["position"+suffix+" = "] = expr;
    else if (variable == "v")
        expressions["velocity"+suffix+" = "] = expr;
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    else if (variable == "")
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        expressions["sum[3*index+"+cl.intToString(component)+"] = "] = expr;
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    else {
        for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
            if (variable == integrator.getPerDofVariableName(i))
                expressions["perDof"+suffix.substr(1)+perDofValues->getParameterSuffix(i)+" = "] = expr;
    }
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    if (expressions.size() == 0)
        throw OpenMMException("Unknown per-DOF variable: "+variable);
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    map<string, string> variables;
    variables["x"] = "position"+suffix;
    variables["v"] = "velocity"+suffix;
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    variables[forceName] = "f"+suffix;
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    variables["gaussian"] = "gaussian"+suffix;
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    variables["uniform"] = "uniform"+suffix;
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    variables["m"] = "mass";
    variables["dt"] = "stepSize";
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    if (energyName != "")
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        variables[energyName] = "energy";
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    for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
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        variables[integrator.getGlobalVariableName(i)] = "globals["+cl.intToString(globalVariableIndex[i])+"]";
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    for (int i = 0; i < integrator.getNumPerDofVariables(); i++)
        variables[integrator.getPerDofVariableName(i)] = "perDof"+suffix.substr(1)+perDofValues->getParameterSuffix(i);
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    for (int i = 0; i < (int) parameterNames.size(); i++)
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        variables[parameterNames[i]] = "globals["+cl.intToString(parameterVariableIndex[i])+"]";
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    vector<const TabulatedFunction*> functions;
    vector<pair<string, string> > functionNames;
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    string tempType = (cl.getSupportsDoublePrecision() ? "double" : "float");
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    vector<pair<ExpressionTreeNode, string> > variableNodes;
    findExpressionsForDerivs(expr.getRootNode(), variableNodes);
    for (map<string, string>::const_iterator iter = variables.begin(); iter != variables.end(); ++iter)
        variableNodes.push_back(make_pair(ExpressionTreeNode(new Operation::Variable(iter->first)), iter->second));
    return cl.getExpressionUtilities().createExpressions(expressions, variableNodes, functions, functionNames, "temp"+cl.intToString(component)+"_", tempType);
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}

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void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {
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    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    int numAtoms = cl.getNumAtoms();
    int numSteps = integrator.getNumComputations();
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    bool useDouble = cl.getUseDoublePrecision() || cl.getUseMixedPrecision();
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    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
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        // Initialize various data structures.
        
        const map<string, double>& params = context.getParameters();
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        for (map<string, double>::const_iterator iter = params.begin(); iter != params.end(); ++iter)
            parameterNames.push_back(iter->first);
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        kernels.resize(integrator.getNumComputations());
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        requiredGaussian.resize(integrator.getNumComputations(), 0);
        requiredUniform.resize(integrator.getNumComputations(), 0);
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        needsGlobals.resize(numSteps, false);
        globalExpressions.resize(numSteps);
        stepType.resize(numSteps);
        stepTarget.resize(numSteps);
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        merged.resize(numSteps, false);
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        modifiesParameters = false;
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        map<string, string> defines;
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        defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
        defines["WORK_GROUP_SIZE"] = cl.intToString(OpenCLContext::ThreadBlockSize);
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        // Record information about all the computation steps.

        vector<string> variable(numSteps);
        vector<int> forceGroup;
        vector<vector<Lepton::ParsedExpression> > expression;
        CustomIntegratorUtilities::analyzeComputations(context, integrator, expression, comparisons, blockEnd, invalidatesForces, needsForces, needsEnergy, computeBothForceAndEnergy, forceGroup);
        for (int step = 0; step < numSteps; step++) {
            string expr;
            integrator.getComputationStep(step, stepType[step], variable[step], expr);
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            if (stepType[step] == CustomIntegrator::WhileBlockStart)
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                blockEnd[blockEnd[step]] = step; // Record where to branch back to.
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            if (stepType[step] == CustomIntegrator::ComputeGlobal || stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
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                for (int i = 0; i < (int) expression[step].size(); i++)
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                    globalExpressions[step].push_back(ParsedExpression(replaceDerivFunctions(expression[step][i].getRootNode(), context)).createCompiledExpression());
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        }
        for (int step = 0; step < numSteps; step++) {
            for (int i = 0; i < (int) globalExpressions[step].size(); i++)
                expressionSet.registerExpression(globalExpressions[step][i]);
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        }
        
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        // Record the indices for variables in the CompiledExpressionSet.
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        gaussianVariableIndex = expressionSet.getVariableIndex("gaussian");
        uniformVariableIndex = expressionSet.getVariableIndex("uniform");
        dtVariableIndex = expressionSet.getVariableIndex("dt");
        for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
            globalVariableIndex.push_back(expressionSet.getVariableIndex(integrator.getGlobalVariableName(i)));
        for (int i = 0; i < (int) parameterNames.size(); i++)
            parameterVariableIndex.push_back(expressionSet.getVariableIndex(parameterNames[i]));

        // Record the variable names and flags for the force and energy in each step.

        forceGroupFlags.resize(numSteps, -1);
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        vector<string> forceGroupName;
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        vector<string> energyGroupName;
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        for (int i = 0; i < 32; i++) {
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            stringstream fname;
            fname << "f" << i;
            forceGroupName.push_back(fname.str());
            stringstream ename;
            ename << "energy" << i;
            energyGroupName.push_back(ename.str());
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        }
        vector<string> forceName(numSteps, "f");
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        vector<string> energyName(numSteps, "energy");
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        stepEnergyVariableIndex.resize(numSteps, expressionSet.getVariableIndex("energy"));
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        for (int step = 0; step < numSteps; step++) {
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            if (needsForces[step] && forceGroup[step] > -1)
                forceName[step] = forceGroupName[forceGroup[step]];
            if (needsEnergy[step] && forceGroup[step] > -1) {
                energyName[step] = energyGroupName[forceGroup[step]];
                stepEnergyVariableIndex[step] = expressionSet.getVariableIndex(energyName[step]);
            }
            if (forceGroup[step] > -1)
                forceGroupFlags[step] = 1<<forceGroup[step];
            if (forceGroupFlags[step] == -2 && step > 0)
                forceGroupFlags[step] = forceGroupFlags[step-1];
            if (forceGroupFlags[step] != -2 && savedForces.find(forceGroupFlags[step]) == savedForces.end())
                savedForces[forceGroupFlags[step]] = new OpenCLArray(cl, cl.getForce().getSize(), cl.getForce().getElementSize(), "savedForces");
        }
        
        // Allocate space for storing global values, both on the host and the device.
        
        globalValuesFloat.resize(expressionSet.getNumVariables());
        globalValuesDouble.resize(expressionSet.getNumVariables());
        int elementSize = (cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
        globalValues = new OpenCLArray(cl, expressionSet.getNumVariables(), elementSize, "globalValues");
        for (int i = 0; i < integrator.getNumGlobalVariables(); i++) {
            globalValuesDouble[globalVariableIndex[i]] = initialGlobalVariables[i];
            expressionSet.setVariable(globalVariableIndex[i], initialGlobalVariables[i]);
        }
        for (int i = 0; i < (int) parameterVariableIndex.size(); i++) {
            double value = context.getParameter(parameterNames[i]);
            globalValuesDouble[parameterVariableIndex[i]] = value;
            expressionSet.setVariable(parameterVariableIndex[i], value);
        }
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        int numContextParams = context.getParameters().size();
        localPerDofEnergyParamDerivsFloat.resize(numContextParams);
        localPerDofEnergyParamDerivsDouble.resize(numContextParams);
        perDofEnergyParamDerivs = new OpenCLArray(cl, max(1, numContextParams), elementSize, "perDofEnergyParamDerivs");
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        // Record information about the targets of steps that will be stored in global variables.
        
        for (int step = 0; step < numSteps; step++) {
            if (stepType[step] == CustomIntegrator::ComputeGlobal || stepType[step] == CustomIntegrator::ComputeSum) {
                if (variable[step] == "dt")
                    stepTarget[step].type = DT;
                for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
                    if (variable[step] == integrator.getGlobalVariableName(i))
                        stepTarget[step].type = VARIABLE;
                for (int i = 0; i < (int) parameterNames.size(); i++)
                    if (variable[step] == parameterNames[i]) {
                        stepTarget[step].type = PARAMETER;
                        modifiesParameters = true;
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                    }
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                stepTarget[step].variableIndex = expressionSet.getVariableIndex(variable[step]);
            }
        }

        // Identify which per-DOF steps are going to require global variables or context parameters.

        for (int step = 0; step < numSteps; step++) {
            if (stepType[step] == CustomIntegrator::ComputePerDof || stepType[step] == CustomIntegrator::ComputeSum) {
                for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
                    if (usesVariable(expression[step][0], integrator.getGlobalVariableName(i)))
                        needsGlobals[step] = true;
                for (int i = 0; i < (int) parameterNames.size(); i++)
                    if (usesVariable(expression[step][0], parameterNames[i]))
                        needsGlobals[step] = true;
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            }
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        }
        
        // Determine how each step will represent the position (as just a value, or a value plus a delta).
        
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        hasAnyConstraints = (context.getSystem().getNumConstraints() > 0);
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        vector<bool> storePosAsDelta(numSteps, false);
        vector<bool> loadPosAsDelta(numSteps, false);
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        if (hasAnyConstraints) {
            bool beforeConstrain = false;
            for (int step = numSteps-1; step >= 0; step--) {
                if (stepType[step] == CustomIntegrator::ConstrainPositions)
                    beforeConstrain = true;
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                else if (stepType[step] == CustomIntegrator::ComputePerDof && variable[step] == "x" && beforeConstrain) {
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                    storePosAsDelta[step] = true;
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                    beforeConstrain = false;
                }
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            }
            bool storedAsDelta = false;
            for (int step = 0; step < numSteps; step++) {
                loadPosAsDelta[step] = storedAsDelta;
                if (storePosAsDelta[step] == true)
                    storedAsDelta = true;
                if (stepType[step] == CustomIntegrator::ConstrainPositions)
                    storedAsDelta = false;
            }
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        }
        
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        // Identify steps that can be merged into a single kernel.
        
        for (int step = 1; step < numSteps; step++) {
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            if (invalidatesForces[step-1] || forceGroupFlags[step] != forceGroupFlags[step-1])
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                continue;
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            if (stepType[step-1] == CustomIntegrator::ComputePerDof && stepType[step] == CustomIntegrator::ComputePerDof)
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                merged[step] = true;
        }
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        for (int step = numSteps-1; step > 0; step--)
            if (merged[step]) {
                needsForces[step-1] = (needsForces[step] || needsForces[step-1]);
                needsEnergy[step-1] = (needsEnergy[step] || needsEnergy[step-1]);
                needsGlobals[step-1] = (needsGlobals[step] || needsGlobals[step-1]);
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                computeBothForceAndEnergy[step-1] = (computeBothForceAndEnergy[step] || computeBothForceAndEnergy[step-1]);
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            }
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        // Loop over all steps and create the kernels for them.
        
        for (int step = 0; step < numSteps; step++) {
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            if ((stepType[step] == CustomIntegrator::ComputePerDof || stepType[step] == CustomIntegrator::ComputeSum) && !merged[step]) {
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                // Compute a per-DOF value.
                
                stringstream compute;
                for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
                    const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
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                    compute << buffer.getType()<<" perDofx"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index];\n";
                    compute << buffer.getType()<<" perDofy"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index+1];\n";
                    compute << buffer.getType()<<" perDofz"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index+2];\n";
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                }
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                int numGaussian = 0, numUniform = 0;
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                for (int j = step; j < numSteps && (j == step || merged[j]); j++) {
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                    numGaussian += numAtoms*usesVariable(expression[j][0], "gaussian");
                    numUniform += numAtoms*usesVariable(expression[j][0], "uniform");
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                    compute << "{\n";
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                    if (numGaussian > 0)
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                        compute << "float4 gaussian = gaussianValues[gaussianIndex+index];\n";
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                    if (numUniform > 0)
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                        compute << "float4 uniform = uniformValues[uniformIndex+index];\n";
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                    for (int i = 0; i < 3; i++)
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                        compute << createPerDofComputation(stepType[j] == CustomIntegrator::ComputePerDof ? variable[j] : "", expression[j][0], i, integrator, forceName[j], energyName[j]);
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                    if (variable[j] == "x") {
                        if (storePosAsDelta[j]) {
                            if (cl.getSupportsDoublePrecision())
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                                compute << "posDelta[index] = convert_mixed4(convert_double4(position)-convert_double4(loadPos(posq, posqCorrection, index)));\n";
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                            else
                                compute << "posDelta[index] = position-posq[index];\n";
                        }
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                        else
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                            compute << "storePos(posq, posqCorrection, index, position);\n";
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                    }
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                    else if (variable[j] == "v")
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                        compute << "velm[index] = convert_mixed4(velocity);\n";
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                    else {
                        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
                            const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
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                            compute << "perDofValues"<<cl.intToString(i+1)<<"[3*index] = perDofx"<<cl.intToString(i+1)<<";\n";
                            compute << "perDofValues"<<cl.intToString(i+1)<<"[3*index+1] = perDofy"<<cl.intToString(i+1)<<";\n";
                            compute << "perDofValues"<<cl.intToString(i+1)<<"[3*index+2] = perDofz"<<cl.intToString(i+1)<<";\n";
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                        }
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                    }
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                    if (numGaussian > 0)
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                        compute << "gaussianIndex += NUM_ATOMS;\n";
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                    if (numUniform > 0)
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                        compute << "uniformIndex += NUM_ATOMS;\n";
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                    compute << "}\n";
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                }
                map<string, string> replacements;
                replacements["COMPUTE_STEP"] = compute.str();
                stringstream args;
                for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
                    const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
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                    string valueName = "perDofValues"+cl.intToString(i+1);
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                    args << ", __global " << buffer.getType() << "* restrict " << valueName;
                }
                replacements["PARAMETER_ARGUMENTS"] = args.str();
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                if (loadPosAsDelta[step])
                    defines["LOAD_POS_AS_DELTA"] = "1";
                else if (defines.find("LOAD_POS_AS_DELTA") != defines.end())
                    defines.erase("LOAD_POS_AS_DELTA");
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                cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customIntegratorPerDof, replacements), defines);
                cl::Kernel kernel = cl::Kernel(program, "computePerDof");
                kernels[step].push_back(kernel);
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                requiredGaussian[step] = numGaussian;
                requiredUniform[step] = numUniform;
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                int index = 0;
                kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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                setPosqCorrectionArg(cl, kernel, index++);
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                kernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, cl.getVelm().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, cl.getForce().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, integration.getStepSize().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
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                kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
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                index += 4;
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                kernel.setArg<cl::Buffer>(index++, perDofEnergyParamDerivs->getDeviceBuffer());
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                for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
                    kernel.setArg<cl::Memory>(index++, perDofValues->getBuffers()[i].getMemory());
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                if (stepType[step] == CustomIntegrator::ComputeSum) {
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                    // Create a second kernel for this step that sums the values.

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                    program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
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                    kernel = cl::Kernel(program, useDouble ? "computeDoubleSum" : "computeFloatSum");
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                    kernels[step].push_back(kernel);
                    index = 0;
                    kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
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                    kernel.setArg<cl::Buffer>(index++, summedValue->getDeviceBuffer());
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                    kernel.setArg<cl_int>(index++, 3*numAtoms);
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                }
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            }
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            else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
                // Apply position constraints.

                cl::Program program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
                cl::Kernel kernel = cl::Kernel(program, "applyPositionDeltas");
                kernels[step].push_back(kernel);
                int index = 0;
                kernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
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                setPosqCorrectionArg(cl, kernel, index++);
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                kernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
            }
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        }
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        // Initialize the random number generator.
        
        int maxUniformRandoms = 1;
        for (int i = 0; i < (int) requiredUniform.size(); i++)
            maxUniformRandoms = max(maxUniformRandoms, requiredUniform[i]);
        uniformRandoms = OpenCLArray::create<mm_float4>(cl, maxUniformRandoms, "uniformRandoms");
        randomSeed = OpenCLArray::create<mm_int4>(cl, cl.getNumThreadBlocks()*OpenCLContext::ThreadBlockSize, "randomSeed");
        vector<mm_int4> seed(randomSeed->getSize());
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        int rseed = integrator.getRandomNumberSeed();
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        // A random seed of 0 means use a unique one
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        if (rseed == 0)
            rseed = osrngseed();
        unsigned int r = (unsigned int) (rseed+1);
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        for (int i = 0; i < randomSeed->getSize(); i++) {
            seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
            seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
            seed[i].z = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
            seed[i].w = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
        }
        randomSeed->upload(seed);
        cl::Program randomProgram = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
        randomKernel = cl::Kernel(randomProgram, "generateRandomNumbers");
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        randomKernel.setArg<cl_int>(0, maxUniformRandoms);
        randomKernel.setArg<cl::Buffer>(1, uniformRandoms->getDeviceBuffer());
        randomKernel.setArg<cl::Buffer>(2, randomSeed->getDeviceBuffer());
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        // Create the kernel for computing kinetic energy.

        stringstream computeKE;
        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
            computeKE << buffer.getType()<<" perDofx"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index];\n";
            computeKE << buffer.getType()<<" perDofy"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index+1];\n";
            computeKE << buffer.getType()<<" perDofz"<<cl.intToString(i+1)<<" = perDofValues"<<cl.intToString(i+1)<<"[3*index+2];\n";
        }
        Lepton::ParsedExpression keExpression = Lepton::Parser::parse(integrator.getKineticEnergyExpression()).optimize();
        for (int i = 0; i < 3; i++)
            computeKE << createPerDofComputation("", keExpression, i, integrator, "f", "");
        map<string, string> replacements;
        replacements["COMPUTE_STEP"] = computeKE.str();
        stringstream args;
        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
            string valueName = "perDofValues"+cl.intToString(i+1);
            args << ", __global " << buffer.getType() << "* restrict " << valueName;
        }
        replacements["PARAMETER_ARGUMENTS"] = args.str();
        if (defines.find("LOAD_POS_AS_DELTA") != defines.end())
            defines.erase("LOAD_POS_AS_DELTA");
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        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customIntegratorPerDof, replacements), defines);
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        kineticEnergyKernel = cl::Kernel(program, "computePerDof");
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        int index = 0;
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        kineticEnergyKernel.setArg<cl::Buffer>(index++, cl.getPosq().getDeviceBuffer());
        setPosqCorrectionArg(cl, kineticEnergyKernel, index++);
        kineticEnergyKernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, cl.getVelm().getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, cl.getForce().getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, integration.getStepSize().getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
        kineticEnergyKernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
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        index += 2;
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        kineticEnergyKernel.setArg<cl::Buffer>(index++, uniformRandoms->getDeviceBuffer());
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        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision())
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            kineticEnergyKernel.setArg<cl_double>(index++, 0.0);
        else
            kineticEnergyKernel.setArg<cl_float>(index++, 0.0f);
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        kineticEnergyKernel.setArg<cl::Buffer>(index++, perDofEnergyParamDerivs->getDeviceBuffer());
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        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++)
            kineticEnergyKernel.setArg<cl::Memory>(index++, perDofValues->getBuffers()[i].getMemory());
        keNeedsForce = usesVariable(keExpression, "f");

        // Create a second kernel to sum the values.

        program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
        sumKineticEnergyKernel = cl::Kernel(program, useDouble ? "computeDoubleSum" : "computeFloatSum");
        index = 0;
        sumKineticEnergyKernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
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        sumKineticEnergyKernel.setArg<cl::Buffer>(index++, summedValue->getDeviceBuffer());
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        sumKineticEnergyKernel.setArg<cl_int>(index++, 3*numAtoms);
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    }
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    // Make sure all values (variables, parameters, etc.) are up to date.
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    if (!deviceValuesAreCurrent) {
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        if (useDouble)
            perDofValues->setParameterValues(localPerDofValuesDouble);
        else
            perDofValues->setParameterValues(localPerDofValuesFloat);
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        deviceValuesAreCurrent = true;
    }
    localValuesAreCurrent = false;
    double stepSize = integrator.getStepSize();
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    recordGlobalValue(stepSize, GlobalTarget(DT, dtVariableIndex), integrator);
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    for (int i = 0; i < (int) parameterNames.size(); i++) {
        double value = context.getParameter(parameterNames[i]);
        if (value != globalValuesDouble[parameterVariableIndex[i]]) {
            globalValuesDouble[parameterVariableIndex[i]] = value;
            deviceGlobalsAreCurrent = false;
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        }
    }
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}
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ExpressionTreeNode OpenCLIntegrateCustomStepKernel::replaceDerivFunctions(const ExpressionTreeNode& node, ContextImpl& context) {
    // This is called recursively to identify calls to the deriv() function inside global expressions,
    // and replace them with a custom function that returns the correct value.
    
    const Operation& op = node.getOperation();
    if (op.getId() == Operation::CUSTOM && op.getName() == "deriv") {
        string param = node.getChildren()[1].getOperation().getName();
        if (context.getParameters().find(param) == context.getParameters().end())
            throw OpenMMException("The second argument to deriv() must be a context parameter");
        needsEnergyParamDerivs = true;
        return ExpressionTreeNode(new Operation::Custom("deriv", new DerivFunction(energyParamDerivs, param)));
    }
    else {
        vector<ExpressionTreeNode> children;
        for (int i = 0; i < (int) node.getChildren().size(); i++)
            children.push_back(replaceDerivFunctions(node.getChildren()[i], context));
        return ExpressionTreeNode(op.clone(), children);
    }
}

void OpenCLIntegrateCustomStepKernel::findExpressionsForDerivs(const ExpressionTreeNode& node, vector<pair<ExpressionTreeNode, string> >& variableNodes) {
    // This is called recursively to identify calls to the deriv() function inside per-DOF expressions,
    // and record the code to replace them with.
    
    const Operation& op = node.getOperation();
    if (op.getId() == Operation::CUSTOM && op.getName() == "deriv") {
        string param = node.getChildren()[1].getOperation().getName();
        int index;
        for (index = 0; index < perDofEnergyParamDerivNames.size() && param != perDofEnergyParamDerivNames[index]; index++)
            ;
        if (index == perDofEnergyParamDerivNames.size())
            perDofEnergyParamDerivNames.push_back(param);
        variableNodes.push_back(make_pair(node, "energyParamDerivs["+cl.intToString(index)+"]"));
        needsEnergyParamDerivs = true;
    }
    else {
        for (int i = 0; i < (int) node.getChildren().size(); i++)
            findExpressionsForDerivs(node.getChildren()[i], variableNodes);
    }
}

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void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {
    prepareForComputation(context, integrator, forcesAreValid);
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    int numAtoms = cl.getNumAtoms();
    int numSteps = integrator.getNumComputations();
    
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    // Loop over computation steps in the integrator and execute them.

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    for (int step = 0; step < numSteps; ) {
        int nextStep = step+1;
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        int lastForceGroups = context.getLastForceGroups();
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        if ((needsForces[step] || needsEnergy[step]) && (!forcesAreValid || lastForceGroups != forceGroupFlags[step])) {
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            if (forcesAreValid && savedForces.find(lastForceGroups) != savedForces.end()) {
                // The forces are still valid.  We just need a different force group right now.  Save the old
                // forces in case we need them again.
                
                cl.getForce().copyTo(*savedForces[lastForceGroups]);
                validSavedForces.insert(lastForceGroups);
            }
            else
                validSavedForces.clear();
            
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            // Recompute forces and/or energy.  Figure out what is actually needed
            // between now and the next time they get invalidated again.
            
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            bool computeForce = (needsForces[step] || computeBothForceAndEnergy[step]);
            bool computeEnergy = (needsEnergy[step] || computeBothForceAndEnergy[step]);
            if (!computeEnergy && validSavedForces.find(forceGroupFlags[step]) != validSavedForces.end()) {
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                // We can just restore the forces we saved earlier.
                
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                savedForces[forceGroupFlags[step]]->copyTo(cl.getForce());
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            }
            else {
                recordChangedParameters(context);
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                energy = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
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                if (needsEnergyParamDerivs) {
                    context.getEnergyParameterDerivatives(energyParamDerivs);
                    if (perDofEnergyParamDerivNames.size() > 0) {
                        if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
                            for (int i = 0; i < perDofEnergyParamDerivNames.size(); i++)
                                localPerDofEnergyParamDerivsDouble[i] = energyParamDerivs[perDofEnergyParamDerivNames[i]];
                            perDofEnergyParamDerivs->upload(localPerDofEnergyParamDerivsDouble);
                        }
                        else {
                            for (int i = 0; i < perDofEnergyParamDerivNames.size(); i++)
                                localPerDofEnergyParamDerivsFloat[i] = (float) energyParamDerivs[perDofEnergyParamDerivNames[i]];
                            perDofEnergyParamDerivs->upload(localPerDofEnergyParamDerivsFloat);
                        }
                    }
                }
                forcesAreValid = true;
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            }
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        }
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        if (needsGlobals[step] && !deviceGlobalsAreCurrent) {
            // Upload the global values to the device.
            
            if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision())
                globalValues->upload(globalValuesDouble);
            else {
                for (int j = 0; j < (int) globalValuesDouble.size(); j++)
                    globalValuesFloat[j] = (float) globalValuesDouble[j];
                globalValues->upload(globalValuesFloat);
            }
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        }
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        if (stepType[step] == CustomIntegrator::ComputePerDof && !merged[step]) {
            kernels[step][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredGaussian[step]));
            kernels[step][0].setArg<cl::Buffer>(8, integration.getRandom().getDeviceBuffer());
            kernels[step][0].setArg<cl::Buffer>(10, uniformRandoms->getDeviceBuffer());
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            if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision())
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                kernels[step][0].setArg<cl_double>(11, energy);
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            else
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                kernels[step][0].setArg<cl_float>(11, (cl_float) energy);
            if (requiredUniform[step] > 0)
                cl.executeKernel(randomKernel, numAtoms);
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            cl.executeKernel(kernels[step][0], numAtoms, 128);
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        }
        else if (stepType[step] == CustomIntegrator::ComputeGlobal) {
            expressionSet.setVariable(uniformVariableIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
            expressionSet.setVariable(gaussianVariableIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
            expressionSet.setVariable(stepEnergyVariableIndex[step], energy);
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            recordGlobalValue(globalExpressions[step][0].evaluate(), stepTarget[step], integrator);
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        }
        else if (stepType[step] == CustomIntegrator::ComputeSum) {
            kernels[step][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredGaussian[step]));
            kernels[step][0].setArg<cl::Buffer>(8, integration.getRandom().getDeviceBuffer());
            kernels[step][0].setArg<cl::Buffer>(10, uniformRandoms->getDeviceBuffer());
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            if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision())
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                kernels[step][0].setArg<cl_double>(11, energy);
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            else
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                kernels[step][0].setArg<cl_float>(11, (cl_float) energy);
            if (requiredUniform[step] > 0)
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                cl.executeKernel(randomKernel, numAtoms);
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            cl.clearBuffer(*sumBuffer);
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            cl.executeKernel(kernels[step][0], numAtoms, 128);
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            cl.executeKernel(kernels[step][1], OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
            if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
                double value;
                summedValue->download(&value);
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                recordGlobalValue(value, stepTarget[step], integrator);
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            }
            else {
                float value;
                summedValue->download(&value);
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                recordGlobalValue(value, stepTarget[step], integrator);
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            }
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        }
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        else if (stepType[step] == CustomIntegrator::UpdateContextState) {
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            recordChangedParameters(context);
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            context.updateContextState();
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        }
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        else if (stepType[step] == CustomIntegrator::ConstrainPositions) {
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            if (hasAnyConstraints) {
                cl.getIntegrationUtilities().applyConstraints(integrator.getConstraintTolerance());
                cl.executeKernel(kernels[step][0], numAtoms);
            }
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            cl.getIntegrationUtilities().computeVirtualSites();
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        }
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        else if (stepType[step] == CustomIntegrator::ConstrainVelocities) {
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            cl.getIntegrationUtilities().applyVelocityConstraints(integrator.getConstraintTolerance());
        }
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        else if (stepType[step] == CustomIntegrator::IfBlockStart) {
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            if (!evaluateCondition(step))
                nextStep = blockEnd[step]+1;
        }
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        else if (stepType[step] == CustomIntegrator::WhileBlockStart) {
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            if (!evaluateCondition(step))
                nextStep = blockEnd[step]+1;
        }
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        else if (stepType[step] == CustomIntegrator::BlockEnd) {
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            if (blockEnd[step] != -1)
                nextStep = blockEnd[step]; // Return to the start of a while block.
        }
        if (invalidatesForces[step])
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            forcesAreValid = false;
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        step = nextStep;
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    }
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    recordChangedParameters(context);
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    // Update the time and step count.

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    cl.setTime(cl.getTime()+integrator.getStepSize());
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    cl.setStepCount(cl.getStepCount()+1);
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    cl.reorderAtoms();
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    if (cl.getAtomsWereReordered()) {
        forcesAreValid = false;
        validSavedForces.clear();
    }
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    // Reduce UI lag.
    
#ifdef WIN32
    cl.getQueue().flush();
#endif
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}

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bool OpenCLIntegrateCustomStepKernel::evaluateCondition(int step) {
    expressionSet.setVariable(uniformVariableIndex, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
    expressionSet.setVariable(gaussianVariableIndex, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
    expressionSet.setVariable(stepEnergyVariableIndex[step], energy);
    double lhs = globalExpressions[step][0].evaluate();
    double rhs = globalExpressions[step][1].evaluate();
    switch (comparisons[step]) {
        case CustomIntegratorUtilities::EQUAL:
            return (lhs == rhs);
        case CustomIntegratorUtilities::LESS_THAN:
            return (lhs < rhs);
        case CustomIntegratorUtilities::GREATER_THAN:
            return (lhs > rhs);
        case CustomIntegratorUtilities::NOT_EQUAL:
            return (lhs != rhs);
        case CustomIntegratorUtilities::LESS_THAN_OR_EQUAL:
            return (lhs <= rhs);
        case CustomIntegratorUtilities::GREATER_THAN_OR_EQUAL:
            return (lhs >= rhs);
    }
    throw OpenMMException("Invalid comparison operator");
}

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double OpenCLIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {
    prepareForComputation(context, integrator, forcesAreValid);
    if (keNeedsForce && !forcesAreValid) {
        // Compute the force.  We want to then mark that forces are valid, which means also computing
        // potential energy if any steps will expect it to be valid too.
        
        bool willNeedEnergy = false;
        for (int i = 0; i < integrator.getNumComputations(); i++)
            willNeedEnergy |= needsEnergy[i];
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        energy = context.calcForcesAndEnergy(true, willNeedEnergy, -1);
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        forcesAreValid = true;
    }
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    cl.clearBuffer(*sumBuffer);
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    kineticEnergyKernel.setArg<cl::Buffer>(8, cl.getIntegrationUtilities().getRandom().getDeviceBuffer());
    kineticEnergyKernel.setArg<cl_uint>(9, 0);
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    cl.executeKernel(kineticEnergyKernel, cl.getNumAtoms());
    cl.executeKernel(sumKineticEnergyKernel, OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        double ke;
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        summedValue->download(&ke);
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        return ke;
    }
    else {
        float ke;
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        summedValue->download(&ke);
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        return ke;
    }
}

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void OpenCLIntegrateCustomStepKernel::recordGlobalValue(double value, GlobalTarget target, CustomIntegrator& integrator) {
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    switch (target.type) {
        case DT:
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            if (value != globalValuesDouble[dtVariableIndex])
                deviceGlobalsAreCurrent = false;
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            expressionSet.setVariable(dtVariableIndex, value);
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            globalValuesDouble[dtVariableIndex] = value;
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            cl.getIntegrationUtilities().setNextStepSize(value);
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            integrator.setStepSize(value);
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            break;
        case VARIABLE:
        case PARAMETER:
            expressionSet.setVariable(target.variableIndex, value);
            globalValuesDouble[target.variableIndex] = value;
            deviceGlobalsAreCurrent = false;
            break;
    }
}

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void OpenCLIntegrateCustomStepKernel::recordChangedParameters(ContextImpl& context) {
    if (!modifiesParameters)
        return;
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    for (int i = 0; i < (int) parameterNames.size(); i++) {
        double value = context.getParameter(parameterNames[i]);
        if (value != globalValuesDouble[parameterVariableIndex[i]])
            context.setParameter(parameterNames[i], globalValuesDouble[parameterVariableIndex[i]]);
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    }
}

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void OpenCLIntegrateCustomStepKernel::getGlobalVariables(ContextImpl& context, vector<double>& values) const {
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    if (globalValues == NULL) {
        // The data structures haven't been created yet, so just return the list of values that was given earlier.
        
        values = initialGlobalVariables;
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    }
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    values.resize(numGlobalVariables);
    for (int i = 0; i < numGlobalVariables; i++)
        values[i] = globalValuesDouble[globalVariableIndex[i]];
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}

void OpenCLIntegrateCustomStepKernel::setGlobalVariables(ContextImpl& context, const vector<double>& values) {
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    if (numGlobalVariables == 0)
        return;
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    if (globalValues == NULL) {
        // The data structures haven't been created yet, so just store the list of values.
        
        initialGlobalVariables = values;
        return;
    }
    for (int i = 0; i < numGlobalVariables; i++) {
        globalValuesDouble[globalVariableIndex[i]] = values[i];
        expressionSet.setVariable(globalVariableIndex[i], values[i]);
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    }
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    deviceGlobalsAreCurrent = false;
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}

void OpenCLIntegrateCustomStepKernel::getPerDofVariable(ContextImpl& context, int variable, vector<Vec3>& values) const {
    values.resize(perDofValues->getNumObjects()/3);
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    const vector<int>& order = cl.getAtomIndex();
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        if (!localValuesAreCurrent) {
            perDofValues->getParameterValues(localPerDofValuesDouble);
            localValuesAreCurrent = true;
        }
        for (int i = 0; i < (int) values.size(); i++)
            for (int j = 0; j < 3; j++)
                values[order[i]][j] = localPerDofValuesDouble[3*i+j][variable];
    }
    else {
        if (!localValuesAreCurrent) {
            perDofValues->getParameterValues(localPerDofValuesFloat);
            localValuesAreCurrent = true;
        }
        for (int i = 0; i < (int) values.size(); i++)
            for (int j = 0; j < 3; j++)
                values[order[i]][j] = localPerDofValuesFloat[3*i+j][variable];
    }
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}

void OpenCLIntegrateCustomStepKernel::setPerDofVariable(ContextImpl& context, int variable, const vector<Vec3>& values) {
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    const vector<int>& order = cl.getAtomIndex();
    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
        if (!localValuesAreCurrent) {
            perDofValues->getParameterValues(localPerDofValuesDouble);
            localValuesAreCurrent = true;
        }
        for (int i = 0; i < (int) values.size(); i++)
            for (int j = 0; j < 3; j++)
                localPerDofValuesDouble[3*i+j][variable] = values[order[i]][j];
    }
    else {
        if (!localValuesAreCurrent) {
            perDofValues->getParameterValues(localPerDofValuesFloat);
            localValuesAreCurrent = true;
        }
        for (int i = 0; i < (int) values.size(); i++)
            for (int j = 0; j < 3; j++)
                localPerDofValuesFloat[3*i+j][variable] = (float) values[order[i]][j];
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    }
    deviceValuesAreCurrent = false;
}

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OpenCLApplyAndersenThermostatKernel::~OpenCLApplyAndersenThermostatKernel() {
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    if (atomGroups != NULL)
        delete atomGroups;
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}

void OpenCLApplyAndersenThermostatKernel::initialize(const System& system, const AndersenThermostat& thermostat) {
    randomSeed = thermostat.getRandomNumberSeed();
    map<string, string> defines;
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    defines["NUM_ATOMS"] = cl.intToString(cl.getNumAtoms());
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    cl::Program program = cl.createProgram(OpenCLKernelSources::andersenThermostat, defines);
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    kernel = cl::Kernel(program, "applyAndersenThermostat");
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    cl.getIntegrationUtilities().initRandomNumberGenerator(randomSeed);
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    // Create the arrays with the group definitions.

    vector<vector<int> > groups = AndersenThermostatImpl::calcParticleGroups(system);
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    atomGroups = OpenCLArray::create<int>(cl, cl.getNumAtoms(), "atomGroups");
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    vector<int> atoms(atomGroups->getSize());
    for (int i = 0; i < (int) groups.size(); i++) {
        for (int j = 0; j < (int) groups[i].size(); j++)
            atoms[groups[i][j]] = i;
    }
    atomGroups->upload(atoms);
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}

void OpenCLApplyAndersenThermostatKernel::execute(ContextImpl& context) {
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
        kernel.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
        kernel.setArg<cl::Buffer>(3, cl.getIntegrationUtilities().getStepSize().getDeviceBuffer());
        kernel.setArg<cl::Buffer>(4, cl.getIntegrationUtilities().getRandom().getDeviceBuffer());
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        kernel.setArg<cl::Buffer>(6, atomGroups->getDeviceBuffer());
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    }
    kernel.setArg<cl_float>(0, (cl_float) context.getParameter(AndersenThermostat::CollisionFrequency()));
    kernel.setArg<cl_float>(1, (cl_float) (BOLTZ*context.getParameter(AndersenThermostat::Temperature())));
    kernel.setArg<cl_uint>(5, cl.getIntegrationUtilities().prepareRandomNumbers(cl.getPaddedNumAtoms()));
    cl.executeKernel(kernel, cl.getNumAtoms());
}

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OpenCLApplyMonteCarloBarostatKernel::~OpenCLApplyMonteCarloBarostatKernel() {
    if (savedPositions != NULL)
        delete savedPositions;
    if (moleculeAtoms != NULL)
        delete moleculeAtoms;
    if (moleculeStartIndex != NULL)
        delete moleculeStartIndex;
}

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void OpenCLApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& thermostat) {
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    savedPositions = new OpenCLArray(cl, cl.getPaddedNumAtoms(), cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4), "savedPositions");
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    cl::Program program = cl.createProgram(OpenCLKernelSources::monteCarloBarostat);
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    kernel = cl::Kernel(program, "scalePositions");
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}

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void OpenCLApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) {
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    if (!hasInitializedKernels) {
        hasInitializedKernels = true;

        // Create the arrays with the molecule definitions.

        vector<vector<int> > molecules = context.getMolecules();
        numMolecules = molecules.size();
        moleculeAtoms = OpenCLArray::create<int>(cl, cl.getNumAtoms(), "moleculeAtoms");
        moleculeStartIndex = OpenCLArray::create<int>(cl, numMolecules+1, "moleculeStartIndex");
        vector<int> atoms(moleculeAtoms->getSize());
        vector<int> startIndex(moleculeStartIndex->getSize());
        int index = 0;
        for (int i = 0; i < numMolecules; i++) {
            startIndex[i] = index;
            for (int j = 0; j < (int) molecules[i].size(); j++)
                atoms[index++] = molecules[i][j];
        }
        startIndex[numMolecules] = index;
        moleculeAtoms->upload(atoms);
        moleculeStartIndex->upload(startIndex);

        // Initialize the kernel arguments.
        
        kernel.setArg<cl_int>(3, numMolecules);
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        kernel.setArg<cl::Buffer>(9, cl.getPosq().getDeviceBuffer());
        kernel.setArg<cl::Buffer>(10, moleculeAtoms->getDeviceBuffer());
        kernel.setArg<cl::Buffer>(11, moleculeStartIndex->getDeviceBuffer());
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    }
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    int bytesToCopy = cl.getPosq().getSize()*(cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4));
    cl.getQueue().enqueueCopyBuffer(cl.getPosq().getDeviceBuffer(), savedPositions->getDeviceBuffer(), 0, 0, bytesToCopy);
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    kernel.setArg<cl_float>(0, (cl_float) scaleX);
    kernel.setArg<cl_float>(1, (cl_float) scaleY);
    kernel.setArg<cl_float>(2, (cl_float) scaleZ);
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    setPeriodicBoxArgs(cl, kernel, 4);
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    cl.executeKernel(kernel, cl.getNumAtoms());
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    for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++)
        cl.getPosCellOffsets()[i] = mm_int4(0, 0, 0, 0);
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    lastAtomOrder = cl.getAtomIndex();
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}

void OpenCLApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context) {
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    int bytesToCopy = cl.getPosq().getSize()*(cl.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4));
    cl.getQueue().enqueueCopyBuffer(savedPositions->getDeviceBuffer(), cl.getPosq().getDeviceBuffer(), 0, 0, bytesToCopy);
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}

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OpenCLRemoveCMMotionKernel::~OpenCLRemoveCMMotionKernel() {
    if (cmMomentum != NULL)
        delete cmMomentum;
}

void OpenCLRemoveCMMotionKernel::initialize(const System& system, const CMMotionRemover& force) {
    frequency = force.getFrequency();
    int numAtoms = cl.getNumAtoms();
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    cmMomentum = OpenCLArray::create<mm_float4>(cl, (numAtoms+OpenCLContext::ThreadBlockSize-1)/OpenCLContext::ThreadBlockSize, "cmMomentum");
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    double totalMass = 0.0;
    for (int i = 0; i < numAtoms; i++)
        totalMass += system.getParticleMass(i);
    map<string, string> defines;
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    defines["INVERSE_TOTAL_MASS"] = cl.doubleToString(totalMass == 0 ? 0.0 : 1.0/totalMass);
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    cl::Program program = cl.createProgram(OpenCLKernelSources::removeCM, defines);
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    kernel1 = cl::Kernel(program, "calcCenterOfMassMomentum");
    kernel1.setArg<cl_int>(0, numAtoms);
    kernel1.setArg<cl::Buffer>(1, cl.getVelm().getDeviceBuffer());
    kernel1.setArg<cl::Buffer>(2, cmMomentum->getDeviceBuffer());
    kernel1.setArg(3, OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
    kernel2 = cl::Kernel(program, "removeCenterOfMassMomentum");
    kernel2.setArg<cl_int>(0, numAtoms);
    kernel2.setArg<cl::Buffer>(1, cl.getVelm().getDeviceBuffer());
    kernel2.setArg<cl::Buffer>(2, cmMomentum->getDeviceBuffer());
    kernel2.setArg(3, OpenCLContext::ThreadBlockSize*sizeof(mm_float4), NULL);
}

void OpenCLRemoveCMMotionKernel::execute(ContextImpl& context) {
    cl.executeKernel(kernel1, cl.getNumAtoms());
    cl.executeKernel(kernel2, cl.getNumAtoms());
}