OpenCLKernels.cpp 253 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) 2008-2010 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/CustomCompoundBondForceImpl.h"
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#include "openmm/internal/CustomHbondForceImpl.h"
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#include "openmm/internal/NonbondedForceImpl.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/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 "../src/SimTKUtilities/SimTKOpenMMRealType.h"
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#include "../src/SimTKUtilities/SimTKOpenMMUtilities.h"
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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 Lepton::ExpressionTreeNode;
using Lepton::Operation;
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static string doubleToString(double value) {
    stringstream s;
    s.precision(8);
    s << scientific << value << "f";
    return s.str();
}

static string intToString(int value) {
    stringstream s;
    s << value;
    return s.str();
}

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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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    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
    bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
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    cl.setAtomsWereReordered(false);
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    if (cl.getMoleculesAreInvalid() || (nb.getUseCutoff() && includeNonbonded && cl.getComputeForceCount()%100 == 0)) {
        cl.reorderAtoms(!cl.getMoleculesAreInvalid());
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        nb.updateNeighborListSize();
        cl.setComputeForceCount(cl.getComputeForceCount()+1);
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    }
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    cl.clearAutoclearBuffers();
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    if (includeNonbonded)
        nb.prepareInteractions();
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}

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double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
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    cl.getBondedUtilities().computeInteractions(groups);
    if ((groups&(1<<cl.getNonbondedUtilities().getForceGroup())) != 0)
        cl.getNonbondedUtilities().computeInteractions();
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    cl.reduceForces();
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    cl.getIntegrationUtilities().distributeForcesFromVirtualSites();
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    double sum = 0.0f;
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    if (includeEnergy) {
        OpenCLArray<cl_float>& energy = cl.getEnergyBuffer();
        energy.download();
        for (int i = 0; i < energy.getSize(); i++)
            sum += energy[i];
    }
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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) {
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    OpenCLArray<mm_float4>& posq = cl.getPosq();
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    posq.download();
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    OpenCLArray<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
    positions.resize(numParticles);
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    mm_float4 periodicBoxSize = cl.getPeriodicBoxSize();
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    for (int i = 0; i < numParticles; ++i) {
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        mm_float4 pos = posq[i];
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        mm_int4 offset = cl.getPosCellOffsets()[i];
        positions[order[i]] = Vec3(pos.x-offset.x*periodicBoxSize.x, pos.y-offset.y*periodicBoxSize.y, pos.z-offset.z*periodicBoxSize.z);
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    }
}

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void OpenCLUpdateStateDataKernel::setPositions(ContextImpl& context, const vector<Vec3>& positions) {
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    OpenCLArray<mm_float4>& posq = cl.getPosq();
    OpenCLArray<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
    for (int i = 0; i < numParticles; ++i) {
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        mm_float4& pos = posq[i];
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        const Vec3& p = positions[order[i]];
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        pos.x = (cl_float) p[0];
        pos.y = (cl_float) p[1];
        pos.z = (cl_float) p[2];
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    }
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    for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
        posq[i] = mm_float4(0.0f, 0.0f, 0.0f, 0.0f);
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    posq.upload();
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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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}

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void OpenCLUpdateStateDataKernel::getVelocities(ContextImpl& context, vector<Vec3>& velocities) {
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    OpenCLArray<mm_float4>& velm = cl.getVelm();
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    velm.download();
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    OpenCLArray<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
    velocities.resize(numParticles);
    for (int i = 0; i < numParticles; ++i) {
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        mm_float4 vel = velm[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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    OpenCLArray<mm_float4>& velm = cl.getVelm();
    OpenCLArray<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
    for (int i = 0; i < numParticles; ++i) {
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        mm_float4& vel = velm[i];
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        const Vec3& p = velocities[order[i]];
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        vel.x = (cl_float) p[0];
        vel.y = (cl_float) p[1];
        vel.z = (cl_float) p[2];
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    }
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    for (int i = numParticles; i < cl.getPaddedNumAtoms(); i++)
        velm[i] = mm_float4(0.0f, 0.0f, 0.0f, 0.0f);
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    velm.upload();
}

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void OpenCLUpdateStateDataKernel::getForces(ContextImpl& context, vector<Vec3>& forces) {
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    OpenCLArray<mm_float4>& force = cl.getForce();
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    force.download();
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    OpenCLArray<cl_int>& order = cl.getAtomIndex();
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    int numParticles = context.getSystem().getNumParticles();
    forces.resize(numParticles);
    for (int i = 0; i < numParticles; ++i) {
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        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::getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const {
    mm_float4 box = cl.getPeriodicBoxSize();
    a = Vec3(box.x, 0, 0);
    b = Vec3(0, box.y, 0);
    c = Vec3(0, 0, box.z);
}

void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const {
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    vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
    for (int i = 0; i < (int) contexts.size(); i++)
        contexts[i]->setPeriodicBoxSize(a[0], b[1], c[2]);
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}

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void OpenCLUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream& stream) {
    int version = 1;
    stream.write((char*) &version, sizeof(int));
    double time = cl.getTime();
    stream.write((char*) &time, sizeof(double));
    cl.getPosq().download();
    stream.write((char*) &cl.getPosq()[0], sizeof(mm_float4)*cl.getPosq().getSize());
    cl.getVelm().download();
    stream.write((char*) &cl.getVelm()[0], sizeof(mm_float4)*cl.getVelm().getSize());
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    stream.write((char*) &cl.getAtomIndex()[0], sizeof(cl_int)*cl.getAtomIndex().getSize());
    stream.write((char*) &cl.getPosCellOffsets()[0], sizeof(mm_int4)*cl.getPosCellOffsets().size());
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    mm_float4 box = cl.getPeriodicBoxSize();
    stream.write((char*) &box, sizeof(mm_float4));
    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));
    if (version != 1)
        throw OpenMMException("Checkpoint was created with a different version of OpenMM");
    double time;
    stream.read((char*) &time, sizeof(double));
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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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    stream.read((char*) &cl.getPosq()[0], sizeof(mm_float4)*cl.getPosq().getSize());
    cl.getPosq().upload();
    stream.read((char*) &cl.getVelm()[0], sizeof(mm_float4)*cl.getVelm().getSize());
    cl.getVelm().upload();
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    stream.read((char*) &cl.getAtomIndex()[0], sizeof(cl_int)*cl.getAtomIndex().getSize());
    cl.getAtomIndex().upload();
    stream.read((char*) &cl.getPosCellOffsets()[0], sizeof(mm_int4)*cl.getPosCellOffsets().size());
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    mm_float4 box;
    stream.read((char*) &box, sizeof(mm_float4));
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    for (int i = 0; i < (int) contexts.size(); i++)
        contexts[i]->setPeriodicBoxSize(box.x, box.y, box.z);
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    cl.getIntegrationUtilities().loadCheckpoint(stream);
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    SimTKOpenMMUtilities::loadCheckpoint(stream);
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    for (int i = 0; i < cl.getReorderListeners().size(); i++)
        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;
        defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
        cl::Program program = cl.createProgram(OpenCLKernelSources::constraints, defines);
        applyDeltasKernel = cl::Kernel(program, "applyPositionDeltas");
        applyDeltasKernel.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
        applyDeltasKernel.setArg<cl::Buffer>(1, cl.getIntegrationUtilities().getPosDelta().getDeviceBuffer());
    }
    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 OpenCLVirtualSitesKernel::initialize(const System& system) {
}

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

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class OpenCLHarmonicBondForceInfo : public OpenCLForceInfo {
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public:
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    OpenCLHarmonicBondForceInfo(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 = new OpenCLArray<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["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());
    cl.addForce(new OpenCLHarmonicBondForceInfo(force));
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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");
    
    // 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.
    
    cl.invalidateMolecules();
}

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class OpenCLCustomBondForceInfo : public OpenCLForceInfo {
public:
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    OpenCLCustomBondForceInfo(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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    cl.addForce(new OpenCLCustomBondForceInfo(force));
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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;
    expressions["float dEdR = "] = forceExpression;

    // 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) {
        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customBondGlobals", false, CL_MEM_READ_ONLY);
        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);
            string value = argName+"["+intToString(i)+"]";
            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()<<" bondParams"<<(i+1)<<" = "<<argName<<"[index];\n";
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    }
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    vector<pair<string, string> > functions;
    compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "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::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");
    
    // 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.
    
    cl.invalidateMolecules();
}

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class OpenCLHarmonicAngleForceInfo : public OpenCLForceInfo {
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public:
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    OpenCLHarmonicAngleForceInfo(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 = new OpenCLArray<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["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());
    cl.addForce(new OpenCLHarmonicAngleForceInfo(force));
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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");
    
    // 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.
    
    cl.invalidateMolecules();
}

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class OpenCLCustomAngleForceInfo : public OpenCLForceInfo {
public:
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    OpenCLCustomAngleForceInfo(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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    cl.addForce(new OpenCLCustomAngleForceInfo(force));
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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["float 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) {
        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customAngleGlobals", false, CL_MEM_READ_ONLY);
        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);
            string value = argName+"["+intToString(i)+"]";
            variables[name] = value;
        }
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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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    }
    vector<pair<string, string> > functions;
    compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
    map<string, string> replacements;
    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");
    
    // 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.
    
    cl.invalidateMolecules();
}

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class OpenCLPeriodicTorsionForceInfo : public OpenCLForceInfo {
public:
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    OpenCLPeriodicTorsionForceInfo(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 = new OpenCLArray<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["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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    cl.addForce(new OpenCLPeriodicTorsionForceInfo(force));
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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");
    
    // 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.
    
    cl.invalidateMolecules();
}

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class OpenCLRBTorsionForceInfo : public OpenCLForceInfo {
public:
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    OpenCLRBTorsionForceInfo(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 = new OpenCLArray<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["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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    cl.addForce(new OpenCLRBTorsionForceInfo(force));
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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");
    
    // 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.
    
    cl.invalidateMolecules();
}

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class OpenCLCMAPTorsionForceInfo : public OpenCLForceInfo {
public:
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    OpenCLCMAPTorsionForceInfo(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;
    vector<mm_int2> mapPositionsVec(numMaps);
    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 = new OpenCLArray<mm_float4>(cl, coeffVec.size(), "cmapTorsionCoefficients");
    mapPositions = new OpenCLArray<mm_int2>(cl, numMaps, "cmapTorsionMapPositions");
    torsionMaps = new OpenCLArray<cl_int>(cl, numTorsions, "cmapTorsionMaps");
    coefficients->upload(coeffVec);
    mapPositions->upload(mapPositionsVec);
    torsionMaps->upload(torsionMapsVec);
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    map<string, string> replacements;
    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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    cl.addForce(new OpenCLCMAPTorsionForceInfo(force));
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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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class OpenCLCustomTorsionForceInfo : public OpenCLForceInfo {
public:
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    OpenCLCustomTorsionForceInfo(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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    cl.addForce(new OpenCLCustomTorsionForceInfo(force));
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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;
    expressions["float dEdAngle = "] = forceExpression;

    // 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) {
        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customTorsionGlobals", false, CL_MEM_READ_ONLY);
        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);
            string value = argName+"["+intToString(i)+"]";
            variables[name] = value;
        }
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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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    }
    vector<pair<string, string> > functions;
    compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
    map<string, string> replacements;
    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");
    
    // 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.
    
    cl.invalidateMolecules();
}

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class OpenCLNonbondedForceInfo : public OpenCLForceInfo {
public:
    OpenCLNonbondedForceInfo(int requiredBuffers, const NonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    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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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;
    if (pmeBsplineTheta != NULL)
        delete pmeBsplineTheta;
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    if (pmeBsplineDTheta != NULL)
        delete pmeBsplineDTheta;
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    if (pmeAtomRange != NULL)
        delete pmeAtomRange;
    if (pmeAtomGridIndex != NULL)
        delete pmeAtomGridIndex;
    if (sort != NULL)
        delete sort;
    if (fft != NULL)
        delete fft;
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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();
    sigmaEpsilon = new OpenCLArray<mm_float2>(cl, numParticles, "sigmaEpsilon");
    OpenCLArray<mm_float4>& posq = cl.getPosq();
    vector<mm_float2> sigmaEpsilonVector(numParticles);
    vector<vector<int> > exclusionList(numParticles);
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    double sumSquaredCharges = 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);
        posq[i].w = (float) charge;
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        sigmaEpsilonVector[i] = mm_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
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        exclusionList[i].push_back(i);
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        sumSquaredCharges += charge*charge;
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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);
    }
    posq.upload();
    sigmaEpsilon->upload(sigmaEpsilonVector);
    bool useCutoff = (force.getNonbondedMethod() != NonbondedForce::NoCutoff);
    bool usePeriodic = (force.getNonbondedMethod() != NonbondedForce::NoCutoff && force.getNonbondedMethod() != NonbondedForce::CutoffNonPeriodic);
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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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    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"] = doubleToString(reactionFieldK);
        defines["REACTION_FIELD_C"] = doubleToString(reactionFieldC);
    }
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    if (force.getUseDispersionCorrection() && cl.getContextIndex() == 0)
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        dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(system, force);
    else
        dispersionCoefficient = 0.0;
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    alpha = 0;
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    if (force.getNonbondedMethod() == NonbondedForce::Ewald) {
        // Compute the Ewald parameters.

        int kmaxx, kmaxy, kmaxz;
        NonbondedForceImpl::calcEwaldParameters(system, force, alpha, kmaxx, kmaxy, kmaxz);
        defines["EWALD_ALPHA"] = doubleToString(alpha);
        defines["TWO_OVER_SQRT_PI"] = doubleToString(2.0/sqrt(M_PI));
        defines["USE_EWALD"] = "1";
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        ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
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        // Create the reciprocal space kernels.

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

        int gridSizeX, gridSizeY, gridSizeZ;
        NonbondedForceImpl::calcPMEParameters(system, force, alpha, gridSizeX, gridSizeY, gridSizeZ);
        gridSizeX = OpenCLFFT3D::findLegalDimension(gridSizeX);
        gridSizeY = OpenCLFFT3D::findLegalDimension(gridSizeY);
        gridSizeZ = OpenCLFFT3D::findLegalDimension(gridSizeZ);
        defines["EWALD_ALPHA"] = doubleToString(alpha);
        defines["TWO_OVER_SQRT_PI"] = doubleToString(2.0/sqrt(M_PI));
        defines["USE_EWALD"] = "1";
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        ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
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        pmeDefines["PME_ORDER"] = intToString(PmeOrder);
        pmeDefines["NUM_ATOMS"] = intToString(numParticles);
        pmeDefines["RECIP_EXP_FACTOR"] = doubleToString(M_PI*M_PI/(alpha*alpha));
        pmeDefines["GRID_SIZE_X"] = intToString(gridSizeX);
        pmeDefines["GRID_SIZE_Y"] = intToString(gridSizeY);
        pmeDefines["GRID_SIZE_Z"] = intToString(gridSizeZ);
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        pmeDefines["EPSILON_FACTOR"] = doubleToString(sqrt(ONE_4PI_EPS0));
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        // Create required data structures.

        pmeGrid = new OpenCLArray<mm_float2>(cl, gridSizeX*gridSizeY*gridSizeZ, "pmeGrid");
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        cl.addAutoclearBuffer(pmeGrid->getDeviceBuffer(), pmeGrid->getSize()*2);
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        pmeGrid2 = new OpenCLArray<mm_float2>(cl, gridSizeX*gridSizeY*gridSizeZ, "pmeGrid2");
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        pmeBsplineModuliX = new OpenCLArray<cl_float>(cl, gridSizeX, "pmeBsplineModuliX");
        pmeBsplineModuliY = new OpenCLArray<cl_float>(cl, gridSizeY, "pmeBsplineModuliY");
        pmeBsplineModuliZ = new OpenCLArray<cl_float>(cl, gridSizeZ, "pmeBsplineModuliZ");
        pmeBsplineTheta = new OpenCLArray<mm_float4>(cl, PmeOrder*numParticles, "pmeBsplineTheta");
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        bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
        if (deviceIsCpu)
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            pmeBsplineDTheta = new OpenCLArray<mm_float4>(cl, PmeOrder*numParticles, "pmeBsplineDTheta");
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        pmeAtomRange = new OpenCLArray<cl_int>(cl, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
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        pmeAtomGridIndex = new OpenCLArray<mm_int2>(cl, numParticles, "pmeAtomGridIndex");
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        sort = new OpenCLSort<SortTrait>(cl, cl.getNumAtoms());
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        fft = new OpenCLFFT3D(cl, gridSizeX, gridSizeY, gridSizeZ);

        // Initialize the b-spline moduli.

        int maxSize = max(max(gridSizeX, gridSizeY), gridSizeZ);
        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];
        }

        // 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 ? gridSizeX : dim == 1 ? gridSizeY : gridSizeZ);
            vector<cl_float> 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);
            }
            for (int i = 0; i < ndata; i++)
            {
                if (moduli[i] < 1.0e-7)
                    moduli[i] = (moduli[i-1]+moduli[i+1])*0.5f;
            }
            if (dim == 0)
                pmeBsplineModuliX->upload(moduli);
            else if (dim == 1)
                pmeBsplineModuliY->upload(moduli);
            else
                pmeBsplineModuliZ->upload(moduli);
        }
    }
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    else
        ewaldSelfEnergy = 0.0;

    // 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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        vector<vector<int> > atoms(numExceptions, vector<int>(2));
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        exceptionParams = new OpenCLArray<mm_float4>(cl, numExceptions, "exceptionParams");
        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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        }
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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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    }
    cl.addForce(new OpenCLNonbondedForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
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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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            string file = (deviceIsCpu ? OpenCLKernelSources::pme_cpu : OpenCLKernelSources::pme);
            cl::Program program = cl.createProgram(file, pmeDefines);
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            pmeUpdateBsplinesKernel = cl::Kernel(program, "updateBsplines");
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            pmeAtomRangeKernel = cl::Kernel(program, "findAtomRangeForGrid");
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	    if (!deviceIsCpu)
                pmeZIndexKernel = cl::Kernel(program, "recordZIndex");
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            pmeSpreadChargeKernel = cl::Kernel(program, "gridSpreadCharge");
            pmeConvolutionKernel = cl::Kernel(program, "reciprocalConvolution");
            pmeInterpolateForceKernel = cl::Kernel(program, "gridInterpolateForce");
            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*sizeof(mm_float4), NULL);
            pmeUpdateBsplinesKernel.setArg<cl::Buffer>(3, pmeAtomGridIndex->getDeviceBuffer());
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            if (deviceIsCpu)
                pmeUpdateBsplinesKernel.setArg<cl::Buffer>(6, pmeBsplineDTheta->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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	    if (!deviceIsCpu) {
                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());
            pmeSpreadChargeKernel.setArg<cl::Buffer>(3, pmeGrid->getDeviceBuffer());
            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, cl.getEnergyBuffer().getDeviceBuffer());
            pmeConvolutionKernel.setArg<cl::Buffer>(2, pmeBsplineModuliX->getDeviceBuffer());
            pmeConvolutionKernel.setArg<cl::Buffer>(3, pmeBsplineModuliY->getDeviceBuffer());
            pmeConvolutionKernel.setArg<cl::Buffer>(4, pmeBsplineModuliZ->getDeviceBuffer());
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            interpolateForceThreads = (cl.getDevice().getInfo<CL_DEVICE_LOCAL_MEM_SIZE>() > 2*128*PmeOrder*sizeof(mm_float4) ? 128 : 64);
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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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            if (deviceIsCpu) {
                pmeInterpolateForceKernel.setArg<cl::Buffer>(5, pmeBsplineTheta->getDeviceBuffer());
                pmeInterpolateForceKernel.setArg<cl::Buffer>(6, pmeBsplineDTheta->getDeviceBuffer());
            }
            else
                pmeInterpolateForceKernel.setArg(5, 2*interpolateForceThreads*PmeOrder*sizeof(mm_float4), NULL);
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            if (cl.getSupports64BitGlobalAtomics()) {
                pmeFinishSpreadChargeKernel = cl::Kernel(program, "finishSpreadCharge");
                pmeFinishSpreadChargeKernel.setArg<cl::Buffer>(0, pmeGrid->getDeviceBuffer());
            }
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       }
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    }
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    if (cosSinSums != NULL && cl.getContextIndex() == 0 && includeReciprocal) {
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        mm_float4 boxSize = cl.getPeriodicBoxSize();
        mm_float4 recipBoxSize = mm_float4((float) (2*M_PI/boxSize.x), (float) (2*M_PI/boxSize.y), (float) (2*M_PI/boxSize.z), 0);
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        float recipCoefficient = (float) (ONE_4PI_EPS0*4*M_PI/(boxSize.x*boxSize.y*boxSize.z));
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        ewaldSumsKernel.setArg<mm_float4>(3, recipBoxSize);
        ewaldSumsKernel.setArg<cl_float>(4, recipCoefficient);
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        cl.executeKernel(ewaldSumsKernel, cosSinSums->getSize());
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        ewaldForcesKernel.setArg<mm_float4>(3, recipBoxSize);
        ewaldForcesKernel.setArg<cl_float>(4, recipCoefficient);
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        cl.executeKernel(ewaldForcesKernel, cl.getNumAtoms());
    }
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    if (pmeGrid != NULL && cl.getContextIndex() == 0 && includeReciprocal) {
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        mm_float4 boxSize = cl.getPeriodicBoxSize();
        mm_float4 invBoxSize = cl.getInvPeriodicBoxSize();
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        pmeUpdateBsplinesKernel.setArg<mm_float4>(4, boxSize);
        pmeUpdateBsplinesKernel.setArg<mm_float4>(5, invBoxSize);
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        cl.executeKernel(pmeUpdateBsplinesKernel, cl.getNumAtoms());
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        if (deviceIsCpu) {
            pmeSpreadChargeKernel.setArg<mm_float4>(5, boxSize);
            pmeSpreadChargeKernel.setArg<mm_float4>(6, invBoxSize);
            cl.executeKernel(pmeSpreadChargeKernel, 2*cl.getDevice().getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>(), 1);
        }
        else {
            sort->sort(*pmeAtomGridIndex);
            pmeAtomRangeKernel.setArg<mm_float4>(3, boxSize);
            pmeAtomRangeKernel.setArg<mm_float4>(4, invBoxSize);
            cl.executeKernel(pmeAtomRangeKernel, cl.getNumAtoms());
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            if (cl.getSupports64BitGlobalAtomics()) {
                pmeSpreadChargeKernel.setArg<mm_float4>(5, boxSize);
                pmeSpreadChargeKernel.setArg<mm_float4>(6, invBoxSize);
                cl.executeKernel(pmeSpreadChargeKernel, cl.getNumAtoms(), PmeOrder*PmeOrder*PmeOrder);
                cl.executeKernel(pmeFinishSpreadChargeKernel, pmeGrid->getSize());
            }
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            else {
                pmeZIndexKernel.setArg<mm_float4>(2, boxSize);
                pmeZIndexKernel.setArg<mm_float4>(3, invBoxSize);
                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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        pmeConvolutionKernel.setArg<mm_float4>(5, invBoxSize);
        pmeConvolutionKernel.setArg<cl_float>(6, (float) (1.0/(M_PI*boxSize.x*boxSize.y*boxSize.z)));
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        cl.executeKernel(pmeConvolutionKernel, cl.getNumAtoms());
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        fft->execFFT(*pmeGrid2, *pmeGrid, false);
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        pmeInterpolateForceKernel.setArg<mm_float4>(3, boxSize);
        pmeInterpolateForceKernel.setArg<mm_float4>(4, invBoxSize);
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        cl.executeKernel(pmeInterpolateForceKernel, cl.getNumAtoms(), interpolateForceThreads);
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    }
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    double energy = (includeReciprocal ? ewaldSelfEnergy : 0.0);
    if (dispersionCoefficient != 0.0 && includeDirect) {
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        mm_float4 boxSize = cl.getPeriodicBoxSize();
        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);
        if (chargeProd != 0.0 || epsilon != 0.0)
            exceptions.push_back(i);
    }
    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;
    if ((exceptionParams == NULL && numExceptions > 0) || (exceptionParams != NULL && numExceptions != exceptionParams->getSize()))
        throw OpenMMException("updateParametersInContext: The number of non-excluded exceptions has changed");
    
    // Record the per-particle parameters.
    
    OpenCLArray<mm_float4>& posq = cl.getPosq();
    posq.download();
    vector<mm_float2> sigmaEpsilonVector(force.getNumParticles());
    double sumSquaredCharges = 0.0;
    OpenCLArray<cl_int>& order = cl.getAtomIndex();
    for (int i = 0; i < force.getNumParticles(); i++) {
        int index = order[i];
        double charge, sigma, epsilon;
        force.getParticleParameters(index, charge, sigma, epsilon);
        posq[i].w = (float) charge;
        sigmaEpsilonVector[index] = mm_float2((float) (0.5*sigma), (float) (2.0*sqrt(epsilon)));
        sumSquaredCharges += charge*charge;
    }
    posq.upload();
    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.
    
    NonbondedForce::NonbondedMethod method = force.getNonbondedMethod();
    if (method == NonbondedForce::Ewald || method == NonbondedForce::PME)
        ewaldSelfEnergy = (cl.getContextIndex() == 0 ? -ONE_4PI_EPS0*alpha*sumSquaredCharges/sqrt(M_PI) : 0.0);
    if (force.getUseDispersionCorrection() && cl.getContextIndex() == 0 && (method == NonbondedForce::CutoffPeriodic || method == NonbondedForce::Ewald || method == NonbondedForce::PME))
        dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
    cl.invalidateMolecules();
}

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class OpenCLCustomNonbondedForceInfo : public OpenCLForceInfo {
public:
    OpenCLCustomNonbondedForceInfo(int requiredBuffers, const CustomNonbondedForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    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() {
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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;
};

OpenCLCalcCustomNonbondedForceKernel::~OpenCLCalcCustomNonbondedForceKernel() {
    if (params != NULL)
        delete params;
    if (globals != NULL)
        delete globals;
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    if (tabulatedFunctionParams != NULL)
        delete tabulatedFunctionParams;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
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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)
        ;
    string prefix = "custom"+intToString(forceIndex)+"_";

    // 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 = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customNonbondedGlobals", false, 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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    OpenCLExpressionUtilities::FunctionPlaceholder fp;
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    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
    vector<mm_float4> tabulatedFunctionParamsVec(force.getNumFunctions());
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    for (int i = 0; i < force.getNumFunctions(); i++) {
        string name;
        vector<double> values;
        double min, max;
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        force.getFunctionParameters(i, name, values, min, max);
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        string arrayName = prefix+"table"+intToString(i);
        functionDefinitions.push_back(make_pair(name, arrayName));
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        functions[name] = &fp;
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        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), (float) values.size()-2);
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        vector<mm_float4> f = OpenCLExpressionUtilities::computeFunctionCoefficients(values, min, max);
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        tabulatedFunctions.push_back(new OpenCLArray<mm_float4>(cl, values.size()-1, "TabulatedFunction"));
        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
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        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", 4, sizeof(cl_float4), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
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    }
    if (force.getNumFunctions() > 0) {
        tabulatedFunctionParams = new OpenCLArray<mm_float4>(cl, tabulatedFunctionParamsVec.size(), "tabulatedFunctionParameters", false, CL_MEM_READ_ONLY);
        tabulatedFunctionParams->upload(tabulatedFunctionParamsVec);
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        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(prefix+"functionParams", "float", 4, sizeof(cl_float4), tabulatedFunctionParams->getDeviceBuffer()));
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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;
    forceExpressions["tempEnergy += "] = energyExpression;
    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);
        string value = "globals["+intToString(i)+"]";
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        variables.push_back(makeVariable(name, prefix+value));
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    }
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    stringstream compute;
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    compute << OpenCLExpressionUtilities::createExpressions(forceExpressions, variables, functionDefinitions, prefix+"temp", prefix+"functionParams");
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    map<string, string> replacements;
    replacements["COMPUTE_FORCE"] = compute.str();
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    string source = cl.replaceStrings(OpenCLKernelSources::customNonbonded, replacements);
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    cl.getNonbondedUtilities().addInteraction(useCutoff, usePeriodic, true, force.getCutoffDistance(), exclusionList, source, force.getForceGroup());
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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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        cl.getNonbondedUtilities().addParameter(OpenCLNonbondedUtilities::ParameterInfo(prefix+"params"+intToString(i+1), buffer.getComponentType(), buffer.getNumComponents(), buffer.getSize(), buffer.getMemory()));
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    }
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    if (globals != NULL) {
        globals->upload(globalParamValues);
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        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(prefix+"globals", "float", 1, sizeof(cl_float), globals->getDeviceBuffer()));
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    }
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    cl.addForce(new OpenCLCustomNonbondedForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
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}

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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;
        }
        if (changed)
            globals->upload(globalParamValues);
    }
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    return 0.0;
}
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class OpenCLGBSAOBCForceInfo : public OpenCLForceInfo {
public:
    OpenCLGBSAOBCForceInfo(int requiredBuffers, const GBSAOBCForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    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 = new OpenCLArray<mm_float2>(cl, cl.getPaddedNumAtoms(), "gbsaObcParams");
    bornRadii = new OpenCLArray<cl_float>(cl, cl.getPaddedNumAtoms(), "bornRadii");
    obcChain = new OpenCLArray<cl_float>(cl, cl.getPaddedNumAtoms(), "obcChain");
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    if (cl.getSupports64BitGlobalAtomics()) {
        longBornSum = new OpenCLArray<cl_long>(cl, cl.getPaddedNumAtoms(), "longBornSum");
        longBornForce = new OpenCLArray<cl_long>(cl, cl.getPaddedNumAtoms(), "longBornForce");
        bornForce = new OpenCLArray<cl_float>(cl, cl.getPaddedNumAtoms(), "bornForce");
        cl.addAutoclearBuffer(longBornSum->getDeviceBuffer(), 2*longBornSum->getSize());
        cl.addAutoclearBuffer(longBornForce->getDeviceBuffer(), 2*longBornForce->getSize());
    }
    else {
        bornSum = new OpenCLArray<cl_float>(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), "bornSum");
        bornForce = new OpenCLArray<cl_float>(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), "bornForce");
        cl.addAutoclearBuffer(bornSum->getDeviceBuffer(), bornSum->getSize());
        cl.addAutoclearBuffer(bornForce->getDeviceBuffer(), bornForce->getSize());
    }
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    OpenCLArray<mm_float4>& posq = cl.getPosq();
    int numParticles = force.getNumParticles();
    vector<mm_float2> paramsVector(numParticles);
    const double dielectricOffset = 0.009;
    for (int i = 0; i < numParticles; i++) {
        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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        posq[i].w = (float) charge;
    }
    posq.upload();
    params->upload(paramsVector);
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    prefactor = -ONE_4PI_EPS0*((1.0/force.getSoluteDielectric())-(1.0/force.getSolventDielectric()));
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    bool useCutoff = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff);
    bool usePeriodic = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff && force.getNonbondedMethod() != GBSAOBCForce::CutoffNonPeriodic);
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    string source = OpenCLKernelSources::gbsaObc2;
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    nb.addInteraction(useCutoff, usePeriodic, false, force.getCutoffDistance(), vector<vector<int> >(), source, force.getForceGroup());
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    nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("obcParams", "float", 2, sizeof(cl_float2), params->getDeviceBuffer()));;
    nb.addParameter(OpenCLNonbondedUtilities::ParameterInfo("bornForce", "float", 1, sizeof(cl_float), bornForce->getDeviceBuffer()));;
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    cl.addForce(new OpenCLGBSAOBCForceInfo(nb.getNumForceBuffers(), force));
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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.getForceBufferPerAtomBlock())
            defines["USE_OUTPUT_BUFFER_PER_BLOCK"] = "1";
        if (nb.getUseCutoff())
            defines["USE_CUTOFF"] = "1";
        if (nb.getUsePeriodic())
            defines["USE_PERIODIC"] = "1";
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        defines["CUTOFF_SQUARED"] = doubleToString(nb.getCutoffDistance()*nb.getCutoffDistance());
        defines["PREFACTOR"] = doubleToString(prefactor);
        defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
        defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
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        defines["NUM_BLOCKS"] = OpenCLExpressionUtilities::intToString(cl.getNumAtomBlocks());
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        defines["FORCE_WORK_GROUP_SIZE"] = OpenCLExpressionUtilities::intToString(nb.getForceThreadBlockSize());
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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 if (cl.getSIMDWidth() == 32)
            file = OpenCLKernelSources::gbsaObc_nvidia;
        else
            file = OpenCLKernelSources::gbsaObc_default;
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        cl::Program program = cl.createProgram(file, defines);
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        bool useLong = (cl.getSupports64BitGlobalAtomics() && !deviceIsCpu);
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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 += 2; // The periodic box size arguments are set when the kernel is executed.
            computeBornSumKernel.setArg<cl_uint>(index++, maxTiles);
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            if (cl.getSIMDWidth() == 32 || deviceIsCpu)
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                computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getInteractionFlags().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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        if (cl.getSIMDWidth() == 32) {
            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getExclusionIndices().getDeviceBuffer());
            computeBornSumKernel.setArg<cl::Buffer>(index++, nb.getExclusionRowIndices().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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        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 += 2; // The periodic box size arguments are set when the kernel is executed.
            force1Kernel.setArg<cl_uint>(index++, maxTiles);
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            if (cl.getSIMDWidth() == 32 || deviceIsCpu)
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                force1Kernel.setArg<cl::Buffer>(index++, nb.getInteractionFlags().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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        if (cl.getSIMDWidth() == 32) {
            force1Kernel.setArg<cl::Buffer>(index++, nb.getExclusionIndices().getDeviceBuffer());
            force1Kernel.setArg<cl::Buffer>(index++, nb.getExclusionRowIndices().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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    if (nb.getUseCutoff()) {
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        computeBornSumKernel.setArg<mm_float4>(5, cl.getPeriodicBoxSize());
        computeBornSumKernel.setArg<mm_float4>(6, cl.getInvPeriodicBoxSize());
        force1Kernel.setArg<mm_float4>(7, cl.getPeriodicBoxSize());
        force1Kernel.setArg<mm_float4>(8, cl.getInvPeriodicBoxSize());
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        if (maxTiles < nb.getInteractingTiles().getSize()) {
            maxTiles = nb.getInteractingTiles().getSize();
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            computeBornSumKernel.setArg<cl::Buffer>(4, nb.getInteractingTiles().getDeviceBuffer());
            computeBornSumKernel.setArg<cl_uint>(7, maxTiles);
            force1Kernel.setArg<cl::Buffer>(5, nb.getInteractingTiles().getDeviceBuffer());
            force1Kernel.setArg<cl_uint>(9, maxTiles);
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            if (cl.getSIMDWidth() == 32 || deviceIsCpu) {
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                computeBornSumKernel.setArg<cl::Buffer>(8, nb.getInteractionFlags().getDeviceBuffer());
                force1Kernel.setArg<cl::Buffer>(10, nb.getInteractionFlags().getDeviceBuffer());
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            }
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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.
    
    OpenCLArray<mm_float4>& posq = cl.getPosq();
    posq.download();
    vector<mm_float2> paramsVector(numParticles);
    const double dielectricOffset = 0.009;
    for (int i = 0; i < numParticles; i++) {
        double charge, radius, scalingFactor;
        force.getParticleParameters(i, charge, radius, scalingFactor);
        radius -= dielectricOffset;
        paramsVector[i] = mm_float2((float) radius, (float) (scalingFactor*radius));
        posq[i].w = (float) charge;
    }
    posq.upload();
    params->upload(paramsVector);
    
    // Mark that the current reordering may be invalid.
    
    cl.invalidateMolecules();
}

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class OpenCLCustomGBForceInfo : public OpenCLForceInfo {
public:
    OpenCLCustomGBForceInfo(int requiredBuffers, const CustomGBForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    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 (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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    if (tabulatedFunctionParams != NULL)
        delete tabulatedFunctionParams;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

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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    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)
        ;
    string prefix = "custom"+intToString(forceIndex)+"_";

    // Record parameters and exclusions.

    int numParticles = force.getNumParticles();
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    params = new OpenCLParameterSet(cl, force.getNumPerParticleParameters(), numParticles, "customGBParameters", true);
    computedValues = new OpenCLParameterSet(cl, force.getNumComputedValues(), numParticles, "customGBComputedValues", true);
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    if (force.getNumGlobalParameters() > 0)
        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customGBGlobals", false, CL_MEM_READ_ONLY);
    vector<vector<cl_float> > paramVector(numParticles);
    vector<vector<int> > exclusionList(numParticles);
    for (int i = 0; i < numParticles; i++) {
        vector<double> parameters;
        force.getParticleParameters(i, parameters);
        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];
        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.

    OpenCLExpressionUtilities::FunctionPlaceholder fp;
    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
    vector<mm_float4> tabulatedFunctionParamsVec(force.getNumFunctions());
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    stringstream tableArgs;
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    for (int i = 0; i < force.getNumFunctions(); i++) {
        string name;
        vector<double> values;
        double min, max;
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        force.getFunctionParameters(i, name, values, min, max);
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        string arrayName = prefix+"table"+intToString(i);
        functionDefinitions.push_back(make_pair(name, arrayName));
        functions[name] = &fp;
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        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), (float) values.size()-2);
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        vector<mm_float4> f = OpenCLExpressionUtilities::computeFunctionCoefficients(values, min, max);
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        tabulatedFunctions.push_back(new OpenCLArray<mm_float4>(cl, values.size()-1, "TabulatedFunction"));
        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
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        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(arrayName, "float", 4, sizeof(cl_float4), tabulatedFunctions[tabulatedFunctions.size()-1]->getDeviceBuffer()));
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        tableArgs << ", __global const float4* restrict " << arrayName;
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    }
    if (force.getNumFunctions() > 0) {
        tabulatedFunctionParams = new OpenCLArray<mm_float4>(cl, tabulatedFunctionParamsVec.size(), "tabulatedFunctionParameters", false, CL_MEM_READ_ONLY);
        tabulatedFunctionParams->upload(tabulatedFunctionParamsVec);
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        cl.getNonbondedUtilities().addArgument(OpenCLNonbondedUtilities::ParameterInfo(prefix+"functionParams", "float", 4, sizeof(cl_float4), tabulatedFunctionParams->getDeviceBuffer()));
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        tableArgs << ", __global const float4* " << prefix << "functionParams";
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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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    needParameterGradient = false;
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    for (int i = 1; i < force.getNumComputedValues(); i++) {
        Lepton::ParsedExpression ex = Lepton::Parser::parse(computedValueExpressions[i], functions).optimize();
        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;
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         for (int j = 0; j < i; j++)
            valueDerivExpressions[i].push_back(ex.differentiate(computedValueNames[j]).optimize());
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    }
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    vector<vector<Lepton::ParsedExpression> > energyDerivExpressions(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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    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
    bool useLong = (cl.getSupports64BitGlobalAtomics() && !deviceIsCpu);
    if (useLong) {
        longEnergyDerivs = new OpenCLArray<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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    // 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);
            string value = "globals["+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);
        n2ValueSource << OpenCLExpressionUtilities::createExpressions(n2ValueExpressions, variables, functionDefinitions, "temp", prefix+"functionParams");
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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;
        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"+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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        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();
        map<string, string> defines;
        if (cl.getNonbondedUtilities().getForceBufferPerAtomBlock())
            defines["USE_OUTPUT_BUFFER_PER_BLOCK"] = "1";
        if (useCutoff)
            defines["USE_CUTOFF"] = "1";
        if (usePeriodic)
            defines["USE_PERIODIC"] = "1";
        if (useExclusionsForValue)
            defines["USE_EXCLUSIONS"] = "1";
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        if (cl.getSIMDWidth() == 32)
            defines["WARPS_PER_GROUP"] = OpenCLExpressionUtilities::intToString(cl.getNonbondedUtilities().getForceThreadBlockSize()/OpenCLContext::TileSize);
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        defines["CUTOFF_SQUARED"] = doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
        defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
        defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
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        defines["NUM_BLOCKS"] = OpenCLExpressionUtilities::intToString(cl.getNumAtomBlocks());
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        string file;
        if (deviceIsCpu)
            file = OpenCLKernelSources::customGBValueN2_cpu;
        else if (cl.getSIMDWidth() == 32)
            file = OpenCLKernelSources::customGBValueN2_nvidia;
        else
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            file = OpenCLKernelSources::customGBValueN2_default;
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        cl::Program program = cl.createProgram(cl.replaceStrings(file, replacements), defines);
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        pairValueKernel = cl::Kernel(program, "computeN2Value");
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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.

        stringstream reductionSource, extraArgs;
        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"+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"+intToString(i+1);
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            extraArgs << ", __global " << buffer.getType() << "* restrict global_" << valueName;
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            reductionSource << buffer.getType() << " local_" << valueName << ";\n";
        }
        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++)
            variables[force.getGlobalParameterName(i)] = "globals["+intToString(i)+"]";
        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 << OpenCLExpressionUtilities::createExpressions(valueExpressions, variables, functionDefinitions, "value"+intToString(i)+"_temp", prefix+"functionParams");
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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"+intToString(i+1);
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            reductionSource << "global_" << valueName << "[index] = local_" << valueName << ";\n";
        }
        map<string, string> replacements;
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        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
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        replacements["COMPUTE_VALUES"] = reductionSource.str();
        map<string, string> defines;
        defines["NUM_ATOMS"] = 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["+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]) {
                        string index = intToString(j+1);
                        n2EnergyExpressions["/*"+intToString(i+1)+"*/ deriv"+index+"_1 += "] = energyDerivExpressions[i][2*j];
                        n2EnergyExpressions["/*"+intToString(i+1)+"*/ deriv"+index+"_2 += "] = energyDerivExpressions[i][2*j+1];
                    }
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                }
            }
            else {
                for (int j = 0; j < force.getNumComputedValues(); j++) {
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                    if (needChainForValue[j]) {
                        n2EnergyExpressions["/*"+intToString(i+1)+"*/ deriv"+energyDerivs->getParameterSuffix(j, "_1")+" += "] = energyDerivExpressions[i][2*j];
                        n2EnergyExpressions["/*"+intToString(i+1)+"*/ deriv"+energyDerivs->getParameterSuffix(j, "_2")+" += "] = energyDerivExpressions[i][2*j+1];
                    }
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                }
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            }
            if (exclude)
                n2EnergySource << "if (!isExcluded) {\n";
            n2EnergySource << OpenCLExpressionUtilities::createExpressions(n2EnergyExpressions, variables, functionDefinitions, "temp", prefix+"functionParams");
            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;
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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];
            string paramName = "params"+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];
            string valueName = "values"+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++) {
                string index = intToString(i+1);
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                extraArgs << ", __local float* restrict local_deriv" << index;
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                clearLocal << "local_deriv" << index << "[localAtomIndex] = 0.0f;\n";
                declare1 << "float deriv" << index << "_1 = 0.0f;\n";
                load2 << "float 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 float tempDerivBuffer" << index << "[64];\n";
                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];
                string index = 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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        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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        map<string, string> defines;
        if (cl.getNonbondedUtilities().getForceBufferPerAtomBlock())
            defines["USE_OUTPUT_BUFFER_PER_BLOCK"] = "1";
        if (useCutoff)
            defines["USE_CUTOFF"] = "1";
        if (usePeriodic)
            defines["USE_PERIODIC"] = "1";
        if (anyExclusions)
            defines["USE_EXCLUSIONS"] = "1";
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        if (cl.getSIMDWidth() == 32)
            defines["WARPS_PER_GROUP"] = OpenCLExpressionUtilities::intToString(cl.getNonbondedUtilities().getForceThreadBlockSize()/OpenCLContext::TileSize);
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        defines["CUTOFF_SQUARED"] = doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
        defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
        defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
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        defines["NUM_BLOCKS"] = OpenCLExpressionUtilities::intToString(cl.getNumAtomBlocks());
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        string file;
        if (deviceIsCpu)
            file = OpenCLKernelSources::customGBEnergyN2_cpu;
        else if (cl.getSIMDWidth() == 32)
            file = OpenCLKernelSources::customGBEnergyN2_nvidia;
        else
            file = OpenCLKernelSources::customGBEnergyN2_default;
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        cl::Program program = cl.createProgram(cl.replaceStrings(file, replacements), defines);
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        pairEnergyKernel = cl::Kernel(program, "computeN2Energy");
    }
    {
        // Create the kernel to reduce the derivatives and calculate per-particle energy terms.

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        stringstream compute, extraArgs, reduce;
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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];
            string paramName = "params"+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];
            string valueName = "values"+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];
            string index = 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 (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]") <<
                        " = (1.0f/0xFFFFFFFF)*derivBuffersIn[index+PADDED_NUM_ATOMS*" << intToString(i) << "];\n";
        }
        else {
            for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++)
                reduce << "REDUCE_VALUE(derivBuffers" << intToString(i+1) << ", " << energyDerivs->getBuffers()[i].getType() << ")\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++)
            variables[force.getGlobalParameterName(i)] = "globals["+intToString(i)+"]";
        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["/*"+intToString(i+1)+"*/ energy += "] = parsed;
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            for (int j = 0; j < force.getNumComputedValues(); j++)
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                expressions["/*"+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["/*"+intToString(i+1)+"*/ force.x -= "] = gradx;
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            if (!isZeroExpression(grady))
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                expressions["/*"+intToString(i+1)+"*/ force.y -= "] = grady;
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            if (!isZeroExpression(gradz))
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                expressions["/*"+intToString(i+1)+"*/ force.z -= "] = gradz;
        }
        for (int i = 1; i < force.getNumComputedValues(); i++)
            for (int j = 0; j < i; j++)
                expressions["float dV"+intToString(i)+"dV"+intToString(j)+" = "] = valueDerivExpressions[i][j];
        compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functionDefinitions, "temp", prefix+"functionParams");
        
        // Record values.
        
        compute << "forceBuffers[index] = forceBuffers[index]+force;\n";
        for (int i = 1; i < force.getNumComputedValues(); i++) {
            compute << "float totalDeriv"<<i<<" = dV"<<i<<"dV0";
            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++) {
            string index = intToString(i+1);
            compute << "derivBuffers" << 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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        map<string, string> defines;
        defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
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        defines["PADDED_NUM_ATOMS"] = 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) {
        // Create the kernel to compute chain rule terms for computed values that depend explicitly on particle coordinates.

        stringstream compute, extraArgs;
        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];
            string paramName = "params"+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];
            string valueName = "values"+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];
            string index = 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";
        }
        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++)
            variables[force.getGlobalParameterName(i)] = "globals["+intToString(i)+"]";
        for (int i = 0; i < force.getNumComputedValues(); i++)
            variables[computedValueNames[i]] = "values"+computedValues->getParameterSuffix(i, "[index]");
        for (int i = 1; i < force.getNumComputedValues(); i++) {
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            string is = intToString(i);
            compute << "float4 dV"<<is<<"dR = (float4) 0;\n";
            for (int j = 1; j < i; j++) {
                if (!isZeroExpression(valueDerivExpressions[i][j])) {
                    map<string, Lepton::ParsedExpression> derivExpressions;
                    string js = intToString(j);
                    derivExpressions["float dV"+is+"dV"+js+" = "] = valueDerivExpressions[i][j];
                    compute << OpenCLExpressionUtilities::createExpressions(derivExpressions, variables, functionDefinitions, "temp_"+is+"_"+js, prefix+"functionParams");
                    compute << "dV"<<is<<"dR += dV"<<is<<"dV"<<js<<"*dV"<<js<<"dR;\n";
                }
            }
            map<string, Lepton::ParsedExpression> gradientExpressions;
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            if (!isZeroExpression(valueGradientExpressions[i][0]))
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                gradientExpressions["dV"+is+"dR.x += "] = valueGradientExpressions[i][0];
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            if (!isZeroExpression(valueGradientExpressions[i][1]))
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                gradientExpressions["dV"+is+"dR.y += "] = valueGradientExpressions[i][1];
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            if (!isZeroExpression(valueGradientExpressions[i][2]))
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                gradientExpressions["dV"+is+"dR.z += "] = valueGradientExpressions[i][2];
            compute << OpenCLExpressionUtilities::createExpressions(gradientExpressions, variables, functionDefinitions, "temp", prefix+"functionParams");
        }
        for (int i = 1; i < force.getNumComputedValues(); i++) {
            string is = intToString(i);
            compute << "force -= deriv"<<energyDerivs->getParameterSuffix(i)<<"*dV"<<is<<"dR;\n";
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        }
        map<string, string> replacements;
        replacements["PARAMETER_ARGUMENTS"] = extraArgs.str()+tableArgs.str();
        replacements["COMPUTE_FORCES"] = compute.str();
        map<string, string> defines;
        defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
        cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customGBGradientChainRule, replacements), defines);
        gradientChainRuleKernel = cl::Kernel(program, "computeGradientChainRuleTerms");
    }
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    {
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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);
            string value = "globals["+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["float dV0dR1 = "] = dVdR;
        derivExpressions["float dV0dR2 = "] = dVdR.renameVariables(rename);
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        chainSource << OpenCLExpressionUtilities::createExpressions(derivExpressions, variables, functionDefinitions, prefix+"temp0_", prefix+"functionParams");
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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];
            string paramName = prefix+"params"+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];
            string paramName = prefix+"values"+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) energyDerivs->getBuffers().size(); i++) {
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            if (needChainForValue[i]) { 
                const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
                string paramName = prefix+"dEdV"+intToString(i+1);
                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, force.getCutoffDistance(), 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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    }
    cl.addForce(new OpenCLCustomGBForceInfo(cl.getNonbondedUtilities().getNumForceBuffers(), force));
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    if (useLong)
        cl.addAutoclearBuffer(longEnergyDerivs->getDeviceBuffer(), 2*longEnergyDerivs->getSize());
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    else {
        for (int i = 0; i < (int) energyDerivs->getBuffers().size(); i++) {
            const OpenCLNonbondedUtilities::ParameterInfo& buffer = energyDerivs->getBuffers()[i];
            cl.addAutoclearBuffer(buffer.getMemory(), buffer.getSize()*energyDerivs->getNumObjects()/sizeof(cl_float));
        }
    }
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}

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double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
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    bool deviceIsCpu = (cl.getDevice().getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU);
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    OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
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        maxTiles = (nb.getUseCutoff() ? nb.getInteractingTiles().getSize() : 0);
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        bool useLong = (cl.getSupports64BitGlobalAtomics() && !deviceIsCpu);
        if (useLong) {
            longValueBuffers = new OpenCLArray<cl_long>(cl, cl.getPaddedNumAtoms(), "customGBLongValueBuffers");
            cl.addAutoclearBuffer(longValueBuffers->getDeviceBuffer(), 2*longValueBuffers->getSize());
            cl.clearBuffer(longValueBuffers->getDeviceBuffer(), 2*longValueBuffers->getSize());
        }
        else {
            valueBuffers = new OpenCLArray<cl_float>(cl, cl.getPaddedNumAtoms()*nb.getNumForceBuffers(), "customGBValueBuffers");
            cl.addAutoclearBuffer(valueBuffers->getDeviceBuffer(), valueBuffers->getSize());
            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())*sizeof(cl_float4), NULL);
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        pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusions().getDeviceBuffer());
        pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionIndices().getDeviceBuffer());
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        pairValueKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionRowIndices().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())*sizeof(cl_float), NULL);
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        /// \todo Eliminate this argument and make local to the kernel. For *_default.cl kernel can actually make it TileSize rather than getForceThreadBlockSize as only half the workgroup stores to it as was done with nonbonded_default.cl.
        /// \todo Also make the previous __local argument local as was done with nonbonded_default.cl.
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        pairValueKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*sizeof(cl_float), 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 += 2; // 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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            if (cl.getSIMDWidth() == 32 || deviceIsCpu)
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                pairValueKernel.setArg<cl::Buffer>(index++, nb.getInteractionFlags().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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        if (tabulatedFunctionParams != NULL) {
            for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
                pairValueKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
            pairValueKernel.setArg<cl::Buffer>(index++, tabulatedFunctionParams->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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        if (tabulatedFunctionParams != NULL) {
            for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
                perParticleValueKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
            perParticleValueKernel.setArg<cl::Buffer>(index++, tabulatedFunctionParams->getDeviceBuffer());
        }
        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())*sizeof(cl_float4), 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())*sizeof(cl_float4), NULL);
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        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusions().getDeviceBuffer());
        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionIndices().getDeviceBuffer());
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        pairEnergyKernel.setArg<cl::Buffer>(index++, cl.getNonbondedUtilities().getExclusionRowIndices().getDeviceBuffer());
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        /// \todo Eliminate this argument and make local to the kernel. For *_default.cl kernel can actually make it TileSize rather than getForceThreadBlockSize as only half the workgroup stores to it as was done with nonbonded_default.cl.
        /// \todo Also make the previous __local argument local as was done with nonbonded_default.cl.
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        pairEnergyKernel.setArg(index++, (deviceIsCpu ? OpenCLContext::TileSize : nb.getForceThreadBlockSize())*sizeof(cl_float4), NULL);
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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 += 2; // 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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            if (cl.getSIMDWidth() == 32 || deviceIsCpu)
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                pairEnergyKernel.setArg<cl::Buffer>(index++, nb.getInteractionFlags().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)
                pairEnergyKernel.setArg(index++, nb.getForceThreadBlockSize()*sizeof(cl_float), NULL);
        }
        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 (tabulatedFunctionParams != NULL) {
            for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
                pairEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
            pairEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctionParams->getDeviceBuffer());
        }
        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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        if (useLong)
            perParticleEnergyKernel.setArg<cl::Memory>(index++, longEnergyDerivs->getDeviceBuffer());
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        if (tabulatedFunctionParams != NULL) {
            for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
                perParticleEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
            perParticleEnergyKernel.setArg<cl::Buffer>(index++, tabulatedFunctionParams->getDeviceBuffer());
        }
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        if (needParameterGradient) {
            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 (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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    if (nb.getUseCutoff()) {
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        pairValueKernel.setArg<mm_float4>(10, cl.getPeriodicBoxSize());
        pairValueKernel.setArg<mm_float4>(11, cl.getInvPeriodicBoxSize());
        pairEnergyKernel.setArg<mm_float4>(11, cl.getPeriodicBoxSize());
        pairEnergyKernel.setArg<mm_float4>(12, cl.getInvPeriodicBoxSize());
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        if (maxTiles < nb.getInteractingTiles().getSize()) {
            maxTiles = nb.getInteractingTiles().getSize();
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            pairValueKernel.setArg<cl::Buffer>(8, nb.getInteractingTiles().getDeviceBuffer());
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            pairValueKernel.setArg<cl_uint>(12, maxTiles);
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            pairEnergyKernel.setArg<cl::Buffer>(9, nb.getInteractingTiles().getDeviceBuffer());
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            pairEnergyKernel.setArg<cl_uint>(13, maxTiles);
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            if (cl.getSIMDWidth() == 32 || deviceIsCpu) {
                pairValueKernel.setArg<cl::Buffer>(13, nb.getInteractionFlags().getDeviceBuffer());
                pairEnergyKernel.setArg<cl::Buffer>(14, nb.getInteractionFlags().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)
        cl.executeKernel(gradientChainRuleKernel, cl.getPaddedNumAtoms());
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    return 0.0;
}

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class OpenCLCustomExternalForceInfo : public OpenCLForceInfo {
public:
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    OpenCLCustomExternalForceInfo(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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    cl.addForce(new OpenCLCustomExternalForceInfo(force, system.getNumParticles()));

    // 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 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;
    expressions["float dEdX = "] = forceExpressionX;
    expressions["float dEdY = "] = forceExpressionY;
    expressions["float dEdZ = "] = forceExpressionZ;

    // 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) {
        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customExternalGlobals", false, CL_MEM_READ_ONLY);
        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);
            string value = argName+"["+intToString(i)+"]";
            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<pair<string, string> > functions;
    compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "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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class OpenCLCustomHbondForceInfo : public OpenCLForceInfo {
public:
    OpenCLCustomHbondForceInfo(int requiredBuffers, const CustomHbondForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
    }
    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);
3055
3056
3057
3058
3059
3060
            particles.clear();
            particles.push_back(p1);
            if (p2 > -1)
                particles.push_back(p2);
            if (p3 > -1)
                particles.push_back(p3);
3061
3062
3063
3064
3065
            return;
        }
        index -= force.getNumAcceptors();
        int donor, acceptor;
        force.getExclusionParticles(index, donor, acceptor);
3066
        particles.clear();
3067
        force.getDonorParameters(donor, p1, p2, p3, parameters);
3068
3069
3070
3071
3072
        particles.push_back(p1);
        if (p2 > -1)
            particles.push_back(p2);
        if (p3 > -1)
            particles.push_back(p3);
3073
        force.getAcceptorParameters(acceptor, p1, p2, p3, parameters);
3074
3075
3076
3077
3078
        particles.push_back(p1);
        if (p2 > -1)
            particles.push_back(p2);
        if (p3 > -1)
            particles.push_back(p3);
3079
3080
3081
3082
3083
3084
3085
3086
3087
3088
3089
3090
3091
3092
3093
3094
3095
3096
3097
3098
3099
3100
3101
3102
3103
3104
3105
3106
3107
3108
3109
3110
3111
3112
3113
3114
3115
3116
3117
3118
3119
    }
    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;
3120
3121
3122
3123
    if (donorExclusions != NULL)
        delete donorExclusions;
    if (acceptorExclusions != NULL)
        delete acceptorExclusions;
3124
3125
3126
3127
3128
3129
    if (tabulatedFunctionParams != NULL)
        delete tabulatedFunctionParams;
    for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
        delete tabulatedFunctions[i];
}

3130
3131
3132
3133
3134
3135
3136
3137
3138
3139
3140
3141
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";
}
3142

3143
void OpenCLCalcCustomHbondForceKernel::initialize(const System& system, const CustomHbondForce& force) {
3144
3145
    // Record the lists of donors and acceptors, and the parameters for each one.

3146
3147
3148
3149
    int numContexts = cl.getPlatformData().contexts.size();
    int startIndex = cl.getContextIndex()*force.getNumDonors()/numContexts;
    int endIndex = (cl.getContextIndex()+1)*force.getNumDonors()/numContexts;
    numDonors = endIndex-startIndex;
3150
    numAcceptors = force.getNumAcceptors();
3151
3152
    if (numDonors == 0 || numAcceptors == 0)
        return;
3153
3154
3155
3156
3157
3158
3159
3160
3161
3162
3163
    int numParticles = system.getNumParticles();
    donors = new OpenCLArray<mm_int4>(cl, numDonors, "customHbondDonors");
    acceptors = new OpenCLArray<mm_int4>(cl, numAcceptors, "customHbondAcceptors");
    donorParams = new OpenCLParameterSet(cl, force.getNumPerDonorParameters(), numDonors, "customHbondDonorParameters");
    acceptorParams = new OpenCLParameterSet(cl, force.getNumPerAcceptorParameters(), numAcceptors, "customHbondAcceptorParameters");
    if (force.getNumGlobalParameters() > 0)
        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customHbondGlobals", false, CL_MEM_READ_ONLY);
    vector<vector<cl_float> > donorParamVector(numDonors);
    vector<mm_int4> donorVector(numDonors);
    for (int i = 0; i < numDonors; i++) {
        vector<double> parameters;
3164
        force.getDonorParameters(startIndex+i, donorVector[i].x, donorVector[i].y, donorVector[i].z, parameters);
3165
3166
3167
3168
3169
3170
3171
3172
3173
3174
3175
3176
3177
3178
3179
3180
3181
3182
        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);

3183
    // Select an output buffer index for each donor and acceptor.
3184
3185
3186
3187
3188

    donorBufferIndices = new OpenCLArray<mm_int4>(cl, numDonors, "customHbondDonorBuffers");
    acceptorBufferIndices = new OpenCLArray<mm_int4>(cl, numAcceptors, "customHbondAcceptorBuffers");
    vector<mm_int4> donorBufferVector(numDonors);
    vector<mm_int4> acceptorBufferVector(numAcceptors);
3189
    vector<int> donorBufferCounter(numParticles, 0);
3190
    for (int i = 0; i < numDonors; i++)
3191
3192
3193
        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);
3194
    vector<int> acceptorBufferCounter(numParticles, 0);
3195
    for (int i = 0; i < numAcceptors; i++)
3196
3197
3198
        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);
3199
3200
    donorBufferIndices->upload(donorBufferVector);
    acceptorBufferIndices->upload(acceptorBufferVector);
3201
3202
3203
3204
3205
3206
    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]);
    cl.addForce(new OpenCLCustomHbondForceInfo(maxBuffers, force));
3207
3208
3209

    // Record exclusions.

3210
3211
    vector<mm_int4> donorExclusionVector(numDonors, mm_int4(-1, -1, -1, -1));
    vector<mm_int4> acceptorExclusionVector(numAcceptors, mm_int4(-1, -1, -1, -1));
3212
3213
3214
    for (int i = 0; i < force.getNumExclusions(); i++) {
        int donor, acceptor;
        force.getExclusionParticles(i, donor, acceptor);
3215
3216
3217
        if (donor < startIndex || donor >= endIndex)
            continue;
        donor -= startIndex;
3218
3219
3220
3221
3222
3223
3224
3225
3226
3227
3228
3229
3230
3231
3232
3233
3234
3235
3236
3237
        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");
3238
    }
3239
3240
3241
3242
    donorExclusions = new OpenCLArray<mm_int4>(cl, numDonors, "customHbondDonorExclusions");
    acceptorExclusions = new OpenCLArray<mm_int4>(cl, numDonors, "customHbondAcceptorExclusions");
    donorExclusions->upload(donorExclusionVector);
    acceptorExclusions->upload(acceptorExclusionVector);
3243
3244
3245
3246
3247
3248
3249
3250
3251
3252
3253
3254

    // Record the tabulated functions.

    OpenCLExpressionUtilities::FunctionPlaceholder fp;
    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
    vector<mm_float4> tabulatedFunctionParamsVec(force.getNumFunctions());
    stringstream tableArgs;
    for (int i = 0; i < force.getNumFunctions(); i++) {
        string name;
        vector<double> values;
        double min, max;
3255
        force.getFunctionParameters(i, name, values, min, max);
3256
        string arrayName = "table"+intToString(i);
3257
3258
        functionDefinitions.push_back(make_pair(name, arrayName));
        functions[name] = &fp;
3259
        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), (float) values.size()-2);
3260
        vector<mm_float4> f = OpenCLExpressionUtilities::computeFunctionCoefficients(values, min, max);
3261
3262
        tabulatedFunctions.push_back(new OpenCLArray<mm_float4>(cl, values.size()-1, "TabulatedFunction"));
        tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
3263
        tableArgs << ", __global const float4* restrict " << arrayName;
3264
3265
3266
3267
    }
    if (force.getNumFunctions() > 0) {
        tabulatedFunctionParams = new OpenCLArray<mm_float4>(cl, tabulatedFunctionParamsVec.size(), "tabulatedFunctionParameters", false, CL_MEM_READ_ONLY);
        tabulatedFunctionParams->upload(tabulatedFunctionParamsVec);
3268
        tableArgs << ", __global const float4* restrict functionParams";
3269
3270
    }

3271
    // Record information about parameters.
3272
3273
3274
3275
3276
3277
3278
3279
3280
3281
3282
3283
3284
3285
3286
3287
3288
3289
3290
3291
3292
3293

    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);
        variables[name] = "globals["+intToString(i)+"]";
    }
3294
3295
3296
3297
3298
3299
3300
3301
3302
3303
3304
3305
3306
3307
3308
3309
3310
3311
3312
3313
3314
3315
3316
3317
3318
3319
3320
3321
3322
3323
3324
3325
3326
3327
3328
3329
3330
3331
3332
3333
3334
3335
3336
3337
3338
3339
3340
3341
3342
3343
3344
3345
3346
3347
3348
3349
3350
3351
3352
3353
3354
3355
3356
3357
3358
3359
3360
3361
3362
3363
3364
3365
3366
3367
3368

    // 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) {
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 delta"+deltaName+" = delta("+atomNamesLower[atoms[0]]+", "+atomNamesLower[atoms[1]]+");\n");
            computedDeltas.insert(deltaName);
        }
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float r_"+deltaName+" = sqrt(delta"+deltaName+".w);\n");
        variables[iter->first] = "r_"+deltaName;
        forceExpressions["float dEdDistance"+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) {
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 delta"+deltaName1+" = delta("+atomNamesLower[atoms[1]]+", "+atomNamesLower[atoms[0]]+");\n");
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 delta"+deltaName2+" = delta("+atomNamesLower[atoms[1]]+", "+atomNamesLower[atoms[2]]+");\n");
            computedDeltas.insert(deltaName2);
        }
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float "+angleName+" = computeAngle(delta"+deltaName1+", delta"+deltaName2+");\n");
        variables[iter->first] = angleName;
        forceExpressions["float dEdAngle"+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) {
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 delta"+deltaName1+" = delta("+atomNamesLower[atoms[0]]+", "+atomNamesLower[atoms[1]]+");\n");
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 delta"+deltaName2+" = delta("+atomNamesLower[atoms[2]]+", "+atomNamesLower[atoms[1]]+");\n");
            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
            addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 delta"+deltaName3+" = delta("+atomNamesLower[atoms[2]]+", "+atomNamesLower[atoms[3]]+");\n");
            computedDeltas.insert(deltaName3);
        }
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 "+crossName1+" = computeCross(delta"+deltaName1+", delta"+deltaName2+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 "+crossName2+" = computeCross(delta"+deltaName2+", delta"+deltaName3+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float "+dihedralName+" = computeAngle("+crossName1+", "+crossName2+");\n");
        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;
        forceExpressions["float dEdDihedral"+intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }

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

3369
    if (force.getNumGlobalParameters() > 0)
3370
        extraArgs << ", __global const float* restrict globals";
3371
3372
    for (int i = 0; i < (int) donorParams->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = donorParams->getBuffers()[i];
3373
        extraArgs << ", __global const "+buffer.getType()+"* restrict donor"+buffer.getName();
3374
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, buffer.getType()+" donorParams"+intToString(i+1)+" = donor"+buffer.getName()+"[index];\n");
3375
3376
3377
    }
    for (int i = 0; i < (int) acceptorParams->getBuffers().size(); i++) {
        const OpenCLNonbondedUtilities::ParameterInfo& buffer = acceptorParams->getBuffers()[i];
3378
        extraArgs << ", __global const "+buffer.getType()+"* restrict acceptor"+buffer.getName();
3379
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, buffer.getType()+" acceptorParams"+intToString(i+1)+" = acceptor"+buffer.getName()+"[index];\n");
3380
    }
3381
3382
3383
3384
3385
3386
3387
3388
3389
3390
3391
3392
3393
3394
3395
3396
3397
3398
3399
3400
3401
3402
3403
3404
3405
3406
3407
3408
3409
3410
3411
3412
3413
3414
3415
3416
3417
3418
3419
3420
3421
3422
3423
3424
3425
3426
3427
3428
3429
3430
3431
3432
3433
3434
3435
3436
3437
3438
3439
3440

    // Now evaluate the expressions.

    computeAcceptor << OpenCLExpressionUtilities::createExpressions(forceExpressions, variables, functionDefinitions, "temp", "functionParams");
    forceExpressions["energy += "] = energyExpression;
    computeDonor << OpenCLExpressionUtilities::createExpressions(forceExpressions, variables, functionDefinitions, "temp", "functionParams");

    // 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]];
        string value = "(dEdDistance"+intToString(index)+"/r_"+deltaName+")*delta"+deltaName+".xyz";
        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");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 crossProd = cross(delta"+deltaName2+", delta"+deltaName1+");\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float lengthCross = max(length(crossProd), 1e-6f);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 deltaCross0 = -cross(delta"+deltaName1+", crossProd)*dEdAngle"+intToString(index)+"/(delta"+deltaName1+".w*lengthCross);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 deltaCross2 = cross(delta"+deltaName2+", crossProd)*dEdAngle"+intToString(index)+"/(delta"+deltaName2+".w*lengthCross);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 deltaCross1 = -(deltaCross0+deltaCross2);\n");
        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");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float r = sqrt(delta"+deltaName2+".w);\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 ff;\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.x = (-dEdDihedral"+intToString(index)+"*r)/"+crossName1+".w;\n");
        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");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "ff.w = (dEdDihedral"+intToString(index)+"*r)/"+crossName2+".w;\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 internalF0 = ff.x*"+crossName1+";\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 internalF3 = ff.w*"+crossName2+";\n");
        addDonorAndAcceptorCode(computeDonor, computeAcceptor, "float4 s = ff.y*internalF0 - ff.z*internalF3;\n");
        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;
    defines["PADDED_NUM_ATOMS"] = intToString(cl.getPaddedNumAtoms());
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    defines["NUM_DONORS"] = intToString(numDonors);
    defines["NUM_ACCEPTORS"] = intToString(numAcceptors);
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    defines["M_PI"] = doubleToString(M_PI);
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    if (force.getNonbondedMethod() != CustomHbondForce::NoCutoff) {
        defines["USE_CUTOFF"] = "1";
        defines["CUTOFF_SQUARED"] = doubleToString(force.getCutoffDistance()*force.getCutoffDistance());
    }
    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";
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    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 += 2; // 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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        }
        if (tabulatedFunctionParams != NULL) {
            for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
                donorKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
            donorKernel.setArg<cl::Buffer>(index++, tabulatedFunctionParams->getDeviceBuffer());
        }
        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 += 2; // 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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        }
        if (tabulatedFunctionParams != NULL) {
            for (int i = 0; i < (int) tabulatedFunctions.size(); i++)
                acceptorKernel.setArg<cl::Buffer>(index++, tabulatedFunctions[i]->getDeviceBuffer());
            acceptorKernel.setArg<cl::Buffer>(index++, tabulatedFunctionParams->getDeviceBuffer());
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        }
    }
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    donorKernel.setArg<mm_float4>(8, cl.getPeriodicBoxSize());
    donorKernel.setArg<mm_float4>(9, cl.getInvPeriodicBoxSize());
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    cl.executeKernel(donorKernel, max(numDonors, numAcceptors));
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    acceptorKernel.setArg<mm_float4>(8, cl.getPeriodicBoxSize());
    acceptorKernel.setArg<mm_float4>(9, cl.getInvPeriodicBoxSize());
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    cl.executeKernel(acceptorKernel, max(numDonors, numAcceptors));
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    return 0.0;
}

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class OpenCLCustomCompoundBondForceInfo : public OpenCLForceInfo {
public:
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    OpenCLCustomCompoundBondForceInfo(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;
    if (tabulatedFunctionParams != NULL)
        delete tabulatedFunctionParams;
    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);
    cl.addForce(new OpenCLCustomCompoundBondForceInfo(force));

    // Record the tabulated functions.

    OpenCLExpressionUtilities::FunctionPlaceholder fp;
    map<string, Lepton::CustomFunction*> functions;
    vector<pair<string, string> > functionDefinitions;
    vector<mm_float4> tabulatedFunctionParamsVec(force.getNumFunctions());
    stringstream tableArgs;
    for (int i = 0; i < force.getNumFunctions(); i++) {
        string name;
        vector<double> values;
        double min, max;
        force.getFunctionParameters(i, name, values, min, max);
        functions[name] = &fp;
        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), (float) values.size()-2);
        vector<mm_float4> f = OpenCLExpressionUtilities::computeFunctionCoefficients(values, min, max);
        OpenCLArray<mm_float4>* array = new OpenCLArray<mm_float4>(cl, values.size()-1, "TabulatedFunction");
        tabulatedFunctions.push_back(array);
        array->upload(f);
        string arrayName = cl.getBondedUtilities().addArgument(array->getDeviceBuffer(), "float4");
        functionDefinitions.push_back(make_pair(name, arrayName));
    }
    string functionParamsName;
    if (force.getNumFunctions() > 0) {
        tabulatedFunctionParams = new OpenCLArray<mm_float4>(cl, tabulatedFunctionParamsVec.size(), "tabulatedFunctionParameters", false, CL_MEM_READ_ONLY);
        tabulatedFunctionParams->upload(tabulatedFunctionParamsVec);
        functionParamsName = cl.getBondedUtilities().addArgument(tabulatedFunctionParams->getDeviceBuffer(), "float4");
    }
    
    // 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++) {
        string index = 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);
    }
    if (force.getNumGlobalParameters() > 0) {
        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customCompoundBondGlobals", false, CL_MEM_READ_ONLY);
        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);
            string value = argName+"["+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 = 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++) {
        string index = 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) {
            compute<<"float4 delta"<<deltaName<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<");\n";
            computedDeltas.insert(deltaName);
        }
        compute<<"float r_"<<deltaName<<" = sqrt(delta"<<deltaName<<".w);\n";
        variables[iter->first] = "r_"+deltaName;
        forceExpressions["float dEdDistance"+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) {
            compute<<"float4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[0]]<<");\n";
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
            compute<<"float4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[1]]<<", "<<posNames[atoms[2]]<<");\n";
            computedDeltas.insert(deltaName2);
        }
        compute<<"float "<<angleName<<" = ccb_computeAngle(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        variables[iter->first] = angleName;
        forceExpressions["float dEdAngle"+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) {
            compute<<"float4 delta"<<deltaName1<<" = ccb_delta("<<posNames[atoms[0]]<<", "<<posNames[atoms[1]]<<");\n";
            computedDeltas.insert(deltaName1);
        }
        if (computedDeltas.count(deltaName2) == 0) {
            compute<<"float4 delta"<<deltaName2<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[1]]<<");\n";
            computedDeltas.insert(deltaName2);
        }
        if (computedDeltas.count(deltaName3) == 0) {
            compute<<"float4 delta"<<deltaName3<<" = ccb_delta("<<posNames[atoms[2]]<<", "<<posNames[atoms[3]]<<");\n";
            computedDeltas.insert(deltaName3);
        }
        compute<<"float4 "<<crossName1<<" = ccb_computeCross(delta"<<deltaName1<<", delta"<<deltaName2<<");\n";
        compute<<"float4 "<<crossName2<<" = ccb_computeCross(delta"<<deltaName2<<", delta"<<deltaName3<<");\n";
        compute<<"float "<<dihedralName<<" = ccb_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["float dEdDihedral"+intToString(index)+" = "] = energyExpression.differentiate(iter->first).optimize();
    }

    // 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;
    compute << OpenCLExpressionUtilities::createExpressions(forceExpressions, variables, functionDefinitions, "temp", functionParamsName);

    // Finally, apply forces to atoms.

    vector<string> forceNames;
    for (int i = 0; i < particlesPerBond; i++) {
        string istr = intToString(i+1);
        string forceName = "force"+istr;
        forceNames.push_back(forceName);
        compute<<"float4 "<<forceName<<" = (float4) (0.0f, 0.0f, 0.0f, 0.0f);\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<<OpenCLExpressionUtilities::createExpressions(expressions, variables, functionDefinitions, "coordtemp", functionParamsName);
        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"+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<<"float4 crossProd = cross(delta"<<deltaName2<<", delta"<<deltaName1<<");\n";
        compute<<"float lengthCross = max(length(crossProd), 1e-6f);\n";
        compute<<"float4 deltaCross0 = -cross(delta"<<deltaName1<<", crossProd)*dEdAngle"<<intToString(index)<<"/(delta"<<deltaName1<<".w*lengthCross);\n";
        compute<<"float4 deltaCross2 = cross(delta"<<deltaName2<<", crossProd)*dEdAngle"<<intToString(index)<<"/(delta"<<deltaName2<<".w*lengthCross);\n";
        compute<<"float4 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<<"float r = sqrt(delta"<<deltaName2<<".w);\n";
        compute<<"float4 ff;\n";
        compute<<"ff.x = (-dEdDihedral"<<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"<<intToString(index)<<"*r)/"<<crossName2<<".w;\n";
        compute<<"float4 internalF0 = ff.x*"<<crossName1<<";\n";
        compute<<"float4 internalF3 = ff.w*"<<crossName2<<";\n";
        compute<<"float4 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";
    }
    cl.getBondedUtilities().addInteraction(atoms, compute.str(), force.getForceGroup());
    map<string, string> replacements;
    replacements["M_PI"] = doubleToString(M_PI);
    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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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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    prevStepSize = -1.0;
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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());
        kernel1.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(4, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
        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());
        kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(4, integration.getPosDelta().getDeviceBuffer());
    }
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    if (dt != prevStepSize) {
        vector<mm_float2> stepSizeVec(1);
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        stepSizeVec[0] = mm_float2((cl_float) dt, (cl_float) dt);
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        cl.getIntegrationUtilities().getStepSize().upload(stepSizeVec);
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        prevStepSize = 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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}

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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;
    defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = 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_float>(cl, 3, "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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        kernel2.setArg<cl::Buffer>(1, integration.getPosDelta().getDeviceBuffer());
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        kernel2.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(3, integration.getStepSize().getDeviceBuffer());
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    }
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    double temperature = integrator.getTemperature();
    double friction = integrator.getFriction();
    double stepSize = integrator.getStepSize();
    if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
        // Calculate the integration parameters.

        double tau = (friction == 0.0 ? 0.0 : 1.0/friction);
        double kT = BOLTZ*temperature;
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        double vscale = exp(-stepSize/tau);
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        double fscale = (1-vscale)*tau;
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        double noisescale = sqrt(2*kT/tau)*sqrt(0.5*(1-vscale*vscale)*tau);
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        vector<cl_float> p(params->getSize());
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        p[0] = (cl_float) vscale;
        p[1] = (cl_float) fscale;
        p[2] = (cl_float) noisescale;
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        params->upload(p);
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        integration.getStepSize()[0].y = (cl_float) stepSize;
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        integration.getStepSize().upload();
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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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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;
    defines["NUM_ATOMS"] = 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());
        kernel2.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(3, integration.getPosDelta().getDeviceBuffer());
    }
    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);
        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));
        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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OpenCLIntegrateVariableVerletStepKernel::~OpenCLIntegrateVariableVerletStepKernel() {
}

void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, const VariableVerletIntegrator& 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");
    selectSizeKernel = cl::Kernel(program, "selectVerletStepSize");
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    blockSize = min(min(256, system.getNumParticles()), (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
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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();
    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());
        kernel1.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(4, cl.getForce().getDeviceBuffer());
        kernel1.setArg<cl::Buffer>(5, integration.getPosDelta().getDeviceBuffer());
        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());
        kernel2.setArg<cl::Buffer>(3, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(4, integration.getPosDelta().getDeviceBuffer());
        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());
        selectSizeKernel.setArg(6, blockSize*sizeof(cl_float), NULL);
    }

    // Select the step size to use.

    float maxStepSize = (float)(maxTime-cl.getTime());
    selectSizeKernel.setArg<cl_float>(1, maxStepSize);
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    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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    // Update the time and step count.

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    cl.getIntegrationUtilities().getStepSize().download();
    double dt = cl.getIntegrationUtilities().getStepSize()[0].y;
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    double time = cl.getTime()+dt;
    if (dt == maxStepSize)
        time = maxTime; // Avoid round-off error
    cl.setTime(time);
    cl.setStepCount(cl.getStepCount()+1);
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    return dt;
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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;
    defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
    defines["PADDED_NUM_ATOMS"] = 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_float>(cl, 3, "langevinParams");
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    blockSize = min(256, system.getNumParticles());
    blockSize = max(blockSize, params->getSize());
    blockSize = min(blockSize, (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
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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();
    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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        kernel2.setArg<cl::Buffer>(1, integration.getPosDelta().getDeviceBuffer());
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        kernel2.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
        kernel2.setArg<cl::Buffer>(3, 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());
        selectSizeKernel.setArg(8, params->getSize()*sizeof(cl_float), NULL);
        selectSizeKernel.setArg(9, blockSize*sizeof(cl_float), NULL);
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    }

    // Select the step size to use.

    float maxStepSize = (float)(maxTime-cl.getTime());
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    selectSizeKernel.setArg<cl_float>(0, maxStepSize);
    selectSizeKernel.setArg<cl_float>(1, (cl_float) integrator.getErrorTolerance());
    selectSizeKernel.setArg<cl_float>(2, (cl_float) (integrator.getFriction() == 0.0 ? 0.0 : 1.0/integrator.getFriction()));
    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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    // Update the time and step count.

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    cl.getIntegrationUtilities().getStepSize().download();
    double dt = cl.getIntegrationUtilities().getStepSize()[0].y;
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    double time = cl.getTime()+dt;
    if (dt == maxStepSize)
        time = maxTime; // Avoid round-off error
    cl.setTime(time);
    cl.setStepCount(cl.getStepCount()+1);
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    return dt;
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}

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class OpenCLIntegrateCustomStepKernel::ReorderListener : public OpenCLContext::ReorderListener {
public:
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    ReorderListener(OpenCLContext& cl, OpenCLParameterSet& perDofValues, vector<vector<cl_float> >& localPerDofValues, bool& deviceValuesAreCurrent) :
            cl(cl), perDofValues(perDofValues), localPerDofValues(localPerDofValues), 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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        if (deviceValuesAreCurrent)
            perDofValues.getParameterValues(localPerDofValues);
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        vector<vector<cl_float> > swap(3*numAtoms);
        for (int i = 0; i < numAtoms; i++) {
            swap[3*lastAtomOrder[i]] = localPerDofValues[3*i];
            swap[3*lastAtomOrder[i]+1] = localPerDofValues[3*i+1];
            swap[3*lastAtomOrder[i]+2] = localPerDofValues[3*i+2];
        }
        OpenCLArray<cl_int>& order = cl.getAtomIndex();
        for (int i = 0; i < numAtoms; i++) {
            localPerDofValues[3*i] = swap[3*order[i]];
            localPerDofValues[3*i+1] = swap[3*order[i]+1];
            localPerDofValues[3*i+2] = swap[3*order[i]+2];
        }
        perDofValues.setParameterValues(localPerDofValues);
        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;
    vector<vector<cl_float> >& localPerDofValues;
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    bool& deviceValuesAreCurrent;
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    vector<int> lastAtomOrder;
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};

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OpenCLIntegrateCustomStepKernel::~OpenCLIntegrateCustomStepKernel() {
    if (globalValues != NULL)
        delete globalValues;
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    if (contextParameterValues != NULL)
        delete contextParameterValues;
    if (sumBuffer != NULL)
        delete sumBuffer;
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    if (energy != NULL)
        delete energy;
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    if (uniformRandoms != NULL)
        delete uniformRandoms;
    if (randomSeed != NULL)
        delete randomSeed;
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    if (perDofValues != NULL)
        delete perDofValues;
}

void OpenCLIntegrateCustomStepKernel::initialize(const System& system, const CustomIntegrator& integrator) {
    cl.getPlatformData().initializeContexts(system);
    cl.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
    numGlobalVariables = integrator.getNumGlobalVariables();
    globalValues = new OpenCLArray<cl_float>(cl, max(1, numGlobalVariables), "globalVariables", true);
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    sumBuffer = new OpenCLArray<cl_float>(cl, 3*system.getNumParticles(), "sumBuffer");
    energy = new OpenCLArray<cl_float>(cl, 1, "energy");
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    perDofValues = new OpenCLParameterSet(cl, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables");
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    cl.addReorderListener(new ReorderListener(cl, *perDofValues, localPerDofValues, deviceValuesAreCurrent));
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    prevStepSize = -1.0;
    SimTKOpenMMUtilities::setRandomNumberSeed(integrator.getRandomNumberSeed());
}

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string OpenCLIntegrateCustomStepKernel::createGlobalComputation(const string& variable, const Lepton::ParsedExpression& expr, CustomIntegrator& integrator, const string& energyName) {
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    map<string, Lepton::ParsedExpression> expressions;
    if (variable == "dt")
        expressions["dt[0].y = "] = expr;
    else {
        for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
            if (variable == integrator.getGlobalVariableName(i))
                expressions["globals["+intToString(i)+"] = "] = expr;
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        for (int i = 0; i < (int) parameterNames.size(); i++)
            if (variable == parameterNames[i]) {
                expressions["params["+intToString(i)+"] = "] = expr;
                modifiesParameters = true;
            }
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    }
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    if (expressions.size() == 0)
        throw OpenMMException("Unknown global variable: "+variable);
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    map<string, string> variables;
    variables["dt"] = "dt[0].y";
    variables["uniform"] = "uniform";
    variables["gaussian"] = "gaussian";
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    variables[energyName] = "energy[0]";
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    for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
        variables[integrator.getGlobalVariableName(i)] = "globals["+intToString(i)+"]";
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    for (int i = 0; i < (int) parameterNames.size(); i++)
        variables[parameterNames[i]] = "params["+intToString(i)+"]";
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    vector<pair<string, string> > functions;
    return OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
}

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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 == "")
        expressions["sum[3*index+"+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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    variables[energyName] = "energy[0]";
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    for (int i = 0; i < integrator.getNumGlobalVariables(); i++)
        variables[integrator.getGlobalVariableName(i)] = "globals["+intToString(i)+"]";
    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++)
        variables[parameterNames[i]] = "params["+intToString(i)+"]";
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    vector<pair<string, string> > functions;
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    string tempType = (cl.getSupportsDoublePrecision() ? "double" : "float");
    return OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp"+intToString(component)+"_", "", tempType);
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}

void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {
    OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
    int numAtoms = cl.getNumAtoms();
    int numSteps = integrator.getNumComputations();
    if (!hasInitializedKernels) {
        hasInitializedKernels = true;
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        // Initialize various data structures.
        
        const map<string, double>& params = context.getParameters();
        contextParameterValues = new OpenCLArray<cl_float>(cl, max(1, (int) params.size()), "contextParameters", true);
        for (map<string, double>::const_iterator iter = params.begin(); iter != params.end(); ++iter) {
            contextParameterValues->set(parameterNames.size(), (float) iter->second);
            parameterNames.push_back(iter->first);
        }
        contextParameterValues->upload();
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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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        needsForces.resize(numSteps, false);
        needsEnergy.resize(numSteps, false);
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        forceGroup.resize(numSteps, -2);
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        invalidatesForces.resize(numSteps, false);
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        merged.resize(numSteps, false);
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        modifiesParameters = false;
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        map<string, string> defines;
        defines["NUM_ATOMS"] = intToString(cl.getNumAtoms());
        defines["WORK_GROUP_SIZE"] = intToString(OpenCLContext::ThreadBlockSize);
        
        // Initialize the random number generator.
        
        uniformRandoms = new OpenCLArray<mm_float4>(cl, cl.getNumAtoms(), "uniformRandoms");
        randomSeed = new OpenCLArray<mm_int4>(cl, cl.getNumThreadBlocks()*OpenCLContext::ThreadBlockSize, "randomSeed");
        vector<mm_int4> seed(randomSeed->getSize());
        unsigned int r = integrator.getRandomNumberSeed()+1;
        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");
        randomKernel.setArg<cl::Buffer>(0, uniformRandoms->getDeviceBuffer());
        randomKernel.setArg<cl::Buffer>(1, randomSeed->getDeviceBuffer());
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        // Build a list of all variables that affect the forces, so we can tell which
        // steps invalidate them.
        
        set<string> affectsForce;
        affectsForce.insert("x");
        for (vector<ForceImpl*>::const_iterator iter = context.getForceImpls().begin(); iter != context.getForceImpls().end(); ++iter) {
            const map<string, double> params = (*iter)->getDefaultParameters();
            for (map<string, double>::const_iterator param = params.begin(); param != params.end(); ++param)
                affectsForce.insert(param->first);
        }
        
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        // Record information about all the computation steps.
        
        stepType.resize(numSteps);
        vector<string> variable(numSteps);
        vector<Lepton::ParsedExpression> expression(numSteps);
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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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        for (int step = 0; step < numSteps; step++) {
            string expr;
            integrator.getComputationStep(step, stepType[step], variable[step], expr);
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            if (expr.size() > 0) {
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                expression[step] = Lepton::Parser::parse(expr).optimize();
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                if (usesVariable(expression[step], "f")) {
                    needsForces[step] = true;
                    forceGroup[step] = -1;
                }
                if (usesVariable(expression[step], "energy")) {
                    needsEnergy[step] = true;
                    forceGroup[step] = -1;
                }
                for (int i = 0; i < 32; i++) {
                    if (usesVariable(expression[step], forceGroupName[i])) {
                        if (forceGroup[step] != -2)
                            throw OpenMMException("A single computation step cannot depend on multiple force groups");
                        needsForces[step] = true;
                        forceGroup[step] = 1<<i;
                        forceName[step] = forceGroupName[i];
                    }
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                    if (usesVariable(expression[step], energyGroupName[i])) {
                        if (forceGroup[step] != -2)
                            throw OpenMMException("A single computation step cannot depend on multiple force groups");
                        needsEnergy[step] = true;
                        forceGroup[step] = 1<<i;
                        energyName[step] = energyGroupName[i];
                    }
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                }
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            }
            invalidatesForces[step] = (stepType[step] == CustomIntegrator::ConstrainPositions || affectsForce.find(variable[step]) != affectsForce.end());
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            if (forceGroup[step] == -2 && step > 0)
                forceGroup[step] = forceGroup[step-1];
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        }
        
        // Determine how each step will represent the position (as just a value, or a value plus a delta).
        
        vector<bool> storePosAsDelta(numSteps, false);
        vector<bool> loadPosAsDelta(numSteps, false);
        bool beforeConstrain = false;
        for (int step = numSteps-1; step >= 0; step--) {
            if (stepType[step] == CustomIntegrator::ConstrainPositions)
                beforeConstrain = true;
            else if (stepType[step] == CustomIntegrator::ComputePerDof && variable[step] == "x" && beforeConstrain)
                storePosAsDelta[step] = true;
        }
        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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        // Identify steps that can be merged into a single kernel.
        
        for (int step = 1; step < numSteps; step++) {
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            if (needsForces[step] || needsEnergy[step])
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                continue;
            if (stepType[step-1] == CustomIntegrator::ComputeGlobal && stepType[step] == CustomIntegrator::ComputeGlobal)
                merged[step] = true;
            if (stepType[step-1] == CustomIntegrator::ComputePerDof && stepType[step] == CustomIntegrator::ComputePerDof &&
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                    !usesVariable(expression[step], "uniform"))
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                merged[step] = true;
        }
        
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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];
                    compute << buffer.getType()<<" perDofx"<<intToString(i+1)<<" = perDofValues"<<intToString(i+1)<<"[3*index];\n";
                    compute << buffer.getType()<<" perDofy"<<intToString(i+1)<<" = perDofValues"<<intToString(i+1)<<"[3*index+1];\n";
                    compute << buffer.getType()<<" perDofz"<<intToString(i+1)<<" = perDofValues"<<intToString(i+1)<<"[3*index+2];\n";
                }
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                string convert = (cl.getSupportsDoublePrecision() ? "convert_float4(" : "(");
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                int numGaussian = 0, numUniform = 0;
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                for (int j = step; j < numSteps && (j == step || merged[j]); j++) {
                    compute << "{\n";
                    for (int i = 0; i < 3; i++)
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                        compute << createPerDofComputation(stepType[j] == CustomIntegrator::ComputePerDof ? variable[j] : "", expression[j], i, integrator, forceName[j], energyName[j]);
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                    if (variable[j] == "x") {
                        if (storePosAsDelta[j]) {
                            if (cl.getSupportsDoublePrecision())
                                compute << "posDelta[index] = convert_float4(position-convert_double4(posq[index]));\n";
                            else
                                compute << "posDelta[index] = position-posq[index];\n";
                        }
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                        else
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                            compute << "posq[index] = " << convert << "position);\n";
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                    }
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                    else if (variable[j] == "v")
                        compute << "velm[index] = " << convert << "velocity);\n";
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                    else {
                        for (int i = 0; i < (int) perDofValues->getBuffers().size(); i++) {
                            const OpenCLNonbondedUtilities::ParameterInfo& buffer = perDofValues->getBuffers()[i];
                            compute << "perDofValues"<<intToString(i+1)<<"[3*index] = perDofx"<<intToString(i+1)<<";\n";
                            compute << "perDofValues"<<intToString(i+1)<<"[3*index+1] = perDofy"<<intToString(i+1)<<";\n";
                            compute << "perDofValues"<<intToString(i+1)<<"[3*index+2] = perDofz"<<intToString(i+1)<<";\n";
                        }
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                    }
                    compute << "}\n";
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                    numGaussian += numAtoms*usesVariable(expression[j], "gaussian");
                    numUniform += numAtoms*usesVariable(expression[j], "uniform");
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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];
                    string valueName = "perDofValues"+intToString(i+1);
                    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());
                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++, contextParameterValues->getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
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                kernel.setArg<cl::Buffer>(index++, integration.getRandom().getDeviceBuffer());
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                index++;
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                kernel.setArg<cl::Buffer>(index++, uniformRandoms->getDeviceBuffer());
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                kernel.setArg<cl::Buffer>(index++, energy->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, "computeSum");
                    kernels[step].push_back(kernel);
                    index = 0;
                    kernel.setArg<cl::Buffer>(index++, sumBuffer->getDeviceBuffer());
                    bool found = false;
                    for (int j = 0; j < integrator.getNumGlobalVariables() && !found; j++)
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                        if (variable[step] == integrator.getGlobalVariableName(j)) {
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                            kernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
                            kernel.setArg<cl_uint>(index++, j);
                            found = true;
                        }
                    for (int j = 0; j < (int) parameterNames.size() && !found; j++)
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                        if (variable[step] == parameterNames[j]) {
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                            kernel.setArg<cl::Buffer>(index++, contextParameterValues->getDeviceBuffer());
                            kernel.setArg<cl_uint>(index++, j);
                            found = true;
                            modifiesParameters = true;
                        }
                    if (!found)
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                        throw OpenMMException("Unknown global variable: "+variable[step]);
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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::ComputeGlobal && !merged[step]) {
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                // Compute a global value.

                stringstream compute;
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                for (int i = step; i < numSteps && (i == step || merged[i]); i++)
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                    compute << "{\n" << createGlobalComputation(variable[i], expression[i], integrator, energyName[i]) << "}\n";
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                map<string, string> replacements;
                replacements["COMPUTE_STEP"] = compute.str();
                cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customIntegratorGlobal, replacements), defines);
                cl::Kernel kernel = cl::Kernel(program, "computeGlobal");
                kernels[step].push_back(kernel);
                int index = 0;
                kernel.setArg<cl::Buffer>(index++, integration.getStepSize().getDeviceBuffer());
                kernel.setArg<cl::Buffer>(index++, globalValues->getDeviceBuffer());
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                kernel.setArg<cl::Buffer>(index++, contextParameterValues->getDeviceBuffer());
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                index += 2;
                kernel.setArg<cl::Buffer>(index++, energy->getDeviceBuffer());
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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());
                kernel.setArg<cl::Buffer>(index++, integration.getPosDelta().getDeviceBuffer());
            }
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        }
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        // Create the kernel for summing energy.

        cl::Program program = cl.createProgram(OpenCLKernelSources::customIntegrator, defines);
        sumEnergyKernel = cl::Kernel(program, "computeSum");
        int index = 0;
        sumEnergyKernel.setArg<cl::Buffer>(index++, cl.getEnergyBuffer().getDeviceBuffer());
        sumEnergyKernel.setArg<cl::Buffer>(index++, energy->getDeviceBuffer());
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        sumEnergyKernel.setArg<cl_int>(index++, 0);
        sumEnergyKernel.setArg<cl_int>(index++, cl.getEnergyBuffer().getSize());
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    }
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    // Make sure all values (variables, parameters, etc.) stored on the device are up to date.
    
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    if (!deviceValuesAreCurrent) {
        perDofValues->setParameterValues(localPerDofValues);
        deviceValuesAreCurrent = true;
    }
    localValuesAreCurrent = false;
    double stepSize = integrator.getStepSize();
    if (stepSize != prevStepSize) {
        integration.getStepSize()[0].y = (cl_float) stepSize;
        integration.getStepSize().upload();
        prevStepSize = stepSize;
    }
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    bool paramsChanged = false;
    for (int i = 0; i < (int) parameterNames.size(); i++) {
        float value = (float) context.getParameter(parameterNames[i]);
        if (value != contextParameterValues->get(i)) {
            contextParameterValues->set(i, value);
            paramsChanged = true;
        }
    }
    if (paramsChanged)
        contextParameterValues->upload();
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    // Loop over computation steps in the integrator and execute them.

    for (int i = 0; i < numSteps; i++) {
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        if ((needsForces[i] || needsEnergy[i]) && (!forcesAreValid || context.getLastForceGroups() != forceGroup[i])) {
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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.
            
            bool computeForce = false, computeEnergy = false;
            for (int j = i; ; j++) {
                if (needsForces[j])
                    computeForce = true;
                if (needsEnergy[j])
                    computeEnergy = true;
                if (invalidatesForces[j])
                    break;
                if (j == numSteps-1)
                    j = -1;
                if (j == i-1)
                    break;
            }
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            recordChangedParameters(context);
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            context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroup[i]);
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            if (computeEnergy)
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                cl.executeKernel(sumEnergyKernel, OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
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            forcesAreValid = true;
        }
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        if (stepType[i] == CustomIntegrator::ComputePerDof && !merged[i]) {
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            kernels[i][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredGaussian[i]));
            if (requiredUniform[i] > 0)
                cl.executeKernel(randomKernel, numAtoms);
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            cl.executeKernel(kernels[i][0], numAtoms);
        }
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        else if (stepType[i] == CustomIntegrator::ComputeGlobal && !merged[i]) {
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            kernels[i][0].setArg<cl_float>(3, SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber());
            kernels[i][0].setArg<cl_float>(4, SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
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            cl.executeKernel(kernels[i][0], 1, 1);
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        }
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        else if (stepType[i] == CustomIntegrator::ComputeSum) {
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            kernels[i][0].setArg<cl_uint>(9, integration.prepareRandomNumbers(requiredGaussian[i]));
            if (requiredUniform[i] > 0)
                cl.executeKernel(randomKernel, numAtoms);
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            cl.executeKernel(kernels[i][0], numAtoms);
            cl.executeKernel(kernels[i][1], OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
        }
        else if (stepType[i] == CustomIntegrator::UpdateContextState) {
            recordChangedParameters(context);
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            context.updateContextState();
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        }
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        else if (stepType[i] == CustomIntegrator::ConstrainPositions) {
            cl.getIntegrationUtilities().applyConstraints(integrator.getConstraintTolerance());
            cl.executeKernel(kernels[i][0], numAtoms);
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            cl.getIntegrationUtilities().computeVirtualSites();
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        }
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        else if (stepType[i] == CustomIntegrator::ConstrainVelocities) {
            cl.getIntegrationUtilities().applyVelocityConstraints(integrator.getConstraintTolerance());
        }
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        if (invalidatesForces[i])
            forcesAreValid = false;
    }
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    recordChangedParameters(context);
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    // Update the time and step count.

    cl.setTime(cl.getTime()+stepSize);
    cl.setStepCount(cl.getStepCount()+1);
}

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void OpenCLIntegrateCustomStepKernel::recordChangedParameters(ContextImpl& context) {
    if (!modifiesParameters)
        return;
    contextParameterValues->download();
    for (int i = 0; i < (int) parameterNames.size(); i++) {
        float value = (float) context.getParameter(parameterNames[i]);
        if (value != contextParameterValues->get(i))
            context.setParameter(parameterNames[i], contextParameterValues->get(i));
    }
}

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void OpenCLIntegrateCustomStepKernel::getGlobalVariables(ContextImpl& context, vector<double>& values) const {
    globalValues->download();
    values.resize(numGlobalVariables);
    for (int i = 0; i < numGlobalVariables; i++)
        values[i] = globalValues->get(i);
}

void OpenCLIntegrateCustomStepKernel::setGlobalVariables(ContextImpl& context, const vector<double>& values) {
    for (int i = 0; i < numGlobalVariables; i++)
        globalValues->set(i, (float) values[i]);
    globalValues->upload();
}

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

void OpenCLIntegrateCustomStepKernel::setPerDofVariable(ContextImpl& context, int variable, const vector<Vec3>& values) {
    if (!localValuesAreCurrent) {
        perDofValues->getParameterValues(localPerDofValues);
        localValuesAreCurrent = true;
    }
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    OpenCLArray<cl_int>& order = cl.getAtomIndex();
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    for (int i = 0; i < (int) values.size(); i++)
        for (int j = 0; j < 3; j++)
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            localPerDofValues[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;
    defines["NUM_ATOMS"] = 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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Peter Eastman committed
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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);
    atomGroups = new OpenCLArray<int>(cl, cl.getNumAtoms(), "atomGroups");
    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;
}

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

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

        // Create the arrays with the molecule definitions.

        vector<vector<int> > molecules = context.getMolecules();
        numMolecules = molecules.size();
        moleculeAtoms = new OpenCLArray<int>(cl, cl.getNumAtoms(), "moleculeAtoms");
        moleculeStartIndex = new OpenCLArray<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>(1, numMolecules);
        kernel.setArg<cl::Buffer>(4, cl.getPosq().getDeviceBuffer());
        kernel.setArg<cl::Buffer>(5, moleculeAtoms->getDeviceBuffer());
        kernel.setArg<cl::Buffer>(6, moleculeStartIndex->getDeviceBuffer());
    }
    cl.getQueue().enqueueCopyBuffer(cl.getPosq().getDeviceBuffer(), savedPositions->getDeviceBuffer(), 0, 0, cl.getPosq().getSize()*sizeof(mm_float4));
    kernel.setArg<cl_float>(0, (cl_float) scale);
    kernel.setArg<mm_float4>(2, cl.getPeriodicBoxSize());
    kernel.setArg<mm_float4>(3, cl.getInvPeriodicBoxSize());
    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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}

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

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void OpenCLCalcKineticEnergyKernel::initialize(const System& system) {
    int numParticles = system.getNumParticles();
    masses.resize(numParticles);
    for (int i = 0; i < numParticles; ++i)
        masses[i] = system.getParticleMass(i);
}

double OpenCLCalcKineticEnergyKernel::execute(ContextImpl& context) {
    // We don't currently have a GPU kernel to do this, so we retrieve the velocities and calculate the energy
    // on the CPU.

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    OpenCLArray<mm_float4>& velm = cl.getVelm();
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    velm.download();
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    double energy = 0.0;
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    OpenCLArray<cl_int>& order = cl.getAtomIndex();
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    for (size_t i = 0; i < masses.size(); ++i) {
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        mm_float4 v = velm[i];
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        energy += masses[order[i]]*(v.x*v.x+v.y*v.y+v.z*v.z);
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    }
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    return 0.5*energy;
}
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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();
    cmMomentum = new OpenCLArray<mm_float4>(cl, (numAtoms+OpenCLContext::ThreadBlockSize-1)/OpenCLContext::ThreadBlockSize, "cmMomentum");
    double totalMass = 0.0;
    for (int i = 0; i < numAtoms; i++)
        totalMass += system.getParticleMass(i);
    map<string, string> defines;
    defines["INVERSE_TOTAL_MASS"] = doubleToString(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());
}