Created OpenCL implementation of CustomExternalForce. Also fixed a bug.

platforms/opencl/src/OpenCLKernelFactory.cpp

@@ -54,6 +54,8 @@ KernelImpl* OpenCLKernelFactory::createKernelImpl(std::string name, const Platfo
         return new OpenCLCalcCustomNonbondedForceKernel(name, platform, cl, context.getSystem());
     if (name == CalcGBSAOBCForceKernel::Name())
         return new OpenCLCalcGBSAOBCForceKernel(name, platform, cl);
+    if (name == CalcCustomExternalForceKernel::Name())
+        return new OpenCLCalcCustomExternalForceKernel(name, platform, cl, context.getSystem());
     if (name == IntegrateVerletStepKernel::Name())
         return new OpenCLIntegrateVerletStepKernel(name, platform, cl);
     if (name == IntegrateLangevinStepKernel::Name())

platforms/opencl/src/OpenCLKernels.cpp

@@ -348,7 +348,7 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
     string suffixes[] = {".x", ".y", ".z", ".w"};
     for (int i = 0; i < force.getNumPerBondParameters(); i++) {
         const string& name = force.getPerBondParameterName(i);
-        variables[name] = "exceptionParams"+suffixes[i];
+        variables[name] = "bondParams"+suffixes[i];
     }
     for (int i = 0; i < force.getNumGlobalParameters(); i++) {
         const string& name = force.getGlobalParameterName(i);
@@ -1316,6 +1316,155 @@ double OpenCLCalcGBSAOBCForceKernel::executeEnergy(ContextImpl& context) {
     executeForces(context);
     return 0.0;
 }
+class OpenCLCustomExternalForceInfo : public OpenCLForceInfo {
+public:
+    OpenCLCustomExternalForceInfo(const CustomExternalForce& force, int numParticles) : OpenCLForceInfo(1), force(force), indices(numParticles, -1) {
+        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);
+        for (int i = 0; i < params1.size(); i++)
+            if (params1[i] != params2[i])
+                return false;
+        return true;
+    }
+private:
+    const CustomExternalForce& force;
+    vector<int> indices;
+};
+
+OpenCLCalcCustomExternalForceKernel::~OpenCLCalcCustomExternalForceKernel() {
+    if (params != NULL)
+        delete params;
+    if (indices != NULL)
+        delete indices;
+    if (globals != NULL)
+        delete globals;
+}
+
+void OpenCLCalcCustomExternalForceKernel::initialize(const System& system, const CustomExternalForce& force) {
+    if (force.getNumPerParticleParameters() > 4)
+        throw OpenMMException("OpenCLPlatform only supports four per-particle parameters for custom external forces");
+    numParticles = force.getNumParticles();
+    params = new OpenCLArray<mm_float4>(cl, numParticles, "customExternalParams");
+    indices = new OpenCLArray<cl_int>(cl, numParticles, "customExternalIndices");
+    string extraArguments;
+    if (force.getNumGlobalParameters() > 0) {
+        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customExternalGlobals", false, CL_MEM_READ_ONLY);
+        extraArguments += ", __constant float* globals";
+    }
+    vector<mm_float4> paramVector(numParticles);
+    vector<cl_int> indicesVector(numParticles);
+    for (int i = 0; i < numParticles; i++) {
+        vector<double> parameters;
+        force.getParticleParameters(i, indicesVector[i], parameters);
+        if (parameters.size() > 0)
+            paramVector[i].x = (cl_float) parameters[0];
+        if (parameters.size() > 1)
+            paramVector[i].y = (cl_float) parameters[1];
+        if (parameters.size() > 2)
+            paramVector[i].z = (cl_float) parameters[2];
+        if (parameters.size() > 3)
+            paramVector[i].w = (cl_float) parameters[3];
+    }
+    params->upload(paramVector);
+    indices->upload(indicesVector);
+    cl.addForce(new OpenCLCustomExternalForceInfo(force, system.getNumParticles()));
+
+    // Record information for the expressions.
+
+    vector<string> paramNames;
+    for (int i = 0; i < force.getNumPerParticleParameters(); i++)
+        paramNames.push_back(force.getPerParticleParameterName(i));
+    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);
+    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;
+    variables["x"] = "pos.x";
+    variables["y"] = "pos.y";
+    variables["z"] = "pos.z";
+    string suffixes[] = {".x", ".y", ".z", ".w"};
+    for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
+        const string& name = force.getPerParticleParameterName(i);
+        variables[name] = "particleParams"+suffixes[i];
+    }
+    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
+        const string& name = force.getGlobalParameterName(i);
+        string value = "globals["+intToString(i)+"]";
+        variables[name] = value;
+    }
+    map<string, string> replacements;
+    stringstream compute;
+    vector<pair<string, string> > functions;
+    compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
+    replacements["COMPUTE_FORCE"] = compute.str();
+    replacements["EXTRA_ARGUMENTS"] = extraArguments;
+    cl::Program program = cl.createProgram(cl.loadSourceFromFile("customExternalForce.cl", replacements));
+    kernel = cl::Kernel(program, "computeCustomExternalForces");
+}
+
+void OpenCLCalcCustomExternalForceKernel::executeForces(ContextImpl& context) {
+    if (globals != NULL) {
+        bool changed = false;
+        for (int i = 0; i < 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;
+        kernel.setArg<cl_int>(0, numParticles);
+        kernel.setArg<cl::Buffer>(1, cl.getForceBuffers().getDeviceBuffer());
+        kernel.setArg<cl::Buffer>(2, cl.getEnergyBuffer().getDeviceBuffer());
+        kernel.setArg<cl::Buffer>(3, cl.getPosq().getDeviceBuffer());
+        kernel.setArg<cl::Buffer>(4, params->getDeviceBuffer());
+        kernel.setArg<cl::Buffer>(5, indices->getDeviceBuffer());
+        if (globals != NULL)
+            kernel.setArg<cl::Buffer>(6, globals->getDeviceBuffer());
+    }
+    cl.executeKernel(kernel, numParticles);
+}
+
+double OpenCLCalcCustomExternalForceKernel::executeEnergy(ContextImpl& context) {
+    executeForces(context);
+    return 0.0;
+}
 
 OpenCLIntegrateVerletStepKernel::~OpenCLIntegrateVerletStepKernel() {
 }

platforms/opencl/src/OpenCLKernels.h

@@ -472,6 +472,48 @@ private:
     cl::Kernel reduceBornForceKernel;
 };
 
+/**
+ * This kernel is invoked by CustomExternalForce to calculate the forces acting on the system and the energy of the system.
+ */
+class OpenCLCalcCustomExternalForceKernel : public CalcCustomExternalForceKernel {
+public:
+    OpenCLCalcCustomExternalForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomExternalForceKernel(name, platform),
+            hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
+    }
+    ~OpenCLCalcCustomExternalForceKernel();
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param force      the CustomExternalForce this kernel will be used for
+     */
+    void initialize(const System& system, const CustomExternalForce& force);
+    /**
+     * Execute the kernel to calculate the forces.
+     *
+     * @param context    the context in which to execute this kernel
+     */
+    void executeForces(ContextImpl& context);
+    /**
+     * Execute the kernel to calculate the energy.
+     *
+     * @param context    the context in which to execute this kernel
+     * @return the potential energy due to the CustomExternalForce
+     */
+    double executeEnergy(ContextImpl& context);
+private:
+    int numParticles;
+    bool hasInitializedKernel;
+    OpenCLContext& cl;
+    System& system;
+    OpenCLArray<mm_float4>* params;
+    OpenCLArray<cl_int>* indices;
+    OpenCLArray<cl_float>* globals;
+    std::vector<std::string> globalParamNames;
+    std::vector<cl_float> globalParamValues;
+    cl::Kernel kernel;
+};
+
 /**
  * This kernel is invoked by VerletIntegrator to take one time step.
  */

platforms/opencl/src/OpenCLPlatform.cpp

@@ -55,6 +55,7 @@ OpenCLPlatform::OpenCLPlatform() {
     registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomNonbondedForceKernel::Name(), factory);
     registerKernelFactory(CalcGBSAOBCForceKernel::Name(), factory);
+    registerKernelFactory(CalcCustomExternalForceKernel::Name(), factory);
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
     registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
     registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);

platforms/opencl/src/kernels/customBondForce.cl

@@ -5,13 +5,12 @@
 __kernel void computeCustomBondForces(int numAtoms, int numBonds, __global float4* forceBuffers, __global float* energyBuffer,
         __global float4* posq, __global float4* params, __global int4* indices
         EXTRA_ARGUMENTS) {
-    int index = get_global_id(0);
     float energy = 0.0f;
-    while (index < numBonds) {
-        // Look up the data for this exception.
+    for (int index = get_global_id(0); index < numBonds; index += get_global_size(0)) {
+        // Look up the data for this bond.
 
         int4 atoms = indices[index];
-        float4 exceptionParams = params[index];
+        float4 bondParams = params[index];
         float4 delta = posq[atoms.y]-posq[atoms.x];
 
         // Compute the force.
@@ -30,7 +29,6 @@ __kernel void computeCustomBondForces(int numAtoms, int numBonds, __global float
         forceB.xyz += delta.xyz;
         forceBuffers[offsetA] = forceA;
         forceBuffers[offsetB] = forceB;
-        index += get_global_size(0);
     }
     energyBuffer[get_global_id(0)] += energy;
 }

platforms/opencl/src/kernels/customExternalForce.cl

+/**
+ * Compute custom external forces.
+ */
+
+__kernel void computeCustomExternalForces(int numTerms, __global float4* forceBuffers, __global float* energyBuffer,
+        __global float4* posq, __global float4* params, __global int* indices
+        EXTRA_ARGUMENTS) {
+    float energy = 0.0f;
+    for (int index = get_global_id(0); index < numTerms; index += get_global_size(0)) {
+        // Look up the data for this particle.
+
+        int atom = indices[index];
+        float4 particleParams = params[index];
+        float4 pos = posq[atom];
+
+        // Compute the force.
+
+        COMPUTE_FORCE
+
+        // Record the force on the atom.
+
+        float4 force = forceBuffers[atom];
+        force.x -= dEdX;
+        force.y -= dEdY;
+        force.z -= dEdZ;
+        forceBuffers[atom] = force;
+    }
+    energyBuffer[get_global_id(0)] += energy;
+}

platforms/opencl/tests/TestOpenCLCustomExternalForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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.               *
+ *                                                                            *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the OpenCL implementation of CustomExternalForce.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "OpenCLPlatform.h"
+#include "openmm/CustomExternalForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testForce() {
+    OpenCLPlatform platform;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomExternalForce* forceField = new CustomExternalForce("scale*(x+yscale*(y-y0)^2)");
+    forceField->addPerParticleParameter("y0");
+    forceField->addPerParticleParameter("yscale");
+    forceField->addGlobalParameter("scale", 0.5);
+    vector<double> parameters(2);
+    parameters[0] = 0.5;
+    parameters[1] = 2.0;
+    forceField->addParticle(0, parameters);
+    parameters[0] = 1.5;
+    parameters[1] = 3.0;
+    forceField->addParticle(2, parameters);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(3);
+    positions[0] = Vec3(0, 2, 0);
+    positions[1] = Vec3(0, 0, 1);
+    positions[2] = Vec3(1, 0, 1);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    const vector<Vec3>& forces = state.getForces();
+    ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
+    ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
+}
+
+int main() {
+    try {
+        testForce();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+
+
+

platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp

@@ -106,9 +106,9 @@ int ReferenceCustomExternalIxn::calculateForce( int atomIndex,
 
    // ---------------------------------------------------------------------------------------
 
-   forces[atomIndex][0] += forceExpressionX.evaluate(variables);
-   forces[atomIndex][1] += forceExpressionY.evaluate(variables);
-   forces[atomIndex][2] += forceExpressionZ.evaluate(variables);
+   forces[atomIndex][0] -= forceExpressionX.evaluate(variables);
+   forces[atomIndex][1] -= forceExpressionY.evaluate(variables);
+   forces[atomIndex][2] -= forceExpressionZ.evaluate(variables);
    if (energy != NULL)
        *energy += energyExpression.evaluate(variables);
 

platforms/reference/tests/TestReferenceCustomExternalForce.cpp

@@ -75,9 +75,9 @@ void testForce() {
     context.setPositions(positions);
     State state = context.getState(State::Forces | State::Energy);
     const vector<Vec3>& forces = state.getForces();
-    ASSERT_EQUAL_VEC(Vec3(0.5, 0.5*2.0*2.0*1.5, 0), forces[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
     ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0.5, -0.5*3.0*2.0*1.5, 0), forces[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
     ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
 }