Created OpenCL version of CustomAngleForce

platforms/opencl/src/OpenCLKernelFactory.cpp

@@ -44,6 +44,8 @@ KernelImpl* OpenCLKernelFactory::createKernelImpl(std::string name, const Platfo
         return new OpenCLCalcCustomBondForceKernel(name, platform, cl, context.getSystem());
     if (name == CalcHarmonicAngleForceKernel::Name())
         return new OpenCLCalcHarmonicAngleForceKernel(name, platform, cl, context.getSystem());
+    if (name == CalcCustomAngleForceKernel::Name())
+        return new OpenCLCalcCustomAngleForceKernel(name, platform, cl, context.getSystem());
     if (name == CalcPeriodicTorsionForceKernel::Name())
         return new OpenCLCalcPeriodicTorsionForceKernel(name, platform, cl, context.getSystem());
     if (name == CalcRBTorsionForceKernel::Name())

platforms/opencl/src/OpenCLKernels.cpp

@@ -484,6 +484,161 @@ double OpenCLCalcHarmonicAngleForceKernel::executeEnergy(ContextImpl& context) {
     return 0.0;
 }
 
+class OpenCLCustomAngleForceInfo : public OpenCLForceInfo {
+public:
+    OpenCLCustomAngleForceInfo(int requiredBuffers, const CustomAngleForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
+    }
+    int getNumParticleGroups() {
+        return force.getNumAngles();
+    }
+    void getParticlesInGroup(int index, std::vector<int>& particles) {
+        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 (indices != NULL)
+        delete indices;
+    if (globals != NULL)
+        delete globals;
+}
+
+void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const CustomAngleForce& force) {
+    numAngles = force.getNumAngles();
+    if (numAngles == 0)
+        return;
+    params = new OpenCLParameterSet(cl, force.getNumPerAngleParameters(), numAngles, "customAngleParams");
+    indices = new OpenCLArray<mm_int8>(cl, numAngles, "customAngleIndices");
+    string extraArguments;
+    if (force.getNumGlobalParameters() > 0) {
+        globals = new OpenCLArray<cl_float>(cl, force.getNumGlobalParameters(), "customAngleGlobals", false, CL_MEM_READ_ONLY);
+        extraArguments += ", __constant float* globals";
+    }
+    vector<int> forceBufferCounter(system.getNumParticles(), 0);
+    vector<vector<cl_float> > paramVector(numAngles);
+    vector<mm_int8> indicesVector(numAngles);
+    for (int i = 0; i < numAngles; i++) {
+        int particle1, particle2, particle3;
+        vector<double> parameters;
+        force.getAngleParameters(i, particle1, particle2, particle3, parameters);
+        paramVector[i].resize(parameters.size());
+        for (int j = 0; j < (int) parameters.size(); j++)
+            paramVector[i][j] = (cl_float) parameters[j];
+        indicesVector[i] = mm_int8(particle1, particle2, particle3, forceBufferCounter[particle1]++,
+                forceBufferCounter[particle2]++, forceBufferCounter[particle3]++, 0, 0);
+    }
+    params->setParameterValues(paramVector);
+    indices->upload(indicesVector);
+    int maxBuffers = 1;
+    for (int i = 0; i < (int) forceBufferCounter.size(); i++)
+        maxBuffers = max(maxBuffers, forceBufferCounter[i]);
+    cl.addForce(new OpenCLCustomAngleForceInfo(maxBuffers, force));
+
+    // Record information for the expressions.
+
+    vector<string> paramNames;
+    for (int i = 0; i < force.getNumPerAngleParameters(); i++)
+        paramNames.push_back(force.getPerAngleParameterName(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 forceExpression = energyExpression.differentiate("theta").optimize();
+    map<string, Lepton::ParsedExpression> expressions;
+    expressions["energy += "] = energyExpression;
+    expressions["float dEdR = "] = forceExpression;
+
+    // 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);
+    }
+    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
+        const string& name = force.getGlobalParameterName(i);
+        string value = "globals["+intToString(i)+"]";
+        variables[name] = value;
+    }
+    stringstream compute;
+    for (int i = 0; i < (int) params->getBuffers().size(); i++) {
+        const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
+        extraArguments += ", __global "+buffer.getType()+"* "+buffer.getName();
+        compute<<buffer.getType()<<" angleParams"<<(i+1)<<" = "<<buffer.getName()<<"[index];\n";
+    }
+    vector<pair<string, string> > functions;
+    compute << OpenCLExpressionUtilities::createExpressions(expressions, variables, functions, "temp", "");
+    map<string, string> replacements;
+    replacements["COMPUTE_FORCE"] = compute.str();
+    replacements["EXTRA_ARGUMENTS"] = extraArguments;
+    cl::Program program = cl.createProgram(cl.replaceStrings(OpenCLKernelSources::customAngleForce, replacements));
+    kernel = cl::Kernel(program, "computeCustomAngleForces");
+}
+
+void OpenCLCalcCustomAngleForceKernel::executeForces(ContextImpl& context) {
+    if (numAngles == 0)
+        return;
+    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;
+        kernel.setArg<cl_int>(0, cl.getPaddedNumAtoms());
+        kernel.setArg<cl_int>(1, numAngles);
+        kernel.setArg<cl::Buffer>(2, cl.getForceBuffers().getDeviceBuffer());
+        kernel.setArg<cl::Buffer>(3, cl.getEnergyBuffer().getDeviceBuffer());
+        kernel.setArg<cl::Buffer>(4, cl.getPosq().getDeviceBuffer());
+        kernel.setArg<cl::Buffer>(5, indices->getDeviceBuffer());
+        int nextIndex = 6;
+        if (globals != NULL)
+            kernel.setArg<cl::Buffer>(nextIndex++, globals->getDeviceBuffer());
+        for (int i = 0; i < (int) params->getBuffers().size(); i++) {
+            const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
+            kernel.setArg<cl::Buffer>(nextIndex++, buffer.getBuffer());
+        }
+    }
+    cl.executeKernel(kernel, numAngles);
+}
+
+double OpenCLCalcCustomAngleForceKernel::executeEnergy(ContextImpl& context) {
+    executeForces(context);
+    return 0.0;
+}
+
 class OpenCLPeriodicTorsionForceInfo : public OpenCLForceInfo {
 public:
     OpenCLPeriodicTorsionForceInfo(int requiredBuffers, const PeriodicTorsionForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {

platforms/opencl/src/OpenCLKernels.h

@@ -268,6 +268,48 @@ private:
     cl::Kernel kernel;
 };
 
+/**
+ * This kernel is invoked by CustomAngleForce to calculate the forces acting on the system and the energy of the system.
+ */
+class OpenCLCalcCustomAngleForceKernel : public CalcCustomAngleForceKernel {
+public:
+    OpenCLCalcCustomAngleForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomAngleForceKernel(name, platform),
+            hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
+    }
+    ~OpenCLCalcCustomAngleForceKernel();
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param force      the CustomAngleForce this kernel will be used for
+     */
+    void initialize(const System& system, const CustomAngleForce& 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 CustomAngleForce
+     */
+    double executeEnergy(ContextImpl& context);
+private:
+    int numAngles;
+    bool hasInitializedKernel;
+    OpenCLContext& cl;
+    System& system;
+    OpenCLParameterSet* params;
+    OpenCLArray<mm_int8>* indices;
+    OpenCLArray<cl_float>* globals;
+    std::vector<std::string> globalParamNames;
+    std::vector<cl_float> globalParamValues;
+    cl::Kernel kernel;
+};
+
 /**
  * This kernel is invoked by PeriodicTorsionForce to calculate the forces acting on the system and the energy of the system.
  */

platforms/opencl/src/OpenCLPlatform.cpp

@@ -49,6 +49,7 @@ OpenCLPlatform::OpenCLPlatform() {
     registerKernelFactory(CalcHarmonicBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomBondForceKernel::Name(), factory);
     registerKernelFactory(CalcHarmonicAngleForceKernel::Name(), factory);
+    registerKernelFactory(CalcCustomAngleForceKernel::Name(), factory);
     registerKernelFactory(CalcPeriodicTorsionForceKernel::Name(), factory);
     registerKernelFactory(CalcRBTorsionForceKernel::Name(), factory);
     registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);

platforms/opencl/src/kernels/customAngleForce.cl

+/**
+ * Compute custom angle forces.
+ */
+
+__kernel void computeCustomAngleForces(int numAtoms, int numAngles, __global float4* forceBuffers, __global float* energyBuffer,
+        __global float4* posq, __global int8* indices
+        EXTRA_ARGUMENTS) {
+    float energy = 0.0f;
+    for (int index = get_global_id(0); index < numAngles; index += get_global_size(0)) {
+        int8 atoms = indices[index];
+        float4 a1 = posq[atoms.s0];
+        float4 a2 = posq[atoms.s1];
+        float4 a3 = posq[atoms.s2];
+
+        // Compute the force.
+
+        float4 v0 = a2-a1;
+        float4 v1 = a2-a3;
+        float4 cp = cross(v0, v1);
+        float rp = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
+        rp = max(sqrt(rp), 1.0e-06f);
+        float r21 = v0.x*v0.x + v0.y*v0.y + v0.z*v0.z;
+        float r23 = v1.x*v1.x + v1.y*v1.y + v1.z*v1.z;
+        float dot = v0.x*v1.x + v0.y*v1.y + v0.z*v1.z;
+        float cosine = dot/sqrt(r21*r23);
+        float theta = acos(cosine);
+        COMPUTE_FORCE
+        float4 c21 = cross(v0, cp)*(dEdR/(r21*rp));
+        float4 c23 = cross(cp, v1)*(dEdR/(r23*rp));
+
+        // Record the force on each of the three atoms.
+
+        unsigned int offsetA = atoms.s0+atoms.s3*numAtoms;
+        unsigned int offsetB = atoms.s1+atoms.s4*numAtoms;
+        unsigned int offsetC = atoms.s2+atoms.s5*numAtoms;
+        float4 forceA = forceBuffers[offsetA];
+        float4 forceB = forceBuffers[offsetB];
+        float4 forceC = forceBuffers[offsetC];
+        forceA.xyz += c21.xyz;
+        forceB.xyz -= c21.xyz+c23.xyz;
+        forceC.xyz += c23.xyz;
+        forceBuffers[offsetA] = forceA;
+        forceBuffers[offsetB] = forceB;
+        forceBuffers[offsetC] = forceC;
+    }
+    energyBuffer[get_global_id(0)] += energy;
+}

platforms/opencl/tests/TestOpenCLCustomAngleForce.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) 2008-2010 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 CustomAngleForce.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "OpenCLPlatform.h"
+#include "openmm/CustomAngleForce.h"
+#include "openmm/HarmonicAngleForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "../src/sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testAngles() {
+    OpenCLPlatform platform;
+
+    // Create a system using a CustomAngleForce.
+
+    System customSystem;
+    customSystem.addParticle(1.0);
+    customSystem.addParticle(1.0);
+    customSystem.addParticle(1.0);
+    customSystem.addParticle(1.0);
+    CustomAngleForce* custom = new CustomAngleForce("scale*k*(theta-theta0)^2");
+    custom->addPerAngleParameter("theta0");
+    custom->addPerAngleParameter("k");
+    custom->addGlobalParameter("scale", 0.5);
+    vector<double> parameters(2);
+    parameters[0] = 1.5;
+    parameters[1] = 0.8;
+    custom->addAngle(0, 1, 2, parameters);
+    parameters[0] = 2.0;
+    parameters[1] = 0.5;
+    custom->addAngle(1, 2, 3, parameters);
+    customSystem.addForce(custom);
+
+    // Create an identical system using a HarmonicAngleForce.
+
+    System harmonicSystem;
+    harmonicSystem.addParticle(1.0);
+    harmonicSystem.addParticle(1.0);
+    harmonicSystem.addParticle(1.0);
+    harmonicSystem.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    HarmonicAngleForce* harmonic = new HarmonicAngleForce();
+    harmonic->addAngle(0, 1, 2, 1.5, 0.8);
+    harmonic->addAngle(1, 2, 3, 2.0, 0.5);
+    harmonicSystem.addForce(harmonic);
+
+    // Set the atoms in various positions, and verify that both systems give identical forces and energy.
+
+    init_gen_rand(0);
+    vector<Vec3> positions(4);
+    VerletIntegrator integrator1(0.01);
+    VerletIntegrator integrator2(0.01);
+    for (int i = 0; i < 10; i++) {
+        Context c1(customSystem, integrator1, platform);
+        Context c2(harmonicSystem, integrator2, platform);
+        for (int j = 0; j < (int) positions.size(); j++)
+            positions[j] = Vec3(5.0*genrand_real2(), 5.0*genrand_real2(), 5.0*genrand_real2());
+        c1.setPositions(positions);
+        c2.setPositions(positions);
+        State s1 = c1.getState(State::Forces | State::Energy);
+        State s2 = c2.getState(State::Forces | State::Energy);
+        const vector<Vec3>& forces = s1.getForces();
+        ASSERT_EQUAL_VEC(s1.getForces()[0], s2.getForces()[0], TOL);
+        ASSERT_EQUAL_VEC(s1.getForces()[1], s2.getForces()[1], TOL);
+        ASSERT_EQUAL_VEC(s1.getForces()[2], s2.getForces()[2], TOL);
+        ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
+    }
+}
+
+int main() {
+    try {
+        testAngles();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+
+
+