DPDIntegrator (#4799)

* Created DPDIntegrator class

* Reference implementation of DPDIntegrator

* Build neighbor list for DPDIntegrator

* Minor fixes

* Documentation for DPDIntegrator

* Python API for DPDIntegrator

* Preliminary OpenCL implementation of DPDIntegrator

* Enable USE_PERIODIC

* Use updated positions in DPD thermostat

* Working on neighbor list for OpenCL DPDIntegrator

* ReorderListener for particle types

* Serialization for DPDIntegrator

* CUDA implementation of DPDIntegrator

* HIP implementation of DPDIntegrator

* Fixed compile error in Python wrapper

* Fixed compile error in wrappers

* Fixed uninitialized memory in reference neighbor list

* Added DPDIntegrator to C++ API docs

* Fixed incorrect launch size

* Fixed nan in DPD random number generator

* Minor optimizations

* Improved load balancing

* Fixed an indexing error

* Neighbor list uses the maximum cutoff of any force

* Fixed HIP compilation error

* Fixed access to invalid memory

* Added test case for diffusion coefficient

* Try to debug segfaults on CI

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Possible fix

* Debugging

* Debugging

* Debugging

* Use correct block size on CPU OpenCL

* Workaround for bug in Intel's OpenCL for CPUs

* Removed an unnecessary define

* Removed debugging code

* Include Dart

* More Intel workarounds

* Workaround for error in NVIDIA OpenCL

serialization/src/DPDIntegratorProxy.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) 2025 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/DPDIntegratorProxy.h"
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+DPDIntegratorProxy::DPDIntegratorProxy() : SerializationProxy("DPDIntegrator") {
+
+}
+
+void DPDIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const DPDIntegrator& integrator = *reinterpret_cast<const DPDIntegrator*>(object);
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
+    node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
+    node.setDoubleProperty("temperature", integrator.getTemperature());
+    node.setDoubleProperty("defaultFriction", integrator.getDefaultFriction());
+    node.setDoubleProperty("defaultCutoff", integrator.getDefaultCutoff());
+    node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
+    node.setIntProperty("integrationForceGroups", integrator.getIntegrationForceGroups());
+    SerializationNode& types = node.createChildNode("ParticleTypes");
+    for (auto type: integrator.getParticleTypes())
+        types.createChildNode("Type").setIntProperty("particle", type.first).setIntProperty("type", type.second);
+    SerializationNode& pairs = node.createChildNode("TypePairs");
+    for (int i = 0; i < integrator.getNumTypePairs(); i++) {
+        int type1, type2;
+        double friction, cutoff;
+        integrator.getTypePairParameters(i, type1, type2, friction, cutoff);
+        pairs.createChildNode("Pair").setIntProperty("type1", type1).setIntProperty("type2", type2).setDoubleProperty("friction", friction).setDoubleProperty("cutoff", cutoff);
+    }
+}
+
+void* DPDIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    DPDIntegrator *integrator = new DPDIntegrator(node.getDoubleProperty("temperature"),
+                                                            node.getDoubleProperty("defaultFriction"),
+                                                            node.getDoubleProperty("defaultCutoff"),
+                                                            node.getDoubleProperty("stepSize"));
+    integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
+    integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
+    integrator->setIntegrationForceGroups(node.getIntProperty("integrationForceGroups", 0xFFFFFFFF));
+    const SerializationNode& types = node.getChildNode("ParticleTypes");
+    for (auto& type: types.getChildren())
+        integrator->setParticleType(type.getIntProperty("particle"), type.getIntProperty("type"));
+    const SerializationNode& pairs = node.getChildNode("TypePairs");
+    for (auto& pair: pairs.getChildren())
+        integrator->addTypePair(pair.getIntProperty("type1"), pair.getIntProperty("type2"), pair.getDoubleProperty("friction"), pair.getDoubleProperty("cutoff"));
+    return integrator;
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -47,6 +47,7 @@
 #include "openmm/CustomManyParticleForce.h"
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/CustomTorsionForce.h"
+#include "openmm/DPDIntegrator.h"
 #include "openmm/GayBerneForce.h"
 #include "openmm/GBSAOBCForce.h"
 #include "openmm/HarmonicAngleForce.h"
@@ -87,6 +88,7 @@
 #include "openmm/serialization/CustomManyParticleForceProxy.h"
 #include "openmm/serialization/CustomNonbondedForceProxy.h"
 #include "openmm/serialization/CustomTorsionForceProxy.h"
+#include "openmm/serialization/DPDIntegratorProxy.h"
 #include "openmm/serialization/GayBerneForceProxy.h"
 #include "openmm/serialization/GBSAOBCForceProxy.h"
 #include "openmm/serialization/HarmonicAngleForceProxy.h"
@@ -148,6 +150,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(Discrete1DFunction), new Discrete1DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Discrete2DFunction), new Discrete2DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Discrete3DFunction), new Discrete3DFunctionProxy());
+    SerializationProxy::registerProxy(typeid(DPDIntegrator), new DPDIntegratorProxy());
     SerializationProxy::registerProxy(typeid(GayBerneForce), new GayBerneForceProxy());
     SerializationProxy::registerProxy(typeid(GBSAOBCForce), new GBSAOBCForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicAngleForce), new HarmonicAngleForceProxy());

serialization/tests/TestSerializeDPDIntegrator.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) 2025 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/DPDIntegrator.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerializeDPDIntegrator() {
+    // Create an integrator.
+
+    DPDIntegrator integrator(120.0, 1.1, 1.2, 0.05);
+    integrator.setRandomNumberSeed(4);
+    integrator.setIntegrationForceGroups(3);
+    integrator.setParticleType(1, 3);
+    integrator.setParticleType(3, 8);
+    integrator.addTypePair(0, 3, 1.5, 2.1);
+    integrator.addTypePair(3, 8, 0.5, 0.9);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<DPDIntegrator>(&integrator, "Integrator", buffer);
+    DPDIntegrator* copy = XmlSerializer::deserialize<DPDIntegrator>(buffer);
+
+    // Compare the two integrators to see if they are identical.
+
+    DPDIntegrator& integrator2 = *copy;
+    ASSERT_EQUAL(integrator.getTemperature(), integrator2.getTemperature());
+    ASSERT_EQUAL(integrator.getDefaultFriction(), integrator2.getDefaultFriction());
+    ASSERT_EQUAL(integrator.getDefaultCutoff(), integrator2.getDefaultCutoff());
+    ASSERT_EQUAL(integrator.getStepSize(), integrator2.getStepSize());
+    ASSERT_EQUAL(integrator.getRandomNumberSeed(), integrator2.getRandomNumberSeed());
+    ASSERT_EQUAL(integrator.getIntegrationForceGroups(), integrator2.getIntegrationForceGroups());
+    for (int i = 0; i < 10; i++)
+        ASSERT_EQUAL(integrator.getParticleType(i), integrator2.getParticleType(i));
+    ASSERT_EQUAL_CONTAINERS(integrator.getParticleTypes(), integrator2.getParticleTypes());
+    ASSERT_EQUAL(integrator.getNumTypePairs(), integrator2.getNumTypePairs());
+    for (int i = 0; i < integrator.getNumTypePairs(); i++) {
+        int a1, a2, b1, b2;
+        double f1, f2, c1, c2;
+        integrator.getTypePairParameters(i, a1, b1, f1, c1);
+        integrator.getTypePairParameters(i, a2, b2, f2, c2);
+        ASSERT_EQUAL(a1, a2);
+        ASSERT_EQUAL(b1, b2);
+        ASSERT_EQUAL(f1, f2);
+        ASSERT_EQUAL(c1, c2);
+    }
+}
+
+int main() {
+    try {
+        testSerializeDPDIntegrator();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

tests/TestDPDIntegrator.h

+/* -------------------------------------------------------------------------- *
+ *                                   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) 2025 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "openmm/CustomExternalForce.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/DPDIntegrator.h"
+#include "SimTKOpenMMRealType.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+double computeEnergy(Context& context) {
+    const System& system = context.getSystem();
+    double dt = context.getIntegrator().getStepSize();
+    State state = context.getState(State::Energy | State::Velocities | State::Forces);
+    double energy = state.getPotentialEnergy();
+    for (int i = 0; i < system.getNumParticles(); i++) {
+        double m = system.getParticleMass(i);
+        Vec3 v = state.getVelocities()[i];
+        v += (0.5*dt/m)*state.getForces()[i];
+        energy += 0.5*m*v.dot(v);
+    }
+    return energy;
+}
+
+void testConservationLaws() {
+    const int numParticles = 8;
+    const double temp = 100.0;
+    const double boxSize = 5.0;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    DPDIntegrator integrator(temp, 3.0, 2.5, 0.002);
+    NonbondedForce* forceField = new NonbondedForce();
+    forceField->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    forceField->setCutoffDistance(2.5);
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(2.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; ++i)
+        positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+    velocities[0][0] = 2.0;
+
+    // The integrator should conserve momentum.
+
+    Vec3 initialMomentum = system.getParticleMass(0)*velocities[0];
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    for (int i = 0; i < 100; i++) {
+        integrator.step(1);
+        State state = context.getState(State::Velocities);
+        Vec3 momentum;
+        for (int j = 0; j < numParticles; j++)
+            momentum += system.getParticleMass(j)*state.getVelocities()[j];
+        ASSERT_EQUAL_VEC(initialMomentum, momentum, 1e-5);
+    }
+
+    // If we set the friction to 0, it should also conserve energy.
+
+    integrator.setDefaultFriction(0.0);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    double energy = computeEnergy(context);
+    for (int i = 0; i < 100; i++) {
+        integrator.step(1);
+        State state = context.getState(State::Velocities | State::Energy);
+        Vec3 momentum;
+        for (int j = 0; j < numParticles; j++)
+            momentum += system.getParticleMass(j)*state.getVelocities()[j];
+        ASSERT_EQUAL_VEC(initialMomentum, momentum, 1e-5);
+        ASSERT_EQUAL_TOL(energy, computeEnergy(context), 0.02);
+    }
+}
+
+void testDiffusion() {
+    const int gridWidth = 10;
+    const int numParticles = gridWidth*gridWidth*gridWidth;
+    const double density = 3.0;
+    const double boxSize = pow(numParticles/density, 1.0/3.0);
+    const double cutoff = 1.0;
+    const double friction = 6.75;
+    const double dt = 0.04;
+    const double temp = 1.0/BOLTZ; // So kT = 1.0 kJ/mol
+    
+    // Create a periodic box of particles.
+    
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    HarmonicBondForce* force = new HarmonicBondForce();
+    force->setUsesPeriodicBoundaryConditions(true);
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0);
+    system.addForce(force);
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    double scale = boxSize/gridWidth;
+    for (int i = 0; i < gridWidth; i++)
+        for (int j = 0; j < gridWidth; j++)
+            for (int k = 0; k < gridWidth; k++)
+                positions[i*gridWidth*gridWidth + j*gridWidth + k] = scale*Vec3(i+0.1*genrand_real2(sfmt), j+0.1*genrand_real2(sfmt), k+0.1*genrand_real2(sfmt));
+    DPDIntegrator integrator(temp, friction, cutoff, dt);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(temp, 0);
+    
+    // Simulate it and compute the diffusion coefficient.
+    
+    integrator.step(100);
+    State state1 = context.getState(State::Positions);
+    integrator.step(1000);
+    State state2 = context.getState(State::Positions);
+    double r2 = 0.0;
+    for (int i = 0; i < numParticles; i++) {
+        Vec3 delta = state1.getPositions()[i]-state2.getPositions()[i];
+        r2 += delta.dot(delta);
+    }
+    r2 /= numParticles;
+    double diffusion = r2/6.0/(state2.getTime()-state1.getTime());
+
+    // Compare to a value computed with LAMMPS.
+
+    ASSERT_USUALLY_EQUAL_TOL(0.5203, diffusion, 0.05);
+}
+
+void testTemperature() {
+    const int numParticles = 100;
+    const double temp = 100.0;
+    const double boxSize = 8.0;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    DPDIntegrator integrator(temp, 20.0, 2.5, 0.002);
+    NonbondedForce* force = new NonbondedForce();
+    force->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    force->setCutoffDistance(2.5);
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(2.0);
+        force->addParticle((i%2 == 0 ? 0.1 : -0.1), 0.2, 1.0);
+        bool close = true;
+        while (close) {
+            positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+            close = false;
+            for (int j = 0; j < i; ++j) {
+                Vec3 delta = positions[i]-positions[j];
+                if (delta.dot(delta) < 0.1)
+                    close = true;
+            }
+        }
+    }
+    force->addException(0, numParticles-1, 0.0, 0.0, 0.0); // So there will be an off-diagonal tile with exclusions
+    system.addForce(force);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(temp, 0);
+    
+    // Let it equilibrate.
+    
+    integrator.step(1000);
+    
+    // Now run it for a while and see if the temperature is correct.
+    
+    double ke = 0.0;
+    int steps = 5000;
+    for (int i = 0; i < steps; ++i) {
+        State state = context.getState(State::Energy);
+        ke += state.getKineticEnergy();
+        integrator.step(1);
+    }
+    ke /= steps;
+    double expected = 0.5*numParticles*3*BOLTZ*temp;
+    ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.08);
+}
+
+void testTypePairs() {
+    const int numParticles = 8;
+    const double temp = 100.0;
+    System system;
+    DPDIntegrator integrator(temp, 1.0, 2.0, 0.01);
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(2.0);
+        positions[i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
+        if (i > 3) {
+            positions[i][0] += 5.0;
+            integrator.setParticleType(i, 1);
+        }
+    }
+    integrator.addTypePair(1, 1, 0.0, 2.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+
+    // The integrator should not affect the second cluster of particles.  The friction
+    // for their mutual interactions is 0, and they're outside the cutoff distance from
+    // the first cluster.
+    
+    integrator.step(10);
+    State state = context.getState(State::Positions);
+    for (int i = 0; i < 4; i++)
+        for (int j = 0; j < 3; j++)
+            ASSERT(positions[i][j] != state.getPositions()[i][j]);
+    for (int i = 4; i < numParticles; i++)
+        for (int j = 0; j < 3; j++)
+            ASSERT_EQUAL_TOL(positions[i][j], state.getPositions()[i][j], 1e-6);
+}
+
+void testConstraints() {
+    const int numParticles = 8;
+    const int numConstraints = 5;
+    const double temp = 100.0;
+    System system;
+    DPDIntegrator integrator(temp, 2.0, 1.5, 0.01);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
+    forceField->setCutoffDistance(10.0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(10.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(1, 2, 1.0);
+    system.addConstraint(2, 3, 1.0);
+    system.addConstraint(4, 5, 1.0);
+    system.addConstraint(6, 7, 1.0);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+
+    // Simulate it and see whether the constraints remain satisfied.
+
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions);
+        for (int j = 0; j < numConstraints; ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 1e-4);
+        }
+        integrator.step(1);
+    }
+}
+
+void testConstrainedMasslessParticles() {
+    System system;
+    system.addParticle(0.0);
+    system.addParticle(1.0);
+    system.addConstraint(0, 1, 1.5);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    DPDIntegrator integrator(300.0, 2.0, 3.0, 0.01);
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
+void testRandomSeed() {
+    const int numParticles = 8;
+    const double temp = 100.0;
+    System system;
+    DPDIntegrator integrator(temp, 2.0, 5.0, 0.01);
+    NonbondedForce* forceField = new NonbondedForce();
+    forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
+    forceField->setCutoffDistance(10.0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(2.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    system.addForce(forceField);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
+        velocities[i] = Vec3(0, 0, 0);
+    }
+
+    // Try twice with the same random seed.
+
+    integrator.setRandomNumberSeed(5);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state1 = context.getState(State::Positions);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state2 = context.getState(State::Positions);
+
+    // Try twice with a different random seed.
+
+    integrator.setRandomNumberSeed(10);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state3 = context.getState(State::Positions);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state4 = context.getState(State::Positions);
+
+    // Compare the results.
+
+    for (int i = 0; i < numParticles; i++) {
+        for (int j = 0; j < 3; j++) {
+            ASSERT_EQUAL_TOL(state1.getPositions()[i][j], state2.getPositions()[i][j], 1e-7);
+            ASSERT_EQUAL_TOL(state3.getPositions()[i][j], state4.getPositions()[i][j], 1e-7);
+            ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
+        }
+    }
+}
+
+void testInitialTemperature() {
+    // Check temperature initialization for a collection of randomly placed particles
+    const int numParticles = 50000;
+    const int nDoF = 3 * numParticles;
+    const double targetTemperature = 300;
+    System system;
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    std::vector<Vec3> positions(numParticles);
+
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        positions[i][0] = genrand_real2(sfmt);
+        positions[i][1] = genrand_real2(sfmt);
+        positions[i][2] = genrand_real2(sfmt);
+    }
+
+    DPDIntegrator integrator(300, 25, 0.5, 0.001);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(targetTemperature);
+    auto velocities = context.getState(State::Velocities).getVelocities();
+    double kineticEnergy = 0;
+    for(const auto &v : velocities) kineticEnergy += 0.5 * v.dot(v);
+    double temperature = (2*kineticEnergy / (nDoF*BOLTZ));
+    ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
+}
+
+void testForceGroups() {
+    System system;
+    system.addParticle(1.0);
+    DPDIntegrator integrator(0.0, 1.0, 1.0, 0.01);
+    integrator.setIntegrationForceGroups(1<<1);
+    CustomExternalForce* f1 = new CustomExternalForce("x");
+    f1->addParticle(0);
+    f1->setForceGroup(1);
+    CustomExternalForce* f2 = new CustomExternalForce("y");
+    f2->addParticle(0);
+    f2->setForceGroup(2);
+    system.addForce(f1);
+    system.addForce(f2);
+    Context context(system, integrator, platform);
+    context.setPositions(vector<Vec3>(1));
+
+    // Take one step and verify that the position was updated based only on f1.
+
+    integrator.step(1);
+    Vec3 pos = context.getState(State::Positions).getPositions()[0];
+    ASSERT(pos[0] < 0);
+    ASSERT(pos[1] == 0);
+    ASSERT(pos[2] == 0);
+}
+
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        initializeTests(argc, argv);
+        testConservationLaws();
+        testDiffusion();
+        testTemperature();
+        testTypePairs();
+        testConstraints();
+        testConstrainedMasslessParticles();
+        testRandomSeed();
+        testInitialTemperature();
+        testForceGroups();
+        runPlatformTests();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

wrappers/generateWrappers.py

@@ -92,7 +92,8 @@ class WrapperGenerator:
                             'bool OpenMM::Continuous3DFunction::operator!=',
                             'bool OpenMM::Discrete1DFunction::operator!=',
                             'bool OpenMM::Discrete2DFunction::operator!=',
-                            'bool OpenMM::Discrete3DFunction::operator!='
+                            'bool OpenMM::Discrete3DFunction::operator!=',
+                            'const std::map<int, int>& OpenMM::DPDIntegrator::getParticleTypes'
                            ]
         self.skipMethods = [s.replace(' ', '') for s in self.skipMethods]
         self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -509,6 +509,11 @@ UNITS = {
 ("NoseHooverIntegrator", "setMaximumPairDistance") : (None, ("unit.nanometer",)),
 ("DrudeNoseHooverIntegrator", "getMaxDrudeDistance") : ("unit.nanometer", ()),
 ("DrudeNoseHooverIntegrator", "setMaxDrudeDistance") : (None, ("unit.nanometer",)),
+("DPDIntegrator", "getDefaultFriction") : ("unit.picosecond**-1", ()),
+("DPDIntegrator", "setDefaultFriction") : (None, ("unit.picosecond**-1",)),
+("DPDIntegrator", "getDefaultCutoff") : ("unit.nanometer", ()),
+("DPDIntegrator", "setDefaultCutoff") : (None, ("unit.nanometer",)),
+("DPDIntegrator", "getParticleTypes") : (None, ()),
 ("LocalEnergyMinimizer", "minimize") : (None, (None, "unit.kilojoules_per_mole/unit.nanometer", None)),
 ("ATMForce", "getForce") : (None, ()),
 ("ATMForce", "getPerturbationEnergy") :  ('unit.kilojoule_per_mole', ()),