Add hipification of CUDA platform

Port changes in CUDA backend to HIP

Fix a warning about arithmetic operations on void* in HipArray::uploadSubArray

Fix "Error Initializing context ROCm 5.3.0"

    https://github.com/StreamHPC/openmm-hip/issues/3


    hipDeviceSetCacheConfig returns hipErrorNotSupported on 5.3
Co-authored-by: Nick Curtis <nicholas.curtis@amd.com>

platforms/hip/tests/TestHipNonbondedForce.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestNonbondedForce.h"
+#include <hip/hip_runtime.h>
+
+void testParallelComputation(NonbondedForce::NonbondedMethod method) {
+    System system;
+    const int numParticles = 200;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0);
+    NonbondedForce* force = new NonbondedForce();
+    for (int i = 0; i < numParticles; i++)
+        force->addParticle(i%2-0.5, 0.5, 1.0);
+    force->setNonbondedMethod(method);
+    system.addForce(force);
+    system.setDefaultPeriodicBoxVectors(Vec3(5,0,0), Vec3(0,5,0), Vec3(0,0,5));
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = Vec3(5*genrand_real2(sfmt), 5*genrand_real2(sfmt), 5*genrand_real2(sfmt));
+    for (int i = 0; i < numParticles; ++i)
+        for (int j = 0; j < i; ++j) {
+            Vec3 delta = positions[i]-positions[j];
+            if (delta.dot(delta) < 0.1)
+                force->addException(i, j, 0, 1, 0);
+        }
+
+    // Create two contexts, one with a single device and one with two devices.
+
+    VerletIntegrator integrator1(0.01);
+    Context context1(system, integrator1, platform);
+    context1.setPositions(positions);
+    State state1 = context1.getState(State::Forces | State::Energy);
+    VerletIntegrator integrator2(0.01);
+    string deviceIndex = platform.getPropertyValue(context1, HipPlatform::HipDeviceIndex());
+    map<string, string> props;
+    props[HipPlatform::HipDeviceIndex()] = deviceIndex+","+deviceIndex;
+    Context context2(system, integrator2, platform, props);
+    context2.setPositions(positions);
+    State state2 = context2.getState(State::Forces | State::Energy);
+
+    // See if they agree.
+
+    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
+
+    // Modify some particle parameters and see if they still agree.
+
+    for (int i = 0; i < numParticles; i += 5) {
+        double charge, sigma, epsilon;
+        force->getParticleParameters(i, charge, sigma, epsilon);
+        force->setParticleParameters(i, 0.9*charge, sigma, epsilon);
+    }
+    force->updateParametersInContext(context1);
+    force->updateParametersInContext(context2);
+    state1 = context1.getState(State::Forces | State::Energy);
+    state2 = context2.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
+}
+
+void testReordering() {
+    // Check that reordering of atoms doesn't alter their positions.
+
+    const int numParticles = 200;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(2.1, 6, 0), Vec3(-1.5, -0.5, 6));
+    NonbondedForce *nonbonded = new NonbondedForce();
+    nonbonded->setNonbondedMethod(NonbondedForce::PME);
+    system.addForce(nonbonded);
+    vector<Vec3> positions;
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        nonbonded->addParticle(0.0, 0.0, 0.0);
+        positions.push_back(Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5)*20);
+    }
+    VerletIntegrator integrator(0.001);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    integrator.step(1);
+    State state = context.getState(State::Positions | State::Velocities);
+    for (int i = 0; i < numParticles; i++) {
+        ASSERT_EQUAL_VEC(positions[i], state.getPositions()[i], 1e-6);
+    }
+}
+
+void testDeterministicForces() {
+    // Check that the HipDeterministicForces property works correctly.
+
+    const int numParticles = 1000;
+    System system;
+    system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(2.1, 6, 0), Vec3(-1.5, -0.5, 6));
+    NonbondedForce *nonbonded = new NonbondedForce();
+    nonbonded->setNonbondedMethod(NonbondedForce::PME);
+    system.addForce(nonbonded);
+    vector<Vec3> positions;
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        nonbonded->addParticle(i%2 == 0 ? 1 : -1, 1, 0);
+        positions.push_back(Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5)*6);
+    }
+    VerletIntegrator integrator(0.001);
+    map<string, string> properties;
+    properties[HipPlatform::HipDeterministicForces()] = "true";
+    Context context(system, integrator, platform, properties);
+    context.setPositions(positions);
+    State state1 = context.getState(State::Forces);
+    State state2 = context.getState(State::Forces);
+
+    // All forces should be *exactly* equal.
+
+    for (int i = 0; i < numParticles; i++) {
+        ASSERT_EQUAL(state1.getForces()[i][0], state2.getForces()[i][0]);
+        ASSERT_EQUAL(state1.getForces()[i][1], state2.getForces()[i][1]);
+        ASSERT_EQUAL(state1.getForces()[i][2], state2.getForces()[i][2]);
+    }
+}
+
+bool canRunHugeTest() {
+    // Create a minimal context just to see which device is being used.
+
+    System system;
+    system.addParticle(1.0);
+    VerletIntegrator integrator(1.0);
+    Context context(system, integrator, platform);
+    int deviceIndex = stoi(platform.getPropertyValue(context, HipPlatform::HipDeviceIndex()));
+
+    // Find out how much memory the device has.
+
+    hipDevice_t device;
+    hipDeviceGet(&device, deviceIndex);
+    size_t memory;
+    hipDeviceTotalMem(&memory, device);
+
+    // Only run the huge test if the device has at least 4 GB of memory.
+
+    return (memory >= 4*(size_t(1)<<30));
+}
+
+void runPlatformTests() {
+    testParallelComputation(NonbondedForce::NoCutoff);
+    testParallelComputation(NonbondedForce::Ewald);
+    testParallelComputation(NonbondedForce::PME);
+    testReordering();
+    testDeterministicForces();
+    if (canRunHugeTest())
+        testHugeSystem();
+}

platforms/hip/tests/TestHipNoseHooverIntegrator.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) 2019 Stanford University and the Authors.           *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Andreas Krämer and Andrew C. Simmmonett                           *
+ * 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 "HipTests.h"
+#include "TestNoseHooverIntegrator.h"
+
+void runPlatformTests() {
+}

platforms/hip/tests/TestHipPeriodicTorsionForce.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestPeriodicTorsionForce.h"
+
+void testParallelComputation() {
+    System system;
+    const int numParticles = 200;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0);
+    PeriodicTorsionForce* force = new PeriodicTorsionForce();
+    for (int i = 3; i < numParticles; i++)
+        force->addTorsion(i-3, i-2, i-1, i, 2, 1.1, i);
+    system.addForce(force);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = Vec3(i, i%2, i%3);
+    VerletIntegrator integrator1(0.01);
+    Context context1(system, integrator1, platform);
+    context1.setPositions(positions);
+    State state1 = context1.getState(State::Forces | State::Energy);
+    VerletIntegrator integrator2(0.01);
+    string deviceIndex = platform.getPropertyValue(context1, HipPlatform::HipDeviceIndex());
+    map<string, string> props;
+    props[HipPlatform::HipDeviceIndex()] = deviceIndex+","+deviceIndex;
+    Context context2(system, integrator2, platform, props);
+    context2.setPositions(positions);
+    State state2 = context2.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
+}
+
+void runPlatformTests() {
+    testParallelComputation();
+}

platforms/hip/tests/TestHipRBTorsionForce.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestRBTorsionForce.h"
+
+void testParallelComputation() {
+    System system;
+    const int numParticles = 200;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0);
+    RBTorsionForce* force = new RBTorsionForce();
+    for (int i = 3; i < numParticles; i++)
+        force->addTorsion(i-3, i-2, i-1, i, 2, 0.1*i, 0.5*i, i, 1, 1);
+    system.addForce(force);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = Vec3(i, i%2, i%3);
+    VerletIntegrator integrator1(0.01);
+    Context context1(system, integrator1, platform);
+    context1.setPositions(positions);
+    State state1 = context1.getState(State::Forces | State::Energy);
+    VerletIntegrator integrator2(0.01);
+    string deviceIndex = platform.getPropertyValue(context1, HipPlatform::HipDeviceIndex());
+    map<string, string> props;
+    props[HipPlatform::HipDeviceIndex()] = deviceIndex+","+deviceIndex;
+    Context context2(system, integrator2, platform, props);
+    context2.setPositions(positions);
+    State state2 = context2.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
+}
+
+void runPlatformTests() {
+    testParallelComputation();
+}

platforms/hip/tests/TestHipRMSDForce.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) 2018 Stanford University and the Authors.           *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestRMSDForce.h"
+
+void runPlatformTests() {
+}

platforms/hip/tests/TestHipRandom.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) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 Hip implementation of random number generation.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "HipArray.h"
+#include "HipContext.h"
+#include "HipIntegrationUtilities.h"
+#include "openmm/System.h"
+#include "openmm/Context.h"
+#include "HipPlatform.h"
+#include "openmm/VerletIntegrator.h"
+#include "SimTKOpenMMRealType.h"
+#include <iostream>
+
+using namespace OpenMM;
+using namespace std;
+
+HipPlatform platform;
+
+void testGaussian() {
+    int numAtoms = 5000;
+    System system;
+    for (int i = 0; i < numAtoms; i++)
+        system.addParticle(1.0);
+    HipPlatform::PlatformData platformData(NULL, system, "", "true", platform.getPropertyDefaultValue("HipPrecision"), "false",
+            platform.getPropertyDefaultValue(HipPlatform::HipCompiler()), platform.getPropertyDefaultValue(HipPlatform::HipTempDirectory()),
+            platform.getPropertyDefaultValue(HipPlatform::HipHostCompiler()), platform.getPropertyDefaultValue(HipPlatform::HipDisablePmeStream()), "false", 1, NULL);
+    HipContext& context = *platformData.contexts[0];
+    context.initialize();
+    context.getIntegrationUtilities().initRandomNumberGenerator(0);
+    HipArray& random = context.getIntegrationUtilities().getRandom();
+    context.getIntegrationUtilities().prepareRandomNumbers(random.getSize());
+    const int numValues = random.getSize()*4;
+    vector<float4> values(numValues);
+    random.download(values);
+    float* data = reinterpret_cast<float*>(&values[0]);
+    double mean = 0.0;
+    double var = 0.0;
+    double skew = 0.0;
+    double kurtosis = 0.0;
+    for (int i = 0; i < numValues; i++) {
+        double value = data[i];
+        mean += value;
+        var += value*value;
+        skew += value*value*value;
+        kurtosis += value*value*value*value;
+    }
+    mean /= numValues;
+    var /= numValues;
+    skew /= numValues;
+    kurtosis /= numValues;
+    double c2 = var-mean*mean;
+    double c3 = skew-3*var*mean+2*mean*mean*mean;
+    double c4 = kurtosis-4*skew*mean-3*var*var+12*var*mean*mean-6*mean*mean*mean*mean;
+    ASSERT_EQUAL_TOL(0.0, mean, 3.0/sqrt((double)numValues));
+    ASSERT_EQUAL_TOL(1.0, c2, 3.0/pow(numValues, 1.0/3.0));
+    ASSERT_EQUAL_TOL(0.0, c3, 3.0/pow(numValues, 1.0/4.0));
+    ASSERT_EQUAL_TOL(0.0, c4, 3.0/pow(numValues, 1.0/4.0));
+}
+
+void testRandomVelocities() {
+    // Create a system.
+
+    const int numParticles = 10000;
+    const double temperture = 100.0;
+    System system;
+    VerletIntegrator integrator(0.01);
+    for (int i = 0; i < numParticles; ++i)
+        system.addParticle(10.0+sin(0.1*i));
+    for (int i = 0; i < numParticles-1; ++i)
+        system.addConstraint(i, i+1, 1.0);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; ++i)
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+    context.setPositions(positions);
+
+    // Ask the context to generate random velocities.
+
+    context.setVelocitiesToTemperature(temperture);
+    State state = context.getState(State::Velocities);
+
+    // See if they respect constraints.
+
+    for (int i = 1; i < numParticles; i++) {
+        Vec3 v1 = state.getVelocities()[i-1];
+        Vec3 v2 = state.getVelocities()[i];
+        double vel = (v1-v2).dot(positions[i-1]-positions[i]);
+        ASSERT_EQUAL_TOL(0.0, vel, 2e-5);
+    }
+
+    // See if the temperature is correct.
+
+    double ke = 0;
+    for (int i = 0; i < numParticles; i++) {
+        Vec3 v = state.getVelocities()[i];
+        ke += 0.5*system.getParticleMass(i)*v.dot(v);
+    }
+    double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temperture;
+    ASSERT_USUALLY_EQUAL_TOL(expected, ke, 4/sqrt((double) numParticles));
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        if (argc > 1)
+            platform.setPropertyDefaultValue("HipPrecision", string(argv[1]));
+        testGaussian();
+        testRandomVelocities();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/hip/tests/TestHipSettle.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) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestSettle.h"
+
+void runPlatformTests() {
+}

platforms/hip/tests/TestHipSort.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) 2008-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 Hip implementation of sorting.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "HipArray.h"
+#include "HipContext.h"
+#include "HipSort.h"
+#include "sfmt/SFMT.h"
+#include "openmm/System.h"
+#include <iostream>
+#include <cmath>
+#include <set>
+
+using namespace OpenMM;
+using namespace std;
+
+HipPlatform platform;
+
+class SortTrait : public HipSort::SortTrait {
+    int getDataSize() const {return 4;}
+    int getKeySize() const {return 4;}
+    const char* getDataType() const {return "float";}
+    const char* getKeyType() const {return "float";}
+    const char* getMinKey() const {return "-3.40282e+38f";}
+    const char* getMaxKey() const {return "3.40282e+38f";}
+    const char* getMaxValue() const {return "3.40282e+38f";}
+    const char* getSortKey() const {return "value";}
+};
+
+void verifySorting(vector<float> array) {
+    // Sort the array.
+
+    System system;
+    system.addParticle(0.0);
+    HipPlatform::PlatformData platformData(NULL, system, "", "true", platform.getPropertyDefaultValue("HipPrecision"), "false",
+            platform.getPropertyDefaultValue(HipPlatform::HipCompiler()), platform.getPropertyDefaultValue(HipPlatform::HipTempDirectory()),
+            platform.getPropertyDefaultValue(HipPlatform::HipHostCompiler()), platform.getPropertyDefaultValue(HipPlatform::HipDisablePmeStream()), "false", 1, NULL);
+    HipContext& context = *platformData.contexts[0];
+    context.initialize();
+    HipArray data(context, array.size(), 4, "sortData");
+    data.upload(array);
+    HipSort sort(context, new SortTrait(), array.size());
+    sort.sort(data);
+    vector<float> sorted;
+    data.download(sorted);
+
+    // Verify that it is in sorted order.
+
+    for (int i = 1; i < (int) sorted.size(); i++)
+        ASSERT(sorted[i-1] <= sorted[i]);
+
+    // Make sure the sorted array contains the same values as the original one.
+
+    multiset<float> elements1(array.begin(), array.end());
+    multiset<float> elements2(sorted.begin(), sorted.end());
+    ASSERT(elements1 == elements2);
+}
+
+void testUniformValues() {
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    vector<float> array(10000);
+    for (int i = 0; i < (int) array.size(); i++)
+        array[i] = (float) genrand_real2(sfmt);
+    verifySorting(array);
+}
+
+void testLogValues() {
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    vector<float> array(10000);
+    for (int i = 0; i < (int) array.size(); i++)
+        array[i] = (float) log(genrand_real2(sfmt));
+    verifySorting(array);
+}
+
+void testShortList() {
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    vector<float> array(500);
+    for (int i = 0; i < (int) array.size(); i++)
+        array[i] = (float) log(genrand_real2(sfmt));
+    verifySorting(array);
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        if (argc > 1)
+            platform.setPropertyDefaultValue("HipPrecision", string(argv[1]));
+        testUniformValues();
+        testLogValues();
+        testShortList();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/hip/tests/TestHipVariableLangevinIntegrator.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) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestVariableLangevinIntegrator.h"
+
+void runPlatformTests() {
+}

platforms/hip/tests/TestHipVariableVerletIntegrator.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) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestVariableVerletIntegrator.h"
+
+void runPlatformTests() {
+}

platforms/hip/tests/TestHipVerletIntegrator.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) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestVerletIntegrator.h"
+
+void runPlatformTests() {
+}

platforms/hip/tests/TestHipVirtualSites.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) 2012-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2020 Advanced Micro Devices, Inc.                   *
+ * Authors: Peter Eastman, Nicholas Curtis                                    *
+ * 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 "HipTests.h"
+#include "TestVirtualSites.h"
+
+/**
+ * Make sure that atom reordering respects virtual sites.
+ */
+void testReordering() {
+    const double cutoff = 2.0;
+    const double boxSize = 20.0;
+    System system;
+    NonbondedForce* nonbonded = new NonbondedForce();
+    system.addForce(nonbonded);
+    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
+    nonbonded->setCutoffDistance(cutoff);
+    vector<Vec3> positions;
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    // Create linear molecules with TwoParticleAverage virtual sites.
+
+    for (int i = 0; i < 50; i++) {
+        int start = system.getNumParticles();
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        system.addParticle(0.0);
+        system.setVirtualSite(start+2, new TwoParticleAverageSite(start, start+1, 0.4, 0.6));
+        system.addConstraint(start, start+1, 2.0);
+        for (int i = 0; i < 3; i++) {
+            nonbonded->addParticle(0, 0.2, 1);
+            for (int j = 0; j < i; j++)
+                nonbonded->addException(start+i, start+j, 0, 1, 0);
+        }
+        Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+        positions.push_back(pos);
+        positions.push_back(pos+Vec3(2, 0, 0));
+        positions.push_back(Vec3());
+    }
+
+    // Create planar molecules with ThreeParticleAverage virtual sites.
+
+    for (int i = 0; i < 50; i++) {
+        int start = system.getNumParticles();
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        system.addParticle(0.0);
+        system.setVirtualSite(start+3, new ThreeParticleAverageSite(start, start+1, start+2, 0.3, 0.5, 0.2));
+        system.addConstraint(start, start+1, 1.0);
+        system.addConstraint(start, start+2, 1.0);
+        system.addConstraint(start+1, start+2, sqrt(2.0));
+        for (int i = 0; i < 4; i++) {
+            nonbonded->addParticle(0, 0.2, 1);
+            for (int j = 0; j < i; j++)
+                nonbonded->addException(start+i, start+j, 0, 1, 0);
+        }
+        Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+        positions.push_back(pos);
+        positions.push_back(pos+Vec3(1, 0, 0));
+        positions.push_back(pos+Vec3(0, 1, 0));
+        positions.push_back(Vec3());
+    }
+
+    // Create tetrahedral molecules with OutOfPlane virtual sites.
+
+    for (int i = 0; i < 50; i++) {
+        int start = system.getNumParticles();
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        system.addParticle(0.0);
+        system.setVirtualSite(start+3, new OutOfPlaneSite(start, start+1, start+2, 0.3, 0.5, 0.2));
+        system.addConstraint(start, start+1, 1.0);
+        system.addConstraint(start, start+2, 1.0);
+        system.addConstraint(start+1, start+2, sqrt(2.0));
+        for (int i = 0; i < 4; i++) {
+            nonbonded->addParticle(0, 0.2, 1);
+            for (int j = 0; j < i; j++)
+                nonbonded->addException(start+i, start+j, 0, 1, 0);
+        }
+        Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+        positions.push_back(pos);
+        positions.push_back(pos+Vec3(1, 0, 0));
+        positions.push_back(pos+Vec3(0, 1, 0));
+        positions.push_back(Vec3());
+    }
+
+    // Simulate it and check conservation laws.
+
+    LangevinIntegrator integrator(300.0, 0.1, 0.002);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.applyConstraints(0.0001);
+    for (int i = 0; i < 1000; i++) {
+        State state = context.getState(State::Positions);
+        const vector<Vec3>& pos = state.getPositions();
+        for (int j = 0; j < 150; j += 3)
+            ASSERT_EQUAL_VEC(pos[j]*0.4+pos[j+1]*0.6, pos[j+2], 1e-5);
+        for (int j = 150; j < 350; j += 4)
+            ASSERT_EQUAL_VEC(pos[j]*0.3+pos[j+1]*0.5+pos[j+2]*0.2, pos[j+3], 1e-5);
+        for (int j = 350; j < 550; j += 4) {
+            Vec3 v12 = pos[j+1]-pos[j];
+            Vec3 v13 = pos[j+2]-pos[j];
+            Vec3 cross = v12.cross(v13);
+            ASSERT_EQUAL_VEC(pos[j]+v12*0.3+v13*0.5+cross*0.2, pos[j+3], 1e-5);
+        }
+        integrator.step(1);
+    }
+}
+
+void runPlatformTests() {
+    testReordering();
+}