Consolidate Drude platform tests

plugins/drude/platforms/cuda/tests/CMakeLists.txt

@@ -6,6 +6,7 @@ ENABLE_TESTING()
 
 INCLUDE_DIRECTORIES(${CUDA_INCLUDE_DIR})
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/plugins/drude/tests)
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/tests)
 
 # Automatically create tests using files named "Test*.cpp"
 FILE(GLOB TEST_PROGS "*Test*.cpp")

plugins/drude/platforms/cuda/tests/CudaDrudeTests.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) 2013 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 "CudaTests.h"
+
+extern "C" void registerDrudeCudaKernelFactories();
+
+using namespace OpenMM;
+
+void setupKernels (int argc, char* argv[]) {
+    registerDrudeCudaKernelFactories();
+    platform = dynamic_cast<CudaPlatform&>(Platform::getPlatformByName("CUDA"));
+    initializeTests(argc, argv);
+}

plugins/drude/platforms/cuda/tests/TestCudaDrudeForce.cpp

@@ -29,185 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of DrudeForce.
- */
+#include "CudaDrudeTests.h"
+#include "TestDrudeForce.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "openmm/DrudeForce.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" void registerDrudeCudaKernelFactories();
-
-void validateForce(System& system, vector<Vec3>& positions, double expectedEnergy) {
-    // Given a System containing a Drude force, check that its energy has the expected value.
-    
-    VerletIntegrator integ(1.0);
-    Platform& platform = Platform::getPlatformByName("CUDA");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy | State::Forces);
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
-    
-    // Try moving each particle along each axis, and see if the energy changes by the correct amount.
-    
-    double offset = 1e-2;
-    for (int i = 0; i < system.getNumParticles(); i++)
-        for (int j = 0; j < 3; j++) {
-            vector<Vec3> offsetPos = positions;
-            offsetPos[i][j] = positions[i][j]-offset;
-            context.setPositions(offsetPos);
-            double e1 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
-            offsetPos[i][j] = positions[i][j]+offset;
-            context.setPositions(offsetPos);
-            double e2 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
-            ASSERT_EQUAL_TOL(state.getForces()[i][j], (e1-e2)/(2*offset), 1e-3);
-        }
-}
-
-void testSingleParticle() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(-1, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-    validateForce(system, positions, 0.5*k*3*3);
-}
-
-void testAnisotropicParticle() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double a1 = 0.8;
-    const double a2 = 1.1;
-    const double k1 = k/a1;
-    const double k2 = k/a2;
-    const double k3 = k/(3-a1-a2);
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, 2, 3, 4, charge, alpha, a1, a2);
-    system.addForce(drude);
-    vector<Vec3> positions(5);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0.1, -0.5, 0.8);
-    positions[2] = Vec3(0, 2, 0);
-    positions[3] = Vec3(1, 2, 0);
-    positions[4] = Vec3(1, 2, 3);
-    validateForce(system, positions, 0.5*k1*0.5*0.5 + 0.5*k2*0.8*0.8 + 0.5*k3*0.1*0.1);
-}
-
-double computeScreening(double r, double thole, double alpha1, double alpha2) {
-    double u = r*thole/pow(alpha1*alpha2, 1.0/6.0);
-    return 1.0-(1.0+u/2)*exp(-u);
-}
-
-void testThole() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double thole = 2.5;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    drude->addParticle(3, 2, -1, -1, -1, charge, alpha, 1, 1);
-    drude->addScreenedPair(0, 1, thole);
-    system.addForce(drude);
-    vector<Vec3> positions(4);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, -0.5, 0);
-    positions[2] = Vec3(1, 0, 0);
-    positions[3] = Vec3(1, 0, 0.3);
-    double energySpring1 = 0.5*k*0.5*0.5;
-    double energySpring2 = 0.5*k*0.3*0.3;
-    double energyDipole = 0.0;
-    double q[] = {-charge, charge, -charge, charge};
-    for (int i = 0; i < 2; i++)
-        for (int j = 2; j < 4; j++) {
-            Vec3 delta = positions[i]-positions[j];
-            double r = sqrt(delta.dot(delta));
-            energyDipole += ONE_4PI_EPS0*q[i]*q[j]*computeScreening(r, thole, alpha, alpha)/r;
-        }
-    validateForce(system, positions, energySpring1+energySpring2+energyDipole);
-}
-
-void testChangingParameters() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    Platform& platform = Platform::getPlatformByName("CUDA");
-    
-    // Create the system.
-    
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(-1, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-    
-    // Check the energy.
-    
-    VerletIntegrator integ(1.0);
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(0.5*k*3*3, state.getPotentialEnergy(), 1e-5);
-    
-    // Modify the parameters.
-    
-    const double k2 = ONE_4PI_EPS0*2.2;
-    const double charge2 = 0.3;
-    const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
-    drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
-    drude->updateParametersInContext(context);
-    state = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(0.5*k2*3*3, state.getPotentialEnergy(), 1e-5);
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        registerDrudeCudaKernelFactories();
-        if (argc > 1)
-            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", std::string(argv[1]));
-        testSingleParticle();
-        testAnisotropicParticle();
-        testThole();
-        testChangingParameters();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,230 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of DrudeLangevinIntegrator.
- */
+#include "CudaDrudeTests.h"
+#include "TestDrudeLangevinIntegrator.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VirtualSite.h"
-#include "openmm/DrudeForce.h"
-#include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeCudaKernelFactories();
-
-void testSinglePair() {
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double mass1 = 1.0;
-    const double mass2 = 0.1;
-    const double totalMass = mass1+mass2;
-    const double reducedMass = (mass1*mass2)/(mass1+mass2);
-    const double maxDistance = 0.05;
-    System system;
-    system.addParticle(mass1);
-    system.addParticle(mass2);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, 0, 0);
-    DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
-    integ.setMaxDrudeDistance(maxDistance);
-    Platform& platform = Platform::getPlatformByName("CUDA");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    
-    // Equilibrate.
-    
-    integ.step(1000);
-    
-    // Compute the internal and center of mass temperatures.
-    
-    double keCM = 0, keInternal = 0;
-    int numSteps = 10000;
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(10);
-        State state = context.getState(State::Velocities | State::Positions);
-        const vector<Vec3>& vel = state.getVelocities();
-        Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
-        keCM += 0.5*totalMass*velCM.dot(velCM);
-        Vec3 velInternal = vel[0]-vel[1];
-        keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
-        Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
-        double distance = sqrt(delta.dot(delta));
-        ASSERT(distance <= maxDistance*(1+1e-6));
-    }
-    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
-    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
-}
-
-void testWater() {
-    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
-    // and Drude particles.
-    
-    const int gridSize = 4;
-    const int numMolecules = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    System system;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nonbonded->setCutoffDistance(1.0);
-    for (int i = 0; i < numMolecules; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(15.6); // O
-        system.addParticle(0.4);  // D
-        system.addParticle(1.0);  // H1
-        system.addParticle(1.0);  // H2
-        system.addParticle(0.0);  // M
-        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
-        nonbonded->addParticle(-1.71636, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(-1.11466, 1, 0);
-        for (int j = 0; j < 5; j++)
-            for (int k = 0; k < j; k++)
-                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
-        system.addConstraint(startIndex, startIndex+2, 0.09572);
-        system.addConstraint(startIndex, startIndex+3, 0.09572);
-        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
-        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
-    }
-    vector<Vec3> positions;
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-                positions.push_back(pos+Vec3(0.09572, 0, 0));
-                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check the temperature.
-    
-    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.0005);
-    Platform& platform = Platform::getPlatformByName("CUDA");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    context.applyConstraints(1e-5);
-    
-    // Equilibrate.
-    
-    integ.step(1000);
-    
-    // Compute the internal and center of mass temperatures.
-    
-    double ke = 0;
-    int numSteps = 10000;
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(1);
-        ke += context.getState(State::Energy).getKineticEnergy();
-    }
-    ke /= numSteps;
-    int numStandardDof = 3*3*numMolecules-system.getNumConstraints();
-    int numDrudeDof = 3*numMolecules;
-    int numDof = numStandardDof+numDrudeDof;
-    double expectedTemp = (numStandardDof*temperature+numDrudeDof*temperatureDrude)/numDof;
-    ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.02);
-}
-
-void testForceEnergyConsistency() {
-    // Create a box of polarizable particles.
-    
-    const int gridSize = 3;
-    const int numAtoms = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    System system;
-    vector<Vec3> positions;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::PME);
-    nonbonded->setCutoffDistance(1.0);
-    nonbonded->setUseSwitchingFunction(true);
-    nonbonded->setSwitchingDistance(0.9);
-    nonbonded->setEwaldErrorTolerance(5e-5);
-    for (int i = 0; i < numAtoms; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(1.0);
-        system.addParticle(1.0);
-        nonbonded->addParticle(1.0, 0.3, 1.0);
-        nonbonded->addParticle(-1.0, 0.3, 1.0);
-        nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
-    }
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check that force and energy remain consistent.
-    
-    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
-    Platform& platform = Platform::getPlatformByName("CUDA");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State prevState;
-    for (int i = 0; i < 100; i++) {
-        State state = context.getState(State::Energy | State::Forces | State::Positions);
-        if (i > 0) {
-            double expectedEnergyChange = 0;
-            for (int j = 0; j < system.getNumParticles(); j++) {
-                Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
-                expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
-            }
-            ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
-        }
-        prevState = state;
-        integ.step(1);
-    }
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        registerDrudeCudaKernelFactories();
-        if (argc > 1)
-            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", string(argv[1]));
-        testSinglePair();
-        testWater();
-        testForceEnergyConsistency();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/platforms/cuda/tests/TestCudaDrudeNoseHoover.cpp

@@ -29,33 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-//#include "ReferenceTests.h"
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "openmm/DrudeForce.h"
-#include "CudaPlatform.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeCudaKernelFactories();
-
-void runPlatformTests() { }
-
+#include "CudaDrudeTests.h"
 #include "TestDrudeNoseHoover.h"
 
-Platform& initializePlatform(int argc, char* argv[]) {
-    registerDrudeCudaKernelFactories();
-    if (argc > 1) Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", std::string(argv[1]));   
-    return Platform::getPlatformByName("CUDA");
-}
-
-
+void runPlatformTests() {}

plugins/drude/platforms/cuda/tests/TestCudaDrudeSCFIntegrator.cpp

@@ -29,116 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CUDA implementation of DrudeSCFIntegrator.
- */
+#include "CudaDrudeTests.h"
+#include "TestDrudeSCFIntegrator.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VirtualSite.h"
-#include "openmm/DrudeForce.h"
-#include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeCudaKernelFactories();
-
-void testWater() {
-    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
-    // and Drude particles.
-    
-    const int gridSize = 4;
-    const int numMolecules = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    System system;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nonbonded->setCutoffDistance(1.0);
-    for (int i = 0; i < numMolecules; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(15.6); // O
-        system.addParticle(0.4);  // D
-        system.addParticle(1.0);  // H1
-        system.addParticle(1.0);  // H2
-        system.addParticle(0.0);  // M
-        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
-        nonbonded->addParticle(-1.71636, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(-1.11466, 1, 0);
-        for (int j = 0; j < 5; j++)
-            for (int k = 0; k < j; k++)
-                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
-        system.addConstraint(startIndex, startIndex+2, 0.09572);
-        system.addConstraint(startIndex, startIndex+3, 0.09572);
-        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
-        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
-    }
-    vector<Vec3> positions;
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-                positions.push_back(pos+Vec3(0.09572, 0, 0));
-                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check energy conservation and the total force on the Drude particles.
-    
-    DrudeSCFIntegrator integ(0.0005);
-    Platform& platform = Platform::getPlatformByName("CUDA");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    context.applyConstraints(1e-5);
-    context.setVelocitiesToTemperature(300.0);
-    State state = context.getState(State::Energy);
-    double initialEnergy;
-    int numSteps = 1000;
-    double maxNorm = (platform.getPropertyValue(context, "Precision") == "double" ? 1.0 : 5.0);
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(1);
-        state = context.getState(State::Energy | State::Forces);
-        if (i == 0)
-            initialEnergy = state.getPotentialEnergy()+state.getKineticEnergy();
-        else
-            ASSERT_EQUAL_TOL(initialEnergy, state.getPotentialEnergy()+state.getKineticEnergy(), 0.01);
-        const vector<Vec3>& force = state.getForces();
-        double norm = 0.0;
-        for (int j = 1; j < (int) force.size(); j += 5)
-            norm += sqrt(force[j].dot(force[j]));
-        norm = (norm/numMolecules);
-        ASSERT(norm < maxNorm);
-    }
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        registerDrudeCudaKernelFactories();
-        if (argc > 1)
-            Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", string(argv[1]));
-        testWater();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/platforms/opencl/tests/CMakeLists.txt

@@ -6,6 +6,7 @@ ENABLE_TESTING()
 
 INCLUDE_DIRECTORIES(${OPENCL_INCLUDE_DIR})
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/plugins/drude/tests)
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/opencl/tests)
 
 # Automatically create tests using files named "Test*.cpp"
 FILE(GLOB TEST_PROGS "*Test*.cpp")

plugins/drude/platforms/opencl/tests/OpenCLDrudeTests.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) 2013 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 "OpenCLTests.h"
+
+extern "C" void registerDrudeOpenCLKernelFactories();
+
+using namespace OpenMM;
+
+void setupKernels (int argc, char* argv[]) {
+    registerDrudeOpenCLKernelFactories();
+    platform = dynamic_cast<OpenCLPlatform&>(Platform::getPlatformByName("OpenCL"));
+    initializeTests(argc, argv);
+}

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeForce.cpp

@@ -29,185 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of DrudeForce.
- */
+#include "OpenCLDrudeTests.h"
+#include "TestDrudeForce.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "openmm/DrudeForce.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" void registerDrudeOpenCLKernelFactories();
-
-void validateForce(System& system, vector<Vec3>& positions, double expectedEnergy) {
-    // Given a System containing a Drude force, check that its energy has the expected value.
-    
-    VerletIntegrator integ(1.0);
-    Platform& platform = Platform::getPlatformByName("OpenCL");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy | State::Forces);
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
-    
-    // Try moving each particle along each axis, and see if the energy changes by the correct amount.
-    
-    double offset = 1e-2;
-    for (int i = 0; i < system.getNumParticles(); i++)
-        for (int j = 0; j < 3; j++) {
-            vector<Vec3> offsetPos = positions;
-            offsetPos[i][j] = positions[i][j]-offset;
-            context.setPositions(offsetPos);
-            double e1 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
-            offsetPos[i][j] = positions[i][j]+offset;
-            context.setPositions(offsetPos);
-            double e2 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
-            ASSERT_EQUAL_TOL(state.getForces()[i][j], (e1-e2)/(2*offset), 1e-3);
-        }
-}
-
-void testSingleParticle() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(-1, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-    validateForce(system, positions, 0.5*k*3*3);
-}
-
-void testAnisotropicParticle() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double a1 = 0.8;
-    const double a2 = 1.1;
-    const double k1 = k/a1;
-    const double k2 = k/a2;
-    const double k3 = k/(3-a1-a2);
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, 2, 3, 4, charge, alpha, a1, a2);
-    system.addForce(drude);
-    vector<Vec3> positions(5);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0.1, -0.5, 0.8);
-    positions[2] = Vec3(0, 2, 0);
-    positions[3] = Vec3(1, 2, 0);
-    positions[4] = Vec3(1, 2, 3);
-    validateForce(system, positions, 0.5*k1*0.5*0.5 + 0.5*k2*0.8*0.8 + 0.5*k3*0.1*0.1);
-}
-
-double computeScreening(double r, double thole, double alpha1, double alpha2) {
-    double u = r*thole/pow(alpha1*alpha2, 1.0/6.0);
-    return 1.0-(1.0+u/2)*exp(-u);
-}
-
-void testThole() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double thole = 2.5;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    drude->addParticle(3, 2, -1, -1, -1, charge, alpha, 1, 1);
-    drude->addScreenedPair(0, 1, thole);
-    system.addForce(drude);
-    vector<Vec3> positions(4);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, -0.5, 0);
-    positions[2] = Vec3(1, 0, 0);
-    positions[3] = Vec3(1, 0, 0.3);
-    double energySpring1 = 0.5*k*0.5*0.5;
-    double energySpring2 = 0.5*k*0.3*0.3;
-    double energyDipole = 0.0;
-    double q[] = {-charge, charge, -charge, charge};
-    for (int i = 0; i < 2; i++)
-        for (int j = 2; j < 4; j++) {
-            Vec3 delta = positions[i]-positions[j];
-            double r = sqrt(delta.dot(delta));
-            energyDipole += ONE_4PI_EPS0*q[i]*q[j]*computeScreening(r, thole, alpha, alpha)/r;
-        }
-    validateForce(system, positions, energySpring1+energySpring2+energyDipole);
-}
-
-void testChangingParameters() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    Platform& platform = Platform::getPlatformByName("OpenCL");
-    
-    // Create the system.
-    
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(-1, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-    
-    // Check the energy.
-    
-    VerletIntegrator integ(1.0);
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(0.5*k*3*3, state.getPotentialEnergy(), 1e-5);
-    
-    // Modify the parameters.
-    
-    const double k2 = ONE_4PI_EPS0*2.2;
-    const double charge2 = 0.3;
-    const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
-    drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
-    drude->updateParametersInContext(context);
-    state = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(0.5*k2*3*3, state.getPotentialEnergy(), 1e-5);
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        registerDrudeOpenCLKernelFactories();
-        if (argc > 1)
-            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", std::string(argv[1]));
-        testSingleParticle();
-        testAnisotropicParticle();
-        testThole();
-        testChangingParameters();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,230 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of DrudeLangevinIntegrator.
- */
+#include "OpenCLDrudeTests.h"
+#include "TestDrudeLangevinIntegrator.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VirtualSite.h"
-#include "openmm/DrudeForce.h"
-#include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeOpenCLKernelFactories();
-
-void testSinglePair() {
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double mass1 = 1.0;
-    const double mass2 = 0.1;
-    const double totalMass = mass1+mass2;
-    const double reducedMass = (mass1*mass2)/(mass1+mass2);
-    const double maxDistance = 0.05;
-    System system;
-    system.addParticle(mass1);
-    system.addParticle(mass2);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, 0, 0);
-    DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
-    integ.setMaxDrudeDistance(maxDistance);
-    Platform& platform = Platform::getPlatformByName("OpenCL");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    
-    // Equilibrate.
-    
-    integ.step(1000);
-    
-    // Compute the internal and center of mass temperatures.
-    
-    double keCM = 0, keInternal = 0;
-    int numSteps = 10000;
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(10);
-        State state = context.getState(State::Velocities | State::Positions);
-        const vector<Vec3>& vel = state.getVelocities();
-        Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
-        keCM += 0.5*totalMass*velCM.dot(velCM);
-        Vec3 velInternal = vel[0]-vel[1];
-        keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
-        Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
-        double distance = sqrt(delta.dot(delta));
-        ASSERT(distance <= maxDistance*(1+1e-6));
-    }
-    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
-    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
-}
-
-void testWater() {
-    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
-    // and Drude particles.
-    
-    const int gridSize = 4;
-    const int numMolecules = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    System system;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nonbonded->setCutoffDistance(1.0);
-    for (int i = 0; i < numMolecules; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(15.6); // O
-        system.addParticle(0.4);  // D
-        system.addParticle(1.0);  // H1
-        system.addParticle(1.0);  // H2
-        system.addParticle(0.0);  // M
-        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
-        nonbonded->addParticle(-1.71636, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(-1.11466, 1, 0);
-        for (int j = 0; j < 5; j++)
-            for (int k = 0; k < j; k++)
-                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
-        system.addConstraint(startIndex, startIndex+2, 0.09572);
-        system.addConstraint(startIndex, startIndex+3, 0.09572);
-        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
-        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
-    }
-    vector<Vec3> positions;
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-                positions.push_back(pos+Vec3(0.09572, 0, 0));
-                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check the temperature.
-    
-    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.0005);
-    Platform& platform = Platform::getPlatformByName("OpenCL");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    context.applyConstraints(1e-5);
-    
-    // Equilibrate.
-    
-    integ.step(1000);
-    
-    // Compute the internal and center of mass temperatures.
-    
-    double ke = 0;
-    int numSteps = 10000;
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(1);
-        ke += context.getState(State::Energy).getKineticEnergy();
-    }
-    ke /= numSteps;
-    int numStandardDof = 3*3*numMolecules-system.getNumConstraints();
-    int numDrudeDof = 3*numMolecules;
-    int numDof = numStandardDof+numDrudeDof;
-    double expectedTemp = (numStandardDof*temperature+numDrudeDof*temperatureDrude)/numDof;
-    ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.02);
-}
-
-void testForceEnergyConsistency() {
-    // Create a box of polarizable particles.
-    
-    const int gridSize = 3;
-    const int numAtoms = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    System system;
-    vector<Vec3> positions;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::PME);
-    nonbonded->setCutoffDistance(1.0);
-    nonbonded->setUseSwitchingFunction(true);
-    nonbonded->setSwitchingDistance(0.9);
-    nonbonded->setEwaldErrorTolerance(5e-5);
-    for (int i = 0; i < numAtoms; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(1.0);
-        system.addParticle(1.0);
-        nonbonded->addParticle(1.0, 0.3, 1.0);
-        nonbonded->addParticle(-1.0, 0.3, 1.0);
-        nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
-    }
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check that force and energy remain consistent.
-    
-    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
-    Platform& platform = Platform::getPlatformByName("OpenCL");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State prevState;
-    for (int i = 0; i < 100; i++) {
-        State state = context.getState(State::Energy | State::Forces | State::Positions);
-        if (i > 0) {
-            double expectedEnergyChange = 0;
-            for (int j = 0; j < system.getNumParticles(); j++) {
-                Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
-                expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
-            }
-            ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
-        }
-        prevState = state;
-        integ.step(1);
-    }
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        registerDrudeOpenCLKernelFactories();
-        if (argc > 1)
-            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", string(argv[1]));
-        testSinglePair();
-        testWater();
-        testForceEnergyConsistency();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeNoseHoover.cpp

@@ -29,32 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-//#include "ReferenceTests.h"
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "openmm/DrudeForce.h"
-#include "OpenCLPlatform.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeOpenCLKernelFactories();
-
-void runPlatformTests() { }
-
+#include "OpenCLDrudeTests.h"
 #include "TestDrudeNoseHoover.h"
 
-Platform& initializePlatform(int argc, char* argv[]) {
-    registerDrudeOpenCLKernelFactories();
-    if (argc > 1) Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", std::string(argv[1]));   
-    return Platform::getPlatformByName("OpenCL");
-}
-
+void runPlatformTests() {}

plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp

@@ -29,116 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the OpenCL implementation of DrudeSCFIntegrator.
- */
+#include "OpenCLDrudeTests.h"
+#include "TestDrudeSCFIntegrator.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VirtualSite.h"
-#include "openmm/DrudeForce.h"
-#include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeOpenCLKernelFactories();
-
-void testWater() {
-    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
-    // and Drude particles.
-    
-    const int gridSize = 4;
-    const int numMolecules = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    System system;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nonbonded->setCutoffDistance(1.0);
-    for (int i = 0; i < numMolecules; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(15.6); // O
-        system.addParticle(0.4);  // D
-        system.addParticle(1.0);  // H1
-        system.addParticle(1.0);  // H2
-        system.addParticle(0.0);  // M
-        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
-        nonbonded->addParticle(-1.71636, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(-1.11466, 1, 0);
-        for (int j = 0; j < 5; j++)
-            for (int k = 0; k < j; k++)
-                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
-        system.addConstraint(startIndex, startIndex+2, 0.09572);
-        system.addConstraint(startIndex, startIndex+3, 0.09572);
-        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
-        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
-    }
-    vector<Vec3> positions;
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-                positions.push_back(pos+Vec3(0.09572, 0, 0));
-                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check energy conservation and the total force on the Drude particles.
-    
-    DrudeSCFIntegrator integ(0.0005);
-    Platform& platform = Platform::getPlatformByName("OpenCL");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    context.applyConstraints(1e-5);
-    context.setVelocitiesToTemperature(300.0);
-    State state = context.getState(State::Energy);
-    double initialEnergy;
-    int numSteps = 1000;
-    double maxNorm = (platform.getPropertyValue(context, "Precision") == "double" ? 1.0 : 5.0);
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(1);
-        state = context.getState(State::Energy | State::Forces);
-        if (i == 0)
-            initialEnergy = state.getPotentialEnergy()+state.getKineticEnergy();
-        else
-            ASSERT_EQUAL_TOL(initialEnergy, state.getPotentialEnergy()+state.getKineticEnergy(), 0.01);
-        const vector<Vec3>& force = state.getForces();
-        double norm = 0.0;
-        for (int j = 1; j < (int) force.size(); j += 5)
-            norm += sqrt(force[j].dot(force[j]));
-        norm = (norm/numMolecules);
-        ASSERT(norm < maxNorm);
-    }
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        registerDrudeOpenCLKernelFactories();
-        if (argc > 1)
-            Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", string(argv[1]));
-        testWater();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/platforms/reference/tests/CMakeLists.txt

@@ -5,6 +5,7 @@ ENABLE_TESTING()
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/include)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/openmmapi/include/openmm)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/src)
+INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/reference/tests)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/plugins/drude/tests)
 
 SET(SHARED_OPENMM_DRUDE_TARGET OpenMMDrude)

plugins/drude/platforms/reference/tests/ReferenceDrudeTests.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) 2013 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 "ReferenceTests.h"
+
+extern "C" void registerDrudeReferenceKernelFactories();
+
+using namespace OpenMM;
+
+void setupKernels (int argc, char* argv[]) {
+    registerDrudeReferenceKernelFactories();
+    platform = dynamic_cast<ReferencePlatform&>(Platform::getPlatformByName("Reference"));
+    initializeTests(argc, argv);
+}

plugins/drude/platforms/reference/tests/TestReferenceDrudeForce.cpp

@@ -29,185 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the Reference implementation of DrudeForce.
- */
+#include "ReferenceDrudeTests.h"
+#include "TestDrudeForce.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "openmm/DrudeForce.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
-
-void validateForce(System& system, vector<Vec3>& positions, double expectedEnergy) {
-    // Given a System containing a Drude force, check that its energy has the expected value.
-    
-    VerletIntegrator integ(1.0);
-    Platform& platform = Platform::getPlatformByName("Reference");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy | State::Forces);
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
-    
-    // Try moving each particle along each axis, and see if the energy changes by the correct amount.
-    
-    double offset = 1e-3;
-    for (int i = 0; i < system.getNumParticles(); i++)
-        for (int j = 0; j < 3; j++) {
-            vector<Vec3> offsetPos = positions;
-            offsetPos[i][j] = positions[i][j]-offset;
-            context.setPositions(offsetPos);
-            double e1 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
-            offsetPos[i][j] = positions[i][j]+offset;
-            context.setPositions(offsetPos);
-            double e2 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
-            ASSERT_EQUAL_TOL(state.getForces()[i][j], (e1-e2)/(2*offset), 1e-5);
-        }
-}
-
-void testSingleParticle() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    ASSERT(!drude->usesPeriodicBoundaryConditions());
-    ASSERT(!system.usesPeriodicBoundaryConditions());
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(-1, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-    validateForce(system, positions, 0.5*k*3*3);
-}
-
-void testAnisotropicParticle() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double a1 = 0.8;
-    const double a2 = 1.1;
-    const double k1 = k/a1;
-    const double k2 = k/a2;
-    const double k3 = k/(3-a1-a2);
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, 2, 3, 4, charge, alpha, a1, a2);
-    system.addForce(drude);
-    vector<Vec3> positions(5);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0.1, -0.5, 0.8);
-    positions[2] = Vec3(0, 2, 0);
-    positions[3] = Vec3(1, 2, 0);
-    positions[4] = Vec3(1, 2, 3);
-    validateForce(system, positions, 0.5*k1*0.5*0.5 + 0.5*k2*0.8*0.8 + 0.5*k3*0.1*0.1);
-}
-
-double computeScreening(double r, double thole, double alpha1, double alpha2) {
-    double u = r*thole/pow(alpha1*alpha2, 1.0/6.0);
-    return 1.0-(1.0+u/2)*exp(-u);
-}
-
-void testThole() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double thole = 2.5;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    drude->addParticle(3, 2, -1, -1, -1, charge, alpha, 1, 1);
-    drude->addScreenedPair(0, 1, thole);
-    system.addForce(drude);
-    vector<Vec3> positions(4);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, -0.5, 0);
-    positions[2] = Vec3(1, 0, 0);
-    positions[3] = Vec3(1, 0, 0.3);
-    double energySpring1 = 0.5*k*0.5*0.5;
-    double energySpring2 = 0.5*k*0.3*0.3;
-    double energyDipole = 0.0;
-    double q[] = {-charge, charge, -charge, charge};
-    for (int i = 0; i < 2; i++)
-        for (int j = 2; j < 4; j++) {
-            Vec3 delta = positions[i]-positions[j];
-            double r = sqrt(delta.dot(delta));
-            energyDipole += ONE_4PI_EPS0*q[i]*q[j]*computeScreening(r, thole, alpha, alpha)/r;
-        }
-    validateForce(system, positions, energySpring1+energySpring2+energyDipole);
-}
-
-void testChangingParameters() {
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    Platform& platform = Platform::getPlatformByName("Reference");
-    
-    // Create the system.
-    
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(-1, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-    
-    // Check the energy.
-    
-    VerletIntegrator integ(1.0);
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(0.5*k*3*3, state.getPotentialEnergy(), 1e-5);
-    
-    // Modify the parameters.
-    
-    const double k2 = ONE_4PI_EPS0*2.2;
-    const double charge2 = 0.3;
-    const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
-    drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
-    drude->updateParametersInContext(context);
-    state = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(0.5*k2*3*3, state.getPotentialEnergy(), 1e-5);
-}
-
-int main() {
-    try {
-        registerDrudeReferenceKernelFactories();
-        testSingleParticle();
-        testAnisotropicParticle();
-        testThole();
-        testChangingParameters();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,287 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the Reference implementation of DrudeLangevinIntegrator.
- */
+#include "ReferenceDrudeTests.h"
+#include "TestDrudeLangevinIntegrator.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VirtualSite.h"
-#include "openmm/DrudeForce.h"
-#include "openmm/DrudeLangevinIntegrator.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
-
-void testSinglePair() {
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    const double k = ONE_4PI_EPS0*1.5;
-    const double charge = 0.1;
-    const double alpha = ONE_4PI_EPS0*charge*charge/k;
-    const double mass1 = 1.0;
-    const double mass2 = 0.1;
-    const double totalMass = mass1+mass2;
-    const double reducedMass = (mass1*mass2)/(mass1+mass2);
-    const double maxDistance = 0.05;
-    System system;
-    system.addParticle(mass1);
-    system.addParticle(mass2);
-    DrudeForce* drude = new DrudeForce();
-    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
-    system.addForce(drude);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, 0, 0);
-    DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
-    integ.setMaxDrudeDistance(maxDistance);
-    Platform& platform = Platform::getPlatformByName("Reference");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    
-    // Equilibrate.
-    
-    integ.step(1000);
-    
-    // Compute the internal and center of mass temperatures.
-    
-    double keCM = 0, keInternal = 0;
-    int numSteps = 10000;
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(10);
-        State state = context.getState(State::Velocities | State::Positions);
-        const vector<Vec3>& vel = state.getVelocities();
-        Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
-        keCM += 0.5*totalMass*velCM.dot(velCM);
-        Vec3 velInternal = vel[0]-vel[1];
-        keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
-        Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
-        double distance = sqrt(delta.dot(delta));
-        ASSERT(distance <= maxDistance*(1+1e-6));
-    }
-    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
-    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
-}
-
-void testWater() {
-    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
-    // and Drude particles.
-    
-    const int gridSize = 3;
-    const int numMolecules = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    System system;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nonbonded->setCutoffDistance(1.0);
-    for (int i = 0; i < numMolecules; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(15.6); // O
-        system.addParticle(0.4);  // D
-        system.addParticle(1.0);  // H1
-        system.addParticle(1.0);  // H2
-        system.addParticle(0.0);  // M
-        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
-        nonbonded->addParticle(-1.71636, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(-1.11466, 1, 0);
-        for (int j = 0; j < 5; j++)
-            for (int k = 0; k < j; k++)
-                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
-        system.addConstraint(startIndex, startIndex+2, 0.09572);
-        system.addConstraint(startIndex, startIndex+3, 0.09572);
-        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
-        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
-    }
-    vector<Vec3> positions;
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-                positions.push_back(pos+Vec3(0.09572, 0, 0));
-                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check the temperature.
-    
-    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.0005);
-    Platform& platform = Platform::getPlatformByName("Reference");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    context.applyConstraints(1e-5);
-    
-    // Equilibrate.
-    
-    integ.step(500);
-    
-    // Compute the internal and center of mass temperatures.
-    
-    double ke = 0;
-    int numSteps = 4000;
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(1);
-        ke += context.getState(State::Energy).getKineticEnergy();
-    }
-    ke /= numSteps;
-    int numStandardDof = 3*3*numMolecules-system.getNumConstraints();
-    int numDrudeDof = 3*numMolecules;
-    int numDof = numStandardDof+numDrudeDof;
-    double expectedTemp = (numStandardDof*temperature+numDrudeDof*temperatureDrude)/numDof;
-    ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.03);
-}
-
-void testForceEnergyConsistency() {
-    // Create a box of polarizable particles.
-    
-    const int gridSize = 3;
-    const int numAtoms = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    const double temperature = 300.0;
-    const double temperatureDrude = 10.0;
-    System system;
-    vector<Vec3> positions;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::PME);
-    nonbonded->setCutoffDistance(1.0);
-    nonbonded->setUseSwitchingFunction(true);
-    nonbonded->setSwitchingDistance(0.9);
-    nonbonded->setEwaldErrorTolerance(5e-5);
-    for (int i = 0; i < numAtoms; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(1.0);
-        system.addParticle(1.0);
-        nonbonded->addParticle(1.0, 0.3, 1.0);
-        nonbonded->addParticle(-1.0, 0.3, 1.0);
-        nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
-    }
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check that force and energy remain consistent.
-    
-    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
-    Platform& platform = Platform::getPlatformByName("Reference");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State prevState;
-    for (int i = 0; i < 100; i++) {
-        State state = context.getState(State::Energy | State::Forces | State::Positions);
-        if (i > 0) {
-            double expectedEnergyChange = 0;
-            for (int j = 0; j < system.getNumParticles(); j++) {
-                Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
-                expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
-            }
-            ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
-        }
-        prevState = state;
-        integ.step(1);
-    }
-}
-
-void testInitialTemperature() {
-    // Check temperature initialization for a collection of randomly placed particles
-    const int numRealParticles = 500000;
-    const int numParticles = 2 * numRealParticles;
-    const int nDoF = 3 * numRealParticles;
-    const double targetTemperature = 300;
-    const double drudeTemperature = 1;
-    const double realMass = 10;
-    const double drudeMass = 1;
-    System system;
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    std::vector<Vec3> positions(numParticles);
-    DrudeForce* drude = new DrudeForce();
-
-    for (int i = 0; i < numRealParticles; i++) {
-        system.addParticle(realMass);
-        system.addParticle(drudeMass);
-        positions[2*i][0] = genrand_real2(sfmt);
-        positions[2*i][1] = genrand_real2(sfmt);
-        positions[2*i][2] = genrand_real2(sfmt);
-        positions[2*i+1][0] = positions[2*i][0] + 0.01*genrand_real2(sfmt);
-        positions[2*i+1][1] = positions[2*i][1] + 0.01*genrand_real2(sfmt);
-        positions[2*i+1][2] = positions[2*i][2] + 0.01*genrand_real2(sfmt);
-        drude->addParticle(2*i+1, 2*i, -1, -1, -1, -1.0, 0.001, 1, 1);
-    }
-    system.addForce(drude);
-
-    DrudeLangevinIntegrator integrator(targetTemperature, 25, drudeTemperature, 25, 0.001);
-    Platform& platform = Platform::getPlatformByName("Reference");
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    context.setVelocitiesToTemperature(targetTemperature);
-    auto velocities = context.getState(State::Velocities).getVelocities();
-    double comKineticEnergy = 0;
-    double relKineticEnergy = 0;
-    for (int i = 0; i < numRealParticles; i++) {
-        int m1 = realMass;
-        int m2 = drudeMass;
-        Vec3 v1 = velocities[2*i];
-        Vec3 v2 = velocities[2*i + 1];
-        double invMass = 1.0 / (m1 + m2);
-        double redMass = m1 * m2 * invMass;
-        double fracM1 = m1 * invMass;
-        double fracM2 = m2 * invMass;
-        Vec3 comVelocity = fracM1 * v1 + fracM2 * v2;
-        Vec3 relVelocity = v2 - v1;
-
-        comKineticEnergy += 0.5 * (m1 + m2) * comVelocity.dot(comVelocity);
-        relKineticEnergy += 0.5 * redMass * relVelocity.dot(relVelocity);
-    }
-    double comTemperature = (2*comKineticEnergy / (nDoF*BOLTZ));
-    double relTemperature = (2*relKineticEnergy / (nDoF*BOLTZ));
-    std::cout << comTemperature << std::endl;
-    std::cout << relTemperature << std::endl;
-    //ASSERT_USUALLY_EQUAL_TOL(targetTemperature, temperature, 0.01);
-}
-
-int main() {
-    try {
-        registerDrudeReferenceKernelFactories();
-        testInitialTemperature();
-        testSinglePair();
-        testWater();
-        testForceEnergyConsistency();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/platforms/reference/tests/TestReferenceDrudeNoseHoover.cpp

@@ -29,22 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-//#include "ReferenceTests.h"
-#include "openmm/Platform.h"
-
-
-using namespace OpenMM;
-using namespace std;
-//extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
-
-
-Platform& initializePlatform(int argc, char* argv[]) {
-/*    registerDrudeReferenceKernelFactories();
-    */
-    return Platform::getPlatformByName("Reference");
-}
-
+#include "ReferenceDrudeTests.h"
 #include "TestDrudeNoseHoover.h"
 
-void runPlatformTests() { }
-
+void runPlatformTests() {}

plugins/drude/platforms/reference/tests/TestReferenceDrudeSCFIntegrator.cpp

@@ -29,113 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the Reference implementation of DrudeSCFIntegrator.
- */
+#include "ReferenceDrudeTests.h"
+#include "TestDrudeSCFIntegrator.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/Platform.h"
-#include "openmm/System.h"
-#include "openmm/VirtualSite.h"
-#include "openmm/DrudeForce.h"
-#include "openmm/DrudeSCFIntegrator.h"
-#include "SimTKOpenMMUtilities.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
-
-void testWater() {
-    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
-    // and Drude particles.
-    
-    const int gridSize = 3;
-    const int numMolecules = gridSize*gridSize*gridSize;
-    const double spacing = 0.6;
-    const double boxSize = spacing*(gridSize+1);
-    System system;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    DrudeForce* drude = new DrudeForce();
-    system.addForce(nonbonded);
-    system.addForce(drude);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    nonbonded->setCutoffDistance(1.0);
-    for (int i = 0; i < numMolecules; i++) {
-        int startIndex = system.getNumParticles();
-        system.addParticle(15.6); // O
-        system.addParticle(0.4);  // D
-        system.addParticle(1.0);  // H1
-        system.addParticle(1.0);  // H2
-        system.addParticle(0.0);  // M
-        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
-        nonbonded->addParticle(-1.71636, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(0.55733, 1, 0);
-        nonbonded->addParticle(-1.11466, 1, 0);
-        for (int j = 0; j < 5; j++)
-            for (int k = 0; k < j; k++)
-                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
-        system.addConstraint(startIndex, startIndex+2, 0.09572);
-        system.addConstraint(startIndex, startIndex+3, 0.09572);
-        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
-        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
-        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
-    }
-    vector<Vec3> positions;
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                Vec3 pos(i*spacing, j*spacing, k*spacing);
-                positions.push_back(pos);
-                positions.push_back(pos);
-                positions.push_back(pos+Vec3(0.09572, 0, 0));
-                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
-                positions.push_back(pos);
-            }
-    
-    // Simulate it and check energy conservation and the total force on the Drude particles.
-    
-    DrudeSCFIntegrator integ(0.0005);
-    Platform& platform = Platform::getPlatformByName("Reference");
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    context.applyConstraints(1e-5);
-    context.setVelocitiesToTemperature(300.0);
-    State state = context.getState(State::Energy);
-    double initialEnergy;
-    int numSteps = 1000;
-    for (int i = 0; i < numSteps; i++) {
-        integ.step(1);
-        state = context.getState(State::Energy | State::Forces);
-        if (i == 0)
-            initialEnergy = state.getPotentialEnergy()+state.getKineticEnergy();
-        else
-            ASSERT_EQUAL_TOL(initialEnergy, state.getPotentialEnergy()+state.getKineticEnergy(), 0.01);
-        const vector<Vec3>& force = state.getForces();
-        double norm = 0.0;
-        for (int j = 1; j < (int) force.size(); j += 5)
-            norm += sqrt(force[j].dot(force[j]));
-        norm = (norm/numMolecules);
-        ASSERT(norm < 1.0);
-    }
-}
-
-int main() {
-    try {
-        registerDrudeReferenceKernelFactories();
-        testWater();
-    }
-    catch(const std::exception& e) {
-        std::cout << "exception: " << e.what() << std::endl;
-        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
-        return 1;
-    }
-    std::cout << "Done" << std::endl;
-    return 0;
-}
+void runPlatformTests() {}

plugins/drude/tests/TestDrudeForce.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) 2013 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/NonbondedForce.h"
+#include "openmm/Platform.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "openmm/DrudeForce.h"
+#include "SimTKOpenMMUtilities.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+void validateForce(System& system, vector<Vec3>& positions, double expectedEnergy) {
+    // Given a System containing a Drude force, check that its energy has the expected value.
+
+    VerletIntegrator integ(1.0);
+    Context context(system, integ, platform);
+    context.setPositions(positions);
+    State state = context.getState(State::Energy | State::Forces);
+    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
+
+    // Try moving each particle along each axis, and see if the energy changes by the correct amount.
+
+    double offset = 1e-3;
+    for (int i = 0; i < system.getNumParticles(); i++)
+        for (int j = 0; j < 3; j++) {
+            vector<Vec3> offsetPos = positions;
+            offsetPos[i][j] = positions[i][j]-offset;
+            context.setPositions(offsetPos);
+            double e1 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
+            offsetPos[i][j] = positions[i][j]+offset;
+            context.setPositions(offsetPos);
+            double e2 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
+            ASSERT_EQUAL_TOL(state.getForces()[i][j], (e1-e2)/(2*offset), 1e-5);
+        }
+}
+
+void testSingleParticle() {
+    const double k = ONE_4PI_EPS0*1.5;
+    const double charge = 0.1;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    DrudeForce* drude = new DrudeForce();
+    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
+    system.addForce(drude);
+    ASSERT(!drude->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(2, 0, 0);
+    validateForce(system, positions, 0.5*k*3*3);
+}
+
+void testAnisotropicParticle() {
+    const double k = ONE_4PI_EPS0*1.5;
+    const double charge = 0.1;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
+    const double a1 = 0.8;
+    const double a2 = 1.1;
+    const double k1 = k/a1;
+    const double k2 = k/a2;
+    const double k3 = k/(3-a1-a2);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    DrudeForce* drude = new DrudeForce();
+    drude->addParticle(1, 0, 2, 3, 4, charge, alpha, a1, a2);
+    system.addForce(drude);
+    vector<Vec3> positions(5);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(0.1, -0.5, 0.8);
+    positions[2] = Vec3(0, 2, 0);
+    positions[3] = Vec3(1, 2, 0);
+    positions[4] = Vec3(1, 2, 3);
+    validateForce(system, positions, 0.5*k1*0.5*0.5 + 0.5*k2*0.8*0.8 + 0.5*k3*0.1*0.1);
+}
+
+double computeScreening(double r, double thole, double alpha1, double alpha2) {
+    double u = r*thole/pow(alpha1*alpha2, 1.0/6.0);
+    return 1.0-(1.0+u/2)*exp(-u);
+}
+
+void testThole() {
+    const double k = ONE_4PI_EPS0*1.5;
+    const double charge = 0.1;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
+    const double thole = 2.5;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    DrudeForce* drude = new DrudeForce();
+    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
+    drude->addParticle(3, 2, -1, -1, -1, charge, alpha, 1, 1);
+    drude->addScreenedPair(0, 1, thole);
+    system.addForce(drude);
+    vector<Vec3> positions(4);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(0, -0.5, 0);
+    positions[2] = Vec3(1, 0, 0);
+    positions[3] = Vec3(1, 0, 0.3);
+    double energySpring1 = 0.5*k*0.5*0.5;
+    double energySpring2 = 0.5*k*0.3*0.3;
+    double energyDipole = 0.0;
+    double q[] = {-charge, charge, -charge, charge};
+    for (int i = 0; i < 2; i++)
+        for (int j = 2; j < 4; j++) {
+            Vec3 delta = positions[i]-positions[j];
+            double r = sqrt(delta.dot(delta));
+            energyDipole += ONE_4PI_EPS0*q[i]*q[j]*computeScreening(r, thole, alpha, alpha)/r;
+        }
+    validateForce(system, positions, energySpring1+energySpring2+energyDipole);
+}
+
+void testChangingParameters() {
+    const double k = ONE_4PI_EPS0*1.5;
+    const double charge = 0.1;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
+
+    // Create the system.
+
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    DrudeForce* drude = new DrudeForce();
+    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
+    system.addForce(drude);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(2, 0, 0);
+
+    // Check the energy.
+
+    VerletIntegrator integ(1.0);
+    Context context(system, integ, platform);
+    context.setPositions(positions);
+    State state = context.getState(State::Energy);
+    ASSERT_EQUAL_TOL(0.5*k*3*3, state.getPotentialEnergy(), 1e-5);
+
+    // Modify the parameters.
+
+    const double k2 = ONE_4PI_EPS0*2.2;
+    const double charge2 = 0.3;
+    const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
+    drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
+    drude->updateParametersInContext(context);
+    state = context.getState(State::Energy);
+    ASSERT_EQUAL_TOL(0.5*k2*3*3, state.getPotentialEnergy(), 1e-5);
+}
+
+void setupKernels(int argc, char* argv[]);
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        setupKernels(argc, argv);
+        testSingleParticle();
+        testAnisotropicParticle();
+        testThole();
+        testChangingParameters();
+        runPlatformTests();
+    }
+    catch(const std::exception& e) {
+        std::cout << "exception: " << e.what() << std::endl;
+        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
+        return 1;
+    }
+    std::cout << "Done" << std::endl;
+    return 0;
+}

plugins/drude/tests/TestDrudeLangevinIntegrator.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) 2013-2016 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/NonbondedForce.h"
+#include "openmm/Platform.h"
+#include "openmm/System.h"
+#include "openmm/VirtualSite.h"
+#include "openmm/DrudeForce.h"
+#include "openmm/DrudeLangevinIntegrator.h"
+#include "SimTKOpenMMUtilities.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSinglePair() {
+    const double temperature = 300.0;
+    const double temperatureDrude = 10.0;
+    const double k = ONE_4PI_EPS0*1.5;
+    const double charge = 0.1;
+    const double alpha = ONE_4PI_EPS0*charge*charge/k;
+    const double mass1 = 1.0;
+    const double mass2 = 0.1;
+    const double totalMass = mass1+mass2;
+    const double reducedMass = (mass1*mass2)/(mass1+mass2);
+    const double maxDistance = 0.05;
+    System system;
+    system.addParticle(mass1);
+    system.addParticle(mass2);
+    DrudeForce* drude = new DrudeForce();
+    drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
+    system.addForce(drude);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(0, 0, 0);
+    DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
+    integ.setMaxDrudeDistance(maxDistance);
+    Context context(system, integ, platform);
+    context.setPositions(positions);
+
+    // Equilibrate.
+
+    integ.step(1000);
+
+    // Compute the internal and center of mass temperatures.
+
+    double keCM = 0, keInternal = 0;
+    int numSteps = 10000;
+    for (int i = 0; i < numSteps; i++) {
+        integ.step(10);
+        State state = context.getState(State::Velocities | State::Positions);
+        const vector<Vec3>& vel = state.getVelocities();
+        Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
+        keCM += 0.5*totalMass*velCM.dot(velCM);
+        Vec3 velInternal = vel[0]-vel[1];
+        keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
+        Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
+        double distance = sqrt(delta.dot(delta));
+        ASSERT(distance <= maxDistance*(1+1e-6));
+    }
+    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
+    ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
+}
+
+void testWater() {
+    // Create a box of SWM4-NDP water molecules.  This involves constraints, virtual sites,
+    // and Drude particles.
+
+    const int gridSize = 3;
+    const int numMolecules = gridSize*gridSize*gridSize;
+    const double spacing = 0.6;
+    const double boxSize = spacing*(gridSize+1);
+    const double temperature = 300.0;
+    const double temperatureDrude = 10.0;
+    System system;
+    NonbondedForce* nonbonded = new NonbondedForce();
+    DrudeForce* drude = new DrudeForce();
+    system.addForce(nonbonded);
+    system.addForce(drude);
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    nonbonded->setCutoffDistance(1.0);
+    for (int i = 0; i < numMolecules; i++) {
+        int startIndex = system.getNumParticles();
+        system.addParticle(15.6); // O
+        system.addParticle(0.4);  // D
+        system.addParticle(1.0);  // H1
+        system.addParticle(1.0);  // H2
+        system.addParticle(0.0);  // M
+        nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
+        nonbonded->addParticle(-1.71636, 1, 0);
+        nonbonded->addParticle(0.55733, 1, 0);
+        nonbonded->addParticle(0.55733, 1, 0);
+        nonbonded->addParticle(-1.11466, 1, 0);
+        for (int j = 0; j < 5; j++)
+            for (int k = 0; k < j; k++)
+                nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
+        system.addConstraint(startIndex, startIndex+2, 0.09572);
+        system.addConstraint(startIndex, startIndex+3, 0.09572);
+        system.addConstraint(startIndex+2, startIndex+3, 0.15139);
+        system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
+        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
+    }
+    vector<Vec3> positions;
+    for (int i = 0; i < gridSize; i++)
+        for (int j = 0; j < gridSize; j++)
+            for (int k = 0; k < gridSize; k++) {
+                Vec3 pos(i*spacing, j*spacing, k*spacing);
+                positions.push_back(pos);
+                positions.push_back(pos);
+                positions.push_back(pos+Vec3(0.09572, 0, 0));
+                positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
+                positions.push_back(pos);
+            }
+
+    // Simulate it and check the temperature.
+
+    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.0005);
+    Context context(system, integ, platform);
+    context.setPositions(positions);
+    context.applyConstraints(1e-5);
+
+    // Equilibrate.
+
+    integ.step(500);
+
+    // Compute the internal and center of mass temperatures.
+
+    double ke = 0;
+    int numSteps = 4000;
+    for (int i = 0; i < numSteps; i++) {
+        integ.step(1);
+        ke += context.getState(State::Energy).getKineticEnergy();
+    }
+    ke /= numSteps;
+    int numStandardDof = 3*3*numMolecules-system.getNumConstraints();
+    int numDrudeDof = 3*numMolecules;
+    int numDof = numStandardDof+numDrudeDof;
+    double expectedTemp = (numStandardDof*temperature+numDrudeDof*temperatureDrude)/numDof;
+    ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.03);
+}
+
+void testForceEnergyConsistency() {
+    // Create a box of polarizable particles.
+
+    const int gridSize = 3;
+    const int numAtoms = gridSize*gridSize*gridSize;
+    const double spacing = 0.6;
+    const double boxSize = spacing*(gridSize+1);
+    const double temperature = 300.0;
+    const double temperatureDrude = 10.0;
+    System system;
+    vector<Vec3> positions;
+    NonbondedForce* nonbonded = new NonbondedForce();
+    DrudeForce* drude = new DrudeForce();
+    system.addForce(nonbonded);
+    system.addForce(drude);
+    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    nonbonded->setNonbondedMethod(NonbondedForce::PME);
+    nonbonded->setCutoffDistance(1.0);
+    nonbonded->setUseSwitchingFunction(true);
+    nonbonded->setSwitchingDistance(0.9);
+    nonbonded->setEwaldErrorTolerance(5e-5);
+    for (int i = 0; i < numAtoms; i++) {
+        int startIndex = system.getNumParticles();
+        system.addParticle(1.0);
+        system.addParticle(1.0);
+        nonbonded->addParticle(1.0, 0.3, 1.0);
+        nonbonded->addParticle(-1.0, 0.3, 1.0);
+        nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
+        drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
+    }
+    for (int i = 0; i < gridSize; i++)
+        for (int j = 0; j < gridSize; j++)
+            for (int k = 0; k < gridSize; k++) {
+                Vec3 pos(i*spacing, j*spacing, k*spacing);
+                positions.push_back(pos);
+                positions.push_back(pos);
+            }
+
+    // Simulate it and check that force and energy remain consistent.
+
+    DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
+    Context context(system, integ, platform);
+    context.setPositions(positions);
+    State prevState;
+    for (int i = 0; i < 100; i++) {
+        State state = context.getState(State::Energy | State::Forces | State::Positions);
+        if (i > 0) {
+            double expectedEnergyChange = 0;
+            for (int j = 0; j < system.getNumParticles(); j++) {
+                Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
+                expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
+            }
+            ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
+        }
+        prevState = state;
+        integ.step(1);
+    }
+}
+
+void testInitialTemperature() {
+    // Check temperature initialization for a collection of randomly placed particles
+    const int numRealParticles = 500000;
+    const int numParticles = 2 * numRealParticles;
+    const int nDoF = 3 * numRealParticles;
+    const double targetTemperature = 300;
+    const double drudeTemperature = 1;
+    const double realMass = 10;
+    const double drudeMass = 1;
+    System system;
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    std::vector<Vec3> positions(numParticles);
+    DrudeForce* drude = new DrudeForce();
+
+    for (int i = 0; i < numRealParticles; i++) {
+        system.addParticle(realMass);
+        system.addParticle(drudeMass);
+        positions[2*i][0] = genrand_real2(sfmt);
+        positions[2*i][1] = genrand_real2(sfmt);
+        positions[2*i][2] = genrand_real2(sfmt);
+        positions[2*i+1][0] = positions[2*i][0] + 0.01*genrand_real2(sfmt);
+        positions[2*i+1][1] = positions[2*i][1] + 0.01*genrand_real2(sfmt);
+        positions[2*i+1][2] = positions[2*i][2] + 0.01*genrand_real2(sfmt);
+        drude->addParticle(2*i+1, 2*i, -1, -1, -1, -1.0, 0.001, 1, 1);
+    }
+    system.addForce(drude);
+
+    DrudeLangevinIntegrator integrator(targetTemperature, 25, drudeTemperature, 25, 0.001);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(targetTemperature);
+    auto velocities = context.getState(State::Velocities).getVelocities();
+    double comKineticEnergy = 0;
+    double relKineticEnergy = 0;
+    for (int i = 0; i < numRealParticles; i++) {
+        int m1 = realMass;
+        int m2 = drudeMass;
+        Vec3 v1 = velocities[2*i];
+        Vec3 v2 = velocities[2*i + 1];
+        double invMass = 1.0 / (m1 + m2);
+        double redMass = m1 * m2 * invMass;
+        double fracM1 = m1 * invMass;
+        double fracM2 = m2 * invMass;
+        Vec3 comVelocity = fracM1 * v1 + fracM2 * v2;
+        Vec3 relVelocity = v2 - v1;
+
+        comKineticEnergy += 0.5 * (m1 + m2) * comVelocity.dot(comVelocity);
+        relKineticEnergy += 0.5 * redMass * relVelocity.dot(relVelocity);
+    }
+    double comTemperature = (2*comKineticEnergy / (nDoF*BOLTZ));
+    double relTemperature = (2*relKineticEnergy / (nDoF*BOLTZ));
+    ASSERT_USUALLY_EQUAL_TOL(targetTemperature, comTemperature, 0.01);
+    ASSERT_USUALLY_EQUAL_TOL(drudeTemperature, relTemperature, 0.01);
+}
+
+void setupKernels(int argc, char* argv[]);
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        setupKernels(argc, argv);
+        testInitialTemperature();
+        testSinglePair();
+        testWater();
+        testForceEnergyConsistency();
+        runPlatformTests();
+    }
+    catch(const std::exception& e) {
+        std::cout << "exception: " << e.what() << std::endl;
+        std::cout << "FAIL - ERROR.  Test failed." << std::endl;
+        return 1;
+    }
+    std::cout << "Done" << std::endl;
+    return 0;
+}