Initial velocity verlet, with some nose hoover implementation

tests/TestNoseHooverThermostat.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) 2019 Stanford University and the Authors.           *
+ * Authors: Andreas Krämer and Andrew C. Simmonett                            *
+ * 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/NoseHooverChain.h"
+#include "openmm/VelocityVerletIntegrator.h"
+#include "openmm/Context.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "SimTKOpenMMRealType.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSingleBond() {
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
+    VelocityVerletIntegrator integrator(0.01);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
+    forceField->addBond(0, 1, 1.5, 1);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+    
+    // This is simply a harmonic oscillator, so compare it to the analytical solution.
+    
+    const double freq = 1.0;
+    State state = context.getState(State::Energy);
+    const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
+    for (int i = 0; i < 1000; ++i) {
+        state = context.getState(State::Positions | State::Velocities | State::Energy);
+        double time = state.getTime();
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        double expectedSpeed = -0.5*freq*std::sin(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+        integrator.step(1);
+    }
+    ASSERT_EQUAL_TOL(10.0, context.getState(0).getTime(), 1e-5);
+}
+
+void testConstraints() {
+    const int numParticles = 8;
+    const int numConstraints = 5;
+    System system;
+    VelocityVerletIntegrator integrator(0.001);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(i%2 == 0 ? 5.0 : 10.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(1, 2, 1.0);
+    system.addConstraint(2, 3, 1.0);
+    system.addConstraint(4, 5, 1.0);
+    system.addConstraint(6, 7, 1.0);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+
+    // Simulate it and see whether the constraints remain satisfied.
+
+    double initialEnergy = 0.0;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
+        for (int j = 0; j < numConstraints; ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 1e-4);
+        }
+        double energy = state.getPotentialEnergy()+state.getKineticEnergy();
+        if (i == 1)
+            initialEnergy = energy;
+        else if (i > 1)
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+        integrator.step(1);
+    }
+}
+void testNHCPropagation() {
+    double temperature = 300; // kelvin
+    double collisionFrequency = 20; // 1/ps
+    int numDOFs = 1;
+    int chainLength = 4;
+    int numMTS = 3;
+    int numYS = 1;
+    std::string label;
+    NoseHooverChain nhc(temperature, collisionFrequency, numDOFs, chainLength, numMTS, numYS, label);
+    
+}
+
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        initializeTests(argc, argv);
+        testSingleBond();
+        testConstraints();
+        runPlatformTests();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

tests/TestVelocityVerletIntegrator.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) 2019 Stanford University and the Authors.           *
+ * Authors: Andreas Krämer and Andrew C. Simmonett                            *
+ * 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/HarmonicBondForce.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/VelocityVerletIntegrator.h"
+#include "SimTKOpenMMRealType.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testVVSingleBond() {
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
+    VelocityVerletIntegrator integrator(0.01);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
+    forceField->addBond(0, 1, 1.5, 1);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+    
+    // This is simply a harmonic oscillator, so compare it to the analytical solution.
+    
+    const double freq = 1.0;
+    State state = context.getState(State::Energy);
+    const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
+    for (int i = 0; i < 1000; ++i) {
+        state = context.getState(State::Positions | State::Velocities | State::Energy);
+        double time = state.getTime();
+        double expectedDist = 1.5+0.5*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        double expectedSpeed = -0.5*freq*std::sin(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+        integrator.step(1);
+    }
+    ASSERT_EQUAL_TOL(10.0, context.getState(0).getTime(), 1e-5);
+}
+
+void testVVConstraints() {
+    const int numParticles = 8;
+    const int numConstraints = 5;
+    System system;
+    VelocityVerletIntegrator integrator(0.001);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(i%2 == 0 ? 5.0 : 10.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(1, 2, 1.0);
+    system.addConstraint(2, 3, 1.0);
+    system.addConstraint(4, 5, 1.0);
+    system.addConstraint(6, 7, 1.0);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+
+    // Simulate it and see whether the constraints remain satisfied.
+
+    double initialEnergy = 0.0;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
+        for (int j = 0; j < numConstraints; ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 1e-4);
+        }
+        double energy = state.getPotentialEnergy()+state.getKineticEnergy();
+        if (i == 1)
+            initialEnergy = energy;
+        else if (i > 1)
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+        integrator.step(1);
+    }
+}
+
+void testVVConstrainedClusters() {
+    const int numParticles = 7;
+    System system;
+    VelocityVerletIntegrator integrator(0.001);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(i > 1 ? 1.0 : 10.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(0, 2, 1.0);
+    system.addConstraint(0, 3, 1.0);
+    system.addConstraint(0, 4, 1.0);
+    system.addConstraint(1, 5, 1.0);
+    system.addConstraint(1, 6, 1.0);
+    system.addConstraint(2, 3, sqrt(2.0));
+    system.addConstraint(2, 4, sqrt(2.0));
+    system.addConstraint(3, 4, sqrt(2.0));
+    system.addConstraint(5, 6, sqrt(2.0));
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    positions[2] = Vec3(-1, 0, 0);
+    positions[3] = Vec3(0, 1, 0);
+    positions[4] = Vec3(0, 0, 1);
+    positions[5] = Vec3(2, 0, 0);
+    positions[6] = Vec3(1, 1, 0);
+    vector<Vec3> velocities(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    for (int i = 0; i < numParticles; ++i)
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+
+    // Simulate it and see whether the constraints remain satisfied.
+
+    double initialEnergy = 0.0;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
+        for (int j = 0; j < system.getNumConstraints(); ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 2e-5);
+        }
+        double energy = state.getPotentialEnergy()+state.getKineticEnergy();
+        if (i == 1)
+            initialEnergy = energy;
+        else if (i > 1)
+            ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+        integrator.step(1);
+    }
+}
+
+void testVVConstrainedMasslessParticles() {
+    System system;
+    system.addParticle(0.0);
+    system.addParticle(1.0);
+    system.addConstraint(0, 1, 1.5);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    VelocityVerletIntegrator integrator(0.01);
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        initializeTests(argc, argv);
+        testVVSingleBond();
+        testVVConstraints();
+        testVVConstrainedClusters();
+        testVVConstrainedMasslessParticles();
+        runPlatformTests();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

wrappers/generateWrappers.py

@@ -76,7 +76,20 @@ class WrapperGenerator:
                             'static std::vector<std::string> OpenMM::Platform::loadPluginsFromDirectory',
                             'Vec3 OpenMM::LocalCoordinatesSite::getOriginWeights',
                             'Vec3 OpenMM::LocalCoordinatesSite::getXWeights',
-                            'Vec3 OpenMM::LocalCoordinatesSite::getYWeights']
+                            'Vec3 OpenMM::LocalCoordinatesSite::getYWeights',
+                            'std::string OpenMM::NoseHooverChain::Temperature',
+                            'std::string OpenMM::NoseHooverChain::CollisionFrequency',
+                            'std::string OpenMM::NoseHooverChain::NumDegreesOfFreedom',
+                            'std::string OpenMM::NoseHooverChain::ChainLength',
+                            'std::string OpenMM::NoseHooverChain::NumMultiTimeSteps',
+                            'std::string OpenMM::NoseHooverChain::NumYoshidaSuzukiTimeSteps',
+                            'std::string OpenMM::NoseHooverChain::Force',
+                            'std::string OpenMM::NoseHooverChain::Mass',
+                            'std::string OpenMM::NoseHooverChain::Position',
+                            'std::string OpenMM::NoseHooverChain::Velocity',
+                            'std::string OpenMM::NoseHooverChain::getDefaultLabel',
+                            'std::vector<double> OpenMM::NoseHooverChain::getDefaultYoshidaSuzukiWeights',
+                           ] 
         self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']
         self.nodeByID={}
 

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -66,6 +66,8 @@ SKIP_METHODS = [('State', 'getPositions'),
                 ('IntegrateVariableLangevinStepKernel',),
                 ('IntegrateVariableVerletStepKernel',),
                 ('IntegrateVerletStepKernel',),
+                ('IntegrateVelocityVerletStepKernel',),
+                ('PropagateNoseHooverChainKernel',),
                 ('IntegrateCustomStepKernel',),
                 ('Kernel',),
                 ('KernelFactory',),
@@ -466,6 +468,7 @@ UNITS = {
 ("MonteCarloMembraneBarostat", "getXYMode") : (None, ()),
 ("MonteCarloMembraneBarostat", "getZMode") : (None, ()),
 ("DrudeLangevinIntegrator", "getDrudeFriction") : ("1/unit.picosecond", ()),
+("NoseHooverChain", "getDefaultYoshidaSuzukiWeights") : ("unit.dimensionless", ()),
 ("DrudeSCFIntegrator", "getMinimizationErrorTolerance") : ("unit.kilojoules_per_mole/unit.nanometer", ()),
 ("RPMDIntegrator", "getContractions") : (None, ()),
 ("RPMDIntegrator", "getTotalEnergy") : ("unit.kilojoules_per_mole", ()),