Merge branch 'master' of https://github.com/SimTk/openmm

platforms/cpu/tests/TestCpuLangevinIntegrator.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008-2013 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the reference implementation of LangevinIntegrator.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "CpuPlatform.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/LangevinIntegrator.h"
+#include "SimTKOpenMMRealType.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testSingleBond() {
+    CpuPlatform platform;
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
+    LangevinIntegrator integrator(0, 0.1, 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 damped harmonic oscillator, so compare it to the analytical solution.
+    
+    double freq = std::sqrt(1-0.05*0.05);
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Velocities);
+        double time = state.getTime();
+        double expectedDist = 1.5+0.5*std::exp(-0.05*time)*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*std::exp(-0.05*time)*(0.05*std::cos(freq*time)+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);
+        integrator.step(1);
+    }
+    
+    // Not set the friction to a tiny value and see if it conserves energy.
+    
+    integrator.setFriction(5e-5);
+    context.setPositions(positions);
+    State state = context.getState(State::Energy);
+    double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
+    for (int i = 0; i < 1000; ++i) {
+        state = context.getState(State::Energy);
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+        integrator.step(1);
+    }
+}
+
+void testTemperature() {
+    const int numParticles = 8;
+    const double temp = 100.0;
+    CpuPlatform platform;
+    System system;
+    LangevinIntegrator integrator(temp, 2.0, 0.01);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(2.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; ++i)
+        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
+    context.setPositions(positions);
+    
+    // Let it equilibrate.
+    
+    integrator.step(10000);
+    
+    // Now run it for a while and see if the temperature is correct.
+    
+    double ke = 0.0;
+    for (int i = 0; i < 10000; ++i) {
+        State state = context.getState(State::Energy);
+        ke += state.getKineticEnergy();
+        integrator.step(1);
+    }
+    ke /= 10000;
+    double expected = 0.5*numParticles*3*BOLTZ*temp;
+    ASSERT_USUALLY_EQUAL_TOL(expected, ke, 6/std::sqrt(10000.0));
+}
+
+void testConstraints() {
+    const int numParticles = 8;
+    const double temp = 100.0;
+    CpuPlatform platform;
+    System system;
+    LangevinIntegrator integrator(temp, 2.0, 0.01);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(10.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    for (int i = 0; i < numParticles-1; ++i)
+        system.addConstraint(i, i+1, 1.0);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    
+    // Simulate it and see whether the constraints remain satisfied.
+    
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions);
+        for (int j = 0; j < numParticles-1; ++j) {
+            Vec3 p1 = state.getPositions()[j];
+            Vec3 p2 = state.getPositions()[j+1];
+            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(1.0, dist, 2e-5);
+        }
+        integrator.step(1);
+    }
+}
+
+void testConstrainedMasslessParticles() {
+    CpuPlatform platform;
+    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);
+    LangevinIntegrator integrator(300.0, 2.0, 0.01);
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
+void testRandomSeed() {
+    const int numParticles = 8;
+    const double temp = 100.0;
+    const double collisionFreq = 10.0;
+    CpuPlatform platform;
+    System system;
+    LangevinIntegrator integrator(temp, 2.0, 0.01);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(2.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    system.addForce(forceField);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
+        velocities[i] = Vec3(0, 0, 0);
+    }
+
+    // Try twice with the same random seed.
+
+    integrator.setRandomNumberSeed(5);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state1 = context.getState(State::Positions);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state2 = context.getState(State::Positions);
+
+    // Try twice with a different random seed.
+
+    integrator.setRandomNumberSeed(10);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state3 = context.getState(State::Positions);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state4 = context.getState(State::Positions);
+
+    // Compare the results.
+
+    for (int i = 0; i < numParticles; i++) {
+        for (int j = 0; j < 3; j++) {
+            ASSERT_EQUAL_TOL(state1.getPositions()[i][j], state2.getPositions()[i][j], 1e-5);
+            ASSERT_EQUAL_TOL(state3.getPositions()[i][j], state4.getPositions()[i][j], 1e-5);
+            ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
+        }
+    }
+}
+
+int main() {
+    try {
+        testSingleBond();
+        testTemperature();
+        testConstraints();
+        testConstrainedMasslessParticles();
+        testRandomSeed();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/cpu/tests/TestCpuNeighborList.cpp

@@ -51,6 +51,7 @@ void testNeighborList(bool periodic) {
     const int numParticles = 500;
     const float cutoff = 2.0f;
     const float boxSize[3] = {20.0f, 15.0f, 22.0f};
+    const int blockSize = 8;
     OpenMM_SFMT::SFMT sfmt;
     init_gen_rand(0, sfmt);
     AlignedArray<float> positions(4*numParticles);
@@ -66,15 +67,15 @@ void testNeighborList(bool periodic) {
         }
     }
     ThreadPool threads;
-    CpuNeighborList neighborList;
+    CpuNeighborList neighborList(blockSize);
     neighborList.computeNeighborList(numParticles, positions, exclusions, boxSize, periodic, cutoff, threads);
     
     // Convert the neighbor list to a set for faster lookup.
     
     set<pair<int, int> > neighbors;
     for (int i = 0; i < (int) neighborList.getSortedAtoms().size(); i++) {
-        int blockIndex = i/CpuNeighborList::BlockSize;
-        int indexInBlock = i-blockIndex*CpuNeighborList::BlockSize;
+        int blockIndex = i/blockSize;
+        int indexInBlock = i-blockIndex*blockSize;
         char mask = 1<<indexInBlock;
         for (int j = 0; j < (int) neighborList.getBlockExclusions(blockIndex).size(); j++) {
             if ((neighborList.getBlockExclusions(blockIndex)[j] & mask) == 0) {

platforms/reference/include/ReferenceStochasticDynamics.h

@@ -31,7 +31,7 @@
 
 class ReferenceStochasticDynamics : public ReferenceDynamics {
 
-   private:
+   protected:
 
       std::vector<OpenMM::RealVec> xPrime;
       std::vector<RealOpenMM> inverseMasses;
@@ -99,7 +99,7 @@ class ReferenceStochasticDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      void updatePart1( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
+      virtual void updatePart1( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
                        std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime );
       
       /**---------------------------------------------------------------------------------------
@@ -114,7 +114,7 @@ class ReferenceStochasticDynamics : public ReferenceDynamics {
       
          --------------------------------------------------------------------------------------- */
       
-      void updatePart2( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
+      virtual void updatePart2( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
                        std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime );
       
 };