Converted two more ReferencePlatform tests to platform generic tests

tests/platforms/TestPlatformBrownianIntegrator.cpp.in

+/* -------------------------------------------------------------------------- *
+ *                                   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 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 BrownianIntegrator.
+ */
+
+
+#include "@OPENMM_PLATFORM_NAME@.h"
+
+#include "../../../tests/AssertionUtilities.h"
+#include "OpenMMContext.h"
+#include "StandardMMForceField.h"
+#include "System.h"
+#include "BrownianIntegrator.h"
+#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "../src/sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testSingleBond(Platform& platform) {
+    System system(2, 0);
+    system.setAtomMass(0, 2.0);
+    system.setAtomMass(1, 2.0);
+    double dt = 0.01;
+    BrownianIntegrator integrator(0, 0.1, dt);
+    StandardMMForceField* forceField = new StandardMMForceField(2, 1, 0, 0, 0);
+    forceField->setBondParameters(0, 0, 1, 1.5, 1);
+    system.addForce(forceField);
+    OpenMMContext 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 an overdamped harmonic oscillator, so compare it to the analytical solution.
+    
+    double rate = 2*1.0/0.1;
+    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(-rate*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);
+        if (i > 0) {
+            double expectedSpeed = -0.5*rate*std::exp(-rate*(time-0.5*dt));
+            ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.11);
+            ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.11);
+        }
+        integrator.step(1);
+    }
+}
+
+void testTemperature(Platform& platform) {
+    const int numAtoms = 8;
+    const int numBonds = numAtoms-1;
+    const double temp = 100.0;
+    System system(numAtoms, 0);
+    BrownianIntegrator integrator(temp, 2.0, 0.01);
+    StandardMMForceField* forceField = new StandardMMForceField(numAtoms, numBonds, 0, 0, 0);
+    for (int i = 0; i < numAtoms; ++i) {
+        system.setAtomMass(i, 2.0);
+//        forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    for (int i = 0; i < numBonds; ++i)
+        forceField->setBondParameters(i, i, i+1, 1.0, i);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numAtoms);
+    for (int i = 0; i < numAtoms; ++i)
+        positions[i] = Vec3(i, 0, 0);
+    context.setPositions(positions);
+    
+    // Let it equilibrate.
+    
+    integrator.step(1000);
+    
+    // Now run it for a while and see if the temperature is correct.
+    
+    double pe = 0.0;
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Energy);
+        pe += state.getPotentialEnergy();
+        integrator.step(1);
+    }
+    pe /= 1000;
+    double expected = 0.5*numBonds*BOLTZ*temp;
+    ASSERT_EQUAL_TOL(expected, pe, 3*expected/std::sqrt(1000.0));
+}
+
+void testConstraints(Platform& platform) {
+    const int numAtoms = 8;
+    const double temp = 100.0;
+    System system(numAtoms, numAtoms-1);
+    BrownianIntegrator integrator(temp, 2.0, 0.001);
+    StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0);
+    for (int i = 0; i < numAtoms; ++i) {
+        system.setAtomMass(i, 10.0);
+        forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    for (int i = 0; i < numAtoms-1; ++i)
+        system.setConstraintParameters(i, i, i+1, 1.0);
+    system.addForce(forceField);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numAtoms);
+    vector<Vec3> velocities(numAtoms);
+    init_gen_rand(0);
+    for (int i = 0; i < numAtoms; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-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 < numAtoms-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-4);
+        }
+        integrator.step(1);
+    }
+}
+
+int main() {
+    try {
+    	@OPENMM_PLATFORM_NAME@ platform;    	
+        testSingleBond(platform);
+        testTemperature(platform);
+        testConstraints(platform);
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

tests/platforms/TestPlatformCMMotionRemover.cpp.in

+/* -------------------------------------------------------------------------- *
+ *                                   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 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 AndersenThermostat.
+ */
+
+
+#include "@OPENMM_PLATFORM_NAME@.h"
+
+#include "../../../tests/AssertionUtilities.h"
+#include "CMMotionRemover.h"
+#include "OpenMMContext.h"
+#include "StandardMMForceField.h"
+#include "System.h"
+#include "VerletIntegrator.h"
+#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
+#include "../src/sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+Vec3 calcCM(const vector<Vec3>& values, System& system) {
+    Vec3 cm;
+    for (int j = 0; j < system.getNumAtoms(); ++j) {
+        cm[0] += values[j][0]*system.getAtomMass(j);
+        cm[1] += values[j][1]*system.getAtomMass(j);
+        cm[2] += values[j][2]*system.getAtomMass(j);
+    }
+    return cm;
+}
+
+void testMotionRemoval(Platform& platform) {
+    const int numAtoms = 8;
+    const double temp = 100.0;
+    const double collisionFreq = 10.0;
+    System system(numAtoms, 0);
+    VerletIntegrator integrator(0.01);
+    StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 1, 0, 0, 0);
+    for (int i = 0; i < numAtoms; ++i) {
+        system.setAtomMass(i, i+1);
+        forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    forceField->setBondParameters(0, 2, 3, 2.0, 0.5);
+    system.addForce(forceField);
+    CMMotionRemover* remover = new CMMotionRemover();
+    system.addForce(remover);
+    OpenMMContext context(system, integrator, platform);
+    vector<Vec3> positions(numAtoms);
+    vector<Vec3> velocities(numAtoms);
+    init_gen_rand(0);
+    for (int i = 0; i < numAtoms; ++i) {
+        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
+        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    
+    // Now run it for a while and see if the center of mass remains fixed.
+    
+    Vec3 cmPos = calcCM(context.getState(State::Positions).getPositions(), system);
+    for (int i = 0; i < 1000; ++i) {
+        integrator.step(1);
+        State state = context.getState(State::Positions | State::Velocities);
+        Vec3 pos = calcCM(state.getPositions(), system);
+        ASSERT_EQUAL_VEC(cmPos, pos, 1e-2);
+        Vec3 vel = calcCM(state.getVelocities(), system);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), vel, 1e-2);
+    }
+}
+
+int main() {
+    try {
+        @OPENMM_PLATFORM_NAME@ platform;    	
+        testMotionRemoval(platform);
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}