mirror of
https://github.com/openmm/openmm
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05472c9a81
* Replace SimTK-containing file headers * Update file headers for new Tinker reader files added
288 lines
12 KiB
C++
288 lines
12 KiB
C++
/* -------------------------------------------------------------------------- *
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* OpenMM *
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* -------------------------------------------------------------------------- *
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* This is part of the OpenMM molecular simulation toolkit. *
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* See https://openmm.org/development. *
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* *
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* Portions copyright (c) 2015-2020 Stanford University and the Authors. *
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* Authors: Peter Eastman *
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* Contributors: *
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* *
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* Permission is hereby granted, free of charge, to any person obtaining a *
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* copy of this software and associated documentation files (the "Software"), *
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* to deal in the Software without restriction, including without limitation *
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* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
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* and/or sell copies of the Software, and to permit persons to whom the *
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* Software is furnished to do so, subject to the following conditions: *
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* *
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* The above copyright notice and this permission notice shall be included in *
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* all copies or substantial portions of the Software. *
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* *
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
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* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
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* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
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* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
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* USE OR OTHER DEALINGS IN THE SOFTWARE. *
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* -------------------------------------------------------------------------- */
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#include "openmm/internal/AssertionUtilities.h"
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#include "openmm/BrownianIntegrator.h"
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#include "openmm/CompoundIntegrator.h"
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#include "openmm/Context.h"
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#include "openmm/CustomIntegrator.h"
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#include "openmm/HarmonicBondForce.h"
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#include "openmm/LangevinIntegrator.h"
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#include "openmm/System.h"
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#include "openmm/VerletIntegrator.h"
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#include "SimTKOpenMMRealType.h"
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#include <iostream>
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#include <vector>
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using namespace OpenMM;
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using namespace std;
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const double TOL = 1e-5;
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void testChangingIntegrator() {
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System system;
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system.addParticle(2.0);
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system.addParticle(2.0);
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HarmonicBondForce* bonds = new HarmonicBondForce();
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bonds->addBond(0, 1, 1.5, 1);
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system.addForce(bonds);
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CompoundIntegrator integrator;
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integrator.addIntegrator(new VerletIntegrator(0.01));
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integrator.addIntegrator(new LangevinIntegrator(300.0, 10.0, 0.011));
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integrator.addIntegrator(new BrownianIntegrator(300.0, 10.0, 0.012));
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Context context(system, integrator, platform);
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ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
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vector<Vec3> positions(2);
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positions[0] = Vec3(-1, 0, 0);
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positions[1] = Vec3(1, 0, 0);
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for (int iteration = 0; iteration < 2; ++iteration) {
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context.setPositions(positions);
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// First integrate with the Verlet integrator and compare it to the analytical solution.
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const double freq = 1.0;
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State state = context.getState(State::Energy);
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const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
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for (int i = 0; i < 100; ++i) {
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state = context.getState(State::Positions | State::Velocities | State::Energy);
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double time = state.getTime();
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double expectedDist = 1.5+0.5*std::cos(freq*time);
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ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
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ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
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double expectedSpeed = -0.5*freq*std::sin(freq*time);
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ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
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ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
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double energy = state.getKineticEnergy()+state.getPotentialEnergy();
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ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
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integrator.step(1);
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}
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ASSERT_EQUAL_TOL(100*0.01, context.getState(0).getTime(), 1e-5);
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// Switch to the Langevin integrator and make sure that it heats up.
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integrator.setCurrentIntegrator(1);
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integrator.step(100);
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double ke = 0.0;
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for (int i = 0; i < 1000; ++i) {
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integrator.step(10);
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state = context.getState(State::Energy);
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ke += state.getKineticEnergy();
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}
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double expectedKE = 0.5*2*3*BOLTZ*300.0;
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ASSERT_USUALLY_EQUAL_TOL(expectedKE, ke/1000, 0.1);
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ASSERT_EQUAL_TOL(100*0.01+10100*0.011, context.getState(0).getTime(), 1e-5);
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// Now reinitialize the context and repeat all of these tests to make sure that works correctly.
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context.reinitialize();
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integrator.setCurrentIntegrator(0);
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}
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}
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void testChangingParameters() {
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System system;
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system.addParticle(1.0);
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CompoundIntegrator integrator;
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integrator.addIntegrator(new VerletIntegrator(0.01));
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integrator.addIntegrator(new LangevinIntegrator(300.0, 10.0, 0.02));
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integrator.addIntegrator(new BrownianIntegrator(300.0, 10.0, 0.03));
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// Try getting and setting the step size for different component integrators.
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for (int i = 0; i < 3; i++) {
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integrator.setCurrentIntegrator(i);
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ASSERT_EQUAL_TOL(0.01*(i+1), integrator.getStepSize(), 1e-7);
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}
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for (int i = 0; i < 3; i++) {
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integrator.setCurrentIntegrator(i);
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integrator.setStepSize(0.02*(i+1));
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ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
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}
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for (int i = 0; i < 3; i++) {
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integrator.setCurrentIntegrator(i);
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ASSERT_EQUAL_TOL(0.02*(i+1), integrator.getStepSize(), 1e-7);
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}
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// Try getting and setting the constraint tolerance for different component integrators.
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for (int i = 0; i < 3; i++) {
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integrator.setCurrentIntegrator(i);
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ASSERT_EQUAL_TOL(1e-5, integrator.getConstraintTolerance(), 1e-7);
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}
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for (int i = 0; i < 3; i++) {
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integrator.setCurrentIntegrator(i);
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integrator.setConstraintTolerance(1e-4*(i+1));
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ASSERT_EQUAL_TOL(1e-4*(i+1), integrator.getConstraintTolerance(), 1e-7);
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}
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for (int i = 0; i < 3; i++) {
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integrator.setCurrentIntegrator(i);
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ASSERT_EQUAL_TOL(1e-4*(i+1), integrator.getConstraintTolerance(), 1e-7);
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}
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}
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void testDifferentStepSizes() {
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System system;
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system.addParticle(2.0);
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system.addParticle(2.0);
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HarmonicBondForce* bonds = new HarmonicBondForce();
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bonds->addBond(0, 1, 1.5, 1);
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system.addForce(bonds);
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CompoundIntegrator integrator;
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integrator.addIntegrator(new VerletIntegrator(0.005));
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integrator.addIntegrator(new VerletIntegrator(0.01));
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Context context(system, integrator, platform);
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ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
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vector<Vec3> positions(2);
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positions[0] = Vec3(-1, 0, 0);
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positions[1] = Vec3(1, 0, 0);
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context.setPositions(positions);
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// Integrate with the first Verlet integrator and compare it to the analytical solution.
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const double freq = 1.0;
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double expectedTime = 0;
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for (int i = 0; i < 100; ++i) {
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State state = context.getState(State::Positions);
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double time = state.getTime();
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ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
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double expectedDist = 1.5+0.5*std::cos(freq*time);
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ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
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ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
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integrator.step(1);
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expectedTime += 0.005;
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}
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// Now switch to the second Verlet integrator which has a different step size.
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integrator.setCurrentIntegrator(1);
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for (int i = 0; i < 100; ++i) {
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State state = context.getState(State::Positions);
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double time = state.getTime();
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ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
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double expectedDist = 1.5+0.5*std::cos(freq*time);
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ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
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ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
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integrator.step(1);
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expectedTime += 0.01;
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}
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// Finally, switch back to the first one again.
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integrator.setCurrentIntegrator(0);
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for (int i = 0; i < 100; ++i) {
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State state = context.getState(State::Positions);
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double time = state.getTime();
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ASSERT_EQUAL_TOL(expectedTime, time, 1e-5);
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double expectedDist = 1.5+0.5*std::cos(freq*time);
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ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
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ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
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integrator.step(1);
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expectedTime += 0.005;
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}
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}
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void testCheckpoint() {
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// Test that member integrators get loaded correctly from checkpoints.
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System system;
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system.addParticle(1.0);
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CustomIntegrator* custom = new CustomIntegrator(0.001);
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custom->addGlobalVariable("a", 1.0);
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custom->addPerDofVariable("b", 2.0);
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CompoundIntegrator integrator;
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integrator.addIntegrator(custom);
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integrator.addIntegrator(new VerletIntegrator(0.005));
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Context context(system, integrator, platform);
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vector<Vec3> positions(1, Vec3());
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context.setPositions(positions);
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custom->setGlobalVariable(0, 5.0);
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vector<Vec3> b1(1, Vec3(1, 2, 3));
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custom->setPerDofVariable(0, b1);
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stringstream checkpoint;
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context.createCheckpoint(checkpoint);
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custom->setGlobalVariable(0, 10.0);
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vector<Vec3> b2(1, Vec3(4, 5, 6));
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custom->setPerDofVariable(0, b2);
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integrator.setCurrentIntegrator(1);
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context.loadCheckpoint(checkpoint);
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ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
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ASSERT_EQUAL(5.0, custom->getGlobalVariable(0));
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vector<Vec3> b3;
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custom->getPerDofVariable(0, b3);
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ASSERT_EQUAL_VEC(b1[0], b3[0], 1e-6);
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}
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void testSaveParameters() {
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// Test that integrator variables get loaded correctly from States.
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System system;
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system.addParticle(1.0);
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CustomIntegrator* custom = new CustomIntegrator(0.001);
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custom->addGlobalVariable("a", 1.0);
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custom->addPerDofVariable("b", 2.0);
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CompoundIntegrator integrator;
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integrator.addIntegrator(custom);
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integrator.addIntegrator(new VerletIntegrator(0.005));
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Context context(system, integrator, platform);
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vector<Vec3> positions(1, Vec3());
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context.setPositions(positions);
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custom->setGlobalVariable(0, 5.0);
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vector<Vec3> b1(1, Vec3(1, 2, 3));
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custom->setPerDofVariable(0, b1);
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State savedState = context.getState(State::IntegratorParameters);
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custom->setGlobalVariable(0, 10.0);
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vector<Vec3> b2(1, Vec3(4, 5, 6));
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custom->setPerDofVariable(0, b2);
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integrator.setCurrentIntegrator(1);
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context.setState(savedState);
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ASSERT_EQUAL(0, integrator.getCurrentIntegrator());
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ASSERT_EQUAL(5.0, custom->getGlobalVariable(0));
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vector<Vec3> b3;
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custom->getPerDofVariable(0, b3);
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ASSERT_EQUAL_VEC(b1[0], b3[0], 1e-6);
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}
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void runPlatformTests();
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int main(int argc, char* argv[]) {
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try {
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initializeTests(argc, argv);
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testChangingIntegrator();
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testChangingParameters();
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testDifferentStepSizes();
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testCheckpoint();
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testSaveParameters();
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runPlatformTests();
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}
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catch(const exception& e) {
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cout << "exception: " << e.what() << endl;
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return 1;
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}
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cout << "Done" << endl;
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return 0;
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}
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