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) 2012-2024 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/AndersenThermostat.h"
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#include "openmm/Context.h"
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#include "openmm/LangevinIntegrator.h"
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#include "openmm/NonbondedForce.h"
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#include "openmm/System.h"
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#include "openmm/VerletIntegrator.h"
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#include "sfmt/SFMT.h"
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#include <iostream>
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#include <sstream>
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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 compareStates(State& s1, State& s2) {
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ASSERT_EQUAL_TOL(s1.getTime(), s2.getTime(), TOL);
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int numParticles = s1.getPositions().size();
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for (int i = 0; i < numParticles; i++) {
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ASSERT_EQUAL_VEC(s1.getPositions()[i], s2.getPositions()[i], TOL);
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ASSERT_EQUAL_VEC(s1.getVelocities()[i], s2.getVelocities()[i], TOL);
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Vec3 a1, b1, c1, a2, b2, c2;
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s1.getPeriodicBoxVectors(a1, b1, c1);
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s2.getPeriodicBoxVectors(a2, b2, c2);
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ASSERT_EQUAL_VEC(a1, a2, TOL);
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ASSERT_EQUAL_VEC(b1, b2, TOL);
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ASSERT_EQUAL_VEC(c1, c2, TOL);
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for (map<string, double>::const_iterator iter = s1.getParameters().begin(); iter != s1.getParameters().end(); ++iter)
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ASSERT_EQUAL(iter->second, (*s2.getParameters().find(iter->first)).second);
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}
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}
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void testSetState() {
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const int numParticles = 10;
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const double boxSize = 3.0;
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const double temperature = 200.0;
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System system;
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system.addForce(new AndersenThermostat(0.0, 100.0));
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NonbondedForce* nonbonded = new NonbondedForce();
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system.addForce(nonbonded);
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nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
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vector<Vec3> positions(numParticles);
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OpenMM_SFMT::SFMT sfmt;
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init_gen_rand(0, sfmt);
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for (int i = 0; i < numParticles; i++) {
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system.addParticle(1.0);
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nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
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positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
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}
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VerletIntegrator integrator(0.001);
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Context context(system, integrator, platform);
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context.setPositions(positions);
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context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
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context.setParameter(AndersenThermostat::Temperature(), temperature);
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// Run for a little while.
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integrator.step(100);
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// Record the current state.
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State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
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// Continue the simulation for a few more steps and record a partial state.
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integrator.step(10);
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State s2 = context.getState(State::Positions);
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// Restore the original state and see if everything gets restored correctly.
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context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
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context.setParameter(AndersenThermostat::Temperature(), temperature+10);
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context.setState(s1);
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State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
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compareStates(s1, s3);
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// Set the partial state and see if the correct things were set.
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context.setState(s2);
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State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
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for (int i = 0; i < numParticles; i++) {
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ASSERT_EQUAL_VEC(s2.getPositions()[i], s4.getPositions()[i], TOL);
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ASSERT_EQUAL_VEC(s1.getVelocities()[i], s4.getVelocities()[i], TOL);
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}
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}
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void testMultipleDevices() {
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const int numParticles = 100;
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const double boxSize = 5.0;
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const double temperature = 200.0;
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System system;
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system.addForce(new AndersenThermostat(0.0, 100.0));
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NonbondedForce* nonbonded = new NonbondedForce();
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system.addForce(nonbonded);
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nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
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vector<Vec3> positions(numParticles);
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OpenMM_SFMT::SFMT sfmt;
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init_gen_rand(0, sfmt);
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for (int i = 0; i < numParticles; i++) {
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system.addParticle(1.0);
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nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
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bool clash;
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do {
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clash = false;
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positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
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for (int j = 0; j < i; j++) {
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Vec3 delta = positions[i]-positions[j];
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if (sqrt(delta.dot(delta)) < 0.1)
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clash = true;
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}
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} while (clash);
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}
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VerletIntegrator integrator(0.001);
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Context context(system, integrator, platform);
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context.setPositions(positions);
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context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
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context.setParameter(AndersenThermostat::Temperature(), temperature);
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// Run for a little while.
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integrator.step(100);
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// Record the current state and make a checkpoint.
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State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
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stringstream stream1(ios_base::out | ios_base::in | ios_base::binary);
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context.createCheckpoint(stream1);
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// Continue the simulation for a few more steps and record the state again.
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integrator.step(10);
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State s2 = context.getState(State::Positions | State::Velocities | State::Parameters);
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// Restore from the checkpoint and see if everything gets restored correctly.
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context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
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context.setParameter(AndersenThermostat::Temperature(), temperature+10);
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context.loadCheckpoint(stream1);
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State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
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compareStates(s1, s3);
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// Now simulate from there and see if the trajectory is identical.
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integrator.step(10);
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State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
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compareStates(s2, s4);
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// Create a new Context that uses multiple devices.
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map<string, string> props;
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try {
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string deviceIndex = platform.getPropertyValue(context, "DeviceIndex");
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props["DeviceIndex"] = deviceIndex+","+deviceIndex;
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}
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catch (OpenMMException& ex) {
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// This platform doesn't have a DeviceIndex property.
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}
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VerletIntegrator integrator2(0.001);
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Context context2(system, integrator2, platform, props);
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context2.setPositions(positions);
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context2.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
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context2.setParameter(AndersenThermostat::Temperature(), temperature);
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// Now repeat all of the above tests with it.
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integrator2.step(100);
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State s5 = context2.getState(State::Positions | State::Velocities | State::Parameters);
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stringstream stream2(ios_base::out | ios_base::in | ios_base::binary);
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context2.createCheckpoint(stream2);
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integrator2.step(10);
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State s6 = context2.getState(State::Positions | State::Velocities | State::Parameters);
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context2.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
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context2.setParameter(AndersenThermostat::Temperature(), temperature+10);
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context2.loadCheckpoint(stream2);
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State s7 = context2.getState(State::Positions | State::Velocities | State::Parameters);
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compareStates(s5, s7);
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integrator2.step(10);
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State s8 = context2.getState(State::Positions | State::Velocities | State::Parameters);
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compareStates(s6, s8);
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// See if a checkpoint created from one Context can be loaded into a different one.
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VerletIntegrator integrator3(0.001);
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Context context3(system, integrator3, platform);
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stream1.seekg(0, stream1.beg);
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context3.loadCheckpoint(stream1);
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State s9 = context3.getState(State::Positions | State::Velocities | State::Parameters | State::Energy);
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compareStates(s1, s9);
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}
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void testLangevin() {
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const int numParticles = 10;
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const double boxSize = 3.0;
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System system;
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NonbondedForce* nonbonded = new NonbondedForce();
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system.addForce(nonbonded);
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nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
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vector<Vec3> positions(numParticles);
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OpenMM_SFMT::SFMT sfmt;
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init_gen_rand(0, sfmt);
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for (int i = 0; i < numParticles; i++) {
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system.addParticle(1.0);
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nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
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positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
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}
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LangevinIntegrator integrator(300.0, 1.0, 0.001);
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Context context(system, integrator, platform);
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context.setPositions(positions);
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context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
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// Run for a little while.
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integrator.step(100);
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// Record the current state and make a checkpoint.
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State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
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stringstream stream1(ios_base::out | ios_base::in | ios_base::binary);
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context.createCheckpoint(stream1);
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// Continue the simulation for a few more steps and record the state again.
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integrator.step(10);
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State s2 = context.getState(State::Positions | State::Velocities | State::Parameters);
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// Restore from the checkpoint and see if everything gets restored correctly.
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context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
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context.loadCheckpoint(stream1);
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State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
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compareStates(s1, s3);
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// Now simulate from there and see if the trajectory is identical.
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integrator.step(10);
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State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
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compareStates(s2, s4);
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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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testSetState();
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testMultipleDevices();
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testLangevin();
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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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