void testSerialization() {
// Create a Force.
NonbondedForce force;
force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
force.setCutoffDistance(2.0);
force.setEwaldErrorTolerance(1e-3);
force.setReactionFieldDielectric(50.0);
force.setUseDispersionCorrection(false);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
force.addException(0, 1, 2, 0.5, 0.1);
force.addException(1, 2, 0.2, 0.4, 0.2);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<NonbondedForce>(&force, "Force", buffer);
NonbondedForce* copy = XmlSerializer::deserialize<NonbondedForce>(buffer);
// Compare the two forces to see if they are identical.
NonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getParticleParameters(i, charge1, sigma1, epsilon1);
force2.getParticleParameters(i, charge2, sigma2, epsilon2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
for (int i = 0; i < force.getNumExceptions(); i++) {
int a1, a2, b1, b2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getExceptionParameters(i, a1, b1, charge1, sigma1, epsilon1);
force2.getExceptionParameters(i, a2, b2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(a1, a2);
ASSERT_EQUAL(b1, b2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
}
void testPeriodic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addException(0, 1, 0.0, 1.0, 0.0);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 2.0;
nonbonded->setCutoffDistance(cutoff);
system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
positions[2] = Vec3(3, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
const double force = ONE_4PI_EPS0*(1.0)*(1.0-2.0*krf*1.0);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(2*ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL);
}
void testForceEnergyConsistency() {
// Create a box of polarizable particles.
const int gridSize = 3;
const int numAtoms = gridSize*gridSize*gridSize;
const double spacing = 0.6;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
const double temperatureDrude = 10.0;
System system;
vector<Vec3> positions;
NonbondedForce* nonbonded = new NonbondedForce();
DrudeForce* drude = new DrudeForce();
system.addForce(nonbonded);
system.addForce(drude);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setCutoffDistance(1.0);
nonbonded->setUseSwitchingFunction(true);
nonbonded->setSwitchingDistance(0.9);
nonbonded->setEwaldErrorTolerance(5e-5);
for (int i = 0; i < numAtoms; i++) {
int startIndex = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
nonbonded->addParticle(1.0, 0.3, 1.0);
nonbonded->addParticle(-1.0, 0.3, 1.0);
nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
}
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos(i*spacing, j*spacing, k*spacing);
positions.push_back(pos);
positions.push_back(pos);
}
// Simulate it and check that force and energy remain consistent.
DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
context.setPositions(positions);
State prevState;
for (int i = 0; i < 100; i++) {
State state = context.getState(State::Energy | State::Forces | State::Positions);
if (i > 0) {
double expectedEnergyChange = 0;
for (int j = 0; j < system.getNumParticles(); j++) {
Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
}
ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
}
prevState = state;
integ.step(1);
}
}
void testParallelComputation(NonbondedForce::NonbondedMethod method) {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
NonbondedForce* force = new NonbondedForce();
for (int i = 0; i < numParticles; i++)
force->addParticle(i%2-0.5, 0.5, 1.0);
force->setNonbondedMethod(method);
system.addForce(force);
system.setDefaultPeriodicBoxVectors(Vec3(5,0,0), Vec3(0,5,0), Vec3(0,0,5));
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(5*genrand_real2(sfmt), 5*genrand_real2(sfmt), 5*genrand_real2(sfmt));
for (int i = 0; i < numParticles; ++i)
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
force->addException(i, j, 0, 1, 0);
}
// Create two contexts, one with a single device and one with two devices.
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
VerletIntegrator integrator2(0.01);
string deviceIndex = platform.getPropertyValue(context1, CudaPlatform::CudaDeviceIndex());
map<string, string> props;
props[CudaPlatform::CudaDeviceIndex()] = deviceIndex+","+deviceIndex;
Context context2(system, integrator2, platform, props);
context2.setPositions(positions);
State state2 = context2.getState(State::Forces | State::Energy);
// See if they agree.
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
// Modify some particle parameters and see if they still agree.
for (int i = 0; i < numParticles; i += 5) {
double charge, sigma, epsilon;
force->getParticleParameters(i, charge, sigma, epsilon);
force->setParticleParameters(i, 0.9*charge, sigma, epsilon);
}
force->updateParametersInContext(context1);
force->updateParametersInContext(context2);
state1 = context1.getState(State::Forces | State::Energy);
state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
/**
* Make sure that atom reordering respects virtual sites.
*/
void testReordering() {
const double cutoff = 2.0;
const double boxSize = 20.0;
System system;
NonbondedForce* nonbonded = new NonbondedForce();
system.addForce(nonbonded);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
nonbonded->setCutoffDistance(cutoff);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
// Create linear molecules with TwoParticleAverage virtual sites.
for (int i = 0; i < 50; i++) {
int start = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(start+2, new TwoParticleAverageSite(start, start+1, 0.4, 0.6));
system.addConstraint(start, start+1, 2.0);
for (int i = 0; i < 3; i++) {
nonbonded->addParticle(0, 0.2, 1);
for (int j = 0; j < i; j++)
nonbonded->addException(start+i, start+j, 0, 1, 0);
}
Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions.push_back(pos);
positions.push_back(pos+Vec3(2, 0, 0));
positions.push_back(Vec3());
}
// Create planar molecules with ThreeParticleAverage virtual sites.
for (int i = 0; i < 50; i++) {
int start = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(start+3, new ThreeParticleAverageSite(start, start+1, start+2, 0.3, 0.5, 0.2));
system.addConstraint(start, start+1, 1.0);
system.addConstraint(start, start+2, 1.0);
system.addConstraint(start+1, start+2, sqrt(2.0));
for (int i = 0; i < 4; i++) {
nonbonded->addParticle(0, 0.2, 1);
for (int j = 0; j < i; j++)
nonbonded->addException(start+i, start+j, 0, 1, 0);
}
Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions.push_back(pos);
positions.push_back(pos+Vec3(1, 0, 0));
positions.push_back(pos+Vec3(0, 1, 0));
positions.push_back(Vec3());
}
// Create tetrahedral molecules with OutOfPlane virtual sites.
for (int i = 0; i < 50; i++) {
int start = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(start+3, new OutOfPlaneSite(start, start+1, start+2, 0.3, 0.5, 0.2));
system.addConstraint(start, start+1, 1.0);
system.addConstraint(start, start+2, 1.0);
system.addConstraint(start+1, start+2, sqrt(2.0));
for (int i = 0; i < 4; i++) {
nonbonded->addParticle(0, 0.2, 1);
for (int j = 0; j < i; j++)
nonbonded->addException(start+i, start+j, 0, 1, 0);
}
Vec3 pos(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions.push_back(pos);
positions.push_back(pos+Vec3(1, 0, 0));
positions.push_back(pos+Vec3(0, 1, 0));
positions.push_back(Vec3());
}
// Simulate it and check conservation laws.
LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform);
context.setPositions(positions);
context.applyConstraints(0.0001);
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions);
const vector<Vec3>& pos = state.getPositions();
for (int j = 0; j < 150; j += 3)
ASSERT_EQUAL_VEC(pos[j]*0.4+pos[j+1]*0.6, pos[j+2], 1e-5);
for (int j = 150; j < 350; j += 4)
ASSERT_EQUAL_VEC(pos[j]*0.3+pos[j+1]*0.5+pos[j+2]*0.2, pos[j+3], 1e-5);
for (int j = 350; j < 550; j += 4) {
Vec3 v12 = pos[j+1]-pos[j];
Vec3 v13 = pos[j+2]-pos[j];
Vec3 cross = v12.cross(v13);
ASSERT_EQUAL_VEC(pos[j]+v12*0.3+v13*0.5+cross*0.2, pos[j+3], 1e-5);
}
integrator.step(1);
}
}
/**
* Make sure that energy, linear momentum, and angular momentum are all conserved
* when using virtual sites.
*/
void testConservationLaws() {
System system;
NonbondedForce* forceField = new NonbondedForce();
system.addForce(forceField);
vector<Vec3> positions;
// Create a linear molecule with a TwoParticleAverage virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(2, new TwoParticleAverageSite(0, 1, 0.4, 0.6));
system.addConstraint(0, 1, 2.0);
for (int i = 0; i < 3; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i, j, 0, 1, 0);
}
positions.push_back(Vec3(0, 0, 0));
positions.push_back(Vec3(2, 0, 0));
positions.push_back(Vec3());
// Create a planar molecule with a ThreeParticleAverage virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(6, new ThreeParticleAverageSite(3, 4, 5, 0.3, 0.5, 0.2));
system.addConstraint(3, 4, 1.0);
system.addConstraint(3, 5, 1.0);
system.addConstraint(4, 5, sqrt(2.0));
for (int i = 0; i < 4; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i+3, j+3, 0, 1, 0);
}
positions.push_back(Vec3(0, 0, 1));
positions.push_back(Vec3(1, 0, 1));
positions.push_back(Vec3(0, 1, 1));
positions.push_back(Vec3());
// Create a tetrahedral molecule with an OutOfPlane virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(10, new OutOfPlaneSite(7, 8, 9, 0.3, 0.5, 0.2));
system.addConstraint(7, 8, 1.0);
system.addConstraint(7, 9, 1.0);
system.addConstraint(8, 9, sqrt(2.0));
for (int i = 0; i < 4; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i+7, j+7, 0, 1, 0);
}
positions.push_back(Vec3(1, 0, -1));
positions.push_back(Vec3(2, 0, -1));
positions.push_back(Vec3(1, 1, -1));
positions.push_back(Vec3());
// Create a molecule with a LocalCoordinatesSite virtual site.
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(14, new LocalCoordinatesSite(11, 12, 13, Vec3(0.3, 0.3, 0.4), Vec3(1.0, -0.5, -0.5), Vec3(0, -1.0, 1.0), Vec3(0.2, 0.2, 1.0)));
system.addConstraint(11, 12, 1.0);
system.addConstraint(11, 13, 1.0);
system.addConstraint(12, 13, sqrt(2.0));
for (int i = 0; i < 4; i++) {
forceField->addParticle(0, 1, 10);
for (int j = 0; j < i; j++)
forceField->addException(i+11, j+11, 0, 1, 0);
}
positions.push_back(Vec3(1, 2, 0));
positions.push_back(Vec3(2, 2, 0));
positions.push_back(Vec3(1, 3, 0));
positions.push_back(Vec3());
// Simulate it and check conservation laws.
VerletIntegrator integrator(0.002);
Context context(system, integrator, platform);
context.setPositions(positions);
context.applyConstraints(0.0001);
int numParticles = system.getNumParticles();
double initialEnergy;
Vec3 initialMomentum, initialAngularMomentum;
for (int i = 0; i < 1000; i++) {
State state = context.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
const vector<Vec3>& pos = state.getPositions();
const vector<Vec3>& vel = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = state.getPotentialEnergy();
for (int j = 0; j < numParticles; j++) {
Vec3 v = vel[j] + f[j]*0.5*integrator.getStepSize();
energy += 0.5*system.getParticleMass(j)*v.dot(v);
}
if (i == 0)
initialEnergy = energy;
else
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
Vec3 momentum;
for (int j = 0; j < numParticles; j++)
momentum += vel[j]*system.getParticleMass(j);
if (i == 0)
initialMomentum = momentum;
else
ASSERT_EQUAL_VEC(initialMomentum, momentum, 0.02);
Vec3 angularMomentum;
for (int j = 0; j < numParticles; j++)
angularMomentum += pos[j].cross(vel[j])*system.getParticleMass(j);
if (i == 0)
initialAngularMomentum = angularMomentum;
else
ASSERT_EQUAL_VEC(initialAngularMomentum, angularMomentum, 0.05);
integrator.step(1);
}
}
void testWithBarostat() {
const int gridSize = 3;
const int numMolecules = gridSize*gridSize*gridSize;
const int numParticles = numMolecules*2;
const int numCopies = 5;
const double spacing = 2.0;
const double cutoff = 3.0;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setCutoffDistance(cutoff);
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setForceGroup(1);
nonbonded->setReciprocalSpaceForceGroup(2);
system.addForce(nonbonded);
system.addForce(new MonteCarloBarostat(0.5, temperature));
// Create a cloud of molecules.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
nonbonded->addParticle(-0.2, 0.2, 0.2);
nonbonded->addParticle(0.2, 0.2, 0.2);
nonbonded->addException(2*i, 2*i+1, 0, 1, 0);
bonds->addBond(2*i, 2*i+1, 1.0, 10000.0);
}
RPMDIntegrator integ(numCopies, temperature, 50.0, 0.001);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
for (int copy = 0; copy < numCopies; copy++) {
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
int index = k+gridSize*(j+gridSize*i);
positions[2*index] = pos;
positions[2*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
}
integ.setPositions(copy, positions);
}
// Check the temperature.
const int numSteps = 500;
integ.step(100);
vector<double> ke(numCopies, 0.0);
for (int i = 0; i < numSteps; i++) {
integ.step(1);
vector<State> state(numCopies);
for (int j = 0; j < numCopies; j++)
state[j] = integ.getState(j, State::Velocities, true);
for (int j = 0; j < numParticles; j++) {
for (int k = 0; k < numCopies; k++) {
Vec3 v = state[k].getVelocities()[j];
ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
}
}
}
double meanKE = 0.0;
for (int i = 0; i < numCopies; i++)
meanKE += ke[i];
meanKE /= numSteps*numCopies;
double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}
void testCoulombLennardJones() {
const int numMolecules = 300;
const int numParticles = numMolecules*2;
const double boxSize = 20.0;
// Create two systems: one with a NonbondedForce, and one using a CustomNonbondedForce to implement the same interaction.
System standardSystem;
System customSystem;
for (int i = 0; i < numParticles; i++) {
standardSystem.addParticle(1.0);
customSystem.addParticle(1.0);
}
NonbondedForce* standardNonbonded = new NonbondedForce();
CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
customNonbonded->addPerParticleParameter("q");
customNonbonded->addPerParticleParameter("sigma");
customNonbonded->addPerParticleParameter("eps");
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<double> params(3);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
standardNonbonded->addParticle(1.0, 0.2, 0.1);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.1;
customNonbonded->addParticle(params);
standardNonbonded->addParticle(-1.0, 0.1, 0.1);
params[0] = -1.0;
params[1] = 0.1;
customNonbonded->addParticle(params);
}
else {
standardNonbonded->addParticle(1.0, 0.2, 0.2);
params[0] = 1.0;
params[1] = 0.2;
params[2] = 0.2;
customNonbonded->addParticle(params);
standardNonbonded->addParticle(-1.0, 0.1, 0.2);
params[0] = -1.0;
params[1] = 0.1;
customNonbonded->addParticle(params);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
standardNonbonded->addException(2*i, 2*i+1, 0.0, 1.0, 0.0);
customNonbonded->addExclusion(2*i, 2*i+1);
}
standardNonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
customNonbonded->setNonbondedMethod(CustomNonbondedForce::NoCutoff);
standardSystem.addForce(standardNonbonded);
customSystem.addForce(customNonbonded);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context context1(standardSystem, integrator1, platform);
Context context2(customSystem, integrator2, platform);
context1.setPositions(positions);
context2.setPositions(positions);
context1.setVelocities(velocities);
context2.setVelocities(velocities);
State state1 = context1.getState(State::Forces | State::Energy);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
}
void testWater() {
// Create a box of SWM4-NDP water molecules. This involves constraints, virtual sites,
// and Drude particles.
const int gridSize = 3;
const int numMolecules = gridSize*gridSize*gridSize;
const double spacing = 0.6;
const double boxSize = spacing*(gridSize+1);
System system;
NonbondedForce* nonbonded = new NonbondedForce();
DrudeForce* drude = new DrudeForce();
system.addForce(nonbonded);
system.addForce(drude);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
nonbonded->setCutoffDistance(1.0);
for (int i = 0; i < numMolecules; i++) {
int startIndex = system.getNumParticles();
system.addParticle(15.6); // O
system.addParticle(0.4); // D
system.addParticle(1.0); // H1
system.addParticle(1.0); // H2
system.addParticle(0.0); // M
nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
nonbonded->addParticle(-1.71636, 1, 0);
nonbonded->addParticle(0.55733, 1, 0);
nonbonded->addParticle(0.55733, 1, 0);
nonbonded->addParticle(-1.11466, 1, 0);
for (int j = 0; j < 5; j++)
for (int k = 0; k < j; k++)
nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
system.addConstraint(startIndex, startIndex+2, 0.09572);
system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
}
vector<Vec3> positions;
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos(i*spacing, j*spacing, k*spacing);
positions.push_back(pos);
positions.push_back(pos);
positions.push_back(pos+Vec3(0.09572, 0, 0));
positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
positions.push_back(pos);
}
// Simulate it and check energy conservation and the total force on the Drude particles.
DrudeSCFIntegrator integ(0.0005);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
context.setPositions(positions);
context.applyConstraints(1e-5);
context.setVelocitiesToTemperature(300.0);
State state = context.getState(State::Energy);
double initialEnergy;
int numSteps = 1000;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
state = context.getState(State::Energy | State::Forces);
if (i == 0)
initialEnergy = state.getPotentialEnergy()+state.getKineticEnergy();
else
ASSERT_EQUAL_TOL(initialEnergy, state.getPotentialEnergy()+state.getKineticEnergy(), 0.01);
const vector<Vec3>& force = state.getForces();
double norm = 0.0;
for (int j = 1; j < (int) force.size(); j += 5)
norm += sqrt(force[j].dot(force[j]));
norm = (norm/numMolecules);
ASSERT(norm < 1.0);
}
}
void testWater() {
// Create a box of SWM4-NDP water molecules. This involves constraints, virtual sites,
// and Drude particles.
const int gridSize = 3;
const int numMolecules = gridSize*gridSize*gridSize;
const double spacing = 0.6;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
const double temperatureDrude = 10.0;
System system;
NonbondedForce* nonbonded = new NonbondedForce();
DrudeForce* drude = new DrudeForce();
system.addForce(nonbonded);
system.addForce(drude);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
nonbonded->setCutoffDistance(1.0);
for (int i = 0; i < numMolecules; i++) {
int startIndex = system.getNumParticles();
system.addParticle(15.6); // O
system.addParticle(0.4); // D
system.addParticle(1.0); // H1
system.addParticle(1.0); // H2
system.addParticle(0.0); // M
nonbonded->addParticle(1.71636, 0.318395, 0.21094*4.184);
nonbonded->addParticle(-1.71636, 1, 0);
nonbonded->addParticle(0.55733, 1, 0);
nonbonded->addParticle(0.55733, 1, 0);
nonbonded->addParticle(-1.11466, 1, 0);
for (int j = 0; j < 5; j++)
for (int k = 0; k < j; k++)
nonbonded->addException(startIndex+j, startIndex+k, 0, 1, 0);
system.addConstraint(startIndex, startIndex+2, 0.09572);
system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
}
vector<Vec3> positions;
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos(i*spacing, j*spacing, k*spacing);
positions.push_back(pos);
positions.push_back(pos);
positions.push_back(pos+Vec3(0.09572, 0, 0));
positions.push_back(pos+Vec3(-0.023999, 0.092663, 0));
positions.push_back(pos);
}
// Simulate it and check the temperature.
DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.0005);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
context.setPositions(positions);
context.applyConstraints(1e-5);
// Equilibrate.
integ.step(500);
// Compute the internal and center of mass temperatures.
double ke = 0;
int numSteps = 4000;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
ke += context.getState(State::Energy).getKineticEnergy();
}
ke /= numSteps;
int numStandardDof = 3*3*numMolecules-system.getNumConstraints();
int numDrudeDof = 3*numMolecules;
int numDof = numStandardDof+numDrudeDof;
double expectedTemp = (numStandardDof*temperature+numDrudeDof*temperatureDrude)/numDof;
ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.03);
}
void testEwaldPME(bool includeExceptions) {
// Use amorphous NaCl system for the tests
const int numParticles = 894;
const double cutoff = 1.2;
const double boxSize = 3.00646;
double tol = 1e-5;
ReferencePlatform reference;
System system;
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
nonbonded->setCutoffDistance(cutoff);
nonbonded->setEwaldErrorTolerance(tol);
for (int i = 0; i < numParticles/2; i++)
system.addParticle(22.99);
for (int i = 0; i < numParticles/2; i++)
system.addParticle(35.45);
for (int i = 0; i < numParticles/2; i++)
nonbonded->addParticle(1.0, 1.0,0.0);
for (int i = 0; i < numParticles/2; i++)
nonbonded->addParticle(-1.0, 1.0,0.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(nonbonded);
vector<Vec3> positions(numParticles);
#include "nacl_amorph.dat"
if (includeExceptions) {
// Add some exclusions.
for (int i = 0; i < numParticles-1; i++) {
Vec3 delta = positions[i]-positions[i+1];
if (sqrt(delta.dot(delta)) < 0.5*cutoff)
nonbonded->addException(i, i+1, i%2 == 0 ? 0.0 : 0.5, 1.0, 0.0);
}
}
// (1) Check whether the Reference and CPU platforms agree when using Ewald Method
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cpuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cpuContext.setPositions(positions);
referenceContext.setPositions(positions);
State cpuState = cpuContext.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
tol = 1e-2;
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
}
tol = 1e-5;
ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);
// (2) Check whether Ewald method in CPU is self-consistent
double norm = 0.0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f = cpuState.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
const double delta = 5e-3;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = cpuState.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
VerletIntegrator integrator3(0.01);
Context cpuContext2(system, integrator3, platform);
cpuContext2.setPositions(positions);
tol = 1e-2;
State cpuState2 = cpuContext2.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (cpuState2.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)
// (3) Check whether the Reference and CPU platforms agree when using PME
nonbonded->setNonbondedMethod(NonbondedForce::PME);
cpuContext.reinitialize();
referenceContext.reinitialize();
cpuContext.setPositions(positions);
referenceContext.setPositions(positions);
cpuState = cpuContext.getState(State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Forces | State::Energy);
tol = 1e-2;
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
}
tol = 1e-5;
ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);
// (4) Check whether PME method in CPU is self-consistent
norm = 0.0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f = cpuState.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = cpuState.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
VerletIntegrator integrator4(0.01);
Context cpuContext3(system, integrator4, platform);
cpuContext3.setPositions(positions);
tol = 1e-2;
State cpuState3 = cpuContext3.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (cpuState3.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)
}
void testSerialization() {
// Create a Force.
NonbondedForce force;
force.setForceGroup(3);
force.setNonbondedMethod(NonbondedForce::CutoffPeriodic);
force.setSwitchingDistance(1.5);
force.setUseSwitchingFunction(true);
force.setCutoffDistance(2.0);
force.setEwaldErrorTolerance(1e-3);
force.setReactionFieldDielectric(50.0);
force.setUseDispersionCorrection(false);
double alpha = 0.5;
int nx = 3, ny = 5, nz = 7;
force.setPMEParameters(alpha, nx, ny, nz);
double dalpha = 0.8;
int dnx = 4, dny = 6, dnz = 7;
force.setLJPMEParameters(dalpha, dnx, dny, dnz);
force.addParticle(1, 0.1, 0.01);
force.addParticle(0.5, 0.2, 0.02);
force.addParticle(-0.5, 0.3, 0.03);
force.addException(0, 1, 2, 0.5, 0.1);
force.addException(1, 2, 0.2, 0.4, 0.2);
force.addGlobalParameter("scale1", 1.0);
force.addGlobalParameter("scale2", 2.0);
force.addParticleParameterOffset("scale1", 2, 1.5, 2.0, 2.5);
force.addExceptionParameterOffset("scale2", 1, -0.1, -0.2, -0.3);
// Serialize and then deserialize it.
stringstream buffer;
XmlSerializer::serialize<NonbondedForce>(&force, "Force", buffer);
NonbondedForce* copy = XmlSerializer::deserialize<NonbondedForce>(buffer);
// Compare the two forces to see if they are identical.
NonbondedForce& force2 = *copy;
ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
ASSERT_EQUAL(force.getNumGlobalParameters(), force2.getNumGlobalParameters());
ASSERT_EQUAL(force.getNumParticleParameterOffsets(), force2.getNumParticleParameterOffsets());
ASSERT_EQUAL(force.getNumExceptionParameterOffsets(), force2.getNumExceptionParameterOffsets());
double alpha2;
int nx2, ny2, nz2;
force2.getPMEParameters(alpha2, nx2, ny2, nz2);
ASSERT_EQUAL(alpha, alpha2);
ASSERT_EQUAL(nx, nx2);
ASSERT_EQUAL(ny, ny2);
ASSERT_EQUAL(nz, nz2);
double dalpha2;
int dnx2, dny2, dnz2;
force2.getLJPMEParameters(dalpha2, dnx2, dny2, dnz2);
ASSERT_EQUAL(dalpha, dalpha2);
ASSERT_EQUAL(dnx, dnx2);
ASSERT_EQUAL(dny, dny2);
ASSERT_EQUAL(dnz, dnz2);
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
}
for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
int index1, index2;
string param1, param2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getParticleParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
force2.getParticleParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(index1, index1);
ASSERT_EQUAL(param1, param2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
int index1, index2;
string param1, param2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getExceptionParameterOffset(i, param1, index1, charge1, sigma1, epsilon1);
force2.getExceptionParameterOffset(i, param2, index2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(index1, index1);
ASSERT_EQUAL(param1, param2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
for (int i = 0; i < force.getNumParticles(); i++) {
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getParticleParameters(i, charge1, sigma1, epsilon1);
force2.getParticleParameters(i, charge2, sigma2, epsilon2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
for (int i = 0; i < force.getNumExceptions(); i++) {
int a1, a2, b1, b2;
double charge1, sigma1, epsilon1;
double charge2, sigma2, epsilon2;
force.getExceptionParameters(i, a1, b1, charge1, sigma1, epsilon1);
force2.getExceptionParameters(i, a2, b2, charge2, sigma2, epsilon2);
ASSERT_EQUAL(a1, a2);
ASSERT_EQUAL(b1, b2);
ASSERT_EQUAL(charge1, charge2);
ASSERT_EQUAL(sigma1, sigma2);
ASSERT_EQUAL(epsilon1, epsilon2);
}
}
void testChangingParameters() {
const int numMolecules = 600;
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 20.0;
const double tol = 2e-3;
ReferencePlatform reference;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
NonbondedForce* nonbonded = new NonbondedForce();
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
nonbonded->addParticle(-1.0, 0.2, 0.1);
nonbonded->addParticle(1.0, 0.1, 0.1);
}
else {
nonbonded->addParticle(-1.0, 0.2, 0.2);
nonbonded->addParticle(1.0, 0.1, 0.2);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
system.addConstraint(2*i, 2*i+1, 1.0);
nonbonded->addException(2*i, 2*i+1, 0.0, 0.15, 0.0);
}
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
// See if Reference and Cuda give the same forces and energies.
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cuContext.setPositions(positions);
referenceContext.setPositions(positions);
State cuState = cuContext.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(cuState.getForces()[i], referenceState.getForces()[i], tol);
ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
// Now modify parameters and see if they still agree.
for (int i = 0; i < numParticles; i += 5) {
double charge, sigma, epsilon;
nonbonded->getParticleParameters(i, charge, sigma, epsilon);
nonbonded->setParticleParameters(i, 1.5*charge, 1.1*sigma, 1.7*epsilon);
}
nonbonded->updateParametersInContext(cuContext);
nonbonded->updateParametersInContext(referenceContext);
cuState = cuContext.getState(State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(cuState.getForces()[i], referenceState.getForces()[i], tol);
ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}
void testLargeSystem() {
const int numMolecules = 600;
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 20.0;
const double tol = 2e-3;
ReferencePlatform reference;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
NonbondedForce* nonbonded = new NonbondedForce();
HarmonicBondForce* bonds = new HarmonicBondForce();
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
nonbonded->addParticle(-1.0, 0.2, 0.1);
nonbonded->addParticle(1.0, 0.1, 0.1);
}
else {
nonbonded->addParticle(-1.0, 0.2, 0.2);
nonbonded->addParticle(1.0, 0.1, 0.2);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
bonds->addBond(2*i, 2*i+1, 1.0, 0.1);
nonbonded->addException(2*i, 2*i+1, 0.0, 0.15, 0.0);
}
// Try with cutoffs but not periodic boundary conditions, and make sure the cl and Reference
// platforms agree.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
system.addForce(bonds);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cuContext.setPositions(positions);
cuContext.setVelocities(velocities);
referenceContext.setPositions(positions);
referenceContext.setVelocities(velocities);
State cuState = cuContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(cuState.getPositions()[i], referenceState.getPositions()[i], tol);
ASSERT_EQUAL_VEC(cuState.getVelocities()[i], referenceState.getVelocities()[i], tol);
ASSERT_EQUAL_VEC(cuState.getForces()[i], referenceState.getForces()[i], tol);
}
ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
// Now do the same thing with periodic boundary conditions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
cuContext.reinitialize();
referenceContext.reinitialize();
cuContext.setPositions(positions);
cuContext.setVelocities(velocities);
referenceContext.setPositions(positions);
referenceContext.setVelocities(velocities);
cuState = cuContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++) {
double dx = cuState.getPositions()[i][0]-referenceState.getPositions()[i][0];
double dy = cuState.getPositions()[i][1]-referenceState.getPositions()[i][1];
double dz = cuState.getPositions()[i][2]-referenceState.getPositions()[i][2];
ASSERT_EQUAL_TOL(fmod(cuState.getPositions()[i][0]-referenceState.getPositions()[i][0], boxSize), 0, tol);
ASSERT_EQUAL_TOL(fmod(cuState.getPositions()[i][1]-referenceState.getPositions()[i][1], boxSize), 0, tol);
ASSERT_EQUAL_TOL(fmod(cuState.getPositions()[i][2]-referenceState.getPositions()[i][2], boxSize), 0, tol);
ASSERT_EQUAL_VEC(cuState.getVelocities()[i], referenceState.getVelocities()[i], tol);
ASSERT_EQUAL_VEC(cuState.getForces()[i], referenceState.getForces()[i], tol);
}
ASSERT_EQUAL_TOL(cuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}
