void testHarmonicBonds() {
const int numParticles = 10;
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
// Create a chain of particles connected by harmonic bonds.
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
positions[i] = Vec3(i, 0, 0);
if (i > 0)
bonds->addBond(i-1, i, 1+0.1*i, 1);
}
// Minimize it and check that all bonds are at their equilibrium distances.
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
LocalEnergyMinimizer::minimize(context, 1e-5);
State state = context.getState(State::Positions);
for (int i = 1; i < numParticles; i++) {
Vec3 delta = state.getPositions()[i]-state.getPositions()[i-1];
ASSERT_EQUAL_TOL(1+0.1*i, sqrt(delta.dot(delta)), 1e-4);
}
}
void testSingleBond() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
VariableVerletIntegrator integrator(1e-6);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply a harmonic oscillator, so compare it to the analytical solution.
const double freq = 1.0;;
State state = context.getState(State::Energy);
const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 1000; ++i) {
state = context.getState(State::Positions | State::Velocities | State::Energy);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
double expectedSpeed = -0.5*freq*std::sin(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05);
integrator.step(1);
}
}
void testParallelComputation() {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
HarmonicBondForce* force = new HarmonicBondForce();
for (int i = 1; i < numParticles; i++)
force->addBond(i-1, i, 1.1, i);
system.addForce(force);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(i, 0, 0);
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);
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);
}
void testTemperature() {
const int numParticles = 8;
const int numBonds = numParticles-1;
const double temp = 10.0;
System system;
BrownianIntegrator integrator(temp, 2.0, 0.01);
HarmonicBondForce* forceField = new HarmonicBondForce();
for (int i = 0; i < numParticles; ++i)
system.addParticle(2.0);
for (int i = 0; i < numBonds; ++i)
forceField->addBond(i, i+1, 1.0, 5.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(i, 0, 0);
context.setPositions(positions);
// Let it equilibrate.
integrator.step(10000);
// Now run it for a while and see if the temperature is correct.
double pe = 0.0;
const int steps = 50000;
for (int i = 0; i < steps; ++i) {
State state = context.getState(State::Energy);
pe += state.getPotentialEnergy();
integrator.step(1);
}
pe /= steps;
double expected = 0.5*numBonds*BOLTZ*temp;
ASSERT_USUALLY_EQUAL_TOL(expected, pe, 0.1*expected);
}
void testSingleBond() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
double dt = 0.01;
BrownianIntegrator integrator(0, 0.1, dt);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// This is simply an overdamped harmonic oscillator, so compare it to the analytical solution.
double rate = 2*1.0/(0.1*2.0);
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 ValidateOpenMM::writeHarmonicBondForce( FILE* filePtr, const HarmonicBondForce& harmonicBondForce ) const {
(void) fprintf( filePtr, "HarmonicBondForce %d\n", harmonicBondForce.getNumBonds() );
for(int ii = 0; ii < harmonicBondForce.getNumBonds(); ii++ ){
int particle1, particle2;
double length, k;
harmonicBondForce.getBondParameters( ii, particle1, particle2, length, k );
(void) fprintf( filePtr, "%8d %8d %8d %14.7e %14.7e\n", ii, particle1, particle2, length, k);
}
}
/**
* Test a multiple time step r-RESPA integrator.
*/
void testRespa() {
const int numParticles = 8;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
CustomIntegrator integrator(0.002);
integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
for (int i = 0; i < 2; i++) {
integrator.addComputePerDof("v", "v+0.5*(dt/2)*f0/m");
integrator.addComputePerDof("x", "x+(dt/2)*v");
integrator.addComputePerDof("v", "v+0.5*(dt/2)*f0/m");
}
integrator.addComputePerDof("v", "v+0.5*dt*f1/m");
HarmonicBondForce* bonds = new HarmonicBondForce();
for (int i = 0; i < numParticles-2; i++)
bonds->addBond(i, i+1, 1.0, 0.5);
system.addForce(bonds);
NonbondedForce* nb = new NonbondedForce();
nb->setCutoffDistance(2.0);
nb->setNonbondedMethod(NonbondedForce::Ewald);
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i%2 == 0 ? 5.0 : 10.0);
nb->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
nb->setForceGroup(1);
nb->setReciprocalSpaceForceGroup(0);
system.addForce(nb);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and monitor energy conservations.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Energy);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
if (i == 1)
initialEnergy = energy;
else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05);
integrator.step(2);
}
}
/**
* Test a Monte Carlo integrator that uses global variables and depends on energy.
*/
void testMonteCarlo() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
CustomIntegrator integrator(0.1);
const double kT = BOLTZ*300.0;
integrator.addGlobalVariable("kT", kT);
integrator.addGlobalVariable("oldE", 0);
integrator.addGlobalVariable("accept", 0);
integrator.addPerDofVariable("oldx", 0);
integrator.addComputeGlobal("oldE", "energy");
integrator.addComputePerDof("oldx", "x");
integrator.addComputePerDof("x", "x+dt*gaussian");
integrator.addComputeGlobal("accept", "step(exp((oldE-energy)/kT)-uniform)");
integrator.addComputePerDof("x", "accept*x + (1-accept)*oldx");
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 2.0, 10.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// Compute the histogram of distances and see if it satisfies a Boltzmann distribution.
const int numBins = 100;
const double maxDist = 4.0;
const int numIterations = 5000;
vector<int> counts(numBins, 0);
for (int i = 0; i < numIterations; ++i) {
integrator.step(10);
State state = context.getState(State::Positions);
Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
double dist = sqrt(delta.dot(delta));
if (dist < maxDist)
counts[(int) (numBins*dist/maxDist)]++;
}
vector<double> expected(numBins, 0);
double sum = 0;
for (int i = 0; i < numBins; i++) {
double dist = (i+0.5)*maxDist/numBins;
expected[i] = dist*dist*exp(-5.0*(dist-2)*(dist-2)/kT);
sum += expected[i];
}
for (int i = 0; i < numBins; i++)
ASSERT_USUALLY_EQUAL_TOL((double) counts[i]/numIterations, expected[i]/sum, 0.01);
}
void testMotionRemoval() {
const int numParticles = 8;
const double temp = 100.0;
const double collisionFreq = 10.0;
ReferencePlatform platform;
System system;
VerletIntegrator integrator(0.01);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(2, 3, 2.0, 0.5);
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i+1);
nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(nonbonded);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-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);
}
}
void testWithoutThermostat() {
const int numParticles = 20;
const int numCopies = 10;
const double temperature = 300.0;
const double mass = 2.0;
// Create a chain of particles.
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
for (int i = 0; i < numParticles; i++) {
system.addParticle(mass);
if (i > 0)
bonds->addBond(i-1, i, 1.0, 1000.0);
}
RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
integ.setApplyThermostat(false);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<vector<Vec3> > positions(numCopies);
for (int i = 0; i < numCopies; i++) {
positions[i].resize(numParticles);
for (int j = 0; j < numParticles; j++)
positions[i][j] = Vec3(0.95*j, 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt));
integ.setPositions(i, positions[i]);
}
// Simulate it and see if the energy remains constant.
double initialEnergy;
int numSteps = 100;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
double energy = integ.getTotalEnergy();
if (i == 0)
initialEnergy = energy;
else
ASSERT_EQUAL_TOL(initialEnergy, energy, 1e-4);
}
}
void testBonds() {
ReferencePlatform platform;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 0.8);
forceField->addBond(1, 2, 1.2, 0.7);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
forceField->setBondParameters(0, 0, 1, 1.6, 0.9);
forceField->setBondParameters(1, 1, 2, 1.3, 0.8);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
}
}
/**
* Test a simple leapfrog integrator on a single bond.
*/
void testSingleBond() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
const double dt = 0.01;
CustomIntegrator integrator(dt);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
integrator.setKineticEnergyExpression("m*v1*v1/2; v1=v+0.5*dt*f/m");
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
vector<Vec3> velocities(2);
velocities[0] = Vec3(-0.5*dt*0.5*0.5, 0, 0);
velocities[1] = Vec3(0.5*dt*0.5*0.5, 0, 0);
context.setVelocities(velocities);
// This is simply a harmonic oscillator, so compare it to the analytical solution.
const double freq = 1.0;;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities | State::Energy);
double time = state.getTime();
double expectedDist = 1.5+0.5*std::cos(freq*time);
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 1e-4);
double expectedSpeed = -0.5*freq*std::sin(freq*(time-dt/2));
ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 1e-4);
ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 1e-4);
double energy = state.getKineticEnergy()+state.getPotentialEnergy();
ASSERT_EQUAL_TOL(0.5*0.5*0.5, energy, 1e-4);
integrator.step(1);
}
}
void testBond() {
// Create a system using a CustomCompoundBondForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, "0.5*kb*((distance(p1,p2)-b0)^2+(distance(p2,p3)-b0)^2)+0.5*ka*(angle(p2,p3,p4)-a0)^2+kt*(1+cos(dihedral(p1,p2,p3,p4)-t0))");
custom->addPerBondParameter("kb");
custom->addPerBondParameter("ka");
custom->addPerBondParameter("kt");
custom->addPerBondParameter("b0");
custom->addPerBondParameter("a0");
custom->addPerBondParameter("t0");
vector<int> particles(4);
particles[0] = 0;
particles[1] = 1;
particles[2] = 3;
particles[3] = 2;
vector<double> parameters(6);
parameters[0] = 1.5;
parameters[1] = 0.8;
parameters[2] = 0.6;
parameters[3] = 1.1;
parameters[4] = 2.9;
parameters[5] = 1.3;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
// Create an identical system using standard forces.
System standardSystem;
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.1, 1.5);
bonds->addBond(1, 3, 1.1, 1.5);
standardSystem.addForce(bonds);
HarmonicAngleForce* angles = new HarmonicAngleForce();
angles->addAngle(1, 3, 2, 2.9, 0.8);
standardSystem.addForce(angles);
PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
standardSystem.addForce(torsions);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
vector<Vec3> positions(4);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[3] = 1.3;
custom->setBondParameters(0, particles, parameters);
custom->updateParametersInContext(c1);
bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
bonds->updateParametersInContext(c2);
{
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = s1.getForces();
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
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 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);
}
void testHbond() {
// Create a system using a CustomHbondForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomHbondForce* custom = new CustomHbondForce("0.5*kr*(distance(d1,a1)-r0)^2 + 0.5*ktheta*(angle(a1,d1,d2)-theta0)^2 + 0.5*kpsi*(angle(d1,a1,a2)-psi0)^2 + kchi*(1+cos(n*dihedral(a3,a2,a1,d1)-chi0))");
custom->addPerDonorParameter("r0");
custom->addPerDonorParameter("theta0");
custom->addPerDonorParameter("psi0");
custom->addPerAcceptorParameter("chi0");
custom->addPerAcceptorParameter("n");
custom->addGlobalParameter("kr", 0.4);
custom->addGlobalParameter("ktheta", 0.5);
custom->addGlobalParameter("kpsi", 0.6);
custom->addGlobalParameter("kchi", 0.7);
vector<double> parameters(3);
parameters[0] = 1.5;
parameters[1] = 1.7;
parameters[2] = 1.9;
custom->addDonor(1, 0, -1, parameters);
parameters.resize(2);
parameters[0] = 2.1;
parameters[1] = 2;
custom->addAcceptor(2, 3, 4, parameters);
custom->setCutoffDistance(10.0);
customSystem.addForce(custom);
// Create an identical system using HarmonicBondForce, HarmonicAngleForce, and PeriodicTorsionForce.
System standardSystem;
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
HarmonicBondForce* bond = new HarmonicBondForce();
bond->addBond(1, 2, 1.5, 0.4);
standardSystem.addForce(bond);
HarmonicAngleForce* angle = new HarmonicAngleForce();
angle->addAngle(0, 1, 2, 1.7, 0.5);
angle->addAngle(1, 2, 3, 1.9, 0.6);
standardSystem.addForce(angle);
PeriodicTorsionForce* torsion = new PeriodicTorsionForce();
torsion->addTorsion(1, 2, 3, 4, 2, 2.1, 0.7);
standardSystem.addForce(torsion);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt));
c1.setPositions(positions);
c2.setPositions(positions);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters.resize(3);
parameters[0] = 1.4;
parameters[1] = 1.7;
parameters[2] = 1.9;
custom->setDonorParameters(0, 1, 0, -1, parameters);
parameters.resize(2);
parameters[0] = 2.2;
parameters[1] = 2;
custom->setAcceptorParameters(0, 2, 3, 4, parameters);
bond->setBondParameters(0, 1, 2, 1.4, 0.4);
torsion->setTorsionParameters(0, 1, 2, 3, 4, 2, 2.2, 0.7);
custom->updateParametersInContext(c1);
bond->updateParametersInContext(c2);
torsion->updateParametersInContext(c2);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
/**
* Test evaluating force groups separately.
*/
void testForceGroups() {
System system;
system.addParticle(2.0);
system.addParticle(2.0);
CustomIntegrator integrator(0.01);
integrator.addPerDofVariable("outf", 0);
integrator.addPerDofVariable("outf1", 0);
integrator.addPerDofVariable("outf2", 0);
integrator.addGlobalVariable("oute", 0);
integrator.addGlobalVariable("oute1", 0);
integrator.addGlobalVariable("oute2", 0);
integrator.addComputePerDof("outf", "f");
integrator.addComputePerDof("outf1", "f1");
integrator.addComputePerDof("outf2", "f2");
integrator.addComputeGlobal("oute", "energy");
integrator.addComputeGlobal("oute1", "energy1");
integrator.addComputeGlobal("oute2", "energy2");
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.5, 1.1);
bonds->setForceGroup(1);
system.addForce(bonds);
NonbondedForce* nb = new NonbondedForce();
nb->addParticle(0.2, 1, 0);
nb->addParticle(0.2, 1, 0);
nb->setForceGroup(2);
system.addForce(nb);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
// See if the various forces are computed correctly.
integrator.step(1);
vector<Vec3> f, f1, f2;
double e1 = 0.5*1.1*0.5*0.5;
double e2 = 138.935456*0.2*0.2/2.0;
integrator.getPerDofVariable(0, f);
integrator.getPerDofVariable(1, f1);
integrator.getPerDofVariable(2, f2);
ASSERT_EQUAL_VEC(Vec3(1.1*0.5, 0, 0), f1[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-1.1*0.5, 0, 0), f1[1], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-138.935456*0.2*0.2/4.0, 0, 0), f2[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(138.935456*0.2*0.2/4.0, 0, 0), f2[1], 1e-5);
ASSERT_EQUAL_VEC(f1[0]+f2[0], f[0], 1e-5);
ASSERT_EQUAL_VEC(f1[1]+f2[1], f[1], 1e-5);
ASSERT_EQUAL_TOL(e1, integrator.getGlobalVariable(1), 1e-5);
ASSERT_EQUAL_TOL(e2, integrator.getGlobalVariable(2), 1e-5);
ASSERT_EQUAL_TOL(e1+e2, integrator.getGlobalVariable(0), 1e-5);
// Make sure they also match the values returned by the Context.
State s = context.getState(State::Forces | State::Energy, false);
State s1 = context.getState(State::Forces | State::Energy, false, 2);
State s2 = context.getState(State::Forces | State::Energy, false, 4);
vector<Vec3> c, c1, c2;
c = context.getState(State::Forces, false).getForces();
c1 = context.getState(State::Forces, false, 2).getForces();
c2 = context.getState(State::Forces, false, 4).getForces();
ASSERT_EQUAL_VEC(f[0], c[0], 1e-5);
ASSERT_EQUAL_VEC(f[1], c[1], 1e-5);
ASSERT_EQUAL_VEC(f1[0], c1[0], 1e-5);
ASSERT_EQUAL_VEC(f1[1], c1[1], 1e-5);
ASSERT_EQUAL_VEC(f2[0], c2[0], 1e-5);
ASSERT_EQUAL_VEC(f2[1], c2[1], 1e-5);
ASSERT_EQUAL_TOL(s.getPotentialEnergy(), integrator.getGlobalVariable(0), 1e-5);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), integrator.getGlobalVariable(1), 1e-5);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), integrator.getGlobalVariable(2), 1e-5);
}
void testWithoutThermostat() {
const int numParticles = 20;
const int numCopies = 10;
const double temperature = 300.0;
const double mass = 2.0;
// Create a chain of particles.
System system;
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
for (int i = 0; i < numParticles; i++) {
system.addParticle(mass);
if (i > 0)
bonds->addBond(i-1, i, 1.0, 1000.0);
}
RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
integ.setApplyThermostat(false);
Platform& platform = Platform::getPlatformByName("CUDA");
Context context(system, integ, platform);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<vector<Vec3> > positions(numCopies);
for (int i = 0; i < numCopies; i++) {
positions[i].resize(numParticles);
for (int j = 0; j < numParticles; j++)
positions[i][j] = Vec3(0.95*j, 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt));
integ.setPositions(i, positions[i]);
}
// Simulate it and see if the energy remains constant.
double initialEnergy;
int numSteps = 100;
const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const double wn = numCopies*BOLTZ*temperature/hbar;
const double springConstant = mass*wn*wn;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
// Sum the energies of all the copies.
double energy = 0.0;
for (int j = 0; j < numCopies; j++) {
State state = integ.getState(j, State::Positions | State::Energy);
positions[j] = state.getPositions();
energy += state.getPotentialEnergy()+state.getKineticEnergy();
}
// Add the energy from the springs connecting copies.
for (int j = 0; j < numCopies; j++) {
int previous = (j == 0 ? numCopies-1 : j-1);
for (int k = 0; k < numParticles; k++) {
Vec3 delta = positions[j][k]-positions[previous][k];
energy += 0.5*springConstant*delta.dot(delta);
}
}
if (i == 0)
initialEnergy = energy;
else
ASSERT_EQUAL_TOL(initialEnergy, energy, 1e-4);
}
}
void testEnergyEthane(int applyBornRadiiScaling) {
ReferencePlatform platform;
const int numParticles = 8;
System system;
LangevinIntegrator integrator(0, 0.1, 0.01);
// harmonic bond
double C_HBondDistance = 0.1097;
double C_CBondDistance = 0.1504;
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, C_HBondDistance, 0.0);
bonds->addBond(2, 1, C_HBondDistance, 0.0);
bonds->addBond(3, 1, C_HBondDistance, 0.0);
bonds->addBond(1, 4, C_CBondDistance, 0.0);
bonds->addBond(5, 4, C_HBondDistance, 0.0);
bonds->addBond(6, 4, C_HBondDistance, 0.0);
bonds->addBond(7, 4, C_HBondDistance, 0.0);
system.addForce(bonds);
double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
int AM1_BCC = 1;
H_charge = -0.053;
C_charge = -3.0*H_charge;
if (AM1_BCC) {
C_radius = 0.180;
C_gamma = -0.2863;
H_radius = 0.125;
H_gamma = 0.2437;
}
else {
C_radius = 0.215;
C_gamma = -1.1087;
H_radius = 0.150;
H_gamma = 0.1237;
}
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
GBVIForce* forceField = new GBVIForce();
if (applyBornRadiiScaling) {
forceField->setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
}
else {
forceField->setBornRadiusScalingMethod(GBVIForce::NoScaling);
}
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
forceField->addParticle(H_charge, H_radius, H_gamma);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
forceField->addBond(0, 1, C_HBondDistance);
forceField->addBond(2, 1, C_HBondDistance);
forceField->addBond(3, 1, C_HBondDistance);
forceField->addBond(1, 4, C_CBondDistance);
forceField->addBond(5, 4, C_HBondDistance);
forceField->addBond(6, 4, C_HBondDistance);
forceField->addBond(7, 4, C_HBondDistance);
std::vector<pair<int, int> > bondExceptions;
std::vector<double> bondDistances;
bondExceptions.push_back(pair<int, int>(0, 1));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(2, 1));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(3, 1));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(1, 4));
bondDistances.push_back(C_CBondDistance);
bondExceptions.push_back(pair<int, int>(5, 4));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(6, 4));
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(7, 4));
bondDistances.push_back(C_HBondDistance);
nonbonded->createExceptionsFromBonds(bondExceptions, 0.0, 0.0);
system.addForce(forceField);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0.5480, 1.7661, 0.0000);
positions[1] = Vec3(0.7286, 0.8978, 0.6468);
positions[2] = Vec3(0.4974, 0.0000, 0.0588);
positions[3] = Vec3(0.0000, 0.9459, 1.4666);
positions[4] = Vec3(2.1421, 0.8746, 1.1615);
positions[5] = Vec3(2.3239, 0.0050, 1.8065);
positions[6] = Vec3(2.8705, 0.8295, 0.3416);
positions[7] = Vec3(2.3722, 1.7711, 1.7518);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// Take a small step in the direction of the energy gradient.
double norm = 0.0;
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
forceSum[1] += f[1];
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
const double delta = 1e-4;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = state.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
context.setPositions(positions);
State state2 = context.getState(State::Energy);
// See whether the potential energy changed by the expected amount.
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/delta, 0.01)
}
