void testAnisotropicParticle() {
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double a1 = 0.8;
const double a2 = 1.1;
const double k1 = k/a1;
const double k2 = k/a2;
const double k3 = k/(3-a1-a2);
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
DrudeForce* drude = new DrudeForce();
drude->addParticle(1, 0, 2, 3, 4, charge, alpha, a1, a2);
system.addForce(drude);
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0.1, -0.5, 0.8);
positions[2] = Vec3(0, 2, 0);
positions[3] = Vec3(1, 2, 0);
positions[4] = Vec3(1, 2, 3);
validateForce(system, positions, 0.5*k1*0.5*0.5 + 0.5*k2*0.8*0.8 + 0.5*k3*0.1*0.1);
}
void testThole() {
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double thole = 2.5;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
DrudeForce* drude = new DrudeForce();
drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
drude->addParticle(3, 2, -1, -1, -1, charge, alpha, 1, 1);
drude->addScreenedPair(0, 1, thole);
system.addForce(drude);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, -0.5, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 0.3);
double energySpring1 = 0.5*k*0.5*0.5;
double energySpring2 = 0.5*k*0.3*0.3;
double energyDipole = 0.0;
double q[] = {-charge, charge, -charge, charge};
for (int i = 0; i < 2; i++)
for (int j = 2; j < 4; j++) {
Vec3 delta = positions[i]-positions[j];
double r = sqrt(delta.dot(delta));
energyDipole += ONE_4PI_EPS0*q[i]*q[j]*computeScreening(r, thole, alpha, alpha)/r;
}
validateForce(system, positions, energySpring1+energySpring2+energyDipole);
}
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 testSinglePair() {
const double temperature = 300.0;
const double temperatureDrude = 10.0;
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double mass1 = 1.0;
const double mass2 = 0.1;
const double totalMass = mass1+mass2;
const double reducedMass = (mass1*mass2)/(mass1+mass2);
const double maxDistance = 0.05;
System system;
system.addParticle(mass1);
system.addParticle(mass2);
DrudeForce* drude = new DrudeForce();
drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
system.addForce(drude);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 0, 0);
DrudeLangevinIntegrator integ(temperature, 20.0, temperatureDrude, 20.0, 0.003);
integ.setMaxDrudeDistance(maxDistance);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
context.setPositions(positions);
// Equilibrate.
integ.step(1000);
// Compute the internal and center of mass temperatures.
double keCM = 0, keInternal = 0;
int numSteps = 10000;
for (int i = 0; i < numSteps; i++) {
integ.step(10);
State state = context.getState(State::Velocities | State::Positions);
const vector<Vec3>& vel = state.getVelocities();
Vec3 velCM = vel[0]*(mass1/totalMass) + vel[1]*(mass2/totalMass);
keCM += 0.5*totalMass*velCM.dot(velCM);
Vec3 velInternal = vel[0]-vel[1];
keInternal += 0.5*reducedMass*velInternal.dot(velInternal);
Vec3 delta = state.getPositions()[0]-state.getPositions()[1];
double distance = sqrt(delta.dot(delta));
ASSERT(distance <= maxDistance*(1+1e-6));
}
ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperature, keCM/numSteps, 0.1);
ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
}
void testSingleParticle() {
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
DrudeForce* drude = new DrudeForce();
drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
system.addForce(drude);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(2, 0, 0);
validateForce(system, positions, 0.5*k*3*3);
}
void testChangingParameters() {
const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1;
const double alpha = ONE_4PI_EPS0*charge*charge/k;
Platform& platform = Platform::getPlatformByName("OpenCL");
// Create the system.
System system;
system.addParticle(1.0);
system.addParticle(1.0);
DrudeForce* drude = new DrudeForce();
drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
system.addForce(drude);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(2, 0, 0);
// Check the energy.
VerletIntegrator integ(1.0);
Context context(system, integ, platform);
context.setPositions(positions);
State state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(0.5*k*3*3, state.getPotentialEnergy(), 1e-5);
// Modify the parameters.
const double k2 = ONE_4PI_EPS0*2.2;
const double charge2 = 0.3;
const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
drude->updateParametersInContext(context);
state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(0.5*k2*3*3, state.getPotentialEnergy(), 1e-5);
}
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);
}
