void CudaIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
cu.setAsCurrent();
CudaIntegrationUtilities& integration = cu.getIntegrationUtilities();
int numAtoms = cu.getNumAtoms();
int paddedNumAtoms = cu.getPaddedNumAtoms();
double dt = integrator.getStepSize();
if (dt != prevStepSize) {
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
vector<double2> stepSizeVec(1);
stepSizeVec[0] = make_double2(dt, dt);
cu.getIntegrationUtilities().getStepSize().upload(stepSizeVec);
}
else {
vector<float2> stepSizeVec(1);
stepSizeVec[0] = make_float2((float) dt, (float) dt);
cu.getIntegrationUtilities().getStepSize().upload(stepSizeVec);
}
prevStepSize = dt;
}
// Call the first integration kernel.
CUdeviceptr posCorrection = (cu.getUseMixedPrecision() ? cu.getPosqCorrection().getDevicePointer() : 0);
void* args1[] = {&numAtoms, &paddedNumAtoms, &cu.getIntegrationUtilities().getStepSize().getDevicePointer(), &cu.getPosq().getDevicePointer(), &posCorrection,
&cu.getVelm().getDevicePointer(), &cu.getForce().getDevicePointer(), &integration.getPosDelta().getDevicePointer()};
cu.executeKernel(kernel1, args1, numAtoms);
// Apply constraints.
integration.applyConstraints(integrator.getConstraintTolerance());
// Call the second integration kernel.
void* args2[] = {&numAtoms, &cu.getIntegrationUtilities().getStepSize().getDevicePointer(), &cu.getPosq().getDevicePointer(), &posCorrection,
&cu.getVelm().getDevicePointer(), &integration.getPosDelta().getDevicePointer()};
cu.executeKernel(kernel2, args2, numAtoms);
// Update the positions of virtual sites and Drude particles.
integration.computeVirtualSites();
minimize(context, integrator.getMinimizationErrorTolerance());
// Update the time and step count.
cu.setTime(cu.getTime()+dt);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
}
void ReferenceIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& force = extractForces(context);
// Update the positions and velocities.
int numParticles = particleInvMass.size();
vector<RealVec> xPrime(numParticles);
RealOpenMM dt = integrator.getStepSize();
for (int i = 0; i < numParticles; i++) {
if (particleInvMass[i] != 0.0) {
vel[i] += force[i]*particleInvMass[i]*dt;
xPrime[i] = pos[i]+vel[i]*dt;
}
}
// Apply constraints.
if (constraints != NULL)
constraints->apply(numParticles, pos, xPrime, particleInvMass);
// Record the constrained positions and velocities.
RealOpenMM dtInv = 1.0/dt;
for (int i = 0; i < numParticles; i++) {
if (particleInvMass[i] != 0.0) {
vel[i] = (xPrime[i]-pos[i])*dtInv;
pos[i] = xPrime[i];
}
}
// Update the positions of virtual sites and Drude particles.
ReferenceVirtualSites::computePositions(context.getSystem(), pos);
minimize(context, integrator.getMinimizationErrorTolerance());
data.time += integrator.getStepSize();
data.stepCount++;
}
double ReferenceIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize(), constraints);
}
void ReferenceIntegrateDrudeSCFStepKernel::initialize(const System& system, const DrudeSCFIntegrator& integrator, const DrudeForce& force) {
// Identify Drude particles.
for (int i = 0; i < force.getNumParticles(); i++) {
int p, p1, p2, p3, p4;
double charge, polarizability, aniso12, aniso34;
force.getParticleParameters(i, p, p1, p2, p3, p4, charge, polarizability, aniso12, aniso34);
drudeParticles.push_back(p);
}
// Record particle masses.
vector<RealOpenMM> particleMass;
for (int i = 0; i < system.getNumParticles(); i++) {
double mass = system.getParticleMass(i);
particleMass.push_back(mass);
particleInvMass.push_back(mass == 0.0 ? 0.0 : 1.0/mass);
}
// Prepare constraints.
int numConstraints = system.getNumConstraints();
if (numConstraints > 0) {
vector<pair<int, int> > constraintIndices(numConstraints);
vector<RealOpenMM> constraintDistances(numConstraints);
for (int i = 0; i < numConstraints; ++i) {
int particle1, particle2;
double distance;
system.getConstraintParameters(i, particle1, particle2, distance);
constraintIndices[i].first = particle1;
constraintIndices[i].second = particle2;
constraintDistances[i] = static_cast<RealOpenMM>(distance);
}
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(system, angles);
constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, particleMass, angles, (RealOpenMM)integrator.getConstraintTolerance());
}
// Initialize the energy minimizer.
minimizerPos = lbfgs_malloc(drudeParticles.size()*3);
if (minimizerPos == NULL)
throw OpenMMException("DrudeSCFIntegrator: Failed to allocate memory");
lbfgs_parameter_init(&minimizerParams);
minimizerParams.linesearch = LBFGS_LINESEARCH_BACKTRACKING_STRONG_WOLFE;
if (sizeof(RealOpenMM) < 8)
minimizerParams.xtol = 1e-7;
}
double CudaIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
return cu.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}