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++;
}
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();
}
double ReferenceIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize(), constraints);
}
double CudaIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
return cu.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}