void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system, const DrudeLangevinIntegrator& integrator, const DrudeForce& force) {
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
// Identify particle pairs and ordinary particles.
set<int> particles;
for (int i = 0; i < system.getNumParticles(); i++) {
particles.insert(i);
double mass = system.getParticleMass(i);
particleMass.push_back(mass);
particleInvMass.push_back(mass == 0.0 ? 0.0 : 1.0/mass);
}
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);
particles.erase(p);
particles.erase(p1);
pairParticles.push_back(make_pair(p, p1));
double m1 = system.getParticleMass(p);
double m2 = system.getParticleMass(p1);
pairInvTotalMass.push_back(1.0/(m1+m2));
pairInvReducedMass.push_back((m1+m2)/(m1*m2));
}
normalParticles.insert(normalParticles.begin(), particles.begin(), particles.end());
}
void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system, const DrudeLangevinIntegrator& integrator, const DrudeForce& force) {
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
// Identify particle pairs and ordinary particles.
set<int> particles;
vector<RealOpenMM> particleMass;
for (int i = 0; i < system.getNumParticles(); i++) {
particles.insert(i);
double mass = system.getParticleMass(i);
particleMass.push_back(mass);
particleInvMass.push_back(mass == 0.0 ? 0.0 : 1.0/mass);
}
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);
particles.erase(p);
particles.erase(p1);
pairParticles.push_back(make_pair(p, p1));
double m1 = system.getParticleMass(p);
double m2 = system.getParticleMass(p1);
pairInvTotalMass.push_back(1.0/(m1+m2));
pairInvReducedMass.push_back((m1+m2)/(m1*m2));
}
normalParticles.insert(normalParticles.begin(), particles.begin(), particles.end());
// 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());
}
}
void CudaIntegrateDrudeLangevinStepKernel::initialize(const System& system, const DrudeLangevinIntegrator& integrator, const DrudeForce& force) {
cu.getPlatformData().initializeContexts(system);
cu.getIntegrationUtilities().initRandomNumberGenerator((unsigned int) integrator.getRandomNumberSeed());
// Identify particle pairs and ordinary particles.
set<int> particles;
vector<int> normalParticleVec;
vector<int2> pairParticleVec;
for (int i = 0; i < system.getNumParticles(); i++)
particles.insert(i);
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);
particles.erase(p);
particles.erase(p1);
pairParticleVec.push_back(make_int2(p, p1));
}
normalParticleVec.insert(normalParticleVec.begin(), particles.begin(), particles.end());
normalParticles = CudaArray::create<int>(cu, max((int) normalParticleVec.size(), 1), "drudeNormalParticles");
pairParticles = CudaArray::create<int2>(cu, max((int) pairParticleVec.size(), 1), "drudePairParticles");
if (normalParticleVec.size() > 0)
normalParticles->upload(normalParticleVec);
if (pairParticleVec.size() > 0)
pairParticles->upload(pairParticleVec);
// Create kernels.
map<string, string> defines;
defines["NUM_ATOMS"] = cu.intToString(cu.getNumAtoms());
defines["PADDED_NUM_ATOMS"] = cu.intToString(cu.getPaddedNumAtoms());
defines["NUM_NORMAL_PARTICLES"] = cu.intToString(normalParticleVec.size());
defines["NUM_PAIRS"] = cu.intToString(pairParticleVec.size());
map<string, string> replacements;
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaDrudeKernelSources::drudeLangevin, defines, "");
kernel1 = cu.getKernel(module, "integrateDrudeLangevinPart1");
kernel2 = cu.getKernel(module, "integrateDrudeLangevinPart2");
hardwallKernel = cu.getKernel(module, "applyHardWallConstraints");
prevStepSize = -1.0;
}
double ReferenceIntegrateDrudeLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize(), constraints);
}
void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& force = extractForces(context);
// Update velocities of ordinary particles.
const RealOpenMM vscale = exp(-integrator.getStepSize()*integrator.getFriction());
const RealOpenMM fscale = (1-vscale)/integrator.getFriction();
const RealOpenMM kT = BOLTZ*integrator.getTemperature();
const RealOpenMM noisescale = sqrt(2*kT*integrator.getFriction())*sqrt(0.5*(1-vscale*vscale)/integrator.getFriction());
for (int i = 0; i < (int) normalParticles.size(); i++) {
int index = normalParticles[i];
RealOpenMM invMass = particleInvMass[index];
if (invMass != 0.0) {
RealOpenMM sqrtInvMass = sqrt(invMass);
for (int j = 0; j < 3; j++)
vel[index][j] = vscale*vel[index][j] + fscale*invMass*force[index][j] + noisescale*sqrtInvMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
// Update velocities of Drude particle pairs.
const RealOpenMM vscaleDrude = exp(-integrator.getStepSize()*integrator.getDrudeFriction());
const RealOpenMM fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction();
const RealOpenMM kTDrude = BOLTZ*integrator.getDrudeTemperature();
const RealOpenMM noisescaleDrude = sqrt(2*kTDrude*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
for (int i = 0; i < (int) pairParticles.size(); i++) {
int p1 = pairParticles[i].first;
int p2 = pairParticles[i].second;
RealOpenMM mass1fract = pairInvTotalMass[i]/particleInvMass[p1];
RealOpenMM mass2fract = pairInvTotalMass[i]/particleInvMass[p2];
RealOpenMM sqrtInvTotalMass = sqrt(pairInvTotalMass[i]);
RealOpenMM sqrtInvReducedMass = sqrt(pairInvReducedMass[i]);
RealVec cmVel = vel[p1]*mass1fract+vel[p2]*mass2fract;
RealVec relVel = vel[p2]-vel[p1];
RealVec cmForce = force[p1]+force[p2];
RealVec relForce = force[p2]*mass1fract - force[p1]*mass2fract;
for (int j = 0; j < 3; j++) {
cmVel[j] = vscale*cmVel[j] + fscale*pairInvTotalMass[i]*cmForce[j] + noisescale*sqrtInvTotalMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
relVel[j] = vscaleDrude*relVel[j] + fscaleDrude*pairInvReducedMass[i]*relForce[j] + noisescaleDrude*sqrtInvReducedMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
vel[p1] = cmVel-relVel*mass2fract;
vel[p2] = cmVel+relVel*mass1fract;
}
// Update the particle positions.
int numParticles = particleInvMass.size();
vector<RealVec> xPrime(numParticles);
RealOpenMM dt = integrator.getStepSize();
for (int i = 0; i < numParticles; i++)
if (particleInvMass[i] != 0.0)
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];
}
}
ReferenceVirtualSites::computePositions(context.getSystem(), pos);
data.time += integrator.getStepSize();
data.stepCount++;
}
void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& force = extractForces(context);
// Update velocities of ordinary particles.
const RealOpenMM vscale = exp(-integrator.getStepSize()*integrator.getFriction());
const RealOpenMM fscale = (1-vscale)/integrator.getFriction();
const RealOpenMM kT = BOLTZ*integrator.getTemperature();
const RealOpenMM noisescale = sqrt(2*kT*integrator.getFriction())*sqrt(0.5*(1-vscale*vscale)/integrator.getFriction());
for (int i = 0; i < (int) normalParticles.size(); i++) {
int index = normalParticles[i];
RealOpenMM invMass = particleInvMass[index];
if (invMass != 0.0) {
RealOpenMM sqrtInvMass = sqrt(invMass);
for (int j = 0; j < 3; j++)
vel[index][j] = vscale*vel[index][j] + fscale*invMass*force[index][j] + noisescale*sqrtInvMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
// Update velocities of Drude particle pairs.
const RealOpenMM vscaleDrude = exp(-integrator.getStepSize()*integrator.getDrudeFriction());
const RealOpenMM fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction();
const RealOpenMM kTDrude = BOLTZ*integrator.getDrudeTemperature();
const RealOpenMM noisescaleDrude = sqrt(2*kTDrude*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
for (int i = 0; i < (int) pairParticles.size(); i++) {
int p1 = pairParticles[i].first;
int p2 = pairParticles[i].second;
RealOpenMM mass1fract = pairInvTotalMass[i]/particleInvMass[p1];
RealOpenMM mass2fract = pairInvTotalMass[i]/particleInvMass[p2];
RealOpenMM sqrtInvTotalMass = sqrt(pairInvTotalMass[i]);
RealOpenMM sqrtInvReducedMass = sqrt(pairInvReducedMass[i]);
RealVec cmVel = vel[p1]*mass1fract+vel[p2]*mass2fract;
RealVec relVel = vel[p2]-vel[p1];
RealVec cmForce = force[p1]+force[p2];
RealVec relForce = force[p2]*mass1fract - force[p1]*mass2fract;
for (int j = 0; j < 3; j++) {
cmVel[j] = vscale*cmVel[j] + fscale*pairInvTotalMass[i]*cmForce[j] + noisescale*sqrtInvTotalMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
relVel[j] = vscaleDrude*relVel[j] + fscaleDrude*pairInvReducedMass[i]*relForce[j] + noisescaleDrude*sqrtInvReducedMass*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
vel[p1] = cmVel-relVel*mass2fract;
vel[p2] = cmVel+relVel*mass1fract;
}
// Update the particle positions.
int numParticles = particleInvMass.size();
vector<RealVec> xPrime(numParticles);
RealOpenMM dt = integrator.getStepSize();
for (int i = 0; i < numParticles; i++)
if (particleInvMass[i] != 0.0)
xPrime[i] = pos[i]+vel[i]*dt;
// Apply constraints.
extractConstraints(context).apply(pos, xPrime, particleInvMass, integrator.getConstraintTolerance());
// 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];
}
}
// Apply hard wall constraints.
const RealOpenMM maxDrudeDistance = integrator.getMaxDrudeDistance();
if (maxDrudeDistance > 0) {
const RealOpenMM hardwallscaleDrude = sqrt(kTDrude);
for (int i = 0; i < (int) pairParticles.size(); i++) {
int p1 = pairParticles[i].first;
int p2 = pairParticles[i].second;
RealVec delta = pos[p1]-pos[p2];
RealOpenMM r = sqrt(delta.dot(delta));
RealOpenMM rInv = 1/r;
if (rInv*maxDrudeDistance < 1.0) {
// The constraint has been violated, so make the inter-particle distance "bounce"
// off the hard wall.
if (rInv*maxDrudeDistance < 0.5)
throw OpenMMException("Drude particle moved too far beyond hard wall constraint");
RealVec bondDir = delta*rInv;
RealVec vel1 = vel[p1];
RealVec vel2 = vel[p2];
RealOpenMM mass1 = particleMass[p1];
RealOpenMM mass2 = particleMass[p2];
RealOpenMM deltaR = r-maxDrudeDistance;
RealOpenMM deltaT = dt;
RealOpenMM dotvr1 = vel1.dot(bondDir);
RealVec vb1 = bondDir*dotvr1;
RealVec vp1 = vel1-vb1;
if (mass2 == 0) {
// The parent particle is massless, so move only the Drude particle.
if (dotvr1 != 0.0)
deltaT = deltaR/abs(dotvr1);
if (deltaT > dt)
deltaT = dt;
dotvr1 = -dotvr1*hardwallscaleDrude/(abs(dotvr1)*sqrt(mass1));
RealOpenMM dr = -deltaR + deltaT*dotvr1;
pos[p1] += bondDir*dr;
vel[p1] = vp1 + bondDir*dotvr1;
}
else {
// Move both particles.
RealOpenMM invTotalMass = pairInvTotalMass[i];
RealOpenMM dotvr2 = vel2.dot(bondDir);
RealVec vb2 = bondDir*dotvr2;
RealVec vp2 = vel2-vb2;
RealOpenMM vbCMass = (mass1*dotvr1 + mass2*dotvr2)*invTotalMass;
dotvr1 -= vbCMass;
dotvr2 -= vbCMass;
if (dotvr1 != dotvr2)
deltaT = deltaR/abs(dotvr1-dotvr2);
if (deltaT > dt)
deltaT = dt;
RealOpenMM vBond = hardwallscaleDrude/sqrt(mass1);
dotvr1 = -dotvr1*vBond*mass2*invTotalMass/abs(dotvr1);
dotvr2 = -dotvr2*vBond*mass1*invTotalMass/abs(dotvr2);
RealOpenMM dr1 = -deltaR*mass2*invTotalMass + deltaT*dotvr1;
RealOpenMM dr2 = deltaR*mass1*invTotalMass + deltaT*dotvr2;
dotvr1 += vbCMass;
dotvr2 += vbCMass;
pos[p1] += bondDir*dr1;
pos[p2] += bondDir*dr2;
vel[p1] = vp1 + bondDir*dotvr1;
vel[p2] = vp2 + bondDir*dotvr2;
}
}
}
}
ReferenceVirtualSites::computePositions(context.getSystem(), pos);
data.time += integrator.getStepSize();
data.stepCount++;
}
double CudaIntegrateDrudeLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
return cu.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
}
void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
cu.setAsCurrent();
CudaIntegrationUtilities& integration = cu.getIntegrationUtilities();
int numAtoms = cu.getNumAtoms();
// Compute integrator coefficients.
double stepSize = integrator.getStepSize();
double vscale = exp(-stepSize*integrator.getFriction());
double fscale = (1-vscale)/integrator.getFriction()/(double) 0x100000000;
double noisescale = sqrt(2*BOLTZ*integrator.getTemperature()*integrator.getFriction())*sqrt(0.5*(1-vscale*vscale)/integrator.getFriction());
double vscaleDrude = exp(-stepSize*integrator.getDrudeFriction());
double fscaleDrude = (1-vscaleDrude)/integrator.getDrudeFriction()/(double) 0x100000000;
double noisescaleDrude = sqrt(2*BOLTZ*integrator.getDrudeTemperature()*integrator.getDrudeFriction())*sqrt(0.5*(1-vscaleDrude*vscaleDrude)/integrator.getDrudeFriction());
double maxDrudeDistance = integrator.getMaxDrudeDistance();
double hardwallscaleDrude = sqrt(BOLTZ*integrator.getDrudeTemperature());
if (stepSize != prevStepSize) {
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
double2 ss = make_double2(0, stepSize);
integration.getStepSize().upload(&ss);
}
else {
float2 ss = make_float2(0, (float) stepSize);
integration.getStepSize().upload(&ss);
}
prevStepSize = stepSize;
}
// Create appropriate pointer for the precision mode.
float vscaleFloat = (float) vscale;
float fscaleFloat = (float) fscale;
float noisescaleFloat = (float) noisescale;
float vscaleDrudeFloat = (float) vscaleDrude;
float fscaleDrudeFloat = (float) fscaleDrude;
float noisescaleDrudeFloat = (float) noisescaleDrude;
float maxDrudeDistanceFloat =(float) maxDrudeDistance;
float hardwallscaleDrudeFloat = (float) hardwallscaleDrude;
void *vscalePtr, *fscalePtr, *noisescalePtr, *vscaleDrudePtr, *fscaleDrudePtr, *noisescaleDrudePtr, *maxDrudeDistancePtr, *hardwallscaleDrudePtr;
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
vscalePtr = &vscale;
fscalePtr = &fscale;
noisescalePtr = &noisescale;
vscaleDrudePtr = &vscaleDrude;
fscaleDrudePtr = &fscaleDrude;
noisescaleDrudePtr = &noisescaleDrude;
maxDrudeDistancePtr = &maxDrudeDistance;
hardwallscaleDrudePtr = &hardwallscaleDrude;
}
else {
vscalePtr = &vscaleFloat;
fscalePtr = &fscaleFloat;
noisescalePtr = &noisescaleFloat;
vscaleDrudePtr = &vscaleDrudeFloat;
fscaleDrudePtr = &fscaleDrudeFloat;
noisescaleDrudePtr = &noisescaleDrudeFloat;
maxDrudeDistancePtr = &maxDrudeDistanceFloat;
hardwallscaleDrudePtr = &hardwallscaleDrudeFloat;
}
// Call the first integration kernel.
int randomIndex = integration.prepareRandomNumbers(normalParticles->getSize()+2*pairParticles->getSize());
void* args1[] = {&cu.getVelm().getDevicePointer(), &cu.getForce().getDevicePointer(), &integration.getPosDelta().getDevicePointer(),
&normalParticles->getDevicePointer(), &pairParticles->getDevicePointer(), &integration.getStepSize().getDevicePointer(),
vscalePtr, fscalePtr, noisescalePtr, vscaleDrudePtr, fscaleDrudePtr, noisescaleDrudePtr, &integration.getRandom().getDevicePointer(), &randomIndex};
cu.executeKernel(kernel1, args1, numAtoms);
// Apply constraints.
integration.applyConstraints(integrator.getConstraintTolerance());
// Call the second integration kernel.
CUdeviceptr posCorrection = (cu.getUseMixedPrecision() ? cu.getPosqCorrection().getDevicePointer() : 0);
void* args2[] = {&cu.getPosq().getDevicePointer(), &posCorrection, &integration.getPosDelta().getDevicePointer(),
&cu.getVelm().getDevicePointer(), &integration.getStepSize().getDevicePointer()};
cu.executeKernel(kernel2, args2, numAtoms);
// Apply hard wall constraints.
void* hardwallArgs[] = {&cu.getPosq().getDevicePointer(), &posCorrection, &cu.getVelm().getDevicePointer(),
&pairParticles->getDevicePointer(), &integration.getStepSize().getDevicePointer(), maxDrudeDistancePtr, hardwallscaleDrudePtr};
cu.executeKernel(hardwallKernel, hardwallArgs, pairParticles->getSize());
integration.computeVirtualSites();
// Update the time and step count.
cu.setTime(cu.getTime()+stepSize);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
}