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;
}