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;
}
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;
}
void CudaCalcDrudeForceKernel::initialize(const System& system, const DrudeForce& force) {
cu.setAsCurrent();
int numContexts = cu.getPlatformData().contexts.size();
int startParticleIndex = cu.getContextIndex()*force.getNumParticles()/numContexts;
int endParticleIndex = (cu.getContextIndex()+1)*force.getNumParticles()/numContexts;
int numParticles = endParticleIndex-startParticleIndex;
if (numParticles > 0) {
// Create the harmonic interaction .
vector<vector<int> > atoms(numParticles, vector<int>(5));
particleParams = CudaArray::create<float4>(cu, numParticles, "drudeParticleParams");
vector<float4> paramVector(numParticles);
for (int i = 0; i < numParticles; i++) {
double charge, polarizability, aniso12, aniso34;
force.getParticleParameters(startParticleIndex+i, atoms[i][0], atoms[i][1], atoms[i][2], atoms[i][3], atoms[i][4], charge, polarizability, aniso12, aniso34);
double a1 = (atoms[i][2] == -1 ? 1 : aniso12);
double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34);
double a3 = 3-a1-a2;
double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
if (atoms[i][2] == -1) {
atoms[i][2] = 0;
k1 = 0;
}
if (atoms[i][3] == -1 || atoms[i][4] == -1) {
atoms[i][3] = 0;
atoms[i][4] = 0;
k2 = 0;
}
paramVector[i] = make_float4((float) k1, (float) k2, (float) k3, 0.0f);
}
particleParams->upload(paramVector);
map<string, string> replacements;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(particleParams->getDevicePointer(), "float4");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaDrudeKernelSources::drudeParticleForce, replacements), force.getForceGroup());
}
int startPairIndex = cu.getContextIndex()*force.getNumScreenedPairs()/numContexts;
int endPairIndex = (cu.getContextIndex()+1)*force.getNumScreenedPairs()/numContexts;
int numPairs = endPairIndex-startPairIndex;
if (numPairs > 0) {
// Create the screened interaction between dipole pairs.
vector<vector<int> > atoms(numPairs, vector<int>(4));
pairParams = CudaArray::create<float2>(cu, numPairs, "drudePairParams");
vector<float2> paramVector(numPairs);
for (int i = 0; i < numPairs; i++) {
int drude1, drude2;
double thole;
force.getScreenedPairParameters(startPairIndex+i, drude1, drude2, thole);
int p2, p3, p4;
double charge1, charge2, polarizability1, polarizability2, aniso12, aniso34;
force.getParticleParameters(drude1, atoms[i][0], atoms[i][1], p2, p3, p4, charge1, polarizability1, aniso12, aniso34);
force.getParticleParameters(drude2, atoms[i][2], atoms[i][3], p2, p3, p4, charge2, polarizability2, aniso12, aniso34);
double screeningScale = thole/pow(polarizability1*polarizability2, 1.0/6.0);
double energyScale = ONE_4PI_EPS0*charge1*charge2;
paramVector[i] = make_float2((float) screeningScale, (float) energyScale);
}
pairParams->upload(paramVector);
map<string, string> replacements;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(pairParams->getDevicePointer(), "float2");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaDrudeKernelSources::drudePairForce, replacements), force.getForceGroup());
}
cu.addForce(new CudaDrudeForceInfo(force));
}
