/*
* Zero forces on all local atoms and optionally on ghosts.
*/
void AtomStorage::zeroForces(bool zeroGhosts)
{
int factor = 2;
// Zero forces for all local atoms
if (nAtom() > atomCapacity_/factor) {
atoms_.zeroForces();
// Optimization to allow sequential access
} else {
AtomIterator atomIter;
begin(atomIter);
for( ; atomIter.notEnd(); ++atomIter){
atomIter->force().zero();
}
}
// If using reverse communication, zero ghost atoms
if (zeroGhosts && nGhost()) {
if (nGhost() > ghostCapacity_/factor) {
ghosts_.zeroForces();
// Optimization to allow sequential access
} else {
GhostIterator ghostIter;
begin(ghostIter);
for( ; ghostIter.notEnd(); ++ghostIter){
ghostIter->force().zero();
}
}
}
}
/*
* Second half of two-step velocity-Verlet integrator.
*/
void NphIntegrator::integrateStep2()
{
Vector dv;
double prefactor; // = 0.5*dt/mass
AtomIterator atomIter;
Vector v_fac_2 = Vector((1.0/2.0)*(nu_[0]+mtk_term_2_),
(1.0/2.0)*(nu_[1]+mtk_term_2_),
(1.0/2.0)*(nu_[2]+mtk_term_2_));
Vector exp_v_fac_2 = Vector(exp(-v_fac_2[0]*dt_),
exp(-v_fac_2[1]*dt_),
exp(-v_fac_2[2]*dt_));
// 2nd half of NPH
atomStorage().begin(atomIter);
for ( ; atomIter.notEnd(); ++atomIter) {
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
dv[0] = dv[0] * exp_v_fac_[0]*sinhx_fac_v_[0];
dv[1] = dv[1] * exp_v_fac_[1]*sinhx_fac_v_[1];
dv[2] = dv[2] * exp_v_fac_[2]*sinhx_fac_v_[2];
Vector& v = atomIter->velocity();
v[0] = v[0] * exp_v_fac_2[0] + dv[0];
v[1] = v[1] * exp_v_fac_2[1] + dv[1];
v[2] = v[2] * exp_v_fac_2[2] + dv[2];
}
Simulation& sys = simulation();
sys.velocitySignal().notify();
sys.computeKineticStress();
sys.computeKineticEnergy();
sys.computeVirialStress();
// Advance barostat
if (sys.domain().isMaster()) {
T_kinetic_ = sys.kineticEnergy()*2.0/ndof_;
Tensor stress = sys.virialStress();
stress += sys.kineticStress();
P_curr_diag_ = Vector(stress(0,0), stress(1,1), stress(2,2));
double P_curr = (1.0/3.0)*stress.trace();
double mtk_term = (1.0/2.0)*dt_*T_kinetic_/W_;
double V = sys.boundary().volume();
if (mode_ == Cubic) {
nu_[0] += (1.0/2.0)*dt_*V/W_*(P_curr - P_target_) + mtk_term;
nu_[1] = nu_[2] = nu_[0];
} else if (mode_ == Tetragonal) {
nu_[0] += (1.0/2.0)*dt_*V/W_*(P_curr_diag_[0] - P_target_) + mtk_term;
nu_[1] += (1.0/2.0)*dt_*V/W_*((1.0/2.0)*(P_curr_diag_[1]+P_curr_diag_[2]) - P_target_) + mtk_term;
nu_[2] = nu_[1];
} else if (mode_ == Orthorhombic) {
nu_[0] += (1.0/2.0)*dt_*V/W_*(P_curr_diag_[0] - P_target_) + mtk_term;
nu_[1] += (1.0/2.0)*dt_*V/W_*(P_curr_diag_[1] - P_target_) + mtk_term;
nu_[2] += (1.0/2.0)*dt_*V/W_*(P_curr_diag_[2] - P_target_) + mtk_term;
}
}
#if 0
// output conserved quantity
sys.computePotentialEnergies();
if (sys.domain().isMaster()) {
std::ofstream file;
file.open("NPH.log", std::ios::out | std::ios::app);
double V = sys.boundary().volume();
double barostat_energy = W_*(nu_[0]*nu_[0]+ nu_[1]*nu_[1] + nu_[2]*nu_[2]);
double pe = sys.potentialEnergy();
double ke = sys.kineticEnergy();
file << Dbl(V,20)
<< Dbl(pe,20)
<< Dbl(ke,20)
<< Dbl(barostat_energy,20)
<< std::endl;
file.close();
}
#endif
#ifdef UTIL_MPI
bcast(domain().communicator(), nu_,0);
#endif
}
/*
* First half of two-step velocity-Verlet integrator.
*/
void NphIntegrator::integrateStep1()
{
Vector dv;
AtomIterator atomIter;
Simulation& sys = simulation();
sys.computeVirialStress();
sys.computeKineticStress();
sys.computeKineticEnergy();
if (sys.domain().isMaster()) {
P_target_ = simulation().boundaryEnsemble().pressure();
T_kinetic_ = sys.kineticEnergy()*2.0/ndof_;
Tensor stress = sys.virialStress();
stress += sys.kineticStress();
P_curr_diag_ = Vector(stress(0, 0), stress(1,1), stress(2,2));
double P_curr = (1.0/3.0)*stress.trace();
double mtk_term = (1.0/2.0)*dt_*T_kinetic_/W_;
// Advance barostat
double V = sys.boundary().volume();
if (mode_ == Cubic) {
nu_[0] += (1.0/2.0)*dt_*V/W_*(P_curr - P_target_) + mtk_term;
nu_[1] = nu_[2] = nu_[0];
} else if (mode_ == Tetragonal) {
nu_[0] += (1.0/2.0)*dt_*V/W_*(P_curr_diag_[0] - P_target_) + mtk_term;
nu_[1] += (1.0/2.0)*dt_*V/W_*((1.0/2.0)*(P_curr_diag_[1]+P_curr_diag_[2]) - P_target_) + mtk_term;
nu_[2] = nu_[1];
} else if (mode_ == Orthorhombic) {
nu_[0] += (1.0/2.0)*dt_*V/W_*(P_curr_diag_[0] - P_target_) + mtk_term;
nu_[1] += (1.0/2.0)*dt_*V/W_*(P_curr_diag_[1] - P_target_) + mtk_term;
nu_[2] += (1.0/2.0)*dt_*V/W_*(P_curr_diag_[2] - P_target_) + mtk_term;
}
}
#ifdef UTIL_MPI
bcast(domain().communicator(), nu_,0);
#endif
// Precompute loop invariant quantities
mtk_term_2_ = (nu_[0]+nu_[1]+nu_[2])/ndof_;
Vector v_fac = Vector((1.0/4.0)*(nu_[0]+mtk_term_2_),
(1.0/4.0)*(nu_[1]+mtk_term_2_),
(1.0/4.0)*(nu_[2]+mtk_term_2_));
exp_v_fac_ = Vector(exp(-v_fac[0]*dt_),
exp(-v_fac[1]*dt_),
exp(-v_fac[2]*dt_));
Vector exp_v_fac_2 = Vector(exp(-(2.0*v_fac[0])*dt_),
exp(-(2.0*v_fac[1])*dt_),
exp(-(2.0*v_fac[2])*dt_));
Vector r_fac = Vector((1.0/2.0)*nu_[0],
(1.0/2.0)*nu_[1],
(1.0/2.0)*nu_[2]);
Vector exp_r_fac = Vector(exp(r_fac[0]*dt_),
exp(r_fac[1]*dt_),
exp(r_fac[2]*dt_));
// Coefficients of sinh(x)/x = a_0 + a_2*x^2 + a_4*x^4 + a_6*x^6 + a_8*x^8 + a_10*x^10
const double a[] = {double(1.0), double(1.0/6.0), double(1.0/120.0),
double(1.0/5040.0), double(1.0/362880.0), double(1.0/39916800.0)};
Vector arg_v = Vector(v_fac[0]*dt_, v_fac[1]*dt_, v_fac[2]*dt_);
Vector arg_r = Vector(r_fac[0]*dt_, r_fac[1]*dt_, r_fac[2]*dt_);
sinhx_fac_v_ = Vector(0.0,0.0,0.0);
Vector sinhx_fac_r = Vector(0.0,0.0,0.0);
Vector term_v = Vector(1.0,1.0,1.0);
Vector term_r = Vector(1.0,1.0,1.0);
for (unsigned int i = 0; i < 6; i++) {
sinhx_fac_v_ += Vector(a[0]*term_v[0],
a[1]*term_v[1],
a[2]*term_v[2]);
sinhx_fac_r += Vector(a[0]*term_r[0],
a[1]*term_r[1],
a[2]*term_r[2]);
term_v = Vector(term_v[0] * arg_v[0] * arg_v[0],
term_v[1] * arg_v[1] * arg_v[1],
term_v[2] * arg_v[2] * arg_v[2]);
term_r = Vector(term_r[0] * arg_r[0] * arg_r[0],
term_r[1] * arg_r[1] * arg_r[1],
term_r[2] * arg_r[2] * arg_r[2]);
}
// 1st half of NPH
Vector vtmp;
double prefactor; // = 0.5*dt/mass
atomStorage().begin(atomIter);
for ( ; atomIter.notEnd(); ++atomIter) {
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
dv[0] = dv[0] * exp_v_fac_[0]*sinhx_fac_v_[0];
dv[1] = dv[1] * exp_v_fac_[1]*sinhx_fac_v_[1];
dv[2] = dv[2] * exp_v_fac_[2]*sinhx_fac_v_[2];
Vector& v = atomIter->velocity();
v[0] = v[0] * exp_v_fac_2[0] + dv[0];
v[1] = v[1] * exp_v_fac_2[1] + dv[1];
v[2] = v[2] * exp_v_fac_2[2] + dv[2];
vtmp[0] = v[0]*exp_r_fac[0] *sinhx_fac_r[0];
vtmp[1] = v[1]*exp_r_fac[1] *sinhx_fac_r[1];
vtmp[2] = v[2]*exp_r_fac[2] *sinhx_fac_r[2];
Vector& r = atomIter->position();
r[0] = r[0]*exp_r_fac[0]*exp_r_fac[0] + vtmp[0]*dt_;
r[1] = r[1]*exp_r_fac[1]*exp_r_fac[1] + vtmp[1]*dt_;
r[2] = r[2]*exp_r_fac[2]*exp_r_fac[2] + vtmp[2]*dt_;
}
// Advance box lengths
Vector box_len_scale = Vector(exp(nu_[0]*dt_),
exp(nu_[1]*dt_),
exp(nu_[2]*dt_));
Vector L = sys.boundary().lengths();
L[0] *= box_len_scale[0];
L[1] *= box_len_scale[1];
L[2] *= box_len_scale[2];
// Update box lengths
sys.boundary().setOrthorhombic(L);
}