/*
* Transform all atomic coordinates from generalized to Cartesian.
*/
void AtomStorage::transformGenToCart(const Boundary& boundary)
{
if (isCartesian()) {
UTIL_THROW("Error: Coordinates are Cartesian on entry");
}
Vector r;
if (nAtom()) {
AtomIterator atomIter;
for (begin(atomIter); atomIter.notEnd(); ++atomIter) {
r = atomIter->position();
boundary.transformGenToCart(r, atomIter->position());
}
}
if (nGhost()) {
GhostIterator ghostIter;
for (begin(ghostIter); ghostIter.notEnd(); ++ghostIter) {
r = ghostIter->position();
boundary.transformGenToCart(r, ghostIter->position());
}
}
isCartesian_ = true;
}
/*
* Record current positions of all local atoms and lock storage.
*/
void AtomStorage::makeSnapshot()
{
// Precondition
if (!isCartesian()) {
UTIL_THROW("Error: Coordinates not Cartesian in makeSnapshot");
}
AtomIterator iter;
int i = 0;
for (begin(iter); iter.notEnd(); ++iter) {
snapshot_[i] = iter->position();
++i;
}
locked_ = true;
}
/*
* Return max. sq. displacement of local atoms on this node since snapshot.
*/
double AtomStorage::maxSqDisplacement()
{
if (!isCartesian()) {
UTIL_THROW("Error: Coordinates not Cartesian in maxSqDisplacement");
}
if (!locked_) {
UTIL_THROW("Error: AtomStorage not locked in maxSqDisplacement");
}
Vector dr;
double norm;
double max = 0.0;
AtomIterator iter;
int i = 0;
for (begin(iter); iter.notEnd(); ++iter) {
dr.subtract(iter->position(), snapshot_[i]);
norm = dr.square();
if (norm > max) {
max = norm;
}
++i;
}
return max;
}
/// Increment Structure Factor
void AsymmSF::sample(long iStep)
{
if (isAtInterval(iStep)) {
Vector position;
std::complex<double> expFactor;
double product;
AtomIterator atomIter;
int i, j, typeId;
makeWaveVectors();
// Set all Fourier modes to zero
for (i = 0; i < nWave_; ++i) {
for (j = 0; j < nMode_; ++j) {
fourierModes_(i, j) = std::complex<double>(0.0, 0.0);
}
}
simulation().atomStorage().begin(atomIter);
for ( ; atomIter.notEnd(); ++atomIter) {
position = atomIter->position();
typeId = atomIter->typeId();
// Loop over wavevectors
for (i = 0; i < nWave_; ++i) {
product = position.dot(waveVectors_[i]);
expFactor = exp( product*Constants::Im );
for (j = 0; j < nMode_; ++j) {
fourierModes_(i, j) += modes_(j, typeId)*expFactor;
}
}
}
for (i = 0; i < nWave_; ++i) {
for (j = 0; j < nMode_; ++j) {
totalFourierModes_(i, j) = std::complex<double>(0.0, 0.0);
}
}
#ifdef UTIL_MPI
// Loop over wavevectors
for (int i = 0; i < nWave_; ++i) {
for (int j = 0; j < nMode_; ++j) {
//Sum values from all processors.
simulation().domain().communicator().Reduce(&fourierModes_(i, j), &totalFourierModes_(i, j), 1,
MPI::DOUBLE_COMPLEX, MPI::SUM, 0);
}
}
#else
for (int i = 0; i < nWave_; ++i) {
for (int j = 0; j < nMode_; ++j) {
totalFourierModes_(i, j) = fourierModes_(i, j);
}
}
#endif
if (simulation().domain().isMaster()) {
// Increment structure factors
double volume = simulation().boundary().volume();
double norm;
for (j = 0; j < nMode_; ++j) {
double maxValue = 0.0;
IntVector maxIntVector;
double maxQ;
for (i = 1; i < nWave_; ++i) {
norm = std::norm(totalFourierModes_(i, j));
if ( double(norm/volume) >= maxValue ) {
maxValue = double(norm/volume);
maxIntVector = waveIntVectors_[i];
maxQ = waveVectors_[i].abs();
}
structureFactors_(i, j) += norm/volume;
}
maximumValue_[j].insert(maximumValue_[j].end(), 1, maxValue);
maximumWaveIntVector_[j].insert(maximumWaveIntVector_[j].end(), 1, maxIntVector);
maximumQ_[j].insert(maximumQ_[j].end(), 1, maxQ);
}
}
++nSample_;
}
}
/*
* 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);
}