int sipg_sem_1d<FLOAT_TYPE>::solve()
{
stiffness_matrix_generation.start(); // start timer
compute_stiffness_matrix();
stiffness_matrix_generation.stop(); // stop timer
compute_rhs_vector();
#ifdef USE_LAPACK
std::vector<int> ipiv(_vec_size,0); // pivot
_u = _rhs;
linear_system_solution.start(); // start timer
int info = lapacke_gesv( LAPACK_ROW_MAJOR,
_vec_size,
1,
_A.data(),
_vec_size,
ipiv.data(),
_u.data(),
1 );
#else
ConjugateGradient<Eigen::SparseMatrix<FLOAT_TYPE> > cg;
cg.compute(_A);
_u = cg.solve(_rhs);
#endif
linear_system_solution.stop(); // stop timer
compute_err_norms();
return info;
}
void ATC_TransferThermal::post_final_integrate()
{
//ATC_Transfer::post_final_integrate();
double dt = lammpsInterface_->dt();
double dtLambda = dt*0.5;
// predict thermostat contributions
// compute sources based on predicted FE temperature
prescribedDataMgr_->set_sources(simTime_+.5*dt,sources_);
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
thermostat_.compute_boundary_flux(fields_);
compute_atomic_sources(temperatureMask_,fields_,atomicSources_);
thermostat_.apply_pre_corrector(dtLambda,lammpsInterface_->ntimestep());
// Determine FE contributions to d theta/dt
// Compute atom-integrated rhs
// parallel communication happens within FE_Engine
compute_rhs_vector(temperatureMask_,fields_,rhs_,FE_DOMAIN);
// For flux matching, add 1/2 of "drag" power
thermostat_.add_to_rhs(rhs_);
extrinsicModelManager_.post_final_integrate();
// add in atomic FE contributions for verlet method
if (integrationType_==TimeIntegrator::VERLET) {
DENS_MAT atomicPower(nLocal_,1);
compute_atomic_power(atomicPower,
lammpsInterface_->vatom(),
lammpsInterface_->fatom());
DENS_MAT nodalAtomicPower(nNodes_,1);
restrict_volumetric_quantity(atomicPower,nodalAtomicPower);
nodalAtomicPower *= 2.;
if (timeFilterManager_.filter_variables())
update_filter_implicit(fieldRateNdFiltered_[TEMPERATURE],nodalAtomicPower,dt);
else
fieldRateNdFiltered_[TEMPERATURE] = nodalAtomicPower;
if (!timeFilterManager_.filter_variables() || timeFilterManager_.filter_dynamics())
rhs_[TEMPERATURE] += fieldRateNdFiltered_[TEMPERATURE];
else
rhs_[TEMPERATURE] += nodalAtomicPower;
}
// Finish updating temperature
DENS_MAT R_theta(nNodes_,1);
apply_inverse_mass_matrix(rhs_[TEMPERATURE],TEMPERATURE);
R_theta = (rhs_[TEMPERATURE] - dot_fields_[TEMPERATURE])*dt;
if (timeFilterManager_.filter_dynamics())
gear1_4_correct(fields_[TEMPERATURE],dot_fields_[TEMPERATURE],
ddot_fields_[TEMPERATURE],dddot_fields_[TEMPERATURE],
R_theta,dt);
else
gear1_3_correct(fields_[TEMPERATURE],dot_fields_[TEMPERATURE],
ddot_fields_[TEMPERATURE],R_theta,dt);
// only requirecd for poor man's fractional step
if (pmfcOn_) {
DENS_MAT atomicKineticEnergy(nLocal_,1);
compute_atomic_kinetic_energy(atomicKineticEnergy,
lammpsInterface_->vatom());
DENS_MAT temperatureNd(nNodes_,1);
project_md_volumetric_quantity(atomicKineticEnergy,
temperatureNd,
TEMPERATURE);
temperatureNd *= 2.;
dot_fields_[TEMPERATURE] = 1.0/dt * ( temperatureNd - oldFieldTemp_);
fields_[TEMPERATURE] = temperatureNd;
}
// fix nodes, non-group bcs applied through FE
set_fixed_nodes();
// compute sources based on final FE updates
prescribedDataMgr_->set_sources(simTime_+.5*dt,sources_);
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
thermostat_.compute_boundary_flux(fields_);
compute_atomic_sources(temperatureMask_,fields_,atomicSources_);
// apply corrector phase of thermostat
thermostat_.apply_post_corrector(dtLambda,lammpsInterface_->ntimestep());
// add in MD contributions to time derivative
// update filtered temperature
DENS_MAT atomicKineticEnergy(nLocal_,1);
compute_atomic_kinetic_energy(atomicKineticEnergy,
lammpsInterface_->vatom());
DENS_MAT temperatureNd(nNodes_,1);
project_md_volumetric_quantity(atomicKineticEnergy,temperatureNd,TEMPERATURE);
temperatureNd *= 2.;
if (!timeFilterManager_.filter_dynamics())
fieldNdFiltered_[TEMPERATURE] = temperatureNd;
else if (integrationType_==TimeIntegrator::VERLET)
update_filter_implicit(fieldNdFiltered_[TEMPERATURE],temperatureNd,dt);
simTime_ += .5*dt;
output();
}