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lammps/lib/atc/ATC_TransferThermal.cpp
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ATC_TransferThermal.cpp
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// ATC_Transfer headers
#include "ATC_TransferThermal.h"
#include "ATC_Error.h"
#include "LammpsInterface.h"
#include "PrescribedDataManager.h"
// Other Headers
#include <vector>
#include <set>
#include <utility>
namespace ATC {
ATC_TransferThermal::ATC_TransferThermal(string groupName,
string matParamFile,
ExtrinsicModelType extrinsicModel)
: ATC_Transfer(),
thermostat_(this),
pmfcOn_(false)
{
// assign default "internal" group
int igroup = lammpsInterface_->find_group(groupName.c_str());
groupbit_ |= lammpsInterface_->group_bit(igroup);
igroups_.insert(igroup);
// Allocate PhysicsModel
create_physics_model(THERMAL, matParamFile);
// create extrinsic physics model
if (extrinsicModel != NO_MODEL) {
extrinsicModelManager_.create_model(extrinsicModel,matParamFile);
}
simTime_ = 0.;
integrationType_ = TimeIntegrator::VERLET;
atomicOutputMask_.insert("temperature");
// set up field data based on physicsModel
physicsModel_->get_num_fields(fieldSizes_,fieldMask_);
// output variable vector info:
// output[1] = total coarse scale thermal energy
// output[2] = average temperature
vectorFlag_ = 1;
sizeVector_ = 2;
globalFreq_ = 1;
extVector_ = 1;
if (extrinsicModel != NO_MODEL)
sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);
}
ATC_TransferThermal::~ATC_TransferThermal()
{
}
void ATC_TransferThermal::initialize()
{
// Base class initalizations
ATC_Transfer::initialize();
if (!timeFilterManager_.filter_dynamics()) {
DENS_VEC atomicKineticEnergy(nLocal_);
compute_atomic_kinetic_energy(atomicKineticEnergy, lammpsInterface_->vatom());
project_volumetric_quantity(atomicKineticEnergy,fieldNdFiltered_[TEMPERATURE],TEMPERATURE);
fieldNdFiltered_[TEMPERATURE] *= 2.;
}
thermostat_.initialize();
extrinsicModelManager_.initialize();
if (!initialized_) {
// initialize sources based on initial FE temperature
double dt = lammpsInterface_->dt();
prescribedDataMgr_->set_sources(simTime_+.5*dt,sources_);
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
thermostat_.compute_boundary_flux(fields_);
compute_atomic_sources(fieldMask_,fields_,atomicSources_);
}
if (timeFilterManager_.need_reset()) {
init_filter();
timeFilterManager_.initialize();
}
// reset integration field mask
temperatureMask_.reset(NUM_FIELDS,NUM_FLUX);
temperatureMask_ = false;
for (int i = 0; i < NUM_FLUX; i++)
temperatureMask_(TEMPERATURE,i) = fieldMask_(TEMPERATURE,i);
initialized_ = true;
if (pmfcOn_) {
oldFieldTemp_.reset(nNodes_,1);
}
// read in field data if necessary
if (useRestart_) {
OUTPUT_LIST data;
read_restart_data(restartFileName_,data);
useRestart_ = false;
}
}
void ATC_TransferThermal::init_filter()
{
// NOTE assume total filtered time derivatives are zero
ATC_Transfer::init_filter();
if (integrationType_==TimeIntegrator::VERLET) {
// initialize restricted fields
// NOTE: comment in to initialize fieldRateNdOld_ to current time deriviative
// current assumption is that it is zero
//DenseMatrix<double> atomicPower(nLocal_,1);
//compute_atomic_power(atomicPower,
// lammpsInterface_->vatom(),
// lammpsInterface_->fatom());
//restrict(atomicPower,fieldRateNdOld_[TEMPERATURE]);
//fieldRateNdOld *= 2.;
DENS_MAT atomicKineticEnergy(nLocal_,1);
DENS_MAT nodalAtomicTemperature(nNodes_,1);
compute_atomic_temperature(atomicKineticEnergy,
lammpsInterface_->vatom());
restrict(atomicKineticEnergy, nodalAtomicTemperature);
nodalAtomicTemperature *= 2.;
fieldNdOld_[TEMPERATURE] = nodalAtomicTemperature;
}
if (timeFilterManager_.end_equilibrate()) { // set up correct initial lambda power to enforce initial temperature rate of 0
if (integrationType_==TimeIntegrator::VERLET) {
if (equilibriumStart_) {
if (thermostat_.get_thermostat_type()==Thermostat::FLUX) { // based on FE equation
DENS_MAT vdotflamMat(-2.*fieldRateNdFiltered_[TEMPERATURE]); // note 2 is for 1/2 vdotflam addition
thermostat_.reset_lambda_power(vdotflamMat);
}
else { // based on MD temperature equation
DENS_MAT vdotflamMat(-1.*fieldRateNdFiltered_[TEMPERATURE]);
thermostat_.reset_lambda_power(vdotflamMat);
}
}
}
}
else { // set up space for filtered atomic power
// should set up all data structures common to equilibration and filtering,
// specifically filtered atomic power
if (integrationType_==TimeIntegrator::FRACTIONAL_STEP) {
dot_atomicTemp.reset(nNodes_,1);
dot_atomicTempOld.reset(nNodes_,1);
dot_dot_atomicTemp.reset(nNodes_,1);
dot_dot_atomicTempOld.reset(nNodes_,1);
}
}
}
void ATC_TransferThermal::compute_md_mass_matrix(FieldName thisField,
map<FieldName,DIAG_MAT> & massMats)
{
if (thisField == TEMPERATURE) {
DENS_VEC atomicCapacity(nLocal_);
atomicCapacity = nsd_*(LammpsInterface::instance()->kBoltzmann());
DENS_VEC nodalAtomicCapacity(nNodes_);
restrict_volumetric_quantity(atomicCapacity,nodalAtomicCapacity);
massMats[thisField].reset(nodalAtomicCapacity);
}
}
void ATC_TransferThermal::finish()
{
// base class
ATC_Transfer::finish();
// nothing specific to thermal
}
bool ATC_TransferThermal::modify(int narg, char **arg)
{
bool foundMatch = false;
int argIndx = 0;
// check to see if input is a transfer class command
// check derived class before base class
if (strcmp(arg[argIndx],"transfer")==0) {
argIndx++;
// pass-through to thermostat
if (strcmp(arg[argIndx],"thermal")==0) {
argIndx++;
if (strcmp(arg[argIndx],"control")==0) {
argIndx++;
foundMatch = thermostat_.modify(narg-argIndx,&arg[argIndx]);
}
}
// switch for equilibrium filtering start
/*! \page man_equilibrium_start fix_modify AtC transfer equilibrium_start
\section syntax
fix_modify AtC transfer equilibrium_start <on|off>
\section examples
<TT> fix_modify atc transfer equilibrium_start on </TT> \n
\section description
Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.
\section restrictions
only needed before filtering is begun
\section related
see \ref man_time_filter
\section default
on
*/
else if (strcmp(arg[argIndx],"equilibrium_start")==0) {
argIndx++;
if (strcmp(arg[argIndx],"on")==0) {
equilibriumStart_ = true;
foundMatch = true;
}
else if (strcmp(arg[argIndx],"off")==0) {
equilibriumStart_ = false;
foundMatch = true;
}
}
// time integration scheme
/*! \page man_time_integration fix_modify AtC transfer pmfc
\section syntax
fix_modify AtC transfer pmfc <on|off>
\section examples
<TT> fix_modify atc transfer pmfc on </TT>
\section description
Switches the poor man's fractional step algorithm on where the finite element data lags the exact atomic data by one time step for overlap nodes
\section restrictions
\section related
\section default
off
*/
else if (strcmp(arg[argIndx],"pmfc")==0) {
if (integrationType_!=TimeIntegrator::VERLET || timeFilterManager_.filter_dynamics())
throw ATC_Error(0,"Can only use poor man's fractional step with Verlet integration without filtering");
pmfcOn_ = !pmfcOn_;
foundMatch = true;
}
}
// no match, call base class parser
if (!foundMatch) {
foundMatch = ATC_Transfer::modify(narg, arg);
}
return foundMatch;
}
//--------------------------------------------------
// pack_fields
// bundle all allocated field matrices into a list
// for output needs
//--------------------------------------------------
void ATC_TransferThermal::pack_thermal_fields(OUTPUT_LIST & data)
{
data["ddFieldTemp"] = & oldFieldTemp_;
data["lambdaPowerFiltered"] = &(thermostat_.get_filtered_lambda_power());
}
//--------------------------------------------------
// write_restart_file
// bundle matrices that need to be saved and call
// fe_engine to write the file
//--------------------------------------------------
void ATC_TransferThermal::write_restart_data(string fileName, OUTPUT_LIST & data)
{
pack_thermal_fields(data);
ATC_Transfer::write_restart_data(fileName,data);
}
//--------------------------------------------------
// write_restart_file
// bundle matrices that need to be saved and call
// fe_engine to write the file
//--------------------------------------------------
void ATC_TransferThermal::read_restart_data(string fileName, OUTPUT_LIST & data)
{
pack_thermal_fields(data);
ATC_Transfer::read_restart_data(fileName,data);
}
void ATC_TransferThermal::reset_nlocal()
{
ATC_Transfer::reset_nlocal();
thermostat_.reset_nlocal();
}
void ATC_TransferThermal::pre_init_integrate()
{
//ATC_Transfer::pre_init_integrate();
double dt = lammpsInterface_->dt();
double dtLambda = 0.5*dt;
if (pmfcOn_) {
oldFieldTemp_ = fields_[TEMPERATURE];
}
// Apply thermostat to atom velocities
thermostat_.apply_pre_predictor(dtLambda,lammpsInterface_->ntimestep());
// Predict nodal temperatures and time derivatives based on FE data
// 4th order Gear
// switch call based on filter
if (timeFilterManager_.filter_dynamics())
gear1_4_predict(fields_[TEMPERATURE],dot_fields_[TEMPERATURE],
ddot_fields_[TEMPERATURE],dddot_fields_[TEMPERATURE],dt);
else
gear1_3_predict(fields_[TEMPERATURE],dot_fields_[TEMPERATURE],
ddot_fields_[TEMPERATURE],dt);
extrinsicModelManager_.pre_init_integrate();
// fixed values, non-group bcs handled through FE
set_fixed_nodes();
simTime_ += .5*dt;
}
void ATC_TransferThermal::post_init_integrate()
{
// Nothing to do here
//ATC_Transfer::post_init_integrate();
}
void ATC_TransferThermal::pre_final_integrate()
{
ATC_Transfer::pre_final_integrate();
}
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();
}
//--------------------------------------------------------------------
// compute_vector
//--------------------------------------------------------------------
// this is for direct output to lammps thermo
double ATC_TransferThermal::compute_vector(int n)
{
// output[1] = total coarse scale thermal energy
// output[2] = average temperature
double mvv2e = lammpsInterface_->mvv2e(); // convert to lammps energy units
if (n == 0) {
Array<FieldName> mask(1);
FIELDS energy;
mask(0) = TEMPERATURE;
feEngine_->compute_energy(mask, // NOTE make this a base class function
fields_,
physicsModel_,
elementToMaterialMap_,
energy,
&elementMask_);
double phononEnergy = mvv2e * energy[TEMPERATURE].col_sum();
return phononEnergy;
}
else if (n == 1) {
double aveT = fields_[TEMPERATURE].col_sum()/nNodes_;
return aveT;
}
else if (n > 1) {
double extrinsicValue = extrinsicModelManager_.compute_vector(n);
return extrinsicValue;
}
return 0.;
}
//--------------------------------------------------------------------
// output
//--------------------------------------------------------------------
void ATC_TransferThermal::output()
{
double dt = lammpsInterface_->dt();
double step = (double) lammpsInterface_->ntimestep();
++stepCounter_;
if ((outputFrequency_ > 0)
&& ((stepCounter_ ==1) || (stepCounter_ % outputFrequency_ == 0)) ) {
OUTPUT_LIST output_data;
// Add some outputs only on Proc 0
if (lammpsInterface_->comm_rank() == 0) {
// base class output
ATC_Transfer::output();
// global data
double T_mean = fields_[TEMPERATURE].col_sum(0)/nNodes_;
feEngine_->add_global("temperature_mean", T_mean);
double T_stddev = fields_[TEMPERATURE].col_stdev(0);
feEngine_->add_global("temperature_std_dev", T_stddev);
double Ta_mean = fieldNdFiltered_[TEMPERATURE].col_sum(0)/nNodes_;
feEngine_->add_global("atomic_temperature_mean", Ta_mean);
double Ta_stddev = fieldNdFiltered_[TEMPERATURE].col_stdev(0);
feEngine_->add_global("atomic_temperature_std_dev", Ta_stddev);
// mesh data
output_data["nodalAtomicTemperature"] = & fieldNdFiltered_[TEMPERATURE];
output_data["dot_temperature"] = & dot_fields_[TEMPERATURE];
output_data["ddot_temperature"] = & ddot_fields_[TEMPERATURE];
output_data["nodalAtomicPower"] = & fieldRateNdFiltered_[TEMPERATURE];
// auxilliary data
thermostat_.output(dt,output_data);
extrinsicModelManager_.output(dt,output_data);
}
// Output fe data on proc 0
if (lammpsInterface_->comm_rank() == 0) {
feEngine_->write_data(simTime_, fields_, & output_data);
}
}
if ((outputFrequencyAtom_ > 0)
&& ((stepCounter_ ==1) || (stepCounter_ % outputFrequencyAtom_ == 0)) )
atomic_output();
}
void ATC_TransferThermal::set_ghost_atoms()
{
// Nothing to do here
}
};
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