forked from lijiext/lammps
716 lines
27 KiB
C++
716 lines
27 KiB
C++
// ATC_Transfer headers
|
|
#include "ATC_CouplingEnergy.h"
|
|
#include "Thermostat.h"
|
|
#include "ATC_Error.h"
|
|
#include "PrescribedDataManager.h"
|
|
#include "FieldManager.h"
|
|
|
|
// Other Headers
|
|
#include <vector>
|
|
#include <set>
|
|
#include <utility>
|
|
#include <typeinfo>
|
|
|
|
using std::string;
|
|
|
|
namespace ATC {
|
|
|
|
//--------------------------------------------------------
|
|
//--------------------------------------------------------
|
|
// Class ATC_CouplingEnergy
|
|
//--------------------------------------------------------
|
|
//--------------------------------------------------------
|
|
|
|
//--------------------------------------------------------
|
|
// Constructor
|
|
//--------------------------------------------------------
|
|
ATC_CouplingEnergy::ATC_CouplingEnergy(string groupName,
|
|
double ** & perAtomArray,
|
|
LAMMPS_NS::Fix * thisFix,
|
|
string matParamFile,
|
|
ExtrinsicModelType extrinsicModel)
|
|
: ATC_Coupling(groupName,perAtomArray,thisFix),
|
|
nodalAtomicHeatCapacity_(NULL),
|
|
nodalAtomicKineticTemperature_(NULL),
|
|
nodalAtomicConfigurationalTemperature_(NULL)
|
|
{
|
|
// Allocate PhysicsModel
|
|
create_physics_model(THERMAL, matParamFile);
|
|
|
|
// create extrinsic physics model
|
|
if (extrinsicModel != NO_MODEL) {
|
|
extrinsicModelManager_.create_model(extrinsicModel,matParamFile);
|
|
}
|
|
|
|
// Defaults
|
|
set_time();
|
|
bndyIntType_ = FE_INTERPOLATION;
|
|
|
|
// set up field data based on physicsModel
|
|
physicsModel_->num_fields(fieldSizes_,fieldMask_);
|
|
|
|
// set up atomic regulator
|
|
atomicRegulator_ = new Thermostat(this);
|
|
|
|
// set up physics specific time integrator and thermostat
|
|
timeIntegrators_[TEMPERATURE] = new ThermalTimeIntegrator(this,TimeIntegrator::GEAR);
|
|
|
|
// default physics
|
|
temperatureDef_ = KINETIC;
|
|
|
|
// output variable vector info:
|
|
// output[1] = total coarse scale thermal energy
|
|
// output[2] = average temperature
|
|
vectorFlag_ = 1;
|
|
sizeVector_ = 2;
|
|
scalarVectorFreq_ = 1;
|
|
extVector_ = 1;
|
|
if (extrinsicModel != NO_MODEL)
|
|
sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);
|
|
|
|
// create PE per atom ccompute
|
|
//lammpsInterface_->create_compute_pe_peratom();
|
|
}
|
|
|
|
//--------------------------------------------------------
|
|
// Destructor
|
|
//--------------------------------------------------------
|
|
ATC_CouplingEnergy::~ATC_CouplingEnergy()
|
|
{
|
|
// clear out all managed memory to avoid conflicts with dependencies on class member data
|
|
interscaleManager_.clear();
|
|
}
|
|
|
|
//--------------------------------------------------------
|
|
// initialize
|
|
// sets up all the necessary data
|
|
//--------------------------------------------------------
|
|
void ATC_CouplingEnergy::initialize()
|
|
{
|
|
// Base class initalizations
|
|
ATC_Coupling::initialize();
|
|
|
|
// resetting precedence:
|
|
// time integrator -> thermostat -> time filter
|
|
// init_filter uses fieldRateNdFiltered which comes from the time integrator,
|
|
// which is why the time integrator is initialized first
|
|
|
|
// other initializations
|
|
if (reset_methods()) {
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->initialize();
|
|
}
|
|
atomicRegulator_->initialize();
|
|
}
|
|
extrinsicModelManager_.initialize();
|
|
// reset thermostat power for time filter initial conditions for special cases
|
|
if (timeFilterManager_.need_reset()) {
|
|
init_filter();
|
|
}
|
|
// clears need for reset
|
|
timeFilterManager_.initialize();
|
|
ghostManager_.initialize();
|
|
|
|
if (!initialized_) {
|
|
// initialize sources based on initial FE temperature
|
|
double dt = lammpsInterface_->dt();
|
|
prescribedDataMgr_->set_sources(time()+0.5*dt,sources_);
|
|
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
|
|
atomicRegulator_->compute_boundary_flux(fields_);
|
|
compute_atomic_sources(fieldMask_,fields_,atomicSources_);
|
|
|
|
// read in field data if necessary
|
|
if (useRestart_) {
|
|
RESTART_LIST data;
|
|
read_restart_data(restartFileName_,data);
|
|
useRestart_ = false;
|
|
}
|
|
|
|
// set consistent initial conditions, if requested
|
|
if (!timeFilterManager_.filter_dynamics()) {
|
|
if (consistentInitialization_) {
|
|
|
|
DENS_MAT & temperature(fields_[TEMPERATURE].set_quantity());
|
|
DENS_MAN * nodalAtomicTemperature(interscaleManager_.dense_matrix("NodalAtomicTemperature"));
|
|
const DENS_MAT & atomicTemperature(nodalAtomicTemperature->quantity());
|
|
const INT_ARRAY & nodeType(nodalGeometryType_->quantity());
|
|
for (int i = 0; i<nNodes_; ++i) {
|
|
|
|
if (nodeType(i,0)==MD_ONLY)
|
|
temperature(i,0) = atomicTemperature(i,0);
|
|
}
|
|
}
|
|
}
|
|
initialized_ = true;
|
|
}
|
|
|
|
// 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);
|
|
}
|
|
|
|
//--------------------------------------------------------
|
|
// construct_methods
|
|
// have managers instantiate requested algorithms
|
|
// and methods
|
|
//--------------------------------------------------------
|
|
void ATC_CouplingEnergy::construct_methods()
|
|
{
|
|
ATC_Coupling::construct_methods();
|
|
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->construct_methods();
|
|
}
|
|
atomicRegulator_->construct_methods();
|
|
}
|
|
|
|
//--------------------------------------------------------
|
|
// construct_transfers
|
|
// constructs needed transfer operators
|
|
//--------------------------------------------------------
|
|
void ATC_CouplingEnergy::construct_transfers()
|
|
{
|
|
ATC_Coupling::construct_transfers();
|
|
|
|
// always need kinetic energy
|
|
AtomicEnergyForTemperature * atomicTwiceKineticEnergy = new TwiceKineticEnergy(this);
|
|
AtomicEnergyForTemperature * atomEnergyForTemperature = NULL;
|
|
|
|
// Appropriate per-atom quantity based on desired temperature definition
|
|
if (temperatureDef_==KINETIC) {
|
|
atomEnergyForTemperature = atomicTwiceKineticEnergy;
|
|
}
|
|
else if (temperatureDef_==TOTAL) {
|
|
if (timeIntegrators_[TEMPERATURE]->time_integration_type() != TimeIntegrator::FRACTIONAL_STEP)
|
|
throw ATC_Error("ATC_CouplingEnergy:construct_transfers() on the fractional step time integrator can be used with non-kinetic defitions of the temperature");
|
|
|
|
// kinetic energy
|
|
interscaleManager_.add_per_atom_quantity(atomicTwiceKineticEnergy,
|
|
"AtomicTwiceKineticEnergy");
|
|
|
|
// atomic potential energy
|
|
ComputedAtomQuantity * atomicPotentialEnergy = new ComputedAtomQuantity(this,
|
|
lammpsInterface_->compute_pe_name(),
|
|
1./(lammpsInterface_->mvv2e()));
|
|
interscaleManager_.add_per_atom_quantity(atomicPotentialEnergy,
|
|
"AtomicPotentialEnergy");
|
|
|
|
// reference potential energy
|
|
AtcAtomQuantity<double> * atomicReferencePotential;
|
|
if (!initialized_) {
|
|
atomicReferencePotential = new AtcAtomQuantity<double>(this);
|
|
interscaleManager_.add_per_atom_quantity(atomicReferencePotential,
|
|
"AtomicReferencePotential");
|
|
atomicReferencePotential->set_memory_type(PERSISTENT);
|
|
}
|
|
else {
|
|
atomicReferencePotential = static_cast<AtcAtomQuantity<double> * >(interscaleManager_.per_atom_quantity("AtomicReferencePotential"));
|
|
}
|
|
nodalRefPotentialEnergy_ = new AtfShapeFunctionRestriction(this,
|
|
atomicReferencePotential,
|
|
shpFcn_);
|
|
interscaleManager_.add_dense_matrix(nodalRefPotentialEnergy_,
|
|
"NodalAtomicReferencePotential");
|
|
|
|
// fluctuating potential energy
|
|
AtomicEnergyForTemperature * atomicFluctuatingPotentialEnergy =
|
|
new FluctuatingPotentialEnergy(this,
|
|
atomicPotentialEnergy,
|
|
atomicReferencePotential);
|
|
interscaleManager_.add_per_atom_quantity(atomicFluctuatingPotentialEnergy,
|
|
"AtomicFluctuatingPotentialEnergy");
|
|
|
|
// atomic total energy
|
|
atomEnergyForTemperature = new MixedKePeEnergy(this,1,1);
|
|
|
|
// kinetic temperature measure for post-processing
|
|
// nodal restriction of the atomic energy quantity for the temperature definition
|
|
AtfShapeFunctionRestriction * nodalAtomicTwiceKineticEnergy = new AtfShapeFunctionRestriction(this,
|
|
atomicTwiceKineticEnergy,
|
|
shpFcn_);
|
|
interscaleManager_.add_dense_matrix(nodalAtomicTwiceKineticEnergy,
|
|
"NodalAtomicTwiceKineticEnergy");
|
|
nodalAtomicKineticTemperature_ = new AtfShapeFunctionMdProjection(this,
|
|
nodalAtomicTwiceKineticEnergy,
|
|
TEMPERATURE);
|
|
interscaleManager_.add_dense_matrix(nodalAtomicKineticTemperature_,
|
|
"NodalAtomicKineticTemperature");
|
|
|
|
// potential temperature measure for post-processing (must multiply by 2 for configurational temperature
|
|
// nodal restriction of the atomic energy quantity for the temperature definition
|
|
AtfShapeFunctionRestriction * nodalAtomicFluctuatingPotentialEnergy = new AtfShapeFunctionRestriction(this,
|
|
atomicFluctuatingPotentialEnergy,
|
|
shpFcn_);
|
|
interscaleManager_.add_dense_matrix(nodalAtomicFluctuatingPotentialEnergy,
|
|
"NodalAtomicFluctuatingPotentialEnergy");
|
|
nodalAtomicConfigurationalTemperature_ = new AtfShapeFunctionMdProjection(this,
|
|
nodalAtomicFluctuatingPotentialEnergy,
|
|
TEMPERATURE);
|
|
interscaleManager_.add_dense_matrix(nodalAtomicConfigurationalTemperature_,
|
|
"NodalAtomicConfigurationalTemperature");
|
|
}
|
|
|
|
// register the per-atom quantity for the temperature definition
|
|
interscaleManager_.add_per_atom_quantity(atomEnergyForTemperature,
|
|
"AtomicEnergyForTemperature");
|
|
|
|
// nodal restriction of the atomic energy quantity for the temperature definition
|
|
AtfShapeFunctionRestriction * nodalAtomicEnergy = new AtfShapeFunctionRestriction(this,
|
|
atomEnergyForTemperature,
|
|
shpFcn_);
|
|
interscaleManager_.add_dense_matrix(nodalAtomicEnergy,
|
|
"NodalAtomicEnergy");
|
|
|
|
// nodal atomic temperature field
|
|
|
|
AtfShapeFunctionMdProjection * nodalAtomicTemperature = new AtfShapeFunctionMdProjection(this,
|
|
nodalAtomicEnergy,
|
|
TEMPERATURE);
|
|
interscaleManager_.add_dense_matrix(nodalAtomicTemperature,
|
|
"NodalAtomicTemperature");
|
|
|
|
if (!useFeMdMassMatrix_) {
|
|
// classical thermodynamic heat capacity of the atoms
|
|
HeatCapacity * heatCapacity = new HeatCapacity(this);
|
|
interscaleManager_.add_per_atom_quantity(heatCapacity,
|
|
"AtomicHeatCapacity");
|
|
|
|
// atomic thermal mass matrix
|
|
nodalAtomicHeatCapacity_ = new AtfShapeFunctionRestriction(this,
|
|
heatCapacity,
|
|
shpFcn_);
|
|
interscaleManager_.add_dense_matrix(nodalAtomicHeatCapacity_,
|
|
"NodalAtomicHeatCapacity");
|
|
}
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->construct_transfers();
|
|
}
|
|
atomicRegulator_->construct_transfers();
|
|
}
|
|
|
|
//---------------------------------------------------------
|
|
// init_filter
|
|
// sets up the time filtering operations in all objects
|
|
//---------------------------------------------------------
|
|
void ATC_CouplingEnergy::init_filter()
|
|
{
|
|
|
|
TimeIntegrator::TimeIntegrationType timeIntegrationType = timeIntegrators_[TEMPERATURE]->time_integration_type();
|
|
|
|
|
|
|
|
|
|
if (timeFilterManager_.end_equilibrate()) {
|
|
if (timeIntegrationType==TimeIntegrator::GEAR) {
|
|
if (equilibriumStart_) {
|
|
|
|
|
|
|
|
if (atomicRegulator_->regulator_target()==AtomicRegulator::DYNAMICS) { // based on FE equation
|
|
DENS_MAT vdotflamMat(-2.*(nodalAtomicFields_[TEMPERATURE].quantity())); // note 2 is for 1/2 vdotflam addition
|
|
atomicRegulator_->reset_lambda_contribution(vdotflamMat);
|
|
}
|
|
else { // based on MD temperature equation
|
|
DENS_MAT vdotflamMat(-1.*(nodalAtomicFields_[TEMPERATURE].quantity()));
|
|
atomicRegulator_->reset_lambda_contribution(vdotflamMat);
|
|
}
|
|
}
|
|
}
|
|
else if (timeIntegrationType==TimeIntegrator::FRACTIONAL_STEP) {
|
|
if (equilibriumStart_) {
|
|
DENS_MAT powerMat(-1.*(nodalAtomicFields_[TEMPERATURE].quantity()));
|
|
atomicRegulator_->reset_lambda_contribution(powerMat);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
//---------------------------------------------------------
|
|
// compute_md_mass_matrix
|
|
// compute the mass matrix arising from only atomistic
|
|
// quadrature and contributions as a summation
|
|
//---------------------------------------------------------
|
|
void ATC_CouplingEnergy::compute_md_mass_matrix(FieldName thisField,
|
|
DIAG_MAT & massMat)
|
|
{
|
|
|
|
if (thisField == TEMPERATURE)
|
|
massMat.reset(nodalAtomicHeatCapacity_->quantity());
|
|
}
|
|
|
|
//--------------------------------------------------------
|
|
// finish
|
|
// final clean up after a run
|
|
//--------------------------------------------------------
|
|
void ATC_CouplingEnergy::finish()
|
|
{
|
|
// base class
|
|
ATC_Coupling::finish();
|
|
|
|
atomicRegulator_->finish();
|
|
}
|
|
|
|
//--------------------------------------------------------
|
|
// modify
|
|
// parses inputs and modifies state of the filter
|
|
//--------------------------------------------------------
|
|
bool ATC_CouplingEnergy::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
|
|
|
|
// pass-through to thermostat
|
|
if (strcmp(arg[argIndx],"control")==0) {
|
|
argIndx++;
|
|
foundMatch = atomicRegulator_->modify(narg-argIndx,&arg[argIndx]);
|
|
}
|
|
|
|
// pass-through to timeIntegrator class
|
|
else if (strcmp(arg[argIndx],"time_integration")==0) {
|
|
argIndx++;
|
|
foundMatch = timeIntegrators_[TEMPERATURE]->modify(narg-argIndx,&arg[argIndx]);
|
|
}
|
|
|
|
// switch for the kind of temperature being used
|
|
/*! \page man_temperature_definition fix_modify AtC temperature_definition
|
|
\section syntax
|
|
fix_modify AtC temperature_definition <kinetic|total>
|
|
|
|
\section examples
|
|
<TT> fix_modify atc temperature_definition kinetic </TT> \n
|
|
|
|
\section description
|
|
Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.
|
|
|
|
\section restrictions
|
|
This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.
|
|
|
|
\section default
|
|
kinetic
|
|
*/
|
|
else if (strcmp(arg[argIndx],"temperature_definition")==0) {
|
|
argIndx++;
|
|
string_to_temperature_def(arg[argIndx],temperatureDef_);
|
|
if (temperatureDef_ == TOTAL) {
|
|
setRefPE_ = true;
|
|
}
|
|
foundMatch = true;
|
|
needReset_ = true;
|
|
}
|
|
|
|
// no match, call base class parser
|
|
if (!foundMatch) {
|
|
foundMatch = ATC_Coupling::modify(narg, arg);
|
|
}
|
|
|
|
return foundMatch;
|
|
|
|
}
|
|
|
|
//--------------------------------------------------
|
|
// pack_fields
|
|
// bundle all allocated field matrices into a list
|
|
// for output needs
|
|
//--------------------------------------------------
|
|
void ATC_CouplingEnergy::pack_thermal_fields(RESTART_LIST & data)
|
|
{
|
|
atomicRegulator_->pack_fields(data);
|
|
}
|
|
|
|
//--------------------------------------------------
|
|
// write_restart_file
|
|
// bundle matrices that need to be saved and call
|
|
// fe_engine to write the file
|
|
//--------------------------------------------------
|
|
void ATC_CouplingEnergy::write_restart_data(string fileName, RESTART_LIST & data)
|
|
{
|
|
pack_thermal_fields(data);
|
|
ATC_Method::write_restart_data(fileName,data);
|
|
}
|
|
|
|
//--------------------------------------------------
|
|
// read_restart_file
|
|
// bundle matrices that need to be saved and call
|
|
// fe_engine to write the file
|
|
//--------------------------------------------------
|
|
void ATC_CouplingEnergy::read_restart_data(string fileName, RESTART_LIST & data)
|
|
{
|
|
pack_thermal_fields(data);
|
|
ATC_Method::read_restart_data(fileName,data);
|
|
}
|
|
|
|
//--------------------------------------------------
|
|
void ATC_CouplingEnergy::reset_nlocal()
|
|
{
|
|
ATC_Coupling::reset_nlocal();
|
|
atomicRegulator_->reset_nlocal();
|
|
}
|
|
|
|
//--------------------------------------------------
|
|
// reset_atom_materials
|
|
// update the atom materials map
|
|
//--------------------------------------------------
|
|
void ATC_CouplingEnergy::reset_atom_materials()
|
|
{
|
|
ATC_Coupling::reset_atom_materials();
|
|
atomicRegulator_->reset_atom_materials(elementToMaterialMap_,
|
|
atomElement_);
|
|
}
|
|
|
|
#ifdef OBSOLETE
|
|
//--------------------------------------------------------
|
|
// mid_init_integrate
|
|
// time integration between the velocity update and
|
|
// the position lammps update of Verlet step 1
|
|
//--------------------------------------------------------
|
|
void ATC_CouplingEnergy::mid_init_integrate()
|
|
{
|
|
// CONTINUOUS VELOCITY UPDATE
|
|
|
|
ATC_Coupling::mid_init_integrate();
|
|
double dt = lammpsInterface_->dt();
|
|
|
|
// Compute nodal velocity at n+1/2
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->mid_initial_integrate1(dt);
|
|
}
|
|
|
|
atomicRegulator_->apply_mid_predictor(dt,lammpsInterface_->ntimestep());
|
|
|
|
extrinsicModelManager_.mid_init_integrate();
|
|
}
|
|
|
|
//--------------------------------------------------------
|
|
// post_init_integrate
|
|
// time integration after the lammps atomic updates of
|
|
// Verlet step 1
|
|
//--------------------------------------------------------
|
|
void ATC_CouplingEnergy::post_init_integrate()
|
|
{
|
|
double dt = lammpsInterface_->dt();
|
|
|
|
// Compute nodal velocity at n+1
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->post_initial_integrate1(dt);
|
|
}
|
|
|
|
// Update kinetostat quantities if displacement is being regulated
|
|
atomicRegulator_->apply_post_predictor(dt,lammpsInterface_->ntimestep());
|
|
|
|
// Update extrisic model
|
|
extrinsicModelManager_.post_init_integrate();
|
|
|
|
// fixed values, non-group bcs handled through FE
|
|
set_fixed_nodes();
|
|
|
|
update_time(0.5);
|
|
|
|
ATC_Coupling::post_init_integrate();
|
|
}
|
|
#endif
|
|
//--------------------------------------------------------
|
|
// post_final_integrate
|
|
// integration after the second stage lammps atomic
|
|
// update of Verlet step 2
|
|
//--------------------------------------------------------
|
|
void ATC_CouplingEnergy::post_final_integrate()
|
|
{
|
|
double dt = lammpsInterface_->dt();
|
|
|
|
// update changes in atomic energy or from atomic work, if needed
|
|
// this is here to simplify computing changes in total atomic energy
|
|
// even though all the data needed is available by pre_final_integrate
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->pre_final_integrate1(dt);
|
|
}
|
|
|
|
// Set prescribed sources for current time
|
|
prescribedDataMgr_->set_sources(time()+0.5*dt,sources_);
|
|
|
|
// predictor step in extrinsic model
|
|
extrinsicModelManager_.pre_final_integrate();
|
|
|
|
// predict thermostat contributions
|
|
// compute sources based on predicted FE temperature
|
|
|
|
if (timeIntegrators_[TEMPERATURE]->has_final_predictor()) {
|
|
// set state-based sources
|
|
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
|
|
atomicRegulator_->compute_boundary_flux(fields_);
|
|
compute_atomic_sources(temperatureMask_,fields_,atomicSources_);
|
|
}
|
|
|
|
// Compute thermostat forces
|
|
atomicRegulator_->apply_pre_corrector(dt,lammpsInterface_->ntimestep());
|
|
|
|
// Determine FE contributions to d theta/dt
|
|
// Compute atom-integrated rhs
|
|
// parallel communication happens within FE_Engine
|
|
|
|
|
|
|
|
// Determine FE contributions to dT/dt-----------------------
|
|
compute_rhs_vector(temperatureMask_,fields_,rhs_,FE_DOMAIN);
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->add_to_rhs();
|
|
}
|
|
// For flux matching, add appropriate fraction of "drag" power
|
|
|
|
atomicRegulator_->add_to_rhs(rhs_);
|
|
|
|
// final phase predictor step
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->post_final_integrate1(dt);
|
|
}
|
|
|
|
// fix nodes, non-group bcs applied through FE
|
|
set_fixed_nodes();
|
|
|
|
// corrector step extrinsic model
|
|
extrinsicModelManager_.post_final_integrate();
|
|
|
|
// correct thermostat and finish
|
|
if (timeIntegrators_[TEMPERATURE]->has_final_corrector()) {
|
|
// set state-based sources
|
|
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
|
|
atomicRegulator_->compute_boundary_flux(fields_);
|
|
compute_atomic_sources(temperatureMask_,fields_,atomicSources_);
|
|
}
|
|
|
|
// finish FE temperature update
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->post_final_integrate2(dt);
|
|
}
|
|
|
|
// apply corrector phase of thermostat
|
|
atomicRegulator_->apply_post_corrector(dt,lammpsInterface_->ntimestep());
|
|
|
|
// finalalize time filtering
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->post_final_integrate3(dt);
|
|
}
|
|
|
|
// Fix nodes, non-group bcs applied through FE
|
|
set_fixed_nodes();
|
|
|
|
update_time(0.5);
|
|
|
|
output();
|
|
ATC_Coupling::post_final_integrate(); // adds next step to computes
|
|
}
|
|
|
|
//--------------------------------------------------------------------
|
|
// compute_vector
|
|
//--------------------------------------------------------------------
|
|
// this is for direct output to lammps thermo
|
|
double ATC_CouplingEnergy::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);
|
|
FIELD_MATS energy;
|
|
mask(0) = TEMPERATURE;
|
|
|
|
feEngine_->compute_energy(mask,
|
|
fields_,
|
|
physicsModel_,
|
|
elementToMaterialMap_,
|
|
energy,
|
|
&(elementMask_->quantity()));
|
|
|
|
double phononEnergy = mvv2e * energy[TEMPERATURE].col_sum();
|
|
return phononEnergy;
|
|
}
|
|
else if (n == 1) {
|
|
double aveT = (fields_[TEMPERATURE].quantity()).col_sum()/nNodes_;
|
|
return aveT;
|
|
}
|
|
else if (n > 1) {
|
|
double extrinsicValue = extrinsicModelManager_.compute_vector(n);
|
|
return extrinsicValue;
|
|
}
|
|
|
|
return 0.;
|
|
|
|
}
|
|
|
|
//--------------------------------------------------------------------
|
|
// output
|
|
//--------------------------------------------------------------------
|
|
void ATC_CouplingEnergy::output()
|
|
{
|
|
if (output_now()) {
|
|
feEngine_->departition_mesh();
|
|
|
|
// avoid possible mpi calls
|
|
if (nodalAtomicKineticTemperature_)
|
|
_keTemp_ = nodalAtomicKineticTemperature_->quantity();
|
|
if (nodalAtomicConfigurationalTemperature_)
|
|
_peTemp_ = nodalAtomicConfigurationalTemperature_->quantity();
|
|
|
|
OUTPUT_LIST outputData;
|
|
|
|
// base class output
|
|
ATC_Method::output();
|
|
|
|
// push atc fields time integrator modifies into output arrays
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->post_process();
|
|
}
|
|
|
|
// auxilliary data
|
|
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
|
|
(_tiIt_->second)->output(outputData);
|
|
}
|
|
atomicRegulator_->output(outputData);
|
|
extrinsicModelManager_.output(outputData);
|
|
|
|
DENS_MAT & temperature(nodalAtomicFields_[TEMPERATURE].set_quantity());
|
|
DENS_MAT & dotTemperature(dot_fields_[TEMPERATURE].set_quantity());
|
|
DENS_MAT & ddotTemperature(ddot_fields_[TEMPERATURE].set_quantity());
|
|
DENS_MAT & rocTemperature(nodalAtomicFieldsRoc_[TEMPERATURE].set_quantity());
|
|
DENS_MAT & fePower(rhs_[TEMPERATURE].set_quantity());
|
|
if (lammpsInterface_->rank_zero()) {
|
|
// global data
|
|
double T_mean = (fields_[TEMPERATURE].quantity()).col_sum(0)/nNodes_;
|
|
feEngine_->add_global("temperature_mean", T_mean);
|
|
double T_stddev = (fields_[TEMPERATURE].quantity()).col_stdev(0);
|
|
feEngine_->add_global("temperature_std_dev", T_stddev);
|
|
double Ta_mean = (nodalAtomicFields_[TEMPERATURE].quantity()).col_sum(0)/nNodes_;
|
|
feEngine_->add_global("atomic_temperature_mean", Ta_mean);
|
|
double Ta_stddev = (nodalAtomicFields_[TEMPERATURE].quantity()).col_stdev(0);
|
|
feEngine_->add_global("atomic_temperature_std_dev", Ta_stddev);
|
|
|
|
// different temperature measures, if appropriate
|
|
if (nodalAtomicKineticTemperature_)
|
|
outputData["kinetic_temperature"] = & _keTemp_;
|
|
|
|
if (nodalAtomicConfigurationalTemperature_) {
|
|
_peTemp_ *= 2; // account for full temperature
|
|
outputData["configurational_temperature"] = & _peTemp_;
|
|
}
|
|
|
|
// mesh data
|
|
outputData["NodalAtomicTemperature"] = &temperature;
|
|
outputData["dot_temperature"] = &dotTemperature;
|
|
outputData["ddot_temperature"] = &ddotTemperature;
|
|
outputData["NodalAtomicPower"] = &rocTemperature;
|
|
outputData["fePower"] = &fePower;
|
|
|
|
// write data
|
|
feEngine_->write_data(output_index(), fields_, & outputData);
|
|
}
|
|
feEngine_->partition_mesh();
|
|
}
|
|
}
|
|
};
|