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// ATC transfer headers
#include "SpeciesTimeIntegrator.h"
#include "TransferOperator.h"
#include "ATC_CouplingMass.h"
#include "TimeFilter.h"
#include "LammpsInterface.h"
#include "ATC_Error.h"
#include "PerAtomQuantityLibrary.h"
#include "AtomToMoleculeTransfer.h"
#include "MoleculeSet.h"
using std::pair;
using std::map;
using std::string;
namespace ATC {
//--------------------------------------------------------
//--------------------------------------------------------
// Class SpeciesTimeIntegrator
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
// Grab data from ATC
//--------------------------------------------------------
SpeciesTimeIntegrator::SpeciesTimeIntegrator(ATC_CouplingMass * atc,
TimeIntegrationType timeIntegrationType) :
TimeIntegrator(atc, timeIntegrationType),
moleculeIds_(atc->molecule_ids())
{
// do nothing
}
//--------------------------------------------------------
// modify
// parses inputs and modifies state of the filter
//--------------------------------------------------------
bool SpeciesTimeIntegrator::modify(int /* narg */, char ** /* arg */)
{
bool match = false;
// no parsing needed
return match;
}
//--------------------------------------------------------
// construct_methods
// creates algorithm objects
//--------------------------------------------------------
void SpeciesTimeIntegrator::construct_methods()
{
if (atc_->reset_methods()) {
if (timeIntegrationMethod_) delete timeIntegrationMethod_;
if (timeFilterManager_->need_reset()) {
switch (timeIntegrationType_) {
case FRACTIONAL_STEP: {
timeFilter_ = timeFilterManager_->construct(TimeFilterManager::EXPLICIT_IMPLICIT);
atc_->set_mass_mat_time_filter(SPECIES_CONCENTRATION,TimeFilterManager::EXPLICIT);
break;
}
default:
throw ATC_Error("Unknown time integration type in SpeciesTimeIntegrator::Initialize()");
}
}
if (timeFilterManager_->filter_dynamics()) {
switch (timeIntegrationType_) {
case FRACTIONAL_STEP: {
timeIntegrationMethod_ = new SpeciesTimeIntegratorFractionalStepFiltered(this,
moleculeIds_);
}
default:
throw ATC_Error("Unknown time integration type in SpeciesTimeIntegrator::Initialize()");
}
}
else {
timeIntegrationMethod_ = new SpeciesTimeIntegratorFractionalStep(this,
moleculeIds_);
}
}
}
//--------------------------------------------------------
// pack_fields
// add persistent variables to data list
//--------------------------------------------------------
void SpeciesTimeIntegrator::pack_fields(RESTART_LIST & data)
{
TimeIntegrator::pack_fields(data);
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class SpeciesIntegrationMethod
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
// Grab data from ATC
//--------------------------------------------------------
SpeciesIntegrationMethod::SpeciesIntegrationMethod(SpeciesTimeIntegrator * speciesTimeIntegrator,
const map<string,pair<MolSize,int> > & moleculeIds) :
TimeIntegrationMethod(speciesTimeIntegrator),
timeFilter_(speciesTimeIntegrator->time_filter()),
massDensity_(atc_->field(MASS_DENSITY)),
nodalAtomicMassDensityOut_(atc_->nodal_atomic_field(MASS_DENSITY)),
nodalAtomicMassDensity_(nullptr),
speciesConcentration_(atc_->field(SPECIES_CONCENTRATION)),
nodalAtomicSpeciesConcentration_(nullptr),
nodalAtomicSpeciesConcentrationFiltered_(speciesTimeIntegrator->nodal_atomic_species_concentration_filtered()),
moleculeIds_(moleculeIds)
{
// do nothing
}
//--------------------------------------------------------
// construct_transfers
// sets up all the necessary transfer operators
//--------------------------------------------------------
void SpeciesIntegrationMethod::construct_transfers()
{
InterscaleManager & interscaleManager = atc_->interscale_manager();
// get existing data
nodalAtomicMassDensity_ = interscaleManager.dense_matrix(field_to_intrinsic_name(MASS_DENSITY));
if (atc_->has_tracked_species())
nodalAtomicSpeciesConcentration_ = interscaleManager.dense_matrix(field_to_intrinsic_name(SPECIES_CONCENTRATION));
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class SpeciesTimeIntegratorFractionalStep
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
SpeciesTimeIntegratorFractionalStep::SpeciesTimeIntegratorFractionalStep(SpeciesTimeIntegrator * speciesTimeIntegrator,
const map<string,pair<MolSize,int> > & moleculeIds) :
SpeciesIntegrationMethod(speciesTimeIntegrator,moleculeIds)
{
// do nothing
}
//--------------------------------------------------------
// initialize
// initialize all data
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStep::initialize()
{
SpeciesIntegrationMethod::initialize();
TimeFilterManager * timeFilterManager = atc_->time_filter_manager();
if (timeFilterManager->need_reset()) {
timeFilter_->initialize();
}
if (!timeFilterManager->end_equilibrate()) {
nodalAtomicSpeciesConcentrationFiltered_ = nodalAtomicSpeciesConcentration_->quantity();
}
pre_final_integrate1(0.);
}
//--------------------------------------------------------
// pre_initial_integrate1
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStep::pre_initial_integrate1(double dt)
{
const DENS_MAT & my(nodalAtomicSpeciesConcentration_->quantity());
// updated filtered energy using explicit-implicit scheme
timeFilter_->apply_pre_step1(nodalAtomicSpeciesConcentrationFiltered_.set_quantity(),
my,dt);
}
//--------------------------------------------------------
// pre_final_integrate1
// first time integration computations
// before FractionalStep step 2
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStep::pre_final_integrate1(double /* dt */)
{
// Compute MD contribution to FEM equation
massDensity_ = nodalAtomicMassDensity_->quantity();
speciesConcentration_ = nodalAtomicSpeciesConcentration_->quantity();
atc_->set_fixed_nodes();
}
//--------------------------------------------------------
// post_final_integrate2
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStep::post_final_integrate2(double dt)
{
timeFilter_->apply_post_step1(
nodalAtomicSpeciesConcentrationFiltered_.set_quantity(),
nodalAtomicSpeciesConcentration_->quantity(),dt);
speciesConcentration_ = nodalAtomicSpeciesConcentrationFiltered_.quantity();
}
//--------------------------------------------------------
// post_process
// post processing of variables before output
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStep::post_process()
{
map<string,pair<MolSize,int> >::const_iterator molecule;
for (molecule = moleculeIds_.begin(); molecule != moleculeIds_.end(); molecule++) {
DENS_MAN & nodalMoleculeMassDensityOut(atc_->tagged_dens_man(molecule->first));
DENS_MAN * nodalMoleculeMassDensity((atc_->interscale_manager()).dense_matrix("NodalMoleculeMassDensity"+molecule->first));
nodalMoleculeMassDensityOut = nodalMoleculeMassDensity->quantity();
}
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class SpeciesTimeIntegratorFractionalStepFiltered
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
// Grab data from ATC
//--------------------------------------------------------
SpeciesTimeIntegratorFractionalStepFiltered::SpeciesTimeIntegratorFractionalStepFiltered(
SpeciesTimeIntegrator * speciesTimeIntegrator,
const map<string,pair<MolSize,int> > & moleculeIds) :
SpeciesTimeIntegratorFractionalStep(speciesTimeIntegrator,moleculeIds)
{
throw ATC_Error("SpeciesTimeIntegratorFractionalStepFiltered work in progress");
// do nothing
}
//--------------------------------------------------------
// pre_initial_integrate1
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStepFiltered::pre_final_integrate1(double /* dt */)
{
}
};
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