Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F107268873
ATC_CouplingMass.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sun, Apr 6, 12:13
Size
9 KB
Mime Type
text/x-c
Expires
Tue, Apr 8, 12:13 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
25385669
Attached To
rLAMMPS lammps
ATC_CouplingMass.cpp
View Options
// ATC_Transfer headers
#include "ATC_CouplingMass.h"
#include "ATC_Error.h"
#include "FE_Engine.h"
#include "SpeciesTimeIntegrator.h"
#include "PrescribedDataManager.h"
#include "ExtrinsicModelElectrostatic.h"
#include "PoissonSolver.h"
#include "ChargeRegulator.h"
#include "ConcentrationRegulator.h"
#include "PerAtomQuantityLibrary.h"
#include "TransferOperator.h"
#include "AtomToMoleculeTransfer.h"
#include "MoleculeSet.h"
#include "FieldManager.h"
// Other Headers
#include <vector>
#include <set>
#include <utility>
using ATC_Utility::to_string;
using std::map;
using std::string;
using std::pair;
namespace ATC {
//--------------------------------------------------------
//--------------------------------------------------------
// Class ATC_CouplingMass
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
ATC_CouplingMass::ATC_CouplingMass(string groupName,
double **& perAtomArray,
LAMMPS_NS::Fix * thisFix,
string matParamFile,
ExtrinsicModelType extrinsicModel)
: ATC_Coupling(groupName,perAtomArray,thisFix),
resetNlocal_(false)
{
// Allocate PhysicsModel
create_physics_model(SPECIES, matParamFile);
// create extrinsic physics model
if (extrinsicModel != NO_MODEL) {
extrinsicModelManager_.create_model(extrinsicModel,matParamFile);
}
// Defaults
set_time();
bndyIntType_ = NO_QUADRATURE;
// set up field data based on physicsModel
physicsModel_->num_fields(fieldSizes_,fieldMask_);
// regulator
atomicRegulator_ = new ConcentrationRegulator(this);
// set up physics specific time integrator
//WIP_JAT should be species concentration
timeIntegrators_[MASS_DENSITY] = new SpeciesTimeIntegrator(this,TimeIntegrator::FRACTIONAL_STEP);
// output variable vector info:
// output[1] = system mass density
vectorFlag_ = 1;
sizeVector_ = 0;
scalarVectorFreq_ = 1;
extVector_ = 1;
if (extrinsicModel != NO_MODEL)
sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);
sizeVector_ += atomicRegulator_->size_vector(sizeVector_);
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
ATC_CouplingMass::~ATC_CouplingMass()
{
interscaleManager_.clear();
}
//--------------------------------------------------------
// modify
// parses inputs and modifies state
//--------------------------------------------------------
bool ATC_CouplingMass::modify(int narg, char **arg)
{
bool match = false;
// check to see if it is a transfer class command
// check derived class before base class
int argIndex = 0;
// pass-through to concentration regulator
if (strcmp(arg[argIndex],"control")==0) {
argIndex++;
if (strcmp(arg[argIndex],"concentration")==0) {
argIndex++;
match = atomicRegulator_->modify(narg-argIndex,&arg[argIndex]);
}
}
// no match, call base class parser
if (!match) {
match = ATC_Coupling::modify(narg, arg);
}
return match;
}
//--------------------------------------------------------
// initialize
// sets up all the necessary data
//--------------------------------------------------------
void ATC_CouplingMass::initialize()
{
fieldSizes_[SPECIES_CONCENTRATION] = ntracked();
// Base class initalizations
ATC_Coupling::initialize();
// reset integration field mask
intrinsicMask_.reset(NUM_FIELDS,NUM_FLUX);
intrinsicMask_ = false;
}
void ATC_CouplingMass::construct_transfers()
{
ATC_Coupling::construct_transfers();
FieldManager fmgr(this);
atomicFields_[MASS_DENSITY] = fmgr.nodal_atomic_field(MASS_DENSITY, field_to_intrinsic_name(MASS_DENSITY));
if (has_tracked_species()) {
atomicFields_[SPECIES_CONCENTRATION] = fmgr.nodal_atomic_field(SPECIES_CONCENTRATION, field_to_intrinsic_name(SPECIES_CONCENTRATION));
//if (atomicRegulator_->needs_temperature()) {
atomicFields_[TEMPERATURE] = fmgr.nodal_atomic_field(KINETIC_TEMPERATURE, field_to_intrinsic_name(TEMPERATURE));
//atomicFields_[TEMPERATURE] = fmgr.nodal_atomic_field(TEMPERATURE, field_to_intrinsic_name(TEMPERATURE));
field(TEMPERATURE) = atomicFields_[TEMPERATURE]->quantity();
//}
}
else {
throw ATC_Error("ATC_CouplingMass: no tracked species");
}
//==========================================================================
// add molecule mass density transfer operators
//==========================================================================
map<string,pair<MolSize,int> >::const_iterator molecule;
FundamentalAtomQuantity * mass = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS,
PROC_GHOST);
for (molecule = moleculeIds_.begin(); molecule != moleculeIds_.end(); molecule++) {
const string moleculeName = molecule->first;
SmallMoleculeSet * smallMoleculeSet = interscaleManager_.small_molecule_set(moleculeName);
SPAR_MAN * shpFcnMol = interscaleManager_.sparse_matrix("ShapeFunction"+moleculeName);
AtomToSmallMoleculeTransfer<double> * moleculeMass =
new AtomToSmallMoleculeTransfer<double>(this,mass,smallMoleculeSet);
interscaleManager_.add_dense_matrix(moleculeMass,"MoleculeMass"+moleculeName);
MotfShapeFunctionRestriction * nodalAtomicMoleculeMass =
new MotfShapeFunctionRestriction(moleculeMass,shpFcnMol);
interscaleManager_.add_dense_matrix(nodalAtomicMoleculeMass,"NodalMoleculeMass"+moleculeName);
AtfShapeFunctionMdProjection * nodalAtomicMoleculeMassDensity =
new AtfShapeFunctionMdProjection(this,nodalAtomicMoleculeMass,MASS_DENSITY);
interscaleManager_.add_dense_matrix(nodalAtomicMoleculeMassDensity,"NodalMoleculeMassDensity"+moleculeName);
}
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->construct_transfers();
}
}
void ATC_CouplingMass::init_filter()
{
ATC_Coupling::init_filter();
}
//WIP_JAT consolidate to coupling when we handle the temperature correctly
//--------------------------------------------------------
// pre_exchange
// prior to exchange of atoms
//--------------------------------------------------------
void ATC_CouplingMass::pre_exchange()
{
ATC_Coupling::pre_exchange();
//if (atomicRegulator_->needs_temperature()) {
field(TEMPERATURE) = atomicFields_[TEMPERATURE]->quantity();
///}
atomicRegulator_->pre_exchange();
if (resetNlocal_) {
this->reset_nlocal();
resetNlocal_ = false;
}
}
//--------------------------------------------------------
// output
// does post-processing steps and outputs data
//--------------------------------------------------------
void ATC_CouplingMass::output()
{
if (output_now()) {
feEngine_->departition_mesh();
OUTPUT_LIST outputData;
// base class output
ATC_Coupling::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);
}
extrinsicModelManager_.output(outputData);
atomicRegulator_->output(outputData);
FIELD_POINTERS::iterator itr;
for (itr=atomicFields_.begin(); itr!=atomicFields_.end();itr++) {
FieldName name = itr->first;
const DENS_MAT & data = (itr->second)->quantity();
outputData[field_to_intrinsic_name(name)] = & data;
}
// compute partial forces
int * type =lammpsInterface_->atom_type();
double ** f =lammpsInterface_->fatom();
for (unsigned int j = 0; j < typeList_.size(); j++) {
string speciesName = typeNames_[j];
int sType = typeList_[j];
double localF[3] = {0,0,0}, F[3] = {0,0,0};
for (int i = 0; i < nLocal_; i++) {
int a = internalToAtom_(i);
if (sType == type[a]) {
double * fa = f[a];
localF[0] += fa[0];
localF[1] += fa[1];
localF[2] += fa[2];
}
}
lammpsInterface_->allsum(localF,F,3);
if (lammpsInterface_->rank_zero()) {
for (int i = 0; i < 3; ++i) {
feEngine_->add_global(speciesName+"_F"+to_string(i+1), F[i]);
}
}
}
if (lammpsInterface_->rank_zero()) {
// tagged data --only for molecule
map<string,DENS_MAN>::iterator densMan;
for (densMan = taggedDensMan_.begin(); densMan != taggedDensMan_.end(); densMan++) {
outputData[densMan->first] = & (densMan->second).set_quantity();
}
feEngine_->write_data(output_index(), fields_, & outputData);
}
// force reset of tagged data to keep in sync
map<string,DENS_MAN>::iterator densMan;
for (densMan = taggedDensMan_.begin(); densMan != taggedDensMan_.end(); densMan++)
(densMan->second).force_reset();
feEngine_->partition_mesh();
}
}
//--------------------------------------------------------------------
// compute_vector
//--------------------------------------------------------------------
// this is for direct output to lammps thermo
double ATC_CouplingMass::compute_vector(int n)
{
return atomicRegulator_->compute_vector(n);
}
};
Event Timeline
Log In to Comment