Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/lib/atc/ATC_CouplingMomentum.cpp
4704ced070e9efficient_neuronet

Last Change
Raw File

ATC_CouplingMomentum.cpp
View Options

// ATC headers
#include "ATC_CouplingMomentum.h"
#include "ATC_Error.h"
#include "LammpsInterface.h"
#include "PrescribedDataManager.h"
#include "PerAtomQuantity.h"
#include "TransferOperator.h"
// Other Headers
#include <vector>
#include <map>
#include <set>
#include <utility>
namespace ATC {
//--------------------------------------------------------
//--------------------------------------------------------
// Class ATC_CouplingMomentum
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
ATC_CouplingMomentum::ATC_CouplingMomentum(string groupName,
double **& perAtomArray,
LAMMPS_NS::Fix * thisFix,
string matParamFile,
PhysicsType intrinsicModel,
ExtrinsicModelType extrinsicModel)
: ATC_Coupling(groupName,perAtomArray,thisFix),
nodalAtomicMass_(NULL),
nodalAtomicCount_(NULL),
boundaryDynamics_(PRESCRIBED),
gamma_(0),mu_(1),kappa_(1),
refPE_(0)
{
// Allocate PhysicsModel
create_physics_model(intrinsicModel, matParamFile);
// create extrinsic physics model
if (extrinsicModel != NO_MODEL) {
extrinsicModelManager_.create_model(extrinsicModel,matParamFile);
}
// set up field data based on physicsModel
physicsModel_->num_fields(fieldSizes_,fieldMask_);
// Defaults
set_time();
bndyIntType_ = FE_INTERPOLATION;
trackCharge_ = false;
// use a kinetostat
atomicRegulator_ = new Kinetostat(this);
// set time integrator and change any defaults based on model type
if (intrinsicModel == ELASTIC) {
trackDisplacement_ = true;
fieldSizes_[DISPLACEMENT] = fieldSizes_[VELOCITY];
timeIntegrators_[VELOCITY] = new MomentumTimeIntegrator(this,TimeIntegrator::VERLET);
}
else if (intrinsicModel == SHEAR) {
atomToElementMapType_ = EULERIAN;
atomToElementMapFrequency_ = 1;
timeIntegrators_[VELOCITY] = new MomentumTimeIntegrator(this,TimeIntegrator::GEAR);
}
// output variable vector info:
// output[1] = total coarse scale kinetic energy
// output[2] = total coarse scale potential energy
// output[3] = total coarse scale energy
scalarFlag_ = 1;
vectorFlag_ = 1;
sizeVector_ = 5;
scalarVectorFreq_ = 1;
extVector_ = 1;
thermoEnergyFlag_ = 1;
if (extrinsicModel != NO_MODEL)
sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
ATC_CouplingMomentum::~ATC_CouplingMomentum()
{
interscaleManager_.clear();
}
//--------------------------------------------------------
// initialize
// sets up all the necessary data
//--------------------------------------------------------
void ATC_CouplingMomentum::initialize()
{
// clear displacement entries if requested
if (!trackDisplacement_) {
fieldSizes_.erase(DISPLACEMENT);
for (int i = 0; i < NUM_FLUX; i++)
fieldMask_(DISPLACEMENT,i) = false;
}
// Base class initalizations
ATC_Coupling::initialize();
// check resetting precedence:
// time integrator -> kinetostat -> time filter
// other initializations
if (reset_methods()) {
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->initialize();
}
atomicRegulator_->initialize();
}
extrinsicModelManager_.initialize();
if (timeFilterManager_.need_reset()) { // reset kinetostat power
init_filter();
}
timeFilterManager_.initialize(); // clears need for reset
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 & velocity(fields_[VELOCITY].set_quantity());
DENS_MAN * nodalAtomicVelocity(interscaleManager_.dense_matrix("NodalAtomicVelocity"));
const DENS_MAT & atomicVelocity(nodalAtomicVelocity->quantity());
const INT_ARRAY & nodeType(nodalGeometryType_->quantity());
for (int i = 0; i<nNodes_; ++i) {
if (nodeType(i,0)==MD_ONLY) {
for (int j = 0; j < nsd_; j++) {
velocity(i,j) = atomicVelocity(i,j);
}
}
}
if (trackDisplacement_) {
DENS_MAT & displacement(fields_[DISPLACEMENT].set_quantity());
DENS_MAN * nodalAtomicDisplacement(interscaleManager_.dense_matrix("NodalAtomicDisplacement"));
const DENS_MAT & atomicDisplacement(nodalAtomicDisplacement->quantity());
for (int i = 0; i<nNodes_; ++i) {
if (nodeType(i,0)==MD_ONLY) {
for (int j = 0; j < nsd_; j++) {
displacement(i,j) = atomicDisplacement(i,j);
}
}
}
}
}
}
initialized_ = true;
}
// reset integration field mask
velocityMask_.reset(NUM_FIELDS,NUM_FLUX);
velocityMask_ = false;
for (int i = 0; i < NUM_FLUX; i++)
velocityMask_(VELOCITY,i) = fieldMask_(VELOCITY,i);
refPE_=0;
refPE_=potential_energy();
}
//--------------------------------------------------------
// construct_methods
// have managers instantiate requested algorithms
// and methods
//--------------------------------------------------------
void ATC_CouplingMomentum::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_CouplingMomentum::construct_transfers()
{
ATC_Coupling::construct_transfers();
// momentum of each atom
AtomicMomentum * atomicMomentum = new AtomicMomentum(this);
interscaleManager_.add_per_atom_quantity(atomicMomentum,
"AtomicMomentum");
// nodal momentum for RHS
AtfShapeFunctionRestriction * nodalAtomicMomentum = new AtfShapeFunctionRestriction(this,
atomicMomentum,
shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicMomentum,
"NodalAtomicMomentum");
// nodal forces
FundamentalAtomQuantity * atomicForce = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_FORCE);
AtfShapeFunctionRestriction * nodalAtomicForce = new AtfShapeFunctionRestriction(this,
atomicForce,
shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicForce,
"NodalAtomicForce");
// nodal velocity derived only from atoms
AtfShapeFunctionMdProjection * nodalAtomicVelocity = new AtfShapeFunctionMdProjection(this,
nodalAtomicMomentum,
VELOCITY);
interscaleManager_.add_dense_matrix(nodalAtomicVelocity,
"NodalAtomicVelocity");
if (trackDisplacement_) {
// mass-weighted (center-of-mass) displacement of each atom
AtomicMassWeightedDisplacement * atomicMassWeightedDisplacement;
if (needXrefProcessorGhosts_ || groupbitGhost_) { // explicit construction on internal group
PerAtomQuantity<double> * atomReferencePositions = interscaleManager_.per_atom_quantity("AtomicInternalReferencePositions");
atomicMassWeightedDisplacement = new AtomicMassWeightedDisplacement(this,atomPositions_,
atomMasses_,
atomReferencePositions,
INTERNAL);
}
else
atomicMassWeightedDisplacement = new AtomicMassWeightedDisplacement(this);
interscaleManager_.add_per_atom_quantity(atomicMassWeightedDisplacement,
"AtomicMassWeightedDisplacement");
// nodal (RHS) mass-weighted displacement
AtfShapeFunctionRestriction * nodalAtomicMassWeightedDisplacement = new AtfShapeFunctionRestriction(this,
atomicMassWeightedDisplacement,
shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicMassWeightedDisplacement,
"NodalAtomicMassWeightedDisplacement");
// nodal displacement derived only from atoms
AtfShapeFunctionMdProjection * nodalAtomicDisplacement = new AtfShapeFunctionMdProjection(this,
nodalAtomicMassWeightedDisplacement,
VELOCITY);
interscaleManager_.add_dense_matrix(nodalAtomicDisplacement,
"NodalAtomicDisplacement");
}
// atomic mass matrix data
if (!useFeMdMassMatrix_) {
// atomic momentum mass matrix
FundamentalAtomQuantity * atomicMass = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
nodalAtomicMass_ = new AtfShapeFunctionRestriction(this,
atomicMass,
shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicMass_,
"AtomicMomentumMassMat");
// atomic dimensionless mass matrix
ConstantQuantity<double> * atomicOnes = new ConstantQuantity<double>(this,1);
interscaleManager_.add_per_atom_quantity(atomicOnes,"AtomicOnes");
nodalAtomicCount_ = new AtfShapeFunctionRestriction(this,
atomicOnes,
shpFcn_);
interscaleManager_.add_dense_matrix(nodalAtomicCount_,
"AtomicDimensionlessMassMat");
}
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_CouplingMomentum::init_filter()
{
ATC_Coupling::init_filter();
if (timeFilterManager_.end_equilibrate() && equilibriumStart_) // set up correct initial lambda forces to enforce initial accerlation
if (atomicRegulator_->coupling_mode()==AtomicRegulator::FLUX || atomicRegulator_->coupling_mode()==AtomicRegulator::GHOST_FLUX)
// nothing needed in other cases since kinetostat force is balanced by boundary flux in FE equations
atomicRegulator_->reset_lambda_contribution(nodalAtomicFieldsRoc_[VELOCITY].quantity());
}
//---------------------------------------------------------
// compute_md_mass_matrix
// compute the mass matrix arising from only atomistic
// quadrature and contributions as a summation
//---------------------------------------------------------
void ATC_CouplingMomentum::compute_md_mass_matrix(FieldName thisField,
DIAG_MAT & massMat)
{
if (thisField == DISPLACEMENT || thisField == VELOCITY)
massMat.reset(nodalAtomicMass_->quantity());
else if (thisField == MASS_DENSITY) { // dimensionless mass matrix
massMat.reset(nodalAtomicCount_->quantity());
}
}
//--------------------------------------------------------
// finish
// final clean up after a run
//--------------------------------------------------------
void ATC_CouplingMomentum::finish()
{
// base class
ATC_Coupling::finish();
atomicRegulator_->finish();
}
//--------------------------------------------------------
// modify
// parses inputs and modifies state of the filter
//--------------------------------------------------------
bool ATC_CouplingMomentum::modify(int narg, char **arg)
{
bool foundMatch = false;
int argIndex = 0;
// check to see if it is a transfer class command
// check derived class before base class
// pass-through to kinetostat
if (strcmp(arg[argIndex],"control")==0) {
argIndex++;
foundMatch = atomicRegulator_->modify(narg-argIndex,&arg[argIndex]);
}
// pass-through to timeIntegrator class
else if (strcmp(arg[argIndex],"time_integration")==0) {
argIndex++;
foundMatch = timeIntegrators_[VELOCITY]->modify(narg-argIndex,&arg[argIndex]);
}
// switch for if displacement is tracked or not
/*! \page man_disp_control fix_modify AtC transfer track_displacement
\section syntax
fix_modify AtC transfer track_displacement <on/off> \n
\section description
Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant.
\section restrictions
Some constitutive models require the displacement field
\section default
on
*/
else if (strcmp(arg[argIndex],"track_displacement")==0) {
argIndex++;
if (strcmp(arg[argIndex],"on")==0) {
trackDisplacement_ = true;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"off")==0) {
trackDisplacement_ = false;
foundMatch = true;
}
if (foundMatch) {
needReset_ = true;
}
}
/*! \page man_boundary_dynamics fix_modify AtC transfer boundary_dynamics
\section syntax
fix_modify AtC transfer boundary_dynamics <type> \n
\section description
\section restrictions
\section default
on
*/
else if (strcmp(arg[argIndex],"boundary_dynamics")==0) {
argIndex++;
gamma_ = 0;
kappa_ = 0;
mu_ = 0;
if (strcmp(arg[argIndex],"damped_harmonic")==0) {
argIndex++;
gamma_ = atof(arg[argIndex++]);
kappa_ = atof(arg[argIndex++]);
mu_ = atof(arg[argIndex++]);
boundaryDynamics_ = DAMPED_HARMONIC;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"prescribed")==0) {
boundaryDynamics_ = PRESCRIBED;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"coupled")==0) {
boundaryDynamics_ = COUPLED;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"none")==0) {
boundaryDynamics_ = NO_BOUNDARY_DYNAMICS;
foundMatch = 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_CouplingMomentum::pack_elastic_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_CouplingMomentum::write_restart_data(string fileName, RESTART_LIST & data)
{
pack_elastic_fields(data);
ATC_Method::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_CouplingMomentum::read_restart_data(string fileName, RESTART_LIST & data)
{
pack_elastic_fields(data);
ATC_Method::read_restart_data(fileName,data);
}
//--------------------------------------------------------
void ATC_CouplingMomentum::reset_nlocal()
{
ATC_Coupling::reset_nlocal();
atomicRegulator_->reset_nlocal();
}
//--------------------------------------------------
// reset_atom_materials
// update the atom materials map
//--------------------------------------------------
void ATC_CouplingMomentum::reset_atom_materials()
{
ATC_Coupling::reset_atom_materials();
atomicRegulator_->reset_atom_materials(elementToMaterialMap_,
atomElement_);
}
//--------------------------------------------------------
// pre_init_integrate
// time integration before the lammps atomic
// integration of the Verlet step 1
//--------------------------------------------------------
void ATC_CouplingMomentum::pre_init_integrate()
{
ATC_Coupling::pre_init_integrate();
double dt = lammpsInterface_->dt();
// get any initial data before its modified
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->pre_initial_integrate1(dt);
}
// apply kinetostat force, if needed
atomicRegulator_->apply_pre_predictor(dt,lammpsInterface_->ntimestep());
// predict nodal velocities
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->pre_initial_integrate2(dt);
}
extrinsicModelManager_.pre_init_integrate();
}
//--------------------------------------------------------
// mid_init_integrate
// time integration between the velocity update and
// the position lammps update of Verlet step 1
//--------------------------------------------------------
void ATC_CouplingMomentum::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_CouplingMomentum::post_init_integrate()
{
// CONTINUOUS DISPLACEMENT UPDATE
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();
// enforce atomic boundary conditions
if (boundaryDynamics_==PRESCRIBED) set_ghost_atoms();
else if (boundaryDynamics_==DAMPED_HARMONIC) initial_integrate_ghost();
else if (boundaryDynamics_==COUPLED) initial_integrate_ghost();
// update time by a half dt
update_time(0.5);
ATC_Coupling::post_init_integrate();
}
//--------------------------------------------------------
// pre_final_integrate
// integration before the second stage lammps atomic
// update of Verlet step 2
//--------------------------------------------------------
void ATC_CouplingMomentum::pre_final_integrate()
{
ATC_Coupling::pre_final_integrate();
if (boundaryDynamics_==DAMPED_HARMONIC) {
apply_ghost_forces();
final_integrate_ghost();
}
else if (boundaryDynamics_==COUPLED) {
add_ghost_forces();
final_integrate_ghost();
}
}
//--------------------------------------------------------
// post_final_integrate
// integration after the second stage lammps atomic
// update of Verlet step 2
//--------------------------------------------------------
void ATC_CouplingMomentum::post_final_integrate()
{
// COMPUTE FORCES FOR FE VELOCITY RHS
double dt = lammpsInterface_->dt();
// updating of data based on atomic forces
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();
if (timeIntegrators_[VELOCITY]->has_final_predictor()) {
// set state-based sources
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
atomicRegulator_->compute_boundary_flux(fields_);
compute_atomic_sources(velocityMask_,fields_,atomicSources_);
}
// Compute kinetostat forces and add kinetostat contributions to FE equations
atomicRegulator_->apply_pre_corrector(dt,lammpsInterface_->ntimestep()); // computes but does not apply kstat, and only for StressFlux
// set state-based RHS
// Determine FE contributions to dv/dt-----------------------
// Compute atom-integrated rhs
// parallel communication happens within FE_Engine
compute_rhs_vector(velocityMask_,fields_,rhs_,FE_DOMAIN);
// Compute and add atomic contributions to FE equations
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->add_to_rhs();
}
// add in kinetostat contributions to FE equations
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();
// CONTINUOUS VELOCITY RHS UPDATE
// corrector step extrinsic model
extrinsicModelManager_.post_final_integrate();
if (timeIntegrators_[VELOCITY]->has_final_corrector()) {
// set state-based sources
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
atomicRegulator_->compute_boundary_flux(fields_);
compute_atomic_sources(velocityMask_,fields_,atomicSources_);
}
// Finish update of FE velocity
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->post_final_integrate2(dt);
}
// Apply kinetostat to atoms
atomicRegulator_->apply_post_corrector(dt,lammpsInterface_->ntimestep());
// finalize time integration
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 by a half dt
update_time(0.5);
output();
ATC_Coupling::post_final_integrate(); // addstep for computes
}
//--------------------------------------------------------
// min_pre_force
// add to interatomic forces for minimize
//--------------------------------------------------------
void ATC_CouplingMomentum::min_pre_force()
{
}
//--------------------------------------------------------
// min_post_force
// add to interatomic forces for minimize
// this determines the search direction
//--------------------------------------------------------
void ATC_CouplingMomentum::min_post_force()
{
// reset positions and shape functions
ATC_Method::min_post_force();
// Set sources
prescribedDataMgr_->set_sources(time(),sources_);
extrinsicModelManager_.set_sources(fields_,extrinsicSources_);
extrinsicModelManager_.pre_final_integrate();
if (outputNow_) {
update_time(1.0);
update_step();
output();
outputNow_ = false;
}
localStep_ += 1;
}
//--------------------------------------------------------
// output
// does post-processing steps and outputs data
//--------------------------------------------------------
void ATC_CouplingMomentum::output()
{
if (output_now()) {
feEngine_->departition_mesh();
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 & velocity(nodalAtomicFields_[VELOCITY].set_quantity());
DENS_MAT & rhs(rhs_[VELOCITY].set_quantity());
if (lammpsInterface_->rank_zero()) {
// mesh data
outputData["NodalAtomicVelocity"] = &velocity;
outputData["FE_Force"] = &rhs;
if (trackDisplacement_) {
outputData["NodalAtomicDisplacement"] = & nodalAtomicFields_[DISPLACEMENT].set_quantity();
}
feEngine_->write_data(output_index(), fields_, & outputData);
}
// force optional variables to reset to keep in sync
if (trackDisplacement_) {
nodalAtomicFields_[DISPLACEMENT].force_reset();
}
feEngine_->partition_mesh();
}
}
//--------------------------------------------------------
// set_ghost_atoms
// sets ghost atom positions to finite element
// displacements based on shape functions
//--------------------------------------------------------
void ATC_CouplingMomentum::set_ghost_atoms()
{
// set atomic displacements based on FE displacements
double ** x = lammpsInterface_->xatom();
// prolong
DenseMatrix<double> ghostAtomData(nLocalGhost_,nsd_);
if (nLocalGhost_>0)
ghostAtomData = (shpFcnGhost_->quantity())*(fields_[DISPLACEMENT].quantity());
for (int i = 0; i < nLocalGhost_; ++i)
for (int j = 0; j < nsd_; ++j)
x[ghostToAtom_(i)][j] = ghostAtomData(i,j)+xref_[ghostToAtom_(i)][j];
}
//--------------------------------------------------------
// add_ghost_forces
// add forces to dynamic ghosts
//--------------------------------------------------------
void ATC_CouplingMomentum::add_ghost_forces()
{
double **x = lammpsInterface_->xatom();
double **v = lammpsInterface_->vatom();
double **f = lammpsInterface_->fatom();
// add forces
DENS_MAT coarseDisp(nLocalGhost_,nsd_);
DENS_MAT coarseVel(nLocalGhost_,nsd_);
if (nLocalGhost_>0) {
coarseDisp = (shpFcnGhost_->quantity())*(fields_[DISPLACEMENT].quantity());
coarseVel = (shpFcnGhost_->quantity())*(fields_[VELOCITY].quantity());
}
// dynamics one-way coupled to real atoms in a well tied to coarse scale
for (int i = 0; i < nLocalGhost_; ++i) {
for (int j = 0; j < nsd_; ++j) {
double du = coarseDisp(i,j)+xref_[ghostToAtom_(i)][j]-x[ghostToAtom_(i)][j];
double dv = coarseVel(i,j)-v[ghostToAtom_(i)][j];
f[ghostToAtom_(i)][j] += mu_*du + gamma_*dv;
}
}
}
void ATC_CouplingMomentum::apply_ghost_forces()
{
double **x = lammpsInterface_->xatom();
double **v = lammpsInterface_->vatom();
double **f = lammpsInterface_->fatom();
// add forces
DENS_MAT coarseDisp(nLocalGhost_,nsd_);
DENS_MAT coarseVel(nLocalGhost_,nsd_);
if (nLocalGhost_>0) {
coarseDisp = (shpFcnGhost_->quantity())*(fields_[DISPLACEMENT].quantity());
coarseVel = (shpFcnGhost_->quantity())*(fields_[VELOCITY].quantity());
}
// dynamics one-way coupled to real atoms in a well tied to coarse scale
for (int i = 0; i < nLocalGhost_; ++i) {
for (int j = 0; j < nsd_; ++j) {
double du = coarseDisp(i,j)+xref_[ghostToAtom_(i)][j]-x[ghostToAtom_(i)][j];
double dv = coarseVel(i,j)-v[ghostToAtom_(i)][j];
f[ghostToAtom_(i)][j] = mu_*du + gamma_*dv;
}
}
}
//--------------------------------------------------------
// initial_integrate_ghost
// does the first step of the Verlet integration for
// ghost atoms, to be used with non-reflecting BCs
//--------------------------------------------------------
void ATC_CouplingMomentum::initial_integrate_ghost()
{
double dtfm;
double **x = lammpsInterface_->xatom();
double **v = lammpsInterface_->vatom();
double **f = lammpsInterface_->fatom();
const int *mask = lammpsInterface_->atom_mask();
int nlocal = lammpsInterface_->nlocal();
double dtv = lammpsInterface_->dt();
double dtf = 0.5 * lammpsInterface_->dt() * lammpsInterface_->ftm2v();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbitGhost_) {
dtfm = dtf / mu_;
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
//--------------------------------------------------------
// final_integrate_ghost
// does the second step of the Verlet integration for
// ghost atoms, to be used with non-reflecting BCs
//--------------------------------------------------------
void ATC_CouplingMomentum::final_integrate_ghost()
{
double dtfm;
double **v = lammpsInterface_->vatom();
double **f = lammpsInterface_->fatom();
const int *mask = lammpsInterface_->atom_mask();
int nlocal = lammpsInterface_->nlocal();
double dtf = 0.5 * lammpsInterface_->dt() * lammpsInterface_->ftm2v();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbitGhost_) {
dtfm = dtf / mu_;
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
}
}
}
//--------------------------------------------------------------------
// compute_scalar : added energy
// this is used in the line search
//--------------------------------------------------------------------
double ATC_CouplingMomentum::compute_scalar(void)
{
double energy = extrinsicModelManager_.compute_scalar();
return energy;
}
//--------------------------------------------------------------------
// kinetic energy
//--------------------------------------------------------------------
double ATC_CouplingMomentum::kinetic_energy(const IntegrationDomainType domain) // const
{
const MATRIX & M = massMats_[VELOCITY].quantity();
const DENS_MAT & velocity(fields_[VELOCITY].quantity());
double kineticEnergy = 0;
for (int j = 0; j < nsd_; j++) {
CLON_VEC v = column(velocity,j);
kineticEnergy += v.dot(M*v);
}
if (domain == FE_DOMAIN) {
Array<FieldName> massMask(1);
massMask(0) = VELOCITY;
feEngine_->compute_lumped_mass_matrix(massMask,fields_,physicsModel_,atomMaterialGroups_,
atomVolume_->quantity(),shpFcn_->quantity(),
Ma_);
const MATRIX & Ma = Ma_[VELOCITY].quantity();
for (int j = 0; j < nsd_; j++) {
CLON_VEC v = column(velocity,j);
kineticEnergy -= v.dot(Ma*v);
}
}
double mvv2e = lammpsInterface_->mvv2e();
kineticEnergy *= 0.5*mvv2e; // convert to LAMMPS units
return kineticEnergy;
}
//--------------------------------------------------------------------
// potential/strain energy
//--------------------------------------------------------------------
double ATC_CouplingMomentum::potential_energy(const IntegrationDomainType domain) const
{
Array<FieldName> mask(1);
mask(0) = VELOCITY;
FIELD_MATS energy;
feEngine_->compute_energy(mask,
fields_,
physicsModel_,
elementToMaterialMap_,
energy,
&(elementMask_->quantity()),
domain);
double potentialEnergy = energy[VELOCITY].col_sum();
double mvv2e = lammpsInterface_->mvv2e();
potentialEnergy *= mvv2e; // convert to LAMMPS units
return potentialEnergy-refPE_;
}
//--------------------------------------------------------------------
// compute_vector
//--------------------------------------------------------------------
// this is for direct output to lammps thermo
double ATC_CouplingMomentum::compute_vector(int n)
{
// output[1] = total coarse scale kinetic energy
// output[2] = total coarse scale potential energy
// output[3] = total coarse scale energy
// output[4] = fe-only coarse scale kinetic energy
// output[5] = fe-only coarse scale potential energy
if (n == 0) {
return kinetic_energy();
}
else if (n == 1) {
return potential_energy();
}
else if (n == 2) {
return kinetic_energy()+potential_energy();
}
else if (n == 3) {
return kinetic_energy(FE_DOMAIN);
}
else if (n == 4) {
return potential_energy(FE_DOMAIN);
}
else if (n > 4) {
double extrinsicValue = extrinsicModelManager_.compute_vector(n);
return extrinsicValue;
}
return 0.;
}
};
c4science · Help