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lammps/lib/atc/ATC_CouplingMomentum.cpp
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ATC_CouplingMomentum.cpp
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// 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>
#include <iostream>
using std::string;
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),
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);
ghostManager_.set_boundary_dynamics(GhostManager::PRESCRIBED);
}
else if (intrinsicModel == SHEAR) {
atomToElementMapType_ = EULERIAN;
atomToElementMapFrequency_ = 1;
timeIntegrators_[VELOCITY] = new MomentumTimeIntegrator(this,TimeIntegrator::GEAR);
ghostManager_.set_boundary_dynamics(GhostManager::NO_BOUNDARY_DYNAMICS);
}
// 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();
// reset integration field mask
intrinsicMask_.reset(NUM_FIELDS,NUM_FLUX);
intrinsicMask_ = false;
for (int i = 0; i < NUM_FLUX; i++)
intrinsicMask_(VELOCITY,i) = fieldMask_(VELOCITY,i);
refPE_=0;
refPE_=potential_energy();
}
//--------------------------------------------------------
// 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");
}
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());
}
//--------------------------------------------------------
// 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_track_displacement fix_modify AtC track_displacement
\section syntax
fix_modify AtC track_displacement <on/off> \n
\section examples
<TT> fix_modify atc track_displacement on </TT> \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;
}
}
else if (strcmp(arg[argIndex],"boundary_dynamics")==0) {
argIndex++;
foundMatch = ghostManager_.modify(narg-argIndex,&arg[argIndex]);
}
// no match, call base class parser
if (!foundMatch) {
foundMatch = ATC_Coupling::modify(narg, arg);
}
return foundMatch;
}
//--------------------------------------------------------
// 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();
}
}
//--------------------------------------------------------------------
// 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.;
}
};
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