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lammps/lib/atc/ATC_CouplingMomentumEnergy.cpp
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ATC_CouplingMomentumEnergy.cpp
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// ATC headers
#include "ATC_CouplingMomentumEnergy.h"
#include "KinetoThermostat.h"
#include "ATC_Error.h"
#include "PrescribedDataManager.h"
#include "FieldManager.h"
// Other Headers
#include <vector>
#include <map>
#include <set>
#include <utility>
#include <typeinfo>
#include <iostream>
using std::string;
namespace ATC {
//--------------------------------------------------------
//--------------------------------------------------------
// Class ATC_CouplingMomentumEnergy
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
ATC_CouplingMomentumEnergy::ATC_CouplingMomentumEnergy(string groupName,
double ** & perAtomArray,
LAMMPS_NS::Fix * thisFix,
string matParamFile,
ExtrinsicModelType extrinsicModel)
: ATC_Coupling(groupName,perAtomArray,thisFix),
nodalAtomicKineticTemperature_(NULL),
nodalAtomicConfigurationalTemperature_(NULL),
refPE_(0)
{
// Allocate PhysicsModel
create_physics_model(THERMO_ELASTIC, 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;
// set up atomic regulator
atomicRegulator_ = new KinetoThermostat(this);
// set up physics specific time integrator and thermostat
trackDisplacement_ = true;
fieldSizes_[DISPLACEMENT] = fieldSizes_[VELOCITY];
timeIntegrators_[VELOCITY] = new MomentumTimeIntegrator(this,TimeIntegrator::FRACTIONAL_STEP);
timeIntegrators_[TEMPERATURE] = new ThermalTimeIntegrator(this,TimeIntegrator::FRACTIONAL_STEP);
ghostManager_.set_boundary_dynamics(GhostManager::PRESCRIBED);
// default physics
temperatureDef_ = KINETIC;
// output variable vector info:
// output[1] = total coarse scale mechanical kinetic energy
// output[2] = total coarse scale mechanical potential energy
// output[3] = total coarse scale mechanical energy
// output[1] = total coarse scale thermal energy
// output[2] = average temperature
scalarFlag_ = 1;
vectorFlag_ = 1;
sizeVector_ = 5;
scalarVectorFreq_ = 1;
extVector_ = 1;
if (extrinsicModel != NO_MODEL)
sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
ATC_CouplingMomentumEnergy::~ATC_CouplingMomentumEnergy()
{
// 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_CouplingMomentumEnergy::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);
for (int i = 0; i < NUM_FLUX; i++)
intrinsicMask_(TEMPERATURE,i) = fieldMask_(TEMPERATURE,i);
refPE_=0;
refPE_=potential_energy();
}
//--------------------------------------------------------
// construct_transfers
// constructs needed transfer operators
//--------------------------------------------------------
void ATC_CouplingMomentumEnergy::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");
}
// always need fluctuating velocity and kinetic energy
FtaShapeFunctionProlongation * atomicMeanVelocity = new FtaShapeFunctionProlongation(this,&fields_[VELOCITY],shpFcn_);
interscaleManager_.add_per_atom_quantity(atomicMeanVelocity,
field_to_prolongation_name(VELOCITY));
FieldManager fieldManager(this);
PerAtomQuantity<double> * fluctuatingAtomicVelocity = fieldManager.per_atom_quantity("AtomicFluctuatingVelocity"); // also creates ProlongedVelocity
AtomicEnergyForTemperature * atomicTwiceKineticEnergy = new TwiceKineticEnergy(this,fluctuatingAtomicVelocity);
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_CouplingMomentumEnergy: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");
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_CouplingMomentumEnergy::init_filter()
{
if (timeIntegrators_[TEMPERATURE]->time_integration_type() != TimeIntegrator::FRACTIONAL_STEP) {
throw ATC_Error("ATC_CouplingMomentumEnergy::initialize - method only valid with fractional step time integration");
}
ATC_Coupling::init_filter();
if (timeFilterManager_.end_equilibrate() && equilibriumStart_) {
if (atomicRegulator_->coupling_mode(VELOCITY)==AtomicRegulator::FLUX || atomicRegulator_->coupling_mode(VELOCITY)==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(),VELOCITY);
DENS_MAT powerMat(-1.*(nodalAtomicFields_[TEMPERATURE].quantity()));
atomicRegulator_->reset_lambda_contribution(powerMat,TEMPERATURE);
}
}
//--------------------------------------------------------
// modify
// parses inputs and modifies state of the filter
//--------------------------------------------------------
bool ATC_CouplingMomentumEnergy::modify(int narg, char **arg)
{
return false;
}
//--------------------------------------------------------------------
// compute_scalar : added energy
//--------------------------------------------------------------------
double ATC_CouplingMomentumEnergy::compute_scalar(void)
{
double energy = 0.0;
energy += extrinsicModelManager_.compute_scalar();
return energy;
}
//--------------------------------------------------------------------
// total kinetic energy
//--------------------------------------------------------------------
double ATC_CouplingMomentumEnergy::kinetic_energy(void)
{
const MATRIX & M = massMats_[VELOCITY].quantity();
const DENS_MAT & velocity(fields_[VELOCITY].quantity());
double mvv2e = lammpsInterface_->mvv2e();
double kineticEnergy = 0;
DENS_VEC velocitySquared(nNodes_);
for (int i = 0; i < nNodes_; i++)
for (int j = 0; j < nsd_; j++)
velocitySquared(i) += velocity(i,j)*velocity(i,j);
kineticEnergy = (M*velocitySquared).sum();
kineticEnergy *= mvv2e; // convert to LAMMPS units
return kineticEnergy;
}
//--------------------------------------------------------------------
// total potential energy
//--------------------------------------------------------------------
double ATC_CouplingMomentumEnergy::potential_energy(void)
{
Array<FieldName> mask(1);
mask(0) = VELOCITY;
FIELD_MATS energy;
feEngine_->compute_energy(mask,
fields_,
physicsModel_,
elementToMaterialMap_,
energy,
&(elementMask_->quantity()));
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_CouplingMomentumEnergy::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] = total coarse scale thermal energy
// output[5] = average temperature
double mvv2e = lammpsInterface_->mvv2e(); // convert to lammps energy units
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 == 4) {
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 == 5) {
double aveT = (fields_[TEMPERATURE].quantity()).col_sum()/nNodes_;
return aveT;
}
else if (n > 5) {
double extrinsicValue = extrinsicModelManager_.compute_vector(n);
return extrinsicValue;
}
return 0.;
}
//--------------------------------------------------------------------
// output
//--------------------------------------------------------------------
void ATC_CouplingMomentumEnergy::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 & velocity(nodalAtomicFields_[VELOCITY].set_quantity());
DENS_MAT & rhs(rhs_[VELOCITY].set_quantity());
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["NodalAtomicVelocity"] = &velocity;
outputData["FE_Force"] = &rhs;
if (trackDisplacement_)
outputData["NodalAtomicDisplacement"] = & nodalAtomicFields_[DISPLACEMENT].set_quantity();
outputData["NodalAtomicTemperature"] = &temperature;
outputData["dot_temperature"] = &dotTemperature;
outputData["ddot_temperature"] = &ddotTemperature;
outputData["NodalAtomicPower"] = &rocTemperature;
outputData["fePower"] = &fePower;
feEngine_->write_data(output_index(), fields_, & outputData);
}
// hence propagation is performed on proc 0 but not others.
// The real fix is to have const data in the output list
// force optional variables to reset to keep in sync
if (trackDisplacement_) {
nodalAtomicFields_[DISPLACEMENT].force_reset();
}
fields_[VELOCITY].propagate_reset();
feEngine_->partition_mesh();
}
}
};
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