ATC_CouplingEnergy.cpp
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Created: Wed, Nov 13, 05:28

ATC_CouplingEnergy.cpp
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	// ATC_Transfer headers
	#include "ATC_CouplingEnergy.h"
	#include "Thermostat.h"
	#include "ATC_Error.h"
	#include "PrescribedDataManager.h"
	#include "FieldManager.h"

	// Other Headers
	#include <vector>
	#include <set>
	#include <utility>
	#include <typeinfo>

	using std::string;

	namespace ATC {

	//--------------------------------------------------------
	//--------------------------------------------------------
	// Class ATC_CouplingEnergy
	//--------------------------------------------------------
	//--------------------------------------------------------

	//--------------------------------------------------------
	// Constructor
	//--------------------------------------------------------
	ATC_CouplingEnergy::ATC_CouplingEnergy(string groupName,
	double ** & perAtomArray,
	LAMMPS_NS::Fix * thisFix,
	string matParamFile,
	ExtrinsicModelType extrinsicModel)
	: ATC_Coupling(groupName,perAtomArray,thisFix),
	nodalAtomicKineticTemperature_(NULL),
	nodalAtomicConfigurationalTemperature_(NULL)
	{
	// Allocate PhysicsModel
	create_physics_model(THERMAL, matParamFile);

	// create extrinsic physics model
	if (extrinsicModel != NO_MODEL) {
	extrinsicModelManager_.create_model(extrinsicModel,matParamFile);
	}

	// Defaults
	set_time();
	bndyIntType_ = FE_INTERPOLATION;

	// set up field data based on physicsModel
	physicsModel_->num_fields(fieldSizes_,fieldMask_);

	// set up atomic regulator
	atomicRegulator_ = new Thermostat(this);

	// set up physics specific time integrator and thermostat
	timeIntegrators_[TEMPERATURE] = new ThermalTimeIntegrator(this,TimeIntegrator::GEAR);

	// default physics
	temperatureDef_ = KINETIC;

	// output variable vector info:
	// output[1] = total coarse scale thermal energy
	// output[2] = average temperature
	vectorFlag_ = 1;
	sizeVector_ = 2;
	scalarVectorFreq_ = 1;
	extVector_ = 1;
	if (extrinsicModel != NO_MODEL)
	sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);
	}

	//--------------------------------------------------------
	// Destructor
	//--------------------------------------------------------
	ATC_CouplingEnergy::~ATC_CouplingEnergy()
	{
	// 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_CouplingEnergy::initialize()
	{
	// 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_(TEMPERATURE,i) = fieldMask_(TEMPERATURE,i);
	}

	//--------------------------------------------------------
	// construct_transfers
	// constructs needed transfer operators
	//--------------------------------------------------------
	void ATC_CouplingEnergy::construct_transfers()
	{
	ATC_Coupling::construct_transfers();

	// always need kinetic energy
	AtomicEnergyForTemperature * atomicTwiceKineticEnergy = new TwiceKineticEnergy(this);
	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_CouplingEnergy: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_CouplingEnergy::init_filter()
	{

	TimeIntegrator::TimeIntegrationType timeIntegrationType = timeIntegrators_[TEMPERATURE]->time_integration_type();




	if (timeFilterManager_.end_equilibrate()) {
	if (timeIntegrationType==TimeIntegrator::GEAR) {
	if (equilibriumStart_) {



	if (atomicRegulator_->regulator_target()==AtomicRegulator::DYNAMICS) { // based on FE equation
	DENS_MAT vdotflamMat(-2.*(nodalAtomicFields_[TEMPERATURE].quantity())); // note 2 is for 1/2 vdotflam addition
	atomicRegulator_->reset_lambda_contribution(vdotflamMat);
	}
	else { // based on MD temperature equation
	DENS_MAT vdotflamMat(-1.*(nodalAtomicFields_[TEMPERATURE].quantity()));
	atomicRegulator_->reset_lambda_contribution(vdotflamMat);
	}
	}
	}
	else if (timeIntegrationType==TimeIntegrator::FRACTIONAL_STEP) {
	if (equilibriumStart_) {
	DENS_MAT powerMat(-1.*(nodalAtomicFields_[TEMPERATURE].quantity()));
	atomicRegulator_->reset_lambda_contribution(powerMat);
	}
	}
	}
	}

	//--------------------------------------------------------
	// modify
	// parses inputs and modifies state of the filter
	//--------------------------------------------------------
	bool ATC_CouplingEnergy::modify(int narg, char **arg)
	{
	bool foundMatch = false;
	int argIndx = 0;

	// check to see if input is a transfer class command
	// check derived class before base class

	// pass-through to thermostat
	if (strcmp(arg[argIndx],"control")==0) {
	argIndx++;
	foundMatch = atomicRegulator_->modify(narg-argIndx,&arg[argIndx]);
	}

	// pass-through to timeIntegrator class
	else if (strcmp(arg[argIndx],"time_integration")==0) {
	argIndx++;
	foundMatch = timeIntegrators_[TEMPERATURE]->modify(narg-argIndx,&arg[argIndx]);
	}

	// switch for the kind of temperature being used
	/*! \page man_temperature_definition fix_modify AtC temperature_definition
	\section syntax
	fix_modify AtC temperature_definition <kinetic\|total>

	\section examples
	<TT> fix_modify atc temperature_definition kinetic </TT> \n

	\section description
	Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.

	\section restrictions
	This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.

	\section default
	kinetic
	*/
	else if (strcmp(arg[argIndx],"temperature_definition")==0) {
	argIndx++;
	string_to_temperature_def(arg[argIndx],temperatureDef_);
	if (temperatureDef_ == TOTAL) {
	setRefPE_ = true;
	}
	foundMatch = true;
	needReset_ = true;
	}

	// no match, call base class parser
	if (!foundMatch) {
	foundMatch = ATC_Coupling::modify(narg, arg);
	}

	return foundMatch;

	}

	//--------------------------------------------------------------------
	// compute_vector
	//--------------------------------------------------------------------
	// this is for direct output to lammps thermo
	double ATC_CouplingEnergy::compute_vector(int n)
	{
	// output[1] = total coarse scale thermal energy
	// output[2] = average temperature

	double mvv2e = lammpsInterface_->mvv2e(); // convert to lammps energy units

	if (n == 0) {
	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 == 1) {
	double aveT = (fields_[TEMPERATURE].quantity()).col_sum()/nNodes_;
	return aveT;
	}
	else if (n > 1) {
	double extrinsicValue = extrinsicModelManager_.compute_vector(n);
	return extrinsicValue;
	}

	return 0.;

	}

	//--------------------------------------------------------------------
	// output
	//--------------------------------------------------------------------
	void ATC_CouplingEnergy::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 & 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["NodalAtomicTemperature"] = &temperature;
	outputData["dot_temperature"] = &dotTemperature;
	outputData["ddot_temperature"] = &ddotTemperature;
	outputData["NodalAtomicPower"] = &rocTemperature;
	outputData["fePower"] = &fePower;

	// write data
	feEngine_->write_data(output_index(), fields_, & outputData);
	}
	feEngine_->partition_mesh();
	}
	}
	};

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