forked from lijiext/lammps
413 lines
17 KiB
C++
413 lines
17 KiB
C++
// ATC_Transfer headers
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#include "ATC_CouplingEnergy.h"
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#include "Thermostat.h"
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#include "ATC_Error.h"
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#include "PrescribedDataManager.h"
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#include "FieldManager.h"
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// Other Headers
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#include <vector>
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#include <set>
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#include <utility>
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#include <typeinfo>
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using std::string;
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namespace ATC {
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//--------------------------------------------------------
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//--------------------------------------------------------
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// Class ATC_CouplingEnergy
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//--------------------------------------------------------
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//--------------------------------------------------------
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//--------------------------------------------------------
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// Constructor
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//--------------------------------------------------------
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ATC_CouplingEnergy::ATC_CouplingEnergy(string groupName,
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double ** & perAtomArray,
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LAMMPS_NS::Fix * thisFix,
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string matParamFile,
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ExtrinsicModelType extrinsicModel)
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: ATC_Coupling(groupName,perAtomArray,thisFix),
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nodalAtomicKineticTemperature_(NULL),
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nodalAtomicConfigurationalTemperature_(NULL)
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{
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// Allocate PhysicsModel
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create_physics_model(THERMAL, matParamFile);
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// create extrinsic physics model
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if (extrinsicModel != NO_MODEL) {
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extrinsicModelManager_.create_model(extrinsicModel,matParamFile);
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}
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// Defaults
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set_time();
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bndyIntType_ = FE_INTERPOLATION;
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// set up field data based on physicsModel
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physicsModel_->num_fields(fieldSizes_,fieldMask_);
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// set up atomic regulator
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atomicRegulator_ = new Thermostat(this);
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// set up physics specific time integrator and thermostat
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timeIntegrators_[TEMPERATURE] = new ThermalTimeIntegrator(this,TimeIntegrator::GEAR);
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// default physics
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temperatureDef_ = KINETIC;
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// output variable vector info:
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// output[1] = total coarse scale thermal energy
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// output[2] = average temperature
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vectorFlag_ = 1;
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sizeVector_ = 2;
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scalarVectorFreq_ = 1;
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extVector_ = 1;
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if (extrinsicModel != NO_MODEL)
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sizeVector_ += extrinsicModelManager_.size_vector(sizeVector_);
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}
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//--------------------------------------------------------
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// Destructor
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//--------------------------------------------------------
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ATC_CouplingEnergy::~ATC_CouplingEnergy()
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{
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// clear out all managed memory to avoid conflicts with dependencies on class member data
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interscaleManager_.clear();
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}
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//--------------------------------------------------------
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// initialize
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// sets up all the necessary data
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//--------------------------------------------------------
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void ATC_CouplingEnergy::initialize()
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{
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// Base class initalizations
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ATC_Coupling::initialize();
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// reset integration field mask
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intrinsicMask_.reset(NUM_FIELDS,NUM_FLUX);
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intrinsicMask_ = false;
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for (int i = 0; i < NUM_FLUX; i++)
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intrinsicMask_(TEMPERATURE,i) = fieldMask_(TEMPERATURE,i);
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}
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//--------------------------------------------------------
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// construct_transfers
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// constructs needed transfer operators
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//--------------------------------------------------------
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void ATC_CouplingEnergy::construct_transfers()
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{
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ATC_Coupling::construct_transfers();
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// always need kinetic energy
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AtomicEnergyForTemperature * atomicTwiceKineticEnergy = new TwiceKineticEnergy(this);
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AtomicEnergyForTemperature * atomEnergyForTemperature = NULL;
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// Appropriate per-atom quantity based on desired temperature definition
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if (temperatureDef_==KINETIC) {
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atomEnergyForTemperature = atomicTwiceKineticEnergy;
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}
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else if (temperatureDef_==TOTAL) {
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if (timeIntegrators_[TEMPERATURE]->time_integration_type() != TimeIntegrator::FRACTIONAL_STEP)
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throw ATC_Error("ATC_CouplingEnergy:construct_transfers() on the fractional step time integrator can be used with non-kinetic defitions of the temperature");
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// kinetic energy
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interscaleManager_.add_per_atom_quantity(atomicTwiceKineticEnergy,
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"AtomicTwiceKineticEnergy");
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// atomic potential energy
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ComputedAtomQuantity * atomicPotentialEnergy = new ComputedAtomQuantity(this,
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lammpsInterface_->compute_pe_name(),
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1./(lammpsInterface_->mvv2e()));
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interscaleManager_.add_per_atom_quantity(atomicPotentialEnergy,
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"AtomicPotentialEnergy");
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// reference potential energy
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AtcAtomQuantity<double> * atomicReferencePotential;
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if (!initialized_) {
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atomicReferencePotential = new AtcAtomQuantity<double>(this);
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interscaleManager_.add_per_atom_quantity(atomicReferencePotential,
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"AtomicReferencePotential");
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atomicReferencePotential->set_memory_type(PERSISTENT);
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}
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else {
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atomicReferencePotential = static_cast<AtcAtomQuantity<double> * >(interscaleManager_.per_atom_quantity("AtomicReferencePotential"));
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}
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nodalRefPotentialEnergy_ = new AtfShapeFunctionRestriction(this,
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atomicReferencePotential,
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shpFcn_);
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interscaleManager_.add_dense_matrix(nodalRefPotentialEnergy_,
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"NodalAtomicReferencePotential");
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// fluctuating potential energy
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AtomicEnergyForTemperature * atomicFluctuatingPotentialEnergy =
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new FluctuatingPotentialEnergy(this,
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atomicPotentialEnergy,
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atomicReferencePotential);
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interscaleManager_.add_per_atom_quantity(atomicFluctuatingPotentialEnergy,
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"AtomicFluctuatingPotentialEnergy");
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// atomic total energy
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atomEnergyForTemperature = new MixedKePeEnergy(this,1,1);
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// kinetic temperature measure for post-processing
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// nodal restriction of the atomic energy quantity for the temperature definition
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AtfShapeFunctionRestriction * nodalAtomicTwiceKineticEnergy = new AtfShapeFunctionRestriction(this,
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atomicTwiceKineticEnergy,
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shpFcn_);
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interscaleManager_.add_dense_matrix(nodalAtomicTwiceKineticEnergy,
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"NodalAtomicTwiceKineticEnergy");
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nodalAtomicKineticTemperature_ = new AtfShapeFunctionMdProjection(this,
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nodalAtomicTwiceKineticEnergy,
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TEMPERATURE);
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interscaleManager_.add_dense_matrix(nodalAtomicKineticTemperature_,
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"NodalAtomicKineticTemperature");
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// potential temperature measure for post-processing (must multiply by 2 for configurational temperature
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// nodal restriction of the atomic energy quantity for the temperature definition
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AtfShapeFunctionRestriction * nodalAtomicFluctuatingPotentialEnergy = new AtfShapeFunctionRestriction(this,
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atomicFluctuatingPotentialEnergy,
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shpFcn_);
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interscaleManager_.add_dense_matrix(nodalAtomicFluctuatingPotentialEnergy,
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"NodalAtomicFluctuatingPotentialEnergy");
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nodalAtomicConfigurationalTemperature_ = new AtfShapeFunctionMdProjection(this,
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nodalAtomicFluctuatingPotentialEnergy,
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TEMPERATURE);
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interscaleManager_.add_dense_matrix(nodalAtomicConfigurationalTemperature_,
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"NodalAtomicConfigurationalTemperature");
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}
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// register the per-atom quantity for the temperature definition
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interscaleManager_.add_per_atom_quantity(atomEnergyForTemperature,
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"AtomicEnergyForTemperature");
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// nodal restriction of the atomic energy quantity for the temperature definition
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AtfShapeFunctionRestriction * nodalAtomicEnergy = new AtfShapeFunctionRestriction(this,
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atomEnergyForTemperature,
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shpFcn_);
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interscaleManager_.add_dense_matrix(nodalAtomicEnergy,
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"NodalAtomicEnergy");
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// nodal atomic temperature field
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AtfShapeFunctionMdProjection * nodalAtomicTemperature = new AtfShapeFunctionMdProjection(this,
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nodalAtomicEnergy,
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TEMPERATURE);
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interscaleManager_.add_dense_matrix(nodalAtomicTemperature,
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"NodalAtomicTemperature");
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for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
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(_tiIt_->second)->construct_transfers();
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}
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atomicRegulator_->construct_transfers();
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}
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//---------------------------------------------------------
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// init_filter
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// sets up the time filtering operations in all objects
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//---------------------------------------------------------
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void ATC_CouplingEnergy::init_filter()
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{
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TimeIntegrator::TimeIntegrationType timeIntegrationType = timeIntegrators_[TEMPERATURE]->time_integration_type();
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if (timeFilterManager_.end_equilibrate()) {
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if (timeIntegrationType==TimeIntegrator::GEAR) {
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if (equilibriumStart_) {
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if (atomicRegulator_->regulator_target()==AtomicRegulator::DYNAMICS) { // based on FE equation
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DENS_MAT vdotflamMat(-2.*(nodalAtomicFields_[TEMPERATURE].quantity())); // note 2 is for 1/2 vdotflam addition
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atomicRegulator_->reset_lambda_contribution(vdotflamMat);
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}
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else { // based on MD temperature equation
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DENS_MAT vdotflamMat(-1.*(nodalAtomicFields_[TEMPERATURE].quantity()));
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atomicRegulator_->reset_lambda_contribution(vdotflamMat);
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}
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}
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}
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else if (timeIntegrationType==TimeIntegrator::FRACTIONAL_STEP) {
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if (equilibriumStart_) {
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DENS_MAT powerMat(-1.*(nodalAtomicFields_[TEMPERATURE].quantity()));
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atomicRegulator_->reset_lambda_contribution(powerMat);
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}
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}
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}
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}
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//--------------------------------------------------------
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// modify
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// parses inputs and modifies state of the filter
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//--------------------------------------------------------
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bool ATC_CouplingEnergy::modify(int narg, char **arg)
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{
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bool foundMatch = false;
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int argIndx = 0;
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// check to see if input is a transfer class command
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// check derived class before base class
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// pass-through to thermostat
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if (strcmp(arg[argIndx],"control")==0) {
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argIndx++;
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foundMatch = atomicRegulator_->modify(narg-argIndx,&arg[argIndx]);
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}
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// pass-through to timeIntegrator class
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else if (strcmp(arg[argIndx],"time_integration")==0) {
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argIndx++;
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foundMatch = timeIntegrators_[TEMPERATURE]->modify(narg-argIndx,&arg[argIndx]);
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}
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// switch for the kind of temperature being used
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/*! \page man_temperature_definition fix_modify AtC temperature_definition
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\section syntax
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fix_modify AtC temperature_definition <kinetic|total>
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\section examples
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<TT> fix_modify atc temperature_definition kinetic </TT> \n
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\section description
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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.
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\section restrictions
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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.
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\section default
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kinetic
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*/
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else if (strcmp(arg[argIndx],"temperature_definition")==0) {
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argIndx++;
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string_to_temperature_def(arg[argIndx],temperatureDef_);
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if (temperatureDef_ == TOTAL) {
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setRefPE_ = true;
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}
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foundMatch = true;
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needReset_ = true;
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}
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// no match, call base class parser
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if (!foundMatch) {
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foundMatch = ATC_Coupling::modify(narg, arg);
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}
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return foundMatch;
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}
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//--------------------------------------------------------------------
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// compute_vector
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//--------------------------------------------------------------------
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// this is for direct output to lammps thermo
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double ATC_CouplingEnergy::compute_vector(int n)
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{
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// output[1] = total coarse scale thermal energy
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// output[2] = average temperature
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double mvv2e = lammpsInterface_->mvv2e(); // convert to lammps energy units
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if (n == 0) {
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Array<FieldName> mask(1);
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FIELD_MATS energy;
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mask(0) = TEMPERATURE;
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feEngine_->compute_energy(mask,
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fields_,
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physicsModel_,
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elementToMaterialMap_,
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energy,
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&(elementMask_->quantity()));
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double phononEnergy = mvv2e * energy[TEMPERATURE].col_sum();
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return phononEnergy;
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}
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else if (n == 1) {
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double aveT = (fields_[TEMPERATURE].quantity()).col_sum()/nNodes_;
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return aveT;
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}
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else if (n > 1) {
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double extrinsicValue = extrinsicModelManager_.compute_vector(n);
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return extrinsicValue;
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}
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return 0.;
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}
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//--------------------------------------------------------------------
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// output
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//--------------------------------------------------------------------
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void ATC_CouplingEnergy::output()
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{
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if (output_now()) {
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feEngine_->departition_mesh();
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// avoid possible mpi calls
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if (nodalAtomicKineticTemperature_)
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_keTemp_ = nodalAtomicKineticTemperature_->quantity();
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if (nodalAtomicConfigurationalTemperature_)
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_peTemp_ = nodalAtomicConfigurationalTemperature_->quantity();
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OUTPUT_LIST outputData;
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// base class output
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ATC_Method::output();
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// push atc fields time integrator modifies into output arrays
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for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
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(_tiIt_->second)->post_process();
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}
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// auxilliary data
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for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
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(_tiIt_->second)->output(outputData);
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}
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atomicRegulator_->output(outputData);
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extrinsicModelManager_.output(outputData);
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DENS_MAT & temperature(nodalAtomicFields_[TEMPERATURE].set_quantity());
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DENS_MAT & dotTemperature(dot_fields_[TEMPERATURE].set_quantity());
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DENS_MAT & ddotTemperature(ddot_fields_[TEMPERATURE].set_quantity());
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DENS_MAT & rocTemperature(nodalAtomicFieldsRoc_[TEMPERATURE].set_quantity());
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DENS_MAT & fePower(rhs_[TEMPERATURE].set_quantity());
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if (lammpsInterface_->rank_zero()) {
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// global data
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double T_mean = (fields_[TEMPERATURE].quantity()).col_sum(0)/nNodes_;
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feEngine_->add_global("temperature_mean", T_mean);
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double T_stddev = (fields_[TEMPERATURE].quantity()).col_stdev(0);
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feEngine_->add_global("temperature_std_dev", T_stddev);
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double Ta_mean = (nodalAtomicFields_[TEMPERATURE].quantity()).col_sum(0)/nNodes_;
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feEngine_->add_global("atomic_temperature_mean", Ta_mean);
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double Ta_stddev = (nodalAtomicFields_[TEMPERATURE].quantity()).col_stdev(0);
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feEngine_->add_global("atomic_temperature_std_dev", Ta_stddev);
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// different temperature measures, if appropriate
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if (nodalAtomicKineticTemperature_)
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outputData["kinetic_temperature"] = & _keTemp_;
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if (nodalAtomicConfigurationalTemperature_) {
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_peTemp_ *= 2; // account for full temperature
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outputData["configurational_temperature"] = & _peTemp_;
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}
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// mesh data
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outputData["NodalAtomicTemperature"] = &temperature;
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outputData["dot_temperature"] = &dotTemperature;
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outputData["ddot_temperature"] = &ddotTemperature;
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outputData["NodalAtomicPower"] = &rocTemperature;
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outputData["fePower"] = &fePower;
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// write data
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feEngine_->write_data(output_index(), fields_, & outputData);
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}
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feEngine_->partition_mesh();
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}
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}
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};
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