forked from lijiext/lammps
509 lines
23 KiB
C++
509 lines
23 KiB
C++
// ATC headers
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#include "ATC_CouplingMomentumEnergy.h"
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#include "KinetoThermostat.h"
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#include "ATC_Error.h"
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#include "PrescribedDataManager.h"
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// Other Headers
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#include <vector>
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#include <map>
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#include <set>
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#include <utility>
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#include <typeinfo>
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#include <iostream>
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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_CouplingMomentumEnergy
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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_CouplingMomentumEnergy::ATC_CouplingMomentumEnergy(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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refPE_(0)
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{
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// Allocate PhysicsModel
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create_physics_model(THERMO_ELASTIC, 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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// set up field data based on physicsModel
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physicsModel_->num_fields(fieldSizes_,fieldMask_);
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// Defaults
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set_time();
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bndyIntType_ = FE_INTERPOLATION;
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trackCharge_ = false;
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// set up atomic regulator
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atomicRegulator_ = new KinetoThermostat(this);
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// set up physics specific time integrator and thermostat
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trackDisplacement_ = true;
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fieldSizes_[DISPLACEMENT] = fieldSizes_[VELOCITY];
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timeIntegrators_[VELOCITY] = new MomentumTimeIntegrator(this,TimeIntegrator::FRACTIONAL_STEP);
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timeIntegrators_[TEMPERATURE] = new ThermalTimeIntegrator(this,TimeIntegrator::FRACTIONAL_STEP);
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ghostManager_.set_boundary_dynamics(GhostManager::PRESCRIBED);
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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 mechanical kinetic energy
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// output[2] = total coarse scale mechanical potential energy
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// output[3] = total coarse scale mechanical energy
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// output[1] = total coarse scale thermal energy
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// output[2] = average temperature
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scalarFlag_ = 1;
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vectorFlag_ = 1;
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sizeVector_ = 5;
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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_CouplingMomentumEnergy::~ATC_CouplingMomentumEnergy()
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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_CouplingMomentumEnergy::initialize()
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{
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// clear displacement entries if requested
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if (!trackDisplacement_) {
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fieldSizes_.erase(DISPLACEMENT);
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for (int i = 0; i < NUM_FLUX; i++)
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fieldMask_(DISPLACEMENT,i) = false;
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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_(VELOCITY,i) = fieldMask_(VELOCITY,i);
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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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refPE_=0;
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refPE_=potential_energy();
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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_CouplingMomentumEnergy::construct_transfers()
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{
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ATC_Coupling::construct_transfers();
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// momentum of each atom
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AtomicMomentum * atomicMomentum = new AtomicMomentum(this);
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interscaleManager_.add_per_atom_quantity(atomicMomentum,
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"AtomicMomentum");
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// nodal momentum for RHS
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AtfShapeFunctionRestriction * nodalAtomicMomentum = new AtfShapeFunctionRestriction(this,
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atomicMomentum,
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shpFcn_);
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interscaleManager_.add_dense_matrix(nodalAtomicMomentum,
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"NodalAtomicMomentum");
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// nodal forces
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FundamentalAtomQuantity * atomicForce = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_FORCE);
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AtfShapeFunctionRestriction * nodalAtomicForce = new AtfShapeFunctionRestriction(this,
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atomicForce,
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shpFcn_);
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interscaleManager_.add_dense_matrix(nodalAtomicForce,
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"NodalAtomicForce");
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// nodal velocity derived only from atoms
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AtfShapeFunctionMdProjection * nodalAtomicVelocity = new AtfShapeFunctionMdProjection(this,
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nodalAtomicMomentum,
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VELOCITY);
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interscaleManager_.add_dense_matrix(nodalAtomicVelocity,
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"NodalAtomicVelocity");
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if (trackDisplacement_) {
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// mass-weighted (center-of-mass) displacement of each atom
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AtomicMassWeightedDisplacement * atomicMassWeightedDisplacement;
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if (needXrefProcessorGhosts_ || groupbitGhost_) { // explicit construction on internal group
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PerAtomQuantity<double> * atomReferencePositions = interscaleManager_.per_atom_quantity("AtomicInternalReferencePositions");
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atomicMassWeightedDisplacement = new AtomicMassWeightedDisplacement(this,atomPositions_,
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atomMasses_,
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atomReferencePositions,
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INTERNAL);
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}
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else
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atomicMassWeightedDisplacement = new AtomicMassWeightedDisplacement(this);
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interscaleManager_.add_per_atom_quantity(atomicMassWeightedDisplacement,
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"AtomicMassWeightedDisplacement");
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// nodal (RHS) mass-weighted displacement
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AtfShapeFunctionRestriction * nodalAtomicMassWeightedDisplacement = new AtfShapeFunctionRestriction(this,
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atomicMassWeightedDisplacement,
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shpFcn_);
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interscaleManager_.add_dense_matrix(nodalAtomicMassWeightedDisplacement,
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"NodalAtomicMassWeightedDisplacement");
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// nodal displacement derived only from atoms
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AtfShapeFunctionMdProjection * nodalAtomicDisplacement = new AtfShapeFunctionMdProjection(this,
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nodalAtomicMassWeightedDisplacement,
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VELOCITY);
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interscaleManager_.add_dense_matrix(nodalAtomicDisplacement,
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"NodalAtomicDisplacement");
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}
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// always need kinetic energy
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FtaShapeFunctionProlongation * atomicMeanVelocity = new FtaShapeFunctionProlongation(this,&fields_[VELOCITY],shpFcn_);
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interscaleManager_.add_per_atom_quantity(atomicMeanVelocity,
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"AtomicMeanVelocity");
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AtomicEnergyForTemperature * atomicTwiceKineticEnergy = new TwiceFluctuatingKineticEnergy(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_CouplingMomentumEnergy: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,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 = 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_CouplingMomentumEnergy::init_filter()
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{
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if (timeIntegrators_[TEMPERATURE]->time_integration_type() != TimeIntegrator::FRACTIONAL_STEP) {
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throw ATC_Error("ATC_CouplingMomentumEnergy::initialize - method only valid with fractional step time integration");
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}
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ATC_Coupling::init_filter();
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if (timeFilterManager_.end_equilibrate() && equilibriumStart_) {
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if (atomicRegulator_->coupling_mode(VELOCITY)==AtomicRegulator::FLUX || atomicRegulator_->coupling_mode(VELOCITY)==AtomicRegulator::GHOST_FLUX)
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// nothing needed in other cases since kinetostat force is balanced by boundary flux in FE equations
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atomicRegulator_->reset_lambda_contribution(nodalAtomicFieldsRoc_[VELOCITY].quantity(),VELOCITY);
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DENS_MAT powerMat(-1.*(nodalAtomicFields_[TEMPERATURE].quantity()));
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atomicRegulator_->reset_lambda_contribution(powerMat,TEMPERATURE);
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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_CouplingMomentumEnergy::modify(int narg, char **arg)
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{
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bool foundMatch = false;
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int argIndex = 0;
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return foundMatch;
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}
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//--------------------------------------------------------------------
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// compute_scalar : added energy
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//--------------------------------------------------------------------
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double ATC_CouplingMomentumEnergy::compute_scalar(void)
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{
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double energy = 0.0;
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energy += extrinsicModelManager_.compute_scalar();
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return energy;
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}
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//--------------------------------------------------------------------
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// total kinetic energy
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//--------------------------------------------------------------------
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double ATC_CouplingMomentumEnergy::kinetic_energy(void)
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{
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const MATRIX & M = massMats_[VELOCITY].quantity();
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const DENS_MAT & velocity(fields_[VELOCITY].quantity());
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double mvv2e = lammpsInterface_->mvv2e();
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double kineticEnergy = 0;
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DENS_VEC velocitySquared(nNodes_);
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for (int i = 0; i < nNodes_; i++)
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for (int j = 0; j < nsd_; j++)
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velocitySquared(i) += velocity(i,j)*velocity(i,j);
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kineticEnergy = (M*velocitySquared).sum();
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kineticEnergy *= mvv2e; // convert to LAMMPS units
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return kineticEnergy;
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}
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//--------------------------------------------------------------------
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// total potential energy
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//--------------------------------------------------------------------
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double ATC_CouplingMomentumEnergy::potential_energy(void)
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{
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Array<FieldName> mask(1);
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mask(0) = VELOCITY;
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FIELD_MATS energy;
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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 potentialEnergy = energy[VELOCITY].col_sum();
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double mvv2e = lammpsInterface_->mvv2e();
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potentialEnergy *= mvv2e; // convert to LAMMPS units
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return potentialEnergy-refPE_;
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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_CouplingMomentumEnergy::compute_vector(int n)
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{
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// output[1] = total coarse scale kinetic energy
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// output[2] = total coarse scale potential energy
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// output[3] = total coarse scale energy
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// output[4] = total coarse scale thermal energy
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// output[5] = 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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return kinetic_energy();
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}
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else if (n == 1) {
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return potential_energy();
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}
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else if (n == 2) {
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return kinetic_energy()+potential_energy();
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}
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else if (n == 4) {
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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 == 5) {
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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 > 5) {
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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_CouplingMomentumEnergy::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 & velocity(nodalAtomicFields_[VELOCITY].set_quantity());
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DENS_MAT & rhs(rhs_[VELOCITY].set_quantity());
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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["NodalAtomicVelocity"] = &velocity;
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outputData["FE_Force"] = &rhs;
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if (trackDisplacement_)
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outputData["NodalAtomicDisplacement"] = & nodalAtomicFields_[DISPLACEMENT].set_quantity();
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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();
|
|
}
|
|
}
|
|
|
|
};
|