// ATC_Transfer headers #include "ATC_CouplingEnergy.h" #include "Thermostat.h" #include "ATC_Error.h" #include "PrescribedDataManager.h" #include "FieldManager.h" // Other Headers #include #include #include #include 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 * atomicReferencePotential; if (!initialized_) { atomicReferencePotential = new AtcAtomQuantity(this); interscaleManager_.add_per_atom_quantity(atomicReferencePotential, "AtomicReferencePotential"); atomicReferencePotential->set_memory_type(PERSISTENT); } else { atomicReferencePotential = static_cast * >(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 \section examples fix_modify atc temperature_definition kinetic \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 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(); } } };