replace tabs and remove trailing whitespace in lib folder with updated script
This commit is contained in:
Axel Kohlmeyer
@ -22,7 +22,7 @@ namespace ATC {
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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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@ -36,12 +36,12 @@ namespace ATC {
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nodalAtomicConfigurationalTemperature_(nullptr),
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refPE_(0)
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{
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// Allocate PhysicsModel
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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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extrinsicModelManager_.create_model(extrinsicModel,matParamFile);
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}
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// set up field data based on physicsModel
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@ -129,14 +129,14 @@ namespace ATC {
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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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@ -144,14 +144,14 @@ namespace ATC {
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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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@ -166,14 +166,14 @@ namespace ATC {
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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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@ -183,7 +183,7 @@ namespace ATC {
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}
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// always need fluctuating velocity and 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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field_to_prolongation_name(VELOCITY));
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@ -267,16 +267,16 @@ namespace ATC {
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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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@ -299,17 +299,17 @@ namespace ATC {
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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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@ -360,7 +360,7 @@ namespace ATC {
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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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feEngine_->compute_energy(mask,
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fields_,
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physicsModel_,
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elementToMaterialMap_,
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@ -371,7 +371,7 @@ namespace ATC {
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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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@ -399,14 +399,14 @@ namespace ATC {
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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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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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@ -435,9 +435,9 @@ namespace ATC {
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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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@ -447,13 +447,13 @@ namespace ATC {
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}
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// auxiliary 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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@ -469,18 +469,18 @@ namespace ATC {
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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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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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@ -491,10 +491,10 @@ namespace ATC {
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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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feEngine_->write_data(output_index(), fields_, & outputData);
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}
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// hence propagation is performed on proc 0 but not others.
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// The real fix is to have const data in the output list
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// force optional variables to reset to keep in sync
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