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replace tabs and remove trailing whitespace in lib folder with updated script

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This commit is contained in:
Axel Kohlmeyer
2021-08-22 20:45:24 -04:00
parent 30821b37e5
commit 92b5b159e5
311 changed files with 9176 additions and 9176 deletions
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102
lib/atc/ExtrinsicModelDriftDiffusion.cpp
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@ -39,7 +39,7 @@ namespace ATC {
string matFileName) :
ExtrinsicModelTwoTemperature(modelManager,modelType,matFileName),
continuityIntegrator_(nullptr),
poissonSolverType_(DIRECT), // ITERATIVE | DIRECT
poissonSolver_(nullptr),
baseSize_(0),
@ -49,34 +49,34 @@ namespace ATC {
schrodingerSolver_(nullptr),
schrodingerPoissonMgr_(),
schrodingerPoissonSolver_(nullptr),
maxConsistencyIter_(0), maxConstraintIter_(1),
maxConsistencyIter_(0), maxConstraintIter_(1),
safe_dEf_(0.1), Ef_shift_(0.0),
oneD_(false), oneDcoor_(0), oneDconserve_(0)
{
// delete base class's version of the physics model
if (physicsModel_) delete physicsModel_;
if (physicsModel_) delete physicsModel_;
if (modelType == DRIFT_DIFFUSION_EQUILIBRIUM) {
physicsModel_ = new PhysicsModelDriftDiffusionEquilibrium(matFileName);
physicsModel_ = new PhysicsModelDriftDiffusionEquilibrium(matFileName);
electronDensityEqn_ = ELECTRON_EQUILIBRIUM;
}
else if (modelType == DRIFT_DIFFUSION_SCHRODINGER) {
physicsModel_ = new PhysicsModelDriftDiffusionSchrodinger(matFileName);
physicsModel_ = new PhysicsModelDriftDiffusionSchrodinger(matFileName);
electronDensityEqn_ = ELECTRON_SCHRODINGER;
maxConsistencyIter_ = 1;
}
else if (modelType == DRIFT_DIFFUSION_SCHRODINGER_SLICE) {
physicsModel_ = new PhysicsModelDriftDiffusionSchrodingerSlice(matFileName);
physicsModel_ = new PhysicsModelDriftDiffusionSchrodingerSlice(matFileName);
electronDensityEqn_ = ELECTRON_SCHRODINGER;
maxConsistencyIter_ = 1;
}
else {
physicsModel_ = new PhysicsModelDriftDiffusion(matFileName);
physicsModel_ = new PhysicsModelDriftDiffusion(matFileName);
}
atc_->useConsistentMassMatrix_(ELECTRON_DENSITY) = true;
rhsMaskIntrinsic_(ELECTRON_TEMPERATURE,SOURCE) = true;
//atc_->fieldMask_(ELECTRON_TEMPERATURE,EXTRINSIC_SOURCE) = true;
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
@ -89,7 +89,7 @@ namespace ATC {
}
//--------------------------------------------------------
// modify
// modify
//--------------------------------------------------------
bool ExtrinsicModelDriftDiffusion::modify(int narg, char **arg)
{
@ -110,9 +110,9 @@ namespace ATC {
nNodes_ = atc_->num_nodes();
rhs_[ELECTRON_DENSITY].reset(nNodes_,1);
rhs_[ELECTRIC_POTENTIAL].reset(nNodes_,1);
// set up electron continuity integrator
Array2D <bool> rhsMask(NUM_TOTAL_FIELDS,NUM_FLUX);
Array2D <bool> rhsMask(NUM_TOTAL_FIELDS,NUM_FLUX);
rhsMask = false;
for (int i = 0; i < NUM_FLUX; i++) {
rhsMask(ELECTRON_DENSITY,i) = atc_->fieldMask_(ELECTRON_DENSITY,i);
@ -121,7 +121,7 @@ namespace ATC {
atc_->set_fixed_nodes();
if (continuityIntegrator_) delete continuityIntegrator_;
if (electronTimeIntegration_ == TimeIntegrator::IMPLICIT) {
if (electronTimeIntegration_ == TimeIntegrator::IMPLICIT) {
continuityIntegrator_ = new FieldImplicitEulerIntegrator(ELECTRON_DENSITY,
physicsModel_, atc_->feEngine_, atc_, rhsMask);
}
@ -142,7 +142,7 @@ namespace ATC {
rhsMask(ELECTRIC_POTENTIAL,i) = atc_->fieldMask_(ELECTRIC_POTENTIAL,i);
}
int type = ATC::LinearSolver::ITERATIVE_SOLVE_SYMMETRIC;
if (poissonSolverType_ == DIRECT) {
if (poissonSolverType_ == DIRECT) {
type = ATC::LinearSolver::DIRECT_SOLVE;
}
if (poissonSolver_) delete poissonSolver_;
@ -154,12 +154,12 @@ namespace ATC {
// set up schrodinger solver
if ( electronDensityEqn_ == ELECTRON_SCHRODINGER ) {
if ( schrodingerSolver_ ) delete schrodingerSolver_;
if ( oneD_ ) {
if ( oneD_ ) {
EfHistory_.reset(oneDslices_.size(),2);
schrodingerSolver_ = new SliceSchrodingerSolver(ELECTRON_DENSITY,
physicsModel_, atc_->feEngine_, atc_->prescribedDataMgr_, atc_,
oneDslices_,oneDdxs_);
}
}
else {
schrodingerSolver_ = new SchrodingerSolver(ELECTRON_DENSITY,
physicsModel_, atc_->feEngine_, atc_->prescribedDataMgr_, atc_);
@ -192,7 +192,7 @@ namespace ATC {
double dt = atc_->lammpsInterface_->dt();
double time = atc_->time();
int step = atc_->step();
if (step % fluxUpdateFreq_ != 0) return;
if (step % fluxUpdateFreq_ != 0) return;
// set Dirchlet data
atc_->set_fixed_nodes();
@ -201,25 +201,25 @@ namespace ATC {
atc_->set_sources();
// subcyle integration of fast electron variable/s
double idt = dt/nsubcycle_;
for (int i = 0; i < nsubcycle_ ; ++i) {
if (electronDensityEqn_ == ELECTRON_CONTINUITY) {
// update continuity eqn
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_DENSITY) )
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_DENSITY) )
continuityIntegrator_->update(idt,time,atc_->fields_,rhs_);
atc_->set_fixed_nodes();
atc_->set_fixed_nodes();
// solve poisson eqn for electric potential
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRIC_POTENTIAL) )
poissonSolver_->solve(atc_->fields(),rhs_);
}
}
else if (electronDensityEqn_ == ELECTRON_SCHRODINGER) {
if ( (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_DENSITY) )
if ( (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_DENSITY) )
|| (! atc_->prescribedDataMgr_->all_fixed(ELECTRIC_POTENTIAL) ) )
schrodingerPoissonSolver_->solve(rhs_,fluxes_);
}
// update electron temperature
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_TEMPERATURE)
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_TEMPERATURE)
&& temperatureIntegrator_ ) {
#ifdef ATC_VERBOSE
ATC::LammpsInterface::instance()->stream_msg_once("start temperature integration...",true,false);
@ -229,10 +229,10 @@ namespace ATC {
ATC::LammpsInterface::instance()->stream_msg_once(" done",false,true);
#endif
}
atc_->set_fixed_nodes();
atc_->set_fixed_nodes();
}
}
//--------------------------------------------------------
// set coupling source terms
@ -249,7 +249,7 @@ namespace ATC {
// output
//--------------------------------------------------------
void ExtrinsicModelDriftDiffusion::output(OUTPUT_LIST & outputData)
{
{
#ifdef ATC_VERBOSE
// ATC::LammpsInterface::instance()->print_msg_once("start output",true,false);
#endif
@ -355,13 +355,13 @@ namespace ATC {
baseSize_(0)
{
// delete base class's version of the physics model
if (physicsModel_) delete physicsModel_;
if (physicsModel_) delete physicsModel_;
if (modelType == CONVECTIVE_DRIFT_DIFFUSION_SCHRODINGER) {
physicsModel_ = new PhysicsModelDriftDiffusionConvectionSchrodinger(matFileName);
physicsModel_ = new PhysicsModelDriftDiffusionConvectionSchrodinger(matFileName);
electronDensityEqn_ = ELECTRON_SCHRODINGER;
}
else {
physicsModel_ = new PhysicsModelDriftDiffusionConvection(matFileName);
physicsModel_ = new PhysicsModelDriftDiffusionConvection(matFileName);
}
atc_->useConsistentMassMatrix_(ELECTRON_VELOCITY) = false;
atc_->useConsistentMassMatrix_(ELECTRON_TEMPERATURE) = false;
@ -388,7 +388,7 @@ namespace ATC {
nsd_ = atc_->nsd();
rhs_[ELECTRON_VELOCITY].reset(nNodes_,nsd_);
atc_->set_fixed_nodes(); // needed to correctly set BC data
// initialize Poisson solver
if (cddmPoissonSolver_) delete cddmPoissonSolver_;
@ -397,9 +397,9 @@ namespace ATC {
rhsMask(ELECTRIC_POTENTIAL,FLUX) = true;
pair<FieldName,FieldName> row_col(ELECTRIC_POTENTIAL,ELECTRIC_POTENTIAL);
SPAR_MAT stiffness;
(atc_->feEngine_)->compute_tangent_matrix(rhsMask,row_col, atc_->fields(), physicsModel_,
(atc_->feEngine_)->compute_tangent_matrix(rhsMask,row_col, atc_->fields(), physicsModel_,
atc_->element_to_material_map(), stiffness);
const BC_SET & bcs = (atc_->prescribedDataMgr_->bcs(ELECTRIC_POTENTIAL))[0];
cddmPoissonSolver_ = new LinearSolver(stiffness, bcs, poissonSolverType_,
@ -427,7 +427,7 @@ namespace ATC {
double dt = atc_->lammpsInterface_->dt();
double time = atc_->time();
int step = atc_->step();
if (step % fluxUpdateFreq_ != 0) return;
if (step % fluxUpdateFreq_ != 0) return;
// set Dirchlet data
atc_->set_fixed_nodes();
@ -436,16 +436,16 @@ namespace ATC {
atc_->set_sources();
// subcyle integration of fast electron variable/s
double idt = dt/nsubcycle_;
for (int i = 0; i < nsubcycle_ ; ++i) {
// update electron temperature mass matrix
atc_->compute_mass_matrix(ELECTRON_VELOCITY,physicsModel_);
// update electron velocity
if (!(atc_->prescribedDataMgr_)->all_fixed(ELECTRON_VELOCITY)) {
//const BCS & bcs
//const BCS & bcs
// = atc_->prescribedDataMgr_->bcs(ELECTRON_VELOCITY);
Array2D <bool> rhsMask(NUM_FIELDS,NUM_FLUX);
Array2D <bool> rhsMask(NUM_FIELDS,NUM_FLUX);
rhsMask = false;
rhsMask(ELECTRON_VELOCITY,SOURCE) = atc_->fieldMask_(ELECTRON_VELOCITY,SOURCE);
rhsMask(ELECTRON_VELOCITY,FLUX) = atc_->fieldMask_(ELECTRON_VELOCITY,FLUX);
@ -455,7 +455,7 @@ namespace ATC {
atc_->compute_rhs_vector(rhsMask, atc_->fields_, rhs, atc_->source_integration(), physicsModel_);
const DENS_MAT & velocityRhs = rhs[ELECTRON_VELOCITY].quantity();
// add a solver for electron momentum
// add a solver for electron momentum
DENS_MAT & velocity = (atc_->field(ELECTRON_VELOCITY)).set_quantity();
for (int j = 0; j < nsd_; ++j) {
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_VELOCITY,j) ) {
@ -477,12 +477,12 @@ namespace ATC {
}
}
}
//atc_->set_fixed_nodes();
if (electronDensityEqn_ == ELECTRON_CONTINUITY) {
// update continuity eqn
Array2D <bool> rhsMask(NUM_FIELDS,NUM_FLUX);
Array2D <bool> rhsMask(NUM_FIELDS,NUM_FLUX);
rhsMask = false;
rhsMask(ELECTRON_DENSITY,FLUX) = atc_->fieldMask_(ELECTRON_DENSITY,FLUX);
rhsMask(ELECTRON_DENSITY,SOURCE) = atc_->fieldMask_(ELECTRON_DENSITY,SOURCE);
@ -490,11 +490,11 @@ namespace ATC {
FIELDS rhs;
rhs[ELECTRON_DENSITY].reset(nNodes_,1);
atc_->compute_rhs_vector(rhsMask, atc_->fields_, rhs, atc_->source_integration(), physicsModel_);
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_DENSITY) )
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRON_DENSITY) )
continuityIntegrator_->update(idt,time,atc_->fields_,rhs);
atc_->set_fixed_nodes();
atc_->set_fixed_nodes();
// solve poisson eqn for electric potential
if (! atc_->prescribedDataMgr_->all_fixed(ELECTRIC_POTENTIAL) ) {
//poissonSolver_->solve(atc_->fields_,rhs_);
rhsMask = false;
@ -507,12 +507,12 @@ namespace ATC {
const CLON_VEC r =column(rhs[ELECTRIC_POTENTIAL].quantity(),0);
cddmPoissonSolver_->solve(x,r);
}
}
}
else if (electronDensityEqn_ == ELECTRON_SCHRODINGER) {
schrodingerPoissonSolver_->solve(rhs_,fluxes_);
}
atc_->set_fixed_nodes();
atc_->set_fixed_nodes();
// update electron temperature mass matrix
atc_->compute_mass_matrix(ELECTRON_TEMPERATURE,physicsModel_);
// update electron temperature
@ -521,11 +521,11 @@ namespace ATC {
temperatureIntegrator_->update(idt,time,atc_->fields_,rhs_);
//}
//else { // lumped mass matrix
//}
}
atc_->set_fixed_nodes();
atc_->set_fixed_nodes();
}
}
@ -536,8 +536,8 @@ namespace ATC {
void ExtrinsicModelDriftDiffusionConvection::output(OUTPUT_LIST & outputData)
{
ExtrinsicModelDriftDiffusion::output(outputData);
//FIELD jouleHeating(atc_->num_nodes(),1);
//set_kinetic_energy_source(atc_->fields(),jouleHeating);
outputData["joule_heating"] = & (atc_->extrinsic_source(TEMPERATURE)).set_quantity();
@ -587,7 +587,7 @@ namespace ATC {
DENS_MAT & velocity((atc_->field(ELECTRON_VELOCITY)).set_quantity());
SPAR_MAT & velocityMassMat = (atc_->consistentMassMats_[ELECTRON_VELOCITY]).set_quantity();
kineticEnergy.reset(nNodes_,1);
for (int j = 0; j < nsd_; j++) {
CLON_VEC myVelocity(velocity,CLONE_COL,j);
DENS_MAT velocityMat(nNodes_,1);