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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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30
lib/atc/SpeciesTimeIntegrator.cpp
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@ -24,7 +24,7 @@ namespace ATC {
//--------------------------------------------------------
// Constructor
// Grab data from ATC
//--------------------------------------------------------
//--------------------------------------------------------
SpeciesTimeIntegrator::SpeciesTimeIntegrator(ATC_CouplingMass * atc,
TimeIntegrationType timeIntegrationType) :
TimeIntegrator(atc, timeIntegrationType),
@ -88,7 +88,7 @@ namespace ATC {
//--------------------------------------------------------
void SpeciesTimeIntegrator::pack_fields(RESTART_LIST & data)
{
TimeIntegrator::pack_fields(data);
}
@ -101,7 +101,7 @@ namespace ATC {
//--------------------------------------------------------
// Constructor
// Grab data from ATC
//--------------------------------------------------------
//--------------------------------------------------------
SpeciesIntegrationMethod::SpeciesIntegrationMethod(SpeciesTimeIntegrator * speciesTimeIntegrator,
const map<string,pair<MolSize,int> > & moleculeIds) :
TimeIntegrationMethod(speciesTimeIntegrator),
@ -124,10 +124,10 @@ namespace ATC {
void SpeciesIntegrationMethod::construct_transfers()
{
InterscaleManager & interscaleManager = atc_->interscale_manager();
// get existing data
nodalAtomicMassDensity_ = interscaleManager.dense_matrix(field_to_intrinsic_name(MASS_DENSITY));
if (atc_->has_tracked_species())
if (atc_->has_tracked_species())
nodalAtomicSpeciesConcentration_ = interscaleManager.dense_matrix(field_to_intrinsic_name(SPECIES_CONCENTRATION));
}
@ -139,7 +139,7 @@ namespace ATC {
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
//--------------------------------------------------------
SpeciesTimeIntegratorFractionalStep::SpeciesTimeIntegratorFractionalStep(SpeciesTimeIntegrator * speciesTimeIntegrator,
const map<string,pair<MolSize,int> > & moleculeIds) :
SpeciesIntegrationMethod(speciesTimeIntegrator,moleculeIds)
@ -161,10 +161,10 @@ namespace ATC {
}
if (!timeFilterManager->end_equilibrate()) {
nodalAtomicSpeciesConcentrationFiltered_ = nodalAtomicSpeciesConcentration_->quantity();
nodalAtomicSpeciesConcentrationFiltered_ = nodalAtomicSpeciesConcentration_->quantity();
}
pre_final_integrate1(0.);
}
@ -172,7 +172,7 @@ namespace ATC {
// pre_initial_integrate1
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStep::pre_initial_integrate1(double dt)
{
{
const DENS_MAT & my(nodalAtomicSpeciesConcentration_->quantity());
// updated filtered energy using explicit-implicit scheme
timeFilter_->apply_pre_step1(nodalAtomicSpeciesConcentrationFiltered_.set_quantity(),
@ -182,15 +182,15 @@ namespace ATC {
//--------------------------------------------------------
// pre_final_integrate1
// first time integration computations
// first time integration computations
// before FractionalStep step 2
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStep::pre_final_integrate1(double /* dt */)
{
// Compute MD contribution to FEM equation
massDensity_ = nodalAtomicMassDensity_->quantity();
massDensity_ = nodalAtomicMassDensity_->quantity();
speciesConcentration_ = nodalAtomicSpeciesConcentration_->quantity();
atc_->set_fixed_nodes();
}
@ -204,7 +204,7 @@ namespace ATC {
timeFilter_->apply_post_step1(
nodalAtomicSpeciesConcentrationFiltered_.set_quantity(),
nodalAtomicSpeciesConcentration_->quantity(),dt);
speciesConcentration_ = nodalAtomicSpeciesConcentrationFiltered_.quantity();
speciesConcentration_ = nodalAtomicSpeciesConcentrationFiltered_.quantity();
}
//--------------------------------------------------------
@ -213,7 +213,7 @@ namespace ATC {
//--------------------------------------------------------
void SpeciesTimeIntegratorFractionalStep::post_process()
{
map<string,pair<MolSize,int> >::const_iterator molecule;
for (molecule = moleculeIds_.begin(); molecule != moleculeIds_.end(); molecule++) {
DENS_MAN & nodalMoleculeMassDensityOut(atc_->tagged_dens_man(molecule->first));