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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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82
lib/atc/FieldManager.cpp
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@ -22,7 +22,7 @@ typedef PerAtomQuantity<double> PAQ;
//-----------------------------------------------------------------------------
//* restricted_atom_quantity
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::restricted_atom_quantity(FieldName field, string name, PAQ * atomicQuantity)
DENS_MAN * FieldManager::restricted_atom_quantity(FieldName field, string name, PAQ * atomicQuantity)
{
if (name == "default") { name = field_to_restriction_name(field); }
DENS_MAN * quantity = interscaleManager_.dense_matrix(name);
@ -35,7 +35,7 @@ typedef PerAtomQuantity<double> PAQ;
atomicQuantity = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
}
else {
if (!atomicQuantity) {
throw ATC_Error("FieldManager::restricted_atom_quantity - need to supply PAQ if restricted quantity does not already exist");
}
@ -68,18 +68,18 @@ typedef PerAtomQuantity<double> PAQ;
if (atc_->kernel_on_the_fly()) {
if (atc_->kernel_based()) {
quantity = new OnTheFlyKernelAccumulationNormalized(atc_, atomic,
atc_->kernel_function(),
atc_->atom_coarsegraining_positions(),
quantity = new OnTheFlyKernelAccumulationNormalized(atc_, atomic,
atc_->kernel_function(),
atc_->atom_coarsegraining_positions(),
normalization);
} else {
quantity = new OnTheFlyMeshAccumulationNormalized(atc_, atomic,
atc_->atom_coarsegraining_positions(),
quantity = new OnTheFlyMeshAccumulationNormalized(atc_, atomic,
atc_->atom_coarsegraining_positions(),
normalization);
}
} else {
quantity = new AtfProjection(atc_, atomic,
atc_->accumulant(),
quantity = new AtfProjection(atc_, atomic,
atc_->accumulant(),
normalization);
}
interscaleManager_.add_dense_matrix(quantity,name);
@ -102,21 +102,21 @@ typedef PerAtomQuantity<double> PAQ;
}
else if (atc_->kernel_on_the_fly()) {
if (atc_->kernel_based()) {
quantity = new OnTheFlyKernelAccumulationNormalizedReferenced(atc_,
atomic,
atc_->kernel_function(),
atc_->atom_coarsegraining_positions(),
quantity = new OnTheFlyKernelAccumulationNormalizedReferenced(atc_,
atomic,
atc_->kernel_function(),
atc_->atom_coarsegraining_positions(),
normalization,
reference);
} else {
quantity = new OnTheFlyMeshAccumulationNormalizedReferenced(atc_,
atomic,
atc_->atom_coarsegraining_positions(),
quantity = new OnTheFlyMeshAccumulationNormalizedReferenced(atc_,
atomic,
atc_->atom_coarsegraining_positions(),
normalization,
reference);
}
} else {
quantity = new AtfProjectionReferenced(atc_, atomic,
quantity = new AtfProjectionReferenced(atc_, atomic,
atc_->accumulant(),
reference,
normalization);
@ -141,14 +141,14 @@ typedef PerAtomQuantity<double> PAQ;
}
else if (atc_->kernel_on_the_fly()) {
if (atc_->kernel_based()) {
quantity = new OnTheFlyKernelAccumulationNormalizedScaled(atc_, atomic,
atc_->kernel_function(),
atc_->atom_coarsegraining_positions(),
quantity = new OnTheFlyKernelAccumulationNormalizedScaled(atc_, atomic,
atc_->kernel_function(),
atc_->atom_coarsegraining_positions(),
normalization,
scale);
} else {
quantity = new OnTheFlyMeshAccumulationNormalizedScaled(atc_, atomic,
atc_->atom_coarsegraining_positions(),
quantity = new OnTheFlyMeshAccumulationNormalizedScaled(atc_, atomic,
atc_->atom_coarsegraining_positions(),
normalization,
scale);
}
@ -203,7 +203,7 @@ typedef PerAtomQuantity<double> PAQ;
return projected_atom_quantity(NUMBER_DENSITY,name,atomic,atc_->accumulant_inverse_volumes());
}
//-----------------------------------------------------------------------------
//* MOMENTUM
//* MOMENTUM
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::momentum(string name)
{
@ -215,7 +215,7 @@ typedef PerAtomQuantity<double> PAQ;
return projected_atom_quantity(MOMENTUM,name,atomic,atc_->accumulant_inverse_volumes());
}
//-----------------------------------------------------------------------------
//* VELOCITY
//* VELOCITY
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::velocity(string name)
{
@ -243,7 +243,7 @@ typedef PerAtomQuantity<double> PAQ;
return v;
}
//-----------------------------------------------------------------------------
//* PROJECTED_VELOCITY
//* PROJECTED_VELOCITY
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::projected_velocity(string name)
{
@ -251,7 +251,7 @@ typedef PerAtomQuantity<double> PAQ;
return projected_atom_quantity(PROJECTED_VELOCITY,name,atomic,atc_->accumulant_inverse_volumes());
}
//-----------------------------------------------------------------------------
//* DISPLACEMENT
//* DISPLACEMENT
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::displacement(string name)
{
@ -261,8 +261,8 @@ typedef PerAtomQuantity<double> PAQ;
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicMassWeightedDisplacement");
if (!atomic) {
FundamentalAtomQuantity * atomMasses = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
FundamentalAtomQuantity * atomPositions = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_POSITION);
FundamentalAtomQuantity * atomMasses = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
FundamentalAtomQuantity * atomPositions = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_POSITION);
atomic = new AtomicMassWeightedDisplacement(atc_,atomPositions, atomMasses, atc_->atom_reference_positions(), INTERNAL);
interscaleManager_.add_per_atom_quantity(atomic,"AtomicMassWeightedDisplacement");
}
@ -296,12 +296,12 @@ typedef PerAtomQuantity<double> PAQ;
return u;
}
//-----------------------------------------------------------------------------
//* REFERENCE_POTENTIAL_ENERGY
//* REFERENCE_POTENTIAL_ENERGY
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::reference_potential_energy(string /* name */)
{
DENS_MAN * rpe = interscaleManager_.dense_matrix(field_to_string(REFERENCE_POTENTIAL_ENERGY));
if (! rpe ) {
if (! rpe ) {
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicReferencePotential");
if (!atomic) {
atomic = new AtcAtomQuantity<double>(atc_);
@ -334,7 +334,7 @@ typedef PerAtomQuantity<double> PAQ;
return rpe;
}
//-----------------------------------------------------------------------------
//* POTENTIAL_ENERGY
//* POTENTIAL_ENERGY
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::potential_energy(string name)
{
@ -352,7 +352,7 @@ typedef PerAtomQuantity<double> PAQ;
}
}
//-----------------------------------------------------------------------------
//* TEMPERATURE
//* TEMPERATURE
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::temperature(string name)
{
@ -367,10 +367,10 @@ typedef PerAtomQuantity<double> PAQ;
{
double Tcoef = 1./((atc_->nsd())*(atc_->lammps_interface())->kBoltzmann());
PAQ * atomic = per_atom_quantity("AtomicTwiceKineticEnergy");
return scaled_projected_atom_quantity(KINETIC_TEMPERATURE,name,atomic,Tcoef,atc_->accumulant_weights());
return scaled_projected_atom_quantity(KINETIC_TEMPERATURE,name,atomic,Tcoef,atc_->accumulant_weights());
}
//-----------------------------------------------------------------------------
//* THERMAL_ENERGY
//* THERMAL_ENERGY
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::thermal_energy(string name)
{
@ -379,7 +379,7 @@ typedef PerAtomQuantity<double> PAQ;
return scaled_projected_atom_quantity(THERMAL_ENERGY,name,atomic,Ecoef,atc_->accumulant_inverse_volumes());
}
//-----------------------------------------------------------------------------
//* KINETIC_ENERGY
//* KINETIC_ENERGY
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::kinetic_energy(string name)
{
@ -405,7 +405,7 @@ typedef PerAtomQuantity<double> PAQ;
return projected_atom_quantity(SPECIES_FLUX,name,atomic,atc_->accumulant_inverse_volumes());
}
//-----------------------------------------------------------------------------
//* INTERNAL_ENERGY
//* INTERNAL_ENERGY
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::internal_energy(string name)
{
@ -417,7 +417,7 @@ typedef PerAtomQuantity<double> PAQ;
return ie;
}
//-----------------------------------------------------------------------------
//* ENERGY
//* ENERGY
//-----------------------------------------------------------------------------
DENS_MAN * FieldManager::energy(string name)
{
@ -454,7 +454,7 @@ typedef PerAtomQuantity<double> PAQ;
return atomic;
}
//-----------------------------------------------------------------------------
//* 2 KE
//* 2 KE
//-----------------------------------------------------------------------------
PAQ * FieldManager::atomic_twice_kinetic_energy()
{
@ -503,7 +503,7 @@ typedef PerAtomQuantity<double> PAQ;
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicSpeciesVelocity");
if (!atomic) {
PAQ * atomVelocity = atomic_fluctuating_velocity();
PAQ * atomSpecies = atomic_species_vector();
PAQ * atomSpecies = atomic_species_vector();
atomic = new SpeciesVelocity(atc_,atomVelocity,atomSpecies);
interscaleManager_.add_per_atom_quantity(atomic, "AtomicSpeciesVelocity");
}
@ -529,8 +529,8 @@ typedef PerAtomQuantity<double> PAQ;
{
PAQ * quantity = interscaleManager_.per_atom_quantity(field_to_prolongation_name(field));
if (!quantity) {
DENS_MAN * coarseQuantity = interscaleManager_.dense_matrix(field_to_string(field));
if (!coarseQuantity) coarseQuantity = nodal_atomic_field(field);
if (!coarseQuantity) throw ATC_Error("can not prolong quantity: " + field_to_string(field) + " no field registered");