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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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326
lib/atc/ATC_Transfer.cpp
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@ -68,7 +68,7 @@ namespace ATC {
LAMMPS_NS::Fix * thisFix,
string matParamFile)
: ATC_Method(groupName,perAtomArray,thisFix),
xPointer_(nullptr),
xPointer_(nullptr),
outputStepZero_(true),
neighborReset_(false),
pairMap_(nullptr),
@ -95,7 +95,7 @@ namespace ATC {
lmp->lattice(cb.cell_vectors, cb.basis_vectors);
cb.inv_atom_volume = 1.0 / lmp->volume_per_atom();
cb.e2mvv = 1.0 / lmp->mvv2e();
cb.atom_mass = lmp->atom_mass(1);
cb.atom_mass = lmp->atom_mass(1);
cb.boltzmann = lmp->boltz();
cb.hbar = lmp->hbar();
cauchyBornStress_ = new StressCauchyBorn(fileId, cb);
@ -103,7 +103,7 @@ namespace ATC {
// Defaults
set_time();
outputFlags_.reset(NUM_TOTAL_FIELDS);
outputFlags_ = false;
fieldFlags_.reset(NUM_TOTAL_FIELDS);
@ -117,20 +117,20 @@ namespace ATC {
for (int i = 0; i < NUM_TOTAL_FIELDS; i++) { outputFields_[i] = nullptr; }
// Hardy requires ref positions for processor ghosts for bond list
//needXrefProcessorGhosts_ = true;
}
//-------------------------------------------------------------------
ATC_Transfer::~ATC_Transfer()
{
interscaleManager_.clear();
if (cauchyBornStress_) delete cauchyBornStress_;
interscaleManager_.clear();
if (cauchyBornStress_) delete cauchyBornStress_;
}
//-------------------------------------------------------------------
// called before the beginning of a "run"
void ATC_Transfer::initialize()
void ATC_Transfer::initialize()
{
if (kernelOnTheFly_ && !readRefPE_ && !setRefPEvalue_) {
if (setRefPE_) {
@ -143,7 +143,7 @@ namespace ATC {
ATC_Method::initialize();
if (!initialized_) {
if (!initialized_) {
if (cauchyBornStress_) cauchyBornStress_->initialize();
}
@ -164,16 +164,16 @@ namespace ATC {
ghostManager_.initialize();
// initialize bond matrix B_Iab
if ((! bondOnTheFly_)
&& ( ( fieldFlags_(STRESS)
|| fieldFlags_(ESHELBY_STRESS)
if ((! bondOnTheFly_)
&& ( ( fieldFlags_(STRESS)
|| fieldFlags_(ESHELBY_STRESS)
|| fieldFlags_(HEAT_FLUX) ) ) ) {
try {
compute_bond_matrix();
}
catch(bad_alloc&) {
compute_bond_matrix();
}
catch(bad_alloc&) {
ATC::LammpsInterface::instance()->print_msg("stress/heat_flux will be computed on-the-fly");
bondOnTheFly_ = true;
}
}
@ -181,7 +181,7 @@ namespace ATC {
// set sample frequency to output if sample has not be specified
if (sampleFrequency_ == 0) sampleFrequency_ = outputFrequency_;
// output for step 0
// output for step 0
if (!initialized_) {
if (outputFrequency_ > 0) {
// initialize filtered data
@ -224,9 +224,9 @@ namespace ATC {
lammpsInterface_->computes_addstep(lammpsInterface_->ntimestep()+sampleFrequency_);
//remap_ghost_ref_positions();
update_peratom_output();
update_peratom_output();
}
//-------------------------------------------------------------------
@ -242,7 +242,7 @@ namespace ATC {
void ATC_Transfer::construct_time_integration_data()
{
if (!initialized_) {
// size arrays for requested/required fields
for(int index=0; index < NUM_TOTAL_FIELDS; ++index) {
if (fieldFlags_(index)) {
@ -298,13 +298,13 @@ namespace ATC {
{
// interpolant
if (!(kernelOnTheFly_)) {
// finite element shape functions for interpolants
// finite element shape functions for interpolants
PerAtomShapeFunction * atomShapeFunctions = new PerAtomShapeFunction(this);
interscaleManager_.add_per_atom_sparse_matrix(atomShapeFunctions,"Interpolant");
shpFcn_ = atomShapeFunctions;
}
// accummulant and weights
this->create_atom_volume();
// accumulants
if (kernelFunction_) {
@ -312,7 +312,7 @@ namespace ATC {
if (kernelOnTheFly_) {
ConstantQuantity<double> * atomCount = new ConstantQuantity<double>(this,1.);
interscaleManager_.add_per_atom_quantity(atomCount,"AtomCount");
OnTheFlyKernelAccumulation * myWeights
OnTheFlyKernelAccumulation * myWeights
= new OnTheFlyKernelAccumulation(this,
atomCount, kernelFunction_, atomCoarseGrainingPositions_);
interscaleManager_.add_dense_matrix(myWeights,
@ -337,7 +337,7 @@ namespace ATC {
if (kernelOnTheFly_) {
ConstantQuantity<double> * atomCount = new ConstantQuantity<double>(this,1.);
interscaleManager_.add_per_atom_quantity(atomCount,"AtomCount");
OnTheFlyMeshAccumulation * myWeights
OnTheFlyMeshAccumulation * myWeights
= new OnTheFlyMeshAccumulation(this,
atomCount, atomCoarseGrainingPositions_);
interscaleManager_.add_dense_matrix(myWeights,
@ -363,13 +363,13 @@ namespace ATC {
// molecule centroid, molecule charge, dipole moment and quadrupole moment calculations KKM add
if (!moleculeIds_.empty()) {
map<string,pair<MolSize,int> >::const_iterator molecule;
InterscaleManager & interscaleManager = this->interscale_manager(); // KKM add, may be we do not need this as interscaleManager_ already exists.
InterscaleManager & interscaleManager = this->interscale_manager(); // KKM add, may be we do not need this as interscaleManager_ already exists.
PerAtomQuantity<double> * atomProcGhostCoarseGrainingPositions_ = interscaleManager.per_atom_quantity("AtomicProcGhostCoarseGrainingPositions");
FundamentalAtomQuantity * mass = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS,PROC_GHOST);
molecule = moleculeIds_.begin();
int groupbit = (molecule->second).second;
smallMoleculeSet_ = new SmallMoleculeSet(this,groupbit);
smallMoleculeSet_->initialize(); // KKM add, why should we?
smallMoleculeSet_->initialize(); // KKM add, why should we?
interscaleManager_.add_small_molecule_set(smallMoleculeSet_,"MoleculeSet");
moleculeCentroid_ = new SmallMoleculeCentroid(this,mass,smallMoleculeSet_,atomProcGhostCoarseGrainingPositions_);
interscaleManager_.add_dense_matrix(moleculeCentroid_,"MoleculeCentroid");
@ -393,7 +393,7 @@ namespace ATC {
// set pointer to positions
// REFACTOR use method's handling of xref/xpointer
set_xPointer();
set_xPointer();
ATC_Method::construct_transfers();
@ -412,7 +412,7 @@ namespace ATC {
}
// for hardy-based fluxes
bool needsBondMatrix = (! bondOnTheFly_ ) &&
(fieldFlags_(STRESS)
|| fieldFlags_(ESHELBY_STRESS)
@ -434,7 +434,7 @@ namespace ATC {
const FE_Mesh * fe_mesh = feEngine_->fe_mesh();
if (!kernelBased_) {
bondMatrix_ = new BondMatrixPartitionOfUnity(lammpsInterface_,*pairMap_,xPointer_,fe_mesh,accumulantInverseVolumes_);
bondMatrix_ = new BondMatrixPartitionOfUnity(lammpsInterface_,*pairMap_,xPointer_,fe_mesh,accumulantInverseVolumes_);
}
else {
bondMatrix_ = new BondMatrixKernel(lammpsInterface_,*pairMap_,xPointer_,fe_mesh,kernelFunction_);
@ -470,7 +470,7 @@ namespace ATC {
FieldManager fmgr(this);
// for(int index=0; index < NUM_TOTAL_FIELDS; ++index)
// for(int index=0; index < NUM_TOTAL_FIELDS; ++index)
for(int i=0; i < numFields_; ++i) {
FieldName index = indices_[i];
if (fieldFlags_(index)) {
@ -492,9 +492,9 @@ namespace ATC {
interscaleManager_.add_per_atom_quantity(c,tag);
int projection = iter->second;
DIAG_MAN * w = nullptr;
if (projection == VOLUME_NORMALIZATION )
if (projection == VOLUME_NORMALIZATION )
{ w = accumulantInverseVolumes_; }
else if (projection == NUMBER_NORMALIZATION )
else if (projection == NUMBER_NORMALIZATION )
{ w = accumulantWeights_; }
if (kernelFunction_ && kernelOnTheFly_) {
OnTheFlyKernelAccumulationNormalized * C = new OnTheFlyKernelAccumulationNormalized(this, c, kernelFunction_, atomCoarseGrainingPositions_, w);
@ -507,7 +507,7 @@ namespace ATC {
outputFieldsTagged_[tag] = C;
}
}
}
//-------------------------------------------------------------------
@ -519,18 +519,18 @@ namespace ATC {
if ((!initialized_) || timeFilterManager_.need_reset()) {
timeFilters_.reset(NUM_TOTAL_FIELDS+nComputes_);
sampleCounter_ = 0;
// for filtered fields
for(int index=0; index < NUM_TOTAL_FIELDS; ++index) {
if (fieldFlags_(index)) {
string name = field_to_string((FieldName) index);
filteredData_[name] = 0.0;
timeFilters_(index) = timeFilterManager_.construct();
timeFilters_(index) = timeFilterManager_.construct();
}
}
// for filtered projected computes
// lists/accessing of fields ( & computes)
map <string,int>::const_iterator iter;
int index = NUM_TOTAL_FIELDS;
@ -546,7 +546,7 @@ namespace ATC {
//-------------------------------------------------------------------
// called after the end of a "run"
void ATC_Transfer::finish()
void ATC_Transfer::finish()
{
// base class
ATC_Method::finish();
@ -560,7 +560,7 @@ namespace ATC {
int argIdx = 0;
// check to see if it is a transfer class command
/*! \page man_hardy_fields fix_modify AtC fields
/*! \page man_hardy_fields fix_modify AtC fields
\section syntax
fix_modify AtC fields <all | none> \n
fix_modify AtC fields <add | delete> <list_of_fields> \n
@ -575,13 +575,13 @@ namespace ATC {
temperature : temperature derived from the relative atomic kinetic energy (as done by ) \n
kinetic_temperature : temperature derived from the full kinetic energy \n
number_density : simple kernel estimation of number of atoms per unit volume \n
stress :
stress :
Cauchy stress tensor for eulerian analysis (atom_element_map), or
1st Piola-Kirchhoff stress tensor for lagrangian analysis \n
transformed_stress :
1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or
transformed_stress :
1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or
Cauchy stress tensor for lagrangian analysis \n
heat_flux : spatial heat flux vector for eulerian,
heat_flux : spatial heat flux vector for eulerian,
or referential heat flux vector for lagrangian \n
potential_energy : potential energy per unit volume \n
kinetic_energy : kinetic energy per unit volume \n
@ -590,23 +590,23 @@ namespace ATC {
energy : total energy (potential + kinetic) per unit volume \n
number_density : number of atoms per unit volume \n
eshelby_stress: configurational stress (energy-momentum) tensor defined by Eshelby
[References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244,
[References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244,
No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335] \n
vacancy_concentration: volume fraction of vacancy content \n
type_concentration: volume fraction of a specific atom type \n
\section examples
<TT> fix_modify AtC fields add velocity temperature </TT>
\section description
Allows modification of the fields calculated and output by the
Allows modification of the fields calculated and output by the
transfer class. The commands are cumulative, e.g.\n
<TT> fix_modify AtC fields none </TT> \n
followed by \n
<TT> fix_modify AtC fields none </TT> \n
followed by \n
<TT> fix_modify AtC fields add velocity temperature </TT> \n
will only output the velocity and temperature fields.
\section restrictions
Must be used with the hardy/field type of AtC fix, see \ref man_fix_atc.
Currently, the stress and heat flux formulas are only correct for
central force potentials, e.g. Lennard-Jones and EAM
Currently, the stress and heat flux formulas are only correct for
central force potentials, e.g. Lennard-Jones and EAM
but not Stillinger-Weber.
\section related
See \ref man_hardy_gradients , \ref man_hardy_rates and \ref man_hardy_computes
@ -615,30 +615,30 @@ namespace ATC {
*/
if (strcmp(arg[argIdx],"fields")==0) {
argIdx++;
if (strcmp(arg[argIdx],"all")==0) {
if (strcmp(arg[argIdx],"all")==0) {
outputFlags_ = true;
match = true;
}
else if (strcmp(arg[argIdx],"none")==0) {
}
else if (strcmp(arg[argIdx],"none")==0) {
outputFlags_ = false;
match = true;
}
else if (strcmp(arg[argIdx],"add")==0) {
}
else if (strcmp(arg[argIdx],"add")==0) {
argIdx++;
for (int i = argIdx; i < narg; ++i) {
FieldName field_name = string_to_field(arg[i]);
outputFlags_(field_name) = true;
outputFlags_(field_name) = true;
}
match = true;
}
else if (strcmp(arg[argIdx],"delete")==0) {
}
else if (strcmp(arg[argIdx],"delete")==0) {
argIdx++;
for (int i = argIdx; i < narg; ++i) {
FieldName field_name = string_to_field(arg[i]);
outputFlags_(field_name) = false;
outputFlags_(field_name) = false;
}
match = true;
}
}
check_field_dependencies();
if (fieldFlags_(DISPLACEMENT)) { trackDisplacement_ = true; }
}
@ -649,17 +649,17 @@ namespace ATC {
- add | delete (keyword) = add or delete the calculation of gradients for the listed output fields \n
- fields (keyword) = \n
gradients can be calculated for all fields listed in \ref man_hardy_fields
\section examples
<TT> fix_modify AtC gradients add temperature velocity stress </TT> \n
<TT> fix_modify AtC gradients delete velocity </TT> \n
\section description
Requests calculation and output of gradients of the fields from the
transfer class. These gradients will be with regard to spatial or material
coordinate for eulerian or lagrangian analysis, respectively, as specified by
coordinate for eulerian or lagrangian analysis, respectively, as specified by
atom_element_map (see \ref man_atom_element_map )
\section restrictions
Must be used with the hardy/field type of AtC fix
Must be used with the hardy/field type of AtC fix
( see \ref man_fix_atc )
\section related
\section default
@ -667,33 +667,33 @@ namespace ATC {
*/
else if (strcmp(arg[argIdx],"gradients")==0) {
argIdx++;
if (strcmp(arg[argIdx],"add")==0) {
if (strcmp(arg[argIdx],"add")==0) {
argIdx++;
FieldName field_name;
for (int i = argIdx; i < narg; ++i) {
field_name = string_to_field(arg[i]);
gradFlags_(field_name) = true;
gradFlags_(field_name) = true;
}
match = true;
}
else if (strcmp(arg[argIdx],"delete")==0) {
}
else if (strcmp(arg[argIdx],"delete")==0) {
argIdx++;
FieldName field_name;
for (int i = argIdx; i < narg; ++i) {
field_name = string_to_field(arg[i]);
gradFlags_(field_name) = false;
gradFlags_(field_name) = false;
}
match = true;
}
}
}
/*! \page man_hardy_rates fix_modify AtC rates
/*! \page man_hardy_rates fix_modify AtC rates
\section syntax
fix_modify AtC rates <add | delete> <list_of_fields> \n
- add | delete (keyword) = add or delete the calculation of rates (time derivatives) for the listed output fields \n
- fields (keyword) = \n
rates can be calculated for all fields listed in \ref man_hardy_fields
\section examples
<TT> fix_modify AtC rates add temperature velocity stress </TT> \n
<TT> fix_modify AtC rates delete stress </TT> \n
@ -703,7 +703,7 @@ namespace ATC {
are the partial time derivatives of the nodal fields, not the full (material) time
derivatives. \n
\section restrictions
Must be used with the hardy/field type of AtC fix
Must be used with the hardy/field type of AtC fix
( see \ref man_fix_atc )
\section related
\section default
@ -711,16 +711,16 @@ namespace ATC {
*/
else if (strcmp(arg[argIdx],"rates")==0) {
argIdx++;
if (strcmp(arg[argIdx],"add")==0) {
if (strcmp(arg[argIdx],"add")==0) {
argIdx++;
FieldName field_name;
for (int i = argIdx; i < narg; ++i) {
field_name = string_to_field(arg[i]);
rateFlags_(field_name) = true;
rateFlags_(field_name) = true;
}
match = true;
}
else if (strcmp(arg[argIdx],"delete")==0) {
}
else if (strcmp(arg[argIdx],"delete")==0) {
argIdx++;
FieldName field_name;
for (int i = argIdx; i < narg; ++i) {
@ -728,7 +728,7 @@ namespace ATC {
rateFlags_(field_name) = false;
}
match = true;
}
}
}
@ -736,7 +736,7 @@ namespace ATC {
\section syntax
fix_modify AtC pair_interactions <on|off> \n
fix_modify AtC bond_interactions <on|off> \n
\section examples
<TT> fix_modify AtC bond_interactions on </TT> \n
\section description
@ -748,27 +748,27 @@ namespace ATC {
*/
if (strcmp(arg[argIdx],"pair_interactions")==0) { // default true
argIdx++;
if (strcmp(arg[argIdx],"on")==0) { hasPairs_ = true; }
if (strcmp(arg[argIdx],"on")==0) { hasPairs_ = true; }
else { hasPairs_ = false;}
match = true;
}
}
if (strcmp(arg[argIdx],"bond_interactions")==0) { // default false
argIdx++;
if (strcmp(arg[argIdx],"on")==0) { hasBonds_ = true; }
if (strcmp(arg[argIdx],"on")==0) { hasBonds_ = true; }
else { hasBonds_ = false;}
match = true;
}
/*! \page man_hardy_computes fix_modify AtC computes
}
/*! \page man_hardy_computes fix_modify AtC computes
\section syntax
fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number> \n
- add | delete (keyword) = add or delete the calculation of an equivalent continuum field
for the specified per-atom compute as volume or number density quantity \n
- per-atom compute id = name/id for per-atom compute,
- per-atom compute id = name/id for per-atom compute,
fields can be calculated for all per-atom computes available from LAMMPS \n
- volume | number (keyword) = field created is a per-unit-volume quantity
or a per-atom quantity as weighted by kernel functions \n
or a per-atom quantity as weighted by kernel functions \n
\section examples
<TT> compute virial all stress/atom </TT> \n
<TT> fix_modify AtC computes add virial volume </TT> \n
@ -782,24 +782,24 @@ namespace ATC {
Must be used with the hardy/field type of AtC fix ( see \ref man_fix_atc ) \n
Per-atom compute must be specified before corresponding continuum field can be requested \n
\section related
See manual page for compute
See manual page for compute
\section default
No defaults exist for this command
*/
else if (strcmp(arg[argIdx],"computes")==0) {
argIdx++;
if (strcmp(arg[argIdx],"add")==0) {
if (strcmp(arg[argIdx],"add")==0) {
argIdx++;
string tag(arg[argIdx++]);
int normalization = NO_NORMALIZATION;
if (narg > argIdx) {
if (strcmp(arg[argIdx],"volume")==0) {
if (strcmp(arg[argIdx],"volume")==0) {
normalization = VOLUME_NORMALIZATION;
}
else if (strcmp(arg[argIdx],"number")==0) {
else if (strcmp(arg[argIdx],"number")==0) {
normalization = NUMBER_NORMALIZATION;
}
else if (strcmp(arg[argIdx],"mass")==0) {
else if (strcmp(arg[argIdx],"mass")==0) {
normalization = MASS_NORMALIZATION;
throw ATC_Error("mass normalized not implemented");
}
@ -807,8 +807,8 @@ namespace ATC {
computes_[tag] = normalization;
nComputes_++;
match = true;
}
else if (strcmp(arg[argIdx],"delete")==0) {
}
else if (strcmp(arg[argIdx],"delete")==0) {
argIdx++;
string tag(arg[argIdx]);
if (computes_.find(tag) != computes_.end()) {
@ -816,10 +816,10 @@ namespace ATC {
nComputes_--;
}
else {
throw ATC_Error(tag+" compute is not in list");
throw ATC_Error(tag+" compute is not in list");
}
match = true;
}
}
}
@ -833,7 +833,7 @@ namespace ATC {
Specifies a frequency at which fields are computed for the case
where time filters are being applied.
\section restrictions
Must be used with the hardy/field AtC fix ( see \ref man_fix_atc )
Must be used with the hardy/field AtC fix ( see \ref man_fix_atc )
and is only relevant when time filters are being used.
\section related
\section default
@ -869,11 +869,11 @@ namespace ATC {
// REFACTOR move this to post_neighbor
void ATC_Transfer::pre_final_integrate()
{
// update time
// update time
update_time(); // time uses step if dt = 0
if ( neighborReset_ && sample_now() ) {
if (! kernelOnTheFly_ ) {
if (!moleculeIds_.empty()) compute_kernel_matrix_molecule(); //KKM add
@ -889,7 +889,7 @@ namespace ATC {
// compute spatially smoothed quantities
double dt = lammpsInterface_->dt();
if ( sample_now() ) {
bool needsBond = (! bondOnTheFly_ ) &&
(fieldFlags_(STRESS)
|| fieldFlags_(ESHELBY_STRESS)
@ -898,7 +898,7 @@ namespace ATC {
if ( needsBond ) {
if (pairMap_->need_reset()) {
// ATC::LammpsInterface::instance()->print_msg("Recomputing bond matrix due to atomReset_ value");
compute_bond_matrix();
compute_bond_matrix();
}
}
time_filter_pre (dt);
@ -923,8 +923,8 @@ namespace ATC {
//-------------------------------------------------------------------
void ATC_Transfer::compute_fields(void)
{
// keep per-atom computes fresh. JAZ and REJ not sure why;
// keep per-atom computes fresh. JAZ and REJ not sure why;
// need to confer with JAT. (JAZ, 4/5/12)
interscaleManager_.lammps_force_reset();
@ -937,16 +937,16 @@ namespace ATC {
}
}
if (fieldFlags_(STRESS))
if (fieldFlags_(STRESS))
compute_stress(hardyData_["stress"].set_quantity());
if (fieldFlags_(HEAT_FLUX))
if (fieldFlags_(HEAT_FLUX))
compute_heatflux(hardyData_["heat_flux"].set_quantity());
// molecule data
if (fieldFlags_(DIPOLE_MOMENT))
compute_dipole_moment(hardyData_["dipole_moment"].set_quantity());
compute_dipole_moment(hardyData_["dipole_moment"].set_quantity());
if (fieldFlags_(QUADRUPOLE_MOMENT))
compute_quadrupole_moment(hardyData_["quadrupole_moment"].set_quantity());
if (fieldFlags_(DISLOCATION_DENSITY))
if (fieldFlags_(DISLOCATION_DENSITY))
compute_dislocation_density(hardyData_["dislocation_density"].set_quantity());
// (2) derived quantities
@ -963,7 +963,7 @@ namespace ATC {
}
}
}
// compute: eshelby stress
// compute: eshelby stress
if (fieldFlags_(ESHELBY_STRESS)) {
{
compute_eshelby_stress(hardyData_["eshelby_stress"].set_quantity(),
@ -985,18 +985,18 @@ namespace ATC {
E,hardyData_["stress"].quantity(),
hardyData_["displacement_gradient"].quantity());
}
// compute: cauchy born stress
// compute: cauchy born stress
if (fieldFlags_(CAUCHY_BORN_STRESS)) {
ATOMIC_DATA::const_iterator tfield = hardyData_.find("temperature");
const DENS_MAT *temp = tfield==hardyData_.end() ? nullptr : &((tfield->second).quantity());
cauchy_born_stress(hardyData_["displacement_gradient"].quantity(),
hardyData_["cauchy_born_stress"].set_quantity(), temp);
}
// compute: cauchy born energy
// compute: cauchy born energy
if (fieldFlags_(CAUCHY_BORN_ENERGY)) {
ATOMIC_DATA::const_iterator tfield = hardyData_.find("temperature");
const DENS_MAT *temp = tfield==hardyData_.end() ? nullptr : &((tfield->second).quantity());
cauchy_born_energy(hardyData_["displacement_gradient"].quantity(),
cauchy_born_energy(hardyData_["displacement_gradient"].quantity(),
hardyData_["cauchy_born_energy"].set_quantity(), temp);
}
// 1st PK transformed to cauchy (lag) or cauchy transformed to 1st PK (eul)
@ -1014,13 +1014,13 @@ namespace ATC {
compute_electric_potential(
hardyData_[field_to_string(ELECTRIC_POTENTIAL)].set_quantity());
}
// compute: rotation and/or stretch from deformation gradient
// compute: rotation and/or stretch from deformation gradient
if (fieldFlags_(ROTATION) || fieldFlags_(STRETCH)) {
compute_polar_decomposition(hardyData_["rotation"].set_quantity(),
hardyData_["stretch"].set_quantity(),
hardyData_["displacement_gradient"].quantity());
}
// compute: rotation and/or stretch from deformation gradient
// compute: rotation and/or stretch from deformation gradient
if (fieldFlags_(CAUCHY_BORN_ELASTIC_DEFORMATION_GRADIENT)) {
compute_elastic_deformation_gradient2(hardyData_["elastic_deformation_gradient"].set_quantity(),
hardyData_["stress"].quantity(),
@ -1082,9 +1082,9 @@ namespace ATC {
F(0,0) += 1.0; F(1,1) += 1.0; F(2,2) += 1.0;
FT = F.transpose();
FTINV = inv(FT);
// volumes are already reference volumes.
PK1 = CAUCHY*FTINV;
PK1 = CAUCHY*FTINV;
matrix_to_vector(k,PK1,myData);
}
}
@ -1094,7 +1094,7 @@ namespace ATC {
}
#endif
}
}// end of compute_fields routine
//-------------------------------------------------------------------
@ -1156,7 +1156,7 @@ namespace ATC {
filteredData_[grad_field] = hardyData_[grad_field];
}
}
// lists/accessing of fields ( & computes)
map <string,int>::const_iterator iter;
int index = NUM_TOTAL_FIELDS;
@ -1177,7 +1177,7 @@ namespace ATC {
void ATC_Transfer::output()
{
feEngine_->departition_mesh();
for(int index=0; index < NUM_TOTAL_FIELDS; ++index) {
if (outputFlags_(index)) {
FieldName fName = (FieldName) index;
@ -1185,7 +1185,7 @@ namespace ATC {
fields_[fName] = filteredData_[name];
}
}
ATC_Method::output();
if (lammpsInterface_->comm_rank() == 0) {
// data
@ -1209,7 +1209,7 @@ namespace ATC {
output_data[grad_name] = & ( filteredData_[grad_name].set_quantity());
}
}
// lists/accessing of fields ( & computes)
map <string,int>::const_iterator iter;
for (iter = computes_.begin(); iter != computes_.end(); iter++) {
@ -1226,7 +1226,7 @@ namespace ATC {
output_data["NodalInverseVolumes"] = &nodalInverseVolumes;
// output
feEngine_->write_data(output_index(), & output_data);
feEngine_->write_data(output_index(), & output_data);
}
feEngine_->partition_mesh();
}
@ -1235,7 +1235,7 @@ namespace ATC {
/////// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
//-------------------------------------------------------------------
// computes nodeData = N*atomData
// computes nodeData = N*atomData
void ATC_Transfer::project(const DENS_MAT & atomData,
DENS_MAT & nodeData)
{
@ -1290,8 +1290,8 @@ namespace ATC {
void ATC_Transfer::project_count_normalized(const DENS_MAT & atomData,
DENS_MAT & nodeData)
{
DENS_MAT tmp;
project(atomData,tmp);
DENS_MAT tmp;
project(atomData,tmp);
nodeData = (accumulantWeights_->quantity())*tmp;
}
@ -1301,7 +1301,7 @@ namespace ATC {
DENS_MAT & nodeData)
{
DENS_MAT tmp;
project(atomData,tmp);
project(atomData,tmp);
nodeData = (accumulantInverseVolumes_->quantity())*tmp;
}
@ -1310,8 +1310,8 @@ namespace ATC {
void ATC_Transfer::project_volume_normalized_molecule(const DENS_MAT & molData,
DENS_MAT & nodeData)
{
DENS_MAT tmp;
project_molecule(molData,tmp);
DENS_MAT tmp;
project_molecule(molData,tmp);
nodeData = (accumulantInverseVolumes_->quantity())*tmp;
}
@ -1320,8 +1320,8 @@ namespace ATC {
void ATC_Transfer::project_volume_normalized_molecule_gradient(const DENS_MAT & molData,
DENS_MAT & nodeData)
{
DENS_MAT tmp;
project_molecule_gradient(molData,tmp);
DENS_MAT tmp;
project_molecule_gradient(molData,tmp);
nodeData = (accumulantInverseVolumes_->quantity())*tmp;
}
@ -1354,14 +1354,14 @@ namespace ATC {
//-------------------------------------------------------------------
// computes "virial" part of heat flux
// This is correct ONLY for pair potentials.
// This is correct ONLY for pair potentials.
void ATC_Transfer::compute_heat_matrix()
{
atomicHeatMatrix_ = pairHeatFlux_->quantity();
}
//-------------------------------------------------------------------
// set xPointer_ to xref or xatom depending on Lagrangian/Eulerian analysis
// set xPointer_ to xref or xatom depending on Lagrangian/Eulerian analysis
void ATC_Transfer::set_xPointer()
{
xPointer_ = xref_;
@ -1386,7 +1386,7 @@ namespace ATC {
fieldFlags_(DISPLACEMENT) = true;
}
if (fieldFlags_(CAUCHY_BORN_STRESS)
|| fieldFlags_(CAUCHY_BORN_ENERGY)
|| fieldFlags_(CAUCHY_BORN_ENERGY)
|| fieldFlags_(CAUCHY_BORN_ESHELBY_STRESS)
|| fieldFlags_(CAUCHY_BORN_ELASTIC_DEFORMATION_GRADIENT)) {
if (! (cauchyBornStress_) ) {
@ -1419,7 +1419,7 @@ namespace ATC {
fieldFlags_(KINETIC_ENERGY) = true;
}
if (fieldFlags_(TEMPERATURE) || fieldFlags_(HEAT_FLUX) ||
fieldFlags_(KINETIC_ENERGY) || fieldFlags_(THERMAL_ENERGY) ||
fieldFlags_(KINETIC_ENERGY) || fieldFlags_(THERMAL_ENERGY) ||
fieldFlags_(ENERGY) || fieldFlags_(INTERNAL_ENERGY) ||
fieldFlags_(KINETIC_ENERGY) || (fieldFlags_(STRESS) &&
atomToElementMapType_ == EULERIAN) ) {
@ -1438,15 +1438,15 @@ namespace ATC {
fieldFlags_(NUMBER_DENSITY) = true;
}
if (fieldFlags_(ROTATION) ||
if (fieldFlags_(ROTATION) ||
fieldFlags_(STRETCH)) {
fieldFlags_(DISPLACEMENT) = true;
}
if (fieldFlags_(ESHELBY_STRESS)
|| fieldFlags_(CAUCHY_BORN_STRESS)
|| fieldFlags_(CAUCHY_BORN_ENERGY)
|| fieldFlags_(CAUCHY_BORN_ESHELBY_STRESS)
|| fieldFlags_(CAUCHY_BORN_ELASTIC_DEFORMATION_GRADIENT)
|| fieldFlags_(CAUCHY_BORN_STRESS)
|| fieldFlags_(CAUCHY_BORN_ENERGY)
|| fieldFlags_(CAUCHY_BORN_ESHELBY_STRESS)
|| fieldFlags_(CAUCHY_BORN_ELASTIC_DEFORMATION_GRADIENT)
|| fieldFlags_(VACANCY_CONCENTRATION)
|| fieldFlags_(ROTATION)
|| fieldFlags_(STRETCH) ) {
@ -1459,8 +1459,8 @@ namespace ATC {
throw ATC_Error("Calculation of stress field not possible with selected pair type.");
}
}
}
}
//============== THIN WRAPPERS ====================================
// OBSOLETE
@ -1492,7 +1492,7 @@ namespace ATC {
// calculate kinetic energy tensor part of stress for Eulerian analysis
if (atomToElementMapType_ == EULERIAN && nLocal_>0) {
compute_kinetic_stress(stress);
compute_kinetic_stress(stress);
}
else {
// zero stress table for Lagrangian analysis or if nLocal_ = 0
@ -1511,7 +1511,7 @@ namespace ATC {
compute_force_matrix();
// calculate force part of stress tensor
local_potential_hardy_stress = atomicBondMatrix_*atomicForceMatrix_;
local_potential_hardy_stress *= 0.5;
local_potential_hardy_stress *= 0.5;
}
}
// global summation of potential part of stress tensor
@ -1570,7 +1570,7 @@ namespace ATC {
compute_kinetic_heatflux(flux);
}
else {
flux.zero(); // zero stress table for Lagrangian analysis
flux.zero(); // zero stress table for Lagrangian analysis
}
// add potential part of heat flux vector
int nrows = flux.nRows();
@ -1628,11 +1628,11 @@ namespace ATC {
// - e^0_I v_I + \sigma^T_I v_I
for (int i = 0; i < nNodes_; i++) {
double e_i = energy(i,0);
flux(i,0) += (e_i + stress(i,0))*velocity(i,0)
flux(i,0) += (e_i + stress(i,0))*velocity(i,0)
+ stress(i,3)*velocity(i,1)+ stress(i,4)*velocity(i,2);
flux(i,1) += (e_i + stress(i,1))*velocity(i,1)
flux(i,1) += (e_i + stress(i,1))*velocity(i,1)
+ stress(i,3)*velocity(i,0)+ stress(i,5)*velocity(i,2);
flux(i,2) += (e_i + stress(i,2))*velocity(i,2)
flux(i,2) += (e_i + stress(i,2))*velocity(i,2)
+ stress(i,4)*velocity(i,0)+ stress(i,5)*velocity(i,1);
}
}
@ -1643,7 +1643,7 @@ namespace ATC {
const DENS_MAT & rho = (restrictedCharge_->quantity());
SPAR_MAT K;
feEngine_->stiffness_matrix(K);
double permittivity = lammpsInterface_->dielectric();
double permittivity = lammpsInterface_->dielectric();
permittivity *= LammpsInterface::instance()->epsilon0();
K *= permittivity;
BC_SET bcs;
@ -1670,7 +1670,7 @@ namespace ATC {
for (int i = 0; i < nLocal_; i++) {
int atomIdx = internalToAtom_(i);
if (type[atomIdx] != 13) {
if (type[atomIdx] != 13) {
atomCnt(i,0) = myAtomicWeights(i,i);
atomic_weight_sum += myAtomicWeights(i,i);
number_atoms++;
@ -1725,7 +1725,7 @@ namespace ATC {
#ifndef H_BASED
F(0,0) += 1.0; F(1,1) += 1.0; F(2,2) += 1.0;
#endif
FT = F.transpose();
FT = F.transpose();
}
else if (atomToElementMapType_ == EULERIAN) {
vector_to_symm_matrix(i,S,P);
@ -1741,9 +1741,9 @@ namespace ATC {
// Q stores (1-H)
Q -= FT.transpose();
DENS_MAT F(3,3);
F = inv(Q);
F = inv(Q);
FT = F.transpose();
ESH = FT*ESH;
ESH = FT*ESH;
}
// copy to global
matrix_to_vector(i,ESH,M);
@ -1761,7 +1761,7 @@ namespace ATC {
DENS_MAT_VEC &h = hField[DISPLACEMENT];
h.assign(nsd_, DENS_MAT(nNodes_,nsd_));
tField.assign(nsd_, DENS_MAT(nNodes_,nsd_));
// each row is the CB stress at a node stored in voigt form
// each row is the CB stress at a node stored in voigt form
T.reset(nNodes_,FieldSizes[CAUCHY_BORN_STRESS]);
const double nktv2p = lammpsInterface_->nktv2p();
const double fact = -lammpsInterface_->mvv2e()*nktv2p;
@ -1779,7 +1779,7 @@ namespace ATC {
DENS_MAT S(nNodes_,6);
symm_dens_mat_vec_to_vector(tField,S);
S *= fact;
// tField/S holds the 2nd P-K stress tensor. Transform to
// Cauchy for EULERIAN analysis, transform to 1st P-K
// for LAGRANGIAN analysis.
@ -1799,7 +1799,7 @@ namespace ATC {
FT = transpose(F);
double J = det(F);
STRESS = F*PK2*FT;
STRESS *= 1/J;
STRESS *= 1/J;
symm_matrix_to_vector(i,STRESS,T);
}
else{
@ -1810,7 +1810,7 @@ namespace ATC {
STRESS = F*PK2;
matrix_to_vector(i,STRESS,T);
}
}
}
//---------------------------------------------------------------------------
@ -1861,7 +1861,7 @@ namespace ATC {
void ATC_Transfer::cauchy_born_entropic_energy(const DENS_MAT &H, DENS_MAT &E, const DENS_MAT &T)
{
FIELD_MATS uField; // uField should contain temperature.
uField[TEMPERATURE] = T;
uField[TEMPERATURE] = T;
GRAD_FIELD_MATS hField;
DENS_MAT_VEC &h = hField[DISPLACEMENT];
h.assign(nsd_, DENS_MAT(nNodes_,nsd_));
@ -1916,13 +1916,13 @@ namespace ATC {
vector_to_matrix(i,H,F);
F(0,0) += 1.0; F(1,1) += 1.0; F(2,2) += 1.0;
FT = F.transpose();
FT = F.transpose();
}
//
double J = det(FT);
FT *= 1/J;
if (atomToElementMapType_ == EULERIAN) {
FT = inv(FT);
FT = inv(FT);
}
S = P*FT;
matrix_to_vector(i,S,stress);
@ -1933,10 +1933,10 @@ namespace ATC {
DENS_MAT & stretch, const DENS_MAT & H)
{
DENS_MAT F(3,3),R(3,3),U(3,3);
for (int i = 0; i < nNodes_; i++) {
for (int i = 0; i < nNodes_; i++) {
vector_to_matrix(i,H,F);
F(0,0) += 1.0; F(1,1) += 1.0; F(2,2) += 1.0;
if (atomToElementMapType_ == EULERIAN) {
if (atomToElementMapType_ == EULERIAN) {
polar_decomposition(F,R,U,false); } // F = V R
else {
polar_decomposition(F,R,U); } // F = R U
@ -1953,12 +1953,12 @@ namespace ATC {
//--------------------------------------------------------------------
void ATC_Transfer::compute_elastic_deformation_gradient(DENS_MAT & Fe,
const DENS_MAT & P, const DENS_MAT & H)
{
// calculate Fe for every node
const double nktv2p = lammpsInterface_->nktv2p();
const double fact = 1.0/ ( lammpsInterface_->mvv2e()*nktv2p );
for (int i = 0; i < nNodes_; i++) {
for (int i = 0; i < nNodes_; i++) {
DENS_VEC Pv = global_vector_to_vector(i,P);
Pv *= fact;
CBElasticTangentOperator tangent(cauchyBornStress_, Pv);
@ -1977,11 +1977,11 @@ namespace ATC {
const double nktv2p = lammpsInterface_->nktv2p();
const double fact = 1.0/ ( lammpsInterface_->mvv2e()*nktv2p );
DENS_MAT F(3,3),R(3,3),U(3,3),PP(3,3),S(3,3);
for (int i = 0; i < nNodes_; i++) {
for (int i = 0; i < nNodes_; i++) {
// get F = RU
vector_to_matrix(i,H,F);
F(0,0) += 1.0; F(1,1) += 1.0; F(2,2) += 1.0;
if (atomToElementMapType_ == EULERIAN) {
if (atomToElementMapType_ == EULERIAN) {
polar_decomposition(F,R,U,false); } // F = V R
else {
polar_decomposition(F,R,U); } // F = R U
@ -1989,7 +1989,7 @@ namespace ATC {
vector_to_matrix(i,P,PP);
//S = PP*transpose(F);
S = inv(F)*PP;
S += S.transpose(); S *= 0.5; // symmetrize
DENS_VEC Sv = to_voigt(S);
Sv *= fact;