2013-08-08 05:34:54 +08:00
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#include "FieldManager.h"
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#include "ATC_Method.h"
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#include "LammpsInterface.h"
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#include "PerAtomQuantity.h"
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#include "TransferOperator.h"
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2013-08-22 07:06:07 +08:00
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using std::string;
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2013-08-08 05:34:54 +08:00
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namespace ATC {
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typedef PerAtomQuantity<double> PAQ;
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//-----------------------------------------------------------------------------
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//*
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//-----------------------------------------------------------------------------
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FieldManager::FieldManager(ATC_Method * atc):
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atc_(atc),
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interscaleManager_(atc->interscale_manager())
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{};
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//-----------------------------------------------------------------------------
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//* restricted_atom_quantity
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::restricted_atom_quantity(FieldName field, string name, PAQ * atomicQuantity)
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{
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if (name == "default") { name = field_to_restriction_name(field); }
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DENS_MAN * quantity = interscaleManager_.dense_matrix(name);
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if (!quantity){
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if (field == CHARGE_DENSITY) {
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atomicQuantity = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_CHARGE);
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}
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else if (field == MASS_DENSITY) {
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atomicQuantity = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
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}
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else {
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if (!atomicQuantity) {
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throw ATC_Error("FieldManager::restricted_atom_quantity - need to supply PAQ if restricted quantity does not already exist");
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}
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}
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quantity = new AtfShapeFunctionRestriction(atc_,atomicQuantity,atc_->accumulant());
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interscaleManager_.add_dense_matrix(quantity,name);
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}
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return quantity;
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}
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//-----------------------------------------------------------------------------
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//* restricted_atom_quantity
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//-----------------------------------------------------------------------------
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2013-08-22 07:06:07 +08:00
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DENS_MAN * FieldManager::projected_atom_quantity(FieldName field,string name, PAQ * atomic, DIAG_MAN * normalization)
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2013-08-08 05:34:54 +08:00
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{
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if (atc_->use_md_mass_normalization()) {
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if (name == "default") { name = field_to_intrinsic_name(field); }
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DENS_MAN * quantity = interscaleManager_.dense_matrix(name);
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if (!quantity) {
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DENS_MAN * restricted = restricted_atom_quantity(field,field_to_restriction_name(field),atomic);
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2013-08-22 07:06:07 +08:00
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quantity = new AtfShapeFunctionMdProjection(atc_,restricted,use_mass_matrix(field));
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2013-08-08 05:34:54 +08:00
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interscaleManager_.add_dense_matrix(quantity,name);
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}
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return quantity;
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}
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else {
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if (name == "default") { name = field_to_string(field); }
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DENS_MAN * quantity = interscaleManager_.dense_matrix(name);
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if (quantity) return quantity;
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if (atc_->kernel_on_the_fly()) {
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if (atc_->kernel_based()) {
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quantity = new OnTheFlyKernelAccumulationNormalized(atc_, atomic,
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2013-08-22 07:06:07 +08:00
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atc_->kernel_function(),
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atc_->atom_coarsegraining_positions(),
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normalization);
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2013-08-08 05:34:54 +08:00
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} else {
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quantity = new OnTheFlyMeshAccumulationNormalized(atc_, atomic,
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2013-08-22 07:06:07 +08:00
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atc_->atom_coarsegraining_positions(),
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normalization);
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2013-08-08 05:34:54 +08:00
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}
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} else {
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quantity = new AtfProjection(atc_, atomic,
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atc_->accumulant(),
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normalization);
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}
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interscaleManager_.add_dense_matrix(quantity,name);
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return quantity;
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}
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}
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//-----------------------------------------------------------------------------
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//* referenced_projected_atom_quantity
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//-----------------------------------------------------------------------------
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2013-08-22 07:06:07 +08:00
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DENS_MAN * FieldManager::referenced_projected_atom_quantity(FieldName field,string name, PAQ * atomic, DENS_MAN * reference, DIAG_MAN * normalization)
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2013-08-08 05:34:54 +08:00
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{
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if (name == "default") { name = field_to_string(field); }
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DENS_MAN * quantity = interscaleManager_.dense_matrix(name);
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if (quantity) return quantity;
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if (atc_->use_md_mass_normalization()) {
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DENS_MAN * restricted = restricted_atom_quantity(field,field_to_restriction_name(field),atomic);
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2013-08-22 07:06:07 +08:00
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quantity = new AtfShapeFunctionMdProjectionReferenced(atc_,restricted,reference,use_mass_matrix(field));
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2013-08-08 05:34:54 +08:00
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}
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else if (atc_->kernel_on_the_fly()) {
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if (atc_->kernel_based()) {
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quantity = new OnTheFlyKernelAccumulationNormalizedReferenced(atc_,
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atomic,
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atc_->kernel_function(),
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atc_->atom_coarsegraining_positions(),
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normalization,
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reference);
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} else {
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quantity = new OnTheFlyMeshAccumulationNormalizedReferenced(atc_,
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atomic,
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atc_->atom_coarsegraining_positions(),
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normalization,
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reference);
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}
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} else {
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quantity = new AtfProjectionReferenced(atc_, atomic,
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atc_->accumulant(),
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reference,
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normalization);
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}
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interscaleManager_.add_dense_matrix(quantity,name);
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return quantity;
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}
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//-----------------------------------------------------------------------------
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//* scaled_projected_atom_quantity
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//-----------------------------------------------------------------------------
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2013-08-22 07:06:07 +08:00
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DENS_MAN * FieldManager::scaled_projected_atom_quantity(FieldName field,string name, PAQ * atomic, double scale, DIAG_MAN * normalization)
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2013-08-08 05:34:54 +08:00
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{
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if (name == "default") { name = field_to_string(field); }
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DENS_MAN * quantity = interscaleManager_.dense_matrix(name);
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if (quantity) return quantity;
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if (atc_->use_md_mass_normalization()) {
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DENS_MAN * restricted = restricted_atom_quantity(field,field_to_restriction_name(field),atomic);
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2013-08-22 07:06:07 +08:00
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quantity = new AtfShapeFunctionMdProjectionScaled(atc_,restricted,scale,use_mass_matrix(field));
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2013-08-08 05:34:54 +08:00
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}
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else if (atc_->kernel_on_the_fly()) {
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if (atc_->kernel_based()) {
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quantity = new OnTheFlyKernelAccumulationNormalizedScaled(atc_, atomic,
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atc_->kernel_function(),
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atc_->atom_coarsegraining_positions(),
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normalization,
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scale);
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} else {
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quantity = new OnTheFlyMeshAccumulationNormalizedScaled(atc_, atomic,
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atc_->atom_coarsegraining_positions(),
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normalization,
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scale);
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}
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} else {
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quantity = new AtfProjectionScaled(atc_, atomic,
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atc_->accumulant(),
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scale,
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normalization);
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}
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interscaleManager_.add_dense_matrix(quantity,name);
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return quantity;
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}
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//-----------------------------------------------------------------------------
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//* CHARGE_DENSITY
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::charge_density(string name)
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{
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FundamentalAtomQuantity * atomic = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_CHARGE);
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2013-08-22 07:06:07 +08:00
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return projected_atom_quantity(CHARGE_DENSITY,name,atomic,atc_->accumulant_inverse_volumes());
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2013-08-08 05:34:54 +08:00
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}
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//-----------------------------------------------------------------------------
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//* MASS_DENSITY
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::mass_density(string name)
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{
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FundamentalAtomQuantity * atomic = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
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2013-08-22 07:06:07 +08:00
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return projected_atom_quantity(MASS_DENSITY,name,atomic,atc_->accumulant_inverse_volumes());
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2013-08-08 05:34:54 +08:00
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}
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//-----------------------------------------------------------------------------
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//* SPECIES_CONCENTRATION
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::species_concentration(string name)
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{
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2013-08-22 07:06:07 +08:00
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PerAtomQuantity<double> * atomTypeVector = interscaleManager_.per_atom_quantity("atom_species_vector");
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if (!atomTypeVector) {
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atomTypeVector = new AtomTypeVector(atc_,atc_->type_list(),atc_->group_list());
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interscaleManager_.add_per_atom_quantity(atomTypeVector,"atom_species_vector");
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2013-08-08 05:34:54 +08:00
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}
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2013-08-22 07:06:07 +08:00
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return projected_atom_quantity(SPECIES_CONCENTRATION,name,atomTypeVector,atc_->accumulant_inverse_volumes());
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2013-08-08 05:34:54 +08:00
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}
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//-----------------------------------------------------------------------------
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//* NUMBER_DENSITY
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::number_density(string name)
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{
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PAQ * atomic = interscaleManager_.per_atom_quantity("atomNumber");
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if (!atomic) {
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atomic = new AtomNumber(atc_);
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interscaleManager_.add_per_atom_quantity(atomic, "atomNumber");
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}
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2013-08-22 07:06:07 +08:00
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return projected_atom_quantity(NUMBER_DENSITY,name,atomic,atc_->accumulant_inverse_volumes());
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2013-08-08 05:34:54 +08:00
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}
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//-----------------------------------------------------------------------------
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//* MOMENTUM
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::momentum(string name)
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{
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PAQ * atomic = interscaleManager_.per_atom_quantity("atomMomentum");
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if (!atomic) {
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atomic = new AtomicMomentum(atc_);
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interscaleManager_.add_per_atom_quantity(atomic, "atomMomentum");
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}
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2013-08-22 07:06:07 +08:00
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return projected_atom_quantity(MOMENTUM,name,atomic,atc_->accumulant_inverse_volumes());
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2013-08-08 05:34:54 +08:00
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}
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//-----------------------------------------------------------------------------
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//* VELOCITY
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::velocity(string name)
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{
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if (name == "default") { name = field_to_string(VELOCITY); }
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DENS_MAN * v = interscaleManager_.dense_matrix(name);
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if (v) return v;
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if (atc_->use_md_mass_normalization()) {
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PAQ * atomic = interscaleManager_.per_atom_quantity("atomMomentum");
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if (!atomic) {
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atomic = new AtomicMomentum(atc_);
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interscaleManager_.add_per_atom_quantity(atomic, "atomMomentum");
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}
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DENS_MAN * restricted = restricted_atom_quantity(VELOCITY,field_to_restriction_name(VELOCITY),atomic);
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v = new AtfShapeFunctionMdProjection(atc_,restricted,VELOCITY);
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}
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else {
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DENS_MAN* p = interscaleManager_.dense_matrix(field_to_string(MOMENTUM));
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if (!p) p = nodal_atomic_field(MOMENTUM);
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DENS_MAN* m = interscaleManager_.dense_matrix(field_to_string(MASS_DENSITY));
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if (!m) m = nodal_atomic_field(MASS_DENSITY);
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v = new DenseMatrixQuotient(p,m);
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}
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interscaleManager_.add_dense_matrix(v,field_to_string(VELOCITY));
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return v;
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}
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//-----------------------------------------------------------------------------
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//* PROJECTED_VELOCITY
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::projected_velocity(string name)
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{
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FundamentalAtomQuantity * atomic = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_VELOCITY);
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2013-08-22 07:06:07 +08:00
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return projected_atom_quantity(PROJECTED_VELOCITY,name,atomic,atc_->accumulant_inverse_volumes());
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2013-08-08 05:34:54 +08:00
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}
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//-----------------------------------------------------------------------------
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//* DISPLACEMENT
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//-----------------------------------------------------------------------------
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DENS_MAN * FieldManager::displacement(string name)
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{
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if (name == "default") { name = field_to_string(DISPLACEMENT); }
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DENS_MAN * u = interscaleManager_.dense_matrix(name);
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if (u) return u;
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PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicMassWeightedDisplacement");
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if (!atomic) {
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FundamentalAtomQuantity * atomMasses = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
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FundamentalAtomQuantity * atomPositions = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_POSITION);
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atomic = new AtomicMassWeightedDisplacement(atc_,atomPositions, atomMasses, atc_->atom_reference_positions(), INTERNAL);
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interscaleManager_.add_per_atom_quantity(atomic,"AtomicMassWeightedDisplacement");
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}
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if (atc_->use_md_mass_normalization()) {
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DENS_MAN * restricted = restricted_atom_quantity(DISPLACEMENT,field_to_restriction_name(DISPLACEMENT),atomic);
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u = new AtfShapeFunctionMdProjection(atc_,restricted,VELOCITY);
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}
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else {
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DENS_MAN * q = NULL;
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if (atc_->kernel_on_the_fly()) {
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if (atc_->kernel_based()) {
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q = new OnTheFlyKernelAccumulationNormalized(atc_, atomic,
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atc_->kernel_function(),
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atc_->atom_coarsegraining_positions(),
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atc_->accumulant_inverse_volumes());
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} else {
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q = new OnTheFlyMeshAccumulationNormalized(atc_, atomic,
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atc_->atom_coarsegraining_positions(),
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atc_->accumulant_inverse_volumes());
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}
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} else {
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q = new AtfProjection(atc_, atomic,
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atc_->accumulant(),
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atc_->accumulant_inverse_volumes());
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}
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interscaleManager_.add_dense_matrix(q,"CoarseGrainedAMWD");
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DENS_MAN* m = interscaleManager_.dense_matrix(field_to_string(MASS_DENSITY));
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u = new DenseMatrixQuotient(q,m);
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}
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interscaleManager_.add_dense_matrix(u,name);
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return u;
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}
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//-----------------------------------------------------------------------------
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//* REFERENCE_POTENTIAL_ENERGY
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//-----------------------------------------------------------------------------
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2019-10-20 23:24:13 +08:00
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DENS_MAN * FieldManager::reference_potential_energy(string /* name */)
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2013-08-08 05:34:54 +08:00
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{
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2013-08-22 07:06:07 +08:00
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DENS_MAN * rpe = interscaleManager_.dense_matrix(field_to_string(REFERENCE_POTENTIAL_ENERGY));
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if (! rpe ) {
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PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicReferencePotential");
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if (!atomic) {
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atomic = new AtcAtomQuantity<double>(atc_);
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interscaleManager_.add_per_atom_quantity(atomic, "AtomicReferencePotential");
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atomic->set_memory_type(PERSISTENT);
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}
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SPAR_MAN * referenceAccumulant = interscaleManager_.sparse_matrix("ReferenceAccumulant");
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if (!referenceAccumulant) {
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referenceAccumulant = new SPAR_MAN();
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referenceAccumulant->set_memory_type(PERSISTENT);
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interscaleManager_.add_sparse_matrix(referenceAccumulant,
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"ReferenceAccumulant");
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}
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DIAG_MAN * referenceAccumulantInverseVolumes = interscaleManager_.diagonal_matrix("ReferenceAccumulantInverseVolumes");
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|
if (!referenceAccumulantInverseVolumes) {
|
|
|
|
referenceAccumulantInverseVolumes = new DIAG_MAN();
|
|
|
|
referenceAccumulantInverseVolumes->set_memory_type(PERSISTENT);
|
|
|
|
interscaleManager_.add_diagonal_matrix(referenceAccumulantInverseVolumes,
|
|
|
|
"ReferenceAccumulantInverseVolumes");
|
|
|
|
}
|
|
|
|
|
|
|
|
rpe = new AtfProjection(atc_, atomic,
|
|
|
|
referenceAccumulant,
|
|
|
|
referenceAccumulantInverseVolumes);
|
|
|
|
interscaleManager_.add_dense_matrix(rpe,field_to_string(REFERENCE_POTENTIAL_ENERGY));
|
|
|
|
rpe->set_memory_type(PERSISTENT);
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
2013-08-22 07:06:07 +08:00
|
|
|
return rpe;
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* POTENTIAL_ENERGY
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::potential_energy(string name)
|
|
|
|
{
|
|
|
|
PerAtomQuantity<double> * atomic = interscaleManager_.per_atom_quantity("AtomicPotentialEnergy");
|
2013-08-22 07:06:07 +08:00
|
|
|
if (!atomic) {
|
|
|
|
atomic = new ComputedAtomQuantity(atc_,(atc_->lammps_interface())->compute_pe_name(), atc_->pe_scale());
|
|
|
|
interscaleManager_.add_per_atom_quantity(atomic,"AtomicPotentialEnergy");
|
|
|
|
}
|
|
|
|
DENS_MAN * reference = interscaleManager_.dense_matrix(field_to_string(REFERENCE_POTENTIAL_ENERGY));
|
|
|
|
if (reference) {
|
|
|
|
return referenced_projected_atom_quantity(POTENTIAL_ENERGY,name,atomic,reference,atc_->accumulant_inverse_volumes());
|
|
|
|
}
|
|
|
|
else {
|
|
|
|
return projected_atom_quantity(POTENTIAL_ENERGY,name,atomic,atc_->accumulant_inverse_volumes());
|
|
|
|
}
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* TEMPERATURE
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::temperature(string name)
|
|
|
|
{
|
|
|
|
double Tcoef = 1./((atc_->nsd())*(atc_->lammps_interface())->kBoltzmann());
|
|
|
|
PAQ * atomic = per_atom_quantity("AtomicTwiceFluctuatingKineticEnergy");
|
2013-08-22 07:06:07 +08:00
|
|
|
return scaled_projected_atom_quantity(TEMPERATURE,name,atomic,Tcoef,atc_->accumulant_weights());
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* KINETIC_TEMPERATURE
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::kinetic_temperature(string name)
|
|
|
|
{
|
|
|
|
double Tcoef = 1./((atc_->nsd())*(atc_->lammps_interface())->kBoltzmann());
|
|
|
|
PAQ * atomic = per_atom_quantity("AtomicTwiceKineticEnergy");
|
2013-08-22 07:06:07 +08:00
|
|
|
return scaled_projected_atom_quantity(KINETIC_TEMPERATURE,name,atomic,Tcoef,atc_->accumulant_weights());
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* THERMAL_ENERGY
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::thermal_energy(string name)
|
|
|
|
{
|
|
|
|
double Ecoef = 0.5*atc_->ke_scale();
|
|
|
|
PAQ * atomic = per_atom_quantity("AtomicTwiceFluctuatingKineticEnergy");
|
2013-08-22 07:06:07 +08:00
|
|
|
return scaled_projected_atom_quantity(THERMAL_ENERGY,name,atomic,Ecoef,atc_->accumulant_inverse_volumes());
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* KINETIC_ENERGY
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::kinetic_energy(string name)
|
|
|
|
{
|
|
|
|
double Ecoef = 0.5*atc_->ke_scale();
|
|
|
|
PAQ * atomic = per_atom_quantity("AtomicTwiceKineticEnergy");
|
2013-08-22 07:06:07 +08:00
|
|
|
return scaled_projected_atom_quantity(KINETIC_ENERGY,name,atomic,Ecoef,atc_->accumulant_inverse_volumes());
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* CHARGE_FLUX
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::charge_flux(string name)
|
|
|
|
{
|
|
|
|
|
|
|
|
PAQ * atomic = per_atom_quantity("AtomicChargeVelocity");
|
2013-08-22 07:06:07 +08:00
|
|
|
return projected_atom_quantity(CHARGE_FLUX,name,atomic,atc_->accumulant_inverse_volumes());
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* SPECIES_FLUX
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::species_flux(string name)
|
|
|
|
{
|
|
|
|
PAQ * atomic = per_atom_quantity("AtomicSpeciesVelocity");
|
2013-08-22 07:06:07 +08:00
|
|
|
return projected_atom_quantity(SPECIES_FLUX,name,atomic,atc_->accumulant_inverse_volumes());
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|
2013-08-22 07:06:07 +08:00
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* INTERNAL_ENERGY
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::internal_energy(string name)
|
|
|
|
{
|
|
|
|
if (name == "default") { name = field_to_string(INTERNAL_ENERGY); }
|
|
|
|
DENS_MAN * te = thermal_energy(field_to_string(THERMAL_ENERGY));
|
|
|
|
DENS_MAN * pe = potential_energy(field_to_string(POTENTIAL_ENERGY));
|
|
|
|
DenseMatrixSum * ie = new DenseMatrixSum(te,pe);
|
|
|
|
interscaleManager_.add_dense_matrix(ie,name);
|
|
|
|
return ie;
|
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* ENERGY
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
DENS_MAN * FieldManager::energy(string name)
|
|
|
|
{
|
|
|
|
if (name == "default") { name = field_to_string(ENERGY); }
|
|
|
|
DENS_MAN * ke = kinetic_energy(field_to_string(KINETIC_ENERGY));
|
|
|
|
DENS_MAN * pe = potential_energy(field_to_string(POTENTIAL_ENERGY));
|
|
|
|
DenseMatrixSum * e = new DenseMatrixSum(ke,pe);
|
|
|
|
interscaleManager_.add_dense_matrix(e,name);
|
|
|
|
|
|
|
|
return e;
|
|
|
|
}
|
|
|
|
|
|
|
|
|
2013-08-08 05:34:54 +08:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
//=============================================================================
|
|
|
|
//* PER ATOM QUANTITIES
|
|
|
|
//=============================================================================
|
|
|
|
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* 2 KE '
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
PAQ * FieldManager::atomic_twice_fluctuating_kinetic_energy()
|
|
|
|
{
|
|
|
|
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicTwiceFluctuatingKineticEnergy");
|
|
|
|
if (!atomic) {
|
|
|
|
FundamentalAtomQuantity * atomMass = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
|
|
|
|
FundamentalAtomQuantity * atomVelocity = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_VELOCITY);
|
|
|
|
PAQ * vbar = per_atom_quantity(field_to_prolongation_name(VELOCITY));
|
|
|
|
atomic = new TwiceFluctuatingKineticEnergy(atc_,atomVelocity,atomMass,vbar);
|
|
|
|
interscaleManager_.add_per_atom_quantity(atomic, "AtomicTwiceFluctuatingKineticEnergy");
|
|
|
|
}
|
|
|
|
return atomic;
|
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* 2 KE
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
PAQ * FieldManager::atomic_twice_kinetic_energy()
|
|
|
|
{
|
|
|
|
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicTwiceKineticEnergy");
|
|
|
|
if (!atomic) {
|
|
|
|
FundamentalAtomQuantity * atomMass = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_MASS);
|
|
|
|
FundamentalAtomQuantity * atomVelocity = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_VELOCITY);
|
|
|
|
atomic = new TwiceKineticEnergy(atc_,atomVelocity,atomMass);
|
|
|
|
interscaleManager_.add_per_atom_quantity(atomic, "AtomicTwiceKineticEnergy");
|
|
|
|
}
|
|
|
|
return atomic;
|
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* v'
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
PAQ * FieldManager::atomic_fluctuating_velocity()
|
|
|
|
{
|
|
|
|
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicFluctuatingVelocity");
|
|
|
|
if (!atomic) {
|
|
|
|
FundamentalAtomQuantity * atomVelocity = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_VELOCITY);
|
|
|
|
PAQ * atomMeanVelocity = per_atom_quantity(field_to_prolongation_name(VELOCITY));
|
|
|
|
atomic = new FluctuatingVelocity(atc_,atomVelocity,atomMeanVelocity);
|
|
|
|
interscaleManager_.add_per_atom_quantity(atomic, "AtomicFluctuatingVelocity");
|
|
|
|
}
|
|
|
|
return atomic;
|
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* q v'
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
PAQ * FieldManager::atomic_charge_velocity()
|
|
|
|
{
|
|
|
|
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicChargeVelocity");
|
|
|
|
if (!atomic) {
|
|
|
|
PAQ * atomVelocity = atomic_fluctuating_velocity();
|
|
|
|
FundamentalAtomQuantity * atomCharge = interscaleManager_.fundamental_atom_quantity(LammpsInterface::ATOM_CHARGE);
|
|
|
|
atomic = new ChargeVelocity(atc_,atomVelocity,atomCharge);
|
|
|
|
interscaleManager_.add_per_atom_quantity(atomic, "AtomicChargeVelocity");
|
|
|
|
}
|
|
|
|
return atomic;
|
|
|
|
}
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* m^a v'
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
PAQ * FieldManager::atomic_species_velocity()
|
|
|
|
{
|
|
|
|
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicSpeciesVelocity");
|
|
|
|
if (!atomic) {
|
|
|
|
PAQ * atomVelocity = atomic_fluctuating_velocity();
|
|
|
|
PAQ * atomSpecies = atomic_species_vector();
|
|
|
|
atomic = new SpeciesVelocity(atc_,atomVelocity,atomSpecies);
|
|
|
|
interscaleManager_.add_per_atom_quantity(atomic, "AtomicSpeciesVelocity");
|
|
|
|
}
|
|
|
|
return atomic;
|
|
|
|
}
|
|
|
|
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* [0 1 0 0 ] for type 2 atom
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
PAQ * FieldManager::atomic_species_vector()
|
|
|
|
{
|
|
|
|
PAQ * atomic = interscaleManager_.per_atom_quantity("AtomicSpeciesVector");
|
|
|
|
if (!atomic) {
|
|
|
|
atomic = new AtomTypeVector(atc_,atc_->type_list(),atc_->group_list());
|
|
|
|
interscaleManager_.add_per_atom_quantity(atomic,"AtomicSpeciesVector");
|
|
|
|
}
|
|
|
|
return atomic;
|
|
|
|
}
|
2013-08-22 07:06:07 +08:00
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
//* Prolonged coarse scale field
|
|
|
|
//-----------------------------------------------------------------------------
|
|
|
|
PAQ * FieldManager::prolonged_field(FieldName field)
|
|
|
|
{
|
|
|
|
PAQ * quantity = interscaleManager_.per_atom_quantity(field_to_prolongation_name(field));
|
|
|
|
if (!quantity) {
|
|
|
|
|
2014-11-21 02:59:03 +08:00
|
|
|
|
2013-08-08 05:34:54 +08:00
|
|
|
DENS_MAN * coarseQuantity = interscaleManager_.dense_matrix(field_to_string(field));
|
2013-08-22 07:06:07 +08:00
|
|
|
if (!coarseQuantity) coarseQuantity = nodal_atomic_field(field);
|
|
|
|
if (!coarseQuantity) throw ATC_Error("can not prolong quantity: " + field_to_string(field) + " no field registered");
|
|
|
|
if (atc_->kernel_on_the_fly()) {
|
|
|
|
quantity = new OnTheFlyShapeFunctionProlongation(atc_,
|
|
|
|
coarseQuantity,atc_->atom_coarsegraining_positions());
|
|
|
|
} else {
|
|
|
|
quantity = new FtaShapeFunctionProlongation(atc_,
|
|
|
|
coarseQuantity,atc_->interpolant());
|
|
|
|
}
|
|
|
|
interscaleManager_.add_per_atom_quantity(quantity,
|
|
|
|
field_to_prolongation_name(field));
|
|
|
|
}
|
|
|
|
return quantity;
|
|
|
|
}
|
2013-08-08 05:34:54 +08:00
|
|
|
}
|