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rename tdace_*.h/cpp -> grace_fs_*.h/cpp
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Yury Lysogorskiy committed Sep 11, 2024
1 parent a47f5db commit bb4d1d0
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Showing 3 changed files with 59 additions and 52 deletions.
4 changes: 3 additions & 1 deletion ML-PACE/ace/ace_b_evaluator.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,7 @@ ACEBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, co
throw std::invalid_argument("ACEBEvaluator: basis set is not assigned");
}
per_atom_calc_timer.start();
setup_timer.start();
DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0;
DOUBLE_TYPE r_norm;
DOUBLE_TYPE xn, yn, zn, r_xyz;
Expand Down Expand Up @@ -214,7 +215,6 @@ ACEBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, co
const Array1D<DOUBLE_TYPE> &gr = basis_set->radial_functions->gr;
const Array1D<DOUBLE_TYPE> &dgr = basis_set->radial_functions->dgr;
setup_timer.stop();
A_construction_timer.start();

int jj_actual = 0;
SPECIES_TYPE type_j = 0;
Expand Down Expand Up @@ -267,6 +267,8 @@ ACEBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, co


//ALGORITHM 1: Atomic base A
A_construction_timer.start();

for (jj = 0; jj < jnum_actual; ++jj) {
r_norm = r_norms(jj);
mu_j = elements(jj);
Expand Down
74 changes: 39 additions & 35 deletions ML-PACE/ace/tdace_evaluator.cpp → ML-PACE/ace/grace_fs_evaluator.cpp
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
//
// Created by Yury Lysogorskiy on 24.06.24
//
#include "ace/tdace_evaluator.h"
#include "ace/grace_fs_evaluator.h"
#include "ace-evaluator/ace_types.h"
#include "ace/ace_yaml_input.h"
#include "ace-evaluator/ace_radial.h"
Expand All @@ -10,7 +10,7 @@
#define sqr(x) ((x)*(x))
const DOUBLE_TYPE pi = 3.14159265358979323846264338327950288419; // pi

void TDACEEmbeddingSpecification::from_YAML(YAML_PACE::Node emb_yaml) {
void GRACEFSEmbeddingSpecification::from_YAML(YAML_PACE::Node emb_yaml) {
this->type = emb_yaml["type"].as<string>();
this->FS_parameters = emb_yaml["params"].as<vector<double>>();
if (this->FS_parameters.size() % 2 == 0)
Expand All @@ -21,7 +21,7 @@ void TDACEEmbeddingSpecification::from_YAML(YAML_PACE::Node emb_yaml) {
// this->ndensity = emb_yaml["ndensity"].as<DENSITY_TYPE>();
}

void TDACERadialFunction::from_YAML(YAML_PACE::Node bond_yaml) {
void GRACEFSRadialFunction::from_YAML(YAML_PACE::Node bond_yaml) {

this->radbasename = bond_yaml["radbasename"].as<string>();

Expand All @@ -40,7 +40,7 @@ void TDACERadialFunction::from_YAML(YAML_PACE::Node bond_yaml) {
this->crad.set_flatten_vector(crad_flat);

auto Z_flat = bond_yaml["Z"].as<vector<DOUBLE_TYPE>>();
this->Z.init(Z_shape[0], Z_shape[1]);
this->Z.init(Z_shape[0], Z_shape[1], "Z");
Z.set_flatten_vector(Z_flat);


Expand All @@ -51,7 +51,7 @@ void TDACERadialFunction::from_YAML(YAML_PACE::Node bond_yaml) {
if (bond_yaml["dcut_in"]) dcut_in = bond_yaml["dcut_in"].as<DOUBLE_TYPE>();
}

void TDACEBasisFunction::from_YAML(YAML_PACE::Node node) {
void GRACEFSBasisFunction::from_YAML(YAML_PACE::Node node) {
this->mu0 = node["mu0"].as<SPECIES_TYPE>();

this->ns = node["ns"].as<NS_TYPE>();
Expand All @@ -73,7 +73,7 @@ void TDACEBasisFunction::from_YAML(YAML_PACE::Node node) {
throw invalid_argument("ndensity != coeff.size");
}

void TDACEBasisFunction::print() const {
void GRACEFSBasisFunction::print() const {
cout << "TDACEBasisFunction(mu0=" << this->mu0 << ", rank=" << (int) this->rank << endl;
int rank = this->rank;

Expand All @@ -85,11 +85,11 @@ void TDACEBasisFunction::print() const {
cout << ")" << endl;
}

TDACEBasisSet::TDACEBasisSet(const string &filename) {
GRACEFSBasisSet::GRACEFSBasisSet(const string &filename) {
this->load(filename);
}

void TDACEBasisSet::load(const string &filename) {
void GRACEFSBasisSet::load(const string &filename) {
this->filename = filename;

if (!if_file_exist(filename)) {
Expand Down Expand Up @@ -122,9 +122,9 @@ void TDACEBasisSet::load(const string &filename) {
for (const auto &mu_functions_node: YAML_input["functions"]) {
SPECIES_TYPE mu0 = mu_functions_node.first.as<SPECIES_TYPE>();
const auto &functions_list = mu_functions_node.second;
vector<TDACEBasisFunction> basis_functions_vec;
vector<GRACEFSBasisFunction> basis_functions_vec;
for (const auto &func_node: functions_list) {
TDACEBasisFunction func;
GRACEFSBasisFunction func;
func.from_YAML(func_node);
basis_functions_vec.emplace_back(func);
if (func.rank > rankmax)
Expand Down Expand Up @@ -171,7 +171,7 @@ void TDACEBasisSet::load(const string &filename) {
else this->scale = 1.0;
}

void TDACEBasisSet::convert_to_flatten_arrays() {
void GRACEFSBasisSet::convert_to_flatten_arrays() {
ranks_flatten.resize(nelements);
ndensity_flatten.resize(nelements);
num_ms_combs_flatten.resize(nelements);
Expand Down Expand Up @@ -262,9 +262,9 @@ void TDACEBasisSet::convert_to_flatten_arrays() {
}
}

void TDACEBasisSet::FS_values_and_derivatives(Array1D<DOUBLE_TYPE> &rhos, DOUBLE_TYPE &value,
Array1D<DOUBLE_TYPE> &derivatives,
SPECIES_TYPE mu_i) {
void GRACEFSBasisSet::FS_values_and_derivatives(Array1D<DOUBLE_TYPE> &rhos, DOUBLE_TYPE &value,
Array1D<DOUBLE_TYPE> &derivatives,
SPECIES_TYPE mu_i) {
DOUBLE_TYPE F, DF = 0, wpre, mexp;
DENSITY_TYPE ndensity = this->ndensitymax;

Expand All @@ -283,7 +283,7 @@ void TDACEBasisSet::FS_values_and_derivatives(Array1D<DOUBLE_TYPE> &rhos, DOUBLE
}
}

void TDACEBasisSet::print_functions() {
void GRACEFSBasisSet::print_functions() {
for (int el = 0; el < nelements; el++) {
printf("============================= Element: %d =====================\n", el);
for (const auto &func: basis[el]) {
Expand All @@ -292,12 +292,12 @@ void TDACEBasisSet::print_functions() {
}
}

void TDACEBEvaluator::set_basis(TDACEBasisSet &basis_set) {
void GRACEFSBEvaluator::set_basis(GRACEFSBasisSet &basis_set) {
this->basis_set = basis_set;
init(this->basis_set);
}

void TDACEBEvaluator::init(TDACEBasisSet &basis_set) {
void GRACEFSBEvaluator::init(GRACEFSBasisSet &basis_set) {
A.init(basis_set.nradmax + 1, basis_set.lmax + 1, "A");

rhos.init(basis_set.ndensitymax, "rhos");
Expand Down Expand Up @@ -329,7 +329,7 @@ void TDACEBEvaluator::init(TDACEBasisSet &basis_set) {
}


void TDACEBEvaluator::resize_neighbours_cache(int max_jnum) {
void GRACEFSBEvaluator::resize_neighbours_cache(int max_jnum) {
if (R_cache.get_dim(0) < max_jnum) {

//TODO: implement grow
Expand Down Expand Up @@ -360,7 +360,7 @@ void TDACEBEvaluator::resize_neighbours_cache(int max_jnum) {
}


void TDACEBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) {
void GRACEFSBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) {
per_atom_calc_timer.start();

setup_timer.start();
Expand All @@ -382,11 +382,11 @@ void TDACEBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *t

int j, jj, func_ind, ms_ind;

DOUBLE_TYPE Y{0}, Y_DR{0.};
DOUBLE_TYPE B{0.};
DOUBLE_TYPE dB{0};
DOUBLE_TYPE Y, Y_DR;
DOUBLE_TYPE B;
DOUBLE_TYPE dB;
Array1D<DOUBLE_TYPE> A_cache(basis_set.rankmax);
ACEDRealYcomponent grad_phi_nlm{0}, DY{0.};
ACEDRealYcomponent grad_phi_nlm, DY;

//size is +1 of max to avoid out-of-boundary array access in double-triangular scheme
Array1D<DOUBLE_TYPE> A_forward_prod(basis_set.rankmax + 1);
Expand Down Expand Up @@ -495,6 +495,8 @@ void TDACEBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *t

//loop for computing A's
// for rank > 1
// A_construction_timer2.start();

for (n = 0; n < basis_set.nradmax; n++) {
auto &A_lm = A(n);
for (l = 0; l <= basis_set.lmax; l++) {
Expand All @@ -512,6 +514,7 @@ void TDACEBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *t

}
}
// A_construction_timer2.stop();

} //end loop over neighbours
A_construction_timer.stop();
Expand Down Expand Up @@ -687,8 +690,9 @@ void TDACEBEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *t
per_atom_calc_timer.stop();
}

void TDACEBEvaluator::init_timers() {
void GRACEFSBEvaluator::init_timers() {
A_construction_timer.init();
A_construction_timer2.init();
forces_calc_loop_timer.init();
energy_calc_timer.init();
per_atom_calc_timer.init();
Expand All @@ -698,7 +702,7 @@ void TDACEBEvaluator::init_timers() {
}


void TDACEBEvaluator::load_active_set(const string &asi_filename) {
void GRACEFSBEvaluator::load_active_set(const string &asi_filename) {
cnpy::npz_t asi_npz = cnpy::npz_load(asi_filename);
if (asi_npz.size() != this->basis_set.nelements) {
stringstream ss;
Expand Down Expand Up @@ -746,7 +750,7 @@ void TDACEBEvaluator::load_active_set(const string &asi_filename) {
}


void TDACERadialFunction::init() {
void GRACEFSRadialFunction::init() {

gr.init(nradbasemax, "gr");
dgr.init(nradbasemax, "dgr");
Expand All @@ -765,7 +769,7 @@ void TDACERadialFunction::init() {
* @param rc
* @param x
*/
void TDACERadialFunction::simplified_bessel(DOUBLE_TYPE rc, DOUBLE_TYPE x) {
void GRACEFSRadialFunction::simplified_bessel(DOUBLE_TYPE rc, DOUBLE_TYPE x) {
if (x < rc) {
gr(0) = simplified_bessel_aux(x, rc, 0);
dgr(0) = dsimplified_bessel_aux(x, rc, 0);
Expand All @@ -784,8 +788,8 @@ void TDACERadialFunction::simplified_bessel(DOUBLE_TYPE rc, DOUBLE_TYPE x) {
}
}

void TDACERadialFunction::radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, string radbasename, DOUBLE_TYPE r,
DOUBLE_TYPE cut_in, DOUBLE_TYPE dcut_in) {
void GRACEFSRadialFunction::radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, string radbasename, DOUBLE_TYPE r,
DOUBLE_TYPE cut_in, DOUBLE_TYPE dcut_in) {
/*lam is given by the formula (24), that contains cut */
if (r <= cut_in - dcut_in || r >= cut) {
gr.fill(0);
Expand All @@ -799,14 +803,14 @@ void TDACERadialFunction::radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE
}
}

void TDACERadialFunction::all_radfunc(DOUBLE_TYPE r) {
void GRACEFSRadialFunction::all_radfunc(DOUBLE_TYPE r) {

// set up radial functions
radbase(rad_lamba, rcut, dcut, radbasename, r, 0, 0); //update gr, dgr
radfunc(); // update fr(nr, l), dfr(nr, l)
}

void TDACERadialFunction::radfunc() {
void GRACEFSRadialFunction::radfunc() {
DOUBLE_TYPE frval, dfrval;
for (NS_TYPE n = 0; n < nradmax; n++) {
for (LS_TYPE l = 0; l <= lmax; l++) {
Expand All @@ -824,23 +828,23 @@ void TDACERadialFunction::radfunc() {
}
}

void TDACERadialFunction::setuplookupRadspline() {
void GRACEFSRadialFunction::setuplookupRadspline() {
using namespace std::placeholders;
splines_gk.setupSplines(gr.get_size(),
std::bind(&TDACERadialFunction::radbase, this, this->rad_lamba,
std::bind(&GRACEFSRadialFunction::radbase, this, this->rad_lamba,
this->rcut, this->dcut,
this->radbasename,
_1, 0, 0),//update gr, dgr
gr.get_data(),
dgr.get_data(), deltaSplineBins, this->rcut);

splines_rnl.setupSplines(fr.get_size(),
std::bind(&TDACERadialFunction::all_radfunc, this, _1), // update fr(nr, l), dfr(nr, l)
std::bind(&GRACEFSRadialFunction::all_radfunc, this, _1), // update fr(nr, l), dfr(nr, l)
fr.get_data(),
dfr.get_data(), deltaSplineBins, rcut);
}

void TDACERadialFunction::evaluate(DOUBLE_TYPE r, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j) {
void GRACEFSRadialFunction::evaluate(DOUBLE_TYPE r, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j) {
splines_gk.calcSplines(r);
for (NS_TYPE nr = 0; nr < nradbasemax; nr++) {
gr(nr) = splines_gk.values(nr);
Expand Down
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