[FIX] Fixed DataSet creation from .xyz input files.

src/DataSet/DataSet.h

@@ -376,7 +376,6 @@ namespace lib4neuro {
         */
         LIB4NEURO_API void MPI_gather_data_on_master( );
 
-
         [[nodiscard]] LIB4NEURO_API arma::Mat<double>* get_inputs_matrix();
 
         [[nodiscard]] LIB4NEURO_API arma::Mat<double>* get_outputs_matrix();

src/Reader/XYZReader.cpp

@@ -208,34 +208,27 @@ void lib4neuro::XYZReader::transform_input_to_acsf(std::unordered_map<ELEMENT_SY
         /* Save Cartesian coordinates into the vector */
         for(auto el : *this->element_list) { /* Iterate over particles */
             for(unsigned int i = 0; i < n_coords_per_particle; i++) { /* Iterate over all coordinates of a single particle */
-                if(this->ignore_charge && i < 3) { /* Skip charge */
-                    cartesian_coords.at(i) = configuration.first.at(idx);
-                }
-
+                cartesian_coords.at(i) = configuration.first.at(idx);
                 idx++;
             }
+
+            if(this->ignore_charge) {
+                idx++; //skips charge - TODO add support for charge!
+            }
+
             particles.emplace_back(std::make_pair(el, cartesian_coords));
         }
 
-//        std::vector<std::vector<double>> coords_check;
-//        std::vector<double> single_coords_check;
-
         /* Transform Cartesian coordinates into ACSFs */
         std::vector<double> single_particle_coords;
-//        double coord_val;
         std::vector<std::pair<ELEMENT_SYMBOL, std::vector<double>>> acsf_coords_prep;
         for(size_t i = 0; i < particles.size(); i++) { /* Iterate over all the particles */
-//            single_coords_check.clear();
             single_particle_coords.clear();
 
             /* Compute vector of ACSF coordinates for a single particle */
             for (auto sym_func : *element_description[particles.at(i).first]->getSymmetryFunctions()) {
-//                coord_val = sym_func->eval(i, particles);
-//                acsf_coords.emplace_back(coord_val);
-//                single_coords_check.emplace_back(coord_val);
                 single_particle_coords.emplace_back(sym_func->eval(i, particles));
             }
-//            coords_check.emplace_back(single_coords_check);
 
             /* Store coordinates in a canonic order */
             unsigned int element_ind = 0;
@@ -256,9 +249,6 @@ void lib4neuro::XYZReader::transform_input_to_acsf(std::unordered_map<ELEMENT_SY
                         break;
                     }
 
-//                    std::cout << arma::norm(arma::conv_to<arma::Col<double>>::from(single_particle_coords)) << " "
-//                              << arma::norm(arma::conv_to<arma::Col<double>>::from(acsf_coords_prep.at(element_ind-1).second)) << std::endl;
-
                     if(arma::norm(arma::conv_to<arma::Col<double>>::from(single_particle_coords)) >
                         arma::norm(arma::conv_to<arma::Col<double>>::from(acsf_coords_prep.at(element_ind-1).second))) {
                         break;
@@ -317,9 +307,7 @@ lib4neuro::ELEMENT_SYMBOL lib4neuro::XYZReader::get_element_symbol(std::string s
 
 std::shared_ptr<lib4neuro::DataSet>
 lib4neuro::XYZReader::get_acsf_data_set(std::unordered_map<ELEMENT_SYMBOL, Element*>& element_description) {
-//    if(acsf_data_set == nullptr) {
-        this->transform_input_to_acsf(element_description);
-//    }
+    this->transform_input_to_acsf(element_description);
     return this->acsf_data_set;
 }