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PeizeLinPeizeLin
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1. add namespace Read_Txt_Stru
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‎source/Makefile.Objects‎

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@@ -246,6 +246,7 @@ read_atoms.o\
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read_cell_pseudopots.o\
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read_dm.o\
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read_txt_tools.o\
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read_txt_stru.o\
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write_pot.o\
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write_rho.o\
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write_rho_cube.o\

‎source/src_io/CMakeLists.txt‎

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@@ -24,6 +24,7 @@ add_library(
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read_dm.cpp
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read_rho.cpp
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read_txt_tools.cpp
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read_txt_stru.cpp
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restart.cpp
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rwstream.cpp
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to_wannier90.cpp

‎source/src_io/read_txt_stru.cpp‎

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//=======================
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// AUTHOR : Peize Lin
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// DATE : 2021-12-08
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//=======================
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#include "read_txt_stru.h"
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#include "read_txt_tools.h"
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#include <algorithm>
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namespace Read_Txt_Stru
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{
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//lat_info:
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// {
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// Lattice_Constant: [30.0, Bohr],
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// Lattice_Vectors:
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// [1.0, 0.0, 0.0,
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// 0.0, 1.0, 0.0,
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// 0.0, 0.0, 1.0],
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// Atomic_Positions: [Cartesian, Angstrom]
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// }
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//elements_info:
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// {
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// O: {
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// Pseudo_Potantial: [O_ONCV_PBE-1.0.upf],
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// Numerical_Orbital: [orb_O.dat]
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// },
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// C: {
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// Pseudo_Potantial: [C_ONCV_PBE-1.0.upf]
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// }
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// }
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//atoms:
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// [
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// [O, 0, 0, 0],
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// [H, 0, 0, 3, Force, 1, 1, 1]
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// ]
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std::tuple<
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std::map<std::string, std::vector<std::string>>,
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std::map<std::string, std::map<std::string, std::vector<std::string>>>,
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std::vector<std::vector<std::string>>>
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read_stru(const std::string &file_name)
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{
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const std::set<std::string> labels_lat = {"Lattice_Constant", "Lattice_Vectors", "Atomic_Positions"};
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std::set<std::string> labels = {"Element", "Atoms"};
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labels.insert(labels_lat.begin(), labels_lat.end());
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std::vector<std::vector<std::string>> stru = Read_Txt_Tools::read_file_to_vector(file_name, {"#","\\"});
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std::map<std::string, std::vector<std::string>> lat_info;
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std::map<std::string, std::map<std::string, std::vector<std::string>>> elements_info;
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std::vector<std::vector<std::string>> atoms_info;
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while(!stru.empty())
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{
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std::vector<std::vector<std::string>> stru_one = Read_Txt_Tools::cut_paragraph(stru, labels);
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if(stru_one[0][0]=="Element")
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{
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std::map<std::string, std::vector<std::string>> &element_info = elements_info[stru_one[0][1]];
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for(auto ptr=stru_one.begin()+1; ptr<stru_one.end(); ++ptr)
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{
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element_info[(*ptr)[0]] = std::vector<std::string>(ptr->begin()+1, ptr->end());
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}
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}
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else if(stru_one[0][0]=="Atoms")
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{
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// [
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// [O, 0, 0, 0],
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// [H, 0, 0, 3],
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// [Force, 1, 1, 1]
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// ]
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if(stru_one[0].size()==1)
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{
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atoms_info.insert(atoms_info.end(), stru_one.begin()+1, stru_one.end());
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}
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else
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{
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std::vector<std::string> atom0 = std::vector<std::string>(stru_one[0].begin()+1, stru_one[0].end());
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atoms_info.push_back(std::move(atom0));
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atoms_info.insert(atoms_info.end(), stru_one.begin()+1, stru_one.end());
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}
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}
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else
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{
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const auto ptr = std::find(labels_lat.begin(), labels_lat.end(), stru_one[0][0]);
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if(ptr!=labels_lat.end())
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{
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const std::vector<std::string> data = Read_Txt_Tools::chain(stru_one);
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lat_info[data[0]] = std::vector<std::string>(data.begin()+1, data.end());
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}
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else
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throw std::invalid_argument(stru_one[0][0]);
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}
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}
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std::set<std::string> elements_label;
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for(const auto & i : elements_info)
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elements_label.insert(i.first);
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std::vector<std::vector<std::string>> atoms_info_new = Read_Txt_Stru::organize_atom_info(std::move(atoms_info), elements_label);
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return make_tuple(std::move(lat_info), std::move(elements_info), std::move(atoms_info_new));
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}
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// atoms_info_old:
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// [
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// [H, 0, 0, 0],
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// [O, 0, 0, 3],
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// [Force, 1, 1, 1]
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// ]
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// atoms_info_new:
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// [
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// [H, 0, 0, 0],
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// [O, 0, 0, 3, Force, 1, 1, 1]
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// ]
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std::vector<std::vector<std::string>> organize_atom_info(
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std::vector<std::vector<std::string>> &&atoms_info_old,
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const std::set<std::string> &elements_label)
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{
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std::vector<std::vector<std::string>> atoms_info_new;
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while(!atoms_info_old.empty())
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{
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const std::vector<std::vector<std::string>> atom_one = Read_Txt_Tools::cut_paragraph(atoms_info_old, elements_label);
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atoms_info_new.push_back(Read_Txt_Tools::chain(atom_one));
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}
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return atoms_info_new;
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}
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}

‎source/src_io/read_txt_stru.h‎

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//=======================
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// AUTHOR : Peize Lin
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// DATE : 2021-12-08
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//=======================
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#ifndef READ_TXT_STRU_H
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#define READ_TXT_STRU_H
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#include <tuple>
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#include <vector>
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#include <map>
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#include <set>
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#include <string>
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namespace Read_Txt_Stru
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{
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//lat_info:
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// {
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// Lattice_Constant: [30.0, Bohr],
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// Lattice_Vectors:
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// [1.0, 0.0, 0.0,
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// 0.0, 1.0, 0.0,
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// 0.0, 0.0, 1.0],
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// Atomic_Positions: [Cartesian, Angstrom]
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// }
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//elements_info:
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// {
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// O: {
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// Pseudo_Potantial: [O_ONCV_PBE-1.0.upf],
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// Numerical_Orbital: [orb_O.dat]
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// },
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// C: {
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// Pseudo_Potantial: [C_ONCV_PBE-1.0.upf]
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// }
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// }
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//atoms:
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// [
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// [O, 0, 0, 0],
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// [H, 0, 0, 3, Force, 1, 1, 1]
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// ]
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std::tuple<
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std::map<std::string, std::vector<std::string>>,
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std::map<std::string, std::map<std::string, std::vector<std::string>>>,
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std::vector<std::vector<std::string>>>
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read_stru(const std::string &file_name);
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// atoms_info_old:
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// [
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// [H, 0, 0, 0],
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// [O, 0, 0, 3],
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// [Force, 1, 1, 1]
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// ]
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// atoms_info_new:
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// [
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// [H, 0, 0, 0],
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// [O, 0, 0, 3, Force, 1, 1, 1]
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// ]
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std::vector<std::vector<std::string>> organize_atom_info(
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std::vector<std::vector<std::string>> &&atoms_info_old,
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const std::set<std::string> &elements_label);
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}
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#endif

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