feat(species-lookup): added function to get species from a and z

meson.build

@@ -18,7 +18,7 @@
 #   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 #
 # *********************************************************************** #
-project('libcomposition', 'cpp', version: 'v1.5.2', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
+project('libcomposition', 'cpp', version: 'v1.6.0', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
 
 # Add default visibility for all C++ targets
 add_project_arguments('-fvisibility=default', language: 'cpp')

src/composition/include/fourdst/composition/atomicSpecies.h

@@ -1,9 +1,12 @@
 #pragma once
+
+
 #include <string_view>
 #include <string>
 #include <iostream>
 #include <limits>
 
+
 /**
  * @namespace fourdst::atomic
  * @brief Contains classes and functions related to atomic data, such as properties of atomic species.

src/composition/include/fourdst/composition/elements.h

@@ -0,0 +1,248 @@
+#pragma once
+
+#include <unordered_map>
+#include <cstdint>
+#include <string>
+
+namespace fourdst::atomic {
+    static const std::unordered_map<uint8_t, std::string> element_symbol_map = {
+        {1u, "H"},
+        {2u, "He"},
+        {3u, "Li"},
+        {4u, "Be"},
+        {5u, "B"},
+        {6u, "C"},
+        {7u, "N"},
+        {8u, "O"},
+        {9u, "F"},
+        {10u, "Ne"},
+        {11u, "Na"},
+        {12u, "Mg"},
+        {13u, "Al"},
+        {14u, "Si"},
+        {15u, "P"},
+        {16u, "S"},
+        {17u, "Cl"},
+        {18u, "Ar"},
+        {19u, "K"},
+        {20u, "Ca"},
+        {21u, "Sc"},
+        {22u, "Ti"},
+        {23u, "V"},
+        {24u, "Cr"},
+        {25u, "Mn"},
+        {26u, "Fe"},
+        {27u, "Co"},
+        {28u, "Ni"},
+        {29u, "Cu"},
+        {30u, "Zn"},
+        {31u, "Ga"},
+        {32u, "Ge"},
+        {33u, "As"},
+        {34u, "Se"},
+        {35u, "Br"},
+        {36u, "Kr"},
+        {37u, "Rb"},
+        {38u, "Sr"},
+        {39u, "Y"},
+        {40u, "Zr"},
+        {41u, "Nb"},
+        {42u, "Mo"},
+        {43u, "Tc"},
+        {44u, "Ru"},
+        {45u, "Rh"},
+        {46u, "Pd"},
+        {47u, "Ag"},
+        {48u, "Cd"},
+        {49u, "In"},
+        {50u, "Sn"},
+        {51u, "Sb"},
+        {52u, "Te"},
+        {53u, "I"},
+        {54u, "Xe"},
+        {55u, "Cs"},
+        {56u, "Ba"},
+        {57u, "La"},
+        {58u, "Ce"},
+        {59u, "Pr"},
+        {60u, "Nd"},
+        {61u, "Pm"},
+        {62u, "Sm"},
+        {63u, "Eu"},
+        {64u, "Gd"},
+        {65u, "Tb"},
+        {66u, "Dy"},
+        {67u, "Ho"},
+        {68u, "Er"},
+        {69u, "Tm"},
+        {70u, "Yb"},
+        {71u, "Lu"},
+        {72u, "Hf"},
+        {73u, "Ta"},
+        {74u, "W"},
+        {75u, "Re"},
+        {76u, "Os"},
+        {77u, "Ir"},
+        {78u, "Pt"},
+        {79u, "Au"},
+        {80u, "Hg"},
+        {81u, "Tl"},
+        {82u, "Pb"},
+        {83u, "Bi"},
+        {84u, "Po"},
+        {85u, "At"},
+        {86u, "Rn"},
+        {87u, "Fr"},
+        {88u, "Ra"},
+        {89u, "Ac"},
+        {90u, "Th"},
+        {91u, "Pa"},
+        {92u, "U"},
+        {93u, "Np"},
+        {94u, "Pu"},
+        {95u, "Am"},
+        {96u, "Cm"},
+        {97u, "Bk"},
+        {98u, "Cf"},
+        {99u, "Es"},
+        {100u, "Fm"},
+        {101u, "Md"},
+        {102u, "No"},
+        {103u, "Lr"},
+        {104u, "Rf"},
+        {105u, "Db"},
+        {106u, "Sg"},
+        {107u, "Bh"},
+        {108u, "Hs"},
+        {109u, "Mt"},
+        {110u, "Ds"},
+        {111u, "Rg"},
+        {112u, "Cn"},
+        {113u, "Nh"},
+        {114u, "Fl"},
+        {115u, "Mc"},
+        {116u, "Lv"},
+        {117u, "Ts"},
+        {118u, "Og"}
+    };
+    static const std::unordered_map<std::string, uint8_t> symbol_element_map = {
+        {"H", 1u},
+        {"He", 2u},
+        {"Li", 3u},
+        {"Be", 4u},
+        {"B", 5u},
+        {"C", 6u},
+        {"N", 7u},
+        {"O", 8u},
+        {"F", 9u},
+        {"Ne", 10u},
+        {"Na", 11u},
+        {"Mg", 12u},
+        {"Al", 13u},
+        {"Si", 14u},
+        {"P", 15u},
+        {"S", 16u},
+        {"Cl", 17u},
+        {"Ar", 18u},
+        {"K", 19u},
+        {"Ca", 20u},
+        {"Sc", 21u},
+        {"Ti", 22u},
+        {"V", 23u},
+        {"Cr", 24u},
+        {"Mn", 25u},
+        {"Fe", 26u},
+        {"Co", 27u},
+        {"Ni", 28u},
+        {"Cu", 29u},
+        {"Zn", 30u},
+        {"Ga", 31u},
+        {"Ge", 32u},
+        {"As", 33u},
+        {"Se", 34u},
+        {"Br", 35u},
+        {"Kr", 36u},
+        {"Rb", 37u},
+        {"Sr", 38u},
+        {"Y", 39u},
+        {"Zr", 40u},
+        {"Nb", 41u},
+        {"Mo", 42u},
+        {"Tc", 43u},
+        {"Ru", 44u},
+        {"Rh", 45u},
+        {"Pd", 46u},
+        {"Ag", 47u},
+        {"Cd", 48u},
+        {"In", 49u},
+        {"Sn", 50u},
+        {"Sb", 51u},
+        {"Te", 52u},
+        {"I", 53u},
+        {"Xe", 54u},
+        {"Cs", 55u},
+        {"Ba", 56u},
+        {"La", 57u},
+        {"Ce", 58u},
+        {"Pr", 59u},
+        {"Nd", 60u},
+        {"Pm", 61u},
+        {"Sm", 62u},
+        {"Eu", 63u},
+        {"Gd", 64u},
+        {"Tb", 65u},
+        {"Dy", 66u},
+        {"Ho", 67u},
+        {"Er", 68u},
+        {"Tm", 69u},
+        {"Yb", 70u},
+        {"Lu", 71u},
+        {"Hf", 72u},
+        {"Ta", 73u},
+        {"W", 74u},
+        {"Re", 75u},
+        {"Os", 76u},
+        {"Ir", 77u},
+        {"Pt", 78u},
+        {"Au", 79u},
+        {"Hg", 80u},
+        {"Tl", 81u},
+        {"Pb", 82u},
+        {"Bi", 83u},
+        {"Po", 84u},
+        {"At", 85u},
+        {"Rn", 86u},
+        {"Fr", 87u},
+        {"Ra", 88u},
+        {"Ac", 89u},
+        {"Th", 90u},
+        {"Pa", 91u},
+        {"U", 92u},
+        {"Np", 93u},
+        {"Pu", 94u},
+        {"Am", 95u},
+        {"Cm", 96u},
+        {"Bk", 97u},
+        {"Cf", 98u},
+        {"Es", 99u},
+        {"Fm", 100u},
+        {"Md", 101u},
+        {"No", 102u},
+        {"Lr", 103u},
+        {"Rf", 104u},
+        {"Db", 105u},
+        {"Sg", 106u},
+        {"Bh", 107u},
+        {"Hs", 108u},
+        {"Mt", 109u},
+        {"Ds", 110u},
+        {"Rg", 111u},
+        {"Cn", 112u},
+        {"Nh", 113u},
+        {"Fl", 114u},
+        {"Mc", 115u},
+        {"Lv", 116u},
+        {"Ts", 117u},
+        {"Og", 118u}
+    };
+};

src/composition/include/fourdst/composition/species.h

@@ -16,6 +16,7 @@
 #include <string>
 #include <limits> // Required for std::numeric_limits
 #include "fourdst/composition/atomicSpecies.h"
+#include "fourdst/composition/elements.h"
 
 namespace fourdst::atomic {
     static const Species n_1("n-1", "n", 1, 1, 0, 1, 0.0, "B-", 782.347, 609.8, "/2+*", "-=100", 1.0086649159, 0.00047);
@@ -7137,6 +7138,12 @@ namespace fourdst::atomic {
         {"Og-294", Og_294},
         {"Og-295", Og_295},
     };
+
+    inline Species az_to_species(const int a, const int z) {
+        const std::string element_symbol = element_symbol_map.at(static_cast<uint8_t>(z));
+        const std::string species_symbol = element_symbol + "-" + std::to_string(a);
+        return species.at(species_symbol);
+    };
 }; // namespace fourdst::atomic
 #ifndef SERIF_SPECIES_N_1
     #define SERIF_SPECIES_N_1

src/composition/meson.build

@@ -45,6 +45,12 @@ composition_dep = declare_dependency(
 composition_headers = files(
   'include/fourdst/composition/composition.h',
   'include/fourdst/composition/atomicSpecies.h',
-  'include/fourdst/composition/species.h'
+  'include/fourdst/composition/species.h',
+  'include/fourdst/composition/elements.h'
 )
 install_headers(composition_headers, subdir : 'fourdst/fourdst/composition')
+
+composition_exception_headers = files(
+    'include/fourdst/composition/exceptions/exceptions_composition.h',
+)
+install_headers(composition_exception_headers, subdir : 'fourdst/fourdst/composition/exceptions')

tests/composition/compositionTest.cpp

@@ -429,3 +429,7 @@ TEST_F(compositionTest, getRegisteredSpecies) {
     EXPECT_EQ(*it1, fourdst::atomic::H_1);
 }
 
+TEST_F(compositionTest, getSpeciesFromAZ) {
+    EXPECT_EQ(fourdst::atomic::O_12, fourdst::atomic::az_to_species(12, 8));
+}
+

utils/atomic/format.py

@@ -222,6 +222,7 @@ def formatHeader(dataFrame):
 #include <string>
 #include <limits> // Required for std::numeric_limits
 #include "fourdst/composition/atomicSpecies.h"
+#include "fourdst/composition/elements.h"
 
 namespace fourdst::atomic {{
     // Instantiate all species as static const objects.
@@ -231,6 +232,12 @@ namespace fourdst::atomic {{
     static const std::unordered_map<std::string, const Species*> species = {{
         {'\n        '.join([f'{{"{row["el"].strip()}-{row["a"]}", {mkInstanceName(row)}}},' for index, row in dataFrame.iterrows()])}
     }};
+    Species az_to_species(const int a, const int z) {{
+    const std::string element_symbol = element_symbol_map.at(static_cast<uint8_t>(z));
+        const std::string species_symbol = element_symbol + "-" + std::to_string(a);
+        return species.at(species_symbol);
+    }};
+
 }}; // namespace fourdst::atomic
 """
     return header