build(libcomposition): brought working build system into libcomposition

.gitignore

@@ -0,0 +1,91 @@
+# Python
+__pycache__/
+*.py[cod]
+*.pyo
+*.pyd
+*.env
+*.venv
+env/
+venv/
+ENV/
+ENV.bak/
+*.egg-info/
+dist/
+build/
+*.egg
+
+# C and C++ (using Meson)
+build/
+*.o
+*.a
+*.so
+*.d
+*.dSYM/
+*.exe
+*.out
+*.obj
+*.dll
+*.lib
+*.pdb
+*.exp
+*.log
+*.stackdump
+
+# Fortran
+*.mod
+*.o
+*.a
+*.so
+*.exe
+*.out
+
+# Doxygen
+html/
+latex/
+xml/
+man/
+rtf/
+tags
+
+## Misc
+*.swp
+*._DS_Store
+*.DS_Store
+*.bak
+*.tmp
+*.log
+*.cache
+*.private
+*.private/
+
+subprojects/mfem/
+subprojects/tetgen/
+subprojects/yaml-cpp/
+subprojects/quill/
+subprojects/googletest-*/
+subprojects/opat-core/
+subprojects/pybind11*/
+subprojects/packagecache/
+subprojects/hypre/
+subprojects/qhull/
+subprojects/cppad/
+subprojects/libconfig/
+subprojects/libconstants/
+subprojects/liblogging/
+
+qhull.wrap
+
+.vscode/
+
+*.log
+mpi-install-log.txt
+
+output/
+
+.boost_installed
+4DSSE_logs/
+.last_build_flags
+
+.idea/
+
+scratch/

assets/static/atomic/include/atomicSpecies.h

@@ -5,7 +5,7 @@
 #include <iostream>
 #include "atomicSpecies.h"
 
-namespace serif::atomic {
+namespace fourdst::atomic {
     struct Species {
         std::string m_name; //< Name of the species
         std::string m_el; //< Element symbol
@@ -101,9 +101,9 @@ namespace serif::atomic {
 
 namespace std {
     template<>
-    struct hash<serif::atomic::Species> {
+    struct hash<fourdst::atomic::Species> {
-        size_t operator()(const serif::atomic::Species& s) const noexcept {
+        size_t operator()(const fourdst::atomic::Species& s) const noexcept {
             return std::hash<std::string>()(s.m_name);
         }
     };
-} // namespace std
+} // namespace std

assets/static/atomic/include/species.h

@@ -4,7 +4,7 @@
 #include <string>
 #include "atomicSpecies.h"
 
-namespace serif::atomic {
+namespace fourdst::atomic {
     static const Species n_1("n-1", "n", 1, 1, 0, 1, 0.0, "B-", 782.347, 1.0086649159, 0.00047);
     static const Species H_1("H-1", "H", -1, 0, 1, 1, 0.0, "B-", std::numeric_limits<double>::quiet_NaN(), 1.007825031898, 1.4e-05);
     static const Species H_2("H-2", "H", 0, 1, 1, 2, 1112.2831, "B-", std::numeric_limits<double>::quiet_NaN(), 2.014101777844, 1.5e-05);

assets/static/meson.build

@@ -0,0 +1 @@
+subdir('atomic')

build-config/fourdst/libconfig/meson.build

@@ -0,0 +1,2 @@
+config_p = subproject('libconfig')
+config_dep  = config_p.get_variable('config_dep')

build-config/fourdst/libconstants/meson.build

@@ -0,0 +1,2 @@
+const_p = subproject('libconstants')
+const_dep  = const_p.get_variable('const_dep')

build-config/fourdst/liblogging/meson.build

@@ -0,0 +1,6 @@
+logging_p = subproject('liblogging')
+
+logging_dep  = logging_p.get_variable('logging_dep')
+quill_dep = logging_p.get_variable('quill_dep')
+
+log_dep = [logging_dep, quill_dep]

build-config/fourdst/meson.build

@@ -0,0 +1,3 @@
+subdir('libconstants')
+subdir('liblogging')
+subdir('libconfig')

build-config/meson.build

@@ -1,24 +1,5 @@
 cmake = import('cmake')
 
-subdir('mfem')
+subdir('fourdst')
-subdir('yaml-cpp')
-subdir('quill')
-subdir('boost')
-subdir('opatIO')
-subdir('mpi')
-subdir('hypre')
-subdir('pybind')
 subdir('cppad')
 
-# Set the config file error handling options
-configErr = get_option('config_error_handling')
-
-# build up any -D flags we need
-commonCppArgs = []
-if configErr == 'warn'
-    commonCppArgs += ['-DCONFIG_WARN']
-elif configErr == 'harsh'
-    commonCppArgs += ['-DCONFIG_HARSH']
-endif
-
-add_project_arguments(commonCppArgs, language: 'cpp')

meson.build

@@ -0,0 +1,42 @@
+# ***********************************************************************
+#
+#   Copyright (C) 2025 -- The 4D-STAR Collaboration
+#   File Author: Emily Boudreaux
+#   Last Modified: June 21, 2025
+#
+#   libcomposition is free software; you can use it and/or modify
+#   it under the terms and restrictions the GNU General Library Public
+#   License version 3 (GPLv3) as published by the Free Software Foundation.
+#
+#   libcomposition is distributed in the hope that it will be useful,
+#   but WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+#   See the GNU Library General Public License for more details.
+#
+#   You should have received a copy of the GNU Library General Public License
+#   along with this software; if not, write to the Free Software
+#   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+#
+# *********************************************************************** #
+project('libcomposition', 'cpp', version: 'v1.0.0', 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')
+
+cpp = meson.get_compiler('cpp')
+subdir('build-config')
+subdir('assets/static')
+subdir('src')
+subdir('tests')
+
+pkg = import('pkgconfig')
+pkg.generate(
+    name: 'libcomposition',
+    description: 'Composition module for SERiF and related projects',
+    version: meson.project_version(),
+    libraries: [libcomposition],
+    subdirs: ['libcomposition'],
+    filebase: 'libcomposition',
+    install_dir: join_paths(get_option('libdir'), 'pkgconfig')
+)
+

readme.md

@@ -0,0 +1,23 @@
+# libcomposition
+
+libcomposition is the chemistry tracking tool used by SERiF and related products.
+
+This has been broken out of the main serif project to allow for more modularity
+
+## Building
+In order to build libconstants you need `meson>=1.5.0`. This can be installed with `pip`
+
+```bash
+pip install "meson>=1.5.0"
+```
+
+Then from the root libcomposition directory it is as simple as
+
+```bash
+meson setup build --buildtype=release
+meson compile -C build
+meson test -C build
+```
+
+this will auto generate a pkg-config file for you so that linking other libraries to libcomposition is easy.
+

src/composition/meson.build

@@ -8,10 +8,10 @@ composition_headers = files(
 )
 
 dependencies = [
-    probe_dep,
-    quill_dep,
     species_weight_dep,
     const_dep,
+    config_dep,
+    log_dep
 ]
 
 # Define the libcomposition library so it can be linked against by other parts of the build system
@@ -30,4 +30,4 @@ composition_dep = declare_dependency(
 )
 
 # Make headers accessible
-install_headers(composition_headers, subdir : 'SERiF/composition')
+install_headers(composition_headers, subdir : 'libcomposition/composition')

src/composition/private/composition.cpp

@@ -33,13 +33,13 @@
 #include "atomicSpecies.h"
 #include "species.h"
 
-namespace serif::composition {
+namespace fourdst::composition {
 
-    CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(serif::atomic::species.at("H-1")),
+    CompositionEntry::CompositionEntry() : m_symbol("H-1"), m_isotope(fourdst::atomic::species.at("H-1")),
                                            m_initialized(false) {
     }
 
-    CompositionEntry::CompositionEntry(const std::string& symbol, const bool massFracMode) : m_symbol(symbol), m_isotope(serif::atomic::species.at(symbol)), m_massFracMode(massFracMode) {
+    CompositionEntry::CompositionEntry(const std::string& symbol, const bool massFracMode) : m_symbol(symbol), m_isotope(fourdst::atomic::species.at(symbol)), m_massFracMode(massFracMode) {
         setSpecies(symbol);
     }
 
@@ -56,11 +56,11 @@ namespace serif::composition {
         if (m_initialized) {
             throw std::runtime_error("Composition entry is already initialized.");
         }
-        if (serif::atomic::species.count(symbol) == 0) {
+        if (fourdst::atomic::species.count(symbol) == 0) {
             throw std::runtime_error("Invalid symbol.");
         }
         m_symbol = symbol;
-        m_isotope = serif::atomic::species.at(symbol);
+        m_isotope = fourdst::atomic::species.at(symbol);
         m_initialized = true;
     }
 
@@ -101,7 +101,7 @@ namespace serif::composition {
         return m_relAbundance;
     }
 
-    serif::atomic::Species CompositionEntry::isotope() const {
+    fourdst::atomic::Species CompositionEntry::isotope() const {
         return m_isotope;
     }
 
@@ -258,7 +258,7 @@ namespace serif::composition {
     }
 
     bool Composition::isValidSymbol(const std::string& symbol) {
-        return serif::atomic::species.contains(symbol);
+        return fourdst::atomic::species.contains(symbol);
     }
 
     double Composition::setMassFraction(const std::string& symbol, const double& mass_fraction) {
@@ -652,7 +652,7 @@ namespace serif::composition {
         return m_compositions.count(symbol) > 0;
     }
 
-    bool Composition::contains(const serif::atomic::Species &isotope) const {
+    bool Composition::contains(const fourdst::atomic::Species &isotope) const {
         // Check if the isotope's symbol is in the composition
         if (!m_finalized) {
             LOG_ERROR(m_logger, "Composition has not been finalized.");
@@ -696,4 +696,4 @@ namespace serif::composition {
         return os;
     }
 
-} // namespace serif::composition
+} // namespace fourdst::composition

src/composition/public/composition.h

@@ -27,12 +27,12 @@
 
 #include <utility>
 
-#include "probe.h"
 #include "config.h"
+#include "logging.h"
 
 #include "atomicSpecies.h"
 
-namespace serif::composition {
+namespace fourdst::composition {
     struct CanonicalComposition {
         double X = 0.0; ///< Mass fraction of Hydrogen.
         double Y = 0.0; ///< Mass fraction of Helium.
@@ -63,7 +63,7 @@ namespace serif::composition {
      */
     struct CompositionEntry {
         std::string m_symbol; ///< The chemical symbol of the species.
-        serif::atomic::Species m_isotope; ///< The isotope of the species.
+        fourdst::atomic::Species m_isotope; ///< The isotope of the species.
         bool m_massFracMode = true; ///< The mode of the composition entry. True if mass fraction, false if number fraction.   
 
         double m_massFraction = 0.0; ///< The mass fraction of the species.
@@ -142,7 +142,7 @@ namespace serif::composition {
          * @brief Gets the isotope of the species.
          * @return The isotope of the species.
          */
-        serif::atomic::Species isotope() const;
+        fourdst::atomic::Species isotope() const;
 
         /**
          * @brief Gets the mode of the composition entry.
@@ -215,8 +215,8 @@ namespace serif::composition {
      */
     class Composition {
     private:
-        serif::config::Config& m_config = serif::config::Config::getInstance();
+        fourdst::config::Config& m_config = fourdst::config::Config::getInstance();
-        serif::probe::LogManager& m_logManager = serif::probe::LogManager::getInstance();
+        fourdst::logging::LogManager& m_logManager = fourdst::logging::LogManager::getInstance();
         quill::Logger* m_logger = m_logManager.getLogger("log");
 
         bool m_finalized = false; ///< True if the composition is finalized.
@@ -473,7 +473,7 @@ namespace serif::composition {
         */
         bool hasSymbol(const std::string& symbol) const;
 
-        bool contains(const serif::atomic::Species& isotope) const;
+        bool contains(const fourdst::atomic::Species& isotope) const;
 
         /**
         * @brief Sets the composition mode.
@@ -508,4 +508,4 @@ namespace serif::composition {
         Composition operator+(const Composition& other) const;
 
     };
-}; // namespace serif::composition
+}; // namespace fourdst::composition

src/meson.build

@@ -0,0 +1 @@
+subdir('composition')

subprojects/libconfig.wrap

@@ -0,0 +1,7 @@
+[wrap-git]
+url = https://github.com/4D-STAR/libconfig.git
+revision = v1.0.0
+depth = 1
+
+[provide]
+libconfig = config_dep

subprojects/libconstants.wrap

@@ -0,0 +1,7 @@
+[wrap-git]
+url = https://github.com/4D-STAR/libconstants.git
+revision = v1.1
+depth = 1
+
+[provide]
+libconstants = const_dep

subprojects/liblogging.wrap

@@ -0,0 +1,7 @@
+[wrap-git]
+url = https://github.com/4D-STAR/liblogging.git
+revision = v1.0.1
+depth = 1
+
+[provide]
+liblogging = logging_dep

subprojects/quill.wrap

@@ -0,0 +1,2 @@
+[wrap-redirect]
+filename = liblogging/subprojects/quill.wrap

subprojects/yaml-cpp.wrap

@@ -0,0 +1,2 @@
+[wrap-redirect]
+filename = libconfig/subprojects/yaml-cpp.wrap

tests/composition/compositionTest.cpp

@@ -19,20 +19,20 @@ class compositionTest : public ::testing::Test {};
  * @brief Test the constructor of the composition class.
  */
 TEST_F(compositionTest, isotopeMasses) {
-    EXPECT_NO_THROW(serif::atomic::species.at("H-1"));
+    EXPECT_NO_THROW(fourdst::atomic::species.at("H-1"));
-    EXPECT_DOUBLE_EQ(serif::atomic::species.at("H-1").mass(), 1.007825031898);
+    EXPECT_DOUBLE_EQ(fourdst::atomic::species.at("H-1").mass(), 1.007825031898);
-    EXPECT_DOUBLE_EQ(serif::atomic::species.at("He-3").mass(), 3.0160293219700001);
+    EXPECT_DOUBLE_EQ(fourdst::atomic::species.at("He-3").mass(), 3.0160293219700001);
-    EXPECT_DOUBLE_EQ(serif::atomic::species.at("He-4").mass(),4.0026032541300003);
+    EXPECT_DOUBLE_EQ(fourdst::atomic::species.at("He-4").mass(),4.0026032541300003);
 }
 
 TEST_F(compositionTest, constructor) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    EXPECT_NO_THROW(serif::composition::Composition comp);
+    EXPECT_NO_THROW(fourdst::composition::Composition comp);
 }
 
 TEST_F(compositionTest, registerSymbol) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     EXPECT_NO_THROW(comp.registerSymbol("H-1"));
     EXPECT_NO_THROW(comp.registerSymbol("He-4"));
     EXPECT_THROW(comp.registerSymbol("H-19"), std::runtime_error);
@@ -46,8 +46,8 @@ TEST_F(compositionTest, registerSymbol) {
 }
 
 TEST_F(compositionTest, setGetComposition) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     comp.registerSymbol("H-1");
     comp.registerSymbol("He-4");
 
@@ -72,8 +72,8 @@ TEST_F(compositionTest, setGetComposition) {
 }
 
 TEST_F(compositionTest, setGetNumberFraction) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     comp.registerSymbol("H-1", false);
     comp.registerSymbol("He-4", false);
 
@@ -89,8 +89,8 @@ TEST_F(compositionTest, setGetNumberFraction) {
 }
 
 TEST_F(compositionTest, subset) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     comp.registerSymbol("H-1");
     comp.registerSymbol("He-4");
     comp.setMassFraction("H-1", 0.6);
@@ -98,14 +98,14 @@ TEST_F(compositionTest, subset) {
     EXPECT_NO_THROW(comp.finalize());
 
     std::vector<std::string> symbols = {"H-1"};
-    serif::composition::Composition subsetComp = comp.subset(symbols, "norm");
+    fourdst::composition::Composition subsetComp = comp.subset(symbols, "norm");
     EXPECT_TRUE(subsetComp.finalize());
     EXPECT_DOUBLE_EQ(subsetComp.getMassFraction("H-1"), 1.0);
 }
 
 TEST_F(compositionTest, finalizeWithNormalization) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     comp.registerSymbol("H-1");
     comp.registerSymbol("He-4");
     comp.setMassFraction("H-1", 0.3);
@@ -116,8 +116,8 @@ TEST_F(compositionTest, finalizeWithNormalization) {
 }
 
 TEST_F(compositionTest, finalizeWithoutNormalization) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     comp.registerSymbol("H-1");
     comp.registerSymbol("He-4");
     comp.setMassFraction("H-1", 0.5);
@@ -128,8 +128,8 @@ TEST_F(compositionTest, finalizeWithoutNormalization) {
 }
 
 TEST_F(compositionTest, getComposition) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     comp.registerSymbol("H-1");
     comp.registerSymbol("He-4");
     comp.setMassFraction("H-1", 0.6);
@@ -143,8 +143,8 @@ TEST_F(compositionTest, getComposition) {
 }
 
 TEST_F(compositionTest, setCompositionMode) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     comp.registerSymbol("H-1");
     comp.registerSymbol("He-4");
     comp.setMassFraction("H-1", 0.6);
@@ -165,8 +165,8 @@ TEST_F(compositionTest, setCompositionMode) {
 }
 
 TEST_F(compositionTest, hasSymbol) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp;
+    fourdst::composition::Composition comp;
     comp.registerSymbol("H-1");
     comp.registerSymbol("He-4");
     comp.setMassFraction("H-1", 0.6);
@@ -180,28 +180,28 @@ TEST_F(compositionTest, hasSymbol) {
 }
 
 TEST_F(compositionTest, mix) {
-    serif::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
+    fourdst::config::Config::getInstance().loadConfig(EXAMPLE_FILENAME);
-    serif::composition::Composition comp1;
+    fourdst::composition::Composition comp1;
     comp1.registerSymbol("H-1");
     comp1.registerSymbol("He-4");
     comp1.setMassFraction("H-1", 0.6);
     comp1.setMassFraction("He-4", 0.4);
     EXPECT_NO_THROW(comp1.finalize());
 
-    serif::composition::Composition comp2;
+    fourdst::composition::Composition comp2;
     comp2.registerSymbol("H-1");
     comp2.registerSymbol("He-4");
     comp2.setMassFraction("H-1", 0.4);
     comp2.setMassFraction("He-4", 0.6);
     EXPECT_NO_THROW(comp2.finalize());
 
-    serif::composition::Composition mixedComp = comp1 + comp2;
+    fourdst::composition::Composition mixedComp = comp1 + comp2;
     EXPECT_TRUE(mixedComp.finalize());
     EXPECT_DOUBLE_EQ(mixedComp.getMassFraction("H-1"), 0.5);
     EXPECT_DOUBLE_EQ(mixedComp.getMassFraction("He-4"), 0.5);
 
-    serif::composition::Composition mixedComp2 = comp1.mix(comp2, 0.25);
+    fourdst::composition::Composition mixedComp2 = comp1.mix(comp2, 0.25);
     EXPECT_TRUE(mixedComp2.finalize());
     EXPECT_DOUBLE_EQ(mixedComp2.getMassFraction("H-1"), 0.45);
     EXPECT_DOUBLE_EQ(mixedComp2.getMassFraction("He-4"), 0.55);
-}
+}

tests/meson.build

@@ -0,0 +1,7 @@
+# Google Test dependency
+gtest_dep = dependency('gtest', main: true, required : true)
+gtest_main = dependency('gtest_main', required: true)
+gtest_nomain_dep = dependency('gtest', main: false, required : true)
+
+# Subdirectories for unit and integration tests
+subdir('composition')

utils/atomic/convertWeightsToHeader.py

@@ -0,0 +1,151 @@
+import pandas as pd
+
+# Define fixed-width column specifications based on the format:
+# a1 (width 1), i3 (width 3), i5 (width 5), i5 (width 5), i5 (width 5),
+# 1x (skip 1), a3 (width 3), a4 (width 4), 1x (skip 1),
+# f14.6 (width 14), f12.6 (width 12), f13.5 (width 13),
+# 1x (skip 1), f10.5 (width 10), 1x (skip 1),
+# a2 (width 2), f13.5 (width 13), f11.5 (width 11),
+# 1x (skip 1), i3 (width 3), 1x (skip 1),
+# f13.6 (width 13), f12.6 (width 12)
+# Compute cumulative positions (0-indexed):
+colSpecs = [
+    (0, 1),    # control
+    (1, 4),    # NZ
+    (4, 9),    # N
+    (9, 14),   # Z
+    (14, 19),  # A
+    # skip 1 char at position 19; next field starts at 20
+    (20, 23),  # el
+    (23, 27),  # o
+    # skip 1 char at position 27; next field starts at 28
+    (28, 42),  # massExcess (f14.6)
+    (42, 54),  # massExcessUnc (f12.6)
+    (54, 67),  # bindingEnergy (f13.5)
+    # skip 1 char at position 67; next field starts at 68
+    (68, 78),  # bindingEnergyUnc (f10.5)
+    # skip 1 char at position 78; next field starts at 79
+    (79, 81),  # betaCode (a2)
+    (81, 94),  # betaDecayEnergy (f13.5)
+    (94, 105), # betaDecayEnergyUnc (f11.5)
+    # skip 1 char at position 105; next field starts at 106
+    (106, 109),# atomicMassInt (i3)
+    # skip 1 char at position 109; next field starts at 110
+    (110, 123),# atomicMassFrac (f13.6)
+    (123, 135) # atomicMassUnc (f12.6)
+]
+
+# Define column names (using camelCase for variables)
+columnNames = [
+    "control",
+    "nz",
+    "n",
+    "z",
+    "a",
+    "el",
+    "o",
+    "massExcess",
+    "massExcessUnc",
+    "bindingEnergy",
+    "bindingEnergyUnc",
+    "betaCode",
+    "betaDecayEnergy",
+    "betaDecayEnergyUnc",
+    "atomicMassInt",
+    "atomicMassFrac",
+    "atomicMassUnc"
+]
+
+def combine_atomic_mass(row):
+    """
+    Combine the integer and fractional parts of the atomic mass.
+    For example, if atomicMassInt is '1' and atomicMassFrac is '008664.91590',
+    this function returns float('1008664.91590').
+    """
+    intPart = str(row["atomicMassInt"]).strip()
+    fracPart = str(row["atomicMassFrac"]).strip()
+    try:
+        combined = int(intPart) + float(fracPart)/1e6
+        return combined
+    except ValueError:
+        return None
+
+def mkInstanceName(row):
+    """
+    Make a c++ instance name from the element and atomic number.
+    """
+    speciesName = f"{row['el'].strip()}-{row['a']}"
+    return speciesName.replace("-", "_")
+
+def formatSpecies(row):
+    """
+    Format c++ instantiation of Species struct from row data.
+    """
+    name = f"{row['el'].strip()}-{row['a']}"
+    instanceName = name.replace("-", "_")
+    nz = int(row['nz'])
+    n = int(row['n'])
+    z = int(row['z'])
+    a = int(row['a'])
+    bindingEnergy = float(row['bindingEnergy'])
+    atomicMass = float(row['atomicMass'])
+    atomicMassUnc = float(row['atomicMassUnc'])
+    NaN = "std::numeric_limits<double>::quiet_NaN()"
+    try:
+        betaDecayEnergy = float(row['betaDecayEnergy'].replace("#", "").replace("*", ""))
+    except ValueError:
+        betaDecayEnergy = NaN
+    instantiation = f"static const Species {instanceName}(\"{name}\", \"{row['el']}\", {nz}, {n}, {z}, {a}, {bindingEnergy}, \"{row['betaCode']}\", {betaDecayEnergy}, {atomicMass}, {atomicMassUnc});"
+    return instantiation, instanceName
+
+def formatSpeciesDefines(row):
+    instanceName = f"SERIF_SPECIES_{formatSpecies(row)[1]}"
+    define = f"""#ifndef {instanceName.upper()}
+    #define {instanceName.upper()}
+#endif // {instanceName.upper()}"""
+    return define
+
+def formatHeader(dataFrame):
+    """
+    Format c++ header file from DataFrame.
+    """
+    header = f"""#pragma once
+#include <unordered_map>
+#include <string_view>
+#include <string>
+#include "atomicSpecies.h"
+
+namespace fourdst::atomic {{
+    {'\n    '.join([formatSpecies(row)[0] for index, row in dataFrame.iterrows()])}
+    static const std::unordered_map<std::string, Species> species = {{
+        {'\n        '.join([f'{{"{row["el"].strip()}-{row["a"]}", {mkInstanceName(row)}}},' for index, row in dataFrame.iterrows()])}
+    }};
+}}; // namespace fourdst::atomic
+
+{'\n'.join([formatSpeciesDefines(row) for index, row in dataFrame.iterrows()])}
+"""
+    return header
+
+if __name__ == "__main__":
+    import argparse 
+    import os
+    parser = argparse.ArgumentParser(description="Convert mass data to c++ header file.")
+    parser.add_argument("input", help="Input file path.")
+    parser.add_argument("-o", "--output", help="Output file path.", default="../../assets/static/atomic/include/species.h")
+    args = parser.parse_args()
+
+
+    if not os.path.exists(args.input):
+        raise FileNotFoundError(f"File not found: {args.input}")
+
+    # Read the file (adjust the skiprows value if your header differs)
+    dataFrame = pd.read_fwf(args.input, colspecs=colSpecs, names=columnNames, skiprows=36)
+
+    # Combine the two atomic mass fields into one float column
+    dataFrame["atomicMass"] = dataFrame.apply(combine_atomic_mass, axis=1)
+    dataFrame.drop(columns=["atomicMassInt", "atomicMassFrac"], inplace=True)
+
+    # Format the header
+    header = formatHeader(dataFrame)
+    with open(args.output, "w") as f:
+        f.write(header)

utils/atomic/readme.md

@@ -0,0 +1,13 @@
+# Information
+Simple python utility for turning the file assets/atomic/weights.dat into a c++ header which can be included to provide easy access to all atomic weights inside 4DSSE
+
+## Requirments
+In order to use this utility you will need
+
+- Python
+- Pandas
+
+## Usage
+```bash
+python convertWeightsToHeader.py <path/to/weights.dat> -o atomicWeights.h
+```