feat(reaclib): reworked how I store reactions to avoid stack overflows

assets/static/reaclib/readme.md

@@ -1 +1 @@
-Use the utility `utils/reaclib/generateEmbeddedReaclibHeader.py` to generate reaclib.h
+Use the utility `utils/reaclib/format.py` to generate reacitons.bin

meson.build

@@ -24,6 +24,10 @@ project('GridFire', 'cpp', version: '0.0.1a', default_options: ['cpp_std=c++23']
 add_project_arguments('-fvisibility=default', language: 'cpp')
 # We disable these because of CppAD
 add_project_arguments('-Wno-bitwise-instead-of-logical', language: 'cpp')
+
+# For Eigen
+add_project_arguments('-Wno-deprecated-declarations', language: 'cpp')
+
 llevel = get_option('log_level')
 
 logbase='QUILL_COMPILE_ACTIVE_LOG_LEVEL_'
@@ -52,9 +56,6 @@ add_project_arguments(log_argument, language: 'cpp')
 cpp = meson.get_compiler('cpp')
 
 subdir('build-config')
-subdir('assets/static')
-
-
 
 subdir('src')
 subdir('tests')
@@ -64,7 +65,13 @@ pkg.generate(
     name: 'gridfire',
     description: 'GridFire nuclear reaction network solver',
     version: meson.project_version(),
-    libraries: [libnetwork, libcomposition, libconfig, libconst, liblogging],
+    libraries: [
+        libnetwork,
+        libcomposition,
+        libconfig,
+        libconst,
+        liblogging
+    ],
     subdirs: ['gridfire'],
     filebase: 'gridfire',
     install_dir: join_paths(get_option('libdir'), 'pkgconfig')

src/network/include/gridfire/reaction/reaclib.h

@@ -0,0 +1,19 @@
+#pragma once
+
+#include "gridfire/reaction/reaction.h"
+
+namespace gridfire::reaclib {
+
+    static bool s_initialized = false;
+
+    /**
+     * @brief Provides global access to the fully initialized REACLIB reaction set.
+     *
+     * This function uses a singleton pattern to ensure the reaction data is loaded
+     * from the embedded binary only once, the very first time it is requested.
+     *
+     * @return A constant reference to the application-wide reaction set.
+     */
+    const reaction::LogicalReactionSet& get_all_reactions();
+
+} // namespace gridfire::reaclib

utils/bin_to_header.py

@@ -0,0 +1,34 @@
+import sys
+
+def main():
+    if len(sys.argv) != 4:
+        print("Usage: python bin_to_header.py <input_binary> <output_header> <variable_name>")
+        sys.exit(1)
+
+    input_file = sys.argv[1]
+    output_file = sys.argv[2]
+    variable_name = sys.argv[3]
+
+    try:
+        with open(input_file, 'rb') as f_in:
+            data = f_in.read()
+
+        with open(output_file, 'w') as f_out:
+            f_out.write(f'#pragma once\n\n')
+            f_out.write(f'#include <cstddef>\n\n')
+            f_out.write(f'const unsigned char {variable_name}[] = {{\n    ')
+            
+            for i, byte in enumerate(data):
+                f_out.write(f'0x{byte:02x}, ')
+                if (i + 1) % 16 == 0:
+                    f_out.write('\n    ')
+            
+            f_out.write('\n};\n\n')
+            f_out.write(f'const size_t {variable_name}_len = sizeof({variable_name});\n')
+
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        sys.exit(1)
+
+if __name__ == '__main__':
+    main()

utils/reaclib/format.py

@@ -1,3 +1,68 @@
+"""
+REACLIB Reaction Formatting and Parsing Utilities
+================================================
+
+This module provides utilities for parsing, formatting, and analyzing nuclear reaction
+data in the REACLIB format. It includes tools for extracting reaction information,
+computing reaction rates, and exporting data for use in C++ or binary formats.
+
+Algorithms and Quantum Number Accounting
+----------------------------------------
+The core of this module is the quantum number bookkeeping performed in
+`determine_reaction_type`, which ensures conservation of baryon number (A),
+charge (Z), and handles leptonic and photonic processes:
+
+- **Baryon Number Conservation**: The difference in total mass number (A) between
+  reactants and products must be zero. If not, an assertion error is raised.
+- **Charge Conservation**: The difference in total charge (Z) is checked:
+    - |ΔZ| = 1: Indicates a weak process (beta decay or electron/positron capture).
+      The code distinguishes between electron/positron as projectile or ejectile
+      based on the sign of ΔZ and the Q-value.
+    - ΔZ = 0: If the number of nuclei changes by ±1, photons are involved
+      (radiative capture or photodisintegration).
+- **Projectiles and Ejectiles**: The heaviest reactant is considered the target,
+  and the heaviest product is the residual. Other nuclei are projectiles/ejectiles.
+  Special handling is provided for light nuclei (p, d, t, n, a).
+
+Usage Examples
+--------------
+Parse a REACLIB file and export to CSV:
+
+    python format.py path/to/reaclib/file -o output.csv -f csv
+
+Programmatic usage:
+
+    from utils.reaclib.format import parse_reaclib_entry, extract_groups
+
+    entry = '''1
+    h1 he4 c12 mg24    wkb    1.234e+00
+    1.234e+01 2.345e+02 3.456e+03 4.567e+04 5.678e+05 6.789e+06 7.890e+07
+    '''
+    match, reverse = parse_reaclib_entry(entry)
+    if match:
+        reaction = extract_groups(match, reverse)
+        print(reaction)
+
+Functions
+---------
+- `parse_reaclib_entry(entry)`: Parse a REACLIB entry string.
+- `extract_groups(match, reverse)`: Extracts a Reaction object from a regex match.
+- `determine_reaction_type(reactants, products, qValue)`: Determines projectiles,
+  ejectiles, and reaction type using quantum number accounting.
+- `evaluate_rate(coeffs, T9)`: Computes the reaction rate at temperature T9.
+- `format_cpp_identifier(name)`: Formats a species name for C++ code.
+- `create_reaction_dataframe(reactions)`: Converts a list of Reaction objects to a DataFrame.
+- `write_reactions_binary(reactions, output_path)`: Writes reactions to a binary file.
+
+Classes
+-------
+- `Reaction`: Dataclass representing a nuclear reaction.
+- `ReaclibParseError`: Exception for parsing errors.
+
+See function/class docstrings for further details.
+
+"""
+
 import re
 import sys
 from collections import defaultdict
@@ -10,8 +75,10 @@ from serif.constants import Constants
 import hashlib
 from collections import Counter
 import math
+import argparse
+import pandas as pd
+import struct
 
-#import dataclasses
 from dataclasses import dataclass
 
 @dataclass
@@ -22,10 +89,10 @@ class Reaction:
     chapter: int
     qValue: float
     coeffs: List[float]
-    projectile: str        # added
-    ejectile: str         # added
-    rpName: str           # added
-    reactionType: str     # added (e.g. "(p,γ)")
+    projectile: str
+    ejectile: str
+    rpName: str
+    reactionType: str
     reverse: bool
     def format_rp_name(self) -> str:
         return self.rpName
@@ -36,6 +103,26 @@ class Reaction:
 
 
 def evaluate_rate(coeffs: List[float], T9: float) -> float:
+    """
+    Evaluate the REACLIB reaction rate at a given temperature.
+
+    Parameters
+    ----------
+    coeffs : list of float
+        The 7 REACLIB coefficients (a0..a6) for the reaction.
+    T9 : float
+        Temperature in units of 10^9 K.
+
+    Returns
+    -------
+    float
+        The reaction rate at the specified temperature.
+
+    Notes
+    -----
+    The rate is computed as:
+        rate = exp(a0 + a1/T9 + a2/T9^{1/3} + a3*T9^{1/3} + a4*T9 + a5*T9^{5/3} + a6*ln(T9))
+    """
     rateExponent: float = coeffs[0] + \
                         coeffs[1] / T9 + \
                         coeffs[2] / (T9 ** (1/3)) + \
@@ -46,7 +133,18 @@ def evaluate_rate(coeffs: List[float], T9: float) -> float:
     return np.exp(rateExponent)
 
 class ReaclibParseError(Exception):
-    """Custom exception for parsing errors."""
+    """
+    Exception raised for errors encountered while parsing REACLIB entries.
+
+    Parameters
+    ----------
+    message : str
+        Description of the error.
+    line_num : int, optional
+        Line number where the error occurred.
+    line_content : str, optional
+        Content of the problematic line.
+    """
     def __init__(self, message, line_num=None, line_content=None):
         self.line_num = line_num
         self.line_content = line_content
@@ -60,16 +158,50 @@ class ReaclibParseError(Exception):
 
 
 def format_cpp_identifier(name: str) -> str:
-    name_map = {'p': 'H_1', 'd': 'H_2', 't': 'H_3', 'n': 'n_1', 'a': 'He_4'}
+    """
+    Convert a REACLIB species name to a C++-friendly identifier.
+
+    Parameters
+    ----------
+    name : str
+        The REACLIB species name (e.g., 'h1', 'he4', 'c12', 'p', 'a').
+
+    Returns
+    -------
+    str
+        The formatted C++ identifier (e.g., 'H-1', 'He-4', 'C-12', etc.).
+    """
+    name_map = {'p': 'H-1', 'd': 'H-2', 't': 'H-3', 'n': 'n-1', 'a': 'He-4'}
     if name.lower() in name_map:
         return name_map[name.lower()]
     match = re.match(r"([a-zA-Z]+)(\d+)", name)
     if match:
         element, mass = match.groups()
-        return f"{element.capitalize()}_{mass}"
-    return f"{name.capitalize()}_1"
+        return f"{element.capitalize()}-{mass}"
+    return f"{name.capitalize()}-1"
 
 def parse_reaclib_entry(entry: str) -> tuple[Match[str] | None, bool]:
+    """
+    Parse a single REACLIB entry string using a regular expression.
+
+    Parameters
+    ----------
+    entry : str
+        The REACLIB entry as a string (typically 4 lines).
+
+    Returns
+    -------
+    match : re.Match or None
+        The regex match object if parsing was successful, else None.
+    reverse : bool
+        True if the entry is marked as a reverse reaction, else False.
+
+    Notes
+    -----
+    The function uses a regular expression to extract chapter, reactants/products,
+    label, Q-value, and coefficients. The 'reverse' flag is determined by the
+    character at a fixed position in the entry.
+    """
     pattern = re.compile(r"""^([1-9]|1[0-1])\r?\n
 [ \t]*
 ((?:[A-Za-z0-9-*]+[ \t]+)*
@@ -93,6 +225,23 @@ def parse_reaclib_entry(entry: str) -> tuple[Match[str] | None, bool]:
 
 
 def get_rp(group: str, chapter: int) -> Tuple[List[str], List[str]]:
+    """
+    Split a REACLIB group string into reactants and products based on chapter.
+
+    Parameters
+    ----------
+    group : str
+        The whitespace-separated list of species.
+    chapter : int
+        The REACLIB chapter number (determines reactant/product count).
+
+    Returns
+    -------
+    reactants : list of str
+        List of reactant species names.
+    products : list of str
+        List of product species names.
+    """
     rpGroupings = {
         1: (1, 1), 2: (1, 2), 3: (1, 3), 4: (2, 1), 5: (2, 2),
         6: (2, 3), 7: (2, 4), 8: (3, 1), 9: (3, 2), 10: (4, 2), 11: (1, 4)
@@ -104,6 +253,24 @@ def get_rp(group: str, chapter: int) -> Tuple[List[str], List[str]]:
     return reactants, products
 
 def translate_names_to_species(names: List[str]) -> List[Species]:
+    """
+    Convert a list of REACLIB species names to Species objects.
+
+    Parameters
+    ----------
+    names : list of str
+        List of REACLIB species names (e.g., 'h1', 'he4', 'c12', etc.).
+
+    Returns
+    -------
+    list of Species
+        List of Species objects corresponding to the names.
+
+    Raises
+    ------
+    ReaclibParseError
+        If a species name cannot be found in the species database.
+    """
     sp = list()
     split_alpha_digits = lambda inputString: re.match(r'([A-Za-z]+)[-+*]?(\d+)$', inputString).groups()
     for name in names:
@@ -118,25 +285,44 @@ def translate_names_to_species(names: List[str]) -> List[Species]:
             raise ReaclibParseError(f"Species '{name}' not found in species database.", line_content=name)
     return sp
 
-
-
 def determine_reaction_type(reactants: List[str],
                             products: List[str],
                             qValue: float
-                            ) -> Tuple[str, List[str], List[str], str]:
+                            ) -> Tuple[str, List[str], List[str], str, str, str]:
     """
-    Return (targetToken, projectiles, ejectiles, residualToken)
+    Analyze a reaction for quantum number conservation and classify projectiles/ejectiles.
 
-    • targetToken  – the nucleus that appears before the parenthesis (A)
-    • projectiles  – every explicit projectile that must be written inside ‘( … )’
-    • ejectiles    – every explicit ejectile that must be written after the comma
-    • residualToken– the main heavy product that appears after the parenthesis (D)
+    Parameters
+    ----------
+    reactants : list of str
+        List of reactant species names.
+    products : list of str
+        List of product species names.
+    qValue : float
+        Q-value of the reaction (MeV).
 
-    Photons and neutrinos are added / omitted exactly the way JINA REACLIB expects:
-      – γ is explicit only when it is a **projectile** (photodisintegration)
-      – ν/ν̄ are never explicit
+    Returns
+    -------
+    targetToken : str
+        Name of the heaviest reactant (target nucleus).
+    projectiles : list of str
+        List of projectile names (including leptons/photons if present).
+    ejectiles : list of str
+        List of ejectile names (including leptons/photons if present).
+    residualToken : str
+        Name of the heaviest product (residual nucleus).
+    reactionKey : str
+        Unique string key for the reaction.
+    rType : str
+        String representation of the reaction type.
+
+    Notes
+    -----
+    This function performs quantum number bookkeeping:
+    - Checks baryon and charge conservation.
+    - Identifies weak (leptonic) and photonic processes.
+    - Determines projectiles/ejectiles based on mass and reaction type.
     """
-
     if abs(qValue - 4.621) < 1e-6:
         print("Looking at he3(he3, 2p)he4")
     # --- helper look-ups ----------------------------------------------------
@@ -197,10 +383,9 @@ def determine_reaction_type(reactants: List[str],
     # 2.  Photon bookkeeping (ΔZ = 0) ----------------------------------------
     # -----------------------------------------------------------------------
     if dZ == 0:
-        # Two → one nucleus  and exothermic  ⇒ radiative capture (γ ejectile, implicit)
+        # Two → one nucleus  and exothermic  ⇒ radiative capture (γ ejectile, (seems to normally be implicit, but I am writing it explicitly))
         if dN == 1 and qValue > 0:
             ejectiles.append("g")
-            pass  # γ is implicit; nothing to write
 
         # One → two nuclei  and endothermic ⇒ photodisintegration (γ projectile, explicit)
         elif dN == -1 and qValue < 0:
@@ -248,6 +433,21 @@ def determine_reaction_type(reactants: List[str],
 
 
 def extract_groups(match: re.Match, reverse: bool) -> Reaction:
+    """
+    Extract a Reaction object from a regex match of a REACLIB entry.
+
+    Parameters
+    ----------
+    match : re.Match
+        The regex match object from `parse_reaclib_entry`.
+    reverse : bool
+        Whether the reaction is a reverse reaction.
+
+    Returns
+    -------
+    Reaction
+        The parsed Reaction dataclass instance.
+    """
     groups = match.groups()
     chapter = int(groups[0].strip())
     rawGroup = groups[1].strip()
@@ -274,6 +474,19 @@ def extract_groups(match: re.Match, reverse: bool) -> Reaction:
     return reaction
 
 def format_emplacment(reaction: Reaction) -> str:
+    """
+    Format a Reaction object as a C++ emplacement statement.
+
+    Parameters
+    ----------
+    reaction : Reaction
+        The Reaction object to format.
+
+    Returns
+    -------
+    str
+        The C++ code string for emplacing the reaction.
+    """
     reactantNames = [f'{format_cpp_identifier(r)}' for r in reaction.reactants]
     productNames = [f'{format_cpp_identifier(p)}' for p in reaction.products]
 
@@ -282,7 +495,6 @@ def format_emplacment(reaction: Reaction) -> str:
 
     label = f"{'_'.join(reactantNames)}_to_{'_'.join(productNames)}_{reaction.label.upper()}"
 
-
     reactants_str = ', '.join(reactants_cpp)
     products_str = ', '.join(products_cpp)
 
@@ -294,101 +506,27 @@ def format_emplacment(reaction: Reaction) -> str:
 
     return emplacment
 
-
-
-
-def generate_reaclib_header(reaclib_filepath: str, culling: float, T9: float, verbose: bool) -> tuple[
-    LiteralString, int | Any, int | Any]:
-    """
-    Parses a JINA REACLIB file using regular expressions and generates a C++ header file string.
-
-    Args:
-        reaclib_filepath: The path to the REACLIB data file.
-        culling: The threshold for culling reactions based on their rates at T9.
-        T9: The temperature in billions of Kelvin to evaluate the reaction rates for culling.
-        verbose: If True, prints additional information about skipped reactions.
-
-    Returns:
-        A string containing the complete C++ header content.
-    """
-    with open(reaclib_filepath, 'r') as file:
-        content = file.read()
-        fileHash = hashlib.sha256(content.encode('utf-8')).hexdigest()
-    # split the file into blocks of 4 lines each
-    lines = content.split('\n')
-    entries = ['\n'.join(lines[i:i+4]) for i in range(0, len(lines), 4) if len(lines[i:i+4]) == 4]
-    reactions = list()
-    for entry in entries:
-        m, r = parse_reaclib_entry(entry)
-        if m is not None:
-            try:
-                reac = extract_groups(m, r)
-            except ReaclibParseError as e:
-                continue
-            if verbose:
-                print(f"Parsed reaction: {reac.format_rp_name()} ({reac.coeffs}) with label {reac.label} (reverse: {reac.reverse})")
-            reactions.append(reac)
-
-    # --- Generate the C++ Header String ---
-    cpp_lines = [
-        "// This file is automatically generated. Do not edit!",
-        "// Generated on: " + str(np.datetime64('now')),
-        "// REACLIB file hash (sha256): " + fileHash,
-        "// Generated from REACLIB data file: " + reaclib_filepath,
-        "// Culling threshold: rate >" + str(culling) + " at T9 = " + str(T9),
-        "// Note that if the culling threshold is set to 0.0, no reactions are culled.",
-        "// Includes %%TOTAL%% reactions.",
-        "// Note: Only reactions with species defined in the atomicSpecies.h header will be included at compile time.",
-        "#pragma once",
-        "#include \"fourdst/composition/atomicSpecies.h\"",
-        "#include \"fourdst/composition/species.h\"",
-        "#include \"reaclib.h\"",
-        "\nnamespace gridfire::reaclib {\n",
-        """    
-    inline void initializeAllReaclibReactions() {
-        if (s_initialized) return; // already initialized
-        s_initialized = true;
-        s_all_reaclib_reactions.clear();
-        s_all_reaclib_reactions.reserve(%%TOTAL%%); // reserve space for total reactions
-    """
-    ]
-    totalSkipped = 0
-    totalIncluded = 0
-    energy = list()
-    energyFile = open('energy.txt', 'w')
-    energyFile.write("name;maxEnergy;QValue,reactants;products;a0;a1;a2;a3;a4;a5;a6\n")
-    for reaction in reactions:
-        maxEnergy = calculate_peak_importance(reaction)
-        energyFile.write(f"{reaction.format_rp_name()};{maxEnergy};{reaction.qValue};{' '.join(reaction.reactants)};{' '.join(reaction.products)};{';'.join([str(x) for x in reaction.coeffs])}\n")
-        energy.append(maxEnergy)
-        reactantNames = [f'{format_cpp_identifier(r)}' for r in reaction.reactants]
-        productNames = [f'{format_cpp_identifier(p)}' for p in reaction.products]
-        reactionName = f"{'_'.join(reactantNames)}_to_{'_'.join(productNames)}_{reaction.label.upper()}"
-        if culling > 0.0:
-            rate = evaluate_rate(reaction.coeffs, T9)
-            if rate < culling:
-                if verbose:
-                    print(f"Skipping reaction {reaction.format_rp_name()} ({reactionName}) with rate {rate:.6e} at T9={T9} (culling threshold: {culling} at T9={T9})")
-                totalSkipped += 1
-                continue
-            else:
-                totalIncluded += 1
-        else:
-            totalIncluded += 1
-
-        defines = ' && '.join(set([f"defined(SERIF_SPECIES_{name.upper().replace('-', '_min_').replace('+', '_add_').replace('*', '_mult_')})" for name in reactantNames + productNames]))
-        cpp_lines.append(f"         #if {defines}")
-        emplacment = format_emplacment(reaction)
-        cpp_lines.append(f"             {emplacment}")
-        cpp_lines.append(f"         #endif // {defines}")
-    cpp_lines.append("\n    }\n} // namespace gridfire::reaclib\n")
-    energyFile.close()
-    #save energy data to a file
-    return "\n".join(cpp_lines), totalSkipped, totalIncluded
-
 def calculate_peak_importance(reaction: Reaction) -> float:
-    TGrid = np.logspace(-3, 2, 100)  # Temperature grid from 0.001 to 100 T9
-    RhoGrid = np.logspace(0.0, 6.0, 100)  # Density grid from 1e0 to 1e3 g/cm^3
+    """
+    Estimate the peak energy importance of a reaction over a grid of T and rho.
+
+    Parameters
+    ----------
+    reaction : Reaction
+        The Reaction object to analyze.
+
+    Returns
+    -------
+    float
+        The maximum energy proxy (rate * |Q|) found over the grid.
+
+    Notes
+    -----
+    The function evaluates the reaction rate over a grid of temperature (T9)
+    and density (rho), multiplies by |Q|, and returns the maximum value.
+    """
+    TGrid = np.logspace(-3, 2, 100)
+    RhoGrid = np.logspace(0.0, 6.0, 100)
     N_A: float = Constants['N_a'].value
     u: float = Constants['u'].value
     max_energy_proxy: float = 0.0
@@ -419,12 +557,10 @@ def calculate_peak_importance(reaction: Reaction) -> float:
                 reactant = {'t': 'H-3', 'a': 'He-4', 'he4': 'He-4', 'd': 'H-2', 'n': 'n-1', 'p': 'H-1'}[reactant]
             else:
                 reactant = '-'.join(split_alpha_digits(reactant)).capitalize()
-                # print(f"Parsing reactant {reactant} using split_alpha_digits")
             reactantMassAMU = species[reactant].mass()
             reactantMassG = reactantMassAMU * u
             mass_term *= (Y_ideal/ reactantMassG)
         except Exception as e:
-            # print(f"Error: Reactant {reactant} not found in species database. (what: {e})")
             return 0.0
 
     for T9 in TGrid:
@@ -438,30 +574,129 @@ def calculate_peak_importance(reaction: Reaction) -> float:
     print(f"For reaction {reaction.format_rp_name()}, max energy proxy: {max_energy_proxy:.6e} MeV")
     return max_energy_proxy
 
-# def smart_cull(reactions: List[Reaction], verbose: bool = False):
+def create_reaction_dataframe(reactions: List[Reaction]) -> pd.DataFrame:
+    """
+    Convert a list of Reaction objects into a pandas DataFrame.
+
+    Parameters
+    ----------
+    reactions : list of Reaction
+        List of Reaction objects.
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with columns for all reaction properties.
+    """
+    reaction_data = []
+    for reaction in reactions:
+        record = {
+            'id': f"{'_'.join(reaction.reactants)}_to_{'_'.join(reaction.products)}_{reaction.label.upper()}",
+            'rpName': reaction.rpName,
+            'chapter': reaction.chapter,
+            'reactants': ' '.join(reaction.reactants),
+            'products': ' '.join(reaction.products),
+            'qValue': reaction.qValue,
+            'is_reverse': reaction.reverse,
+            'label': reaction.label,
+            'a0': reaction.coeffs[0],
+            'a1': reaction.coeffs[1],
+            'a2': reaction.coeffs[2],
+            'a3': reaction.coeffs[3],
+            'a4': reaction.coeffs[4],
+            'a5': reaction.coeffs[5],
+            'a6': reaction.coeffs[6]
+        }
+        reaction_data.append(record)
+        
+    return pd.DataFrame(reaction_data)
+
+def write_reactions_binary(reactions: List[Reaction], output_path: str):
+    """
+    Write a list of Reaction objects to a binary file.
+
+    Parameters
+    ----------
+    reactions : list of Reaction
+        List of Reaction objects to write.
+    output_path : str
+        Path to the output binary file.
+
+    Notes
+    -----
+    Each reaction is packed using struct with a fixed format for chapter, Q-value,
+    coefficients, reverse flag, label, rpName, reactants, and products.
+    """
+    record_format = '<i d 7d ? 8s 64s 128s 128s'
+    
+    with open(output_path, 'wb') as f:
+        for reaction in reactions:
+            label_bytes = reaction.label.encode('utf-8')[:7].ljust(8, b'\0')
+            rpName_bytes = reaction.rpName.encode('utf-8')[:63].ljust(64, b'\0')
+            reactants_str = ' '.join([format_cpp_identifier(x) for x in reaction.reactants])
+            products_str = ' '.join([format_cpp_identifier(x) for x in reaction.products])
+            reactants_bytes = reactants_str.encode('utf-8')[:127].ljust(128, b'\0')
+            products_bytes = products_str.encode('utf-8')[:127].ljust(128, b'\0')
+
+            packed_data = struct.pack(
+                record_format,
+                reaction.chapter,
+                reaction.qValue,
+                *reaction.coeffs,
+                reaction.reverse,
+                label_bytes,
+                rpName_bytes,
+                reactants_bytes,
+                products_bytes
+            )
+            f.write(packed_data)
 
 if __name__ == '__main__':
-    import argparse
-    parser = argparse.ArgumentParser(description="Generate a C++ header from a REACLIB file.")
+    parser = argparse.ArgumentParser(description="Generate a CSV file from a REACLIB file.")
     parser.add_argument("reaclib_file", type=str, help="Path to the REACLIB data file.")
-    parser.add_argument("-o", "--output", type=str, default=None, help="Output file path (default: stdout).")
-    parser.add_argument('-c', "--culling", type=float, default=0.0, help="Culling threshold for reaction rates at T9 (when 0.0, no culling is applied).")
-    parser.add_argument('-T', '--T9', type=float, default=0.01, help="Temperature in billions of Kelvin (default: 0.01) to evaluate the reaction rates for culling.")
+    parser.add_argument("-o", "--output", type=str, default="reactions.csv", help="Output CSV file path.")
     parser.add_argument('-v', '--verbose', action='store_true', help="Enable verbose output.")
+    parser.add_argument('-f', '--format', type=str, choices=['csv', 'bin'], default='bin', help="Output format")
     args = parser.parse_args()
 
     try:
-        cpp_header_string, skipped, included = generate_reaclib_header(args.reaclib_file, args.culling, args.T9, args.verbose)
-        cpp_header_string = cpp_header_string.replace("%%TOTAL%%", str(included))
-        print("--- Generated C++ Header (Success!) ---")
-        if args.output:
-            with open(args.output, 'w') as f:
-                f.write(cpp_header_string)
-            print(f"Header written to {args.output}")
-            print(f"Total reactions included: {included}, Total reactions skipped: {skipped}")
+        with open(args.reaclib_file, 'r') as file:
+            content = file.read()
+        
+        lines = content.split('\n')
+        entries = ['\n'.join(lines[i:i+4]) for i in range(0, len(lines), 4) if len(lines[i:i+4]) == 4 and lines[i].strip()]
+
+        parsed_reactions = []
+        for i, entry in enumerate(entries):
+            m, r = parse_reaclib_entry(entry)
+            if m is not None:
+                try:
+                    reac = extract_groups(m, r)
+                    parsed_reactions.append(reac)
+                except ReaclibParseError as e:
+                    if args.verbose:
+                        print(f"Skipping entry starting at line {i*4 + 1} due to parsing error: {e}", file=sys.stderr)
+                    continue
+        
+        print(f"Successfully parsed {len(parsed_reactions)} reactions from {args.reaclib_file}")
+
+        reaction_df = create_reaction_dataframe(parsed_reactions)
+
+
+        if args.format == 'csv':
+            reaction_df.to_csv(args.output, index=False)
+            print("--- CSV Generation (Success!) ---")
+            print(f"Reaction data written to {args.output}")
         else:
-            print(cpp_header_string)
-    except ReaclibParseError as e:
-        print(f"\n--- PARSING FAILED ---")
+            write_reactions_binary(parsed_reactions, args.output)
+
+            print("--- Binary File Generation (Success!) ---")
+            print(f"Reaction data written to {args.output}")
+
+    except FileNotFoundError:
+        print(f"Error: Input file not found at {args.reaclib_file}", file=sys.stderr)
+        sys.exit(1)
+    except Exception as e:
+        print(f"\n--- AN UNEXPECTED ERROR OCCURRED ---")
         print(e, file=sys.stderr)
         sys.exit(1)

utils/reaclib/readme.md

@@ -18,7 +18,7 @@ Assuming you download that file to your ~/Downloads directory, and it is called
 `results123` then usage is as simple as
 
 ```bash
-python generateEmbeddedReaclibHeader.py ~/Downloads/results123 -o reaclib.h -c 1e-8 -T 0.1
+python format.py ~/Downloads/results123 -o reaclib.h
 ```
 
 This will generate the `reaclib.h` header file in your current directory.