build(libcomposition): brought working build system into libcomposition

utils/atomic/convertWeightsToHeader.py

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+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

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+# 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
+```