Atomic Concentrations

Calculates atomic concentrations from chemical formula or material description.

Description

This code uses a NIST table of Atomic Weights and Isotopic Compositions of naturally occurring isotopes to create material descriptions for later use in MonteCarlo codes.

Output format

material_Id   $ material_name; density=value
isotope_code_1  atomic_concentration_1
isotope_code_2  atomic_concentration_2
...

Where:

• Part after the $ symbol is a Fortran comment
• isotope_code consists of the atomic number and mass number (e.g. 1H -> 1001, 16O -> 8016)
• atomic_concentration is in units of 1 x 10²⁴ atoms/cc

Use cases

1. Chemical formulas

Elements or compounds (e.g. O2, Pb, C10H8O4)

Input:

Chemical composition(e.g. 'H2O', 'C2H4 B0.2'):
---> "H2O"
Density (g / cc): "0.998"
ChemicalCompound name(leave blank to use chemical formula):

Output:

m1	$ H2O; 0.998 g/cc
1001	6.669056E-02
1002	7.670297E-06
8016	3.326808E-02
8017	1.267266E-05
8018	6.836569E-05

2. Element compositions

E.g. steel grades, concrete mixes.

Input:

Chemical composition(e.g. 'H2O', 'C2H4 B0.2'):
---> "Fe0.988 C0.001 Mn0.0045 Si0.0025 S0.0002 P0.0002"
Density (g / cc): "7.87"
ChemicalCompound name(leave blank to use chemical formula): "Steel 10 (AISI 1010)"

Output:

m1	$ Steel 10 (AISI 1010); 7.87 g/cc
6012	3.902425E-04
6013	4.220756E-06
14028	3.889341E-04
14029	1.975816E-05
14030	1.303996E-05
15031	3.059196E-05
25055	3.880704E-04
16032	2.806816E-05
16033	2.216141E-07
16034	1.255813E-06
16036	2.954855E-09
26054	4.899236E-03
26056	7.690753E-02
26057	1.776130E-03
26058	2.363703E-04

3. Mixed input

Chemical compounds with additives/impurities (e.g. 'H2O Mg0.002')

Input:

Chemical composition(e.g. 'H2O', 'C2H4 B0.2'):
---> "C2H4 B0.2"
Density (g / cc): "0.99"
ChemicalCompound name(leave blank to use chemical formula): "Borated polyethylene 20%"

Output:

m1	$ Borated polyethylene 20%; 0.99 g/cc
1001	8.496907E-02
1002	9.772567E-06
5010	2.193555E-03
5011	8.829333E-03
6012	4.203479E-02
6013	4.546368E-04

Classes

ConcentrationConvertor

A class to calculate atomic concentrations of isotopes in a material based on its chemical composition and density.

Attributes

• AVOGADRO (float): Avogadro's number in units of 1/(mol * g/cc).
• data (pd.DataFrame): DataFrame containing isotopic data from the NIST table.
• formula (str): Chemical formula of the material.
• density (float): Density of the material in g/cc.
• material_name (str): Name of the material, either user-provided or derived from the formula.

---

Methods

__init__()

Initializes the ConcentrationConvertor by loading isotopic data, prompting the user for input, and performing the initial calculation.

Attributes:

• AVOGADRO (float): Avogadro's number in units of 1/(mol * g/cc).
• data (pd.DataFrame): DataFrame containing isotopic data from the NIST table.
• formula (str): Chemical formula of the material.
• density (float): Density of the material in g/cc.
• material_name (str): Name of the material, either user-provided or derived from the formula.

---

parse_formula(formula: str)

Parses a material definition into its constituent elements and their quantities.

Args:

• formula (str): The chemical formula as a string (e.g., 'H2O', 'C2H4 B0.2').

Returns:

• list[dict[str, float]]: A list of dictionaries where each dictionary represents a component of the material, consisting of separate chemical elements and their quantities.

Example:

• Input: 'C2H4 B0.2'
• Output: [{'C': 2.0, 'H': 4.0}, {'B': 0.2}]

---

get_isotope_code(atomic_number, mass_number) -> str

Generates a unique isotope code based on the atomic number and mass number.

Args:

• atomic_number (int): The atomic number of the element.
• mass_number (int): The mass number of the isotope.

Returns:

• str: A string representing the isotope code, formatted as a concatenation of the atomic number and the mass number.

Example:

• Input: atomic_number=1, mass_number=2
• Output: '1002'

---

calculate(formula: str, density: float, threshold: float = 1e-6) -> None

Calculates the atomic concentrations of isotopes in a material based on its element composition and density.

Args:

• formula (str): The formula of the material (e.g., 'Al2O3', 'C2H4 B0.2').
• density (float): The density of the material in g/cc.
• threshold (float): Minimum concentration threshold for isotopes to be included in the output.

Returns:

• None: The results are printed to the console.

Output Format:

• First line: ChemicalCompound name and density.
• Subsequent lines: Isotope codes and their atomic concentrations in decimal notation.

Example:

• Input: formula='H2O', density=1.0
• Output:

  m1        $ H2O; 1.0 g/cc
  1001      6.674E-02
  1002      3.326E-02
  

• Input: formula="Fe0.988 C0.001 Mn0.0045 Si0.0025 S0.0002 P0.0002", density=7.87
• Output:

   m1	$ Steel 10; 7.87 g/cc
   6012	3.902425E-04
   6013	4.220756E-06
   14028	3.889341E-04
   14029	1.975816E-05
   ...
  

---

Static Methods

load_isotopic_data(file_path: str) -> pd.DataFrame

Loads isotopic composition data from a CSV file into a pandas DataFrame.

Args:

• file_path (str): The path to the CSV file containing isotopic data.

Returns:

• pd.DataFrame: A DataFrame containing the isotopic composition data.

Raises:

• FileNotFoundError: If the specified file does not exist.
• pd.errors.EmptyDataError: If the file is empty.
• pd.errors.ParserError: If the file cannot be parsed as a CSV.

Example:

• Input: file_path='data/isotopes.csv'
• Output: A DataFrame with columns such as 'Element', 'AtomicNumber', 'MassNumber', etc.