1. Creating the Gas Model

The GasModel contains the information about each gas-phase molecule involved in the simulation.

Properties

• type (str): Molecular type — 'linear', 'non_linear' or 'monoatomic'.

• gas_energy (float): Formation energy (eV).

• gas_molec_weight (float): Molecular weight (amu).

• sym_number (int): Symmetry number (ignored for monoatomic species).

• inertia_moments (list of float): Moments of inertia (amu·Å²).

  • 'linear': 1 value required.

  • 'non_linear': 3 values required.

• degeneracy (int, optional): Ground-state degeneracy (default = 1).

There are several ways to create a GasModel instance:

1. From a dictionary

2. From a CSV file

3. From a Pandas DataFrame

How to create it

You can create a GasModel by providing a dictionary where each key is a species name and each value is a dictionary of properties:

from zacrostools.gas_model import GasModel

species_data = {
    'CO': {
        'type': 'linear',
        'gas_molec_weight': 28.01,
        'sym_number': 1,
        'degeneracy': 1,
        'inertia_moments': [8.973],
        'gas_energy': 1.954
    },
    'O2': {
        'type': 'linear',
        'gas_molec_weight': 32.00,
        'sym_number': 2,
        'degeneracy': 3,
        'inertia_moments': [12.178],
        'gas_energy': 2.613
    },
    'CO2': {
        'type': 'linear',
        'gas_molec_weight': 44.01,
        'sym_number': 2,
        'degeneracy': 1,
        'inertia_moments': [44.317],
        'gas_energy': 0.00
    }
}

gas_model = GasModel.from_dict(species_data)

Alternatively, it can also be created from a CSV file. In this case, the indexes must correspond to the species names:

from zacrostools.gas_model import GasModel

gas_model = GasModel.from_csv('gas_data.csv')

Finally, it can also be created from a Pandas dataframe:

import pandas as pd
from zacrostools.gas_model import GasModel

df = pd.read_csv("gas_data.csv")  # or create dataframe directly
gas_model = GasModel.from_df(df)

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Adding and removing species

Use the add_species method to add a new species.

new_species = {
    'species_name': 'N2',
    'type': 'linear',
    'gas_molec_weight': 28.013,
    'sym_number': 2,
    'degeneracy': 1,
    'inertia_moments': [10.822],
    'gas_energy': 0.00
}
gas_model.add_species(species_info=new_species)

Use the remove_species method to remove species by name.

gas_model.remove_species(['CO2'])

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Accessing gas-phase data

The gas species data is stored internally as a Pandas DataFrame, accessible via the df attribute.

print(gas_model.df)

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Full example

Below is a complete example demonstrating the creation and modification of a GasModel:

from zacrostools.gas_model import GasModel

# Initial gas species data
species_data = {
    'CO': {
        'type': 'linear',
        'gas_molec_weight': 28.01,
        'sym_number': 1,
        'degeneracy': 1,
        'inertia_moments': [8.973],
        'gas_energy': 1.9544267
    },
    'O2': {
        'type': 'linear',
        'gas_molec_weight': 32.00,
        'sym_number': 2,
        'degeneracy': 3,
        'inertia_moments': [12.178],
        'gas_energy': 2.6131292
    }
}

# Create the GasModel instance
gas_model = GasModel.from_dict(species_data)

# Add a new species
gas_model.add_species(species_info={
    'species_name': 'CO2',
    'type': 'linear',
    'gas_molec_weight': 44.01,
    'sym_number': 2,
    'degeneracy': 1,
    'inertia_moments': [44.317],
    'gas_energy': 0.00
})

# Remove an existing species
gas_model.remove_species(['O2'])

# Access the DataFrame
print(gas_model.df)

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