Gas model

Overview

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

Required columns

• type (str): Specifies whether the molecule is 'linear' or 'non_linear'.

• gas_molec_weight (float): Molecular weight in atomic mass units (amu).

• sym_number (int): Symmetry number of the molecule.

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

  • Linear molecules: Provide 1 moment of inertia.

  • Non-linear molecules: Provide 3 moments of inertia.

• gas_energy (float): Formation energy in electronvolts (eV). Do not include the zero-point energy (ZPE).

Optional column

• degeneracy (int): Degeneracy of the ground state, used in calculating the electronic partition function.

  • Default value: 1.

Example data table

index	type	gas_molec_weight	sym_number	degeneracy	inertia_moments	gas_energy
CO	linear	28.01	1	1	[8.973618976566065]	1.9544267
O2	linear	32.00	2	3	[12.178373934770187]	2.6131292
CO2	linear	44.01	2	1	[44.317204709218686]	0.00

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Creating a GasModel

There are several ways to create a GasModel instance:

1. From a dictionary

2. From a CSV file

3. From a Pandas DataFrame

1. From a dictionary

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

Example

from zacrostools.gas_model import GasModel

# Define the gas species data
species_data = {
    'CO': {
        'type': 'linear',
        'gas_molec_weight': 28.01,
        'sym_number': 1,
        'degeneracy': 1,
        'inertia_moments': [8.973618976566065],
        'gas_energy': 1.9544267
    },
    'O2': {
        'type': 'linear',
        'gas_molec_weight': 32.00,
        'sym_number': 2,
        'degeneracy': 3,
        'inertia_moments': [12.178373934770187],
        'gas_energy': 2.6131292
    },
    'CO2': {
        'type': 'linear',
        'gas_molec_weight': 44.01,
        'sym_number': 2,
        'degeneracy': 1,
        'inertia_moments': [44.317204709218686],
        'gas_energy': 0.00
    }
}

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

2. From a CSV file

The CSV should have the required columns and use the species names as the index.

Example CSV (gas_data.csv)

,index,type,gas_molec_weight,sym_number,degeneracy,inertia_moments,gas_energy
CO,linear,28.01,1,1,"[8.973618976566065]",1.9544267
O2,linear,32.00,2,3,"[12.178373934770187]",2.6131292
CO2,linear,44.01,2,1,"[44.317204709218686]",0.00

Loading from CSV

from zacrostools.gas_model import GasModel

# Create the GasModel instance from a CSV file
gas_model = GasModel.from_csv('gas_data.csv')

3. From a Pandas DataFrame

If you already have a DataFrame containing the gas species data, you can create a GasModel directly.

Example

import pandas as pd
from zacrostools.gas_model import GasModel

# Create a DataFrame
data = {
    'type': ['linear', 'linear', 'linear'],
    'gas_molec_weight': [28.01, 32.00, 44.01],
    'sym_number': [1, 2, 2],
    'degeneracy': [1, 3, 1],
    'inertia_moments': [
        [8.973618976566065],
        [12.178373934770187],
        [44.317204709218686]
    ],
    'gas_energy': [1.9544267, 2.6131292, 0.00]
}
df = pd.DataFrame(data, index=['CO', 'O2', 'CO2'])

# Create the GasModel instance
gas_model = GasModel.from_df(df)

---

Adding and removing species

You can modify an existing GasModel by adding or removing species.

Adding a species

Use the add_species method to add a new species.

Example

# Define the new species data
new_species = {
    'species_name': 'N2',
    'type': 'linear',
    'gas_molec_weight': 28.0134,
    'sym_number': 2,
    'degeneracy': 1,
    'inertia_moments': [10.822],
    'gas_energy': 0.00
}

# Add the species to the GasModel
gas_model.add_species(species_info=new_species)

Removing species

Use the remove_species method to remove species by name.

Example

# List of species to remove
species_to_remove = ['CO2']

# Remove species from the GasModel
gas_model.remove_species(species_to_remove)

---

Accessing gas-phase data

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

Example

# View the gas species data
print(gas_model.df)

Output:

     type  gas_molec_weight  sym_number  degeneracy  \
CO  linear            28.010           1           1   
CO2 linear            44.010           2           1   

                     inertia_moments  gas_energy  
CO           [8.973618976566065]     1.9544267  
CO2         [44.317204709218686]     0.00  

---

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': [8.973618976566065],
        'gas_energy': 1.9544267
    },
    'O2': {
        'type': 'linear',
        'gas_molec_weight': 32.00,
        'sym_number': 2,
        'degeneracy': 3,
        'inertia_moments': [12.178373934770187],
        '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': [44.317204709218686],
    'gas_energy': 0.00
})

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

# Access the DataFrame
print(gas_model.df)

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Next steps

With the GasModel defined, you can proceed to:

• Define the EnergeticsModel

• Define the ReactionModel

• Create a LatticeModel

• Assemble the KMCModel

For detailed guidance on these steps, refer to the respective sections in the documentation.