This project is a collective of tools for the preparation of input files for Zacros.

pip install zacrosio

git clone https://github.com/hprats/ZacrosIO.git

Pandas, Scipy

In this example, we create the ZACROS input files for many KMC simulations scanning a wide range of partial pressures and temperatures for the CO oxidation.

import numpy as np
import pandas as pd
from zacrosio.kmc_job import NewKMCJob

job = NewKMCJob(df_gas=pd.read_csv(f'gas_data.csv', index_col=0),
                df_mechanism=pd.read_csv(f'mechanism.csv', index_col=0),
                df_energetics=pd.read_csv(f'energetics.csv', index_col=0),
                lattice_path="lattice_input.dat")

for T in np.linspace(500, 1000, 6):
    for pCO in np.logspace(-4, 0, 10):
        for pO in np.logspace(-4, 0, 10):
            job.create_job_dir(path=f"./co_oxidation_T_{T}_pCO_{pCO}_pO_{pO}",
                               T=T,
                               dict_pressure={'CO': pCO, 'O': pO},
                               reporting='on time 5.0e-1',
                               stopping={'max_steps': 'infinity', 'max_time': 'infinity', 'wall_time': 36000},
                               repeat_cell=[10, 10],
                               list_auto_scaling=['O_diffusion'])

The user must prepare three following Pandas dataframes in advance:

This dataframe contains information about the gas-phase species. Each row corresponds to a gas-phase species, and the following columns are required:

• type (str): 'linear' or 'non_linear'
• gas_molec_weight (float): molecular weight in g/mol, e.g. 16.04
• sym_number (int): symmetry number, e.g. 1
• degeneracy (int): degeneracy of the ground state, for the calculation of the electronic partition function, e.g. 1
• inertia_list (list of floats): moments of intertia in amu*Å2 (1 or 3 elements for linear or non-linear molecules, respectively), e.g. [8.9] # can be obtained from ase.Atoms.get_moments_of_inertia()
• gas_energy (float): formation energy in eV, e.g. -0.42

This dataframe contains information about the steps included in the reaction model, where each row of corresponds to a reversible elementary step. The following columns are required:

• site_types (str): type of adsorption sites, e.g. tM tC
• neighboring (str): connectivity between sites involved, e.g. 1-2. Optional (default: None)
• initial (list): initial configuration, e.g. ['1 * 1','2 CH3** 1','2 CH3** 2']
• final (list): final configuration, e.g. ['1 H_tC* 1','2 CH2** 1','2 CH2** 2']
• activ_eng (float): activation energy in eV, e.g. 1.02
• prox_factor (float): proximity factor, e.g. 0.2. Optional (default: 0.5)
• angles (str): angle between sites, e.g. 1-2-3:180. Optional (default: None)
• vib_list_is (list of floats): list of vibrational modes in meV for the initial state in meV, e.g. [332.7, 196.2, 70.5]
• vib_list_ts (list of floats): list of vibrational modes in meV for the transition state in meV, e.g. [332.7, 196.2]. For non-activated adsorption, define this as an empty list i.e. []
• vib_list_fs (list of floats): list of vibrational modes in meV for the final state in meV, e.g. [332.7, 196.2, 70.5]

Additional required columns for adsorption steps:

• molecule (str): gas-phase molecule involved, e.g. CO
• A_site (float): area of the adsoption site in Å, e.g. 4.28

This dataframe contains information about the clusters included in the cluster expansion, where each row of corresponds to a cluster. The entries corresponding to point clusters and pairwise lateral interactions must end in '_point' and '_pair', respectively (e.g. CH3_point, CH2+H_pair) and the following columns are required:

• cluster_eng (float): cluster formation energy, e.g. -1.23
• site_types (str): type of adsorption sites, e.g. top top
• neighboring (str): connectivity between sites involved, e.g. 1-2
• lattice_state (list): cluster configuration, e.g. ['1 CO* 1','2 CO* 1']
• angles (str): angle between sites, e.g. 1-2-3:180. Optional (default: None)
• graph_multiplicity (int): symmetry number of the cluster, e.g. 2. Optional (default: None)

Path were the lattice_input.dat file is located. This file has to be generated manually in advance.

Hector Prats Garcia