ZacrosIO
===========
This project is a collective of tools for the preparation of input files for Zacros.
## Installation
`pip install zacrosio`
`git clone https://github.com/hprats/ZacrosIO.git`
## Dependencies
Pandas, Scipy
## Example
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'])
## Dataframes required
The user must prepare three following Pandas dataframes in advance:
### 1. df_gas.csv
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
### 2. df_mechanism.csv
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
### 3. df_energetics.csv
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)
### 4. lattice_path (str)
Path were the lattice_input.dat file is located. This file has to be generated manually in advance.
## Contributors
Hector Prats Garcia
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