zacrostools 0.2b0

A collective of tools for the preparation of input files for ZACROS

ZacrosTools

[!WARNING]
This project is under development. The documentation is in preparation.

ZacrosTools is a simple toolkit for the preparation of Zacros input files. It is specially useful when running scans at different pressure and temperature conditions, which may require hundreds of KMC simulations.

Installation

The easiest way to install ZacrosTools is by using pip:

$ pip install zacrostools

Alternatively, it can also be cloned from GitHub:

$ git clone https://github.com/hprats/ZacrosTools.git

The only requirements are scipy and pandas.

How to use it

In ZacrosTools, a KMC model is represented as a KMCModel object zacrostools.kmc_model.KMCModel. In order to use ZacrosTools, three Pandas DataFrames have to be prepared in advance:

Name	Information
gas_data	gas species involved
mechanism_data	reaction model
energetics_data	energetics model

The information required in each of these DataFrames is the following:

1. gas_data

One row for every gas-phase species. The row index has to be the name of the species.

The following columns are required:

• type (str): 'non_linear' or 'linear'
• gas_molec_weight (float): molecular weights (in amu) of the gas species
• sym_number (int): symmetry number of the molecule
• degeneracy (int): degeneracy of the ground state, for the calculation of the electronic partition function. Default value: 1
• intertia_moments (list): moments of inertia for the gas-phase molecule (in amu·Å^2). 1 element for linear molecules, 3 elements for non-linear molecules. Can be obtained from ase.Atoms.get_moments_of_inertia()
• gas_energy (float): formation energy (in eV)

Example:

index	type	gas_molec_weight	sym_number	degeneracy	inertia_moments	gas_energy
CO	linear	28.01	1	1	[8.973619026272551]	1.96
O2	linear	32.0	2	3	[12.178379354326061]	2.6

2. mechanism_data

One row for every elementary step. The row index has to be the name of the step.

The following columns are required:

• site_types (str): the types of each site in the pattern
• initial (list): initial configuration in Zacros format, e.g. ['1 CO* 1','2 * 1']
• final (list): final configuration in Zacros format, e.g. ['1 C* 1','2 O* 1']
• activ_eng (float): activation energy (in eV)
• vib_energies_is (list): vibrational energies for the initial state (in meV)
• vib_energies_ts (list): vibrational energies for the transition state (in meV). For non-activated adsorption, define this as an empty list i.e. []
• vib_energies_fs (list): vibrational energies for the final state (in meV)
• molecule (str): gas-phase molecule involved. Only required for adsorption steps. Default value: None
• area_site (float): area of adsorption site (in Å^2). Only required for adsorption steps. Default value: None

The following columns are optional:

• neighboring (str): connectivity between sites involved, e.g. 1-2. Default value: None
• prox_factor (float): proximity factor. Default value: 0.5
• angles (str): Angle between sites in Zacros format, e.g. '1-2-3:180'. Default value: None

Example:

index	sites	site_types	neighboring	area_site	initial	final	activ_eng	molecule	vib_energies_is	vib_energies_fs	vib_energies_ts	prox_factor
CO_adsorption	1	topC		5.34	['1 * 1']	['1 CO* 1']	0.0	CO	[264.160873]	[240.497465, 82.738219, 60.132962, 60.080258, 7.271753, 6.553359]	[]	0.0
O2_adsorption	2	topC topC	1-2	5.34	['1 * 1', '2 * 1']	['1 O* 1', '2 O* 1']	0.0	O2	[194.973022]	[79.738187, 77.981497, 40.487926, 39.798116, 38.056578, 37.441762]	[]	0.0
CO2_adsorption	1	topC		5.34	['1 * 1']	['1 CO2* 1']	0.0	CO2	[294.059036, 163.752147, 78.494148, 78.310738]	[171.188002, 145.668886, 96.963691, 86.25514, 56.201368, 52.375682, 35.933392, 24.342963, 21.024922]	[]	0.0
CO+O_reaction	2	topC topC	1-2		['1 CO* 1', '2 O* 1']	['1 CO2* 1', '2 * 1']	1.249		[240.448231, 83.18955, 80.04067, 61.668486, 59.849388, 38.271338, 36.143131, 12.378844, 10.126178]	[171.188002, 145.668886, 96.963691, 86.25514, 56.201368, 52.375682, 35.933392, 24.342963, 21.024922]	[217.940927, 81.361728, 66.833494, 56.917831, 50.342099, 37.430358, 19.074043, 12.356398]
CO_dissociation	2	topC topC	1-2		['1 CO* 1', '2 * 1']	['1 C* 1', '2 O* 1']	2.176		[240.497465, 82.738219, 60.132962, 60.080258, 7.271753, 6.553359]	[138.064404, 78.64274, 39.644889, 38.175445, 32.997051, 23.89371]	[129.799624, 55.940895, 41.760039, 33.292377, 20.816034]
CO_diffusion	2	topC topC	1-2		['1 CO* 1', '2 * 1']	['1 * 1', '2 CO* 1']	1.156		[240.497465, 82.738219, 60.132962, 60.080258, 7.271753, 6.553359]	[240.497465, 82.738219, 60.132962, 60.080258, 7.271753, 6.553359]	[218.382388, 53.526855, 47.6122, 28.580404, 6.599679]
C_diffusion	2	topC topC	1-2		['1 C* 1', '2 * 1']	['1 * 1', '2 C* 1']	1.449		[138.207451, 24.592242, 17.986572]	[138.207451, 24.592242, 17.986572]	[85.015794, 66.512731]
O_diffusion	2	topC topC	1-2		['1 O* 1', '2 * 1']	['1 * 1', '2 O* 1']	1.221		[78.662275, 40.796289, 40.348665]	[78.662275, 40.796289, 40.348665]	[56.617104, 49.715199]

3. energetics_data

One row for every cluster. The row index has to be the name of the cluster.

[!TIP]
It is recommended to add _point at the end of the cluster name for one-body terms (e.g. CO_point), and _pair at the end of the name for two-body terms (e.g. CO+CO_pair).

The following columns are required:

• cluster_eng (float): cluster formation energy (in eV)
• site_types (str): the types of each site in the pattern
• lattice_state (list): cluster configuration in Zacros format, e.g. ['1 CO* 1','2 CO* 1'] The following columns are optional:
• neighboring (str): connectivity between sites involved, e.g. 1-2. Default value: None
• angles (str): Angle between sites in Zacros format, e.g. '1-2-3:180'. Default value: None
• graph_multiplicity (int): symmetry number of the cluster, e.g. 2. Default value: 1

Example:

index	cluster_eng	sites	site_types	lattice_state	neighboring	graph_multiplicity
CO2_point	-1.576	1	tC	['1 CO2* 1']
CO_point	0.233	1	tC	['1 CO* 1']
C_point	2.452	1	tC	['1 C* 1']
O_point	-1.333	1	tC	['1 O* 1']
CO2+CO2_pair	-0.062	2	tC tC	['1 CO2* 1', '2 CO2* 1']	1-2	2
CO2+CO_pair	-0.184	2	tC tC	['1 CO2* 1', '2 CO* 1']	1-2
CO2+C_pair	-0.168	2	tC tC	['1 CO2* 1', '2 C* 1']	1-2
CO2+O_pair	-0.162	2	tC tC	['1 CO2* 1', '2 O* 1']	1-2
CO+CO_pair	0.177	2	tC tC	['1 CO* 1', '2 CO* 1']	1-2	2
CO+C_pair	0.117	2	tC tC	['1 CO* 1', '2 C* 1']	1-2
CO+O_pair	-0.032	2	tC tC	['1 CO* 1', '2 O* 1']	1-2
C+C_pair	0.096	2	tC tC	['1 C* 1', '2 C* 1']	1-2	2
C+O_pair	-0.036	2	tC tC	['1 C* 1', '2 O* 1']	1-2
O+O_pair	0.034	2	tC tC	['1 O* 1', '2 O* 1']	1-2	2

Lattice model

Finally, a lattice model is needed to create a KMCModel. Currently, the only way to create a lattice model is by reading a lattice_input.dat file:

from zacrostools.lattice_input import LatticeModel

lattice_model = LatticeModel.from_file('lattice_inputs/lattice_input_Ni111.dat')

Example:

# lattice_input_for_HfC.dat file

lattice periodic_cell

   cell_vectors
   3.27 0.00
   0.00 3.27
   repeat_cell 10 10
   n_cell_sites 2
   n_site_types 2
   site_type_names topHf topC
   site_types topHf topC
   site_coordinates
      0.25 0.25
      0.75 0.75
   neighboring_structure
      1-2 self
      1-1 north
      2-1 north
      2-2 north
      1-1 east
      2-1 east
      2-2 east
      2-1 northeast
   end_neighboring_structure

end_lattice

Contributors

Hector Prats