A high-throughput modeling, calculation, and analysis framework for catalytic reaction processes, it provides key tools for high-throughput design and screening of catalytic materials. The software mainly includes functional modules such as surface structure analysis and information extraction, catalytic surface and various adsorption model construction, automatic construction of primitive reaction processes, automatic extraction of computational data and automatic extraction and construction of descriptors.The software can perform the following computational workflows: adsorption energy calculation and analysis workflow, primitive reaction calculation and analysis workflow, high throughput calculation and automated analysis of adsorption energy and reaction potential of catalytic primitive reaction processes, etc.
Python >= 3.6, <=3.9
ASE >= 3.22.1
CatKit == 0.5.4
numpy >= 1.20.0, <= 1.23.5
rdkit
typerIf you haven't installed Python3.x yet, download the specified version of package and install it.
pip install ase numpy==1.23.5 scikit-learn
pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/FireWorks-2.0.3-py3-none-any.whl
pip install https://raw.githubusercontent.com/stanfordbshan/HTMACat-kit/master/requires_wheel/CatKit-0.5.4-py3-none-any.whl
pip install -U https://github.com/stanfordbshan/HTMACat-kit/releases/download/v1.0.2/HTMACat-1.0.2-py3-none-any.whl
config.yaml should be prepared in your working folder.
Config.yaml file Contains two parts:
StuctInfopartsModelparts
The format of the whole config.yaml is as follows:
StrucInfo:
element: Au
lattype: fcc
latcont: 4.16
facet: ['111','100']
dope:
Cu: [3]
Model:
SML: False
ads:
- ['NH3',1]
- ['NO', 2]
coads:
- ['NH3','O',1,1]StuctInfo parts contains the information about substrate, including:
element: bulk phase elementlattype: lattice typelatcont: lattice parameterfacet: crystal plane, hould be a list, start with[, separate with,and end with], facet index should be a str start with'end with', like'100','111'dope: dope of the substrate, the formate isdope element : [dope type1, dope type2]before:is the doped element, after the:is the dope type, the dope type can be chosen as follows：0corresponds to no doping,1,2and3correspond to surface layers doped with1,2and3atoms, respectively.1Landb1represent surface layer substitution and bulk equivalent proportional substitution.
Model parts contains the adsorption modeling parameters, including:
SML: whether using Smiles toe represent the adsorption speciesads: using- [ adsorbate formular , adsorption sites type]to represent one adsorption status, where adsorption formular should be a str start with'end with'. Different adsorption status should start with new line, adsorption sites type can be chosen from1or2.coads: using- [ads1, ads2, ads1 sites, ads2 sites], ads1 and ads2 is two adsorbate species formular, ads1 sites and ads2 sites is adsorption sites type, can be chosen from1and2.
To avoid ambiguity, it is recommended that SMILES be used when declaring complex species. Users can modify the corresponding parameters to achieve customized modeling according to their research needs.
Running command htmat ads can automate the enumeration and construction of all possible configurations, and ultimately
output structure files in the VASP format, like Au_Cu_111_1_NH_0.vasp,
Furthermore, for the adsorption models on doped surfaces, we use the get_binding_adatom function to determine the
types of surface atoms that the adsorbate binds to in the preliminary configurations. We only select configurations
where the adsorbate is bound to a surface atom that contains a dopant atom, in order to reduce the number of final
output structures.
- Jiaqiang Yang email:jqyang_hust@hust.edu.cn
- Feifeng Wu email:wufeifeng_hust@163.com
- Bin Shan email:bshan@mail.hust.edu.cn
- Materials Design and Nano-Manufacturing Center@HUST:http://www.materialssimulation.com/