吸附构型的高通量建模

(简介),想要进一步了解该软件,请参阅 https://github.com/materialssimulation/HTMACat-kit

输入文件的准备

工作目录中需要准备好``config.yaml``文件

Config.yaml 文件包含 3 个部分

  • StuctInfo 部分

  • Species 部分(可选)

  • Model 部分

config.yaml 文件的典型构成如下:

StrucInfo:
  file: POSCARfile
  struct:
    element: Au
    lattice_type: fcc
    latttice_constant: 4.16
    facet: ['111','100'] #This is comment
    supercell: [3,3]     #Default: [3,3], can be undefined
    layers: 4            #Default: 4, can be undefined
    dope:
      Cu: [3]

# This part alias for Species
Species:
  file:
    'NH3+': NH3+.xyz #struct_file
    'NH3-': NH3-.xyz #struct_file
  sml:
    'O2': O=O #smiles

Model:
  ads:
    - ['NH3+',1]
    - ['NO', 2]
    - [s: 'C(=O)O',1]
    - [f: 'NH3+',1]
    - [s: 'C[Al](C)C',1Al]
  coads:
    - ['NH3','O',1,1]

StuctInfo 部分包含吸附基底的信息, 关键词存在两种形式: filestruct

  • file: 路径,该关键词会从POSCAR文件中读取基底信息

  • struct: 使用该关键词会基于下列参数生成基底:
    • element: bulk phase element

    • lattice_type: lattice type

    • latticd_constant: lattice parameter

    • facet: crystal plane, should be a list, start with [, separate with , and end with ], facet index should be a str start with ' end with ', like '100', '111'

    • supercell: supercell of the substrate in the xy-plane

    • layers: layers of the substrate in z axis

    • dope: dope of the substrate, the formate is dope element : [dope type1, dope type2] before : is the doped element, after the : is the dope type, the dope type can be chosen as follows: 0 corresponds to no doping, 1, 2 and 3 correspond to surface layers doped with 1, 2 and 3 atoms, respectively. 1L and b1 represent surface layer substitution and bulk equivalent proportional substitution.

Species 部分为可选部分,用于物种的重命名:

  • sml: 使用 Smiles 格式表示吸附物种

  • file: 从结构文件中读取吸附物种,如 xyz 文件或 vasp 文件

Model 部分包含吸附建模的参数:

  • ads: 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 from 1 or 2.

  • 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 from 1 and 2.

  • Each adsorbate species formular has three representation:
    • str format such as 'ads1', this format will automatically generate species according to chemical formular

    • smile format such as s: 'ads1' or sml: 'ads1', this format will generate spcecies according to the smile formular

    • file format such as f: 'ads1' or file: 'ads1', this format will read structure from file ‘ads1’, now only ‘xyz’ and ‘vasp’ structure file format is supported

  • New in version 1.0.5: Adding the symbol of the element contained in the adsorbate followed by the type of adsorption site generates a configuration in which all atoms corresponding to that element are adsorbed atoms, and automatically adjusts the orientation so that the adsorbed atom is at the bottom. Such as - [s: 'C[Al](C)C',1Al] will generatte configurations with Al atoms as adsorbed stoms

为了避免歧义,建议在声明复杂物种时使用SMILES。 用户可根据自己的研究需要修改相应参数,实现个性化建模。

程序的运行