**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: .. code-block:: console 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: ``file`` 和 ``struct`` * ``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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~