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: 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 elementlattice_type
: lattice typelatticd_constant
: lattice parameterfacet
: 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-planelayers
: layers of the substrate in z axisdope
: 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:0
corresponds to no doping,1
,2
and3
correspond to surface layers doped with1
,2
and3
atoms, respectively.1L
andb1
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 from1
or2
.coads
: using- [ads1, ads2, ads1 sites, ads2 sites]
,ads1
andads2
is two adsorbate species formular,ads1 sites
andads2 sites
is adsorption sites type, can be chosen from1
and2
.- Each adsorbate species formular has three representation:
str format such as
'ads1'
, this format will automatically generate species according to chemical formularsmile format such as
s: 'ads1'
orsml: 'ads1'
, this format will generate spcecies according to the smile formularfile format such as
f: 'ads1'
orfile: '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。