​软件演示

运行软件：

$ chemrust-nasl-app

定义目标文件路径：

> Filepath of the model cell file: ./scanner_test_models/black_phosphorus.cell

定义新原子：

> Element symbol of the new atom: 78 Pt

定义目标键长：

> What is the target bondlength (Å)? 2.9

定义x方向的坐标范围：

> Enter the fractional coordinate range to search in the direction of x-axis: 0 > Enter the fractional coordinate range to search in the direction of x-axis: 1

定义y方向的坐标范围：

> Enter the fractional coordinate range to search in the direction of y-axis: 0 > Enter the fractional coordinate range to search in the direction of y-axis: 1

定义z方向的坐标范围：

> Enter the fractional coordinate range to search in the direction of z-axis: 0 > Enter the fractional coordinate range to search in the direction of z-axis: 1

定义输出文件夹名称：

> Please name the directory for exported seed files: Pt_2.9_black_phosphorus

定义castep赝势文件夹路径：

> Please specify the location of castep psuedopotentials directory: e.g.: /home/user/Potentials

定义k点精度：

> Quality for k-point sampling? Coarse

定义计算模式：

> Use edft method for the `metals_method` option in CASTEP?(y/n or yes/no) No > Run mode of program Fast 软件输出：

Special multi-coordinated sites search completed. Found 186 multi-coordinated positions; Found 157 possible doubly-coordinated positions; Found 100 possible singly-coordinated positions; Results have been written to Pt_2.9_black_phosphorus

Program Initialization:

The program is currently offered as a CLI (command-line interface) program, which required to be run in a terminal emulator with any proper shell. If it is installed to locations that are included in your shell’s environmental variable list, you can directly call it in the command-line:

chemrust-nasl-app

Or, specify the path to it:

/PATH/TO/THE/BINARY/chemrust-nasl-app

Running Modes:

The program currently offers two running modes: an interactive mode and a read-from-config mode.

Interactive Mode:

The interactive mode will guide you step by step, from giving the input model file (supports .cell from castep and .cif of the International Union of Crystallography), specifying the desired new element and bondlength, to the remaining necessary settings to generate the seed files for computation job submissions. You can enter the interactive mode directly by:

chemrust-nasl-app -m i.

You will need to provide (also see the above Example section):

1. Path to the model. (E.g. ./graphene.cif, ./graphdiyne.cell)

2. Element symbol of the new atom. (E.g. Cu)

3. Target bondlength in Å. (E.g. 2.2)

4. The search range along the x,y,z axes by the fractional coordinates, from 0.0 to 1.0. (Default to 0.0 - 1.0 for searching in the whole lattice)

5. Path to the exported files. (If the path does not exist the program will create it for you automatically)

6. Specify the quality of k-point sampling. (Default is Coarse)

7. Use edft or dm as the electronic minimization method in castep. (It is recommended that use edft for rare-earth elements involved models, while dm is enough for models without rare-earth elements)

8. Running modes of the program. (Fast means generating the resulted models files and castep job files without the relatively time-consuming process of copying the psuedopotentials files to the destination. Full would copy the psuedopotentials. Post is you can execute the copying after Fast has been done. The others are for debug use.)

Read-From-Config Mode:

The read-from-config mode (-m c or --mode c) is meant for faster execution and/or batch processing. It will read from a yaml format file which contains all the required items with the predesignated format offered by us.

An example config.yaml:

model_path: ./scanner_test_models/from_mingzi/NiFeLDH_tem1.cell new_element: Cu target_bondlength: 2.2 x_range: [0.0, 1.0] y_range: [0.0, 1.0] z_range: [0.0, 1.0] export_dir: demo/NiFeLDH_tem1_Cu_2.2 kpoint_quality: Coarse edft: false

Suppose you have the required file config.yaml in the current directory. Run the program in read-from-config mode as follows:

chemrust-nasl-app -m c config.yaml

Help Information:

Try to get the basic help information by:

chemrust-nasl-app -h

New Adsorption Site Locator (NASL) for catalyst materials. Written in rust. Part of the `chemrust` toolchain. This is the binary crate. Usage: chemrust-nasl-app [OPTIONS] [CONFIG_LOC] Arguments: [CONFIG_LOC] Options: -m, --mode <MODE> [possible values: c, i] -h, --help Print help (see more with '--help') -V, --version Print version