精品软件工具--适用于多孔材料吸附性质模拟软件——RASPA的脚本工具集合，可用于并行计算等温线、高通量模拟，zeo+.zip

# RASPA_tools 适用于多孔材料吸附性质模拟软件——RASPA的Python脚本工具集合，可用于并行计算等温线、高通量模拟，zeo++参数自动化计算、批量结果分析等。 A collection of Python scripting tools for RASPA, which can be used for parallel calculation of isotherms, high-throughput simulation, automatic calculation of structural parameters, batch result analysis, etc. **我已经毕业了，这个项目应该不会再维护了，如果有什么问题可以邮箱联系我（luxiuyang123@foxmail.com）** ## 项目结构 (Structure) ``` ├── raspa_parse/ ├── raspa_parse.py //用于解析RASPA输出文件的工具类 ├── zeo_calculate/ //使用zeo++批量计算结构参数 ├── config.ini //配置文件 ├── structral_parameters_screen.py //用于计算结构参数的主程序 ├── isotherms/ //批量计算等温线（支持多线程并行、多组分吸附） ├── config.ini //配置文件 ├── simulation_template.input //RASPA输入文件的模板 ├── main_isotherms.py //计算等温线的主程序 ├── high_throughput_adsorption/ //批量进行吸附模拟 ├── config.ini //配置文件 ├── simulation_template.input //RASPA输入文件的模板 ├── main_adsorption.py //批量进行吸附模拟的主程序 ``` ## 用法 (Usage) 在使用之前，请在你的电脑上安装Python运行环境，版本3.0以上。如果你在使用超算或者计算集群，**请勿**使用相应的作业管理系统（如PBS、LSF等）运行脚本。 Please install the Python runtime environment, version 3.0 or higher, on your computer before using it. If you are using supercomputing or computing clusters, **Don't** run the script using the appropriate job management system (e.g. PBS, LSF, etc.). *** ### zeo_calculate [zeo++](http://www.zeoplusplus.org/ )是一款功能强大的多孔材料结构分析工具，此脚本可极大的简化利用zeo++计算材料的结构参数的操作，并可以批量的进行大规模高通量模拟，支持多线程，并可以自动完成对结果的汇总统计。`zeo_calculate/` 里有两个文件，其中`config.ini`为配置文件，`structral_parameters_screen.py`是运行程序的主函数。 zeo++ is a powerful tool for structural analysis of porous materials. This script greatly simplifies the operation of calculating structural parameters of materials with zeo++, and allows to perform large scale high throughput simulations in batch, supports multi-threading, and can automatically complete summary statistics of the results. There are two files in `zeo_calculate/`, `config.ini` is the configuration file, and `structral_parameters_screen.py` is the main function to run the program. 首先根据自己的需求更改`config.ini`中的参数，注意`zeo++_dir`最好使用绝对路径，`number_of_threads`建议设定为电脑的核心数。 First, change the parameters in `config.ini` to suit your needs, note that `zeo++_dir` is best set to absolute path, and `number_of_threads` is recommended to be set to the number of cores in your computer. ```ini [ZEO_CONFIG] # zeo++ 的安装目录（The installation directory of zeo++） zeo++_dir = /home/luxiuyang/zeo++-0.3 # 需要计算的材料的cif文件所在目录（The CIF files directory of the materials to be calculated） cif_dir = /home/luxiuyang/RASPA_tools/test_cifs # CPU核心数（Number of CPU cores on your computer） number_of_threads = 10 # 计算比表面积所用的分子探针半径（Molecular probe radius used to calculate specific surface area） radius_of_area_probe = 0 # 计算孔隙率、孔体积所用的分子探针半径（Molecular probe radius used to calculate porosity） radius_of_porosity_probe = 0 # 用于计算比表面积的蒙特卡洛采样次数，大多数情况下无需更改 #（The number of Monte Carlo samples used to calculate the specific surface area, # in most cases does not need to be changed） area_monte_carlo_samples = 2000 # 用于计算孔隙率的蒙特卡洛采样次数，大多数情况下无需更改 #（The number of Monte Carlo samples used to calculate the porosity, # in most cases does not need to be changed） porosity_monte_carlo_samples = 100000 # 输出文件的名称，大多数情况下无需更改（The name of the output file, in most cases does not need to be changed） output_file_name = result.csv ``` 接下来运行`structral_parameters_screen.py`，注意要和`config.ini`在一个目录下，可以使用VS Code或Pycharm等IDE，或者直接在终端运行： Next, run `structral_parameters_screen.py`, note that it should be in the same directory as `config.ini`, you can use IDE such as VS Code or Pycharm, or run it directly in the terminal: ```shell python structral_parameters_screen.py ``` 如果配置正确的话，程序会显示进度条，结束之后会在控制台输出"Finish !"，此时可以在当前目录下看到`result.csv`和`zeo_results`，分别是计算结果汇总和zeo++的输出文件。 If the configuration is correct, the program will display a progress bar and output "Finish !" in the console when it finishes, you can see `result.csv` and `zeo_results` in the current directory, which are the summary of the calculation results and the output file of zeo++, respectively. *** ### raspa_parse `raspa_parse.py`提供了简洁友好的API，用于解析RASPA输出文件。`RASPA_Output_Data`是核心类，封装了一系列解析方法，其构造器需传入RASPA输出文件的字符串作为参数。 `raspa_parse.py` provides concise and friendly APIs for parsing RASPA output files. `RASPA_Output_Data` is the core class that encapsulates a set of parsing methods. Its constructor takes a string as an argument from the RASPA output file. | Method | Parameter | Function | Return Value | |:-----------------------------:|:---------------------------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------------------------------------------------------------------------------------------:|:--------------------------------------------------------------------------------------------------------------:| | get_components() | None | get components in the output file | List[string: component name] | | is_finished() | None | Determine whether the output file is finished | True if done, False otherwise | | get_warnings() | None | get warnings in the output file