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.
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├── 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
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++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.
[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:
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.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 | List[string: warning name] |
| get_pressure() | None | get pressure of output file | string:pressure,the unit is Pa |
| get_absolute_adsorption(unit) | unit:The unit of adsorption capacity, optional values:"mol/uc","cm^3/g","mol/kg","mg/g","cm^3/cm^3",default is "cm^3/g" | get absolute adsorption capacities | Dict:{component_name:adsorption_capacity} |
| get_excess_adsorption(unit) | unit:The unit of adsorption capacity, optional values:"mol/uc","cm^3/g","mol/kg","mg/g","cm^3/cm^3",default is "cm^3/g" | get excess adsorption capacities, If HeliumViodFraction is not specified in the simulation.input, the result is the same as get_absolute_adsorption(unit) |
Dict:{component_name:adsorption_capacity} |
| get_adsorption_heat() | None | get adsorption heat (KJ/mol) of components in the output file | Dict:{component_name:heat} |
| get_henry_coefficient() | None | get adsorption heat (mol/kg/Pa) of components in the output file | Dict:{component_name:heat} |
| get_all_adsorption_result | None | Obtain adsorption data for each component in each unit, including absolute and excess adsorption capacities | Dict, the keys are "{component_name}_absolute_{unit}", "{component_name}_excess_{unit}", "finished" and "warning" |
RASPA_Output_Data的构造器需传入RASPA输出文件的字符串作为参数。
RASPA_Output_Data 's constructor takes a string as an argument from the RASPA output file.
from raspa_parse import RASPA_Output_Data
with open('./your_output.data','r') as f:
raspa_str = f.read()
output = RASPA_Output_Data(raspa_str)
print(output.is_finished())
print(output.get_absolute_adsorption())你可以借助RASPA_Output_Data进行快速的批量结果统计，注意当输出文件很大时，会很耗费内存。
You can use RASPA_Output_Data for quick batch result statistics. Note that when the output file is large, it will consume a lot of memory
RASPA 默认情况下只能使用单核计算吸附，但是可以同时提交多个压力点的任务来实现多线程计算等温线。main_isotherms.py 可以自动化的完成上述过程，并快速进行结果汇总（基于RASPA_Output_Data），对于多组分吸附的输出文件也能正常解析。
RASPA can only use single-core computing adsorption by default, but can submit tasks for multiple pressure points at the same time to achieve multi-threads computing isotherms. main_isotherms.py can automate the above process and quickly summarize the results (based on RASPA_Output_Data), and can also parse the output file of multi-components adsorption normally.
首先，根据自己的需求更改config.ini中的参数，注意RSAPA_dir最好使用绝对路径，max_threads建议设定为电脑的核心数。
First, change the parameters in config.ini according to your needs. Note that RSAPA_dir is best set to an absolute path, and max_threads is recommended to be set to the number of cores of your computer.
[ISOTHERM_CONFIG]
# RASPA的安装目录，即/bin, /lib, /share所在目录
# The installation directory of RASPA, that is, the directory where /bin, /lib, /share are located
RASPA_dir = /usr/local/RASPA
# 如果只有1个cif需要计算，设定为cif文件所在位置，
# 如果有多个cif需要计算，设定为cif文件所在目录，程序会遍历目录中所有的cif文件并计算等温线
# If only one CIF needs to be calculated, set this parameter to the location of the CIF file.
# If multiple CIFs need to be calculated, set this parameter to the directory of the CIF files.
# The program will traverse all CIF files in the directory and calculate isotherms
cif_location = ../test_cifs/
# 建议设定为cpu的核心数
# Set this parameter to the number of CPU cores on your computer
max_threads = 10
# 温度的单位是K (The unit is kelvin)
temperature = 298
# 压力的单位是Pa, 可以使用科学计数法，数字之间以英文逗号(",")分隔
# The unit of pressure is Pascal, scientific notation can be used,
# and the numbers are separated by commas (",")
pressures = 100,300,500,1000,5000,10000,5e4,1e5
# 范德华力的截断半径，单位是埃
# Cutoff radius of van der Waals force in Angstroms
CutOffVDM = 12.0接下来，修改simulation_template.input，你可以根据计算需求增加、删除或修改一些RASPA参数，程序会根据此模板动态生成RASPA的输入文件——simulation.input。请注意，下面这几行不能修改：
Next, modify simulation_template.input, you can add, delete or modify some RASPA parameters according to the calculation requirements, and the program will dynamically generate the RASPA input file - simulation.input - based on this template. Please note that the following lines cannot be modified.
FrameworkName {cif_name}
CutOffVDW {cutoff}
UnitCells {unitcell}
ExternalTemperature {temperature}
ExternalPressure {pressure}
最后，运行main_isotherms.py，注意要和config.ini，simulation_template.input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：
Finally, run main_isotherms.py, note that it must be in the same directory as config.ini, simulation_template.input, you can use IDE such as VS Code or Pycharm, or run it directly in the terminal:
python main_isotherms.py在程序运行过程中，控制台会输出RASPA的日志，当前目录下会出现RASPA_Output和results文件夹，里面是分别是RASPA的输出文件和结果汇总文件。运行结束时，控制台会输出"Finish!"。
During the running of the program, the console will output the RASPA log, and the RASPA_Output and results folders will appear in the current directory, which are the RASPA output files and the result summary files respectively. At the end of the run, the console will output "Finish!".
有时我们需要对大量的材料进行吸附模拟，这时候此脚本就会派上用场。笔者对上述的main_isotherms.py稍作修改，便有了main_adsorption.py，支持多线程并行模拟多个材料，并自动完成对模拟结果的汇总，同样支持多组分吸附。
Sometimes we need to perform adsorption simulations on a large number of materials, and this is where this script comes in handy. I modified the above main_isotherms.py a little bit, then there is main_adsorption.py, which supports multi-threads parallel simulation of multiple materials, and automatically completes the aggregation of simulation results, also supports multi-components adsorption.
它的使用方法与main_isotherms.py很接近。首先，根据自己的需求更改config.ini中的参数，注意RSAPA_dir最好使用绝对路径，max_threads建议设定为电脑的核心数。
Its usage is very close to main_isotherms.py. First, change the parameters in config.ini according to your needs. Note that RSAPA_dir is best set to an absolute path, and max_threads is recommended to be set to the number of cores of your computer.
[ADSORPTION_CONFIG]
# RASPA的安装目录，即/bin, /lib, /share所在目录
# The installation directory of RASPA, that is, the directory where /bin, /lib, /share are located
RASPA_dir = /usr/local/RASPA
# 设定为cif文件所在目录，程序会遍历目录中所有的cif文件并使用RASPA进行吸附模拟
# Set this parameter to the directory of the CIF files.
# The program will traverse all the cif files in the directory and use RASPA for adsorption simulation
cif_location = ../test_cifs/
# 建议设定为cpu的核心数
# Set this parameter to the number of CPU cores on your computer
max_threads = 10
# 范德华力的截断半径，单位是埃
# Cutoff radius of van der Waals force in Angstroms
CutOffVDM = 12.0接下来，修改simulation_template.input，你可以根据计算需求增加、删除或修改一些RASPA参数，程序会根据此模板动态生成RASPA的输入文件——simulation.input。请注意，下面这几行不能修改：
Next, modify simulation_template.input, you can add, delete or modify some RASPA parameters according to the calculation requirements, and the program will dynamically generate the RASPA input file - simulation.input - based on this template. Please note that the following lines cannot be modified.
FrameworkName {cif_name}
CutOffVDW {cutoff}
UnitCells {unitcell}
最后，运行main_adsorption.py，注意要和config.ini，simulation_template.input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：
Finally, run main_adsorption.py, note that it must be in the same directory as config.ini, simulation_template.input, you can use IDE such as VS Code or Pycharm, or run it directly in the terminal:
python main_adsorption.py在程序运行过程中，控制台会输出RASPA的日志，当前目录下会出现RASPA_Output文件夹和adsorption_results.csv文件，分别是RASPA的输出文件和结果汇总文件。运行结束时，控制台会输出"Finish!"。
During the running process of the program, the console will output the RASPA log, and the RASPA_Output folder and the adsorption_results.csv file will appear in the current directory, which are the RASPA output files and the result summary file respectively. At the end of the run, the console will output "Finish!".