CRAFTED: An exploratory database of simulated adsorption isotherms of nanoporous materials

Overview The files in this repository compose the Charge-dependent, Reproducible, Accessible, Forcefield-dependent, and Temperature-dependent Exploratory Database (CRAFTED) of adsorption isotherms. This dataset contains the simulation of CO2 and N2 adsorption isotherms on 690 metal-organic frameworks taken from the CoRE-MOF-2014 database and 667 covalent organic frameworks taken from the CURATED-COFs database. The simulations were performed with two force fields (UFF and DREIDING), six partial charge schemes (no charges, Qeq, EQeq, DDEC, MPNN, and PACMOF), and three temperatures (273, 298, 323 K). Contents CIF_FILES/ contains 6 folders (NEUTRAL, DDEC, EQeq, Qeq, MPNN, and PACMOF), each one with 1357 CIF files; FORCEFIELDS/ contains 2 folders (UFF and DREIDING) with the definition of the forcefields; INPUT_FILES/ contains 97,704 input files for the GCMC simulations; ISOTHERM_FILES/ contains 97,704 adsorption isotherms resulting from the GCMC simulation; ENTHALPY_FILES/ contains 97,704 enthalpies of adsorption from the isotherms; RAC_DBSCAN/ contains the RAC and geometrical descriptors to perform the t-NSE + DBSCAN analysis; Licenses The 690 MOF-related CIF files in the DDEC folder were downloaded from CoRE-MOF-2014 and are licensed under the terms of the Creative Commons Attribution 4.0 International license (CC-BY-4.0). The 667 COF-related CIF files in the NEUTRAL folder were downloaded from CURATED-COFs and are licensed under the terms of the MIT license (MIT). Dalar Nazarian, Jeffrey S. Camp, & David S. Sholl. (2016). Computation-Ready Experimental Metal-Organic Framework (CoRE MOF) 2014 DDEC Database [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3986573 Ongari, Daniele, et al. "Building a consistent and reproducible database for adsorption evaluation in covalent–organic frameworks." ACS Central Science 5.10 (2019): 1663-1675. https://doi.org/10.1021/acscentsci.9b00619 Ongari, Daniele, Leopold Talirz, and Berend Smit. "Too many materials and too many applications: An experimental problem waiting for a computational solution." ACS Central Science 6.11 (2020): 1890-1900. https://doi.org/10.1021/acscentsci.0c00988 The CO2.def and N2.def forcefield files were downloaded from RASPA and are licensed under the terms of the MIT license. Dubbeldam, David, et al. "RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials." Molecular Simulation 42.2 (2016): 81-101. https://doi.org/10.1080/08927022.2015.1010082 The remaining MOF-related CIF files in the PACMOF, MPNN, Qeq, EQeq and NEUTRAL folders were derived from those in the DDEC folder and are licensed under the terms of the Creative Commons Attribution 4.0 International license (CC-BY-4.0) from the CoRE-MOF-2014 subset. The remaining COF-related CIF files in the PACMOF, MPNN, Qeq, EQeq and DDEC folders were derived from those in the NEUTRAL folder and are licensed under the terms of the MIT license (MIT) from the CURATED-COFs subset. All remaining files were created by us, and are licensed under the terms of the CDLA-Sharing-1.0 license. Software requirements In order to create a Python environment capable of running the Jupyter notebooks, please install conda and execute conda env create --file environment.yml Usage instructions Execute the command below to run JupyterLab in the appropriate Python environment. conda run --name crafted jupyter-lab数据集概述 本仓库中的文件构成了电荷依赖、可复现、可访问、力场依赖且温度依赖的吸附等温线探索数据库（CRAFTED）。本数据集包含针对690个金属有机骨架（Metal-Organic Frameworks，MOF）与667个共价有机骨架（Covalent Organic Frameworks，COF）的CO₂和N₂吸附等温线模拟数据，其中MOF样本取自CoRE-MOF-2014数据库，COF样本取自CURATED-COFs数据库。模拟计算采用了两种力场（UFF与DREIDING）、六种部分电荷方案（无电荷、Qeq、EQeq、DDEC、MPNN及PACMOF），以及三种温度条件（273、298、323 K）。 数据集内容 CIF_FILES/ 文件夹包含6个子文件夹（NEUTRAL、DDEC、EQeq、Qeq、MPNN及PACMOF），每个子文件夹内均存储1357个CIF文件； FORCEFIELDS/ 文件夹包含2个子文件夹（UFF与DREIDING），用于存储力场定义文件； INPUT_FILES/ 文件夹包含97704个用于巨正则系综蒙特卡洛（Grand Canonical Monte Carlo，GCMC）模拟的输入文件； ISOTHERM_FILES/ 文件夹包含97704条由GCMC模拟得到的吸附等温线数据； ENTHALPY_FILES/ 文件夹包含97704条由吸附等温线计算得到的吸附焓数据； RAC_DBSCAN/ 文件夹包含用于执行t-NSE + DBSCAN分析的RAC与几何描述符。 许可协议 DDEC文件夹内的690个MOF相关CIF文件下载自CoRE-MOF-2014，采用知识共享署名4.0国际许可协议（Creative Commons Attribution 4.0 International License，CC-BY-4.0）进行授权。 NEUTRAL文件夹内的667个COF相关CIF文件下载自CURATED-COFs，采用MIT许可协议（MIT）进行授权。 达拉尔·纳扎里安、杰弗里·S·坎普与戴维·S·肖尔. (2016). 计算就绪型实验金属有机骨架（CoRE MOF）2014 DDEC数据库[数据集]. Zenodo. https://doi.org/10.5281/zenodo.3986573 翁加里·达尼埃尔等. "构建用于共价有机骨架吸附性能评估的一致性可复现数据库". ACS Central Science 5.10 (2019): 1663-1675. https://doi.org/10.1021/acscentsci.9b00619 翁加里·达尼埃尔、利奥波德·塔利尔茨与贝伦德·史密特. "材料与应用过剩：亟待计算解决方案的实验难题". ACS Central Science 6.11 (2020): 1890-1900. https://doi.org/10.1021/acscentsci.0c00988 CO₂.def与N₂.def力场文件下载自RASPA，采用MIT许可协议进行授权。 达布尔德姆·戴维等. "RASPA：用于柔性纳米多孔材料吸附与扩散的分子模拟软件". Molecular Simulation 42.2 (2016): 81-101. https://doi.org/10.1080/08927022.2015.1010082 PACMOF、MPNN、Qeq、EQeq与NEUTRAL文件夹内其余MOF相关CIF文件均源自DDEC文件夹内的文件，沿用CoRE-MOF-2014子集的知识共享署名4.0国际许可协议（CC-BY-4.0）进行授权。 PACMOF、MPNN、Qeq、EQeq与DDEC文件夹内其余COF相关CIF文件均源自NEUTRAL文件夹内的文件，沿用CURATED-COFs子集的MIT许可协议（MIT）进行授权。 其余所有文件均由本文作者创建，采用CDLA-Sharing-1.0许可协议进行授权。 软件环境要求 如需搭建可运行Jupyter笔记本的Python环境，请先安装conda，随后执行以下命令： conda env create --file environment.yml 使用说明 执行以下命令即可在指定Python环境中启动JupyterLab： conda run --name crafted jupyter-lab