Grid Adsorption Energy Descriptors (GrAED) is an adsorption energy sampling tool based on symmetric grids to calculate the adsorption enthalpy and the Henry constants in nanoporous materials as well as statistical quantities used in ML modelling of adsorption process
Check if you have c++11 compiler installed (may work with other compiler but has been tested and mainly used with this compiler).
Tested for c++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Compilation that follows the rules set in the Makefile:
make all
This task is performed by the graed binary and gives adsorption enthalpy, Henry coefficient and statistical quantities of the energy grid.
If you want to run a surface sampling simulation on the structure KAXQIL (CSD code) from CoRE MOF 2019 all-solvent removed with the Dreiding+uff forcefield at 298K with a 12A cutoff for the xenon.
./graed structure/KAXQIL_clean_14.cif forcefield/UFF.def 298 12.0 Xe 0.12 100 0.8
The inputs correspond to the structure cif file, the forcefield definition file (Raspa), the temperature, the cutoff in LJ potential, the atom, the grid spacing, the energy threshold under which the energy is accurately calculated, the relative size of the blocking framework atoms (between 0 and 1).
You should get an output that has values close to this:
KAXQIL_clean_14,-44.626,2.21797,2.14037,10.0172,15.0287,73.1689,0.0300725,0.218192
The results are printed in a comma separated format: structure name, adsorption enthalpy (kJ/mol), standard deviation of Boltzmann weighted energies, skewness, kurtosis, standard deviation of energies, Henry coefficient (mol/kg/Pa), Accessible Surface Area (m2/cm3), Time (s)
This binary is supposed to be used in a high-throughput manner to add rows to a csv file.
The pgrid binary prints out a grid in the grid/ folder using the following command:
./pgrid structure/KAXQIL_clean_14.cif forcefield/UFF.def 298.0 12.0 Xe 0.3 100 0.8
The structure name, the grid size in number of points and the computation time are given as an output, in the following format:
KAXQIL_clean_14,884736,0.590011
The file grid/KAXQIL_clean_14_UFF_0.12_100_Xe.ccp4 is then output from the binary and can be used for further analysis or visualization for instance.
To visualize the grid, use the python file viz/visualize_grid.py. To modify the visualization parameters please refer to the documentation of the python library plotly. To use the file simply run the following command:
python3 viz/visualize_grid.py grid/KAXQIL_clean_14_UFF_0.12_100_Xe.ccp4
This will generate a .html file in viz that can be read by any web broawser (firefox, chrome, etc.) and it will be automatically launched in the browser.
This code has been developped during a PhD thesis co-financed by the CEA and Orano under the supervision of François-Xavier Coudert: https://github.com/fxcoudert
This code includes the library developped in Gemmi: https://github.com/project-gemmi/gemmi.git
The MIT License (MIT)
Copyright (c) 2023 Emmanuel Ren
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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