DOI: 10.5281/zenodo.16808816
title: Single-Site Adsorbate Probability Distribution Model Predictions

description: Metal-organic framework adsorbate probability distributions (APDs) predicted using the APD ML model in the paper <paper> of CH4 at conditions of 1 bar and 298 K, CH4 at conditions of 65 bar and 298 K, and Xe at conditions of 1 bar and 298 K. The development set comes from the ARC-MOF database (primarily hypothetical MOFs), while the test set comes from the MOSAEC-DB (exclusively experimentally characterized MOFs from the CSD). The tarballs in this repository contain the following information:



CH4_1bar_dev_ML_APDs.tar.gz -- ML-predicted APDs of CH4 at 1 bar for MOFs in the development set in CHGCAR format.

CH4_1bar_test_ML_APDs.tar.gz -- ML-predicted APDs of CH4 at 1 bar for MOFs in the test set in CHGCAR format.

CH4_65bar_dev_ML_APDs.tar.gz -- ML-predicted APDs of CH4 at 65 bar for MOFs in the development set in CHGCAR format.

CH4_65bar_test_ML_APDs.tar.gz -- ML-predicted APDs of CH4 at 65 bar for MOFs in the test set in CHGCAR format.

Xe_1bar_dev_ML_APDs.tar.gz -- ML-predicted APDs of Xe at 1 bar for MOFs in the development set in CHGCAR format.

Xe_1bar_test_ML_APDs.tar.gz -- ML-predicted APDs of Xe at 1 bar for MOFs in the test set in CHGCAR format.

CH4_1bar_dev_ML_binding_sites.tar.gz -- Binding sites extracted from the APDs in the CH4_1bar_dev_ML_APDs.tar.gz set using our binding site extraction code (GALA).

CH4_65bar_dev_ML_binding_sites.tar.gz -- Binding sites extracted from the APDs in the CH4_65bar_dev_ML_APDs.tar.gz set using our binding site extraction code (GALA).

Xe_1bar_dev_ML_binding_sites.tar.gz -- Binding sites extracted from the APDs in the Xe_1bar_dev_ML_APDs.tar.gz set using our binding site extraction code (GALA).

CH4_1bar_test_ML_binding_sites.tar.gz -- Binding sites extracted from the APDs in the CH4_1bar_test_ML_APDs.tar.gz set using our binding sites extraction code (GALA).

CH4_65bar_test_ML_binding_sites.tar.gz -- Binding sites extracted from the APDs in the CH4_65bar_test_ML_APDs.tar.gz set using our binding sites extraction code (GALA).

Xe_1bar_test_ML_binding_sites.tar.gz -- Binding sites extracted from the APDs in the Xe_1bar_test_ML_APDs.tar.gz set using our binding sites extraction code (GALA).


The binding_sites.tar.gz files contain one directory per MOF, with the following files/subdirectories in each directory: (Note that "O" represents the adsorbate "CH4", since it is modeled as a single-site, and is following a temporary naming convention in GALA. It does not correspond to an oxygen atom, as the name would imply. "CM" is the centre-of-mass pseudoatom of guest "O". "Xex" is the pseudoatom of guest "Xe".)



FIELD -- a file in DLPOLY FIELD format defining interaction parameters for guest-host binding energy calculations.

GALA.inp -- file containing GALA binding site extraction parameters.

gala.log -- GALA log file.

gala.out -- GALA output file.

slurm-* -- standard output.

DL_poly_BS -- a directory generated by GALA to compute the guest-host interaction energy of each binding site. Each subdirectory within DL_poly_BS contains DLPOLY input/output files for each configuration (i.e., the framework, and each binding site configuration). The <framework>_<guest> subdirectory contains the framework with a randomly placed guest configuration. This configuration is important to get the electrostatic energy of the framework, which is subtracted from the binding site configuration energies in GALA (the charges of the guest, if any, are zeroed out in this configuration). See the GALA documentation for more details on binding energy calculations.

GALA_Output -- a directory generated by GALA containing the following files:



<guest>_binding_sites.cif -- all binding sites in .cif format, with the binding sites listed in the .cif file in order of decreasing occupancy.

<guest>_binding_sites_fractional.xyz -- fractional coordinates of all binding sites in the MOF

<guest>_binding_sites_optimized.cif -- all binding sites optimized using MD as implemented in DLPOLY. In this work, a time-step of 0 ps was used, so this is the same as O_binding_sites.cif.

<guest>_gala_binding_sites.xyz -- the Cartesian xyz coordinates of each binding site, ordered in order of decreasing occupancy. This file also contains the guest-host interaction energy of each site (Ebind), the % of Ebind arising from electrostatics (esp%), the van der Waals interaction energy (Evdw), the electrostatic interaction energy (Eesp), and the relative occupancy in % (occ).  

<guest>_guest_information.xyz -- a file containing adsorbate information, and binding sites listed in order of increasing occupancy, with the absolute occupancy values, fractional, and Cartesian coordinates of each binding site.