Published December 12, 2023 | Version Revised dataset with publicly available data under CC BY-NC-SA 4.0 license
Dataset Open

Supplementary data (CC BY-NC-SA 4.0): A reactive neural network framework for water-loaded acidic zeolites

  • 1. Department of Physical and Macromolecular Chemistry, Charles University, Hlavova 8, 128 43 Praha 2

Description

Content (Creative Commons Attribution Non Commercial Share Alike 4.0 International):

This dataset provides supplementary data to "A reactive neural network framework for water-loaded acidic zeolites". It contains trained Neural Network Potentials (NNP and ΔNNP model), scripts, and all energy and force data used in this work at the (Δ)NNP, ReaxFF, and DFT (SCAN+D3(BJ) and ωB97X-D3(BJ)) level. Energy and forces are stored as ASE trajectory files (traj), readable by the Atomic Simulation Environment (ASE). In addition, this repository contains the generated training database with DFT (SCAN+D3(BJ)) energies and forces as SchNetPack1.0 database (SiAlOH.db) file readable by ASE and SchNetPack version 1.0.

  1. "aimd_simulations.zip" - VASP INCAR file, XDATCAR and traj file for 10 ps AIMD run (Supplementary Figure 6) and NNP level (re-)calculated energies/forces ("aimd_nnp_recalc.traj")
  2. "biased_dynamics.zip" - VASP/Plumed input and output files for DFT (SCAN+D3(BJ)) and NNP level biased dynamics including traj files (Supplementary Figure 12)
  3. "database_input.zip" - structure (cif) files of the initial structures used for database generation (Supplementary Table 1)
  4. "delta_nnp.zip" - (pytorch) ΔNNP model (compatible with SchNetPack version 1.0) together with example scripts 
  5. "error_stats.zip" - traj files of all generalization tests (Figure 1 and Supplementary Figure 4) storing energies/forces at the SCAN+D3(BJ), ReaxFF, and NNP level as well as traj files with ΔNNP and ωB97X-D3(BJ) energies/forces for a subset taken from biased dynamics runs (Supplementary Figure 11)
  6. "md_simulations.zip" - NNP level MD trajectories of all generalization test (Figure 1 and Supplementary Figure 4) runs including an example script for an MD run
  7. "neb_calculations.zip" - traj files and example scripts for NEB calculations at the (Δ)NNP along with the corresponding DFT energy/force data (SCAN+D3(BJ) and ωB97X-D3(BJ))
  8. "nnps.zip" - (pytorch) NNP model files (compatible with SchNetPack version 1.0)
  9. "silica_database.zip" - output files of the single-point (SP) and optimization test runs (Supplementary Figure 1) of pure silica structures together with an example structure optimization script 
  10. "SiAlOH.db" - DFT (SCAN+D3(BJ)) training database as SchNetPack1.0 database file readable by ASE and SchNetPack version 1.0

Files

aimd_simulation.zip

Files (6.6 GB)

Name Size Download all
md5:4641891ea54d3c6a028dabca471cce9e
299.4 MB Preview Download
md5:43c5269dd25a6956ad7359d7c6b2fb95
202.1 MB Preview Download
md5:77a4cd224b71cd87ed0e649e6dfc1ab3
15.0 kB Preview Download
md5:17f8273b9244f5d4d4509341b995c89b
3.5 MB Preview Download
md5:73be2c8b13d24a8f8a6369f6a9154678
103.3 MB Preview Download
md5:e66bdefc8d57a34037af3c6eec59a48c
4.2 GB Preview Download
md5:7fdc91fb89fc7f44c92af2dfcafe7f19
688.1 kB Preview Download
md5:e4cff3933b15bd4aa264313e8fbe0649
10.4 MB Preview Download
md5:3e7882b2e52dc2a666e7fab58e23830b
1.8 GB Download
md5:81ddd5f6f108bb1aab587b31131837ea
12.8 MB Preview Download

Additional details

Related works

Is published in
Publication: 10.1038/s41467-024-48609-2 (DOI)
Is supplement to
Preprint: arXiv:2307.00911 (arXiv)

Dates

Created
2023-12-12