Supplementary information for the article: Isobutanol Dehydration Catalyzed by (100) Surface of Ferrierite: From Static DFT to Machine Learning Accelerated Molecular Dynamics
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2026
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| author | Skladanová, Katarína Gešvandtnerová, Monika Sola, Emeline Chizallet, Céline Pigeon, Thomas Badawi, Michael Bucko, Tomas |
| author_facet | Skladanová, Katarína Gešvandtnerová, Monika Sola, Emeline Chizallet, Céline Pigeon, Thomas Badawi, Michael Bucko, Tomas |
| contents | <p>This record contains the input/output files and necessary scripts needed to reproduce the results presented in the article: Isobutanol Dehydration Catalyzed by (100) Surface of Ferrierite: From Static DFT to Machine Learning Accelerated Molecular Dynamics; by Katarína Skladanová, Monika Gešvandtnerová, Emeline Sola, Céline Chizallet, Thomas Pigeon, Michael Badawi, and Tomáš Bučko.</p> <p>Files are organized in the subfolders as follows.</p> <p>Supplementary_files_static/ - includes relaxed transition-state (TS), reactant (R), and product (P) geometries for the conversion of isobutanol to linear (subfolder linear) and branched butenes (subfolder branched), along with the OUTCAR files obtained from the vibrational analysis. Further details can be found in Sec. 2 of the main text. The POTCAR files were generated using default PAW potentials (PBE datasets version 52). To accelerate the vibrational analysis, Selective dynamics was employed to split the calculation into several runs, each treating only a subset of atoms (hence the multiple POSCAR/OUTCAR files in some folders).</p> <p>vibFreq_multi.tgz - contains the Python 3 script vibFreq_multi.py, which can be used to recover the vibrational frequencies of the full system by running it in a directory containing the unzipped, numbered OUTCAR files (e.g. OUTCAR_0) from the vibrational analysis.</p> <p>Supplementary_files_dftMD_linear_Model_A/ and Supplementary_files_mlffMD_*/ - includes INCAR, ICONST, IRCCAR, POSCAR, and REPORT files from explicit DFT (Supplementary_files_dftMD_linear_Model_A) and MLFF-accelerated molecular dynamics (MD) simulations performed along the intrinsic reaction coordinate (IRC) for the conversion of isobutanol to linear (subfolder linear) and branched butenes (subfolder branched), documenting the simulation settings (INCAR), reaction-coordinate definition (ICONST and IRCCAR), starting structures (POSCAR), and trajectory outputs (REPORT). Further details, including the description of Models A, B, and C can be found in Sec. 2 of the main text. For a general introduction to VASP file formats and the IRC workflow, see the VASP Wiki documentation. For computational reasons, the simulations were continued over multiple runs; consequently, the starting structure is provided in the numbered file POSCAR.1, and the trajectory output is distributed across multiple REPORT files (e.g., report.1, report.2).</p> <p>Supplementary_files_training+testingMLFF/ - includes INCAR, POSCAR, and ML_AB files used for MLFF refitting, along with MLFF-MD trajectories (stored in numbered vasprun.xml files) and the associated ML_AB_mlff and ML_AB_dft files for the conversion of isobutanol to linear (subfolder linear) and branched (subfolder branched) butenes, used for MLFF validation and MLPT. Each vasprun.xml file contains 10 000 structures, and each ML_AB_mlff and ML_AB_dft file provides energies and forces for 400 structures sampled from the MLFF-MD trajectory, with the energies and forces in ML_AB_dft recalculated using single-point DFT.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_19049864 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Supplementary information for the article: Isobutanol Dehydration Catalyzed by (100) Surface of Ferrierite: From Static DFT to Machine Learning Accelerated Molecular Dynamics Skladanová, Katarína Gešvandtnerová, Monika Sola, Emeline Chizallet, Céline Pigeon, Thomas Badawi, Michael Bucko, Tomas acidic zeolites dehydration isomerization alcohol biobutanol molecular dynamics free energy of activation density functional theory machine learning <p>This record contains the input/output files and necessary scripts needed to reproduce the results presented in the article: Isobutanol Dehydration Catalyzed by (100) Surface of Ferrierite: From Static DFT to Machine Learning Accelerated Molecular Dynamics; by Katarína Skladanová, Monika Gešvandtnerová, Emeline Sola, Céline Chizallet, Thomas Pigeon, Michael Badawi, and Tomáš Bučko.</p> <p>Files are organized in the subfolders as follows.</p> <p>Supplementary_files_static/ - includes relaxed transition-state (TS), reactant (R), and product (P) geometries for the conversion of isobutanol to linear (subfolder linear) and branched butenes (subfolder branched), along with the OUTCAR files obtained from the vibrational analysis. Further details can be found in Sec. 2 of the main text. The POTCAR files were generated using default PAW potentials (PBE datasets version 52). To accelerate the vibrational analysis, Selective dynamics was employed to split the calculation into several runs, each treating only a subset of atoms (hence the multiple POSCAR/OUTCAR files in some folders).</p> <p>vibFreq_multi.tgz - contains the Python 3 script vibFreq_multi.py, which can be used to recover the vibrational frequencies of the full system by running it in a directory containing the unzipped, numbered OUTCAR files (e.g. OUTCAR_0) from the vibrational analysis.</p> <p>Supplementary_files_dftMD_linear_Model_A/ and Supplementary_files_mlffMD_*/ - includes INCAR, ICONST, IRCCAR, POSCAR, and REPORT files from explicit DFT (Supplementary_files_dftMD_linear_Model_A) and MLFF-accelerated molecular dynamics (MD) simulations performed along the intrinsic reaction coordinate (IRC) for the conversion of isobutanol to linear (subfolder linear) and branched butenes (subfolder branched), documenting the simulation settings (INCAR), reaction-coordinate definition (ICONST and IRCCAR), starting structures (POSCAR), and trajectory outputs (REPORT). Further details, including the description of Models A, B, and C can be found in Sec. 2 of the main text. For a general introduction to VASP file formats and the IRC workflow, see the VASP Wiki documentation. For computational reasons, the simulations were continued over multiple runs; consequently, the starting structure is provided in the numbered file POSCAR.1, and the trajectory output is distributed across multiple REPORT files (e.g., report.1, report.2).</p> <p>Supplementary_files_training+testingMLFF/ - includes INCAR, POSCAR, and ML_AB files used for MLFF refitting, along with MLFF-MD trajectories (stored in numbered vasprun.xml files) and the associated ML_AB_mlff and ML_AB_dft files for the conversion of isobutanol to linear (subfolder linear) and branched (subfolder branched) butenes, used for MLFF validation and MLPT. Each vasprun.xml file contains 10 000 structures, and each ML_AB_mlff and ML_AB_dft file provides energies and forces for 400 structures sampled from the MLFF-MD trajectory, with the energies and forces in ML_AB_dft recalculated using single-point DFT.</p> |
| title | Supplementary information for the article: Isobutanol Dehydration Catalyzed by (100) Surface of Ferrierite: From Static DFT to Machine Learning Accelerated Molecular Dynamics |
| topic | acidic zeolites dehydration isomerization alcohol biobutanol molecular dynamics free energy of activation density functional theory machine learning |
| url | https://doi.org/10.5281/zenodo.19049864 |