Data for "Computational vibrational spectra for formic acid adsorbed on magnetite surfaces from DFT calculations"

This dataset contains input files for and output data of density functional theroy calculations (DFT) for obtaining the vibrational frequencies of formic acid and formate molecules adsorbed on the magnetite (001) and (111) surfaces. The DFT calculations were performed with the Vienna Ab Initio Simulation Package (VASP). Further details on the computational settings, related calculations such as structural pre-relaxations and vibrational spectra can be found in the corresponding publications (DOIs: 10.1038/s42004-019-0197-1, 10.1021/acs.jpclett.1c00209, 10.15480/882.3791, 10.1039/D5CP00848D).

The accompanying README file provides a summary of the basic information on this dataset, a detailed descriptions of all included files, and explains the research context, methodological aspects.

Provided files:
INCAR_vib_prototyp.txt : Prototypical VASP INCAR file for calculation of vibrational properties using DFPT, particularly for magnetite. The number atoms and the center of mass have to be adjusted for the used simulation cell. Also other settings might have to adapted depending on the studied materials.

The POSCAR files contain the atomic coordinates used for the calculations of the vibrational properties. The POSCAR files follow the structure for VASP calculations, for using them other codes adaptions might be necessary. The disp zip-files hold xyz files containing snapshots of the atomic positions during vibrations with a given wave number. The file names follow the same nomenclature. "Filetype"_"material"-"surface"_"adsorbate"-"coverage"-"adsorption mode"-"adsorption geometry" with the following possibilities:
- Filetype: POSCAR / disp
- Material: fe3o4
- Surface: 001 / 111
- Adsorbate: FA (Formic acid or formate)
- Coverage: tm / hm / fm (third / half / full monolayer, defined as the number of adsorbates divided by the number of Fe ions in the top surface layer)
- Adsorption mode: mol / dis (molecular / dissociative adsorption)
- Adsorption geometry: bd / md / qdr / chel / qdc (bi-dentate / mono-dentate / quasi-dentate-restgroup_H / chelating / quasi-bi-dentate-carboxy_H)
additional geometrical information: int / tet / parallel / triangle (specifying placement or orientation of adsorbates), H1/2/3/4NN (nearest neighbour shell of surface O atoms where carboxy H atoms bind to, measured from the surface Fe where adsorbate binds to)

Provided scripts:
Several python scripts are provided for processing and visualising DFT/DFPT output data. The provided scripts are currently not well documented and should only be used with care and at your own risk. We accept no liability.
- plotIR.py (for plotting calculated IR spectra)
- vibrations.py (for creating snapshots for vibrational motions for animations)
- poscarRW.py (for reading and writing POSCAR files)
- xyzRW.py (for reading and writing XYZ files)

The DFT calculations were performed with the Vienna Ab Initio Simulation Package (VASP, version 5.4.4). Further details on the computational settings, related calculations such as structural pre-relaxations and vibrational spectra can be found in the the accompanying README file and the corresponding publications (DOIs: 10.1038/s42004-019-0197-1, 10.1021/acs.jpclett.1c00209, 10.15480/882.3791, 10.1039/D5CP00848D).

Using the output of the DFT/DFPT calculations (mainly the OUTCAR for VASP calculations, which are not provided here), IR spectra and animations of the vibrational motions of the atoms can be calculated and visualised. First the vibrational intensities have to be calculated. This can be done, e.g., using the tool "VASP-infrared-intensities" by David Karhanek (https://github.com/dakarhanek/VASP-infrared-intensities). The results can be plotted for obtaining IR spectra. Here, we are supplying an own python script "plotIR.py" for that. Moreover, the eigenvectors of the vibrational motions can be used to produce animations of the vibrations. Here, we provide an python script "vibrations.py" for producing snapshots of the motions as xyz-files. The vibrations.py script is using two additionally provided scripts "poscarRW.py" and "xyzRW.py" for reading and writing POSCAR and XYZ files. The provided scripts are currently not well documented and should only be used with care and at your own risk. We accept no liability.

From the xyz-files, animations of the vibrational modes can be created using additional software such as VMD (Visual Molecular Dynamics, https://www.ks.uiuc.edu/Research/vmd/).