README.md

VaspGibbs

Installation

pip install VaspGibbs

Usage

In a folder with a finished vasp calculation, run

vasp_gibbs

vasp_gibbs will rerun Vasp to obtain vibration modes and output the gibbs free energy of your system.

Use -o (only) or -t(top) to specify a set of atoms for which to calculate vibration modes. Examples:

• -o C O would only compute vibration modes associated with C and O keeping all other atoms fixed.
• -o 1 3 6 would compute vibration modes associated with the first, third and sixth atoms in the POSCAR keeping all other atoms fixed.
• -t 10 would compute vibration modes associated with the first 10 atoms starting from the top of the unit cell along the c axis.

This can be useful when computing free energy differences between systems where one part of the system does not change, e.g. adsorption free energies.

To run vasp in parallel call:

vasp_gibbs -n [number of proc] -m [mpi executable] -v [vasp executable]

By default srun and vasp_std are used.

VaspGibbs will automatically compute the moment of inertia and symmetry of your molecule and compute rotational and translational contributions if you specify that the system is a molecule with the -m flag.

The temperature and pressure can be set using the -T and -P flags.

Output

All outputs can be found in the VaspGibbs.md file. It contains the following information:

Rotational properties

Property	Value
Sigma	x
P. axes
I~1	x eV/THz^2
I~2	x eV/THz^2
I~3	x eV/THz^2

Energy corrections

Type	Z	E (eV)	S (eV/K)	F (eV)
ZPE	N/A	x	N/A	N/A
Electronic	x	x	x	x
Vibrational	x	x	x	x
Rotational	x	x	x	x
Translational	x	x	x	x

Thermodynamic Quantities

Quantity	Value
Enthalpy	x eV
Entropy	x eV/K
Gibbs Free Energy	x eV
G - E_dft	x eV
TS	x eV

Online Ressources

• https://pubs.acs.org/doi/abs/10.1021/jp407468t (Supporting Information)
• https://gaussian.com/thermo/
• https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html
• https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Statistical_Thermodynamics_(Jeschke)/06%3A_Partition_Functions_of_Gases/6.04%3A_Rotational_Partition_Function
• https://vaspkit.com/tutorials.html#thermo-energy-correction
• https://uregina.ca/~eastalla/entropy.pdf (https://doi.org/10.1063/1.473958)

Citation

@software{therrien2023vaspgibbs,
  author       = {Félix Therrien},
  title        = {{VaspGibbs: A simple way to obtain Gibbs free 
                   energy from Vasp calculations}},
  month        = apr,
  year         = 2023,
  publisher    = {Zenodo},
  version      = {v0.2.1},
  doi          = {10.5281/zenodo.7874413},
  url          = {https://doi.org/10.5281/zenodo.7874413}
}

Under development

Results have been checked with J. Phys. Chem. C 2013, 117, 49. More validation needs to be done; use with care.

Next steps: more testing, add to pypi, PV term for solids with Murnaghan equation, hindered translator and rotor?

Let me know if you would like new features to be added!