VaspGibbs: A simple way to obtain Gibbs free energy from Vasp calculations
Bibliographic record
Abstract
VaspGibbs A simple way to get Gibbs free energy from Vasp calculations Installation pip install vaspgibbs Latest version: 0.2.0 (beta) 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) 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?
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.007 |
| Meta-epidemiology (narrow) | 0.004 | 0.004 |
| Meta-epidemiology (broad) | 0.004 | 0.004 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.004 | 0.005 |
| Open science | 0.010 | 0.004 |
| Research integrity | 0.004 | 0.009 |
| Insufficient payload (model declined to judge) | 0.354 | 0.141 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".