Atomistic Simulation Packages

Group's RAWP

Atomic Simulation Environment (ASE)

ASE is a python-based tool that offers vast options to generate and manipulate inputs and outputs from a wide range of simulation packages, including the ones the group employs.

Most of the scripts the group is developing are in python and most of them use the capability and functionality of ASE.

Vienna Ab initio Simulation Package (VASP)

The group owns a licence of VASP, an efficient package for periodic calculations based on planewaves. All the inputs and outputs details as well as the tags defining specific actions are described in the vaspwiki, a guide pdf version is also available.

Hands-on

The best way to learn about VASP's background, methods and usage is practising with these hands-on seesions. There are also multiple sources explaining the background and offering scripts for analysing VASP outputs.

Inputs

VASP only requires four inputs files in addition to the submission script (machine dependent):

INCAR: what to do and how to do it. Here some examples for optimisations, single-points, NEBs, dimers and frequencies calculations. To use GPU nodes, the INCAR file needs some adjustments according to the current setup.

KPOINTS: where the wavefunction is measured. It can be integrated (recomended) in the INCAR file through the KSPACING tag.

POSCAR: the structure. It contains the periodic cell (lattice) and the xyz coordinates of each atom in direct or Cartisian coordinates of the initial structure.

POTCAR: which elements form the structure. It should contains the elements in the same order than POSCAR. Commonly, it is catenated in the submission script from a common source (a shared or private folder in the machine) and deleted at the end of the calculation as it remains invariable (but it is functional dependent!).

Outputs

VASP writes many output files depending on what is required and specified in the INCAR file. Some of these files can be very large (Gb) although are quite easy to generate, therefore it is not worth to store them. Common output files from an optimisation calculation worth saving are:

CONTCAR: optimised structure. It has the same shape than POSCAR with the optimised atomic coordinates (and lattices if allowed).

OSZICAR: energy summary. It summarises the electronic and ionic convergance along the optimisiation process.

OUTCAR: the results. It contains information regarding the structure, the potentials, the what and how, the energies and forces at each optimisation step and k-point.

Resources

There are many software and scripts able to handle VASP files. Find relevan ones in its official Resources web. The group commonly uses VESTA, p4vasp and Jmol as visualisers and for manipulation of structures.

OTHERS

The group also uses ORCA, DL_poly, GULP and any other suitable software to proceed with the investigation.