Convert VASP OUTCAR to extxyz file for NequIP input

vasp_to_extxyz.py

from ase.io import read, write

# outcar contanining one (single-point) or multiple (trajectory) DFT frames
in_filename = './OUTCAR'
out_filename = 'nequip-data.extxyz'

# read all frames into a list of ase.Atoms objects
all_atoms = read(in_filename, format='vasp-out', index=':')

for curr_atoms in enumerate(all_atoms): 
  write('out_filename', curr_atoms, append=True, format='extxyz')

Hi, Thank you for the code
i don't think its taking into consideration all the frames (at least for me), i ran the code on a system with 390 atom and 37 frame, i confirmed that using dpdata package as follow:

but when i read the same file with ase.io.read i get the following:

normally this shouldn't be happening since index is settled to all (':') , maybe there is something that i'm not seeing it !
Can you help me with that please ?

the list i'm getting has a length of 1 instead of 37 (num of frames)

Hm, this worked for me in the past, and looking at the code here it does indeed iterate over frames:

@reader
def read_vasp_out(filename='OUTCAR', index=-1):
    """Import OUTCAR type file.

    Reads unitcell, atom positions, energies, and forces from the OUTCAR file
    and attempts to read constraints (if any) from CONTCAR/POSCAR, if present.
    """
    # "filename" is actually a file-descriptor thanks to @reader
    g = iread_vasp_out(filename, index=index)
    # Code borrowed from formats.py:read
    if isinstance(index, (slice, str)):
        # Return list of atoms
        return list(g)
    else:
        # Return single atoms object
        return next(g)

Can I ask what is in 220.OUTCAR, does it come from an AIMD simulation?

yes 200.OUTCAR come from an AIMD simulation

it worked fine with dpdata package and i can't see why its not working with ase

Hm, that seems more like a question for the ASE folks, I'm sorry I can't help you much here.

Unrelated to previous comments: there is a glitch in reading OUTCAR's with ase if one (a) installs ase with anaconda and (b) uses spin-polarized calculations in (c) VASP 6. It manifests as an AssertionError. It can be fixed by taking vasp_outcar_parsers.py from the ase GitLab repo (tested 2022.12.02) and substituting that for the anaconda-installed one.

hello,
I replaced the vasp-out file,but still I am getting this error: ase.io.ParseError: Did not find required property positions during parse. My outcar files include positions but the script can not find any. thanks

This one works.

from ase.io import read, write

Read all frames from OUTCAR

atoms_list = read('OUTCAR', index=':')

Write all frames to a single EXTXYZ file

write('output.extxyz', atoms_list)