make NEB initial POSCAR with specified atom not affected by PBC.

nebmake.py

#!/usr/bin/env python3

import copy
from pathlib import Path
import shutil
from sys import argv

import numpy as np
from ase.io import read as poscar_reader
from ase import Atoms


def lerp(IS: Atoms, FS: Atoms, nimages: int, *, inopbc=None):
    ispos = IS.get_scaled_positions()
    fspos = FS.get_scaled_positions()
    dist  = (fspos - ispos + 0.5) % 1 - 0.5

    lerped_pos = np.linspace(ispos,
                             ispos + dist,
                             nimages + 2)

    if inopbc is not None:
        lerped_pos[:, inopbc - 1, :] = np.linspace(ispos[inopbc-1, :],
                                                   fspos[inopbc-1, :],
                                                   nimages + 2)

    lerped_cell = np.linspace(IS.get_cell(),
                              FS.get_cell(),
                              nimages + 2)

    ret = []
    for i in range(nimages + 2):
        TS = copy.deepcopy(IS)
        TS.set_scaled_positions(lerped_pos[i])
        TS.set_cell(lerped_cell[i])
        ret.append(TS)

    return ret


def gen_neb(isname: str, fsname: str, nimages: int, inopbc):
    IS = poscar_reader(isname, index = 0)
    FS = poscar_reader(fsname, index = 0)

    TSS = lerp(Atoms(IS), Atoms(FS), nimages, inopbc=inopbc)

    for ii in range(nimages + 2):
        dirname = "{:02d}".format(ii)
        print(dirname)
        Path(dirname).mkdir(parents=True, exist_ok=True)

        if 0 == ii:
            shutil.copy2(argv[1], dirname+'/POSCAR')
        elif nimages + 1 == ii:
            shutil.copy2(argv[2], dirname+'/POSCAR')
        else:
            TSS[ii].write(dirname+'/POSCAR', vasp5=True)
        pass
        shutil.copy2('KPOINTS', dirname)
        shutil.copy2('INCAR', dirname)


if '__main__' == __name__:
    assert (len(argv) >= 4), "Usage: nebmake.py POSCAR_init POSCAR_fin NIMAGES [inopbc]"

    isfname = argv[1]
    fsfname = argv[2]
    nimages = int(argv[3])

    if len(argv) == 5:
        inopbc = int(argv[4])
    else:
        inopbc = None

    gen_neb(isfname, fsfname, nimages, inopbc)