2. 转换POSCAR为lammps.data
1. 师弟版（好用）
==记得使用时需要把poscar中下面的速度分量和空格都删除干净，不然会报错==
python “this file” OUTCAR.input data.output
# convert VASP OUTCAT to lammps .data (atomic)
#
# usage:
# python "this file" OUTCAR.input data.output
#
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ###
import numpy as np
from sys import argv
def anls_poscar(file_name: str):
with open(file_name, 'r') as f:
lines = f.readlines()
bloom_factor = float(lines[1])
lat = np.array([i.split() for i in lines[2: 5]]).astype(float)
lat = bloom_factor * lat
ele_and_num = lines[5][:-1] + ":" + lines[6][:-1]
pos_d = None
if (lines[7][0] == 'd') or (lines[7][0] == 'D'):
# direct coord.
pos_d = np.array([i.split() for i in lines[8:]]).astype(float)
elif (lines[7][0] == 'c') or (lines[7][0] == 'C'):
# cartesian
pos_c = np.array([i.split() for i in lines[8:]]).astype(float)
pos_d = direct2pos(lat, pos_c, False)
return lat, pos_d, ele_and_num
def direct2pos(lat, pos, direction=True):
"""
lat = [[Ax, Ay, Az],
[Bx, By, Bz],
[Cx, Cy, Cz]]
Pos = [n, 3]
:return: if True: return cart = [n, 3]
if False: return direct = [n, 3]
"""
if direction:
return pos @ lat
else:
return pos @ np.linalg.inv(lat)
def clip_ny_norm(x):
return x / np.linalg.norm(x)
def cart2lams(lat):
"""
vasp (POSCAR) Coordinate System:
O = [[ax, ay, az],
[bx, by, bz],
[cx, cy, cz]]
:return:
lammps Coordinate System:
O' = [[xhi - xlo, 0, 0],
[xy, yhi - ylo, 0],
[xz, yz, zhi - zlo]]
"""
ax = (lat[0] ** 2).sum() ** 0.5
a_hat = clip_ny_norm(lat[0])
bx = (lat[1] * a_hat).sum()
by = np.linalg.norm(np.cross(a_hat, lat[1]))
cx = (lat[2] * a_hat).sum()
cy = (lat[2] * np.cross(clip_ny_norm(np.cross(lat[0], lat[1])), a_hat)).sum()
cz = np.abs((lat[2] * clip_ny_norm(np.cross(lat[0], lat[1]))).sum())
new = np.array([
[ax, 0, 0],
[bx, by, 0],
[cx, cy, cz]
])
return new
def write_lmp_atomic_data(filename, lmp_lat, pos_c, strr):
new_coo = pos_c
Z_of_type = strr.split(':')[0].split()
n_type = strr.split(':')[1].split()
new_ele = [[i] * int(n_type[i - 1]) for i in range(1, len(n_type) + 1)]
new_ele = sum(new_ele, [])
# write
with open(filename, "w") as f:
f.writelines("%s (written by ARES-NNP)\n\n" % str(filename + strr))
f.writelines("%i atoms\n" % len(new_coo))
f.writelines("%i atom types\n" % len(Z_of_type))
f.writelines("0.0 %.17f xlo xhi\n" % lmp_lat[0][0])
f.writelines("0.0 %.17f ylo yhi\n" % lmp_lat[1][1])
f.writelines("0.0 %.17f zlo zhi\n" % lmp_lat[2][2])
f.writelines(
" %18.12f %18.12f %18.12f xy xz yz\n\n\n" % (lmp_lat[1][0], lmp_lat[2][0], lmp_lat[2][1]))
f.writelines("Atoms\n\n")
index_list = np.arange(1, len(new_coo) + 1)
for i, ele, coo in zip(index_list, new_ele, new_coo):
f.writelines("{0:>6} {1:>3} {2:20.12f} {3:20.12f} {4:20.12f}\n".format(i, ele, coo[0], coo[1], coo[2]))
if __name__ == '__main__':
filename = argv[2]
lat, pos, strr = anls_poscar(argv[1])
crs_para = np.linalg.norm(lat, axis=1)
exg = np.argsort(crs_para)[::-1]
lat = lat[exg, :]
pos = pos[:, exg]
lmp_lat = cart2lams(lat)
inv = np.linalg.inv(lat) @ lmp_lat
pos_c = direct2pos(lat, pos, True) @ inv
write_lmp_atomic_data(filename, lmp_lat, pos_c, strr)
2.pymatgen版（有时出错）
from pymatgen.io.lammps.data import LammpsData
from pymatgen.io.vasp.inputs import Poscar
poscar = Poscar.from_file("POSCAR")
structure=poscar.structure
lammps_data = LammpsData.from_structure(structure)
lammps_data.write_file("data.kysio")
#poscar2=Poscar(structure)
#poscar2.write_file('super.vasp')
3. 转换lammps.data为POSCAR
- 用ovito转
from pymatgen.io.lammps.data import LammpsData
from pymatgen.io.vasp.inputs import Poscar
lammps_data = LammpsData.from_file("data.KYSO")
structure = lammps_data.structure
poscar = Poscar(structure)
poscar.write_file("POSCAR")
转载请注明来源 有问题可通过github提交issue