"""
Simple parser for VESTA.
This module contains the parser for VESTA.
"""
from pymatgen.core import Structure
from pymatgen.core import Lattice
# ==================================================
vesta_key = [ # VESTA Keywords.
"#VESTA_FORMAT_VERSION",
"ATOMM",
"ATOMP",
"ATOMS",
"ATOMT",
"BKGRC",
"BONDM",
"BONDP",
"BONDS",
"CELLP",
"COMPS",
"CONTR",
"CRYSTAL",
"DISPF",
"DLATM",
"DLBND",
"DLPLY",
"DPTHQ",
"FORMM",
"FORMP",
"FORMS",
"GROUP",
"HBOND",
"HKLPM",
"HKLPP",
"ISURF",
"LABEL",
"LBLAT",
"LBLSP",
"LIGHT0",
"LIGHT1",
"LIGHT2",
"LIGHT3",
"LMATRIX",
"LORIENT",
"LTRANSL",
"MODEL",
"PLN2D",
"POLYM",
"POLYP",
"POLYS",
"PROJT",
"SBOND",
"SCENE",
"SECCL",
"SECTP",
"SECTS",
"SHAPE",
"SITET",
"SPLAN",
"STRUC",
"STYLE",
"SURFM",
"SURFS",
"SYMOP",
"TEX3P",
"TEXCL",
"THERI",
"TITLE",
"UCOLP",
"VECTR",
"VECTS",
"VECTT",
]
# ==================================================
[docs]
def parse_vesta(filename):
"""
parse VESTA file.
Args:
filename (str): filename.
Returns:
- (dict) -- VESTA keyword - content dict.
"""
data = []
with open(filename) as f:
for line in f:
d = line.split(" ")
d = [i.replace("\n", "") for i in d if i.replace("\n", "") != ""]
if d:
data += [d + ["\n"]]
data = sum(data, [])
pos = sorted([(data.index(i), i) if i in data else (-1, i) for i in vesta_key], key=lambda x: x[0])
dic = {}
for i in range(len(pos) - 1):
if pos[i][0] != -1:
if pos[i + 1][0] - pos[i][0] != 1:
dic[pos[i][1]] = (" ".join(data[pos[i][0] + 1 : pos[i + 1][0]])).strip()
else:
dic[pos[i][1]] = ""
return dic
# ==================================================
[docs]
def create_structure_vesta(vesta_dict):
"""
create Structure from vesta dict.
Args:
vesta_dict (dict): vesta dict.
Returns:
- (Structure) -- structure.
"""
space_group = int(vesta_dict["GROUP"].split(" ")[0])
lattice = [float(i) for i in vesta_dict["CELLP"].split("\n")[0].split(" ") if i != ""]
sites = [[j for j in i.split(" ") if j != ""] for i in vesta_dict["STRUC"].split("\n")[:-1:2]]
species = [i[1] for i in sites]
coords = [[float(i[4]), float(i[5]), float(i[6])] for i in sites]
lattice = Lattice.from_parameters(*lattice)
structure = Structure.from_spacegroup(space_group, lattice, species, coords)
return structure
