# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
from __future__ import annotations
from typing import Optional
from sisl import Atom, AtomicOrbital, Atoms, Orbital, PeriodicTable
from sisl._array import arrayi
from sisl._internal import set_module
from sisl.unit.siesta import unit_convert
from ..sile import add_sile, sile_fh_open
from .sile import SileSiesta
__all__ = ["orbindxSileSiesta"]
Bohr2Ang = unit_convert("Bohr", "Ang")
@set_module("sisl.io.siesta")
class orbindxSileSiesta(SileSiesta):
"""Orbital information file"""
[docs]
@sile_fh_open()
def read_lattice_nsc(self):
"""Reads the supercell number of supercell information"""
# First line contains no no_s
line = self.readline().split()
no_s = int(line[1])
self.readline()
self.readline()
nsc = [0] * 3
def int_abs(i):
return abs(int(i))
for _ in range(no_s):
line = self.readline().split()
isc = list(map(int_abs, line[12:15]))
if isc[0] > nsc[0]:
nsc[0] = isc[0]
if isc[1] > nsc[1]:
nsc[1] = isc[1]
if isc[2] > nsc[2]:
nsc[2] = isc[2]
return arrayi([n * 2 + 1 for n in nsc])
[docs]
@sile_fh_open()
def read_basis(self, basis: Optional[Atoms] = None) -> Atoms:
"""Returns a set of atoms corresponding to the basis-sets in the ORB_INDX file
The specie names have a short field in the ORB_INDX file, hence the name may
not necessarily be the same as provided in the species block
Parameters
----------
basis :
list of atoms used for the species index
"""
# First line contains no no_s
line = self.readline().split()
no = int(line[0])
self.readline()
self.readline()
pt = PeriodicTable()
if basis is None:
def crt_atom(i_s, spec, orbs):
# The user has not specified an atomic basis
i = pt.Z(spec)
if isinstance(i, int):
return Atom(i, orbs)
else:
return Atom(-1, orbs, tag=spec)
else:
def crt_atom(i_s, spec, orbs):
# Get the atom and add the orbitals
return basis[i_s].copy(orbitals=orbs)
# Now we begin by reading the atoms
atoms = []
orbs = []
specs = []
ia = 1
i_s = 0
for _ in range(no):
line = self.readline().split()
i_a = int(line[1])
spec = line[3]
if i_a != ia:
if i_s not in specs:
atoms.append(crt_atom(i_s, spec, orbs))
specs.append(i_s)
ia = i_a
orbs = []
i_s = int(line[2]) - 1
if i_s in specs:
continue
nlmz = list(map(int, line[5:9]))
P = line[9] == "T"
rc = float(line[11]) * Bohr2Ang
# Create the orbital
o = AtomicOrbital(n=nlmz[0], l=nlmz[1], m=nlmz[2], zeta=nlmz[3], P=P, R=rc)
orbs.append(o)
if i_s not in specs:
atoms.append(crt_atom(i_s, spec, orbs))
specs.append(i_s)
# Now re-arrange the atoms and create the Atoms object
return Atoms([atoms[i] for i in specs])
add_sile("ORB_INDX", orbindxSileSiesta, gzip=True)