def generate_periodic_zgnr(
width_n: int,
bond_dist: float = DEFAULT_CC_DIST,
vacuum_sep: float = 15,
hydrogen: bool = True,
):
assert width_n > 0
# the way we count is a bit off, so subtract one here to fix it
width_n -= 1
# put vacuum separation in terms of the bond distance
vacuum_sep /= bond_dist
cell = zgnr_unit_cell(vacuum_sep=vacuum_sep)
cell.make_supercell([1, width_n // 2 + 1, 1])
if width_n % 2 == 0:
# need to remove the two topmost atoms
cell.remove_sites(np.argsort(cell.cart_coords[:, 1])[-2:])
# add vacuum separation
cell = add_vacuum_sep(cell, vy=vacuum_sep, vz=vacuum_sep)
# center new structure
cell = center_structure(cell)
if hydrogen:
add_hydrogen(cell, cutoff=1.05, dist=DEFAULT_CH_DIST / DEFAULT_CC_DIST)
# scale to bond distances
return Structure(
lattice=Lattice(matrix=cell.lattice.matrix * bond_dist),
species=cell.species,
coords=cell.frac_coords,
)
def generate_periodic_agnr(
width_n: int,
bond_dist: float = DEFAULT_CC_DIST,
vacuum_sep: float = 15,
hydrogen: bool = True,
):
assert width_n >= 2
# put vacuum separation in terms of the bond distance
vacuum_sep /= bond_dist
cell = agnr_unit_cell(vacuum_sep=vacuum_sep)
if width_n % 2 == 0:
cell.make_supercell([1, width_n // 2, 1])
else:
cell.make_supercell([1, width_n // 2 + 1, 1])
# need to remove the two topmost atoms
cell.remove_sites(np.argsort(cell.cart_coords[:, 1])[-2:])
# add vacuum separation
cell = add_vacuum_sep(cell, vy=vacuum_sep, vz=vacuum_sep)
# center new structure
cell = center_structure(cell)
if hydrogen:
add_hydrogen(cell, cutoff=1.05, dist=DEFAULT_CH_DIST / DEFAULT_CC_DIST)
# scale to bond distances
cell.lattice = Lattice(matrix=cell.lattice.matrix * bond_dist)
return cell
def _generate_finite_agnr_from_periodic(
periodic_gnr: Structure,
length_m: int,
bond_dist: float,
vacuum_sep: float,
hydrogen: bool,
):
assert length_m >= 2
cell = periodic_gnr
if length_m % 2 == 0:
cell.make_supercell([length_m // 2, 1, 1])
else:
num_to_remove = cell.num_sites // 2
cell.make_supercell([length_m // 2 + 1, 1, 1])
# remove rightmost atoms
to_remove = np.argsort(cell.cart_coords[:, 0])[-num_to_remove:]
cell.remove_sites(to_remove)
# put vacuum separation in terms of the bond distance
vacuum_sep /= bond_dist
cell = add_vacuum_sep(cell, vx=vacuum_sep, vy=vacuum_sep, vz=vacuum_sep)
# center new structure
cell = center_structure(cell)
# kill off any lone carbons or those with only 1 bond
n_bonds = np.array([len(b) for b in calculate_bond_list(cell, cutoff=1.1)])
cell.remove_sites(np.where(n_bonds <= 1)[0])
if hydrogen:
add_hydrogen(cell, cutoff=1.05, dist=DEFAULT_CH_DIST / DEFAULT_CC_DIST)
# scale to bond distances
cell.lattice = Lattice(matrix=cell.lattice.matrix * bond_dist)
return cell
def run_gnr(args):
if not args["periodic"] and not args["length"]:
print("missing --length argument for finite gnr", file=sys.stderr)
sys.exit(1)
elif args["periodic"]:
if args["zigzag"]:
name = "z"
func = generate_periodic_zgnr
else:
name = "a"
func = generate_periodic_agnr
if not args["output"]:
args["output"] = f"periodic-{name}gnr-{args['width']}.vasp"
os.chdir('output')
gnr = func(args["width"], hydrogen=not args["no_hydrogen"])
if args["length"]:
gnr.make_supercell([args["length"], 1, 1])
#For edge structures
start = time.time()
if args["zigzag"]:
edge_combinations = zgnr_edge_types(gnr)
else:
edge_combinations = agnr_edge_types(gnr)
print(len(edge_combinations))
print(time.time() - start)
for i, cell in enumerate(edge_combinations):
add_hydrogen(cell,
cutoff=1.05,
dist=DEFAULT_CH_DIST / DEFAULT_CC_DIST)
cell.lattice = Lattice(matrix=cell.lattice.matrix *
DEFAULT_CC_DIST)
cell.to(filename=
f"periodic-{name}gnr-w{args['width']}xl{args['length']}-" +
str(i) + ".vasp",
fmt="poscar")
# gnr.to(filename=args["output"], fmt="poscar")
else:
if args["zigzag"]:
print("only periodic zigzag GNR generation is supported",
file=sys.stderr)
sys.exit(1)
if not args["output"]:
args[
"output"] = f"finite-gnr-{args['width']}x{args['length']}.vasp"
gnr = generate_finite_agnr(args["width"],
args["length"],
hydrogen=not args["no_hydrogen"])
gnr.to(filename=args["output"], fmt="poscar")
def process_structure(s: Structure):
# kill off any lone carbons or those with only 1 bond
from pyputil.structure.bonds import calculate_bond_list
n_bonds = np.array([len(b) for b in calculate_bond_list(s)])
s.remove_sites(np.where(n_bonds <= 1)[0])
# add hydrogen atoms on the edges
add_hydrogen(s, cutoff=1.05, dist=DEFAULT_CH_DIST / DEFAULT_CC_DIST)
# scale coordinates to bond distance
s.lattice = Lattice(matrix=s.lattice.matrix * bond_dist)
return s