def write_cif(placed_all, fixed_bonds, scaled_params, sc_unit_cell, cifname,
charges):
sc_a, sc_b, sc_c, sc_alpha, sc_beta, sc_gamma = scaled_params
zs = 0.5
#opath = os.path.join('cifs', cifname)
opath = cifname
coords = []
sps = []
for l in placed_all:
vec = list(map(float, l[1:4]))
cvec = np.dot(np.linalg.inv(sc_unit_cell), vec)
coord = [
np.round(cvec[0], 10),
np.round(cvec[1], 10),
np.round(cvec[2], 10)
]
coords.append(coord)
sps.append(re.sub('[0-9]', '', l[0]))
lat = Lattice.from_parameters(sc_a, sc_b, sc_c, sc_alpha, sc_beta,
sc_gamma)
st = Structure(lat, sps, coords)
st.sort()
min_d = st.distance_matrix + np.eye(len(st)) * 1000
if min_d.min() < 1.0:
print("! %s", opath)
return
with open(opath, 'w') as out:
out.write('data_' + cifname[0:-4] + '\n')
out.write('_audit_creation_date ' +
datetime.datetime.today().strftime('%Y-%m-%d') + '\n')
out.write("_audit_creation_method 'tobacco_3.0'" + '\n')
out.write("_symmetry_space_group_name_H-M 'P1'" + '\n')
out.write('_symmetry_Int_Tables_number 1' + '\n')
out.write('_symmetry_cell_setting triclinic' + '\n')
out.write('loop_' + '\n')
out.write('_symmetry_equiv_pos_as_xyz' + '\n')
out.write(' x,y,z' + '\n')
out.write('_cell_length_a ' + str(sc_a) + '\n')
out.write('_cell_length_b ' + str(sc_b) + '\n')
out.write('_cell_length_c ' + str(sc_c) + '\n')
out.write('_cell_angle_alpha ' + str(sc_alpha) + '\n')
out.write('_cell_angle_beta ' + str(sc_beta) + '\n')
out.write('_cell_angle_gamma ' + str(sc_gamma) + '\n')
out.write('loop_' + '\n')
out.write('_atom_site_label' + '\n')
out.write('_atom_site_type_symbol' + '\n')
out.write('_atom_site_fract_x' + '\n')
out.write('_atom_site_fract_y' + '\n')
out.write('_atom_site_fract_z' + '\n')
if charges:
out.write('_atom_site_charge' + '\n')
for l in placed_all:
vec = list(map(float, l[1:4]))
cvec = np.dot(np.linalg.inv(sc_unit_cell), vec)
if charges:
out.write('{:7} {:>4} {:>15} {:>15} {:>15} {:>15}'.format(
l[0], re.sub('[0-9]', '',
l[0]), "%.10f" % (np.round(cvec[0], 10) + zs),
"%.10f" % (np.round(cvec[1], 10) + zs),
"%.10f" % (np.round(cvec[2], 10) + zs), l[4]))
out.write('\n')
else:
out.write('{:7} {:>4} {:>15} {:>15} {:>15}'.format(
l[0], re.sub('[0-9]', '',
l[0]), "%.10f" % (np.round(cvec[0], 10) + zs),
"%.10f" % (np.round(cvec[1], 10) + zs),
"%.10f" % (np.round(cvec[2], 10) + zs)))
out.write('\n')
out.write('loop_' + '\n')
out.write('_geom_bond_atom_site_label_1' + '\n')
out.write('_geom_bond_atom_site_label_2' + '\n')
out.write('_geom_bond_distance' + '\n')
out.write('_geom_bond_site_symmetry_2' + '\n')
out.write('_ccdc_geom_bond_type' + '\n')
for e in fixed_bonds:
out.write('{:7} {:>7} {:>5} {:>7} {:>3}'.format(
e[0], e[1], "%.3f" % float(e[2]), e[3], e[4]))
out.write('\n')
import math
from pymatgen import Structure, Molecule, Lattice
import os
os.chdir(
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/slab/gulp/nonstochio/La-vac/two'
)
m = Molecule.from_file('tail.xyz')
l = Lattice.from_lengths_and_angles([11.46615, 15.2882, 50], [90, 90, 90])
s = Structure(l, m.species, m.cart_coords, coords_are_cartesian=True)
s.make_supercell([[4, 0, 0], [0, 3, 0], [0, 0, 1]])
s.make_supercell([[1, 1, 0], [1, -1, 0], [0, 0, 1]])
s.sort()
# ll = Lattice.from_lengths_and_angles([s.lattice.a / 2, s.lattice.b / 2, s.lattice.c], s.lattice.angles)
ll = Lattice.from_lengths_and_angles(s.lattice.abc, s.lattice.angles)
s = Structure(ll, s.species, s.cart_coords, coords_are_cartesian=True)
indi = []
for i, site in enumerate(s.sites):
if site.x + site.y < ll.b / math.sqrt(2):
indi.append(i)
# s.remove_sites(indi)
# s = Structure(ll, s.species, s.cart_coords, coords_are_cartesian=True)
# s.to('POSCAR', 'POSCAR')
s.to('POSCAR', 'CONTCAR')
