def make_struc(formula, spacegroup, sc=1):
"""
Creates the crystal structure using ASE.
:param alat: Lattice parameter in angstrom
:return: structure object converted from ase
"""
#src_dir = 'bronze' if('Cu' in formula) else 'steel'
src_dir = 'base'
cif_in = read("./{}_cifs/{}_{}.cif".format(src_dir, formula, spacegroup))
supercell = make_supercell(cif_in, [[sc, 0, 0], [0, sc, 0], [0, 0, sc]])
structure = Struc(ase2struc(supercell))
#structure = make_supercell(structure, [[sc,0,0],[0,sc,0],[0,0,sc]])
#fecell = bulk('Fe', cell, a=alat)
#fecell = make_supercell(fecell, [[2,0,0],[0,2,0],[0,0,2]])
# check how your cell looks like
#write('s.cif', gecell)
#if(cell == 'bcc' and (mag=='non' or mag=='ferro')):
# fecell.set_atomic_numbers([26,26,26,26,26,26,26,26])
# print(fecell)
#elif(cell == 'bcc' and mag == 'anti'):
# fecell.set_atomic_numbers([26,27,26,27,26,27,26,27])
# print(fecell)
#else:
#fecell.set_atomic_numbers([26, 27,26,27,26,27,26,27,26, 27,26,27,26,27,26,27])
# print(fecell)
#structure = Struc(ase2struc(fecell))
#print(structure.species)
return structure
def make_struc():
slab_ideal=fcc110('Au',size=(4,2,8), a=4.163737636, vacuum=20)
#slab_ideal=fcc110('Au',size=(4,8,i), vacuum=20)
write('slab_ideal.struct',slab_ideal)
slab_ideal.edit()
#natoms_100=(len(slab_100.numbers))
#print ('positions',slab_ideal.positions)
natoms_ideal=len(slab_ideal.positions)
#print(natoms_ideal)
struc_ideal=Struc(ase2struc(slab_ideal))
return natoms_ideal,struc_ideal
def make_struc(formula, spacegroup, sc=1):
"""
Creates the crystal structure using ASE.
:param alat: Lattice parameter in angstrom
:return: structure object converted from ase
"""
#src_dir = 'bronze' if('Cu' in formula) else 'steel'
src_dir = 'bronze' if (('C' in formula) and ('S' in formula)) else 'base'
cif_in = read("./{}_cifs/{}_{}.cif".format(src_dir, formula, spacegroup))
supercell = make_supercell(cif_in, [[sc, 0, 0], [0, sc, 0], [0, 0, sc]])
structure = Struc(ase2struc(supercell))
return structure
def make_struc(alat):
"""
Creates the crystal structure using ASE.
:param alat: Lattice parameter in angstrom
:return: structure object converted from ase
"""
unitcell = crystal('Au', [(0, 0, 0)], spacegroup=225, cellpar=[alat, alat, alat, 90, 90, 90])
#unitcell.edit()
natoms_unitcell=(len(unitcell.numbers))
print('number of atoms in the bulk is', natoms_unitcell)
structure = Struc(ase2struc(unitcell))
return structure
def make_struc(alat):
"""
Creates the crystal structure using ASE.
:param alat: Lattice parameter in angstrom
:return: structure object converted from ase
"""
unitcell = crystal('Al', [(0, 0, 0)],
spacegroup=225,
cellpar=[alat, alat, alat, 90, 90, 90])
#multiplier = numpy.identity(3) * 2
#ase_supercell = make_supercell(unitcell, multiplier)
structure = Struc(ase2struc(unitcell))
return structure
def make_struc(alat):
"""
Creates the crystal structure using ASE.
:param alat: Lattice parameter in angstrom
:return: structure object converted from ase
"""
fecell = bulk('Fe', 'hcp', a=alat)
# check how your cell looks like
#write('s.cif', gecell)
print(fecell, fecell.get_atomic_numbers())
fecell.set_atomic_numbers([26, 27])
structure = Struc(ase2struc(fecell))
print(structure.species)
return structure
def make_struc(alat, displacement=0):
"""
Creates the crystal structure using ASE.
:param alat: Lattice parameter in angstrom
:return: structure object converted from ase
"""
lattice = alat * numpy.identity(3)
symbols = ['Pb', 'Ti', 'O', 'O', 'O']
sc_pos = [[0,0,0], [0.5,0.5,0.5 + displacement], [0,0.5,0.5], [0.5,0,0.5], [0.5,0.5,0]]
perov = Atoms(symbols=symbols, scaled_positions=sc_pos, cell=lattice)
# check how your cell looks like
# write('s.cif', perov)
structure = Struc(ase2struc(perov))
return structure
def make_struc(size):
"""
Creates the crystal structure using ASE.
:param size: supercell multiplier
:return: structure object converted from ase
"""
alat = 4.10
unitcell = crystal('Al', [(0, 0, 0)],
spacegroup=225,
cellpar=[alat, alat, alat, 90, 90, 90])
multiplier = numpy.identity(3) * size
supercell = make_supercell(unitcell, multiplier)
structure = Struc(ase2struc(supercell))
return structure
def make_struc(alat):
"""
Creates the crystal structure using ASE.
:param alat: Lattice parameter in angstrom
:return: structure object converted from ase
"""
# set primitive_cell=False if you want to create a simple cubic unit cell with 8 atoms
gecell = crystal('Ge', [(0, 0, 0)],
spacegroup=227,
cellpar=[alat, alat, alat, 90, 90, 90],
primitive_cell=True)
# check how your cell looks like
# write('s.cif', gecell)
structure = Struc(ase2struc(gecell))
return structure
def make_struc(size):
"""
Creates the crystal structure using ASE.
:param size: supercell multiplier
:return: structure object converted from ase
"""
alat = 5.1
lattice = alat * numpy.identity(3)
symbols = ['Ag', 'I', 'Ag', 'I']
sc_positions = [[1 / 2, 0, 1 / 4], [0, 0, 0], [1, 1 / 2, 3 / 4],
[1 / 2, 1 / 2, 1 / 2]]
unitcell = Atoms(symbols=symbols,
scaled_positions=sc_positions,
cell=lattice)
multiplier = numpy.identity(3) * size
supercell = make_supercell(unitcell, multiplier)
structure = Struc(ase2struc(supercell))
return structure
def make_struc(i):
slab_ideal = fcc110('Au', size=(16, 16, 40), a=4.0800000183054, vacuum=i)
#slab_ideal=fcc110('Au',size=(4,8,i), vacuum=20)
write('slab_ideal.struct', slab_ideal)
#slab_ideal.edit()
#natoms_100=(len(slab_100.numbers))
list_z = [
slab_ideal.positions[i][2] for i in range(len(slab_ideal.positions))
]
min_z = min(list_z)
list_x_top_row = []
for i in range(len(slab_ideal.positions)):
if slab_ideal.positions[i][2] == min_z:
list_x_top_row.append(slab_ideal.positions[i][0])
list_x_top_row_concise = list(set(list_x_top_row))
list_x_top_row_concise.sort()
select_list_x = list_x_top_row_concise[
1::2] #this slices list_x_top_row_concise using even index
atoms_to_delete = []
atoms_to_delete_index = []
for i in range(len(slab_ideal.positions)):
if slab_ideal.positions[i][
0] in select_list_x and slab_ideal.positions[i][2] == min_z:
atoms_to_delete.append(slab_ideal.positions[i])
atoms_to_delete_index.append(i)
atoms_to_delete_index.sort()
atoms_to_delete_index.reverse()
#to delete atoms in slab to create the 1*2 missing row reconstruction
for i in atoms_to_delete_index:
slab_ideal.pop(i)
#slab_ideal.edit()
#print('list of atoms is',slab_ideal.positions)
#print('list_x_top_row',list_x_top_row)
#print('list_x_top_row_concise',list_x_top_row_concise)
#print ('min z is',min_z)
#print('select_list_x',select_list_x)
#print('atoms_to_delete',atoms_to_delete)
print('atoms_to_delete_index', atoms_to_delete_index)
natoms_ideal = len(slab_ideal.positions)
print('number of atoms left', natoms_ideal)
struc_ideal = Struc(ase2struc(slab_ideal))
return natoms_ideal, struc_ideal
