def POSCAR_writer(self,fname="/POSCAR"):
vac = 15 # vacuum spacing
c = vac + np.sum(self.dz) + np.sum(self.zsep)
c = self.nlayers * 6 + 10
a0 = np.mean(self.a0) # let the combined lattice constant be the averaged value
A0 = [[1*a0, 0, 0],
[-0.5*a0, sqrt(3)/2*a0, 0],
[0, 0, c]]
# relax the atomic positions in the z direction
relax = [[False, False, True] for x in range(self.nlayers*3)]
# create atomic positions for all layers in Cartesian coordinate
coords = np.zeros([self.nlayers*3,3])
z_here = 0
for l in range(self.nlayers):
relax[l*3][2]=False # do not relax the z position of the metal
z_here = z_here + self.dz[l]
if l > 0:
z_here = z_here + self.zsep[l]
if self.alignment[l] == 0: # 0 deg.
coords_here = np.array([[0, 0, 0],
[1./3, 2./3, -self.zsep[l]],
[1./3, 2./3, self.zsep[l]]])
else: # 180 deg.
coords_here = [[1./3, 2./3, 0],
[0, 0, -self.zsep[l]],
[0, 0, self.zsep[l]]]
coords[l*3:(l+1)*3][:] = coords_here
coords[l*3:(l+1)*3,2] += z_here
coords[l*3:(l+1)*3,2] = coords[l*3:(l+1)*3,2] / c
for i in range(3):
if coords[l*3+i,2] < 0:
coords[l*3+i,2] += 1
# For 0 deg. stacking, the AB stacking is the stable stacking config.
# Need to shift by (1/3,1/3,0) for every
for l in range(self.nlayers):
if self.alignment[l] == 0:
coords[l*3:,0] += 1./3
coords[l*3:,1] -= 1./3
layers = struct.Structure(A0,self.mat,coords,coords_are_cartesian=False)
out = inputs.Poscar(layers)
out.selective_dynamics=relax
out.write_file(os.getcwd()+fname)
def export_dict(self, format="poscar", filename="./POSCAR"):
"""
Export edited structure.
Arguments
---------
fortmat: str
Format of export data (default: "poscar").
filename: str
File name (directory) of exported file (default: "./POSCAR").
"""
struct = pymatgen.Structure.from_dict(self.struct_dict)
if format is "poscar":
with open(filename, mode="w") as file:
file.writelines(str(vasp_inputs.Poscar(struct)))
else:
raise UndefinedFormatError(format)
def __init__(self,
struct,
format="structure",
filename="undefined",
atom_num_limit=0,
output_original_struct_if_modified="True",
output_format="poscar",
output_path="./"):
"""
Arguments
---------
struct: (Structure data)
Original structure data, which can be pymatgen.Structure,
poscar, cif, or any other what pymatgen can handle.
format: str
Format of read data.
filename: str
File name of read data.
atom_num_limit: int
The lower limit of the number of atoms in the unit cell.
output_original_struct_if_modified: bool
If this flag is True, output original structure
if it is modified in make_supercell_enough_large method.
output_format: str
Format of output data of modified original structure.
output_path: str
Path to the output file.
"""
if format is "structure":
self.struct = struct
else:
self.struct = pymatgen.Structure.from_str(open(struct).read(),
fmt=format)
self.filename = filename
struct_if_modified = self.make_supercell_enough_large(atom_num_limit)
if output_original_struct_if_modified and struct_if_modified:
if output_format is "poscar":
with open(output_path + "POSCAR_" + filename + "_modified",
mode="w") as file:
file.writelines(str(vasp_inputs.Poscar(self.struct)))
else:
raise UndefinedFormatError(format)
self.struct_dict = self.struct.as_dict()
cell = Structure(
lattice=np.array([[lattice_parameter[i, 9], 0, 0],
[0, lattice_parameter[i, 10], 0],
[0, 0, lattice_parameter[i, 11]]]) * j,
species=[
'Rh', 'Rh', 'Rh', 'Rh', 'Rh', 'Rh', 'Rh', 'Rh', 'Fe', 'Fe',
'Fe', 'Fe', z_atoms[i], z_atoms[i], z_atoms[i], z_atoms[i]
],
coords=[(0.25, 0.25, 0.25), (0.75, 0.25, 0.75), (0.25, 0.75, 0.75),
(0.75, 0.75, 0.25), (0.5, 0.5, 0.0), (0.0, 0.0, 0.0),
(0.5, 0.0, 0.5), (0.0, 0.5, 0.5), (0.5, 0.0, 0.0),
(0.0, 0.5, 0.0), (0.0, 0.0, 0.5), (0.5, 0.5, 0.5),
(0.25, 0.75, 0.25), (0.75, 0.25, 0.25), (0.25, 0.25, 0.75),
(0.75, 0.75, 0.75)],
)
poscar = inputs.Poscar(cell)
potcar = inputs.Potcar(symbols=['Rh_pv', 'Fe', z_potentials[i]],
functional="PBE_54")
kpoints = inputs.Kpoints(kpts=[[7, 7, 7]])
incar = inputs.Incar({
'LCHARG': True,
'LWAVE': True,
'ICHARG': 1,
'IBRION': 2,
'ISIF': 3,
'POTIM': 0.1,
'PREC': 'Accurate',
'ENCUT': 460,
slabgen = SlabGenerator(structure, (0, 0, 1),
size * structure.lattice.c,
15,
center_slab=True)
slabs = slabgen.get_slabs(symmetrize=True)
print("Number of slabs:", len(slabs))
for i in range(len(slabs)):
if not os.path.isdir('slab/ION/regular/{}/{:.0f}/{}'.format(
z_atoms[k], size, i)):
os.makedirs('slab/ION/regular/{}/{:.0f}/{}'.format(
z_atoms[k], size, i))
poscar = inputs.Poscar(slabs[i], sort_structure=True)
paw = [z_potentials[s.symbol] for s in slabs[i].types_of_species]
potcar = inputs.Potcar(symbols=paw, functional="PBE_54")
kpoints = inputs.Kpoints.automatic_density(slabs[i], 5000)
incar = inputs.Incar({
'LCHARG': True,
'LWAVE': True,
'ICHARG': 1,
'IBRION': 2,
'ISIF': 2,
'POTIM': 0.1,
'PREC': 'Accurate',
'ENCUT': 460,
for i in range(len(z_atoms)):
for key in magmoms.keys():
for j in np.arange(0.8, 1.425, 0.025):
if not os.path.isdir('ca/regular/{}/{}/{:.3f}'.format(z_atoms[i], key, j)):
os.makedirs('ca/regular/{}/{}/{:.3f}'.format(z_atoms[i], key, j))
structure = Structure.from_file('{}/ION/isif7/regular/{}/{}/CONTCAR'.format(os.getcwd(), z_atoms[i], key))
D = np.array([[(j)**(-1.0/3.0), 0, 0],
[0, (j)**(-1.0/3.0), 0],
[0, 0, (j)**(2.0/3.0)]])
structure.lattice = np.dot(structure.lattice.matrix, D)
poscar = inputs.Poscar(structure)
potcar = inputs.Potcar(symbols=['Rh_pv', 'Fe', z_potentials[i]], functional="PBE_54")
kpoints = inputs.Kpoints(kpts = [[7, 7, 7]])
incar = inputs.Incar({'LCHARG' : True,
'LWAVE' : True,
'ICHARG' : 1,
'IBRION' : 2,
'ISIF' : 2,
'POTIM' : 0.1,
'PREC' : 'Accurate',
'ENCUT' : 460,
'EDIFF' : 1e-7,
'EDIFFG' : 1e-3,
slabgen = SlabGenerator(structure, (0, 0, 1),
size * structure.lattice.c,
10,
center_slab=True)
slabs = slabgen.get_slabs(symmetrize=True)
print("Number of slabs:", len(slabs))
for i in range(len(slabs)):
if not os.path.isdir('slab/test_distance/regular/Al/{:.0f}/{}'.format(
size, i)):
os.makedirs('slab/test_distance/regular/Al/{:.0f}/{}'.format(
size, i))
poscar = inputs.Poscar(slabs[i])
paw = [z_potentials[s.symbol] for s in slabs[i].types_of_species]
potcar = inputs.Potcar(symbols=paw, functional="PBE_54")
kpoints = inputs.Kpoints.automatic_density(slabs[i], 5000)
incar = inputs.Incar({
'LCHARG': True,
'LWAVE': True,
'ICHARG': 1,
'IBRION': 2,
'ISIF': 2,
'POTIM': 0.1,
'PREC': 'Accurate',
'ENCUT': 460,
def relax_off(self,fname="./POSCAR-unit"): # turn off selective dynamics
relax_struct=struct.Structure.from_file(fname)
relax_poscar=inputs.Poscar(relax_struct,selective_dynamics=None)
relax = [[False, False, False] for x in range(self.nlayers*3)]
relax_poscar.write_file(fname)