def test():
#atoms=gen_pnma('LaMnO3',out_of_phase_rotation=1.5)
#atoms=gen_pnma('LaMnO3',JT_d=0.2)
#atoms=gen_pnma('LaMnO3',in_phase_tilting=0.6)
atoms = gen_distorted_perovskite('LaMnO3',
out_of_phase_rotation=0.0,
JT_d=0.0,
in_phase_tilting=0.9,
breathing=0.0)
vesta_view(atoms)
def test():
atoms=gen_P21c_perovskite(name='YNiO3', cell=[3.7,3.7,3.7],
supercell_matrix=[[1, -1, 0], [1, 1, 0], [0, 0, 2]],
modes=dict(
#R2_m_O1=0.8, #breathing
#R3_m_O1=1.0,
#R3_m_O2=1.0, # R3-[O1:c:dsp]A2u(b), O, out-of-plane-stagger, inplane antiphase
#R5_m_O1=1.2, # R5-[O1:c:dsp]Eu(a), O a-
#R5_m_O2=1.2, # R5-[O1:c:dsp]Eu(a), O b-
#R5_m_O3=1.0, # R5-[O1:c:dsp]Eu(c), O c-
#X5_m_A1=1.0, # [Nd1:a:dsp]T1u(a), A , Antiferro mode
#R4_m_A1=0.5, # R4-[Nd1:a:dsp]T1u(a), A , Antipolar mode in Pnma
#R4_m_A2=0.5, # R4-[Nd1:a:dsp]T1u(b), A, Antipolar mode in Pnma
R4_m_A3=0.0, # R4-[Nd1:a:dsp]T1u(c), A, Unusual
#R4_m_A3=0.0, # R4-[Nd1:a:dsp]T1u(c), A, Unusual
#R4_m_O1=0.0, # R4-[O1:c:dsp]Eu(a), O, Unusual
#R4_m_O2=0.0, # R4-[O1:c:dsp]Eu(b), O, Unusual
#R4_m_O3=0.0, # R4-[O1:c:dsp]Eu(c), O, Unusual
#M2_p_O1=1.2, # M2+[O1:c:dsp]Eu(a), O, In phase rotation c+
#M3_p_O1=0.1, # M3+[O1:c:dsp]A2u(a), O, D-type JT inplane stagger
#M5_p_O1=1.0, # M5+[O1:c:dsp]Eu(a), O, Out of phase tilting
#M4_p_O1=1.0 , # M4+[O1:c:dsp]A2u(a), O, in-plane-breathing (not in P21/c)
G_Ax=0.0,
G_Ay=0.0,
G_Az=0.0,
G_Sx=0.0,
G_Sy=0.0,
G_Sz=0.0,
G_Axex=0.0,
G_Axey=0.0,
G_Axez=0.0,
G_Lx=0.0,
G_Ly=0.0,
G_Lz=0.0,
#G_G4x=0.1,
#G_G4y=0.1,
#G_G4z=0.1,
)
)
#write('P4mm.vasp', atoms, vasp5=True)
vesta_view(atoms)
def test_distortion():
amp=np.random.random(6)
atoms=gen_P21c_perovskite(
'NdNiO3',
cell=[3.785415]*3,
supercell_matrix=[[1, -1, 0], [1, 1, 0], [0, 0, 2]],
modes=dict(
#R2_m_O1=amp[0]*0.1, # R2-[O1:c:dsp]A2u(a), O, breathing
#R3_m_O1=-0.0023, # R3-[O1:c:dsp]A2u(a), O JT inplane-stagger, out-of-plane antiphase
#R3_m_O2=amp[1], # R3-[O1:c:dsp]A2u(b), O, out-of-plane-stagger, inplane antiphase
#R4_m_A1=amp[2], # R4-[Nd1:a:dsp]T1u(a), A
#R4_m_A2=0.0, # R4-[Nd1:a:dsp]T1u(b), A
#R4_m_A3=0.0, # R4-[Nd1:a:dsp]T1u(c), A
#R4_m_O1=0.0, # R4-[O1:c:dsp]Eu(a), O
#R4_m_O2=0.0, # R4-[O1:c:dsp]Eu(b), O
#R4_m_O3=0.0, # R4-[O1:c:dsp]Eu(c), O
R5_m_O1=0.81457, # R5-[O1:c:dsp]Eu(a), O a-
R5_m_O2=0.81457, # R5-[O1:c:dsp]Eu(b), O b-
R5_m_O3=0.81457, # R5-[O1:c:dsp]Eu(c), O c- (not in Pnma)
#X3_m_A1=0.0, # X3-[Nd1:a:dsp]T1u(a), What's this..
#X3_m_O1=0.0, # X3-[O1:c:dsp]A2u(a)
#X5_m_A1=0.3219, # [Nd1:a:dsp]T1u(a), A , Antiferro mode
#Z5_m_A2=0.3219, # [Nd1:a:dsp]T1u(b), A , save as above
#X5_m_O1=-0.06299, # [Nd1:a:dsp]T1u(a), O , Antiferro mode
#Z5_m_O2=-0.06299, # [Nd1:a:dsp]T1u(b), O , same as above
#M2_p_O1=0.739, # M2+[O1:c:dsp]Eu(a), O, In phase rotation
#M3_p_O1=0.00412, # M3+[O1:c:dsp]A2u(a), O, D-type JT inplane stagger
#M5_p_O1=0.00015, # M5+[O1:c:dsp]Eu(a), O, Out of phase tilting
#M5_p_O2=-0.00015, # M5+[O1:c:dsp]Eu(b), O, Out of phase tilting, -above
#M4_p_O1=0.0 , # M4+[O1:c:dsp]A2u(a), O, in-plane-breathing (not in P21/c)
)
)
vesta_view(atoms)
#write("NNO_br%s.vasp"%br,atoms, vasp5=True)
return amp, atoms
"""
if name is not None:
symbols=string2symbols(name)
A, B, O, _, _ = symbols
atoms = PerovskiteCubic([A, B, O], latticeconstant=latticeconstant)
direction_dict = {
'A': ([1, 0, 0], [0, 1, 0], [0, 0, 2]),
'C': ([1, -1, 0], [1, 1, 0], [0, 0, 1]),
'G': ([0, 1, 1], [1, 0, 1], [1, 1, 0]),
'FM': np.eye(3),
}
size_dict = {'A': (1, 1, 2), 'C': (1, 1, 1), 'G': (1, 1, 1)}
A, B, O = atoms.get_chemical_symbols()[0:3]
if mag_order == 'PM':
atoms = atoms
elif mag_order == 'FM':
atoms = atoms
atoms = set_element_mag(atoms, B, [m])
else:
atoms.translate([0.045] * 3)
atoms = normalize(atoms)
atoms = make_supercell(atoms, direction_dict[mag_order])
atoms.translate([-0.045] * 3)
atoms = set_element_mag(atoms, B, [m, -m])
return atoms
if __name__ == '__main__':
atoms = gen_primitive(name='LaMnO3',mag_order='C')
vesta_view(atoms)
def test():
mylwf = LWF.load_nc(fname='./Downfolded_hr.nc')
atoms = lwf_to_atoms(mylwf,
scmat=np.diag([5, 5, 5]),
amplist=[[(0, 0, 0), 0, 1], [(0, 0, 0), 1, 1]])
vesta_view(atoms)
#!/usr/bin/env python
from pyDFTutils.perovskite.frozen_mode import gen_distorted_perovskite
from pyDFTutils.ase_utils import vesta_view
from pyDFTutils.ase_utils import substitute_atoms
from ase.io import write
def gen():
atoms = gen_distorted_perovskite(
name='NdNiO3',
cell=[3.79, 3.79, 3.79],
#supercell_matrix=[[1, -1, 0], [1, 1, -2], [1, 1, 1]],
#supercell_matrix=[[1, 1, 1.0], [-1, 1, 1.0], [0, -2, 1.0]],
supercell_matrix=[[1, 1, 2.0], [-1, 1, 2.0], [0, -2, 2.0]],
out_of_phase_rotation=0.4,
in_phase_rotation=0.3,
#in_phase_tilting=0.3,
#JT_a=1.35,
#JT_d=1.05,
#breathing=0.5
)
#atom=substitute_atoms(atoms,['Ni5','Ni10'],['Ga','Ga'])
return atoms
write('P21c.cif', gen())
vesta_view(gen())