def test_map_to_primitive(self):
sc_atoms = read('data/supercell.vasp')
patoms = gen_primitive(name="SrMnO3",
latticeconstant=7.6266083947907566 / 2,
mag_order='FM',
m=3)
ilist, Rlist = map_to_primitive(sc_atoms, patoms)
print(Rlist)
def test():
from pyDFTutils.perovskite.cubic_perovskite import gen_primitive
from pyDFTutils.ase_utils import symbol_number
from ase.io import read
patoms = gen_primitive(name="SrMnO3",
latticeconstant=7.6266083947907566 / 2,
mag_order='FM',
m=3)
syms = list(symbol_number(patoms).keys())
atoms = read('./supercell444/flip_Mn12_-3_-3/POSCAR')
#ilist, Rlist = map_to_primitive(atoms, patoms)
d = OijuFitter(atoms=patoms, sc_atoms=atoms, scell=np.eye(3) * 4, nspin=1)
d.fit(ijdict={
(1, 2): (1, 1, (0, 0, 1)),
(1, 3): (1, 1, (0, 1, 0)),
(1, 5): (1, 1, (1, 0, 0))
},
fname_template=name_template)
d.write_netcdf_scalarij(fname='Oiju_scalarij.nc')
read_Oiju_netcdf(fname='Oiju_scalarij.nc')
def gen_distorted_perovskite(name,
cell=[3.9, 3.9, 3.9],
supercell_matrix=[[1, -1, 0], [1, 1, 0],
[0, 0, 2]],
out_of_phase_rotation=0.0,
in_phase_rotation=0.0,
in_phase_tilting=0.0,
breathing=0.0,
JT_d=0.0,
JT_a=0.0):
atoms = gen_primitive(name=name, mag_order='PM', latticeconstant=3.9)
spos = atoms.get_scaled_positions()
#atoms.set_cell([3.5,3.5,3.9,90,90,90])
atoms.set_cell(cell)
atoms.set_scaled_positions(spos)
#from ase.io import write
#write('cubic_LaMnO3.cif',atoms)
dcell = distorted_cell(atoms, supercell_matrix=supercell_matrix)
eigvec = np.zeros(15)
eig_breathing = np.array(perovskite_mode.R2p)
eig_JT_d = np.array(perovskite_mode.M2)
eig_in_phase_tilting = np.array(perovskite_mode.X5_3)
eig_out_of_phase_rotation_x = np.array(perovskite_mode.R25_1)
eig_out_of_phase_rotation_y = np.array(perovskite_mode.R25_2)
eig_in_phase_rotation_z = np.array(perovskite_mode.M3)
disp_br = dcell._get_displacements(eigvec=eig_breathing,
q=[0.5, 0.5, 0.5],
amplitude=breathing,
argument=0)
#disp2=dcell._get_displacements(eigvec=out_of_phase_rotation,q=[0.5,0.5,0.5],amplitude=0.55,argument=0)
disp_jt = dcell._get_displacements(eigvec=eig_JT_d,
q=[0.5, 0.5, 0.0],
amplitude=JT_d,
argument=0)
disp_tilting = dcell._get_displacements(eigvec=eig_in_phase_tilting,
q=[0.0, 0.0, 0.5],
amplitude=in_phase_tilting,
argument=0)
disp_rotx = dcell._get_displacements(eigvec=eig_out_of_phase_rotation_x,
q=[0.5, 0.5, 0.5],
amplitude=out_of_phase_rotation,
argument=0)
disp_roty = dcell._get_displacements(eigvec=eig_out_of_phase_rotation_y,
q=[0.5, 0.5, 0.5],
amplitude=out_of_phase_rotation,
argument=0)
disp_rotz = dcell._get_displacements(eigvec=eig_in_phase_rotation_z,
q=[0.5, 0.5, 0.0],
amplitude=in_phase_rotation,
argument=0)
#print(out_of_phase_rotation)
#print(disp_rotx)
#print(disp_jt)
#print disp.shape
newcell = dcell._get_cell_with_modulation(disp_jt + disp_rotx + disp_roty +
disp_rotz + disp_br +
disp_tilting)
newcell = Atoms(newcell)
print(spglib.get_spacegroup(newcell))
#vesta_view(newcell)
return newcell
def gen_P21c_perovskite(
name,
cell=[3.9, 3.9, 3.9],
supercell_matrix=[[1, -1, 0], [1, 1, 0], [0, 0, 2]],
modes=dict(
R2_m_O1=0.0, # R2-[O1:c:dsp]A2u(a), O, breathing
R3_m_O1=
0.0, # R3-[O1:c:dsp]A2u(a), O JT inplane-stagger, out-of-plane antiphase
R3_m_O2=
0.0, # R3-[O1:c:dsp]A2u(b), O, out-of-plane-stagger, inplane antiphase, Unusual.
R4_m_A1=0.0, # R4-[Nd1:a:dsp]T1u(a), A , Unusual
R4_m_A2=0.0, # R4-[Nd1:a:dsp]T1u(b), 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
R5_m_O1=0.0, # R5-[O1:c:dsp]Eu(a), O a-
R5_m_O2=0.0, # R5-[O1:c:dsp]Eu(b), O b-
R5_m_O3=0.0, # R5-[O1:c:dsp]Eu(c), O c-
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=0.0, # [Nd1:a:dsp]T1u(a), A , Antiferro mode
#X5_m_A2=0.0, # [Nd1:a:dsp]T1u(b), A , save as above
#X5_m_O1=0.0, # [Nd1:a:dsp]T1u(a), O , Antiferro mode
#X5_m_O2=0.0, # [Nd1:a:dsp]T1u(b), O , same as above
#M2_p_O1=0.0, # M2+[O1:c:dsp]Eu(a), O, In phase rotation c+
Z5_m_A1=0.0, # [Nd1:a:dsp]T1u(a), A , Antiferro mode
Z5_m_A2=0.0, # [Nd1:a:dsp]T1u(b), A , save as above
Z5_m_O1=0.0, # [Nd1:a:dsp]T1u(a), O , Antiferro mode
Z5_m_O2=0.0, # [Nd1:a:dsp]T1u(b), O , same as above
M2_p_O1=0.0, # M2+[O1:c:dsp]Eu(a), O, In phase rotation
M3_p_O1=0.0, # M3+[O1:c:dsp]A2u(a), O, D-type JT inplane stagger
M5_p_O1=0.0, # M5+[O1:c:dsp]Eu(a), O, Out of phase tilting
M5_p_O2=0.0, # M5+[O1:c:dsp]Eu(a), O, Out of phase tilting
M4_p_O1=0.0, # 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=0.0,
G_G4y=0.0,
G_G4z=0.0,
)):
atoms = gen_primitive(name=name, mag_order='PM', latticeconstant=cell[0])
spos = atoms.get_scaled_positions()
atoms.set_cell(cell)
atoms.set_scaled_positions(spos)
dcell = distorted_cell(atoms, supercell_matrix=supercell_matrix)
eigvec = np.zeros(15)
mode_dict = {
'R2_m_O1': perovskite_mode.R2p,
'R3_m_O1': perovskite_mode.
R12p_1, # R3-[O1:c:dsp]A2u(a), O JT inplane-stagger, out-of-plane antiphase
'R3_m_O2': perovskite_mode.
R12p_2, # R3-[O1:c:dsp]A2u(b), O, out-of-plane-stagger, inplane antiphase
'R4_m_A1': perovskite_mode.R15_1, # R4-[Nd1:a:dsp]T1u(a), A
'R4_m_A2': perovskite_mode.R15_2, # R4-[Nd1:a:dsp]T1u(b), A
'R4_m_A3': perovskite_mode.R15_3, # R4-[Nd1:a:dsp]T1u(c), A
'R4_m_O1': perovskite_mode.R15_4, # R4-[O1:c:dsp]Eu(a), O
'R4_m_O2': perovskite_mode.R15_5, # R4-[O1:c:dsp]Eu(b), O
'R4_m_O3': perovskite_mode.R15_6, # R4-[O1:c:dsp]Eu(c), O
'R5_m_O1': perovskite_mode.
R25_1, # R5-[O1:c:dsp]Eu(a), O, out-of-phase rotation a-
'R5_m_O2': perovskite_mode.R25_2, # R5-[O1:c:dsp]Eu(b), O, b-
'R5_m_O3': perovskite_mode.
R25_3, # R5-[O1:c:dsp]Eu(c), O, c-. For Pnma. Do not use.
#'X3_m_A1':perovskite_mode., # X3-[Nd1:a:dsp]T1u(a), What's this..
#'X3_m_O1':perovskite_mode., # X3-[O1:c:dsp]A2u(a)
'Z5_m_A1':
perovskite_mode.Z5p_1, # [Nd1:a:dsp]T1u(a), A , Antiferro mode
'Z5_m_A2':
perovskite_mode.Z5p_2, # [Nd1:a:dsp]T1u(b), A , save as above
'Z5_m_O1':
perovskite_mode.Z5p_3, # [Nd1:a:dsp]T1u(b), O , same as above
'Z5_m_O2':
perovskite_mode.Z5p_4, # [Nd1:a:dsp]T1u(b), O , same as above
'M2_p_O1':
perovskite_mode.M3, # M2+[O1:c:dsp]Eu(a), O, In phase rotation
'M3_p_O1': perovskite_mode.
M2, # M3+[O1:c:dsp]A2u(a), O, D-type JT inplane stagger
'M5_p_O1':
perovskite_mode.M5_1, # M5+[O1:c:dsp]Eu(a), O, Out of phase tilting
'M5_p_O2': perovskite_mode.
M5_2, # M5+[O1:c:dsp]Eu(b), O, Out of phase tilting, -above
'M4_p_O1': perovskite_mode.
M4, # M4+[O1:c:dsp]A2u(a), O, in-plane-breathing (not in P21/c)
}
# add Gamma modes to mode_dict
Gamma_mode_dict = Gamma_modes(atoms.get_chemical_symbols())
mode_dict.update(Gamma_mode_dict)
mode_disps = {}
qdict = {
'G': [0, 0, 0],
#'X':[0,0.0,0.5],
'M': [0.5, 0.5, 0],
'R': [0.5, 0.5, 0.5],
'Z': [0.0, 0.0, 0.5]
}
disps = 0.0 #np.zeros(3,dtype='complex128')
for name, amp in modes.items():
eigvec = np.array(mode_dict[name])
disp = dcell._get_displacements(eigvec=eigvec,
q=qdict[name[0]],
amplitude=amp,
argument=0)
disps += disp
newcell = dcell._get_cell_with_modulation(disps)
newcell = Atoms(newcell)
print(spglib.get_spacegroup(newcell))
#vesta_view(newcell)
return newcell
def gen_RNiO3(a=3.709, c=3.709, rot_R=1.0, rot_M=1.0, jt=0.0, br=0.00):
atoms = gen_primitive(name='YNiO3', mag_order='PM', latticeconstant=3.7094)
spos = atoms.get_scaled_positions()
atoms.set_cell([a, a, c, 90, 90, 90])
atoms.set_scaled_positions(spos)
from ase.io import write
dcell = distorted_cell(atoms, supercell_matrix=np.eye(3) * 2)
dcell = distorted_cell(atoms,
supercell_matrix=[[1, -1, 0], [1, 1, 0], [0, 0, 2]])
eigvec = np.zeros(15)
eigvec[6] = 1
eigvec[10] = 1
breathing = np.array(perovskite_mode.R2p)
JT_d = np.array(perovskite_mode.M2)
in_phase_tilting_A1 = np.array(perovskite_mode.X5p_1)
in_phase_tilting_A2 = np.array(perovskite_mode.X5p_2)
in_phase_tilting_O1 = np.array(perovskite_mode.X5p_3)
in_phase_tilting_O2 = np.array(perovskite_mode.X5p_4)
in_phase_rotation = np.array(perovskite_mode.M3)
out_of_phase_rotation_x = np.array(perovskite_mode.R25_1)
out_of_phase_rotation_y = np.array(perovskite_mode.R25_2)
# R2- breathing 0.1
disp_br = dcell._get_displacements(eigvec=breathing,
q=[0.5, 0.5, 0.5],
amplitude=br,
argument=0)
#disp2=dcell._get_displacements(eigvec=out_of_phase_rotation,q=[0.5,0.5,0.5],amplitude=0.55,argument=0)
# M3+ JT 0.1
disp_jt = dcell._get_displacements(eigvec=JT_d,
q=[0.5, 0.5, 0.0],
amplitude=jt,
argument=0)
#disp4=dcell._get_displacements(eigvec=in_phase_tilting,q=[0.0,0.5,0.0],amplitude=0.5,argument=0)
# R5- rotation out 1.07
disp_rotx = dcell._get_displacements(eigvec=out_of_phase_rotation_x,
q=[0.5, 0.5, 0.5],
amplitude=1.07 * rot_R,
argument=0)
disp_roty = dcell._get_displacements(eigvec=out_of_phase_rotation_y,
q=[0.5, 0.5, 0.5],
amplitude=-1.07 * rot_R,
argument=0)
# M2+
disp_rot_zin = dcell._get_displacements(eigvec=in_phase_rotation,
q=[0.5, 0.5, 0.0],
amplitude=0.525 * 2 * rot_M,
argument=0)
#X5-
disp_tilting_A1 = dcell._get_displacements(eigvec=in_phase_tilting_A1,
q=[0.0, 0.0, 0.5],
amplitude=-0.485 * 2,
argument=0)
#print disp_tilting_A1
disp_tilting_A2 = dcell._get_displacements(eigvec=in_phase_tilting_A2,
q=[0.0, 0.0, 0.5],
amplitude=0.485 * 2,
argument=0)
#print disp_tilting_A2
disp_tilting_O1 = dcell._get_displacements(eigvec=in_phase_tilting_O1,
q=[0.0, 0.5, 0.0],
amplitude=-0.168 * 2,
argument=0)
disp_tilting_O2 = dcell._get_displacements(eigvec=in_phase_tilting_O2,
q=[0.0, 0.5, 0.0],
amplitude=0.168 * 2,
argument=0)
#print disp.shape
newcell = dcell._get_cell_with_modulation(
disp_rotx + disp_roty + disp_rot_zin + disp_br + disp_jt
) # +disp_tilting_A1)#+disp_tilting_A2)#+disp_tilting_O1+disp_tilting_O2)
print(spglib.get_spacegroup(newcell))
#vesta_view(newcell)
return newcell