def findspg(atoms):
spg0 = spglib.get_spacegroup(atoms, symprec=0.1)
if spg0:
spg1 = spg0.split()
spg = [str(spg1[0]), int(spg1[1][1:-1])]
else:
spg = []
# print spg0, spg
return spg
def test():
myatoms = gen_STO()
print(find_sym(myatoms))
#print myatoms.get_chemical_symbols()
#natoms,d=ref_atoms_mag(myatoms)
##print ref_atoms_mag(myatoms)[0].get_chemical_symbols()
#old_atoms=rev_ref_atoms(natoms,d)
#print old_atoms.get_chemical_symbols()
#print get_prim_atoms(myatoms)
new_atoms = find_primitive_mag(myatoms)
#print new_atoms.get_chemical_symbols()
print(new_atoms.get_cell())
print(new_atoms.get_scaled_positions())
print(new_atoms.get_volume())
print(spglib.get_spacegroup(new_atoms))
#write('POSCAR',new_atoms,sort=True,vasp5=True)
natoms = normalize(new_atoms)
print(natoms.get_positions())
print(natoms.get_volume())
print(cell_to_cellpar(natoms.get_cell()))
def get_spacegroup(filename=False, format=False):
if filename:
pass
elif os.path.isfile('geometry.in'):
filename='geometry.in'
elif os.path.isfile('POSCAR'):
filename='POSCAR'
else:
raise Exception('No input file!')
if format:
atoms = ase.io.read(filename, format=format)
else:
atoms = ase.io.read(filename)
print("| Threshold / Å | Space group |")
print("|---------------|-------------------|")
for threshold in (1e-5, 1e-4, 5e-4, 1e-3, 5e-3, 1e-2, 5e-2, 1e-1):
print("| {0:0.5f} | {1: <16} |".format(
threshold, spglib.get_spacegroup(atoms, symprec=threshold)))
def find_sym(atoms):
return spglib.get_spacegroup(atoms, symprec=5e-4)
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 get_primitive(input_file='POSCAR',
input_format=None,
output_file=None,
output_format=None,
threshold=1e-5,
angle_tolerance=-1.,
verbose=False):
if output_file is None:
verbose = True
if verbose:
def vprint(*args):
for arg in args:
print(arg,)
print("")
else:
def vprint(*args):
pass
try:
if input_format is None:
A = ase.io.read(input_file)
else:
A = ase.io.read(input_file, format=input_format)
except IOError as e:
raise Exception("I/O error({0}): {1}".format(e.errno, e.strerror))
vprint(
"# Space group: ",
str(
spglib.get_spacegroup(
A, symprec=threshold, angle_tolerance=angle_tolerance)),
'\n')
cell, positions, atomic_numbers = spglib.find_primitive(
A, symprec=threshold, angle_tolerance=angle_tolerance)
if positions is None:
print("This space group doesn't have a more primitive unit cell.")
else:
vprint("Primitive cell vectors:")
vprint(cell, '\n')
vprint("Atomic positions and proton numbers:")
for position, number in zip(positions, atomic_numbers):
vprint(position, '\t', number)
if output_file is None:
pass
else:
atoms = ase.Atoms(
scaled_positions=positions,
cell=cell,
numbers=atomic_numbers,
pbc=True)
if output_format is None:
try:
atoms.write(output_file, vasp5=True)
except TypeError:
atoms.write(output_file)
elif output_format is "vasp":
atoms.write(output_file, format="vasp", vasp5=True)
else:
atoms.write(output_file, format=output_format)
def get_primitive(input_file='POSCAR',
input_format=None,
output_file=None,
output_format=None,
threshold=1e-5,
angle_tolerance=-1.,
verbose=False):
if output_file is None:
verbose = True
if verbose:
def vprint(*args):
for arg in args:
print(arg, )
print("")
else:
def vprint(*args):
pass
try:
if input_format is None:
A = ase.io.read(input_file)
else:
A = ase.io.read(input_file, format=input_format)
except IOError as e:
raise Exception("I/O error({0}): {1}".format(e.errno, e.strerror))
vprint(
"# Space group: ",
str(
spglib.get_spacegroup(A,
symprec=threshold,
angle_tolerance=angle_tolerance)), '\n')
cell, positions, atomic_numbers = spglib.find_primitive(
A, symprec=threshold, angle_tolerance=angle_tolerance)
if positions is None:
print("This space group doesn't have a more primitive unit cell.")
else:
vprint("Primitive cell vectors:")
vprint(cell, '\n')
vprint("Atomic positions and proton numbers:")
for position, number in zip(positions, atomic_numbers):
vprint(position, '\t', number)
if output_file is None:
pass
else:
atoms = ase.Atoms(scaled_positions=positions,
cell=cell,
numbers=atomic_numbers,
pbc=True)
if output_format is None:
try:
atoms.write(output_file, vasp5=True)
except TypeError:
atoms.write(output_file)
elif output_format is "vasp":
atoms.write(output_file, format="vasp", vasp5=True)
else:
atoms.write(output_file, format=output_format)
def view_spacegroup(filename='POSCAR', symprec=1e-3):
atoms = read(filename)
print("SPACEGROUP: %s" % spglib.get_spacegroup(atoms, symprec=symprec))
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
def read_DDB(self,
fname=None,
do_label=True,
workdir=None,
phonon_output_dipdip='phonon_band_dipdip.png',
phonon_output_nodipdip='phonon_band_nodipdip.png'):
"""
read phonon related properties from DDB file.
"""
self.has_phonon = True
ddb = abiopen(fname)
self.ddb_header = ddb.header
self.atoms = ddb.structure.to_ase_atoms()
self.natoms = len(self.atoms)
self.cellpar = self.atoms.get_cell_lengths_and_angles()
self.cell = self.atoms.get_cell().flatten()
self.masses = self.atoms.get_masses()
self.scaled_positions = self.atoms.get_scaled_positions()
self.chemical_symbols = self.atoms.get_chemical_symbols()
self.spgroup_name = spglib.get_spacegroup(self.atoms, symprec=1e-4)
self.ixc = self.ddb_header['ixc']
self.XC = ixc_to_xc(self.ixc)
self.ispin = self.ddb_header['nsppol']
self.spinat = self.ddb_header['spinat']
self.nband = self.ddb_header['nband']
self.ecut = self.ddb_header['ecut']
self.tsmear = self.ddb_header['tsmear']
self.usepaw = self.ddb_header['usepaw']
self.pawecutdg = self.ddb_header['tsmear']
self.nsppol = self.ddb_header['nsppol']
self.nspden = self.ddb_header['nspden']
self.species = [
chemical_symbols[int(i)] for i in self.ddb_header['znucl']
]
self.zion = [int(x) for x in self.ddb_header['zion']]
self.znucl = [int(x) for x in self.ddb_header['znucl']]
emacror, becsr = ddb.anaget_emacro_and_becs()
emacro = emacror[0].cartesian_tensor
becs_array = becsr.values
becs = {}
for i, bec in enumerate(becs_array):
becs[str(i)] = bec
nqpts = ddb._guess_ngqpt()
qpts = tuple(ddb.qpoints.frac_coords)
self.emacro = emacro
self.becs = becs
self.nqpts = nqpts
self.qpts = qpts
for qpt in qpts:
qpt = tuple(qpt)
m = ddb.anaget_phmodes_at_qpoint(qpt)
#self.results['phonon'][qpt]['frequencies'] = m.phfreqs
#self.results['phonon'][qpt][
# 'eigen_displacements'] = m.phdispl_cart
qpoints, evals, evecs, edisps = self.phonon_band(
ddb,
lo_to_splitting=False,
phonon_output_dipdip=phonon_output_dipdip,
phonon_output_nodipdip=phonon_output_nodipdip)
#for i in range(15):
# print(evecs[0, :, i])
self.special_qpts = {
'X': (0, 0.5, 0.0),
'M': (0.5, 0.5, 0),
'R': (0.5, 0.5, 0.5)
}
zb_modes = self.label_zone_boundary_all(qpoints,
evals,
evecs,
label=do_label)
for qname in self.special_qpts:
self.phonon_mode_freqs[qname] = zb_modes[qname][0]
self.phonon_mode_names[qname] = zb_modes[qname][1]
self.phonon_mode_evecs[qname] = zb_modes[qname][2]
Gmodes = self.label_Gamma_all(qpoints, evals, evecs, label=do_label)
self.phonon_mode_freqs['Gamma'] = Gmodes[0]
self.phonon_mode_names['Gamma'] = Gmodes[1]
self.phonon_mode_evecs['Gamma'] = Gmodes[2]
#!/usr/bin/env python
import ase.io.vasp as io
from spglib import spglib
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-f",
"--file",
action="store",
type="string",
dest="file",
default="POSCAR",
help="Path to input file [default: ./POSCAR]")
parser.add_option("-p",
"--prec",
action="store",
type="float",
dest="prec",
default=0.001,
help="Precision for symmetry test [default: 0.001]")
(options, args) = parser.parse_args()
bulk = io.read_vasp(options.file)
spacegroup = spglib.get_spacegroup(bulk, symprec=options.prec)
print "Spacegroup information."
print "-----------------------"
print spacegroup
print "-----------------------"
