def test_magmom(convcell_cr: PhonopyAtoms):
"""Test symmetry search with hmagnetic moments."""
symprec = 1e-5
symmetry_nonspin = Symmetry(convcell_cr, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(symmetry_nonspin.symmetry_operations["rotations"])
spin = [1, -1]
cell_withspin = convcell_cr.copy()
cell_withspin.magnetic_moments = spin
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(symmetry_withspin.symmetry_operations["rotations"])
broken_spin = [1, -2]
cell_brokenspin = convcell_cr.copy()
cell_brokenspin = convcell_cr.copy()
cell_brokenspin.magnetic_moments = broken_spin
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.symmetry_operations["rotations"])
assert (atom_map_nonspin == atom_map_withspin).all()
assert (atom_map_nonspin != atom_map_brokenspin).any()
assert len_sym_nonspin == len_sym_withspin
assert len_sym_nonspin != len_sym_brokenspin
def test_magmom(self):
symprec = 1e-5
cell = read_cell_yaml(os.path.join(data_dir, "Cr.yaml"))
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
self.assertTrue((atom_map_nonspin == atom_map_withspin).all())
self.assertFalse((atom_map_nonspin == atom_map_brokenspin).all())
self.assertTrue(len_sym_nonspin == len_sym_withspin)
self.assertFalse(len_sym_nonspin == len_sym_brokenspin)
def test_magmom(convcell_cr):
symprec = 1e-5
cell = convcell_cr
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
assert (atom_map_nonspin == atom_map_withspin).all()
assert (atom_map_nonspin != atom_map_brokenspin).any()
assert len_sym_nonspin == len_sym_withspin
assert len_sym_nonspin != len_sym_brokenspin
def test_magmom(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(os.path.join(data_dir,"Cr.yaml"))
symmetry_nonspin = Symmetry(cell, symprec=symprec)
atom_map_nonspin = symmetry_nonspin.get_map_atoms()
len_sym_nonspin = len(
symmetry_nonspin.get_symmetry_operations()['rotations'])
spin = [1, -1]
cell_withspin = cell.copy()
cell_withspin.set_magnetic_moments(spin)
symmetry_withspin = Symmetry(cell_withspin, symprec=symprec)
atom_map_withspin = symmetry_withspin.get_map_atoms()
len_sym_withspin = len(
symmetry_withspin.get_symmetry_operations()['rotations'])
broken_spin = [1, -2]
cell_brokenspin = cell.copy()
cell_brokenspin = cell.copy()
cell_brokenspin.set_magnetic_moments(broken_spin)
symmetry_brokenspin = Symmetry(cell_brokenspin, symprec=symprec)
atom_map_brokenspin = symmetry_brokenspin.get_map_atoms()
len_sym_brokenspin = len(
symmetry_brokenspin.get_symmetry_operations()['rotations'])
self.assertTrue((atom_map_nonspin == atom_map_withspin).all())
self.assertFalse((atom_map_nonspin == atom_map_brokenspin).all())
self.assertTrue(len_sym_nonspin == len_sym_withspin)
self.assertFalse(len_sym_nonspin == len_sym_brokenspin)
def _distribute_forces(supercell, disp, forces, filename, symprec):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
symbols = supercell.get_chemical_symbols()
positions = supercell.get_positions()
positions[disp[0]] += disp[1]
cell = Atoms(cell=lattice, positions=positions, symbols=symbols, pbc=True)
symmetry = Symmetry(cell, symprec)
independent_atoms = symmetry.get_independent_atoms()
# Rotation matrices in Cartesian
rotations = []
for r in symmetry.get_symmetry_operations()["rotations"]:
rotations.append(similarity_transformation(lattice.T, r))
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
atoms_in_dot_scf = _get_independent_atoms_in_dot_scf(filename)
if len(forces) != len(atoms_in_dot_scf):
print("%s does not contain necessary information." % filename)
print('Plese check if there are "FGL" lines with')
print('"total forces" are required.')
return False
if len(atoms_in_dot_scf) == natom:
print("It is assumed that there is no symmetrically-equivalent " "atoms in ")
print("'%s' at wien2k calculation." % filename)
force_set = forces
elif len(forces) != len(independent_atoms):
print("Non-equivalent atoms of %s could not be recognized by phonopy." % filename)
return False
else:
# 1. Transform wien2k forces to those on independent atoms
indep_atoms_to_wien2k = []
forces_remap = []
for i, pos_wien2k in enumerate(atoms_in_dot_scf):
for j, pos in enumerate(cell.get_scaled_positions()):
diff = pos_wien2k - pos
diff -= np.rint(diff)
if (abs(diff) < symprec).all():
forces_remap.append(np.dot(rotations[map_operations[j]], forces[i]))
indep_atoms_to_wien2k.append(map_atoms[j])
break
if len(forces_remap) != len(forces):
print("Atomic position mapping between Wien2k and phonopy failed.")
print("If you think this is caused by a bug of phonopy")
print("please report it in the phonopy mainling list.")
return False
# 2. Distribute forces from independent to dependent atoms.
force_set = []
for i in range(natom):
j = indep_atoms_to_wien2k.index(map_atoms[i])
force_set.append(np.dot(rotations[map_operations[i]].T, forces_remap[j]))
return force_set
def _expand_borns(borns, primitive: PhonopyAtoms, prim_symmetry: Symmetry):
# Expand Born effective charges to all atoms in the primitive cell
rotations = prim_symmetry.symmetry_operations["rotations"]
map_operations = prim_symmetry.get_map_operations()
map_atoms = prim_symmetry.get_map_atoms()
for i in range(len(primitive)):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(primitive.cell.T,
rotations[map_operations[i]])
# R_cart^T B R_cart^-T (inverse rotation is required to transform)
borns[i] = similarity_transformation(rot_cartesian.T,
borns[map_atoms[i]])
def get_born_parameters(f, primitive, is_symmetry):
# Read unit conversion factor, damping factor, ...
factors = [float(x) for x in f.readline().split()]
if len(factors) < 1:
print "BORN file format of line 1 is incorrect"
return False
if len(factors) < 2:
factors = factors[0]
# Read dielectric constant
line = f.readline().split()
if not len(line) == 9:
print "BORN file format of line 2 is incorrect"
return False
dielectric = np.reshape([float(x) for x in line], (3, 3))
# Read Born effective charge
symmetry = Symmetry(primitive, is_symmetry=is_symmetry)
independent_atoms = symmetry.get_independent_atoms()
born = np.zeros((primitive.get_number_of_atoms(), 3, 3), dtype=float)
for i in independent_atoms:
line = f.readline().split()
if len(line) == 0:
print "Number of lines for Born effect charge is not enough."
return False
if not len(line) == 9:
print "BORN file format of line %d is incorrect" % (i + 3)
return False
born[i] = np.reshape([float(x) for x in line], (3, 3))
# Expand Born effective charges to all atoms in the primitive cell
rotations = symmetry.get_symmetry_operations()['rotations']
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
for i in range(primitive.get_number_of_atoms()):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(
primitive.get_cell().transpose(), rotations[map_operations[i]])
# R_cart^T B R_cart^-T (inverse rotation is required to transform)
born[i] = similarity_transformation(rot_cartesian.transpose(),
born[map_atoms[i]])
non_anal = {'born': born,
'factor': factors,
'dielectric': dielectric }
return non_anal
def parse_BORN( primitive, filename = "BORN" ):
file = open( filename, 'r' )
# Read unit conversion factor, damping factor, ...
factors = [ float( x ) for x in file.readline().split() ]
if len( factors ) < 1:
print "BORN file format of line 1 is incorrect"
return None
if len( factors ) < 2:
factors.append( Damping_Factor )
# Read dielectric constant
line = file.readline().split()
if 9 < len( line ) or len( line ) < 9:
print "BORN file format of line 2 is incorrect"
return None
dielectric = np.reshape( [ float( x ) for x in line ], ( 3, 3 ) )
# Read Born effective charge
symmetry = Symmetry( primitive )
independent_atoms = symmetry.get_independent_atoms()
born = np.zeros( ( primitive.get_number_of_atoms(), 3, 3 ), dtype=float )
for i in independent_atoms:
line = file.readline().split()
if 9 < len( line ) or len( line ) < 9:
print "BORN file format of line %d is incorrect" % ( i + 3 )
return None
born[ i ] = np.reshape( [ float( x ) for x in line ], ( 3, 3 ) )
# Expand Born effective charges to all atoms in the primitive cell
rotations = symmetry.get_symmetry_operations()['rotations']
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
for i in range( primitive.get_number_of_atoms() ):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(
primitive.get_cell().transpose(), rotations[ map_operations[i] ] )
# R_cart^T B R_cart^-T ( inverse rotation is required to transform )
born[i] = similarity_transformation( rot_cartesian.transpose(),
born[ map_atoms[ i ] ] )
non_anal = {'born': born,
'factor': factors,
'dielectric': dielectric }
return non_anal
def get_born_parameters(f, primitive, is_symmetry):
# Read unit conversion factor, damping factor, ...
factors = [float(x) for x in f.readline().split()]
if len(factors) < 1:
print "BORN file format of line 1 is incorrect"
return False
if len(factors) < 2:
factors = factors[0]
# Read dielectric constant
line = f.readline().split()
if not len(line) == 9:
print "BORN file format of line 2 is incorrect"
return False
dielectric = np.reshape([float(x) for x in line], (3, 3))
# Read Born effective charge
symmetry = Symmetry(primitive, is_symmetry=is_symmetry)
independent_atoms = symmetry.get_independent_atoms()
born = np.zeros((primitive.get_number_of_atoms(), 3, 3), dtype=float)
for i in independent_atoms:
line = f.readline().split()
if len(line) == 0:
print "Number of lines for Born effect charge is not enough."
return False
if not len(line) == 9:
print "BORN file format of line %d is incorrect" % (i + 3)
return False
born[i] = np.reshape([float(x) for x in line], (3, 3))
# Expand Born effective charges to all atoms in the primitive cell
rotations = symmetry.get_symmetry_operations()['rotations']
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
for i in range(primitive.get_number_of_atoms()):
# R_cart = L R L^-1
rot_cartesian = similarity_transformation(
primitive.get_cell().transpose(), rotations[map_operations[i]])
# R_cart^T B R_cart^-T (inverse rotation is required to transform)
born[i] = similarity_transformation(rot_cartesian.transpose(),
born[map_atoms[i]])
non_anal = {'born': born, 'factor': factors, 'dielectric': dielectric}
return non_anal
def test_get_map_operations(self):
symprec = 1e-5
cell = read_cell_yaml(os.path.join(data_dir, "..", "NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
# start = time.time()
symmetry._set_map_operations()
# end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
def test_get_map_operations(self):
symprec = 1e-5
cell = get_unitcell_from_phonopy_yaml(
os.path.join(data_dir,"../NaCl.yaml"))
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
start = time.time()
symmetry._set_map_operations()
end = time.time()
# print(end - start)
map_ops = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
positions = scell.get_scaled_positions()
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
self.assertTrue((diff < symprec).all())
def test_get_map_operations(convcell_nacl):
symprec = 1e-5
cell = convcell_nacl
scell = get_supercell(cell, np.diag([2, 2, 2]), symprec=symprec)
symmetry = Symmetry(scell, symprec=symprec)
map_ops = symmetry.get_map_operations().copy()
# start = time.time()
# symmetry._set_map_operations()
# end = time.time()
# print(end - start)
# map_ops_old = symmetry.get_map_operations().copy()
# assert (map_ops == map_ops_old).all()
map_atoms = symmetry.get_map_atoms()
positions = scell.scaled_positions
rotations = symmetry.symmetry_operations['rotations']
translations = symmetry.symmetry_operations['translations']
for i, (op_i, atom_i) in enumerate(zip(map_ops, map_atoms)):
r_pos = np.dot(rotations[op_i], positions[i]) + translations[op_i]
diff = positions[atom_i] - r_pos
diff -= np.rint(diff)
assert (diff < symprec).all()
def distribute_forces(supercell, disp, forces, filename, symprec):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
symbols = supercell.get_chemical_symbols()
positions = supercell.get_positions()
positions[disp[0]] += disp[1]
cell = Atoms(cell=lattice, positions=positions, symbols=symbols, pbc=True)
symmetry = Symmetry(cell, symprec)
independent_atoms = symmetry.get_independent_atoms()
# Rotation matrices in Cartesian
rotations = []
for r in symmetry.get_symmetry_operations()['rotations']:
rotations.append(similarity_transformation(lattice.T, r))
map_operations = symmetry.get_map_operations()
map_atoms = symmetry.get_map_atoms()
atoms_in_dot_scf = get_independent_atoms_in_dot_scf(filename)
if not len(forces) == len(atoms_in_dot_scf):
print "%s does not contain necessary information." % filename
print "Plese check if there are \"FGL\" lines with"
print "\"total forces\" are required."
return False
if len(atoms_in_dot_scf) == natom:
print "It is assumed that there is no symmetrically-equivalent atoms in "
print "\'%s\' at wien2k calculation." % filename
print ""
force_set = forces
elif not len(forces) == len(independent_atoms):
print "Non-equivalent atoms of %s could not be recognized by phonopy." % filename
return False
else:
# 1. Transform wien2k forces to those on independent atoms
indep_atoms_to_wien2k = []
forces_remap = []
for i, pos_wien2k in enumerate(atoms_in_dot_scf):
for j, pos in enumerate(cell.get_scaled_positions()):
diff = pos_wien2k - pos
diff -= np.rint(diff)
if (abs(diff) < 0.00001).all():
forces_remap.append(
np.dot(forces[i], rotations[map_operations[j]].T))
indep_atoms_to_wien2k.append(map_atoms[j])
break
if not len(forces_remap) == len(forces):
print "Atomic position mapping between Wien2k and phonopy failed."
print "If you think this is caused by a bug of phonopy"
print "please report it in the phonopy mainling list."
return False
# 2. Distribute forces from independent to dependent atoms.
force_set = []
for i in range(natom):
force_set.append(
np.dot(forces_remap[indep_atoms_to_wien2k.index(map_atoms[i])],
rotations[map_operations[i]]))
return force_set
magmom = []
for numxmag in text.split():
if '*' in numxmag:
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
else:
magmom.append(float(numxmag))
return magmom
def parse_incar(filename):
for line in open(filename):
for conf in line.split(';'):
if 'MAGMOM' in conf:
return get_magmom(conf.split('=')[1])
cell = read_vasp("POSCAR")
symmetry = Symmetry(cell, symprec=1e-3)
map_nonspin = symmetry.get_map_atoms()
print "Number of operations w/o spin", len(symmetry.get_symmetry_operations()['rotations'])
magmoms = parse_incar("INCAR")
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-3)
print "Number of operations w spin", len(symmetry.get_symmetry_operations()['rotations'])
map_withspin = symmetry.get_map_atoms()
if ((map_nonspin - map_withspin) == 0).all():
print True
else:
print False
print map_nonspin
print map_withspin
if '*' in numxmag:
num, mag = numxmag.split('*')
magmom += [float(mag)] * int(num)
else:
magmom.append(float(numxmag))
return magmom
def parse_incar(filename):
for line in open(filename):
for conf in line.split(';'):
if 'MAGMOM' in conf:
return get_magmom(conf.split('=')[1])
cell = read_vasp("POSCAR")
symmetry = Symmetry(cell, symprec=1e-3)
map_nonspin = symmetry.get_map_atoms()
print("Number of operations w/o spin %d" %
len(symmetry.get_symmetry_operations()['rotations']))
magmoms = parse_incar("INCAR")
cell.set_magnetic_moments(magmoms)
symmetry = Symmetry(cell, symprec=1e-3)
print("Number of operations w spin %d" %
len(symmetry.get_symmetry_operations()['rotations']))
map_withspin = symmetry.get_map_atoms()
if ((map_nonspin - map_withspin) == 0).all():
print(True)
else:
print(False)
print(map_nonspin)
print(map_withspin)
def get_born_OUTCAR(poscar_filename="POSCAR",
outcar_filename="OUTCAR",
primitive_axis=np.eye(3),
supercell_matrix=np.eye(3, dtype='intc'),
is_symmetry=True,
symmetrize_tensors=False):
ucell = read_vasp(poscar_filename)
scell = get_supercell(ucell, supercell_matrix)
inv_smat = np.linalg.inv(supercell_matrix)
pcell = get_primitive(scell, np.dot(inv_smat, primitive_axis))
u_sym = Symmetry(ucell, is_symmetry=is_symmetry)
p_sym = Symmetry(pcell, is_symmetry=is_symmetry)
lattice = ucell.get_cell().T
outcar = open(outcar_filename)
borns = []
while True:
line = outcar.readline()
if not line:
break
if "NIONS" in line:
num_atom = int(line.split()[11])
if "MACROSCOPIC STATIC DIELECTRIC TENSOR" in line:
epsilon = []
outcar.readline()
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
epsilon.append([float(x) for x in outcar.readline().split()])
if "BORN" in line:
outcar.readline()
line = outcar.readline()
if "ion" in line:
for i in range(num_atom):
born = []
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
born.append([float(x)
for x in outcar.readline().split()][1:])
outcar.readline()
borns.append(born)
borns = np.array(borns, dtype='double')
epsilon = np.array(epsilon, dtype='double')
if symmetrize_tensors:
borns_orig = borns.copy()
point_sym = [similarity_transformation(lattice, r)
for r in u_sym.get_pointgroup_operations()]
epsilon = symmetrize_tensor(epsilon, point_sym)
for i in range(num_atom):
z = borns[i]
site_sym = [similarity_transformation(lattice, r)
for r in u_sym.get_site_symmetry(i)]
borns[i] = symmetrize_tensor(z, site_sym)
rotations = u_sym.get_symmetry_operations()['rotations']
map_atoms = u_sym.get_map_atoms()
borns_copy = np.zeros_like(borns)
for i, m_i in enumerate(map_atoms):
count = 0
for j, r_j in enumerate(u_sym.get_map_operations()):
if map_atoms[j] == m_i:
count += 1
r_cart = similarity_transformation(lattice, rotations[r_j])
borns_copy[i] += similarity_transformation(r_cart, borns[j])
borns_copy[i] /= count
borns = borns_copy
sum_born = borns.sum(axis=0) / len(borns)
borns -= sum_born
if (np.abs(borns_orig - borns) > 0.1).any():
sys.stderr.write(
"Born effective charge symmetrization might go wrong.\n")
p2s = np.array(pcell.get_primitive_to_supercell_map(), dtype='intc')
s_indep_atoms = p2s[p_sym.get_independent_atoms()]
u2u = scell.get_unitcell_to_unitcell_map()
u_indep_atoms = [u2u[x] for x in s_indep_atoms]
reduced_borns = borns[u_indep_atoms].copy()
return reduced_borns, epsilon
