def _get_second_displacements(atom2,
disp2,
cell,
reduced_bond_sym,
symprec,
is_diagonal):
positions = cell.get_scaled_positions()
dds_atom2 = {'number': atom2,
'direction': disp2,
'third_atoms': []}
reduced_bond_sym2 = get_reduced_site_symmetry(reduced_bond_sym,
disp2,
symprec)
third_atoms = get_least_orbits(atom2,
cell,
reduced_bond_sym2,
symprec)
for atom3 in third_atoms:
reduced_plane_sym = get_bond_symmetry(
reduced_bond_sym2,
cell.get_scaled_positions(),
atom2,
atom3,
symprec)
dds_atom3 = get_next_displacements(atom2,
atom3,
reduced_plane_sym,
positions,
symprec,
is_diagonal)
dds_atom2['third_atoms'].append(dds_atom3)
return dds_atom2
def get_fourth_order_displacements(cell,
symmetry,
is_plusminus='auto',
is_diagonal=False):
# Atoms 1, 2, and 3 are defined as follows:
#
# Atom 1: The first displaced atom. Fourth order force constant
# between Atoms 1, 2, 3, and 4 is calculated.
# Atom 2: The second displaced atom. Third order force constant
# between Atoms 2, 3, and 4 is calculated.
# Atom 3: The third displaced atom. Second order force constant
# between Atoms 3 and 4 is calculated.
# Atom 4: Force is mesuared on this atom.
# Least displacements for third order force constants
#
# Data structure
# [{'number': atom1,
# 'displacement': [0.00000, 0.007071, 0.007071],
# 'second_atoms': [ {'number': atom2,
# 'displacement': [0.007071, 0.000000, 0.007071],
# 'third_atoms': [ {'number': atom3,
# 'displacements':
# [[-0.007071, 0.000000, -0.007071],
# ,...]}, {...}, ... ]},
# Least displacements of first atoms (Atom 1) are searched by
# using respective site symmetries of the original crystal.
disps_first = get_least_displacements(symmetry,
is_plusminus=is_plusminus,
is_diagonal=False)
symprec = symmetry.get_symmetry_tolerance()
dds = []
for disp in disps_first:
atom1 = disp[0]
disp1 = disp[1:4]
site_sym = symmetry.get_site_symmetry(atom1)
dds_atom1 = {'number': atom1, 'direction': disp1, 'second_atoms': []}
reduced_site_sym = get_reduced_site_symmetry(site_sym, disp1, symprec)
second_atoms = get_least_orbits(atom1, cell, reduced_site_sym, symprec)
for atom2 in second_atoms:
reduced_bond_sym = get_bond_symmetry(reduced_site_sym,
cell.get_scaled_positions(),
atom1, atom2, symprec)
for disp2 in _get_displacements_second(reduced_bond_sym, symprec,
is_diagonal):
dds_atom2 = _get_second_displacements(atom2, disp2, cell,
reduced_bond_sym,
symprec, is_diagonal)
dds_atom1['second_atoms'].append(dds_atom2)
dds.append(dds_atom1)
write_supercells_with_three_displacements(cell, dds)
return dds
def get_fourth_order_displacements(cell, symmetry, is_plusminus="auto", is_diagonal=False):
# Atoms 1, 2, and 3 are defined as follows:
#
# Atom 1: The first displaced atom. Fourth order force constant
# between Atoms 1, 2, 3, and 4 is calculated.
# Atom 2: The second displaced atom. Third order force constant
# between Atoms 2, 3, and 4 is calculated.
# Atom 3: The third displaced atom. Second order force constant
# between Atoms 3 and 4 is calculated.
# Atom 4: Force is mesuared on this atom.
# Least displacements for third order force constants
#
# Data structure
# [{'number': atom1,
# 'displacement': [0.00000, 0.007071, 0.007071],
# 'second_atoms': [ {'number': atom2,
# 'displacement': [0.007071, 0.000000, 0.007071],
# 'third_atoms': [ {'number': atom3,
# 'displacements':
# [[-0.007071, 0.000000, -0.007071],
# ,...]}, {...}, ... ]},
# Least displacements of first atoms (Atom 1) are searched by
# using respective site symmetries of the original crystal.
disps_first = get_least_displacements(symmetry, is_plusminus=is_plusminus, is_diagonal=False)
symprec = symmetry.get_symmetry_tolerance()
dds = []
for disp in disps_first:
atom1 = disp[0]
disp1 = disp[1:4]
site_sym = symmetry.get_site_symmetry(atom1)
dds_atom1 = {"number": atom1, "direction": disp1, "second_atoms": []}
reduced_site_sym = get_reduced_site_symmetry(site_sym, disp1, symprec)
second_atoms = get_least_orbits(atom1, cell, reduced_site_sym, symprec)
for atom2 in second_atoms:
reduced_bond_sym = get_bond_symmetry(reduced_site_sym, cell.get_scaled_positions(), atom1, atom2, symprec)
for disp2 in _get_displacements_second(reduced_bond_sym, symprec, is_diagonal):
dds_atom2 = _get_second_displacements(atom2, disp2, cell, reduced_bond_sym, symprec, is_diagonal)
dds_atom1["second_atoms"].append(dds_atom2)
dds.append(dds_atom1)
write_supercells_with_three_displacements(cell, dds)
return dds
def _get_second_displacements(atom2, disp2, cell, reduced_bond_sym, symprec,
is_diagonal):
positions = cell.get_scaled_positions()
dds_atom2 = {'number': atom2, 'direction': disp2, 'third_atoms': []}
reduced_bond_sym2 = get_reduced_site_symmetry(reduced_bond_sym, disp2,
symprec)
third_atoms = get_least_orbits(atom2, cell, reduced_bond_sym2, symprec)
for atom3 in third_atoms:
reduced_plane_sym = get_bond_symmetry(reduced_bond_sym2,
cell.get_scaled_positions(),
atom2, atom3, symprec)
dds_atom3 = get_next_displacements(atom2, atom3, reduced_plane_sym,
positions, symprec, is_diagonal)
dds_atom2['third_atoms'].append(dds_atom3)
return dds_atom2
