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 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 -= diff.round()
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