class Phonopy:
def __init__( self,
unitcell,
supercell_matrix,
is_preprocess=True,
distance=0.01,
symprec=1e-5,
factor=VaspToTHz,
is_nosym=False,
log_level=0 ):
self.symprec = symprec
self.unitcell = unitcell
self.supercell_matrix = supercell_matrix
self.distance = distance
self.factor = factor
self.is_nosym = is_nosym
self.log_level = log_level
self.supercell = None
self.__supercell()
self.symmetry = None
self.__symmetry()
if is_preprocess:
self.displacements = None
self.displacement_directions = None
self.supercells_with_displacements = None
self.set_displacements()
# set_post_process
self.primitive = None
self.dynamical_matrix = None
self.is_nac = False
# set_force_constants or set_forces
self.force_constants = None
# set_band_structure
self.__band_structure = None
# set_mesh
self.__mesh = None
# set_thermal_properties
self.__thermal_properties = None
# set_thermal_displacements
self.__thermal_displacements = None
# set_partial_DOS
self.__pdos = None
# set_total_DOS
self.__total_dos = None
def __supercell(self):
self.supercell = get_supercell( self.unitcell,
self.supercell_matrix,
self.symprec )
def get_supercell( self ):
return self.supercell
def set_supercell( self, supercell ):
self.supercell = supercell
def get_primitive( self ):
return self.primitive
def set_primitive( self, primitive ):
self.primitive = primitive
def __symmetry(self):
self.symmetry = Symmetry( self.supercell,
self.symprec,
self.is_nosym )
def get_symmetry(self):
return self.symmetry
def set_displacements( self,
is_plusminus='auto',
is_diagonal=True ):
"""
displacements:
List of displacements in Cartesian coordinates.
See 'set_special_displacements'
displacement_directions:
List of directions with respect to axes. This gives only the
symmetrically non equivalent directions. The format is like:
[[ 0, 1, 0, 0 ],
[ 7, 1, 0, 1 ], ...]
where each list is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: If the direction is displaced or not ( 1, 0, or -1 )
with respect to the axes.
"""
lattice = self.supercell.get_cell()
self.displacements = []
self.displacement_directions = \
get_least_displacements( self.symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
log_level=self.log_level )
for disp in self.displacement_directions:
atom_num = disp[0]
disp_cartesian = np.dot(disp[1:], lattice)
disp_cartesian *= self.distance / np.linalg.norm(disp_cartesian)
self.displacements.append( [ atom_num,
disp_cartesian[0],
disp_cartesian[1],
disp_cartesian[2] ] )
self.__supercells_with_displacements()
def set_special_displacements(self, displacements):
"""
This method orverwrites displacements that were automatically
determined in the post-process.
displacemsts: List of disctionaries
[[ 0, 0.01, 0.00, 0.00 ], ... ]
where each set of elements is defined by:
First value: Atom index in supercell starting with 0
Second to fourth: Displacement in Cartesian coordinates
"""
self.displacements = displacements
self.__supercells_with_displacements()
def get_displacements( self ):
return self.displacements
def get_displacement_directions( self ):
return self.displacement_directions
def print_displacements(self):
print "Least displacements:"
print " Atom Displacement"
print " ----------------------------"
for disp in self.displacements:
print " %4d " % disp[0],
print disp[1:4]
def __supercells_with_displacements(self):
supercells = []
for disp in self.displacements:
positions = self.supercell.get_positions()
positions[disp[0]] += disp[1:4]
supercells.append( Atoms(
numbers = self.supercell.get_atomic_numbers(),
masses = self.supercell.get_masses(),
positions = positions,
cell = self.supercell.get_cell(),
pbc = True ) )
self.supercells_with_displacements = supercells
def get_supercells_with_displacements(self):
return self.supercells_with_displacements
def set_post_process( self,
primitive_matrix,
set_of_forces=None,
force_constants=None,
is_nac=False ):
"""
Set forces to prepare phonon calculations. The order of
'set_of_forces' has to correspond to that of 'displacements'.
primitive_matrix:
Relative axes of primitive cell to the input unit cell.
Relative axes to the supercell is calculated by:
supercell_matrix^-1 * primitive_matrix
Therefore primitive cell lattice is finally calculated by:
( supercell_lattice * ( supercell_matrix )^-1 * primitive_matrix )^T
set_of_forces:
[ [ [ f_1x, f_1y, f_1z ], [ f_2x, f_2y, f_2z ], ... ], # first supercell
[ [ f_1x, f_1y, f_1z ], [ f_2x, f_2y, f_2z ], ... ], # second supercell
... ]
"""
self.is_nac = is_nac
if not set_of_forces == None:
self.set_forces( set_of_forces )
elif not force_constants == None:
self.set_force_constants( force_constants )
elif self.force_constants == None:
print "In set_post_process, set_of_forces or force_constants"
print "has to be set."
sys.exit(1)
# Primitive cell
inv_supercell_matrix = np.linalg.inv( self.supercell_matrix )
self.primitive = Primitive( self.supercell,
np.dot( inv_supercell_matrix, primitive_matrix ),
self.symprec )
# Dynamical Matrix
if self.is_nac:
self.dynamical_matrix = \
DynamicalMatrixNAC( self.supercell,
self.primitive,
self.force_constants,
symprec=self.symprec )
else:
self.dynamical_matrix = \
DynamicalMatrix( self.supercell,
self.primitive,
self.force_constants,
symprec=self.symprec )
def set_nac_params( self, nac_params, method='wang' ):
if self.is_nac:
self.dynamical_matrix.set_nac_params( nac_params, method )
def get_dynamical_matrix( self ):
return self.dynamical_matrix
def set_forces( self,
set_of_forces,
is_tensor_symmetry=False ):
# Forces
forces = []
for i, disp in enumerate( self.displacements ):
forces.append( Forces( disp[0],
disp[1:4],
set_of_forces[i] ) )
# Force constants
self.force_constants = get_force_constants( forces,
self.symmetry,
self.supercell,
is_tensor_symmetry )
def set_force_constants( self, force_constants ):
self.force_constants = force_constants
def symmetrize_force_constants( self, iteration=3 ):
symmetrize_force_constants( self.force_constants, iteration )
def get_force_constants( self ):
return self.force_constants
def get_rotational_condition_of_fc( self ):
return rotational_invariance( self.force_constants,
self.supercell,
self.primitive,
self.symprec )
# Frequency at a q-point
def get_frequencies(self, q):
"""
Calculate phonon frequency
q: k-vector in reduced coordinates of primitive cell
"""
self.dynamical_matrix.set_dynamical_matrix(q)
dm = self.dynamical_matrix.get_dynamical_matrix()
frequencies = []
for eig in np.linalg.eigvalsh(dm):
if eig < 0:
frequencies.append(-np.sqrt(-eig))
else:
frequencies.append(np.sqrt(eig))
return np.array(frequencies) * self.factor
# Band structure
def set_band_structure( self,
bands,
is_eigenvectors=False ):
self.__band_structure = BandStructure( bands,
self.dynamical_matrix,
self.primitive,
is_eigenvectors=is_eigenvectors,
factor=self.factor )
def get_band_structure( self ):
band = self.__band_structure
return ( band.get_distances(),
band.get_qpoints(),
band.get_eigenvalues(),
band.get_eigenvectors() )
def plot_band_structure( self, symbols=None ):
return self.__band_structure.plot_band( symbols )
def write_yaml_band_structure( self ):
self.__band_structure.write_yaml()
# Mesh sampling
def set_mesh( self,
mesh,
shift=None,
is_time_reversal=True,
is_symmetry=True,
is_eigenvectors=False ):
self.__mesh = Mesh( self.dynamical_matrix,
self.primitive,
mesh,
shift=shift,
is_time_reversal=is_time_reversal,
is_symmetry=is_symmetry,
is_eigenvectors=is_eigenvectors,
factor=self.factor,
symprec=self.symprec )
def get_mesh( self ):
return ( self.__mesh.get_weights(),
self.__mesh.get_qpoints(),
self.__mesh.get_eigenvalues(),
self.__mesh.get_eigenvectors() )
def write_yaml_mesh( self ):
self.__mesh.write_yaml()
# Thermal property
def set_thermal_properties( self, t_step=10, t_max=1000, t_min=0,
cutoff_eigenvalue=None ):
if self.__mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
tp = ThermalProperties( self.__mesh.get_eigenvalues(),
weights=self.__mesh.get_weights(),
factor=self.factor,
cutoff_eigenvalue=cutoff_eigenvalue )
tp.set_thermal_properties( t_step, t_max, t_min )
self.__thermal_properties = tp
def get_thermal_properties( self ):
temps, fe, entropy, cv = \
self.__thermal_properties.get_thermal_properties()
return np.array([ temps, fe, entropy, cv ]).transpose()
def plot_thermal_properties( self ):
return self.__thermal_properties.plot_thermal_properties()
def write_yaml_thermal_properties( self ):
self.__thermal_properties.write_yaml()
# Partial DOS
def set_partial_DOS( self,
sigma=None,
omega_min=None,
omega_max=None,
omega_pitch=None ):
if self.__mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
if self.__mesh.get_eigenvectors() == None:
print "Eigenvectors have to be calculated."
sys.exit(1)
pdos = PartialDos( self.__mesh.get_eigenvalues(),
self.__mesh.get_weights(),
self.__mesh.get_eigenvectors(),
factor=self.factor,
sigma=sigma )
pdos.set_draw_area( omega_min,
omega_max,
omega_pitch )
pdos.calculate()
self.__pdos = pdos
def get_partial_DOS( self ):
"""
Retern omegas and partial_dos.
The first element is omegas and the second is partial_dos.
omegas: [ freq1, freq2, ... ]
partial_dos:
[[elem1-freq1, elem1-freq2, ... ],
[elem2-freq1, elem2-freq2, ... ],
... ]
where
elem1: atom1-x compornent
elem2: atom1-y compornent
elem3: atom1-z compornent
elem4: atom2-x compornent
...
"""
return self.__pdos.get_partial_dos()
def plot_partial_DOS( self, pdos_indices ):
return self.__pdos.plot_pdos( pdos_indices )
def write_partial_DOS( self ):
self.__pdos.write()
# Total DOS
def set_total_DOS( self,
sigma=None,
omega_min=None,
omega_max=None,
omega_pitch=None ):
if self.__mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
total_dos = TotalDos( self.__mesh.get_eigenvalues(),
self.__mesh.get_weights(),
factor=self.factor,
sigma=sigma )
total_dos.set_draw_area( omega_min,
omega_max,
omega_pitch )
total_dos.calculate()
self.__total_dos = total_dos
def get_total_DOS( self ):
"""
Retern omegas and total dos.
The first element is omegas and the second is total dos.
omegas: [ freq1, freq2, ... ]
total_dos: [ dos1, dos2, ... ]
"""
return self.__total_dos.get_dos()
def plot_total_DOS( self ):
return self.__total_dos.plot_dos()
def write_total_DOS( self ):
self.__total_dos.write()
# Thermal displacement
def set_thermal_displacements( self,
t_step=10,
t_max=1000,
t_min=0,
projector=None,
cutoff_eigenvalue=None ):
"""
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz)
"""
if self.__mesh==None:
print "set_mesh has to be done before set_thermal_properties"
sys.exit(1)
if self.__mesh.get_eigenvectors() == None:
print "Eigenvectors have to be calculated."
sys.exit(1)
td = ThermalDisplacements( self.__mesh.get_eigenvalues(),
self.__mesh.get_eigenvectors(),
self.__mesh.get_weights(),
self.primitive.get_masses(),
factor=self.factor,
cutoff_eigenvalue=cutoff_eigenvalue )
td.set_temperature_range( t_min, t_max, t_step )
if not projector==None:
td.project_eigenvectors( projector, self.primitive.get_cell() )
td.set_thermal_displacements()
self.__thermal_displacements = td
def plot_thermal_displacements( self, is_legend=False ):
return self.__thermal_displacements.plot_thermal_displacements( is_legend )
def write_yaml_thermal_displacements( self ):
self.__thermal_displacements.write_yaml()
# Thermal displacement
def set_thermal_distances( self,
atom_pairs,
t_step=10,
t_max=1000,
t_min=0,
cutoff_eigenvalue=None ):
"""
atom_pairs: List of list
Mean square distances are calculated for the atom_pairs
e.g. [ [ 1, 2 ], [ 1, 4 ] ]
cutoff_eigenvalue:
phonon modes that have frequencies below cutoff_eigenvalue
are ignored.
e.g. 0.1 (THz)
"""
td = ThermalDistances( self.__mesh.get_eigenvalues(),
self.__mesh.get_eigenvectors(),
self.__mesh.get_weights(),
self.supercell,
self.primitive,
self.__mesh.get_qpoints(),
symprec=self.symprec,
factor=self.factor,
cutoff_eigenvalue=cutoff_eigenvalue )
td.set_temperature_range( t_min, t_max, t_step )
td.set_thermal_distances( atom_pairs )
self.__thermal_distances = td
def write_yaml_thermal_distances( self ):
self.__thermal_distances.write_yaml()
# Q-points mode
def write_yaml_qpoints( self,
qpoints,
is_eigenvectors=False,
factor=VaspToTHz ):
write_yaml_qpoints( qpoints,
self.primitive,
self.dynamical_matrix,
is_eigenvectors=is_eigenvectors,
factor=self.factor )
# Animation
def write_animation( self,
qpoint=None,
anime_type='v_sim',
band_index=None,
amplitude=None,
num_div=None,
shift=None ):
if qpoint==None:
animation = Animation( [0, 0, 0],
self.dynamical_matrix,
self.primitive,
shift=shift )
else:
animation = Animation( qpoint,
self.dynamical_matrix,
self.primitive,
shift=shift )
if anime_type=='v_sim':
animation.write_v_sim( self.factor )
if ( anime_type=='arc' or
anime_type=='xyz' or
anime_type=='jmol' or
anime_type=='poscar' ):
if band_index==None or amplitude==None or num_div==None:
print "Parameters are not correctly set for animation."
sys.exit(1)
if anime_type=='arc' or anime_type==None:
animation.write_arc( band_index,
amplitude,
num_div )
if anime_type=='xyz':
animation.write_xyz( band_index,
amplitude,
num_div,
self.factor )
if anime_type=='jmol':
animation.write_xyz_jmol( amplitude=amplitude,
factor=self.factor )
if anime_type=='poscar':
animation.write_POSCAR( band_index,
amplitude,
num_div )
def write_modulation( self, setting ):
write_modulations( self.dynamical_matrix,
self.primitive,
setting )
