scnc
/
phonopy
mirror of https://github.com/phonopy/phonopy.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Phono3py is going to be modular to be handled from __init__.py.

This commit is contained in:
Atsushi Togo 2014-01-27 23:57:46 +09:00
parent a0effb75ef
commit ded5b75b14
3 changed files with 104 additions and 74 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

62
anharmonic/phonon3/__init__.py
View File

@ -47,15 +47,19 @@ class Phono3py:
self._supercell = None
self._primitive = None
self._phonon_supercell = None
self._phonon_primitive = None
self._build_supercell()
self._build_primitive_cell()
self._build_phonon_supercell()
self._build_phonon_primitive_cell()
# Set supercell and primitive symmetry
# Set supercell, primitive, and phonon supercell symmetries
self._symmetry = None
self._primitive_symmetry = None
self._phonon_supercell_symmetry = None
self._search_symmetry()
self._search_primitive_symmetry()
self._search_phonon_supercell_symmetry()
# Thermal conductivity
self._thermal_conductivity = None # conductivity_RTA object
@ -135,29 +139,37 @@ class Phono3py:
def get_phonon_supercell(self):
return self._phonon_supercell
def get_phonon_primitive(self):
return self._phonon_primitive
def get_symmetry(self):
"""return symmetry of supercell"""
return self._symmetry
def get_primitive_symmetry(self):
"""return symmetry of primitive cell"""
return self._primitive_symmetry
def get_phonon_supercell_symmetry(self):
return self._phonon_supercell_symmetry
def generate_displacements(self,
distance=0.01,
cutoff_pair_distance=None,
is_plusminus='auto',
is_diagonal=True):
self._direction_dataset = get_third_order_displacements(
direction_dataset = get_third_order_displacements(
self._supercell,
self._symmetry,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal)
self._displacement_dataset = direction_to_displacement(
self._direction_dataset,
direction_dataset,
distance,
self._supercell,
cutoff_distance=cutoff_pair_distance)
def set_displacement_dataset(self, dataset):
self._displacement_dataset = dataset
def get_displacement_dataset(self):
return self._displacement_dataset
@ -296,6 +308,13 @@ class Phono3py:
print ("Warning: point group symmetries of supercell and primitive"
"cell are different.")
def _search_phonon_supercell_symmetry(self):
if self._phonon_supercell_matrix is None:
self._phonon_supercell_symmetry = self._symmetry
else:
self._phonon_supercell_symmetry = Symmetry(self._phonon_supercell,
self._symprec,
self._is_symmetry)
def _build_supercell(self):
self._supercell = get_supercell(self._unitcell,
@ -326,20 +345,8 @@ class Phono3py:
Therefore primitive cell lattice is finally calculated by:
(supercell_lattice * (supercell_matrix)^-1 * primitive_matrix)^T
"""
inv_supercell_matrix = np.linalg.inv(self._supercell_matrix)
if self._primitive_matrix is None:
trans_mat = inv_supercell_matrix
else:
trans_mat = np.dot(inv_supercell_matrix, self._primitive_matrix)
self._primitive = get_primitive(
self._supercell, trans_mat, self._symprec)
num_satom = self._supercell.get_number_of_atoms()
num_patom = self._primitive.get_number_of_atoms()
if abs(num_satom * np.linalg.det(trans_mat) - num_patom) < 0.1:
return True
else:
return False
self._primitive = self._get_primitive_cell(
self._supercell, self._supercell_matrix, self._primitive_matrix)
def _build_phonon_supercell(self):
"""
@ -354,6 +361,25 @@ class Phono3py:
else:
self._phonon_supercell = get_supercell(
self._unitcell, self._phonon_supercell_matrix, self._symprec)
def _build_phonon_primitive_cell(self):
self._phonon_primitive = self._get_primitive_cell(
self._phonon_supercell,
self._phonon_supercell_matrix,
self._primitive_matrix)
def _get_primitive_cell(self, supercell, supercell_matrix, primitive_matrix):
if supercell_matrix is None:
inv_supercell_matrix = np.eye(3)
else:
inv_supercell_matrix = np.linalg.inv(supercell_matrix)
if primitive_matrix is None:
t_mat = inv_supercell_matrix
else:
t_mat = np.dot(inv_supercell_matrix, primitive_matrix)
return get_primitive(supercell, t_mat, self._symprec)
class IsotopeScattering:

12
anharmonic/settings.py
View File

@ -23,7 +23,7 @@ class Phono3pySettings(Settings):
self._no_kappa_stars = False
self._read_amplitude = False
self._read_gamma = False
self._supercell_matrix_extra = None
self._phonon_supercell_matrix = None
self._temperatures = None
self._write_amplitude = False
self._write_gamma = False
@ -136,11 +136,11 @@ class Phono3pySettings(Settings):
def get_read_amplitude(self):
return self._read_amplitude
def set_supercell_matrix_extra(self, matrix):
self._supercell_matrix_extra = matrix
def set_phonon_supercell_matrix(self, matrix):
self._phonon_supercell_matrix = matrix
def get_supercell_matrix_extra(self):
return self._supercell_matrix_extra
def get_phonon_supercell_matrix(self):
return self._phonon_supercell_matrix
def set_temperatures(self, temperatures):
self._temperatures = temperatures
@ -394,7 +394,7 @@ class Phono3pyConfParser(ConfParser):
# Supercell size for fc2
if params.has_key('dim_extra'):
self._settings.set_supercell_matrix_extra(params['dim_extra'])
self._settings.set_phonon_supercell_matrix(params['dim_extra'])
# Sets of band indices that are summed
if params.has_key('band_indices'):

104
scripts/phono3py
View File

@ -450,12 +450,14 @@ else:
unitcell_filename = options.cell_poscar
unitcell = read_vasp(unitcell_filename, settings.get_chemical_symbols())
###############################################################
# Create supercells with displacements and exit (pre-process) #
###############################################################
#################################################
# Create supercells with displacements and exit #
#################################################
if options.is_displacement:
cutoff_pair_distance = settings.get_cutoff_pair_distance()
phono3py = Phono3py(unitcell, settings.get_supercell_matrix())
phono3py = Phono3py(unitcell,
settings.get_supercell_matrix(),
symprec=options.symprec)
supercell = phono3py.get_supercell()
phono3py.generate_displacements(
distance=settings.get_displacement_distance(),
@ -488,28 +490,27 @@ if options.is_displacement:
print_end()
sys.exit(0)
symmetry = Symmetry(unitcell, options.symprec)
##############
# Initialize #
##############
phono3py = Phono3py(
unitcell,
settings.get_supercell_matrix(),
primitive_matrix=settings.get_primitive_matrix(),
phonon_supercell_matrix=settings.get_phonon_supercell_matrix(),
symprec=options.symprec)
#########################################
# Calculate third-order force constants #
#########################################
if settings.get_primitive_matrix() is None:
primitive_matrix = np.eye(3, dtype='double')
else:
primitive_matrix = np.array(settings.get_primitive_matrix(), dtype='double')
primitive = get_primitive(
supercell,
np.dot(np.linalg.inv(settings.get_supercell_matrix()), primitive_matrix),
options.symprec)
if settings.get_supercell_matrix_extra() is not None:
primitive_extra = get_primitive(
supercell_extra,
np.dot(np.linalg.inv(settings.get_supercell_matrix_extra()),
primitive_matrix),
options.symprec)
supercell = phono3py.get_supercell()
primitive = phono3py.get_primitive()
phonon_supercell = phono3py.get_phonon_supercell()
phonon_primitive = phono3py.get_phonon_primitive()
symmetry = phono3py.get_symmetry()
mesh = settings.get_mesh_numbers()
mesh_divs = settings.get_mesh_divisors()
#################
# Show settings #
#################
if log_level:
if options.is_translational_symmetry:
print "Translational symmetry:", options.is_translational_symmetry
@ -524,8 +525,8 @@ if log_level:
if settings.get_cutoff_fc3_distance() is not None:
print "FC3 cutoff distance:",
print settings.get_cutoff_fc3_distance()
if settings.get_supercell_matrix_extra() is not None:
print "Extra supercell for fc2 is supplied."
if settings.get_phonon_supercell_matrix() is not None:
print "Supercell for harmonic phonon is introduced."
if settings.get_is_nac():
print "Non-analytical term correction:", settings.get_is_nac()
print "Spacegroup: ", symmetry.get_international_table()
@ -537,24 +538,24 @@ if log_level:
print "------------------ ratio (supercell for fc)/(primitive) --------------------"
for vec in np.dot(supercell.get_cell(), np.linalg.inv(primitive.get_cell())):
print "%5.2f"*3 % tuple(vec)
if log_level and (settings.get_supercell_matrix_extra() is not None):
print "-------------------------- primitive cell extra -----------------------------"
print_cell(primitive_extra)
print "---------------------------- supercell extra --------------------------------"
print_cell(supercell_extra, mapping=primitive_extra.get_supercell_to_primitive_map())
print "---------------- ratio (supercell extra)/(primitive extra) -----------------"
for vec in np.dot(supercell_extra.get_cell(),
np.linalg.inv(primitive_extra.get_cell())):
print "%5.2f"*3 % tuple(vec)
if settings.get_phonon_supercell_matrix() is not None:
print "-------------------- primitive cell for harmonic phonon ---------------------"
print_cell(phonon_primitive)
print "---------------------- supercell for harmonic phonon ------------------------"
print_cell(phonon_supercell, mapping=phonon_primitive.get_supercell_to_primitive_map())
print "--------------- ratio (phonon supercell)/(phonon primitive) -----------------"
for vec in np.dot(phonon_supercell.get_cell(),
np.linalg.inv(phonon_primitive.get_cell())):
print "%5.2f"*3 % tuple(vec)
# Write ir-grid points and grid addresses
#####################################################
# Write ir-grid points and grid addresses, and exit #
#####################################################
if options.write_grid_points:
print "---------------------------------------------------------------------------"
mesh = settings.get_mesh_numbers()
if mesh is None:
print "To write grid points, mesh numbers have to be set."
print "To write grid points, mesh numbers have to be specified."
else:
mesh_divs = settings.get_mesh_divisors()
(grid_points,
coarse_grid_weights,
grid_address) = get_coarse_ir_grid_points(
@ -578,8 +579,10 @@ if options.write_grid_points:
if log_level:
print_end()
sys.exit(0)
# fc2
#######
# fc2 #
#######
if log_level:
print "------------------------------ fc2 ------------------------------"
sys.stdout.flush()
@ -621,15 +624,14 @@ if not options.read_fc2:
print "Writing fc2 to %s..." % filename
write_fc2_to_hdf5(fc2_with_dim, filename=filename)
if settings.get_supercell_matrix_extra()==None:
if settings.get_phonon_supercell_matrix()==None:
fc2 = fc2_with_dim
else:
if log_level:
print "--------------------------- fc2 extra ---------------------------"
sys.stdout.flush()
# fc2 extra (FORCE_SETS_EXTRA)
# phonon fc2 (FORCE_SETS_EXTRA)
if options.read_fc2_extra:
if input_filename is None:
filename = 'fc2_extra.hdf5'
else:
@ -642,7 +644,9 @@ else:
if log_level:
print "Solving fc2 extra..."
forces_second_extra = parse_FORCE_SETS(filename="FORCE_SETS_EXTRA")
fc2 = get_fc2(supercell_extra, symmetry_extra, forces_second_extra)
fc2 = get_fc2(phonon_supercell,
phono3py.get_phonon_supercell_symmetry(),
forces_second_extra)
if options.is_symmetrize_fc2:
set_permutation_symmetry(fc2)
@ -663,10 +667,10 @@ else:
if settings.get_is_nac():
file_exists('BORN', log_level)
if settings.get_supercell_matrix_extra()==None:
if settings.get_phonon_supercell_matrix()==None:
nac_params = parse_BORN(primitive)
else:
nac_params = parse_BORN(primitive_extra)
nac_params = parse_BORN(phonon_primitive)
nac_q_direction = settings.get_nac_q_direction()
else:
nac_params = None
@ -852,12 +856,12 @@ elif settings.get_mesh_numbers() is not None:
else:
freq_scale = options.freq_scale
if settings.get_supercell_matrix_extra() is None:
if settings.get_phonon_supercell_matrix() is None:
supercell_dm = supercell
primitive_dm = primitive
else:
supercell_dm = supercell_extra
primitive_dm = primitive_extra
supercell_dm = phonon_supercell
primitive_dm = phonon_primitive
if log_level: