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Update phonon, phono3py python interfaces

This commit is contained in:
Atsushi Togo 2014-02-03 00:04:37 +09:00
parent 0ba2107165
commit 95791c9969
4 changed files with 65 additions and 18 deletions
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14
anharmonic/phonon3/__init__.py
View File

@ -145,9 +145,14 @@ class Phono3py:
def produce_fc2(self,
forces_fc2,
disp_dataset,
displacement_dataset=None,
is_permutation_symmetry=False,
is_translational_symmetry=False):
if displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = displacement_dataset
if self._log_level:
print "Solving fc2"
for forces, disp1 in zip(forces_fc2, disp_dataset['first_atoms']):
@ -162,10 +167,15 @@ class Phono3py:
def produce_fc3(self,
forces_fc3,
disp_dataset,
displacement_dataset=None,
cutoff_distance=None, # set fc3 zero
is_translational_symmetry=False,
is_permutation_symmetry=False):
if displacement_dataset is None:
disp_dataset = self._displacement_dataset
else:
disp_dataset = displacement_dataset
if self._log_level:
print "Solving fc2"
for forces, disp1 in zip(forces_fc3, disp_dataset['first_atoms']):

47
phonopy/__init__.py
View File

@ -214,7 +214,12 @@ class Phonopy:
return self._factor
unit_conversion_factor = property(get_unit_conversion_factor)
def produce_force_constants(self, calculate_full_force_constants=True):
def produce_force_constants(self,
forces=None,
calculate_full_force_constants=True):
if forces is not None:
self.set_forces(forces)
if calculate_full_force_constants:
self._run_force_constants_from_forces(
decimals=self._force_constants_decimals)
@ -269,7 +274,10 @@ class Phonopy:
disp_cartesian[0],
disp_cartesian[1],
disp_cartesian[2]])
self._build_supercells_with_displacements()
self._displacement_dataset = {
'natom': self._supercell.get_number_of_atoms(),
'first_atoms': [{'number': disp[0], 'displacement': disp[1:4]}
for disp in self._displacements]}
def set_displacements(self, displacements):
"""Set displacements manually
@ -283,7 +291,6 @@ class Phonopy:
"""
self._displacements = displacements
self._build_supercells_with_displacements()
def get_displacements(self):
return self._displacements
@ -293,8 +300,15 @@ class Phonopy:
return self._displacement_directions
displacement_directions = property(get_displacement_directions)
def get_displacement_dataset(self):
return self._displacement_dataset
def get_supercells_with_displacements(self):
return self._supercells_with_displacements
if self._displacement_dataset is None:
return None
else:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def get_dynamical_matrix(self):
return self._dynamical_matrix
@ -303,15 +317,13 @@ class Phonopy:
def set_forces(self, sets_of_forces):
"""
sets_of_forces:
This requires that self._displacements is set in advance.
[[[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
... ]
"""
disps = [{'number': disp[0], 'displacement': disp[1:4], 'forces': forces}
for forces, disp in zip(sets_of_forces, self._displacements)]
self._displacement_dataset = {'natom': len(disps[0]['forces']),
'first_atoms': disps}
for disp, forces in zip(
self._displacement_dataset['first_atoms'], sets_of_forces):
disp['forces'] = forces
def set_force_constants_zero_with_radius(self, cutoff_radius):
cutoff_force_constants(self._force_constants,
@ -323,6 +335,17 @@ class Phonopy:
self._force_constants = force_constants
def set_force_sets(self, force_sets):
print
print ("********************************** Warning"
"**********************************")
print "set_force_sets will be obsolete."
print (" The method name is changed to set_displacement_dataset.")
print ("******************************************"
"**********************************")
print
self._displacement_dataset = force_sets
def set_displacement_dataset(self, displacement_dataset):
"""
displacement_dataset:
{'natom': number_of_atoms_in_supercell,
@ -332,7 +355,7 @@ class Phonopy:
'forces': forces on atoms in supercell},
{...}, ...]}
"""
self._displacement_dataset = force_sets
self._displacement_dataset = displacement_dataset
def symmetrize_force_constants(self, iteration=3):
symmetrize_force_constants(self._force_constants, iteration)
@ -951,9 +974,9 @@ class Phonopy:
def _build_supercells_with_displacements(self):
supercells = []
for disp in self._displacements:
for disp in self._displacement_dataset['first_atoms']:
positions = self._supercell.get_positions()
positions[disp[0]] += disp[1:4]
positions[disp['number']] += disp['displacement']
supercells.append(Atoms(
numbers=self._supercell.get_atomic_numbers(),
masses=self._supercell.get_masses(),

14
phonopy/file_IO.py
View File

@ -205,7 +205,19 @@ def is_forces_read(force_sets, num_atom, filenames):
print "\'%s\' does not contain necessary information." % filenames[i]
return is_read
def write_FORCE_SETS_from_dataset(dataset,
filename='FORCE_SETS',
verbose=False):
displacements = [[x['number'], x['displacement']]
for x in dataset['first_atoms']]
forces = [x['forces'] for x in dataset['first_atoms']]
write_FORCE_SETS(filename,
dataset['natom'],
displacements,
forces,
verbose=verbose)
def write_FORCE_SETS(filename,
natom,
displacements,

8
scripts/phono3py
View File

@ -580,7 +580,7 @@ else:
forces_fc3 = parse_FORCES_FC3(disp_dataset)
phono3py.produce_fc3(
forces_fc3,
disp_dataset,
displacement_dataset=disp_dataset,
cutoff_distance=settings.get_cutoff_fc3_distance(),
is_translational_symmetry=options.is_translational_symmetry,
is_permutation_symmetry=options.is_symmetrize_fc3_r)
@ -619,7 +619,8 @@ else:
file_exists(filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=filename)
forces_fc3 = parse_FORCES_FC3(disp_dataset)
phono3py.produce_fc2(forces_fc3, disp_dataset)
phono3py.produce_fc2(forces_fc3,
displacement_dataset=disp_dataset)
else:
if input_filename is None:
filename = 'disp_fc2.yaml'
@ -630,7 +631,8 @@ else:
file_exists(filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=filename)
forces_fc2 = parse_FORCES_FC2(disp_dataset)
phono3py.produce_fc2(forces_fc2, disp_dataset)
phono3py.produce_fc2(forces_fc2,
displacement_dataset=disp_dataset)
if output_filename is None:
filename = 'fc2.hdf5'