[gpaw-users] Phonon band structure
Jakob Blomquist
jakob.blomqvist at mah.se
Thu Dec 16 16:42:56 CET 2010
Hi
Everytime I try to use GPAW and the phonon module I get a symmetry error
after the first step (when one atom is moved once in one direction).
****************
Writing GPAW-phonon.eq.pckl
Traceback (most recent call last):
File "Al-phonon.py", line 18, in <module>
ph.run()
File "/home/jakob/ase/ase/phonons.py", line 206, in run
forces = atoms_lmn.get_forces()
File "/home/jakob/ase/ase/atoms.py", line 536, in get_forces
forces = self.calc.get_forces(self)
File "/usr/local/lib/python2.6/dist-packages/gpaw/aseinterface.py",
line 61, in get_forces
force_call_to_set_positions=force_call_to_set_positions)
File "/usr/local/lib/python2.6/dist-packages/gpaw/paw.py", line 239,
in calculate
self.set_positions(atomsWriting GPAW-phonon.eq.pckl
Traceback (most recent call last):
File "Al-phonon.py", line 18, in <module>
ph.run()
File "/home/jakob/ase/ase/phonons.py", line 206, in run
forces = atoms_lmn.get_forces()
File "/home/jakob/ase/ase/atoms.py", line 536, in get_forces
forces = self.calc.get_forces(self)
File "/usr/local/lib/python2.6/dist-packages/gpaw/aseinterface.py",
line 61, in get_forces
force_call_to_set_positions=force_call_to_set_positions)
File "/usr/local/lib/python2.6/dist-packages/gpaw/paw.py", line 239,
in calculate
self.set_positions(atoms)
File "/usr/local/lib/python2.6/dist-packages/gpaw/paw.py", line 293,
in set_positions
spos_ac = self.initialize_positions(atoms)
File "/usr/local/lib/python2.6/dist-packages/gpaw/paw.py", line 285,
in initialize_positions
self.wfs.set_positions(spos_ac)
File "/usr/local/lib/python2.6/dist-packages/gpaw/wavefunctions.py",
line 914, in set_positions
WaveFunctions.set_positions(self, spos_ac)
File "/usr/local/lib/python2.6/dist-packages/gpaw/wavefunctions.py",
line 247, in set_positions
self.symmetry.check(spos_ac)
File "/usr/local/lib/python2.6/dist-packages/gpaw/symmetry.py", line
139, in check
raise RuntimeError('Broken symmetry!')
)
File "/usr/local/lib/python2.6/dist-packages/gpaw/paw.py", line 293,
in set_positions
spos_ac = self.initialize_positions(atoms)
File "/usr/local/lib/python2.6/dist-packages/gpaw/paw.py", line 285,
in initialize_positions
self.wfs.set_positions(spos_ac)
File "/usr/local/lib/python2.6/dist-packages/gpaw/wavefunctions.py",
line 914, in set_positions
WaveFunctions.set_positions(self, spos_ac)
File "/usr/local/lib/python2.6/dist-packages/gpaw/wavefunctions.py",
line 247, in set_positions
self.symmetry.check(spos_ac)
File "/usr/local/lib/python2.6/dist-packages/gpaw/symmetry.py", line
139, in check
raise RuntimeError('Broken symmetry!')
************
I use GPAW version 0.7.6383
The latest revision of the ase/phonon.py
and
ase version 3.4.0 stable revision
Any suggestions?
/Jakob Blomquist
Kristen Kaasbjerg wrote:
> I have now added a simple example to the ASE documentation illustrating
> how to use the new phonon module:
>
> https://wiki.fysik.dtu.dk/ase/ase/phonons.html#module-phonons
>
> A few figures will be added soon.
>
> Kristen
>
>
>
>> Dear GPAW-users,
>>
>> I am a post-doc in Kyoto university in Japan. I work for phonopy.
>> The Si band structure may be calculated as follows:
>>
>> from gpaw import GPAW
>> from ase import *
>> from ase.calculators import numeric_force
>> from phonopy import Phonopy
>> import numpy as np
>>
>> # GPAW setting
>> a = 5.404
>> bulk = Atoms(symbols='Si8',
>> positions=[(0, 0, 0),
>> (0, 0.5, 0.5),
>> (0.5, 0, 0.5),
>> (0.5, 0.5, 0),
>> (0.25, 0.25, 0.25),
>> (0.25, 0.75, 0.75),
>> (0.75, 0.25, 0.75),
>> (0.75, 0.75, 0.25)],
>> pbc=True)
>> bulk.set_cell((a, a, a), scale_atoms=True)
>>
>> n = 32
>> calc = GPAW(gpts=(n, n, n),
>> nbands=8*3,
>> width=0.01,
>> kpts=(2, 2, 2),
>> convergence={'eigenstates': 1e-7}
>> )
>>
>> # Phonopy pre-process
>> print "------"
>> print "Phonon"
>> print "------"
>> # 1st arg. is the input unit cell.
>> # 2nd arg. is the supercell lattice relative to the unit cell.
>> # 'distance' is the distance of displacements.
>> # Default symmetry tolerance is 1e-5 in fractional coordinates.
>> phonon = Phonopy(bulk, [[1,0,0],[0,1,0],[0,0,1]], distance=0.01)
>> symmetry = phonon.get_symmetry()
>> print "Space group:", symmetry.get_international_table()
>>
>>
>> phonon.print_displacements()
>> supercells = phonon.get_supercells_with_displacements()
>>
>> # Force calculations
>> set_of_forces = []
>> for scell in supercells:
>> cell = Atoms( symbols=scell.get_chemical_symbols(),
>> scaled_positions=scell.get_scaled_positions(),
>> cell=scell.get_cell(),
>> pbc=True )
>> cell.set_calculator(calc)
>> forces = cell.get_forces()
>> drift_force = forces.sum(axis=0)
>> print " ---------------------------------"
>> print " ", "%11.5f"*3 % tuple(drift_force)
>> # Simple translational invariance
>> for force in forces:
>> force -= drift_force / forces.shape[0]
>> set_of_forces.append(forces)
>>
>> # Phonopy post-process
>> # 1st arg. is a relative lattice to the input unit cell.
>> # 2nd arg. is bunch of the calculated forces.
>> phonon.set_post_process([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]], set_of_forces)
>>
>> # Phonon dispersion relation
>> bands = []
>>
>> q_start = np.array([0.5,0.5,0.0])
>> q_end = np.array([0.0,0.0,0.0])
>> band = []
>> for i in range(51):
>> band.append( q_start + ( q_end - q_start ) / 50 * i )
>>
>> bands.append(band)
>>
>> q_start = np.array([0.0,0.0,0.0])
>> q_end = np.array([0.5,0.0,0.0])
>> band = []
>> for i in range(51):
>> band.append( q_start + ( q_end - q_start ) / 50 * i )
>>
>> bands.append(band)
>>
>> #*********************
>> # Matplotlib required
>> #*********************
>> print "\nPhonon dispersion:"
>> phonon.set_band_structure( bands )
>> phonon.plot_band_structure().show()
>>
>>
>>
>>
>>
>> Togo
>>
>> On Fri, Dec 3, 2010 at 7:02 PM, Kristen Kaasbjerg <kkaa at fysik.dtu.dk> wrote:
>>
>>
>>> If someone finds it useful then why not ?
>>> I should stress though, that the ASE implementation has features for
>>> calculating phonon dispersion and mode visualization with ag.
>>>
>>> By the way, frophon code seem to have been replaced by the Phononpy code:
>>> http://phonopy.sourceforge.net/
>>>
>>> Kristen
>>>
>>>
>>>
>>>> Hi,
>>>>
>>>> by looking at the latest abinit release one can see that they
>>>> "Print out VASP-style POSCAR and FORCES files, for use with PHON or
>>>> frophon codes for frozen phonon calculations."
>>>> http://www.abinit.org/documentation/helpfiles/for-v6.4/release_notes/release_notes.html
>>>>
>>>> Could this way be also interesting for us?
>>>> website of phon: http://www.homepages.ucl.ac.uk/~ucfbdxa/phon/
>>>>
>>>> Marcin
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>>>
>>>
>>
>>
>>
>
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