def run_phonolammps():
n = 2
phlammps = Phonolammps('in.graphene',
supercell_matrix=[[n, 0, 0], [0, n, 0], [0, 0, n]])
unitcell = phlammps.get_unitcell()
force_constants = phlammps.get_force_constants()
supercell_matrix = phlammps.get_supercell_matrix()
print('unitcell')
print('*' * 50)
print(unitcell)
print('force const')
print('*' * 50)
print(force_constants)
print('supercell')
print('*' * 50)
print(supercell_matrix)
from phonopy import Phonopy
phonon = Phonopy(unitcell, supercell_matrix)
print(phonon)
print(dir(phonon))
phonon.set_force_constants(force_constants)
phonon.set_mesh([20, 20, 20])
# phonon.write_yaml_band_structure('band.conf')
# phonon.set_band_structure('band.conf')
# phonon.plot_band_structure().savefig('band.png')
# phonon.set_total_DOS()
# phonon.plot_total_DOS().savefig('dos.png')
phonon.set_thermal_properties()
# print(phonon.get_thermal_properties_dict())
phonon.plot_thermal_properties().savefig('therm.png')
# Integration with phonopy
from phonolammps import Phonolammps
from phonopy import Phonopy
phlammps = Phonolammps('in.lammps',
supercell_matrix=[[3, 0, 0], [0, 3, 0], [0, 0, 3]])
unitcell = phlammps.get_unitcell()
force_constants = phlammps.get_force_constants()
supercell_matrix = phlammps.get_supercell_matrix()
phonon = Phonopy(unitcell, supercell_matrix)
phonon.set_force_constants(force_constants)
phonon.set_mesh([20, 20, 20])
phonon.set_total_DOS()
phonon.plot_total_DOS().show()
phonon.set_thermal_properties()
phonon.plot_thermal_properties().show()
for q, d, freq in zip(q_points, distances, frequencies):
print q, d, freq
phonon.plot_band_structure().show()
# Mesh sampling 20x20x20
phonon.set_mesh([20, 20, 20])
phonon.set_thermal_properties(t_step=10,
t_max=1000,
t_min=0)
# DOS
phonon.set_total_DOS(sigma=0.1)
for omega, dos in np.array(phonon.get_total_DOS()).T:
print "%15.7f%15.7f" % (omega, dos)
phonon.plot_total_DOS().show()
# Thermal properties
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
phonon.plot_thermal_properties().show()
# PDOS
phonon.set_mesh([10, 10, 10],
is_mesh_symmetry=False,
is_eigenvectors=True)
phonon.set_partial_DOS(tetrahedron_method=True)
omegas, pdos = phonon.get_partial_DOS()
pdos_indices = [[0], [1]]
phonon.plot_partial_DOS(pdos_indices=pdos_indices,
legend=pdos_indices).show()
def test_phonolammps():
os.chdir('data')
with open('data.si', 'w') as f:
f.write('''Generated using dynaphopy
8 atoms
1 atom types
0.0000000000 5.4500000000 xlo xhi
0.0000000000 5.4500000000 ylo yhi
0.0000000000 5.4500000000 zlo zhi
0.0000000000 0.0000000000 0.0000000000 xy xz yz
Masses
1 28.0855000000
Atoms
1 1 4.7687500000 4.7687500000 4.7687500000
2 1 4.7687500000 2.0437500000 2.0437500000
3 1 2.0437500000 4.7687500000 2.0437500000
4 1 2.0437500000 2.0437500000 4.7687500000
5 1 0.6812500000 0.6812500000 0.6812500000
6 1 0.6812500000 3.4062500000 3.4062500000
7 1 3.4062500000 0.6812500000 3.4062500000
8 1 3.4062500000 3.4062500000 0.6812500000
''')
with open('si.in', 'w') as f:
f.write('''
units metal
boundary p p p
box tilt large
atom_style atomic
read_data data.si
pair_style tersoff
pair_coeff * * SiCGe.tersoff Si(C)
neighbor 0.3 bin
''')
supercell = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
print(supercell)
phlammps = Phonolammps('si.in', supercell_matrix=supercell)
print(phlammps)
unitcell = phlammps.get_unitcell()
force_constants = phlammps.get_force_constants()
supercell_matrix = phlammps.get_supercell_matrix()
print(unitcell)
print(force_constants)
print(supercell_matrix)
os.chdir('..')
return
phonon = Phonopy(unitcell, supercell_matrix)
phonon.set_force_constants(force_constants)
phonon.set_mesh([20, 20, 20])
phonon.set_total_DOS()
phonon.plot_total_DOS().show()
phonon.set_thermal_properties()
phonon.plot_thermal_properties().show()
class PhononFromModel(object):
"""
This class uses frozen phonon method to calculate the phonon dispersion curves and thermodynamic
properties of a structure.
The steps are as follows:
1. Displaced structures are obtained from pristine structure via phonopy.
2. The forces of each displaced structures are calculated by model
3. The forces are passed to phonopy object and the force constant are produced
4. Phonon is calculated once the force constant matrix is available.
Args:
model (model object): a model object that has a method "calculate_forces" that takes in a list of
structures and return a list of N*3 forces, where N are the number of atoms in each structures
structure (pymatgen structure): a pristine pymatgen structure
atom_disp (float): small displacements in Angstrom
"""
def __init__(self, model=None, structure=None, atom_disp=0.015, **kwargs):
self.model = model
self.structure = structure
self.atom_disp = atom_disp
self.qpoints, self.vertices = get_qpoints_and_vertices(self.structure)
is_plusminus = kwargs.get('is_plusminus', True)
is_diagonal = kwargs.get('is_diagonal', True)
is_trigonal = kwargs.get('is_diagonal', False)
supercell_matrix = kwargs.get('is_diagonal', None)
ph_structure = get_phonopy_structure(self.structure)
if supercell_matrix is None:
supercell_matrix = np.eye(3) * np.array((1, 1, 1))
self.phonon = Phonopy(unitcell=ph_structure, supercell_matrix=supercell_matrix)
self.phonon.generate_displacements(distance=self.atom_disp,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal)
disp_supercells = self.phonon.get_supercells_with_displacements()
# Perfect supercell structure
init_supercell = self.phonon.get_supercell()
# Structure list to be returned
self.structure_list = [get_pmg_structure(init_supercell)]
for c in disp_supercells:
if c is not None:
self.structure_list.append(get_pmg_structure(c))
forces = self.model.calculate_forces(self.structure_list)
self.phonon.set_forces(forces[1:])
self.phonon.produce_force_constants()
logging.info("Force constant produced")
def get_thermo_properties(self, mesh=[8, 8, 8], t_step=10, t_max=3000, t_min=0):
self.phonon.set_mesh(mesh=mesh)
self.phonon.set_thermal_properties(t_step=t_step,
t_max=t_max,
t_min=t_min)
plt = self.phonon.plot_thermal_properties()
return plt
def get_bs_plot(self, points_per_line=50, figsize=(6, 4), ylim=[-1, 5]):
bands = []
bands = append_bands(bands, self.qpoints, points_per_line)
self.phonon.set_band_structure(bands)
q_points, self.distances, self.frequencies, eigvecs = self.phonon.get_band_structure()
special_points = self.phonon._band_structure._special_points
distance = self.phonon._band_structure._distance
plt.figure(figsize=figsize)
for j, (d, f) in enumerate(zip(self.distances, self.frequencies)):
for i, freqs in enumerate(f.T):
if i == 0 and j == 0:
plt.plot(d, freqs, "b-", lw=1)
else:
plt.plot(d, freqs, "b-", lw=1)
for sp in special_points:
plt.axvline(x=sp, linestyle=':', linewidth=1, color='k')
plt.axhline(y=0, linestyle=':', linewidth=1, color='k')
plt.xticks(special_points, ["$\mathrm{%s}$" % i for i in self.vertices])
plt.xlabel("Wave vector")
plt.ylabel("Frequency (THz)")
plt.xlim(0, distance)
plt.ylim(ylim)
plt.yticks(list(range(ylim[0], ylim[-1]+1)))
plt.tight_layout()
return plt
