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')
# Simple API example to calculate the harmonic force constants
from phonolammps import Phonolammps
import numpy as np
phlammps = Phonolammps('in.lammps',
supercell_matrix=np.diag([3, 3, 3]),
primitive_matrix=np.identity(3))
phlammps.plot_phonon_dispersion_bands()
force_constants = phlammps.get_force_constants()
print(force_constants)
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()
from dynaphopy.atoms import Structure
import numpy as np
# calculate harmonic force constants with phonoLAMMPS
phlammps = Phonolammps('in.lammps',
supercell_matrix=np.diag([2, 2, 2]),
primitive_matrix=[[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]],
)
phlammps.plot_phonon_dispersion_bands()
# set force constants for dynaphopy
force_constants = ForceConstants(phlammps.get_force_constants(),
supercell=phlammps.get_supercell_matrix())
# Print harmonic force constants
print('harmonic force constants')
print(force_constants.get_array())
structure = phlammps.get_unitcell()
# define structure for dynaphopy
dp_structure = Structure(cell=structure.get_cell(), # cell_matrix, lattice vectors in rows
scaled_positions=structure.get_scaled_positions(),
atomic_elements=structure.get_chemical_symbols(),
primitive_matrix=phlammps.get_primitve_matrix(),
force_constants=force_constants)