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remove third_order command and ASE based examples to be added in a new pull request

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Axel Kohlmeyer
2019-02-28 15:21:48 -05:00
parent 9298fe7868
commit 7062bc862e
18 changed files with 5 additions and 6532 deletions
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39
examples/USER/phonon/dynamical_matrix_command/GaAs/GaAs.py
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from ase import Atoms, Atom
from ase.calculators.lammpslib import LAMMPSlib
import numpy as np
import matplotlib.pyplot as plt
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
GaAs = Atoms([Atom('Ga', (0.0, 0.0, 0.0)),
Atom('As', (1.413425, 1.413425, 1.413425))],
cell=[(0.0, 2.82685, 2.82685), (2.82685, 0.0, 2.82685), (2.82685, 2.82685, 0.0)],
pbc=True,)
cmds = ["pair_style bop", "pair_coeff * * ../../../../../potentials/GaAs.bop.table Ga As",
"comm_modify cutoff 12"]
mends = ["info system",
"dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
"neigh_modify delay 0"]
N = 5
GaAs = GaAs.repeat([N, N, N])
lammps = LAMMPSlib(lmpcmds=cmds, atom_types={'Ga': 1, 'As': 2}, amendments=mends, log_file='lammps.log')
GaAs.set_calculator(lammps)
GaAs.get_potential_energy()
if rank == 0:
dynmat = np.loadtxt("dynmat.dat")
dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
eigv = np.linalg.eigvals(dynmat)
eigv.sort()
eigv = np.sqrt(np.abs(eigv))/(2*np.pi)
plt.hist(eigv, 80)
plt.xlabel('Frequency (THz)')
plt.show()

39
examples/USER/phonon/dynamical_matrix_command/GaN/GaN.py
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from ase import Atoms, Atom
from ase.calculators.lammpslib import LAMMPSlib
import numpy as np
import matplotlib.pyplot as plt
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
GaN = Atoms([Atom('Ga', (1.59, 0.917986928012, 0.0)),
Atom('Ga', (1.59, -0.917986928012, 2.583)),
Atom('N', (1.59, 0.917986928012, 1.98891)),
Atom('N', (1.59, -0.917986928012, 4.57191))],
cell=[(1.59, -2.75396078403, 0.0), (1.59, 2.75396078403, 0.0), (0.0, 0.0, 5.166)],
pbc=True)
cmds = ["pair_style tersoff", "pair_coeff * * ../../../../../potentials/GaN.tersoff Ga N"]
mends = ["info system",
"dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
"neigh_modify delay 0"]
N = 6
GaN = GaN.repeat([N, N, N])
lammps = LAMMPSlib(lmpcmds=cmds, atom_types={'Ga': 1, 'N': 2}, amendments=mends, log_file='lammps.log')
GaN.set_calculator(lammps)
GaN.get_potential_energy()
if rank == 0:
dynmat = np.loadtxt("dynmat.dat")
dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
eigv = np.linalg.eigvals(dynmat)
eigv.sort()
eigv = np.sqrt(np.abs(eigv))/(2*np.pi)
plt.hist(eigv, 80)
plt.xlabel('Frequency (THz)')
plt.show()

57
examples/USER/phonon/dynamical_matrix_command/Quartz/quartz.py
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@ -1,57 +0,0 @@
from ase import Atoms, Atom
from ase.calculators.lammpslib import LAMMPSlib
import numpy as np
import matplotlib.pyplot as plt
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
quartz = Atoms(
[Atom('Si', (1.1545226, -1.99969180169, 0.0)),
Atom('Si', (1.1545226, 1.99969180169, 3.6036)),
Atom('Si', (2.6069548, 2.15247249027e-16, 1.8018)),
Atom('O', (1.6724232, -0.624132037742, 0.64378314)),
Atom('O', (1.6724232, 0.624132037742, 2.9598186618)),
Atom('O', (2.1623026, -2.49695388906, 4.2473849418)),
Atom('O', (3.5392742, 1.13629495821, 1.1580150582)),
Atom('O', (3.5392742, -1.13629495821, 2.4455813382)),
Atom('O', (2.1623026, 2.49695388906, 4.76161686))],
cell=[(2.458, -4.257380885, 0.0), (2.458, 4.257380885, 0.0), (0.0, 0.0, 5.4054)],
pbc=True,
)
# number of repeats
N = 3
quartz = quartz.repeat([N, N, N])
header = ['units metal',
'atom_style charge',
'atom_modify map array sort 0 0']
cmds = ["pair_style buck/coul/long 10.0 8.0",
"pair_coeff 1 1 0 1 0",
"pair_coeff 1 2 18003.7572 0.20520 133.5381",
"pair_coeff 2 2 1388.7730 0.36232 175.0000",
"kspace_style ewald 1.0e-12",
"set type 1 charge 2.4",
"set type 2 charge -1.2"]
mends = ["dynamical_matrix all eskm 0.000001 file dynmat.dat binary no",
"neigh_modify delay 0"]
lammps = LAMMPSlib(lmpcmds=cmds, lammps_header=header, amendments=mends, log_file='lammps.log')
quartz.set_calculator(lammps)
quartz.get_potential_energy()
if rank == 0:
dynmat = np.loadtxt("dynmat.dat")
dynmat = dynmat.reshape(([int(3*(len(dynmat)/3)**0.5), int(3*(len(dynmat)/3)**0.5)]))
eigv = np.linalg.eigvals(dynmat)
eigv.sort()
plt.hist(33*np.sqrt(np.abs(eigv))/(2*np.pi), 80)
plt.xlabel('Frequency (cm-1)')
plt.show()