Added additional tutorials for the dynamical matrix calculator (4b8621e7) · Commits · 郑智淋 / lammps

examples/USER/phonon/dynamical_matrix_command/GaAs/GaAs.py

0 → 100644

+39 −0

Changes for examples/USER/phonon/dynamical_matrix_command/GaAs/GaAs.py: 39 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		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()

examples/USER/phonon/dynamical_matrix_command/GaN/GaN.py

0 → 100644

+39 −0

Changes for examples/USER/phonon/dynamical_matrix_command/GaN/GaN.py: 39 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		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()

examples/USER/phonon/dynamical_matrix_command/Quartz/quartz.py

0 → 100644

+57 −0

Changes for examples/USER/phonon/dynamical_matrix_command/Quartz/quartz.py: 57 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		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(33np.sqrt(np.abs(eigv))/(2np.pi), 80)
		plt.xlabel('Frequency (cm-1)')
		plt.show()

examples/USER/phonon/dynamical_matrix_command/README.md→examples/USER/phonon/dynamical_matrix_command/Silicon/README.md

+2 −2

Changes for examples/USER/phonon/dynamical_matrix_command/Silicon/README.md: 2 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -7,7 +7,7 @@ This directory contains the ingredients to calculate a dynamical matrix.
		Example:
		```
		NP=4 #number of processors
		mpirun -np $NP lmp_mpi < in.silicon > out.silicon
		mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
		```

		To test out a different silicon example:
		@@ -15,7 +15,7 @@ To test out a different silicon example:
		LMP_FILE=amorphous_silicon.lmp
		cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp
		NP=4 #number of processors
		mpirun -np $NP lmp_mpi < in.silicon > out.silicon
		mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
		```

		## Requires: MANYBODY and MOLECULE packages

examples/USER/phonon/dynamical_matrix_command/Si.opt.tersoff→examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff

+0 −0

File moved.

View file

Admin message