43 lines
1.0 KiB
Python
43 lines
1.0 KiB
Python
"""Made by Charlie Sievers Ph.D. Candidate, UC Davis, Donadio Lab 2019"""
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# from mpi4py import MPI
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from lammps import lammps
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import numpy as np
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# comm = MPI.COMM_WORLD
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# rank = comm.Get_rank()
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""" LAMMPS VARIABLES """
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# data files
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infile = "silicon_input_file.lmp"
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ff_file = "ff-silicon.lmp"
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# full output useful for testing
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lmp = lammps()
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# reduced output useful reducing IO for production runs
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# lmp = lammps(cmdargs=["-screen", "none", "-log", "none"])
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# lammps commands
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lmp.command("atom_style full")
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lmp.command("units metal")
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lmp.command("processors * * *")
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lmp.command("neighbor 1 bin")
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lmp.command("boundary p p p")
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# read data and force field file
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lmp.command("read_data {}".format(infile))
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lmp.file("{}".format(ff_file))
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lmp.command("dynamical_matrix all eskm 0.000001 file dynmat.dat")
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dynmat = np.loadtxt("dynmat.dat")
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dynlen = int(3*np.sqrt(len(dynmat)/3))
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dynmat = dynmat.reshape((dynlen, dynlen))
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eigvals, eigvecs = np.linalg.eig(dynmat)
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# frequencies in THz
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omegas = np.sqrt(np.abs(eigvals))/2/np.pi
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print(omegas)
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