added dynamical matrix python script

# LAMMPS LATTICE DYNAMICS COMMANDS

## DYNAMICAL MATRIX CALCULATOR

This directory contains the ingredients to calculate a dynamical matrix with python.  

Example:

```

python dynmat.py

```

## Requires: MANYBODY and MOLECULE packages and the Python Library Interface

"""Made by Charlie Sievers Ph.D. Candidate, UC Davis, Donadio Lab 2019"""

# from mpi4py import MPI

from lammps import lammps

import numpy as np

# comm = MPI.COMM_WORLD

# rank = comm.Get_rank()

""" LAMMPS  VARIABLES """

# data files

infile = "silicon_input_file.lmp"

ff_file = "ff-silicon.lmp"

# full output useful for testing

lmp = lammps()

# reduced output useful reducing IO for production runs

# lmp = lammps(cmdargs=["-screen", "none", "-log", "none"])

# lammps commands

lmp.command("atom_style full")

lmp.command("units metal")

lmp.command("processors * * *")

lmp.command("neighbor 1 bin")

lmp.command("boundary p p p")

# read data and force field file

lmp.command("read_data {}".format(infile))

lmp.file("{}".format(ff_file))

lmp.command("dynamical_matrix all eskm 0.000001 file dynmat.dat")

dynmat = np.loadtxt("dynmat.dat")

dynlen = int(3*np.sqrt(len(dynmat)/3))

dynmat = dynmat.reshape((dynlen, dynlen))

eigvals, eigvecs = np.linalg.eig(dynmat)

# frequencies in THz

omegas = np.sqrt(np.abs(eigvals))

print(omegas)