added dynamical matrix python script

examples/USER/phonon/dynamical_matrix_command/python/README.md

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+# 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

examples/USER/phonon/dynamical_matrix_command/python/dynmat.py

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+"""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)