Created PyLammps documentation

Based on material presented during MD Workshop at Temple University in
August 2016.

python/examples/pylammps/README

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+# Compile LAMMPS as shared library
+
+git clone https://github.com/lammps/lammps.git
+cd lammps/src
+python Make.py -m mpi -png -s ffmpeg exceptions -a file
+
+make -j 4 mode=shlib auto
+cd ../..
+
+# Install Python package
+
+virtualenv testing
+source testing/bin/activate
+
+(testing) cd lammps/python
+(testing) python install.py
+(testing) pip install jupyter matplotlib mpi4py
+
+(testing) cd ../../examples
+
+# Launch jupter and work inside browser
+
+(testing) jupyter notebook
+
+# Use Ctrl+c to stop jupyter
+
+# finally exit the virtualenv
+(testing) deactivate

python/examples/pylammps/dihedrals/data.dihedral

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+Comment line
+ 
+4 atoms
+0 bonds
+0 angles
+1 dihedrals
+0 impropers
+ 
+1 atom types
+0 bond types
+0 angle types
+1 dihedral types
+0 improper types
+ 
+-5.0   5.0      xlo xhi
+-5.0   5.0      ylo yhi
+-5.0   5.0      zlo zhi
+0.0   0.0   0.0   xy xz yz
+ 
+Atoms # molecular
+
+1      1   1     -1.00000     1.00000      0.00000
+2      1   1     -0.50000     0.00000      0.00000
+3      1   1      0.50000     0.00000      0.00000
+4      1   1      1.00000     1.00000      0.00000
+
+Dihedral Coeffs
+
+1      80.0   1   2
+
+Dihedrals
+
+1      1   1  2  3  4
+

python/examples/pylammps/mpi4py/hello.py

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+from mpi4py import MPI
+
+comm=MPI.COMM_WORLD
+print("Hello from rank %d of %d" % (comm.rank, comm.size))

python/examples/pylammps/mpi4py/in.melt

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+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+#dump		id all atom 50 dump.melt
+
+#dump		2 all image 25 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+#dump		3 all movie 25 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3
+
+thermo		50
+run		250

python/examples/pylammps/mpi4py/melt.py

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+from mpi4py import MPI
+from lammps import PyLammps
+
+L = PyLammps()
+L.file('in.melt')
+
+
+if MPI.COMM_WORLD.rank == 0:
+    pe = L.eval("pe")
+    print("Potential Energy:", pe)