new examples and debugging code changes

examples/mdi/in.sequence.python

@@ -0,0 +1,21 @@
+# MDI engine script to process a series of evaulate, run, minimize commands
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 1 0 1 0 1
+create_box	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix             1 all nve
+
+thermo          10
+
+mdi             engine