Crystal pack

[nasimanousheh]

@jadhao and @kadupitiya In interface.cpp, we can pack the ions like crystal.I updated the examples (not all of them).

There are some issues:

• The potential energy is very high due to repulsion, but after 5000 steps, it goes down; however the real_bath energies are still high.
• When the ions are packed, in lammps I get an error message "Neighbor list overflow, boost neigh_modify one (src/npair_half_bin_atomonly_newton.cpp:114)"

For Positive ion valency (e)= +3 which makes the box full: Positive ion diameter (nm): 0.714; Negative ion diameter (nm): 0.714; Negative ion valency (e) : -1; Concentration (M): 0.9; Confinement size for nano-hub between 2.2 to 4 nm. (less than 2.2 does not work);

I prefer to keep random pack, in some cases like positive ion vacancy = +3 we can switch to crystal pack.

[kadupitiya]

@jadhao: I am approving this to check with nanoHUB.