[REQUEST] Incorporating the name of the simulation into checkpoint/ name

[alisagk]

Checkpoints are written in the checkpoints/ directory. Therefore, all runs in the same directory will write to and read from the same directory. To improve this, it would be good to incorporate the simulation's name into checkpoints/. Then, when restarting, the simulation's name is known and easily accessible.

[haykh]

By default now it uses <simname>.ckpt as the directory for checkpoints as per #112