OSError: [Error] Too many open files (devel branch)

[jkha-unist]

In the devel branch, the updated misc.py causes the programs to open a large number of files simultaneously during a simulation, closing them only upon completion.

For coupled trajectory simulations with a large number of trajectories, this triggers an OSError: [Errno 24] Too many open files, as the system maintains open file descriptors for the entire duration of the simulation. (Currently confirmed for CTv2)