New features & improvement requests

[LiuCMU]

• Accept SDF as the input
• Using Multiple GPUs
• Function API
• Swap date and name in the folder name
• handle IDs with underscore
• Detailed log information by logging in multiple processes
• run from terminal without calling python. For example, type auto3d input.smi --k=1. Thanks @j3mdamas for implementing the entry point feature!
• remove unnecessary variables atom_list and num_atoms here
• new enantiomer check
• different duplicate threshold for cyclic and non-cyclic molecules
• accepts custom NNP
• rename output E_tot to SPE_hartree
• For each Jupyter Notebook documentation in readme.io, state the file link to GitHub