update tutorial

update torchNEP

Update tools.py

Delete nep_model.pt

Update io.py

Update run_deform.py

Update run_gpumd.py

updata tutorial

Update run_radiation_overlap.py

Update run_primary_radiaion.py

Update run_deposit.py

Update run_deposit.py

Update atoms.py

Update run_radiation_overlap.py

Update run_primary_radiaion.py