Fix for Training Process Halting and lmdb script

[mujeebarshad]

Overview

• The fix for the training process was halted because of wrong atom counts.
• lmdb script crashing fixed as well.
• Training process made doable and smooth

[synsis]

I apologize for not responding promptly to the issues. I hadn't logged into GitHub for a long time and missed the notification. I sincerely appreciate your fix to my code. I will review and process your pull request within a week. Thank you for your understanding and patience.