eliminate for loops and use np.sum

[maldil]

Hi Maintainers of this repo,

Thank you very much for your excellent work in Chemml,

I am new to this repository. I am a researcher studying the best practices of evolving data science codes. According to our findings, migration of loop-based computations is a common evolution practice among the developers since it increases performance and code quality. I observed the code in this PR where it could make better use of functions from NumPy and eliminate inefficient loops.

This PR is a minor contribution compared to all the hard work that you have done in this repo. However, I am hoping that it will enhance code quality and, hopefully, performance.