Use a persistent hdf5 file handler

[sanathkeshav]

Uses a file handler to write data (collectively) instead of the results file name. This avoids unnecessary opening and closing of the HDF5 file, which causes a substantial overhead. The file is opened once, and a persistent file handler is stored and used to write outputs, and is closed at the end.

Checklist:

• I made sure that the CI passed before I ask for a review.
• I added a summary of the changes (compared to the last release) in the CHANGELOG.md.
• If necessary, I made changes to the documentation and/or added new content.
• I will remember to squash-and-merge, providing a useful summary of the changes of this PR.