Fix field names in diag_parser.py and add example script

[yut23]

PR summary

Make sure np.genfromtxt() doesn't mess with the field names, add an example script that plots mass fractions over time from species_diag.out, and add a note to the docs.

PR motivation

PR checklist

• test suite needs to be run on this PR
• this PR will change answers in the test suite to more than roundoff level
• all newly-added functions have docstrings as per the coding conventions
• the CHANGES file has been updated, if appropriate
• if appropriate, this change is described in the docs