Alternative lammps parse

[Leimeroth]

Another approach to parsing without readlines() and multiple loops

EDIT (@liamhuber -- correct if I'm wrong about this, Niklas): Intended to solve #671

[coveralls]

Pull Request Test Coverage Report for Build 3095441284

• 16 of 17 (94.12%) changed or added relevant lines in 1 file are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.02%) to 68.274%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/base.py	16	17	94.12%

Totals
Change from base Build 3089757525:	0.02%
Covered Lines:	12090
Relevant Lines:	17708

---

💛 - Coveralls

[pmrv]

Based on this I've found a version that is even more efficient, will push it when I have cleaned it up. In the meantime feel free to merge #657, so you don't need to wait for me.

[jan-janssen]

Using a for loop could be an issue performance wise, is it possible to solve this with arrays as @samwaseda did before?

[Leimeroth]

I am not sure what @samwaseda did, but the previous implementation read in the whole file into memory and then did multiple list comprehensions and initialized seperate StringIO and DataFrame instances for each line, so I assume this is a improvement already.
Anyway @pmrv did some tests and already found a better version so this was not merged yet, but only exists as a reminder.

[Leimeroth]

@pmrv should I merge this or do you want to create a PR for your version?

[jan-janssen]

@pmrv should I merge this or do you want to create a PR for your version?

Can we still do a set of benchmarks before we merge these changes? I have the feeling we are moving back and forth with the LAMMPS parser, so I would like to have clear reasoning why we choose one implementation over another.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[Leimeroth]

up

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[pmrv]

At this point, let's just merge this and revisit with pymatgen parser at some point in the future.