Add initial species in core before seed mechanism

[hwpang]

Motivation or Problem

The current initialization would fail if one uses a pyrms-based reactor with seed mechanism and the seed mechanism contains species that are the initial species. It would fail with an error related to the initial species not in the phase.names.

Description of Changes

I moved the code block for initializing the bath gases and the initial species in front of the seed mechanism code block.

[hwpang]

A bit more detailed explanation for future reference. Currently, when RMG tries to add pressure dependent reactions from the seed mechanism to core that are pressure dependent on the initial species, the code crashes when it tries to make the corresponding core phase(s). This is because the core phase tries to get the index of that initial species from phase.names, but initial species are not yet in the core phase.

[JacksonBurns]

Rebasing with updated CI

[github-actions]

This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days.

[JacksonBurns]

@hwpang this looks simple enough - want to try and revive this one?

[hwpang]

I will close this PR for now as I don't have time to work on it.

[JacksonBurns]

Blocked by #2514

[github-actions]

This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days.