Multi species

[JintaoWu98]

This branch allows us to create a cluster species including multi-individual species. To be more specific, the current arc creates different input Gaussian input files if it receives multispecies. With this new feature, we can combine all the species in one Gaussian input file, followed by the relevant post-processing steps.

[codecov[bot]]

Codecov Report

Attention: 132 lines in your changes are missing coverage. Please review.

Comparison is base (3b46df6) 73.71% compared to head (4aa5282) 73.67%.

Files	Patch %	Lines
arc/scheduler.py	8.69%	121 Missing and 5 partials :warning:
arc/plotter.py	94.44%	1 Missing and 1 partial :warning:
arc/species/species.py	50.00%	1 Missing and 1 partial :warning:
arc/job/adapter.py	83.33%	0 Missing and 1 partial :warning:
arc/job/adapters/common.py	97.14%	0 Missing and 1 partial :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #724 +/- ## ========================================== - Coverage 73.71% 73.67% -0.04% ========================================== Files 99 99 Lines 26992 27180 +188 Branches 5620 5687 +67 ========================================== + Hits 19896 20025 +129 - Misses 5698 5757 +59 Partials 1398 1398 ``` | [Flag](https://app.codecov.io/gh/ReactionMechanismGenerator/ARC/pull/724/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/ReactionMechanismGenerator/ARC/pull/724/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator) | `73.67% <51.47%> (-0.04%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=ReactionMechanismGenerator#carryforward-flags-in-the-pull-request-comment) to find out more.

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[calvinp0]

@JintaoWu98 @alongd

Hi guys, I just wanted to ask, what happens if one species in the multi gauss file failes due to a convergence issue etc. How do we troubleshoot it? Do we rerun all the species again, or will ARC be able to recognise that, for example, 1 of the 3 species in the input.gjf failed and it will only troubleshoot that particular species

[JintaoWu98]

@JintaoWu98 @alongd

Hi guys, I just wanted to ask, what happens if one species in the multi gauss file failes due to a convergence issue etc. How do we troubleshoot it? Do we rerun all the species again, or will ARC be able to recognise that, for example, 1 of the 3 species in the input.gjf failed and it will only troubleshoot that particular species

From my point of view, it can be done individually instead of the whole group to be run again. Because when we are doing the parsing, we slice the big output file into individual ones and investigate the status of each of the species. So when one of the species goes wrong, we can just relaunch the specific one. Though I am not sure if it is being applied currently, could you please comment on that, @alongd? Thanks!

[alongd]

I agree, troubleshooting specific species in the future is the way to go

[alongd]

@JintaoWu98, is this PR ready to be merged? Can you run a multispecies project using the updated brunch to confirm it works as expected?

[JintaoWu98]

@JintaoWu98, is this PR ready to be merged? Can you run a multispecies project using the updated brunch to confirm it works as expected?

Hi @alongd, a multi species project is working as expected. I think it is ready to be merged.