Advertising the atomate2 paper writing

[Zhuoying]

Dear contributors,

We are thrilled to share the commencement of the Atomate2 paper's preparation phase. Our goal is to have the initial draft ready by our upcoming monthly gathering on March 29.

Since Atomate2 is truly a collective endeavor, we want to ensure that every contributor has the opportunity to contribute to the paper (including those who have made minor contributions but would like to do more to qualify for authorship).

Overview

The paper will be split into 5 sections:

1. Introduction & Background (@computron)
2. Atomate2 Design Philosophy & Overview (@utf)
3. Calculators (team)
4. Worklows (team)
5. Conclusion & Future Work (@computron, @utf)

Below, you will find a list of teams categorized according to their workflow and calculator code contributions, compiled to the best of my knowledge. Should there be any oversight or additional workflows you've contributed to that are not mentioned, please do not hesitate to bring them to our attention.

Calculators

• VASP (TBD)
• CP2K (@nwinner)
• ABINIT (@gpetretto, @davidwaroquiers, @VicTrqt, @gmrigna)
• FHI-aims (@tpurcell90, @ansobolev)
• QCHEM (@rdguha1995, @rkingsbury, @rohithsrinivaas)
• Force fields (@matthewkuner @janosh @JaGeo @CompRhys)

We kindly ask each calculator team to prepare the following:

• 300-600 words of text covering implementation, usage notes, and any existing use case/papers using this implementation.
• A summary of the key calculation types implemented.
• No figure needed.

Workflows

• amset (@utf )
• electron phonon (@utf)
• lobster (@JaGeo @naik-aakash)
• elastic (@mjwen @utf @JaGeo)
• harmonic phonon using phonopy (@JaGeo @ab5424)
• anharmonic phonon using hiphive (WIP, @hrushikesh-s @Zhuoying)
• electrode (@jmmshn)
• vasp and cp2k defect (WIP, @jmmshn @nwinner )
• aimd and ffmd (WIP, @gpetretto, @mjwen, @davidwaroquiers,@esoteric-ephemera, @chiang-yuan)
• openMM (WIP, @orionarcher)
• mp (@esoteric-ephemera @Andrew-S-Rosen @janosh)
• magnetic orderings (WIP, @mattmcdermott @mkhorton @guymoore13)
• adsorption (WIP, @itsduowang)
• ferroelectric (WIP, @fraricci)

We kindly ask each workflow team to prepare the following:

• 500-750 words of text covering methodology, usage notes, and any existing use case/papers using this workflow;
• a workflow diagram (will talk more about standardizing the diagram in our next monthly meeting on Mar. 29)
• a "pretty" output collage of plots (from raw data calculated from the workflow).

Welcoming Additional Contributors

There are some contributors to atomate2 who have provided fixes here and there but who have not contributed to major workflows. We want to make it clear that these contributors are still welcome to be included on the atomate2 paper. However, we're suggesting that these people could contribute more to the atomate2 code base, either by fixing an open issue or by adding a new tutorial to the documentation. Currently, we could do with the following tutorials, however, if you have other ideas then please let @utf know.

• How to write your own atomate2 workflow.
• Introduction to the data and document stores.
• An introduction to the input sets framework.
• An introduction to task documents, schemas, and emmet.
• A high level overview of the concepts in atomate2: job/flow makers, input sets, task documents, builders.

If you think you could fit into this category, please reach out to @utf via email and we can chat.

List of tutorial contributors: @QuantumChemist, @ml-evs, @JonathanSchmidt1, @naik-aakash, @JaGeo

Notes

1. We are delighted to hear your thoughts. For example, if you think anyone should be added to the authorship but not currently listed, don't hesitate to let us know.

2. You are encouraged to collaborate within or across teams as you see fit. To simplify the collecting process, we propose nominating the first person listed in each workflow as the team leader by default. However, please feel free to adjust the leadership roles within your teams or to merge different workflow teams if you find it necessary. If any changes occur, we would appreciate a brief notification. I will make ongoing updates to the workflow list based on your feedback for a better track.

Point of contact for accessing collaboration platforms

Overleaf: Please leave your email to @utf for access to our Overleaf project. Zoom meeting: Please leave your email to @Zhuoying for the Google invite (our next meeting will be 8:30 AM on March 29 PST to discuss jobflow-remote and the paper writing) Slack channel: Please leave your email to @Andrew-S-Rosen for the Slack invite.

Your contributions are greatly valued. Any of your feedback and thoughts are welcome!

[Andrew-S-Rosen]

I am very excited about this effort and happy to be involved! Apologies for not being able to make the last couple of meetings --- I've had some conflicts.

In any case, @esoteric-ephemera shall I counter-nominate you for the MP workflow lead? 😉 Of course, I am happy to help write.

[Zhuoying]

In any case, @esoteric-ephemera shall I counter-nominate you for the MP workflow lead? 😉 Of course, I am happy to help write.

@Andrew-S-Rosen Thanks for the nomination. I have put @esoteric-ephemera as the first name of the MP workflow.

Hi @mjwen, since @utf and @JaGeo are the lead of a few workflows, are you interested in being the lead of the elastic workflow?

[mjwen]

@Zhuoying Yes, I'd be happy to!

[JaGeo]

Thank you, @Zhuoying . Could you add @ab5424 to the harmonic phonon workflow as well? Thanks! The implemented workflow was based on a previous implementation in his Master thesis.

(To mention shortly, I also only indirectly contributed to the FHI-aims implementation as it starts from the phonon workflow)

[utf]

Thanks very much for putting this message together @Zhuoying. I would just raise two additional points.

Workflows vs Calculators

I think we should make a distinction in the paper between workflows and force/energy calculators. Many of the workflows are agnostic to the choice of calculator (e.g., elastic, phonon, defect etc). I suggest we therefore have a section before workflows providing a short summary for each calculator.

Welcoming additional contributions

There are some contributors to atomate2 who have provided fixes here and there but who have not contributed to major workflows. I want to make it clear that these contributors are still welcome to be included on the atomate2 paper. However, we're suggesting that these people could contribute more to the atomate2 code base, either by fixing an open issue or by adding a new tutorial to the documentation. Currently, I think we could do with the following tutorials, however, if you have other ideas then please let me know.

• How to write your own atomate2 workflow.
• Introduction to the data and document stores.
• An introduction to the input sets framework.
• An introduction to task documents, schemas, and emmet (@rkingsbury)
• A high level overview of the concepts in atomate2: job/flow makers, input sets, task documents, builders (@QuantumChemist)

If you think you could fit into this category, please reach out to me via email and we can chat.

Notes on the contributor list

Looking through the list, @ansobolev has also contributed to the FHI-aims implementation; @CompRhys added the MACE workflow;

[davidwaroquiers]

Very nice to see this issue open! Just adding @VicTrqt, @gmrigna and @gpetretto to the abinit workflows.

[esoteric-ephemera]

Thanks @Andrew-S-Rosen and @Zhuoying! Might also suggest lumping the EOS workflows (WIP waiting on an emmet release) under the elastic flows.

Would we want to put together an examples directory with jupyter / python notebooks showing typical use? Basically would just mean writing a script to reproduce the figure(s) that we add to the paper

[rdguha1995]

Thanks @Zhuoying for nominating me and @rkingsbury. This is a question to both @Zhuoying and @utf . For DFT code contributions, do we have a blueprint similar to the one for workflows? Or do we plan to have a generalized code-agnostic discussion in the paper?

[tpurcell90]

I'm happy to write about the FHI-aims and help out with the phonon workflow parts as well

[matthewkuner]

@JaGeo I wrote up part of the section for forcefields--could you add the relevant parts about phonons/elastic constants to it? We can figure out what kinds of workflow flowcharts we want to do offline (if that works for you)

[utf]

For DFT code contributions, do we have a blueprint similar to the one for workflows?

@rdguha1995 Good question. I think this would be a reasonable starting point:

• 300-600 words of text covering implementation, usage notes, and any existing use case/papers using this code;
• A summary of the key calculation types implemented.
• No figure needed;

I'll update the original message with this information.

[utf]

@matthewkuner @JaGeo @janosh what do you think about putting the force field part in the "Calculators" section rather than "Workflows" section. Since the force fields can be used for many workflows I think this makes sense, but happy to hear your thoughts.

[janosh]

Since the force fields can be used for many workflows I think this makes sense

agreed!

[JaGeo]

@matthewkuner @JaGeo @janosh what do you think about putting the force field part in the "Calculators" section rather than "Workflows" section. Since the force fields can be used for many workflows I think this makes sense, but happy to hear your thoughts.

Fine with me!

[matthewkuner]

@matthewkuner @JaGeo @janosh what do you think about putting the force field part in the "Calculators" section rather than "Workflows" section. Since the force fields can be used for many workflows I think this makes sense, but happy to hear your thoughts.

Sounds good to me

[JaGeo]

@utf @Zhuoying Can we maybe use slack channel or a Team to navigate the communication? I feel this will be otherwise hard to organize. (Especially the individual workflow, code teams)

[Andrew-S-Rosen]

@utf @Zhuoying Can we maybe use slack channel or a Team to navigate the communication? I feel this will be otherwise hard to organize. (Especially the individual workflow, code teams)

Seconded. Plus the GitHub notifications are too much for me... 😅

[tpurcell90]

@utf @Zhuoying Can we maybe use slack channel or a Team to navigate the communication? I feel this will be otherwise hard to organize. (Especially the individual workflow, code teams)

Seconded. Plus the GitHub notifications are too much for me... 😅

I agree with both of these sentiments

[Zhuoying]

@utf @Zhuoying Can we maybe use slack channel or a Team to navigate the communication? I feel this will be otherwise hard to organize. (Especially the individual workflow, code teams)

@JaGeo Sure, it is a good point (always keep a clear organization for efficient communication in such a collaborative project).

@Andrew-S-Rosen, I remember we already have a slack channel called atomate2-working-group created by you a while ago (for monthly meeting purposes). Would you mind using that slack channel (and inviting more contributors to the channel) for the communication?

[Andrew-S-Rosen]

@Andrew-S-Rosen, I remember we already have a slack channel called atomate2-working-group created by you a while ago (for monthly meeting purposes). Would you mind using that slack channel (and inviting more contributors to the channel) for the communication?

I always love when I solved my own problems without remembering 😆 will do!

[Andrew-S-Rosen]

Just added everyone to the Slack (except @ab5424, whose email I need). Feel free to ping @Zhuoying, @utf, or myself to be added if you don't get an email.

[JaGeo]

@Andrew-S-Rosen @ab5424 's mail address is in your mail 😅

[tpurcell90]

@Andrew-S-Rosen I did not get an email ([email protected])

[QuantumChemist]

Hey everyone :)

@utf, as we agreed, I will work on an atomate2 tutorial for "A high-level overview of the key concepts in atomate2: job/flow makers, input sets, task documents, and builders" to contribute to this paper :) And could I be added to the slack channel, too, please?

[Andrew-S-Rosen]

@QuantumChemist please send me your email and I'll add you. :)

[ml-evs]

Likewise, discussed with @utf and I will work on some tutorials describing the execution mechanisms (fireworks, JF local, JF remote etc) and would be happy to contribute to the paper. I would also like a slack invite please, hopefully you have my email!

[rkingsbury]

Hi all, thank you for including me in this effort. TBH, I would classify my contributions up to this point as mostly "moral support" to @rdguha1995 plus a few code reviews, so I'm not sure I should qualify as a coauthor (yet). That said, I'd be happy to work with @rdguha1995 on the Q-Chem calculator section and also to develop tutorials on one or both of the following:

• An introduction to the input sets framework.
• An introduction to task documents, schemas, and emmet.

Plus some tutorials on specific Q-Chem topics (although perhaps not relevant for the paper).

@Andrew-S-Rosen can you please add me to the Slack? I either missed the invitation or did not get one. Is this a dedicated workspace or a channel in BerkeleyTheory or MP?

[mkhorton]

Tagging @guymoore13 for possible inclusion of additional magnetic workflows.

[mkhorton]

@utf, @Zhuoying, @Andrew-S-Rosen please could you invite me via [email protected], using this email since my current/future contributions to atomate2 will be via Microsoft's open source program. Thank you!

[Zhuoying]

Tagging @guymoore13 for possible inclusion of additional magnetic workflows.

I just added @guymoore13 in the main post for the magnetic workflow.

@mkhorton A Google invite was just sent to your Microsoft email. Please feel free to check!