[REVIEW]: Mold: a LAMMPS package to compute interfacial free energies and nucleation rates

editorialbot commented 11 months ago

Submitting author: !--author-handle-->@AndresRTejedor@lucydot<!--end-editor-- Reviewers: @mattwthompson, @marjanalbooyeh Archive: 10.5281/zenodo.10843863

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editorialbot commented 9 months ago

Done! archive is now 10.5281/zenodo.10641293

lucydot commented 9 months ago

@editorialbot set v1.0.0 as version

editorialbot commented 9 months ago

Done! version is now v1.0.0

lucydot commented 9 months ago

@AndresRTejedor the title and author list on the archive must match exactly that of the paper. Currently, neither do. Please can you update the Zenodo repo accordingly? (ie, title will be "Mold: a LAMMPS package to compute interfacial free energies and nucleation rates" and the author list will match that in the JOSS paper).

lucydot commented 9 months ago

Adjustments to paper

Your reference lists are not formatted correctly. Where there are multiple references, use square brackets separated by semi-colons e.g. [@anderson2020hoomd; @lammps_2022]

In your paper I suggest re-phrasing for clarity:

In the particular case of liquid-to-solid transitions, obtaining this quantity is not straightforward neither experimentally nor computationally. --> In the particular case of liquid-to-solid transitions, it is not straightforward to obtain this quantity through experiment or computation.
Here, we present a computational package integrated in the Molecular Dynamics open-source software LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator)(Thompson et al., 2022), which enables the direct calculation of the interfacial free energy between arbitrarily complex crystal structures and liquids/solutions at coexistence conditions through the Mold Integration method (J. Espinosa et al., 2014). --> Here, we present the computational package Mold, which is integrated in the Molecular Dynamics open-source software LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator)(Thompson et al., 2022). Mold enables direct calculation of the interfacial free energy between arbitrarily complex crystal structures and liquids/solutions at coexistence conditions through the Mold Integration method (J. Espinosa et al., 2014).
implemented to be included in the MD package LAMMPS. --> implemented to work alongside the MD package LAMMPS.

AndresRTejedor commented 9 months ago

Adjustments to paper

Your reference lists are not formatted correctly. Where there are multiple references, use square brackets separated by semi-colons e.g. [@anderson2020hoomd; @lammps_2022]

In your paper I suggest re-phrasing for clarity:

In the particular case of liquid-to-solid transitions, obtaining this quantity is not straightforward neither experimentally nor computationally. --> In the particular case of liquid-to-solid transitions, it is not straightforward to obtain this quantity through experiment or computation.

Here, we present a computational package integrated in the Molecular Dynamics open-source software LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator)(Thompson et al., 2022), which enables the direct calculation of the interfacial free energy between arbitrarily complex crystal structures and liquids/solutions at coexistence conditions through the Mold Integration method (J. Espinosa et al., 2014). --> Here, we present the computational package Mold, which is integrated in the Molecular Dynamics open-source software LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator)(Thompson et al., 2022). Mold enables direct calculation of the interfacial free energy between arbitrarily complex crystal structures and liquids/solutions at coexistence conditions through the Mold Integration method (J. Espinosa et al., 2014).

implemented to be included in the MD package LAMMPS. --> implemented to work alongside the MD package LAMMPS.

Dear @lucydot

Thank you for all your suggestions. We have included your re-phrasing, and also we have corrected the format of the references.

Please let me know if you need any further information.

AndresRTejedor commented 9 months ago

list on the archive must match exactly that of the paper. C

Dear @lucydot

I have updated the repo to match the title and authors in the JOSS paper.

AndresRTejedor commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lucydot commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lucydot commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/1.4896621 is OK
- 10.1063/5.0139699 is OK
- 10.1039/C4CP03948C is OK
- 10.1063/1.5018303 is OK
- 10.1039/C1CP22167A is OK
- 10.1016/j.bpj.2023.03.006 is OK
- 10.1063/1.1747248 is OK
- 10.1038/s41598-021-94309-y is OK
- 10.1039/C6FD00141F is OK
- 10.1016/j.softx.2015.06.001 is OK
- 10.1063/1.3578182 is OK
- 10.1016/j.cossms.2011.07.003 is OK
- 10.1063/1.3153843 is OK
- 10.1080/00268978300100971 is OK
- 10.1039/D1CP01784E is OK
- 10.1103/PhysRevLett.130.118001 is OK
- 10.1063/1.4921185 is OK
- 10.1021/acs.jpcc.5b11221 is OK
- 10.1021/ie50510a027 is OK
- 10.1016/j.actamat.2008.10.020 is OK
- 10.1016/j.jcis.2022.05.029 is OK
- 10.1063/5.0101383 is OK
- 10.1063/1.5098551 is OK
- 10.1073/pnas.1917569117 is OK
- 10.1016/j.bpj.2021.01.031 is OK
- 10.3390/biom11020278 is OK
- 10.1063/5.0101529 is OK
- 10.1063/1.1563248 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1063/1.445633 is OK
- 10.1063/5.0028219 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1063/5.0101746 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 8 months ago

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

\AA
   ^
unexpected control sequence \AA
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

\AA
   ^
unexpected control sequence \AA
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

editorialbot commented 8 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element doi: [facet 'pattern'] The value 'https://doi.org/10.1063/5.0101746' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

AndresRTejedor commented 8 months ago

@editorialbot commands

editorialbot commented 8 months ago

Hello @AndresRTejedor, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

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@editorialbot generate preprint

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@editorialbot list reviewers

AndresRTejedor commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/1.4896621 is OK
- 10.1063/5.0139699 is OK
- 10.1039/C4CP03948C is OK
- 10.1063/1.5018303 is OK
- 10.1039/C1CP22167A is OK
- 10.1016/j.bpj.2023.03.006 is OK
- 10.1063/1.1747248 is OK
- 10.1038/s41598-021-94309-y is OK
- 10.1039/C6FD00141F is OK
- 10.1016/j.softx.2015.06.001 is OK
- 10.1063/1.3578182 is OK
- 10.1016/j.cossms.2011.07.003 is OK
- 10.1063/1.3153843 is OK
- 10.1080/00268978300100971 is OK
- 10.1039/D1CP01784E is OK
- 10.1103/PhysRevLett.130.118001 is OK
- 10.1063/1.4921185 is OK
- 10.1021/acs.jpcc.5b11221 is OK
- 10.1021/ie50510a027 is OK
- 10.1016/j.actamat.2008.10.020 is OK
- 10.1063/5.0101746 is OK
- 10.1016/j.jcis.2022.05.029 is OK
- 10.1063/5.0101383 is OK
- 10.1063/1.5098551 is OK
- 10.1073/pnas.1917569117 is OK
- 10.1016/j.bpj.2021.01.031 is OK
- 10.3390/biom11020278 is OK
- 10.1063/5.0101529 is OK
- 10.1063/1.1563248 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1063/1.445633 is OK
- 10.1063/5.0028219 is OK

MISSING DOIs

- None

INVALID DOIs

- None

AndresRTejedor commented 8 months ago

Dear @lucydot

I have corrected the DOI that was invalid before.

Many thanks

AndresRTejedor commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lucydot commented 8 months ago

@AndresRTejedor there also seems to be an issue with \AA ; it might be as it is used in mathmode. Could you try inserting directly into the markdown (you can copy and paste I have done here: Å) - and see if that works?

AndresRTejedor commented 8 months ago

@lucydot I have included Å directly into the markdown and it seems it worked. Thank you for noticing that.

AndresRTejedor commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lucydot commented 8 months ago

Hi @AndresRTejedor - there are double brackets (( and )) in the paper.md (occuring where there are lists of references). Please can you correct this?

AndresRTejedor commented 8 months ago

@lucydot thank you for noticing it. I have already corrected it.

AndresRTejedor commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lucydot commented 8 months ago

It's also best to avoid the consecutive brackets on line 20/21 and the nested brackets on line 118/119. I suggest removing the brackets around the references by using square brackets around the sentence (see: https://stackoverflow.com/questions/64209134/r-markdown-suppress-parentheses-in-specific-citations), or re-phrasing.

AndresRTejedor commented 8 months ago

I have changed those lines by using brackets instead for the clarification. Please let me know if that works.

AndresRTejedor commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lucydot commented 8 months ago

@AndresRTejedor - hmm, not what I was expecting. I've tried fixing another way (removing square brackets from reference) and issued a PR. Could you merge and then we can check if that looks correct?

https://github.com/AndresRTejedor/Mold/pull/3

AndresRTejedor commented 8 months ago

@lucydot I have already merged your patch. Please let me know if it works now.

lucydot commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lucydot commented 8 months ago

Hi @AndresRTejedor - it hasn't.

I'll message the other editors to see how to include citations without the brackets. There is also the option of re-phrasing to avoid the citation within a bracket. We are very close to being finished!

FYI I'm going on leave for one week starting tomorrow, will check back here on the 18th. Please also note that if you make changes and want to verify correct, you can also check yourself using the @editorialbot generate pdf command.

Best,

Lucy

AndresRTejedor commented 8 months ago

Hi @lucydot , thanks for your help! I hope it can be solved soon for publication!

Can I re-phrase those lines and finish it today?

Many thanks

lucydot commented 7 months ago

Hi @AndresRTejedor - yes, go ahead and re-phrase then we can finish.

AndresRTejedor commented 7 months ago

Hi @lucydot , I re-phrased the corresponding parts. Please let me know if it works now!

AndresRTejedor commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lucydot commented 7 months ago

@AndresRTejedor - I have just spotted that the software version on the Zenodo archive (Lammps) does not match that which is set here (v1.0.0). To ensure consistency, you need to update the version number on Zenodo. To do this I think you can create a v1.0.0 release on Github and then Zenodo should issue a new doi.

AndresRTejedor commented 7 months ago

@lucydot I have created a new release with the correct tag. Here is the doi: 10.5281/zenodo.10843863

lucydot commented 7 months ago

@editorialbot set 10.5281/zenodo.10843863 as archive

editorialbot commented 7 months ago

Done! archive is now 10.5281/zenodo.10843863

lucydot commented 7 months ago

@AndresRTejedor you need to make the archive title and author list match exactly that of the JOSS submission. Please update. I'll re-paste the author to-do list from earlier message below so you can confirm all tasks complete:

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

openjournals / joss-reviews