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

[editorialbot]

Submitting author: !--author-handle-->@AndresRTejedor<!--end-author-handle-- (Andrés R. Tejedor) Repository: https://github.com/AndresRTejedor/Mold Branch with paper.md (empty if default branch): joss Version: LAMMPS 2023 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @mattwthompson, @marjanAlbouye Managing EiC: Kevin M. Moerman

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Couldn't check the bibtex because branch name is incorrect: https://github.com/AndresRTejedor/Mold/tree/joss/joss

[editorialbot]

Couldn't check the bibtex because branch name is incorrect: https://github.com/AndresRTejedor/Mold/tree/joss/joss

[editorialbot]

:warning: An error happened when generating the pdf.

[Kevin-Mattheus-Moerman]

@editorialbot check repository

[editorialbot]

Couldn't check the bibtex because branch name is incorrect: https://github.com/AndresRTejedor/Mold/tree/joss/joss

[Kevin-Mattheus-Moerman]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[Kevin-Mattheus-Moerman]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (358.3 files/s, 201301.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      14           2289           2323           8446
Fortran 77                       1           2563           3075           6890
SVG                              1              0              0           2671
HTML                             9           1069             27           1414
CSS                              4            181             33            721
C++                              2            231            160            630
Markdown                        12            187              0            508
Python                           5             34             27            192
Bourne Shell                     7             27              3            153
TeX                              1             12              0            145
C/C++ Header                     2             47             53             71
YAML                             2             12              4             56
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            61           6656           5712          21906
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Failed to discover a Statement of need section in paper

[Kevin-Mattheus-Moerman]

@editorialbot set joss as branch

[editorialbot]

Done! branch is now joss

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1063/1.4896621 may be a valid DOI for title: The mold integration method for the calculation of the crystal-fluid interfacial free energy from simulations
- 10.1063/5.0139699 may be a valid DOI for title: Effect of pressure on the carbon dioxide hydrate–water interfacial free energy along its dissociation line
- 10.1039/c4cp03948c may be a valid DOI for title: Suppression of sub-surface freezing in free-standing thin films of a coarse-grained model of water
- 10.1063/1.5018303 may be a valid DOI for title: Forward-flux sampling with jumpy order parameters
- 10.1016/j.bpj.2023.03.006 may be a valid DOI for title: Surfactants or scaffolds? RNAs of varying lengths control the thermodynamic stability of condensates differently
- 10.1063/1.1747248 may be a valid DOI for title: The statistical mechanical theory of surface tension
- 10.1101/2021.04.30.442154 may be a valid DOI for title: Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients
- 10.1039/c6fd00141f may be a valid DOI for title: Lattice mold technique for the calculation of crystal nucleation rates
- 10.1016/j.softx.2015.06.001 may be a valid DOI for title: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
- 10.1063/1.3153843 may be a valid DOI for title: Reversible gels of patchy particles: role of the valence
- 10.1080/00268978300100971 may be a valid DOI for title: The pressure tensor at the planar surface of a liquid
- 10.1103/physrevlett.130.118001 may be a valid DOI for title: Direct Calculation of the Interfacial Free Energy between NaCl Crystal and its Aqueous Solution at the Solubility Limit
- 10.1063/1.4921185 may be a valid DOI for title: The crystal-fluid interfacial free energy and nucleation rate of NaCl from different simulation methods
- 10.1021/acs.jpcc.5b11221 may be a valid DOI for title: Ice–water interfacial free energy for the TIP4P, TIP4P/2005, TIP4P/ice, and mW models as obtained from the mold integration technique
- 10.1016/j.actamat.2008.10.020 may be a valid DOI for title: Solidification microstructures and solid-state parallels: Recent developments, future directions
- 10.1063/5.0101746 may be a valid DOI for title: Simulation of the CO2 hydrate–water interfacial energy: The mold integration–guest methodology
- 10.1016/j.jcis.2022.05.029 may be a valid DOI for title: Simulation of the carbon dioxide hydrate-water interfacial energy
- 10.26434/chemrxiv-2022-2k8g5 may be a valid DOI for title: Homogeneous ice nucleation rates for mW and TIP4P/ICE models through Lattice Mold calculations
- 10.1039/c6fd00141f may be a valid DOI for title: Lattice mold technique for the calculation of crystal nucleation rates
- 10.1063/1.5098551 may be a valid DOI for title: Breakdown of the law of rectilinear diameter and related surprises in the liquid-vapor coexistence in systems of patchy particles
- 10.1016/j.bpj.2021.01.031 may be a valid DOI for title: Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model
- 10.3390/biom11020278 may be a valid DOI for title: Valency and binding affinity variations can regulate the multilayered organization of protein condensates with many components
- 10.26434/chemrxiv-2022-sm80v may be a valid DOI for title: Alternating one-phase and two-phase crystallization mechanisms in octahedral patchy colloids
- 10.1063/1.1563248 may be a valid DOI for title: Direct calculation of the crystal–melt interfacial free energies for continuous potentials: Application to the Lennard-Jones system
- 10.1016/j.cpc.2021.108171 may be a valid DOI for title: LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
- 10.1063/5.0028219 may be a valid DOI for title: Shuttleworth equation: A molecular simulations perspective
- 10.1038/124119a0 may be a valid DOI for title: The collected works of J. Willard Gibbs.
- 10.1063/1.445633 may be a valid DOI for title: Molecular dynamics investigation of the crystal–fluid interface. I. Bulk properties
- 10.1063/1.449884 may be a valid DOI for title: Molecular dynamics investigation of the crystal–fluid interface. VI. Excess surface free energies of crystal–liquid systems
- 10.1103/physrevlett.94.086102 may be a valid DOI for title: Crystal structure and interaction dependence of the crystal-melt interfacial free energy
- 10.1063/1.1563248 may be a valid DOI for title: Direct calculation of the crystal–melt interfacial free energies for continuous potentials: Application to the Lennard-Jones system
- 10.1103/physrevlett.100.036104 may be a valid DOI for title: Direct calculation of solid-liquid interfacial free energy for molecular systems: TIP4P ice-water interface
- 10.1016/j.commatsci.2018.08.035 may be a valid DOI for title: Structural and mechanical properties of homogeneous solid-liquid interface of Al modelled with COMB3 potential
- 10.1016/j.commatsci.2013.03.018 may be a valid DOI for title: Molecular dynamics calculation of solid–liquid interfacial free energy and its anisotropy during iron solidification
- 10.1063/1.4967521 may be a valid DOI for title: Obtaining the solid-liquid interfacial free energy via multi-scheme thermodynamic integration: Ag-ethylene glycol interfaces
- 10.1063/5.0028653 may be a valid DOI for title: Computation of solid–fluid interfacial free energy in molecular systems using thermodynamic integration

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

Note to editors, this is a re-submission (see previous submission: https://github.com/openjournals/joss-reviews/issues/5958).

[Kevin-Mattheus-Moerman]

@AndresRTejedor thanks for this re-submission. Initially I rejected this submission based on its apparent small size from the software report over in https://github.com/openjournals/joss-reviews/issues/5958. There I perceived the work to be contained in <50 lines of Python, and <300 lines of C++ (the counts were however based on the joss paper branch). However, after your re-submission, with which you also provided additional information on the functionality/significance of this work, I have triggered this pre-review and have re-run the software report. This time I made sure the report is for the main branch. Now the numbers appear to satisfy our minimum requirements. I apologise for the desk rejection of your first submission.

Furthermore, I've had a fellow member of the editorial board, @lucydot, check this submission in terms of scope, and she believes it may be in scope, and has offered to edit this work.

@AndresRTejedor, in relation to the above software report, what code portions would you say capture the core aspects of this work in terms of functionality and your original work? Is it mainly the Python and C++ code? Or are Fortran and JavaScript codes also your original developments? (I ask the latter as in some cases libraries from others are provided to support the project, and in some cases JavaScript is auto-generated to facilitate a GUI wrapper for instance)

For the moment, @AndresRTejedor, can you please address the above potentially missing DOIs? :point_up: Note also, that you can remove any entries from the .bib file that you do not end up using in the paper. Once you have updated the DOIs, you can rerun the reference check by calling: @editorialbot generate pdf.

[Kevin-Mattheus-Moerman]

@editorialbot invite @lucydot as editor

[editorialbot]

Invitation to edit this submission sent!

[lucydot]

@editorialbot assign me as editor

[editorialbot]

Assigned! @lucydot is now the editor

[lucydot]

Hello @AndresRTejedor I will be your editor for this submission 👋 I point you to the comment from Kevin above; your answer here will also help finding appropriate reviewers.

[AndresRTejedor]

Dear @lucydot

Thank you very much for reconsidering the resubmission of our paper.

Regarding Kevin comments:

-The code is entirely written by the authors of the work apart from the JavaScript which is an auto-generated code. More precisely: The C++ code is the core of the software that must be included in LAMMPS to carry out the simulations either for the Mold Integration or the Lattice Mold techniques. The Python code includes analysis to perform the thermodynamic integration (Mold Integration and Lattice Mold) as well as determining the average nucleation time (Lattice Mold). The Fortran code includes several analysis and running options which are both very useful in the context of liquid-solid interfaces. In particular, for the purpose of this package, it performs the calculation of the largest cluster through a local order parameter to determine the crystallization of the system (Lattice Mold, but mostly Mold Integration).

-The DOIs are missing because the references are copied from Scholar that does not include DOIs. I will include all the DOIs as soon as possible thoughtout this morning. I will re-generate the pdf when everything is ready.

Many thanks for the possitive feeback. Looking forward to continuing the review process.

On behalf of all the authors. Andres

[AndresRTejedor]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[AndresRTejedor]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[lucydot]

Hi @AndresRTejedor -

@AndresRTejedor Thanks for your comments. I've re-read the paper:

• your statement of need section is long and contains scientific context. I suggest breaking this into two sections: statement of need (typically one or two paragraphs: what problem the software solves and target audience) and something along the lines of scientific background. Bear in mind you are towards the upper limit on paper length.
• Please fix the reference DiPasquale2020shuttleworth?

If you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

[AndresRTejedor]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

MetalWalls: A classical molecular dynamics software dedicated to the simulation of electrochemical systems Submitting author: @salanne Handling editor: @richardjgowers (Active) Reviewers: @mattwthompson, @hmacdope Similarity score: 0.8118

FitSNAP: Atomistic machine learning with LAMMPS Submitting author: @rohskopf Handling editor: @jmschrei (Active) Reviewers: @tpurcell90, @bahung Similarity score: 0.8105

Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD Submitting author: @tonigi Handling editor: @labarba (Retired) Reviewers: @jrperilla, @HaoZeke Similarity score: 0.8102

MCSD: A MATLAB Tool for Monte-Carlo Simulations of Diffusion in biological Tissues Submitting author: @davidnsousa Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @nnadeau, @mwacaan Similarity score: 0.8100

NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models Submitting author: @diehlpk Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @vijaysm, @chennachaos Similarity score: 0.8081

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[AndresRTejedor]

Dear @lucydot ,

I have amended the reference DiPasquale2020shuttleworth. Also, I have divided the previous statement of need in two different sections to independently provide the scientific background of the methods we present in our package.

For the Referees I propose the following:

• lorenzo-rovigatti
• merrygoat

Many thanks

[lucydot]

Thanks @AndresRTejedor for the suggestions and update.

@merrygoat, @mattwthompson, @marjanAlbouye - :wave: are you available to review this submission to JOSS?

[mattwthompson]

I'll take on reviewing this

[marjanalbooyeh]

Yes, I’d be happy to review this.

[lucydot]

@editorialbot add @mattwthompson as reviewer

[editorialbot]

@mattwthompson added to the reviewers list!

[lucydot]

@editorialbot add @marjanAlbouye as reviewer

[editorialbot]

@marjanAlbouye added to the reviewers list!

[lucydot]

Thank you for agreeing to review this paper @mattwthompson and @marjanAlbouye ✨

I'm going to ask editorial-bot to start the review, it will appear in a separate thread. There will be instructions at the top of the thread, and please let me know if you have any other questions about the process. We aim to complete reviews in 4-6 weeks, and as it is an iterative process, its best to get started within a week or two.

[lucydot]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6083.