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[PRE REVIEW]: matscipy: materials science at the atomic scale with Python #5646

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@pastewka<!--end-author-handle-- (Lars Pastewka) Repository: https://github.com/libAtoms/matscipy Branch with paper.md (empty if default branch): Version: 0.8.0 Editor: !--editor-->@diehlpk<!--end-editor-- Reviewers: @rashatwi, @mbarzegary, @mastricker Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/33f6a17885367fe629c3a73f27743945/status.svg)](https://joss.theoj.org/papers/33f6a17885367fe629c3a73f27743945)

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editorialbot commented 1 year ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=3.02 s (95.3 files/s, 148259.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
F#                               2              1              0         318016
HTML                             4           9399              8          59776
Python                         185           8925          14960          26810
TeX                              1             67              6           1082
SVG                              1              0             12           1014
C++                              4            301            269            942
C                                3            160            159            751
Jupyter Notebook                 9              0           2154            535
Markdown                         5            100              0            320
Bourne Shell                    28             29             30            259
Meson                           19             46             56            246
YAML                             5             45             29            230
C/C++ Header                     7             98            141            222
DOS Batch                        1             29              1            212
make                             1             29              6            143
Ruby                             1             28             12            106
reStructuredText                 8             67             63            106
XML                              2             12              6             78
TOML                             1              3              0             39
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                           288          19339          17912         410889
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 2529

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1007/BF00186854 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10/chm6f7 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1103/PhysRevB.29.6443 is OK

MISSING DOIs

- 10.1103/physrevb.31.5262 may be a valid DOI for title: Computer simulation of local order in condensed phases of silicon
- 10.1016/j.commatsci.2006.07.013 may be a valid DOI for title: Development of bond-order potentials that can reproduce the elastic constants and melting point of silicon for classical molecular dynamics simulation
- 10.1103/physrevlett.56.632 may be a valid DOI for title: New Empirical Model for the Structural Properties of Silicon
- 10.1103/physrevb.39.5566 may be a valid DOI for title: Modeling solid-state chemistry: Interatomic potentials for multicomponent systems
- 10.1080/14786437508226544 may be a valid DOI for title: The Influence of the Interatomic Force Law and of Kinks on the Propagation of Brittle Cracks
- 10.1007/978-3-7091-8752-4 may be a valid DOI for title: Analysis and simulation of semiconductor devices
- 10.1103/physrevmaterials.7.055601 may be a valid DOI for title: Yielding under compression and the polyamorphic transition in silicon
- 10.1088/0965-0393/17/5/053001 may be a valid DOI for title: A unified framework and performance benchmark of fourteen multiscale atomistic/continuum coupling methods
- 10.1016/j.jmps.2018.05.004 may be a valid DOI for title: The Coupled Atomistic/Discrete-Dislocation method in 3d part I: Concept and algorithms
- 10.1103/physrevb.74.075420 may be a valid DOI for title: Practical Green’s function approach to the simulation of elastic semi-infinite solids
- 10.1103/physrevb.86.075459 may be a valid DOI for title: Seamless elastic boundaries for atomistic calculations
- 10.1201/9781482268171-24 may be a valid DOI for title: Dynamics of viscoplastic deformation in amorphous solids
- 10.1088/2515-7639/ab36ed may be a valid DOI for title: Correlations of non-affine displacements in metallic glasses through the yield transition
- 10.1557/mrc.2019.93 may be a valid DOI for title: Surface flaws control strain localization in the deformation of Cu|Au nanolaminate pillars
- 10.1103/physrevmaterials.4.013603 may be a valid DOI for title: Pattern formation during deformation of metallic nanolaminates
- 10.1103/physrevb.44.4925 may be a valid DOI for title: Computation of ring statistics for network models of solids
- 10.1103/physrevb.78.161402 may be a valid DOI for title: Describing bond-breaking processes by reactive potentials: Importance of an environment-dependent interaction range
- 10.1088/1361-651x/ab45da may be a valid DOI for title: Structural and elastic properties of amorphous carbon from simulated quenching at low rates
- 10.1080/23746149.2022.2093129 may be a valid DOI for title: Interatomic potentials: achievements and challenges
- 10.1016/j.carbon.2015.10.098 may be a valid DOI for title: Activation and mechanochemical breaking of C−C bonds initiate wear of diamond (110) surfaces in contact with silica
- 10.1103/physrevmaterials.2.083601 may be a valid DOI for title: Shear melting of silicon and diamond and the disappearance of the polyamorphic transition under shear
- 10.1103/physrevlett.127.126101 may be a valid DOI for title: Solid-Phase Silicon Homoepitaxy via Shear-Induced Amorphization and Recrystallization
- 10.1007/s11249-011-9864-9 may be a valid DOI for title: Formation and oxidation of linear carbon chains and their role in the wear of carbon materials
- 10.1038/nmat2902 may be a valid DOI for title: Anisotropic mechanical amorphization drives wear in diamond
- 10.1007/s11249-020-01395-6 may be a valid DOI for title: Molecular Simulations of Electrotunable Lubrication: Viscosity and Wall Slip in Aqueous Electrolytes
- 10.1063/5.0153397 may be a valid DOI for title: Molecular simulations of sliding on SDS surfactant films
- 10.1016/j.cpc.2015.07.012 may be a valid DOI for title: Atomsk: A tool for manipulating and converting atomic data files

INVALID DOIs

- https://doi.org/10.1016/j.actamat.2023.118734 is INVALID because of 'https://doi.org/' prefix
- 10.1103/PhysRevLett.124.10550 is INVALID
editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

Kevin-Mattheus-Moerman commented 1 year ago

@pastewka thanks for this submission. I am the AEiC for this track and here to help process initial steps. I will be looking for a handling editor but for the moment, can you start on the points below:

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot invite @diehlpk as editor

editorialbot commented 1 year ago

Invitation to edit this submission sent!

pastewka commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1016/j.actamat.2023.118734 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1016/j.commatsci.2006.07.013 is OK
- 10.1103/PhysRevB.39.5566 is OK
- 10.1103/PhysRevLett.64.1955 is OK
- 10.1088/0959-5309/43/5/301 is OK
- 10.1007/BF00186854 is OK
- 10.1080/14786437508226544 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10.1002/jcc.21224 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1103/PhysRevMaterials.7.055601 is OK
- 10.1088/0965-0393/17/5/053001 is OK
- 10.1016/j.jmps.2018.05.004 is OK
- 10.1103/PhysRevB.74.075420 is OK
- 10.1103/PhysRevB.86.075459 is OK
- 10.1103/PhysRevE.57.7192 is OK
- 10.1088/2515-7639/ab36ed is OK
- 10.1557/mrc.2019.93 is OK
- 10.1103/PhysRevMaterials.4.013603 is OK
- 10.1103/PhysRevB.44.4925 is OK
- 10.1103/PhysRevB.78.161402 is OK
- 10.1088/1361-651X/ab45da is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1016/j.carbon.2015.10.098 is OK
- 10.1103/PhysRevMaterials.2.083601 is OK
- 10.1103/PhysRevLett.127.126101 is OK
- 10.1007/s11249-011-9864-9 is OK
- 10.1038/nmat2902 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1063/5.0153397 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2015.07.012 is OK
- 10.1103/PhysRevB.29.6443 is OK

MISSING DOIs

- 10.1103/physrevlett.56.632 may be a valid DOI for title: New Empirical Model for the Structural Properties of Silicon
- 10.1007/978-3-7091-8752-4 may be a valid DOI for title: Analysis and simulation of semiconductor devices

INVALID DOIs

- 10.1103/PhysRevLett.124.10550 is INVALID
pastewka commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1088/1361-648x/aa680e is OK
- 10.1088/0965-0393/18/1/015012 is OK
- 10.1088/0034-4885/72/2/026501 is OK
- 10.1021/acs.jctc.8b00959 is OK
- 10.1063/1.5035508 is OK
- 10.1039/d0cp01841d is OK
- 10.1103/PhysRevMaterials.4.023601 is OK
- 10.1016/j.actamat.2023.118734 is OK
- 10.1007/s11249-009-9566-8 is OK
- 10.1103/PhysRevB.31.5262 is OK
- 10.1016/j.commatsci.2006.07.013 is OK
- 10.1103/PhysRevLett.56.632 is OK
- 10.1103/PhysRevB.39.5566 is OK
- 10.1103/PhysRevLett.64.1955 is OK
- 10.1088/0959-5309/43/5/301 is OK
- 10.1007/BF00186854 is OK
- 10.1080/14786437508226544 is OK
- 10.1103/PhysRevLett.115.135501 is OK
- 10.1103/PhysRevE.103.033002 is OK
- 10.1002/jcc.21224 is OK
- 10.1007/978-3-7091-8752-4 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1137/040609938 is OK
- 10.1021/ja9621760 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1021/jacs.5b04073 is OK
- 10.1103/PhysRevLett.124.105501 is OK
- 10.1021/acsami.9b18019 is OK
- 10.1007/s11249-021-01508-9 is OK
- 10.3390/ma15093247 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.1103/PhysRevMaterials.7.055601 is OK
- 10.1088/0965-0393/17/5/053001 is OK
- 10.1016/j.jmps.2018.05.004 is OK
- 10.1103/PhysRevB.74.075420 is OK
- 10.1103/PhysRevB.86.075459 is OK
- 10.1103/PhysRevE.57.7192 is OK
- 10.1088/2515-7639/ab36ed is OK
- 10.1557/mrc.2019.93 is OK
- 10.1103/PhysRevMaterials.4.013603 is OK
- 10.1103/PhysRevB.44.4925 is OK
- 10.1103/PhysRevB.78.161402 is OK
- 10.1088/1361-651X/ab45da is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.48550/arXiv.2205.06643 is OK
- 10.1016/j.carbon.2015.10.098 is OK
- 10.1103/PhysRevMaterials.2.083601 is OK
- 10.1103/PhysRevLett.127.126101 is OK
- 10.1007/s11249-011-9864-9 is OK
- 10.1038/nmat2902 is OK
- 10.1007/s11249-020-01395-6 is OK
- 10.1063/5.0153397 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.cpc.2015.07.012 is OK
- 10.1103/PhysRevB.29.6443 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1103/PhysRevMaterials.7.073603 is INVALID
pastewka commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

pastewka commented 1 year ago

@Kevin-Mattheus-Moerman I resolved the issues and the proof looks good. Note that the DOI listed as invalid is for a paper that was literally posted online an hour ago. It should become valid over the next couple of days.

pastewka commented 1 year ago

Note that the issue labels are wrong. Most of the code is actually Python.

pastewka commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

diehlpk commented 1 year ago

@editorialbot add @diehlpk as editor

editorialbot commented 1 year ago

Assigned! @diehlpk is now the editor

pastewka commented 1 year ago

@diehlpk We have the following suggestions for reviewers:

Pierre Hirel (Lille, maintains atoms package) Noam Bernstein (Naval Research Lab) Lucas Hale (NIST, maintains atomman package) Markus Stricker (ICAMS Bochum) Gabor Csanyi (Cambridge)

Let me know if you need contact info.

pastewka commented 1 year ago

@diehlpk Another suggestion is Alexander Stukowski (Ovito GmbH)

diehlpk commented 1 year ago

Hi @pastewka I am back from my vacation and will start working on finding reviewers.

diehlpk commented 1 year ago

Hi @rashatwi do you have time to review this paper?

diehlpk commented 1 year ago

Hi @BrinthanK do you have time to review this paper?

diehlpk commented 1 year ago

Hi @mzkhalid039 do you have time to review this paper?

rashatwi commented 1 year ago

Hi @rashatwi do you have time to review this paper?

Yes

diehlpk commented 1 year ago

@editorialbot add @rashatwi as reviewer

editorialbot commented 1 year ago

@rashatwi added to the reviewers list!

diehlpk commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5668.

diehlpk commented 1 year ago

@pastewka Do you have the GitHub handles of them?

pastewka commented 1 year ago

Yes, I do:

Pierre Hirel (Lille, maintains atoms package) - "pierrehirel" Noam Bernstein (Naval Research Lab) - "bernstei" Lucas Hale (NIST, maintains atomman package) - "lmhale99" Markus Stricker (ICAMS Bochum) - "mastricker" Gabor Csanyi (Cambridge) - "gabor1" Alexander Stukowski (Ovito GmbH) - "stukowski"

diehlpk commented 1 year ago

Hi @pierrehirel do you have time to review this paper?

diehlpk commented 1 year ago

Hi @stukowski do you have time to review this paper?

diehlpk commented 1 year ago

Hi @bernstei do you have time to review this paper?

diehlpk commented 1 year ago

Hi @gabor1 do you have time to review this paper?

diehlpk commented 1 year ago

Hi @mastricker do you have time to review this paper?

gabor1 commented 1 year ago

Hi @gabor1 do you have time to review this paper?

I'm too close to the authors/contributors. The package is hosted under the organisation I co-control.

mastricker commented 1 year ago

Hi I would be happy to review - depends on the timeline. When do you expect a report?

diehlpk commented 1 year ago

Hi I would be happy to review - depends on the timeline. When do you expect a report?

Within the next two months would be great.

bernstei commented 1 year ago

Hi @bernstei do you have time to review this paper?

Is there a full author list and/or abstract I can check before deciding?

diehlpk commented 1 year ago

@editorialbot generate pdf

diehlpk commented 1 year ago

Hi @bernstei do you have time to review this paper?

Is there a full author list and/or abstract I can check before deciding?

Yes, you can run @editorialbot generate pdf to get the latest version of the paper.

editorialbot commented 1 year ago

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

bernstei commented 1 year ago

So, FWIW, I'd be willing to review, but I'm a pretty close collaborator of at least one of the authors (Kermode), and somewhat of a couple of others (Pastewka, Wengert). I feel like I could give an unbiased review, but you should let me know how you feel about that level of previous collaboration.

Also, can you point me at the reviewer guidelines? It's not obvious to me to what extent I'm reviewing the text vs. the software itself, and how much responsibility I'm taking to actually run it as opposed to just make conclusions based on the available documentation.

diehlpk commented 1 year ago

So, FWIW, I'd be willing to review, but I'm a pretty close collaborator of at least one of the authors (Kermode), and somewhat of a couple of others (Pastewka, Wengert). I feel like I could give an unbiased review, but you should let me know how you feel about that level of previous collaboration.

Also, can you point me at the reviewer guidelines? It's not obvious to me to what extent I'm reviewing the text vs. the software itself, and how much responsibility I'm taking to actually run it as opposed to just make conclusions based on the available documentation.

Thanks for letting me know, but I think that is some COI.

diehlpk commented 1 year ago

@mastricker are you still interested?

diehlpk commented 1 year ago

Hi @mbarzegary do you have time to review this paper?

diehlpk commented 1 year ago

Hi @Materials-Informatics-Laboratory do you have time to review this paper?