[REVIEW]: MeMC: A package for monte-carlo simulations of spherical shells

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@vipinagrawal25@fboehm<!--end-editor-- Reviewers: @victorapm, @mgiardino Archive: 10.5281/zenodo.6671531

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (215.0 files/s, 107829.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1            131             92           7546
C++                              9            185            111           1122
Markdown                         2            129              0            600
C/C++ Header                     4             18             33            244
Python                           3             36             37            192
make                             1              7              8             38
Bourne Shell                     1              0              0              5
-------------------------------------------------------------------------------
SUM:                            21            506            281           9747
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 2698

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editorialbot commented 2 years ago

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1017/S0022112086002859 is OK
- 10.1017/S0022112005003368 is OK
- 10.1103/PhysRevE.76.026313 is OK
- 10.1103/PhysRevE.83.036314 is OK
- 10.1103/PhysRevLett.100.184503 is OK
- 10.1103/PhysRevLett.107.184503 is OK
- 10.1063/1.864230 is OK
- 10.1063/1.857985 is OK
- 10.1017/S0022112056000020 is OK
- 10.1017/S002211200500844X is OK
- 10.1103/PhysRevLett.106.074101 is OK
- 10.1016/0032-0633(65)90131-5 is OK
- 10.1086/148912 is OK
- 10.1086/149265 is OK
- 10.1103/PhysRevLett.92.040601 is OK
- 10.1103/PhysRevE.85.036315 is OK
- 10.1103/PhysRevLett.96.168301 is OK
- 10.1103/PhysRevE.70.026405 is OK
- 10.1103/PhysRevFluids.3.053901 is OK
- 10.1017/jfm.2015.650 is OK
- 10.1103/PhysRevFluids.1.033602 is OK
- 10.1063/1.1605952 is OK
- 10.1017/CBO9780511524608.004 is OK
- 10.1051/jp2:1994173 is OK
- 10.1017/jfm.2017.485 is OK
- 10.1146/annurev.fluid.38.050304.092139 is OK
- 10.1103/PhysRevLett.58.2571 is OK

MISSING DOIs

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- 10.1088/0004-637x/697/2/1269 may be a valid DOI for title: Zonal flows and long-lived axisymmetric pressure bumps in magnetorotational turbulence
- 10.2458/azu_uapress_9780816531240-ch024 may be a valid DOI for title: The multifaceted planetesimal formation process
- 10.1016/0009-2509(93)80031-k may be a valid DOI for title: Deposition in porous media and clogging
- 10.1143/ptp.56.1756 may be a valid DOI for title: The gas drag effect on the elliptic motion of a solid body in the primordial solar nebula
- 10.1080/14685240701332475 may be a valid DOI for title: Lagrangian and Eulerian descriptions of inertial particles in random flows
- 10.1103/physreve.87.023016 may be a valid DOI for title: Distribution of velocity gradients and rate of caustic formation in turbulent aerosols at finite Kubo numbers
- 10.1088/1367-2630/9/4/089 may be a valid DOI for title: Asymptotic exponents from low-Reynolds-number flows
- 10.1103/physrevlett.97.174501 may be a valid DOI for title: Lagrangian dynamics and statistical geometric structure of turbulence
- 10.1063/1.2766740 may be a valid DOI for title: Unmixing in random flows
- 10.1007/s10955-007-9307-z may be a valid DOI for title: A Borel transform method for locating singularities of Taylor and Fourier series
- 10.1103/physreve.85.015301 may be a valid DOI for title: Nelkin scaling for the Burgers equation and the role of high-precision calculations
- 10.1103/physreve.68.040101 may be a valid DOI for title: Path coalescence transition and its applications
- 10.1103/physreve.84.045304 may be a valid DOI for title: Distribution of relative velocities in turbulent aerosols
- 10.1017/jfm.2019.294 may be a valid DOI for title: Clustering of rapidly settling, low-inertia particle pairs in isotropic turbulence. Part 2. Comparison of theory and DNS
- 10.1017/jfm.2014.259 may be a valid DOI for title: Prevalence of the sling effect for enhancing collision rates in turbulent suspensions
- 10.1017/jfm.2018.24 may be a valid DOI for title: Small-scale dynamics of settling, bidisperse particles in turbulence
- 10.1103/physrevlett.97.048501 may be a valid DOI for title: Caustic activation of rain showers
- 10.1088/1367-2630/10/7/075015 may be a valid DOI for title: Effects of turbulence on the geometric collision rate of sedimenting droplets. Part 1. Results from direct numerical simulation
- 10.1103/physrevfluids.3.044303 may be a valid DOI for title: Topology of two-dimensional turbulent flows of dust and gas
- 10.1103/physreve.100.013114 may be a valid DOI for title: Clustering and energy spectra in two-dimensional dusty gas turbulence
- 10.1103/physreve.103.033110 may be a valid DOI for title: Reynolds number dependence of Lyapunov exponents of turbulence and fluid particles
- 10.1016/j.bpj.2018.12.003 may be a valid DOI for title: Statistical mechanics of an elastically pinned membrane: static profile and correlations
- 10.1103/physreve.83.050901 may be a valid DOI for title: Effective free energy for pinned membranes
- 10.1016/j.bpj.2019.06.036 may be a valid DOI for title: Statistical mechanics of an elastically pinned membrane: Equilibrium dynamics and power spectrum
- 10.1038/nphys4138 may be a valid DOI for title: Membrane fluctuations mediate lateral interaction between cadherin bonds
- 10.1016/s0006-3495(94)80535-1 may be a valid DOI for title: Self-assembly of membrane junctions.
- 10.1080/00018739700101488 may be a valid DOI for title: Configurations of fluid membranes and vesicles
- 10.1209/epl/i2001-00281-7 may be a valid DOI for title: Fluctuation-induced aggregation of rigid membrane inclusions
- 10.1103/physreve.67.041907 may be a valid DOI for title: Interactions between proteins bound to biomembranes
- 10.1021/ct050293s may be a valid DOI for title: Simulating membrane dynamics in nonhomogeneous hydrodynamic environments
- 10.1039/c6sm01096b may be a valid DOI for title: Formation of semi-dilute adhesion domains driven by weak elasticity-mediated interactions
- 10.1103/physreve.72.031904 may be a valid DOI for title: Fluctuation spectrum of membranes with anchored linear and star polymers
- 10.1103/physreve.73.010401 may be a valid DOI for title: Nonmonotonic fluctuation spectra of membranes pinned or tethered discretely to a substrate
- 10.1016/j.bpj.2017.08.041 may be a valid DOI for title: Mapping cell membrane fluctuations reveals their active regulation and transient heterogeneities
- 10.1039/c5sm01900a may be a valid DOI for title: Monte Carlo study of the frame, fluctuation and internal tensions of fluctuating membranes with fixed area
- 10.1201/9780429497131 may be a valid DOI for title: Statistical thermodynamics of surfaces, interfaces, and membranes
- 10.1209/epl/i1996-00340-1 may be a valid DOI for title: Shape fluctuations of active membranes
- 10.1109/jproc.2004.840301 may be a valid DOI for title: The Design and Implementation of FFTW3
- 10.1016/j.euromechflu.2018.08.002 may be a valid DOI for title: A flow-pattern map for phase separation using the Navier–Stokes–Cahn–Hilliard model
- 10.1103/physrevlett.75.4031 may be a valid DOI for title: Lattice Boltzmann study of hydrodynamic spinodal decomposition
- 10.1103/physrevlett.74.3852 may be a valid DOI for title: Effects of hydrodynamics on phase transition kinetics in two-dimensional binary fluids
- 10.1017/jfm.2021.942 may be a valid DOI for title: Turbulence modulation in buoyancy-driven bubbly flows
- 10.1017/s0022112092001782 may be a valid DOI for title: On the multifractal properties of the energy dissipation derived from turbulence data
- 10.1103/physrevx.7.011002 may be a valid DOI for title: Statistical mechanics of thin spherical shells
- 10.1021/jp054372b may be a valid DOI for title: Mechanical properties of surfactant bilayer membranes from atomistic and coarse-grained molecular dynamics simulations
- 10.1103/physrevlett.64.2094 may be a valid DOI for title: Entropy-driven tension and bending elasticity in condensed-fluid membranes
- 10.1103/physrevlett.82.221 may be a valid DOI for title: Mobility and elasticity of self-assembled membranes
- 10.1016/s0006-3495(00)76304-1 may be a valid DOI for title: Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
- 10.1017/jfm.2017.820 may be a valid DOI for title: The effect of turbulence on mass transfer rates of small inertial particles with surface reactions
- 10.1021/acsnano.6b07302.s001 may be a valid DOI for title: Competition between bending and internal pressure governs the mechanics of fluid nanovesicles
- 10.1073/pnas.202617299 may be a valid DOI for title: Stomatocyte–discocyte–echinocyte sequence of the human red blood cell: Evidence for the bilayer–couple hypothesis from membrane mechanics
- 10.1103/physrevlett.78.2690 may be a valid DOI for title: Nonequilibrium equality for free energy differences
- 10.1088/0034-4885/75/12/126001 may be a valid DOI for title: Stochastic thermodynamics, fluctuation theorems and molecular machines
- 10.1007/s101890170071 may be a valid DOI for title: Universality classes of self-avoiding fixed-connectivity membranes
- 10.1142/9789812565518_0012 may be a valid DOI for title: Triangulated-surface models of fluctuating membranes
- 10.1103/physreva.38.1005 may be a valid DOI for title: Defects in flexible membranes with crystalline order
- 10.1007/978-3-662-05105-4 may be a valid DOI for title: Visualization and mathematics III
- 10.1007/978-3-662-05105-4_2 may be a valid DOI for title: Discrete differential-geometry operators for triangulated 2-manifolds
- 10.1103/physreve.78.051924 may be a valid DOI for title: Elastic properties and mechanical stability of chiral and filled viral capsids
- 10.1529/biophysj.106.081422 may be a valid DOI for title: Mechanical deformation of spherical viruses with icosahedral symmetry
- 10.1021/acssensors.9b00418.s001 may be a valid DOI for title: Label-free surface protein profiling of extracellular vesicles by an electrokinetic sensor
- 10.1007/978-3-642-13193-6_39 may be a valid DOI for title: Robust and Efficient Delaunay triangulations of points on or close to a sphere

INVALID DOIs

- http://dx.doi.org/10.1016/0301-9322(83)90064-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jnnfm.2018.01.008 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/fld.4678 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0022-247X(70)90110-1 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.physrep.2003.08.001 is INVALID because of 'https://doi.org/' prefix

victorapm commented 2 years ago

Review checklist for @victorapm

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/vipinagrawal25/MeMC?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@vipinagrawal25) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

mgiardino commented 2 years ago

Review checklist for @mgiardino

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/vipinagrawal25/MeMC?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@vipinagrawal25) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

fboehm commented 2 years ago

@victorapm & @mgiardino - how are the reviews going? Do you have any questions yet?

mgiardino commented 2 years ago

Hi @fboehm, I'm working on it and indeed I have a question(It's my first JOSS review). Besides the checklist that we are following, do we have to produce some sort of report to gather our comments? I have some advice/comments right now that I wish to communicate to the author, but I'm not sure if I'm supposed to create an issue about it or just write it here as a comment.

victorapm commented 2 years ago

@fboehm, I have the same questions as @mgiardino. Thanks!

fboehm commented 2 years ago

@mgiardino and @victorapm - Thanks for the questions!

You are not required to produce a report with comments. I recognize that such a report may be standard for other journals, but at JOSS we primarily depend on teh checklists. That being said, all comments for improving the package are welcome. You are also welcome to ask questions of the authors. To offer a comment or to ask a question of the authors, please do so in this comment thread. It's helpful, I think, to tag the submitting author if you wish to ask them a question.

If you like, you may also open issues in the submitted software repository (which is distinct from the joss-reviews repo). If you choose this approach, please be sure to link to any opened issues in this thread so that we have a complete record of activity in this thread. Thanks again!

mgiardino commented 2 years ago

Hi @vipinagrawal25, I have to report an issue about the Prerequisites of your README. I've tried the proposed instruction for Ubuntu systems in my Ubuntu 20.04.4 LTS: apt install g++ hdf5 resulting in “cannot found packet hdf5”. Maybe this requirement shall be better specified (which language binding is required? which version? some repo to add?). For example, some possible packets are: libhdf5-dev, libhdf5-cpp-103. Anyway, I finally achieved my compilation task by following your proposed solution on using the h5c++ compiler.

vipinagrawal25 commented 2 years ago

Hi @mgiardino, Thanks for your comment. We were not pedantic in giving installation directives for the hdf5 package in Ubuntu. We have fixed the README.md in the repository. After the installation, we also find that the environment variables for include and library path are not set properly. The user can set these paths manually in the Makefile to compile the package.

Regards Vipin

mgiardino commented 2 years ago

Thank you @vipinagrawal25. One more thing: to successfully execute the python modules, avoiding the error "ModuleNotFoundError: No module named 'h5py'", the h5py module shall be added to the pip installation instruction.

mgiardino commented 2 years ago

Hi @vipinagrawal25 , I've created the issue https://github.com/vipinagrawal25/MeMC/issues/1 to suggest some minor corrections to your README.md file. Regards,

Marco

fboehm commented 2 years ago

@victorapm @mgiardino - how are the reviews going? Is there anything that I might help with? thanks again!

mgiardino commented 2 years ago

Hi @fboehm, I've completed the installation steps and I'm now using my running instance to perform several test runs. With visit I am visualizing the resulting vtks and also trying to analyze them. My comprehension of the involved science domain is very limited, anyway, so my considerations are mostly focused on sw engineering features. About the "Missing DOIs" from editioralbot, are we supposed to use also this information in some way? Cheers,

Marco

victorapm commented 2 years ago

@fboehm, it's going well. The comments above regarding installation helped me. Thanks, @mgiardino. Now, I'm looking at reproducing the results.

I have a question: is it necessary that all authors of the paper have at least one commit in the code repo?

Thanks!

fboehm commented 2 years ago

@mgiardino - Thank you for your question. The missing DOIs should be corrected by the authors, but you need not do anything with them.

@victorapm - Thank you for your question. There is no JOSS policy requiring that authors have at least one commit.

Thank you, @mgiardino and @victorapm for your work on these reviews. @vipinagrawal25 - please ensure that your cited works have accurate dois.

vipinagrawal25 commented 2 years ago

Thank you @vipinagrawal25. One more thing: to successfully execute the python modules, avoiding the error "ModuleNotFoundError: No module named 'h5py'", the h5py module shall be added to the pip installation instruction.

Hi @mgiardino, We have now added the instructions for h5py installation in the readme as well.

vipinagrawal25 commented 2 years ago

Hi @vipinagrawal25 , I've created the issue vipinagrawal25/MeMC#1 to suggest some minor corrections to your README.md file. Regards,

Marco

Hi @mgiardino,

Thanks a lot for the comments. We have now incorporated all of them and closed the issue. Do let us know if you have any further suggestions.

mgiardino commented 2 years ago

Dear @vipinagrawal25, after constructing the membrane, triangulating the surface, running the bin/exe_memc executable, the program gives the following console output message (multiple times): “X0 small roots may not be correct”. I'm not sure if this message shall be seriously taken into consideration, as the results are still being produced. In any case, the output stream is crowded with these messages, maybe this behavior can be confusing for the user.

thecalculon commented 2 years ago

Dear @mgiardino,

The section of code where we evaluate the force exerted by the AFM (Atomic Force Microscopy) tip to Exosome outputs the message "X0 small roots may not be correct". Consider the representative configuration of the Exosome the AFM tip, shown in the figure attached. The AFM tip is modeled as a paraboloid and the force it exerts is very short ranged. Therefore, we assume that the force exerted on a represented point say (x_0, y_0, z_0) on exosome is only from a point (x,y,z) of the tip which is nearest to (x_0, y_0, z_0). Thus, to evaluate the force we first solve for (x,y,z) in the code.

When the value of x_0 (or y_0/z_0) is zero till machine precision, we find the solution to be incorrect. At the same time, if the points representing the surface of Exosome is determined using a Monte-Carlo simulation then, we have observed that this condition (x_0=0) is never satisfied. Therefore, we had never seen the message in our screen as you are observing.

Fortunately, after several attempts on different laptops and servers we were able to reproduce the error. At our end the reason was that the memc config file (conf/dmemc_pos.h5) was not written/read properly. We were able to fix the error by reinstalling the hdf5 library.

To avoid the confusion to the user, we now have changed the error message to the following;

x0 = 0, y0 = 0, z0 = 0; Points representing exosome very small... See section Checking execution status in https://github.com/vipinagrawal25/MeMC/blob/main/README.md

We have also added a section Checking Execution Status in the README file which should enable the user to debug the code properly.

@mgiardino we hope that we were able to help you resolve the error. We welcome all further suggestions.

error

thecalculon commented 2 years ago

Hi @fboehm @mgiardino @victorapm,

I am Vikash Pandey, the second author of the paper and go by the username @thecalculon . Since @vipinagrawal25 is away I will be responding to the reviews for the time being.

mgiardino commented 2 years ago

Dear @thecalculon, thank you for your very interesting explanation! I have reinstalled the hfd5 library and downloaded/recompiled the MeMC code. Now the error messages have disappeared and everything seems OK. The new "Checking Execution Status" section is also helpful. Maybe it should also be declared the dependence of the scriptutils/check_status.py from the matplotlib module.

mgiardino commented 2 years ago

Hi @fboehm, I think my review is pretty complete. The paper is well written and the software behavior is "as expected": great job! The authors were really open to my suggestions and I think that the small corrections performed could also simplify the use of this module. I write here my last comments.

Statement of need The target audience is somewhat implicit.

References The (n.d. …) style references are syntactically correct?

Functionality/Performance No performance claims.

Documentation/Functionality documentation No API or very minimal documentation is provided inline with the source code. The sw usage is well described, but the code is missing any kind of description, considering file, method, or instruction level. No documentation support is provided for the developer trying to understand or contribute to the software logic.

Documentation/Community guidelines I have not found any clear guidelines about contributions for third parties.

fboehm commented 2 years ago

Hi, @thecalculon @vipinagrawal25 - please see the above comments from @mgiardino and make changes as needed. For example, your submission needs to have a statement about guidelines for contributors. Once you've addressed the above issues, we'll proceed further towards publication. thanks again!

fboehm commented 2 years ago

@victorapm - How is the review going? It looks like your checklist has many unchecked boxes. Please feel free to comment in this thread about what changes are needed from the authors.

fboehm commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1017/S0022112086002859 is OK
- 10.1017/S0022112005003368 is OK
- 10.1103/PhysRevE.76.026313 is OK
- 10.1103/PhysRevE.83.036314 is OK
- 10.1103/PhysRevLett.100.184503 is OK
- 10.1103/PhysRevLett.107.184503 is OK
- 10.1063/1.864230 is OK
- 10.1063/1.857985 is OK
- 10.1017/S0022112056000020 is OK
- 10.1017/S002211200500844X is OK
- 10.1103/PhysRevLett.106.074101 is OK
- 10.1016/0032-0633(65)90131-5 is OK
- 10.1086/148912 is OK
- 10.1086/149265 is OK
- 10.1103/PhysRevLett.92.040601 is OK
- 10.1103/PhysRevE.85.036315 is OK
- 10.1103/PhysRevLett.96.168301 is OK
- 10.1103/PhysRevE.70.026405 is OK
- 10.1103/PhysRevFluids.3.053901 is OK
- 10.1017/jfm.2015.650 is OK
- 10.1103/PhysRevFluids.1.033602 is OK
- 10.1063/1.1605952 is OK
- 10.1017/CBO9780511524608.004 is OK
- 10.1051/jp2:1994173 is OK
- 10.1017/jfm.2017.485 is OK
- 10.1146/annurev.fluid.38.050304.092139 is OK
- 10.1103/PhysRevLett.58.2571 is OK

MISSING DOIs

- 10.2307/2313035 may be a valid DOI for title: Vectors, tensors and the basic equations of fluid mechanics
- 10.1016/c2009-1-28537-6 may be a valid DOI for title: Mathematical methods for physicists
- 10.1016/c2013-0-03269-0 may be a valid DOI for title: Mean-field magnetohydrodynamics and dynamo theory
- 10.1016/c2009-0-14608-1 may be a valid DOI for title: The classical theory of fields
- 10.1007/3-540-27223-2_1 may be a valid DOI for title: Fluid mechanics
- 10.1007/3-540-27223-2_1 may be a valid DOI for title: Fluid mechanics
- 10.1016/0029-8018(83)90035-5 may be a valid DOI for title: An album of fluid motion 
- 10.5040/9781350970052 may be a valid DOI for title: Turbulence 
- 10.5040/9781350970052 may be a valid DOI for title: Turbulence
- 10.1016/0032-3861(81)90183-x may be a valid DOI for title: Scaling concepts in polymer physics
- 10.1103/revmodphys.65.851 may be a valid DOI for title: Pattern formation outside of equilibrium
- 10.1103/physreva.23.2673 may be a valid DOI for title: Intermittency in nonlinear dynamics and singularities  at complex time
- 10.1145/103162.103163 may be a valid DOI for title: What Every Computer Scientist Should Know About Floating-Point Arithmetic
- 10.1103/physreva.45.600 may be a valid DOI for title: Stochastic Runge-Kutta algorithms. I. White noise 
- 10.1088/1367-2630/6/1/072 may be a valid DOI for title: Active and passive fields face to face
- 10.1007/bfb0105029 may be a valid DOI for title: Intermittency of passive scalars in delta-correlated flow: Introduction to recent work
- 10.1017/jfm.2012.65 may be a valid DOI for title: Wall accumulation and spatial localization in particle-laden wall ﬂows
- 10.1086/304146 may be a valid DOI for title: The effects of velocity correlation times on the turbulent amplification of magnetic energy
- 10.1088/2041-8205/791/2/l34 may be a valid DOI for title: Fluctuation dynamo at finite correlation times and the Kazantsev spectrum
- 10.1063/1.3276099 may be a valid DOI for title: Singularities of complex-valued solutions of the two-dimensional Burgers system
- 10.1103/physreva.44.r3427 may be a valid DOI for title: Lyapunov exponents for hydromagnetic convection.
- 10.1006/jcph.2002.6995 may be a valid DOI for title: Exponential time differencing for stiff systems 
- 10.1038/nature00983 may be a valid DOI for title: Acceleration of rain initiation by cloud turbulence
- 10.1023/b:joss.0000041740.90705.d5 may be a valid DOI for title: Sticky Behavior of Fluid Particles in the Compressible Kraichnan Model
- 10.1146/annurev.fluid.010908.165210 may be a valid DOI for title: Lagrangian properties of particles in turbulence
- 10.1063/1.3623466 may be a valid DOI for title: Multi-time multi-scale correlation functions in hydrodynamic turbulence
- 10.1103/physreve.67.066310 may be a valid DOI for title: Strong universality in forced and decaying turbulence  in a shell model 
- 10.1063/1.857730 may be a valid DOI for title: A general classification of three-dimensional flow fields
- 10.1063/1.869752 may be a valid DOI for title: Dynamics of the velocity gradient tensor invariants in isotropic turbulence
- 10.1103/physreve.63.056313 may be a valid DOI for title: Statistics of Fourier modes in a turbulent flow
- 10.1109/sc.2002.10052 may be a valid DOI for title: 16.4-Tflops Direct Numerical Simulation of Turbulence by a Fourier Spectral Method on the Earth Simulator
- 10.1103/physrevlett.93.064502 may be a valid DOI for title: Multifractal Statistics of Lagrangian Velocity and Acceleration in Turbulence
- 10.1017/s002211208100181x may be a valid DOI for title:  Numerical study of small-scale intermittency in  three-dimensional turbulence
- 10.1103/physreve.72.056307 may be a valid DOI for title: Structural studies of decaying fluid turbulence: Effect of initial conditions
- 10.1088/1367-2630/9/8/307 may be a valid DOI for title: 2D enslaving of MHD turbulence
- 10.1103/physrevlett.92.054502 may be a valid DOI for title: Critical Magnetic Prandtl Number for Small-Scale Dynamo
- 10.1103/physrevlett.94.164502 may be a valid DOI for title: Numerical Study of Dynamo Action at Low Magnetic Prandtl Numbers
- 10.1103/physrevlett.33.1139 may be a valid DOI for title: Relaxation of Toroidal Plasma and Generation of Reverse Magnetic Field
- 10.1103/physrevlett.81.3144 may be a valid DOI for title: Relaxed State of a Magnetized Plasma with Minimum Dissipation
- 10.1103/physrevlett.84.1196 may be a valid DOI for title: Heliciy Redistribution during Relaxation of Astrophysical Plasmas
- 10.1007/s11207-006-0280-5 may be a valid DOI for title: Solar Arcades as Possible Minimum Dissipative Relaxed States
- 10.1063/1.2828539 may be a valid DOI for title: Theory and simulations of principles of minimum dissipation rate
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INVALID DOIs

- http://dx.doi.org/10.1016/0301-9322(83)90064-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jnnfm.2018.01.008 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/fld.4678 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0022-247X(70)90110-1 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.physrep.2003.08.001 is INVALID because of 'https://doi.org/' prefix

victorapm commented 2 years ago

@victorapm - How is the review going? It looks like your checklist has many unchecked boxes. Please feel free to comment in this thread about what changes are needed from the authors.

Hi @fboehm, I haven't made progress in the last two weeks. I am sorry about that. I am working on the review in this weekend and I plan to finish it in the next two weeks.

Thanks!

fboehm commented 2 years ago

@victorapm - that sounds good! Thank you!

fboehm commented 2 years ago

@vipinagrawal25 @thecalculon - please double-check that the references in paper.md have valid DOIs. If you have in your bib file references that are not used in the paper.md, you may wish to delete them from the bib file.

thecalculon commented 2 years ago

Dear @thecalculon, thank you for your very interesting explanation! I have reinstalled the hfd5 library and downloaded/recompiled the MeMC code. Now the error messages have disappeared and everything seems OK. The new "Checking Execution Status" section is also helpful. Maybe it should also be declared the dependence of the scriptutils/check_status.py from the matplotlib module.

Hi @mgiardino we have updated the Readme.md adding the matplotlib dependency . Since the software is required only when the user is in the debugging phase, we have added the dependency in the section "Checking Execution status"

thecalculon commented 2 years ago

Hi @fboehm, I think my review is pretty complete. The paper is well written and the software behavior is "as expected": great job! The authors were really open to my suggestions and I think that the small corrections performed could also simplify the use of this module. I write here my last comments.

Statement of need The target audience is somewhat implicit.

References The (n.d. …) style references are syntactically correct?

Functionality/Performance No performance claims.

Documentation/Functionality documentation No API or very minimal documentation is provided inline with the source code. The sw usage is well described, but the code is missing any kind of description, considering file, method, or instruction level. No documentation support is provided for the developer trying to understand or contribute to the software logic.

Documentation/Community guidelines I have not found any clear guidelines about contributions for third parties.

Dear @mgiardino, Thank you very much for taking time and reviewing the paper.

Hi @fboehm, we will complete the remaining criterion in the checklist and get back at you as quickly as we can.

thecalculon commented 2 years ago

@editorialbot check references

thecalculon commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

vipinagrawal25 commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1021/acsnano.6b07302 is OK
- 10.1073/pnas.1212268109 is OK

MISSING DOIs

- 10.1103/physrevx.7.011002 may be a valid DOI for title: Statistical mechanics of thin spherical shells
- 10.1073/pnas.202617299 may be a valid DOI for title: Stomatocyte–discocyte–echinocyte sequence of the human red blood cell: Evidence for the bilayer–couple hypothesis from membrane mechanics
- 10.1103/physrevlett.82.221 may be a valid DOI for title: Mobility and elasticity of self-assembled membranes
- 10.1007/s101890170071 may be a valid DOI for title: Universality classes of self-avoiding fixed-connectivity membranes
- 10.1103/physreve.72.031904 may be a valid DOI for title: Fluctuation spectrum of membranes with anchored linear and star polymers
- 10.1142/9789812565518_0012 may be a valid DOI for title: Triangulated-surface models of fluctuating membranes
- 10.1007/978-3-642-13193-6_39 may be a valid DOI for title: Robust and Efficient Delaunay triangulations of points on or close to a sphere
- 10.1529/biophysj.106.081422 may be a valid DOI for title: Mechanical deformation of spherical viruses with icosahedral symmetry
- 10.1103/physreve.78.051924 may be a valid DOI for title: Elastic properties and mechanical stability of chiral and filled viral capsids
- 10.1103/physreva.38.1005 may be a valid DOI for title: Defects in flexible membranes with crystalline order
- 10.1007/978-3-662-05105-4 may be a valid DOI for title: Visualization and mathematics III
- 10.1007/978-3-662-05105-4_2 may be a valid DOI for title: Discrete differential-geometry operators for triangulated 2-manifolds
- 10.1021/acssensors.9b00418.s001 may be a valid DOI for title: Label-free surface protein profiling of extracellular vesicles by an electrokinetic sensor

INVALID DOIs

- None

vipinagrawal25 commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1021/acsnano.6b07302 is OK
- 10.1073/pnas.1212268109 is OK
- 10.1103/physrevx.7.011002 is OK
- 10.1073/pnas.202617299 is OK
- 10.1103/physrevlett.82.221 is OK
- 10.1007/s101890170071 is OK
- 10.1103/physreve.72.031904 is OK
- 10.1103/physrevx.7.011002 is OK
- 10.1007/978-3-642-13193-6_39 is OK
- 10.1529/biophysj.106.081422 is OK
- 10.1103/physreve.78.051924 is OK
- 10.1103/physreva.38.1005 is OK
- 10.1007/978-3-662-05105-4 is OK
- 10.1007/978-3-662-05105-4_2 is OK
- 10.1021/acssensors.9b00418.s001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

vipinagrawal25 commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

victorapm commented 2 years ago

Hi @vipinagrawal25 and @thecalculon, congratulations for your nice work! I have finished my review, the most important points I wanted to highlight are code organization and performance. Please find all my comments below, and let me know if you have questions. Thank you!

[ ] Consider fixing the compilation warnings listed below:

src/init.cpp: In function ‘void init_read_parameters(MBRANE_para*, AFM_para*, MCpara*, char*)’:
src/init.cpp:102:37: warning: format ‘%d’ expects a matching ‘int*’ argument [-Wformat=]
102 |         sscanf(buff,"%lf %lf %d %d %d", &td1, &td2,  &t_n2, &t_n3);
  |                                    ~^
  |                                     |
  |                                     int*
src/init.cpp:80:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
80 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:81:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
81 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:82:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
82 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:90:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
90 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:91:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
91 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:99:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
99 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:100:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
100 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:101:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
101 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:108:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
108 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:109:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
109 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/init.cpp:110:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
110 |         fgets(buff,255,(FILE*)f2);
  |         ~~~~~^~~~~~~~~~~~~~~~~~~~
src/forces_surf.cpp: In function ‘Vec3d determine_xyz_parabola(Vec3d, AFM_para)’:
src/forces_surf.cpp:45:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
45 |         if(fabs(y0)< 1e-15 & fabs(z0)< 1e-15 ){
  |            ~~~~~~~~^~~~~~~
src/forces_surf.cpp:28:9: warning: variable ‘nroot’ set but not used [-Wunused-but-set-variable]
28 |     int nroot;
  |         ^~~~~
src/hdf5_io.cpp: In function ‘void io_read_config(double*, int, char*)’:
src/hdf5_io.cpp:86:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
86 |     fread(Pos, N*sizeof(double), 1, fid);
  |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[ ] Is there a reason to use 60000 MC steps by default? Should this parameter be accessible to the user in the exe_start driver?
[ ] Code organization:
1. Consider generating a library so that external application codes can link to it.
2. Consider moving the bulk of the work performed in the drivers start.cpp and memc.cpp to separate functions located at the src/ folder. This way, you can create a library that distributes those functionalities to external users.
3. I could not find API documentation anywhere. For example, what are the meanings of the input/output parameters used in functions such as monte_carlo_surf2d, pairlj_total_energy, and monte_carlo_3d? Consider using a documentation generator tool such as Doxygen. Note that functions should be annotated to be able to automatically generate the documentation.
4. Add a make clean target (could be the same as make distclean).
[ ] Code performance:
1. Have you considered multithreading, e.g., via OpenMP, to speedup functions that take most of the execution time? For example, Gprof indicates that cal_length takes up to 70% of the execution time of exe_start and bending_energy_ipart takes up to 90% of the execution time of exe_memc. Would it be possible to reduce the execution time of these particular functions?
[ ] Minor changes in the text:
1. Lines 60-61: did you mean: there are two elastic constants to be determined? Can you elaborate on this statement?
2. Line 64: should the definition of R be moved closer to its first appearance, i.e., closer to Equation 3?
3. What is the meaning of K_B in Equation 6?
4. What is the meaning of H in Equation 9?
5. Lines 110-113, 119, 127: which subsubsection are you talking about? I cannot see the numbers.
6. In Equation 17, how \Delta V is computed? Is it simply V - V_0?
7. Line 121-122: remove the text ::: subequations :::
[ ] Add community guidelines which should contain information about how to:
1. Contribute to the software.
2. Report issues or problems with the software.
3. Seek support.
[ ] Add white background to the figure: https://github.com/vipinagrawal25/MeMC/blob/main/paper/fig/describe_theta.png
[ ] Update links in https://github.com/vipinagrawal25/MeMC/blob/main/README.md#example
1. gnuplot: http://www.gnuplot.info/
2. GNU GSL: https://www.gnu.org/software/gsl/

fboehm commented 2 years ago

@vipinagrawal25 and @thecalculon - do you have any questions about the next steps? Thanks again!

vipinagrawal25 commented 2 years ago

@fboehm,

Thank you for the question. The reviewer's comments are very clear and we are modifying the code and text accordingly. We have incorporated most of the suggestions and are in the process of finalizing everything. You will hear from us soon.

Thanks & Regards Vipin & Vikash

vipinagrawal25 commented 2 years ago

@editorialbot generate pdf

openjournals / joss-reviews