How to Modify LAMMPS: From the Prospective of a Particle Method Researcher
, Eve le Guillou 2, Antoine Danzé 2, Irene Moulitsas 2, Iwan H. Sahputra 1,3, Amin Rahmat 1, Carlos Alberto Duque-Daza 1,4, Xiaocheng Shang 5, Khai Ching Ng 6, Mostapha Ariane 7 and Alessio Alexiadis 1,*Round 1
Reviewer 1 Report
The authors have addressed my previous comments.
Author Response
We are happy of having addressed all the comments. We thank the referee for the time he/she spent reviewing the manuscript and for giving us the opportunity to improve its content.
Reviewer 2 Report
the article does not meet the minimum criteria for publication in the journal
Author Response
In his/her comment, the referee does not provide neither an explanation on what are the ‘minimal criteria’ that allegedly the article does not meet, neither a reason of why these are not met. Therefore, on the basis of this comment, we are not in the position to make any modification to the manuscript.
Reviewer 3 Report
Reviewers' comments:
Manuscript ID: ChemEngineering-1090370
Title: How to modify LAMMPS: From the prospective of a Particle method researcher.
Manuscript Type: Article.
Reviewers' comments:
The manuscript describes the How to modify LAMMPS: From the prospective of a Particle method researcher. The manuscript needs a detailed editing. Some markings are made to just illustrate the extent of editing needed. A thorough revision addressing all the concerns is needed and if the authors are prepared to do that it can be considered for a review of the revised manuscript.
The authors need to consider the following comments
- The introduction section should be improved; more related papers must be discussed and superiority, novelty, critical improvement in this study must be clarified.
- Figure 2. Schematic representation of Kelvin-Voigt model. Not clear make clear.
- Please provides the references for all equations and formula.
- Figure 9 - Not clear make clear.
- Figure 10 - Not clear make clear.
- Conclusions: the authors need to improve with more specific short results and conclusions, i.e. academic novelty or technical advantages.
- References: make all references in same format for volume number, page numbers and journal name, because it is difficult to searching and reading.
- Several faults: are added or missing spaces between words: see manuscript file.
Author Response
The introduction section should be improved; more related papers must be discussed and superiority, novelty, critical improvement in this study must be clarified.
We added all publications that, to the best of our knowledge, are related to the theme of the manuscript and rewrote part of the introduction and conclusions. In both the new introduction and the new conclusions we clarify the difference between our study and the available publications explaining that while the available material focuses on Molecular Dynamics, we extend the approach to other particle methods such as SPH, DEM etc.
Figure 2. Schematic representation of Kelvin-Voigt model. Not clear make clear.
Figure 2 has been improved as requested.
Please provides the references for all equations and formula.
All the equations have been properly referenced.
Figure 9 - Not clear make clear.
Figure 10 - Not clear make clear
Both figures shows that the instantaneous data and their trend curve obtained in the simulations are in good agreement with the analytical solution of Sameen & Govindarajan. 

This information has been clarified in the legends of all the subfigures and in the captions.
Conclusions: the authors need to improve with more specific short results and conclusions, i.e. academic novelty or technical advantages.
The conclusions have been modified accordingly.
References: make all references in same format for volume number, page numbers and journal name, because it is difficult to searching and reading.
The format of the references is now consistent.
Several faults: are added or missing spaces between words: see manuscript file.
Fixed.
Reviewer 4 Report
The authors gave a good introduction to the structure of the LAMMPS code and showed how to modify LAMMPS code to implement new algorithms and functions in details. The content of the manuscript would be useful for researchers who not only use LAMMPS to perform simulations but also want to develop their own methods in LAMMPS. My only suggestion is that the authors may remove section 2.1 and 2.2 which only explain basic concepts of the C++ programming language. I believe the most of the readers should know those basic concepts or they could consult the textbook.
Author Response
We believe section 2.1 and 2.2 are necessary for consistency since they introduce the terminology that is used in the rest of the manuscript. Moreover, with this paper, we would also like to attract readers with minimal coding background. This type of reader would probably need to refer to a dedicated textbook for some of the concepts, but, even so, sections 2.1 and 2.2 will still provide a guide on the basic concept that are necessary to understand the rest of the article.
Round 2
Reviewer 3 Report
Reviewers' comments:
The authors revised the manuscript according to the reviewers' comments.
So that I recommended this manuscript accept for publication in ChemEngineering.
This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.
Round 1
Reviewer 1 Report
This manuscript, although fairly well written, does not provide any scientific advancement. Rather, it shows how to modify a widely adopted code, a task that many, many researcher must do anyways in the early stages of their scientific career, whether with lammps or any other major codes. Since this manuscript doesn't report any physical application, it could be, eventually, presented on the arXiv, or sent to some education-oriented journal (maybe journal of chemical education?). Besides this, this article does not even fit with the scopes of ChemEngineering.
Reviewer 2 Report
This is a detailed tutorial for how to modify and contribute to the LAMMPS codebase. The walk through of some of the style classes is a good introduction for people who want to work with the codebase but are not familiar with it. Below are my comments on which I would like to hear feedback from the authors.
- I understand section 3 serves as a basic example showing how to implement a trivial change. However, there is also some overlap between section 3 and 4. In my opinion many of the preliminary concepts in section 3 can also be explained with the example in section 4.
- It would be easier for readers to find out what has changed if you could show a diff between the two files (for example on Page 15), such as a side by side diff view. Likewise for all subsequent side by side comparison of code snippets throughout the manuscript.
Reviewer 3 Report
The authors present a very comprehensive and exhaustive instruction for the use and implementation of LAMMPS code. It is a significant work for a friendly-used program especially suitable for researchers with less-advanced coding skills. I have a small suggestion is that this work can be combined with the online manual, thus more convenient to use.
