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I research the aerodynamics of an air vehicle. I use commercial fluid-dynamics software (we have a commercial license). However, I noticed that most papers dealing similar research use homemade software and write about it in the methods section of their papers.

Should I describe how I operate the commercial software in the methods section of my paper? If not, how should I organize this part of my paper? What aspects should I cover in my paper?

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  • Not how you operate the software, but how you model the flow, separation, turbulence losses etc
    – Solar Mike
    Nov 24, 2017 at 16:35
  • Do you really mean "commercial"?
    – aparente001
    Nov 25, 2017 at 3:25
  • @aparente001 yes it's a commercial software called STAR-CCM+
    – PureLine
    Nov 25, 2017 at 16:27
  • @PureLine - Okay, great, you could also talk about the considerations that led you to choose that package over some others, what made the routines you chose an appropriate choice for your problem, and give a brief description of the algorithm(s). Also, what you put in your comment below Dan's answer looks good.
    – aparente001
    Nov 25, 2017 at 17:49

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Since my background is also CFD, maybe I can help. It is really important to mention what type of scheme you are using and what is the commercial software. Is it based on the finite volume method or finite element method? Is it a cell-centered or vertex-centered scheme? What is the order of convergence of the method you are using, are they first, second or third order in space? Which transient time-stepping scheme are you using? What is the order of convergence of that scheme? Is it implicit, explicit? Etc.

In the end, the commercial software is just the implementation of a numerical scheme that you are using to solve the Navier-Stokes equation. It is important that you highlight the equations you are solving, the type of turbulence modeling you might be using and also the properties and details of the underlying numerical scheme. Then, even if you are using a commercial software package, people will have sufficient details to understand the context of your numerical resolution.

Also, please do not forget to carry out grid-independence studies!

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    Great answer. I would also talk about why you chose the particular routine, and give a bit of an explanation of the routine's algorithm. Also you can talk about choice of parameter values and how you settled on the final values you chose.
    – aparente001
    Nov 25, 2017 at 3:24
  • thanks for your detailed answer, but based on your answer, there will be another problem. Since it's a commercial software, here it is STAR-CCM+, it may would not give you all the information of its implementation. As to STAR-CCM+, the fundamental theory is even incomplete in its manual. Consequently, some underlying details you have mentioned, such as cell-centered or vertex-centered, is hard to presented in my paper. My new question is whether it's proper to neglect the information that I could get from the official manual ?
    – PureLine
    Nov 25, 2017 at 16:20
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    Although you might not be able to know if Star CCM+ is node or cell centered (which I doubt, that information must exist somewhere, maybe you can call a representative), you can know all the rest of the information. What is your time stepping scheme? What is your spatial discretization scheme? All those schemes have a name and you can look up the corresponding litterature on them. What process are you using the solve the Navier-Stokes equations? PISO, SIMPLE, SIMPLEC, etc. All that information must be present in the paper, in my opinion you cannot neglect that and refer to the manual.
    – BlaB
    Nov 25, 2017 at 16:41
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The point of the methods section is to give enough detail so that someone else could reproduce what you did. You should seek to meet that goal within the context of using commercial software (which is not a problem by the way).

Don't describe how to use it (information that could be found in the manual) but how you used it.

Tell all about what analyses you did, what parameters you used, the environment, the version of the software, etc.

Lots of software used in science allows you to enter commands as a script, output a log of actions taken, or both. If this is true if the software you are using, including such files as supplementary material will also help clarify the methods, and give a level of detail not possible in the paper itself.

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  • thanks for your general guideline. I think I get your point. You mean I should give my working platform and the key configuration of the simulation, so that other researchers could examine and reproduce my simulation, am I right ?
    – PureLine
    Nov 25, 2017 at 16:25

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