29

The SIAM Journals, especially SISC (Scientific Computing) and MMS (Multiscale Modeling and Simulation) are obvious established and high-quality choices.


14

I personally have come the way from Gnuplot to Matplotlib with PGFPlots as an intermediate step. I will try to name all aspects of Matplotlib that I like. It is very versatile. You are not limited to line or scatter plots, you can easily do bar plots, images (matrix visualization!), basic 3D plotting and even some animation. You can use Matplotlib as a GUI ...


10

Physical Review E http://pre.aps.org/about Physical Review E (PRE), interdisciplinary in scope, focuses on many-body phenomena, including recent developments in quantum and classical chaos and soft matter physics. It has sections on statistical physics, equilibrium and transport properties of fluids, liquid crystals, complex fluids, polymers, chaos, fluid ...


10

This is not an answer to your question. But if a student came to me asking this question, I would ask him or her to read these articles: You and your research (Hamming) How to choose a good scientific problem (Alon) And a warning: jumping into a "hot" subfield as a student is very dangerous if your advisor is not at the front of that subfield. You're ...


10

The best way to do this to avoid these issues is to publish a paper about what your software package does and the problems it solves and cite your Github repo or website or whatever for access to the software. That way you don't need to give up your copyright on your code, and you can BSD/MIT/GPL it to your heart's content.


9

In addition to all that Bill Barth has already said above, let me mention that people often report the fastest of several runs. The rationale is that the actual run time is the ideal run time plus any number of slow downs resulting from other processes running, OS delays, network delays, etc. Since these are all noise we are not interested in, using the ...


8

Great question and great replies, but I think none addresses the question of persistence adequately, if the goal is to achieve the same standard accorded to the publication itself. (Which may be silly given the chances the code still runs, but may still be at least as useful as the publication all the same). University websites journal supplements aren't ...


8

I think there are several alternatives, but to some extent, it may depend upon the field. For fluid mechanics, there's obviously J. Fluid Mech.. For many areas in microscopic physics, you could send your work to J. Chem. Phys.


8

the planned longevity of TeX comes to mind: “Ever since those beginnings in 1977, the TeX research project that I embarked on was driven by two major goals. The first goal was quality: we wanted to produce documents that were not just nice, but actually the best. (…) The second major goal was archival: to create systems that would be independent of ...


8

You're looking at the wrong metric. In most areas of science, people don't write code at all but still get their papers published. The same is true for more theoretical papers in numerical analysis, proving for example the convergence of a particular scheme. On the other hand, there are papers that discuss particular libraries or implementations. These ...


7

First, an attempt to just answer the question. My (personal and subjective) feeling is that many jobs and funding opportunities right now are tied to applications in biology and energy, and that the hot research topics are in "multi-scale" and "multi-physics" phenomena, as well as uncertainty quantification. However, in your case you need to know what will ...


7

If you're willing to overcome the learning curve of Gnuplot, you can generate top-quality figures with it (as exemplified in http://www.gnuplotting.org/). In particular, I'd recommend using the epslatex terminal as it allows you to use LaTeX to render all the text in the figure (including any mathematical notation that you may wish to input). If you want ...


7

I oftem use Matlab and then save the result as an eps file via print -depsc2 -f1 fig. This saves figure 1 as an eps file named fig.eps. There is also the Plot2Svg from matlab file exchange that can save as svg. This is really nice since you can then open the files in Inkscape or other vector graphics software and edit them. If you are willing to learn new ...


6

Along the same lines as aeismail's answer, International Journal of Numerical Methods in Engineering, and International Journal of Numerical Methods in Fluids could be candidate journals for papers that would otherwise go into Journal of Computational Physics. (These journals are both Wiley journals.)


6

Total running time (wall clock) is the only metric that matters in industry or real life applications: this figure should never be omitted, even if embarrassing. Of course this metric is very dependent on the test environment, so this should be described in detail. All other metrics can (or should be) reported if they provide insight into the problem, or ...


5

The short answer is: it depends. Some journals have a requirement or a guideline to have experimental results that corroborate the numerical simulations. For example, IEEE Transactions on Microwave Theory and Techniques rarely publishes papers that do not have experimental results in one form or another. However, this is very different for IEEE Transactions ...


4

There are many technical challenges that make exact bit-for-bit reproducibility of computational results extremely hard to achieve. At the software level, changes to the code or any of the libraries used by the code can obviously cause different results to be produced. You'd be surprised by the number of support libraries that can end up linked into a ...


4

It is often the case that one can only report the tip of the iceberg of all the work and compromises that went into a piece of software. Reporting performance is nice but the real deal is when the code is made freely accesible on internet, this way, anyone interested can evaluate and reproduce the results. Ideally, if you release the software, you can also ...


4

Although not as good as SIAM journals, Communications in Computational Physics (CiCP) also seems promising.


3

In Stodden, V. 2009. “The Legal Framework for Reproducible Scientific Research.” CiSE. Victoria Stodden recommends publishing the full "research compendium", and lists the following components on p. 38: The research paper The data - including documentation and code for processing the data The experiment — all source code; documentation, parameters, ...


2

Communications in Computational Physics, published with Cambridge University Press http://www.global-sci.com/ Journal of Computational Mathematics: free for both reader and author, published by SMAI http://www.euro-math-soc.eu/news/14/12/5/smai-founds-new-journal-computational-mathematics Journal of Scientific Computing, while not Elsevier, is with ...


2

There is also the Journal of Scientific Computing, which overlaps strongly with JCP in its area of focus.


2

Take a look at http://www.runmycode.org. They host companion sites for code associated with research papers. If the code is R, Matlab, or a few others, it will actually run the code for you. I haven't tried it yet, but I intend to. I think David Donoho and his collaborators use it.


2

I work for Elsevier. My company has started using the Collage framework (developed in response to the Executable Paper Grand Challenge) in journal issues to enable authors to include all of the data and code needed to reproduce the results and figures in their papers. This feature makes it easier for readers to reproduce results reported in the article and ...


2

There have been many attempts at making reproducibility happen and there is a whole literature on this topic. My personal opinion from 15 years of scientific software is that it's unrealistic, as unsatisfactory as I find that answer. The problems are that (i) complex software has bugs and so can't be frozen; (ii) software is never feature complete and so ...


2

For a possible solution to this problem, see my ActivePapers project. In summary, it describes how data and code can be packaged together with explicit dependencies on specific versions of each software component. This makes it possible to exactly reproduce a computation, while also permitting to run updated software on the same data. I should add that ...


2

It sounds like you actually have three pieces of information here -- h, error, and runtime. Plotting accuracy vs runtime isn't that useful if there is no correspondence with h (and so the user of your algorithm can't know how to pick h to get the desired accuracy/runtime). I'd do scatter plots with color of the glyph to indicate h. In this way your ...


2

As Wolfgang said, your metric is wrong. Writing code alone simply isn't ever sufficient to publish a paper. A meaningful paper that is; obviously a lot of garbage gets published. I can think of 3 major areas of computational science publications: Numerics: You developed a new numerical method, or otherwise enhanced/modified an existing one. Results show ...


1

I suggest you use the median to give a statistical estimate. Unlike the mean, the median is not corrupted by outliers.


1

I believe that as far as the choice of language goes, using a standardized one (e.g. C/Fortran/C++) would qualify as "best practice". If a package depends on 10 other libs/packages, especially those written in obscure languages then that obviously is bad for longevity. Many projects end up being orphaned after some time. I dont think major libs/api's like ...


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