We face a reality that we have many codes to do matter modeling simulations (as described here). This is good. But, how good is it, really? For any beginner in computational modeling it is very difficult to choose a code with which to start modeling. Also, as these codes don't talk to each other, it is also hard to move between them.
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4$\begingroup$ This seems a bit like an opinion question, which isn't always a great fit for StackExchange, e.g. meta.stackoverflow.com/a/255471/131896 $\endgroup$– Geoff HutchisonCommented Apr 30, 2020 at 15:05
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6$\begingroup$ I think a question about communicating between codes or moving between codes is a good one. ASE and OpenBabel, for example are designed to help with these types of tasks. $\endgroup$– Geoff HutchisonCommented Apr 30, 2020 at 15:06
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4$\begingroup$ Another possible question could be: "What functionality do current codes presently lack?" If it turns out that there's a lot of functionalities that are in demand, then the question could be asked about whether or not this would work best as a stand-alone code (adding to the huge list of existing codes which is already too much for some people to keep up with) or to incorporate that functionality into some existing code. $\endgroup$– Nike Dattani - No Free TimeCommented Apr 30, 2020 at 18:37
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$\begingroup$ Sounds like an opinion question and hence rephrasing the question will make it better $\endgroup$– ThomasCommented May 1, 2020 at 23:53
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2$\begingroup$ @CodyAldaz While I certainly agree with the general sentiment about mods being circumspect with their powers, in this case the question was reopened by votes from other users. $\endgroup$– Tyberius ♦Commented Jul 25, 2020 at 23:32
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2 Answers
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If you put aside the commercial software like QuantumWise, Materials Studio, Schrodinger that are well-known materials modeling tools and are designed in a very general fashion, other open-source codes in this field more or less are designed for a specific purpose. It's true that LAMMPS, for example, is a general molecular dynamics simulation library, but most of the computational materials scientists that I know, choose their code or software based on literature review and what is the well-known application of that particular software. As I said LAMMPS, for example, is a general molecular dynamics software, but most of the people that I know which work in designing polymers/bio-polymers use GROMACS, not LAMMPS because it has suitable force-fields for that specific area of research and you don't need to reinvent the wheel from scratch.
This was just an example to show how people choose their research software and I hope it helps you.
answered Apr 30, 2020 at 14:00
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I also remember finding it difficult to navigate the landscape of atomistic simulation engines as a Ph.D. student. While there are very extensive lists on Wikipedia, I often found it difficult to understand which of these codes actually are in broad use and for what purpose.
This was one of the motivations for me creating the atomistic.software collection, which strives to combine metadata on all major atomistic simulation engines with annual citation data from Google Scholar from 2010 until today. You can filter by license type (and more), and you can click on each citation count to see the query that was used to obtain it and browse through the articles that are citing the code.
More information in the associated preprint.
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1$\begingroup$ In case you want to weigh in, I just posted a question based on the data from your preprint. See mattermodeling.stackexchange.com/q/6719/243 $\endgroup$– ksousaCommented Sep 9, 2021 at 22:24