Building graphene oxide

General Discussion
1

Hi,
Any suggestions on how can we build a single sheet/layer of Graphene Oxide (GO) on Avogadro? I will be extremely grateful for any inputs/suggestions. Thank you.

With best regards

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While I can’t provide you an answer on this, I suggest to address this question to https://mattermodeling.stackexchange.com/. The number of visitors and the spectrum of the audience is greater, thus chances are higher to identify a solution in the answers provided there or/and receive hints how to solve this. (For the benefit of Avogadro’s user community, you may add a link to the fruitful answer here.)

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Generally, we’ve been moving towards adding plugins / interface to other programs for applications like this.

For GO, there are two fairly commonly used Python packages:

I admit I haven’t used either of them, but from what I can tell, GOPY is maybe a bit more flexible, but only generates PDB files, and MakeGraphitics will generate parameters to use in LAMMPS.

As @Thomas mentioned, if you use them, it would be great if you post back here with your experience. The Matter Modeling stack exchange is also useful for cases like this, where there are likely to be more users.

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Prof. Hutchison, thank you very much for the links. GOPY looks really good, and it seems like it does build topology as well. I haven’t tested it yet, but let’s see if my simulation system crashes or not :slight_smile:

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Hi, I’m new to this board :grinning:

I’ve been using GOPY as well, it’s really great. The problem is, i need to provide accurate lattice parameter and space group of my graphene oxide model, while GOPY will only allow input such as graphene dimension and atomic position. Do you know how i can input lattice parameter and space group in GOPY? I tried to input it in Avogadro after importing it from GOPY, but the structure becomes weird with all the bonds gone.

Hope to get some help from here, thank you.

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I mean, I’m not familiar with the package, but it looks like it takes the default graphene lattice.

I’m not sure I understand what you mean. If you read PDB files, both Avogadro v1 and v2 will attempt to determine bonds based on atomic distances.