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glotzerlab / signac-examples

Examples for the signac framework.
https://signac.io/
BSD 3-Clause "New" or "Revised" License
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New hoomd example #14

Closed atravitz closed 3 years ago

atravitz commented 4 years ago

For a while we've been needing to update some of these examples. Here's a proposed update to the HOOMD-blue example. The most notable change is the addition of a walk-through readme.

mikemhenry commented 4 years ago

I really like this example!

atravitz commented 4 years ago

Okay so the only other thing that might be worth adding, is to store the run_steps in the job document, that way we could introduce the concept that if you need to run the simulation longer, you just need to bump run_steps in the job doc. Maybe that is for a different tutorial, but it is one of the first things that people run into, they want to run their simulation longer since it hasn't equilibrated yet, but if they want to run it longer, they run into issues since it will mess up the state points.

I agree that it's good to encourage this as a default - I'll change it and add a note as to why we store it in the job doc.

csadorf commented 4 years ago

@atravitz I believe this is ready for another round of review? If yes, could you request that?

Besides that, it appears that there are some build issues, any idea what might be going on?

atravitz commented 4 years ago

@atravitz The style of the README has to follow a particular format. The continuous integration I added in #17 (and which used to be enabled long ago) parses the README and runs the commands it finds in code blocks beneath the heading # Usage. The updated text is definitely useful but the list formatting will need to look more like the previous. If you want help or an example, let me know.

Also should status.txt be removed (and added to .gitignore)?

Would breaking the commands into code blocks be sufficient? Should we have print_status.sh in there at all?

bdice commented 4 years ago

Would breaking the commands into code blocks be sufficient? Should we have print_status.sh in there at all?

@atravitz I think so. You can refer to the other examples. The CI will run python flow-test.py flow.hoomd.lj from the projects/ directory, and you can also run that locally to test it.

I don't think we need print_status.sh, you can remove it along with status.txt.

atravitz commented 4 years ago

Would breaking the commands into code blocks be sufficient? Should we have print_status.sh in there at all?

@atravitz I think so. You can refer to the other examples. The CI will run python flow-test.py flow.hoomd.lj from the projects/ directory, and you can also run that locally to test it.

I don't think we need print_status.sh, you can remove it along with status.txt.

@bdice let me know if this looks good to you

bdice commented 3 years ago

I'm going to go ahead and merge this. The PR been stalled for a long time and it is a significant improvement over the existing tutorial.