But changing the values tu use and small real-space cutoff make the error appear!
Not sure if that's the reason. We used different alphas. I'm not sure either. We should check the tests for the new implementation :)
Nowadays we have the same alpha values: https://github.com/lumol-org/lumol/blob/383d4b60fb8145264f4ea42107e8ee89e1c1314b/tests/nist-spce.rs#L72
But it is worth checking it more carefully!
and thanks for taking the time to merge #240!
I rebased #241 on top of master, it is a pretty straightforward PR. I think the main change is the switch from
.zip() methods to a soa_zip! macro in soa-derive
Also, if you are willing to use the input system, you can follow the code in bin/lumol.rs for the lumol binary. If you don't use the input system, you might want to setup a logging backend in your own main to get the warning/error messages.
The
lumol command expects an input toml file. The .rs files in the examples folder show how to use lumol as a library. You don't need an input file there if you specify everything within the source files.
But you have to compile them before they can be ran. The
cargo command above does that for you. Let me know if that works!
(FYI the error message you got is because lumol expects a toml as input and can't parse the comment of the .rs file)
Hello all. I am implementing a similar package for simulating Discrete element method. I just have a question regarding parallel functionality. I implemented the serial version. I need it to make it parallel. I just need some resources so that I can make the code parallel. I need to make the for loops parallel. Can you please help on how to implement parallel for loops in rust?
I want to make those two for loops parallel
Is it at least doable?
Hey @dineshadepu, this has nothing to do with lumol, so I'd rather keep the discussion about this out of this forum. You'll get more answers on http://users.rust-lang.org/. Long story short, we are using rayon, and it is amazing!
Hey @tabedzki, thanks for checking out! I haven't have the opportunity to work on lumol in a while; and my current line of work and funding as a postdoc does not include classical molecular simulation, so you are right that the project is a bit stale right now. However, I am still interested to come back to it when I find some time! I would still be very happy to collaborate and merge contributions though!
Hello Help Center! I am trying to install Lumol by using "cargo install --git https://github.com/lumol-org/lumol" but I am getting an error in my terminal (Mac user) saying "error: multiple packages with binaries found: lumol, lumol_tutorial_potential"
Could you help me? I have already installed a Rust compiler that was linked on your Lumol Installation page using "curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh"
FYI, lumol is still very much alpha software, while it should work it has not yet been thoroughly tested for all possible use cases!
Sorry @tabedzki I though I already answered your question "how does this software perform against something like LAMMPS or GROMACS?". I have very little data on this, but for a very simple system (500 lennard-jones atoms), lumol was as fast a LAMMPS. This would not be the case for very large systems, where LAMMPS MPI parallelism would help a lot.
Hello! I just came around the lumol package. First, it's really wonderfully done. So, thank you. I wanted to contribute. I noticed that the examples in the git repository doesn't work with the current code as it stands. I will put in a few pull requests making the examples consistent.
I wanted to ask if you are interested in extending lumol to account for path integral simulations. Can we discuss a bit about how best to add path integral Monte Carlo and path integral molecular dynamics?
Hello @amartyabose, and thanks a lot for the kind words! I don't have a lot of time to allocate to this package these days since I changed research group and somehow topic, but path integral MD would be a good way for me to bring it back. I'm currently working in one of the group maintaining i-PI, which is another tool for path integral MD.
I'm happy to discuss how to best implement this, maybe the best place is to create a new Github issue? I did not know there was a possibility to do path integral Monte Carlo, do you have some intro paper/review I could read on that?
Hello @Luthaf! i-PI is a wonderful package that I have been using. Between PIMD and PIMC, the quantum classical isomorphism and the ring polymer remains identical. However instead of a molecular dynamics based sampling, a Metropolis Monte Carlo sampling is used. If you want a basic introduction, take a look at https://courses.physics.illinois.edu/phys466/sp2013/lnotes/pimcnotes.pdf
Let me open an issue and put the link there as well. Let's continue the discussion there.