Hi @srmnitc

[jan-janssen]

Hi @srmnitc,

I saw that you stared the repository, so I wanted to give you access. The reason why I removed public access is that some functions do not work at the moment, like extract_atom. Luckily the functions we need inside pyiron, work out of the box https://github.com/pyiron/pyiron/blob/master/pyiron/lammps/interactive.py#L606 .

The general idea is to provide a single core lammps process - running in a jupyter notebook - which then controls a mpi parallel lammps process. Currently this implementation only works with openmpi - figuring this out took me quite some time pyiron/pyiron#516 .

As this scheme is potentially interesting for users of lammps beyond the pyiron community I would be interested to make this a public package. If we get the standard commands working I am pretty sure we can also get Steve Plimpton - the core developer of lammps to implement it in the core lammps code. I met Steve last year when I visited Los Alamos.

So if you are interested to work on this feel free to continue the project, the Lammps developers are always happy about contributions and being named in the Lammps documentation helps to get more people interested in your work - that is what I learned from contributing the Lammps conda forge package https://github.com/lammps/lammps/blob/master/doc/src/Install_conda.rst .

Best regards,

Jan

[srmnitc]

Hi @jan-janssen ,

Thanks for the invite. Yes, I had a quick look and found that it is quite interesting and useful. I think the idea is great, I will try to contribute as I can!

[jan-janssen]

Maybe you can start by testing which functions work. At least the functions implemented in pyiron work already:
https://github.com/pyiron/pyiron/blob/master/pyiron/lammps/sub/lmpmpi.py

In addition I would assume that functions like extract_box should work as well.

For debugging we can write the status of the MPI process to a file:
https://github.com/pyiron/pyiron/blob/master/pyiron/lammps/sub/lmpmpi.py#L65

[srmnitc]

Yes, will do. I have already tested quite a few of them. I am trying to get this working a little bit quickly as it will help my next project quite a bit.

[srmnitc]

@jan-janssen One more question - is there an emphasis on keeping the API same as the lammps one. For example, commands_list and commands_string - this could potentially be combined on the top level to take either kind of input.

[jan-janssen]

That is fine for me.