[ase-users] LAMMPS in ASE

[Noam Bernstein]

> On Mar 16, 2018, at 4:23 PM, Efrem Braun via ase-users <ase-users at listserv.fysik.dtu.dk> wrote:
> 
> Very happy to hear that LAMMPS is being supported! I switched over to the development branch from the Gitlab repo, but unfortunately I'm still having the same issue. Running "ase test" gives me "OK (skipped=71)", "ase test -c lammpsrun" gives me  "OK (skipped=68)", and "ase test -c lammpslib" gives me the same "MPI_ABORT was invoked on rank 0 communicator MPI_COMM_WORLD..." error message that I was getting before. Like I mentioned, I do have LAMMPS working in Python, so I don't know what I could be doing wrong.
> 
> Assuming I'm able to get this fixed, I'd like to ask my more specific question...The LAMMPS potential I'm trying to run has bonds/angles/dihedrals defined. The actual LAMMPS input file reads:
> 
> atom_style      full
> boundary        p p p
> pair_style      lj/cut/coul/long 12.500
> bond_style      harmonic
> angle_style     hybrid fourier cosine/periodic
> dihedral_style  harmonic
> improper_style  fourier
> kspace_style    ewald 0.000001
> dielectric      1.0
> pair_modify     tail yes mix arithmetic
> special_bonds   lj/coul 0.0 0.0 1.0
> box tilt        large
> read_data       data.input
> ...(the actual running follows)
> 
> The "data.input" file is quite similar to what's found in https://gitlab.com/ase/ase/blob/master/ase/test/lammpsdata/lammpsdata.py <https://gitlab.com/ase/ase/blob/master/ase/test/lammpsdata/lammpsdata.py>; the only difference is that there are more atom types and the velocities are not specified.
> 
> I don't think that lammpsrun will work for this, because I see no way to feed a data file in. So lammpslib is probably the only way to go, which is why I've been trying to get it to work. Obviously I'd prefer to figure this out on my own before asking for help, but since I can't get lammpslib working, I can't yet do this. And if I'm told that there's no way to do this with lammpslib anyway, then it'd be nice to know that I shouldn't waste time trying.
> 

I haven’t been keeping up with what version of lammpslib is currently being included in ASE, but there is definitely a version some of us have been working on that can create bonded potentials from the ASE atoms structure (using some lammps syntax that has been added recently, namely “create_bonds single/bond” and the like). I’ll ask the people who (I think) were responsible for the recent improved capability lammpslib and see if there’s a move to add those features as well.  Impropers will need to be added for you, but otherwise it should probably work, and I’m pretty sure there’s a branch someplace that has impropers already, just need to merge it back in.

									Noam


____________
||
|U.S. NAVAL|
|_RESEARCH_|
LABORATORY
Noam Bernstein, Ph.D.
Center for Materials Physics and Technology
U.S. Naval Research Laboratory
T +1 202 404 8628  F +1 202 404 7546
https://www.nrl.navy.mil <https://www.nrl.navy.mil/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20180316/60dd38fe/attachment-0001.html>