[ase-users] LAMMPS in ASE

[Efrem Braun]

Ah, the issue was that the environment variable LAMMPS_POTENTIAL_PATH was
not set, which was what was causing LAMMPS to crash. Setting that before
running the tests got it to work.

(Running the example from the docstring does not require this variable to
be set if NiAlH_jea.eam.alloy is in the current directory, but running the
tests seems to require that it be set regardless. This might be worth
fixing or noting somewhere.)

I'll see if I can get the setup with bonds working and send an update soon.
If anyone has tips on that though, please do shoot them my way.

Efrem Braun

On Fri, Mar 16, 2018 at 1:23 PM, Efrem Braun <efrem.braun at berkeley.edu>
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;
> 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.
>
> Efrem Braun
>
> On Fri, Mar 16, 2018 at 2:03 AM, Simon P. Rittmeyer <
> simon.rittmeyer at tum.de> wrote:
>
>> HI Efrem,
>>
>> we have a modified version of lammpslib.py on the current master branch.
>> With the next release it will be part of ase. So just wait some days until
>> Ask and Jens announce the latest release and check again.
>>
>> Of course, you can also check lammpsrun instead.
>>
>> Best
>> Simon
>>
>> > Am 16.03.2018 um 08:19 schrieb Efrem Braun via ase-users <
>> ase-users at listserv.fysik.dtu.dk>:
>> >
>> > I'm struggling with using LAMMPS in ASE. I can get LAMMPS working and
>> ASE working, but I can't even run the example script in lammpslib (
>> https://svn.fysik.dtu.dk/projects/ase-extra/trunk/ase/calcu
>> lators/lammpslib.py).
>> >
>> > First I get the error that "al" and "h" can't be added together. This
>> is easily fixed by running the setup with the line "alh = Atoms('AlH',
>> cell=(a, a, a), pbc=True)". Then I get an MPI_ABORT error, which I can't
>> figure out. The presence of the first error makes it appear that lammpslib
>> is not being updated/supported by ASE, since this issue was documented a
>> year and a half ago (https://listserv.fysik.dtu.dk
>> /pipermail/ase-users/2016-August/003080.html). So I'm not sure how much
>> effort I should even try to put into trying to figure this out. Is LAMMPS
>> basically not being supported anymore?
>> >
>> > Efrem Braun
>> > _______________________________________________
>> > ase-users mailing list
>> > ase-users at listserv.fysik.dtu.dk
>> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>
>>
>
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