[ase-users] LAMMPS in ASE

[Efrem Braun]

Simon and Noam,

After running my simulations longer, I found that LAMMPS was crashing. I
traced it down to the image flags being changed within LAMMPS when
scatter_atoms() command is issued when the coordinates are negative. I
fixed this by having ASE wrap the coordinates before sending them through
to LAMMPS, but I saw that there was a thread on the LAMMPS listserve that
seemed like this was a version of some other problem that you guys already
encountered (http://lammps.sandia.gov/threads/msg68567.html), so I just
wanted to bring it to your attention in case not wrapping the coordinates
was intentional on your end for some reason.

Anyway, the fix is present in the pull request.

Efrem Braun

On Mon, Mar 19, 2018 at 8:54 PM, Efrem Braun <efrem.braun at berkeley.edu>
wrote:

> Changes documented. I added a test to the lammpslib calculator that shows
> how a data file of arbitrary complexity can be read in. Hopefully it gets
> merged into the code, or I get some feedback on how to improve it.
>
> Efrem Braun
>
> On Sat, Mar 17, 2018 at 7:57 AM, Noam Bernstein <
> noam.bernstein at nrl.navy.mil> wrote:
>
>> On Mar 16, 2018, at 10:30 PM, Efrem Braun <efrem.braun at berkeley.edu>
>> wrote:
>>
>> I *think* I've actually gotten it figured out. The energy and forces I
>> get out of ASE are the same as what I'm getting out of the direct LAMMPS
>> simulation. I don't have the dynamics right yet because I don't have the
>> masses set correctly in ASE, but I should be able to figure this out on
>> Sunday. I'll shoot an update with some documentation then.
>>
>> I did need to make one small update to lammpslib.py to get this working
>> (since I'm using create_atoms=False, which I guess hasn't been used much
>> before), so I sent a pull request in for that.
>>
>>
>> Good to hear.  If you ever need a solution that’s self contained, i.e.
>> doesn’t rely on a data file, purely on information that’s in the ASE Atoms
>> object, say something.
>>
>> 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 <(202)%20404-8628>  F +1 202 404 7546
>> <(202)%20404-7546>
>> https://www.nrl.navy.mil
>>
>>
>
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