[ase-users] ASE LAMMPS: update Atoms object coordinates and use constraints

[Spencer Hills]

Hello,

I am new to ASE and am trying to use it to look at different data types by
calling other functions (ex: LAMMPS). With the ASE atoms object it is very
easy to keep everything stored in one place. I am using lammpsrun.py from
the standard ASE package to write input files from a code, so that I can
make a modular code and not require the user to write lammps input file
everytime they want to run the code.

However, when I use LAMMPS and call the minimize function, I run into some
difficulties. It will minimize the energy correctly (compared to running
lammps with the python library version of it and the same inputs), but it
does not update the positions of the atoms in the atoms object, so I can't
compare the minimized energy to anything else because its a different
arrangement.

Is there a way to update the atoms object with the LAMMPS minimized
structure? I think that I could make it read the trajectory file and
convert that to positions, but I would rather not save the temporary files
in order to do this. Is there a more elegant way to do this? Or is there a
current implementation in ASE?

Additionally, when I call the minimize function, it does not use the
constraints that I assign to it. Right now I am starting simple with one
atom at a fixed position, but this atom does not stay in the same position.

Is there a way to pass the constraints to the LAMMPS input file?

I've looking through some of the mailing list, and have been unable to find
answers to the questions. Any direction, either to previous threads or
general help on this issue would be appreciated!

Thanks,
Spencer Hills
Research Aide
Argonne National Lab
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