I would like to start using python to analyze my data at the moment I use (https://github.com/lammps/lammps/tree/master/tools/matlab). I installed:
conda install -c pyiron lammps, but I am not sure if this the right platform or should I use https://github.com/lammps/lammps/tree/master/tools/python?
Here is an example head of my file I am trying to process.
i$ head dump2_temp_0.1.lammpstrj
ITEM: NUMBER OF ATOMS
ITEM: BOX BOUNDS pp pp pp
ITEM: ATOMS id type xs ys zs
1 1 0 0 0.5
Thank you so much for your help,
Not quite sure what you’re asking.
Are you asking for this? https://pizza.sandia.gov/
Or are you asking how to read data into python in general? (which I’m very positive you can figure out with google, and is not a relevant lammps question)
I am asking what’s the standard why to do it these days. Neither of the github project of Pizza or python seems to be maintained.
If I understand correctly, pyiron lammps is to run simulations and not for post processing and plotting stuff…
Never used pyiron lammps, so someone might respond with something better. Post processing can be done within Lammps itself through the rerun command - depending on what it is that you want to compute. I often find it easier/more flexible myself to do it with my own post-processing routines, though I don’t write them in python.
Off topic but, its not too difficult to program something to read the results of a dump custom.
there is not such thing as "the standard way(tm)", since the needs for
different people and different project can be very different.
people use what serves them well and what they are familiar with. e.g.
i prefer using VMD to post-process trajectory data, since i am very
familiar with Tcl scripting and VMD has a lot of useful extensions for
working with molecular systems.
others use C/C++, Fortran, Python, Perl, Matlab, or one of the tools
listed here: https://lammps.sandia.gov/prepost.html
Pizza.py is not being actively developed, but several
of its tools are included in the LAMMPS distro,
under tools/python. Those scripts should
work fine and show you the kinds of things you
can do with Python processing of LAMMPS output.