[ERROR] LAMMPS Format Option Segfaults

[ejmeitz]

When using the option output_format on both the generate_structure and canonical_configuration (and I expect any binary that has this option) I get an error when using the LAMMPS format.

The command I ran was from the MgO example, but I added the -of 3 option to the end:
canonical_configuration -n 4 -t 300 -mf 20 --quantum -of 3

At line 571 of file type_crystalstructure_io.f90 (unit = 100, file = 'lammps_conf0001')
Fortran runtime error: Expected INTEGER for item 4 in formatted transfer, got REAL
(i10,e20.8,a)
 ^

[mjv500]

Hi - please pull and check (and confirm) if the format fix is ok.

[flokno]

@mjv500 maybe a good motivation to include #10 as well (preferably via a PR that closes both issues, but we can do that manually of course)?

[mjv500]

Good point - I got the message about PRs after having committed. @Ethan - did you succeed with the new commit? M.

…

On Mon, Jan 8, 2024 at 9:35 AM Florian Knoop ***@***.***> wrote: @mjv500 <https://github.com/mjv500> maybe a good motivation to include #10 <#10> as well (preferably via a PR that closes both issues, but we can do that manually of course)? — Reply to this email directly, view it on GitHub <#35 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABWOT3YMZZH75Z7R6TZWFVTYNOVWNAVCNFSM6AAAAABBQQXIJKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBQGU3TAMRQGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Professor Matthieu J Verstraete Fellow, American Physical Society Chair, Steering Committee, European Theoretical Spectroscopy Facility www.etsf.eu Alumnus Fellow, Young Academy of Europe yacadeuro.org Institute for Theoretical Physics (ITP) Department of Physics Buys Ballot Gebouw/Building, Princetonplein 5, office University of Utrecht, 3584 CC Utrecht ITP Secretariat: +31 30 253 5928 E-mail: ***@***.*** Group web page (Liège): http://www.nanomat.ulg.ac.be/ Nanomat lab, Q-Mat center, Université de Liège Département de Physique, Bat. B5a, 4/50 Allée du 6 août, 19 B-4000 Sart Tilman, Liège Belgium Phone : +32 4 366 90 17 European Theoretical Spectroscopy Facility (ETSF) Mail : ***@***.*** ***@***.*** ***@***.***

[ejmeitz]

The error is now on the next item of the format string:

At line 571 of file type_crystalstructure_io.f90 (unit = 100, file = 'lammps_conf0001')
Fortran runtime error: Expected INTEGER for item 5 in formatted transfer, got CHARACTER
(i10,e20.8,2a)
^

[flokno]

Ok @ejmeitz this should fix it: #36

Please confirm on your end and we're good to go

[ejmeitz]

Command runs well now, I believe you need an new (empty) line after the "Masses" heading for it to get parsed right though. With that space it gets parsed correctly. (quite the annoying format in my opinion).

The command also prints Have not fixed velocity output for LAMMMPS yet to the terminal. Not sure if you meant to leave that there.

Here's an example file that LAMMPS generated internally.
initial_structure_LJ.txt

[flokno]

@ejmeitz ok thanks for checking. LAMMPS seems to be a little problematic.

We discussed the issue and tend towards removing native LAMMPS support as we don't use (and maintain) it ourselves. Converting (default) VASP POSCARs to Lammps is as easy as e.g.

ase convert contcar_conf0001 -i vasp lammps.in -o lammps-data (--write-args masses=True)

Would that be fine?

[ejmeitz]

Fine by me, I dont actually use the LAMMPS format was just testing stuff for the JOSS paper and this was the thing that broke. I guess I'd say just remove it as an option rather than leave it half working maybe?

That format is problematic in many ways, I understand why this would be faster.

[flokno]

@ejmeitz ok I removed lammps altogether now. I'll update the docs once we all agree on this.

In case somebody would try to use the lammps interface, we now exit with

 ERROR
 exit code 8: Feature removed

 Native LAMMPS IO was removed, please use external converters.

I also removed the holding stuff from build_things.sh

[flokno]

Public website is also updated