In 8.4.3. AMOEBA and HIPPO force fields — LAMMPS documentation there is a link
https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html which is now 404.
The correct link seems to be Tinker XYZ format (txyz) — Open Babel openbabel-3-1-1 documentation
@initialize
Thanks for reporting. This will be corrected and augmented (the first source in the list should actually be pointing to the Tinker user guide) in the next LAMMPS release/update.
As it turns out, there were quite a few broken or outdated URLs in the manual.
This is to be expected due to the general “bit rot” on the web and we have a tool in the build system for the manual to check for this, but it seems that nobody has used it in quite a while.
You beat me to it, I was in the process of collecting broken link information. You will likely find the same with your tool, but just in case, here’s what I’ve already found (along with alternative links, where applicable):
In region2vmd command — LAMMPS documentation, there is a link https://ks.uiuc.edu/Research/vmd/ that should be https://www.ks.uiuc.edu/Research/vmd/.
In dump netcdf command — LAMMPS documentation, there a link https://trac.mcs.anl.gov/projects/parallel-netcdf/ that does not work.
In 7.4.3. KOKKOS package — LAMMPS documentation, there is a link to (https://)kokkos.org/kokkos-core-wiki/requirements.html that does not work. From looking at their website, I think that the link should be https://kokkos.org/kokkos-core-wiki/get-started/requirements.html
In 4.3. Code design — LAMMPS documentation, there is a link to
https://fmt.dev/latest/syntax.html that should be https://fmt.dev/latest/syntax/
In 2.9. Using LAMMPS in IPython notebooks and Jupyter — LAMMPS documentation, there is a link to https://docs.lammps.org/juypter, beyond the typo in jupyter, I suppose the intended link was https://jupyter.org/. On the same page, there should be a link to https://ipython.org/ instead of https://docs.lammps.org/ipython.
Sorry. Didn’t want to do that. I was just that I remembered that we have the link_check option and that I didn’t recall having done a check for a while, so it was just a natural reaction.
I am now using the “linkcheck” builder that is part of Sphinx, which turns out to be much faster than the “LinkChecker” python module. The only shortcoming is that it returns a lot of false positives to DOIs and commercial websites, so it requires some careful checking. Thus it cannot hurt to have multiple eyes on this. You can launch this test with “make link_check” in the doc folder.
I should probably make this an automated process to be run nightly on the “develop” branch, so that you don’t have to wait for the results. I’ve done that same already with clang’s static code analysis and code coverage reporting for the integrated tests. If you are thinking about doing something similar for the tutorials, contact me directly and I can share what I have (old and new checker).
I will try, thanks.
This is something I had in mind in the past, but out of fear of false positives, I just do a manual check using deadlinkchecker.com. The tutorial website has much, much fewer links than the LAMMPS documentation, so I think that a manual check remains reasonable …
I just updated Collected small changes and fixes by akohlmey · Pull Request #4670 · lammps/lammps · GitHub
This should have all changes that I noticed would be needed.
The check is manual and I capture and inspect the output after removing the known false positives (i.e. all lines referring to DOIs or similar).
Automated nightly link check run is implemented and report is at https://download.lammps.org/linkcheck/