From 407e2f1243561022856022505c00e8c6f464436e Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 11 Jun 2025 12:49:32 -0700 Subject: [PATCH] fix links to LAMMPS docs - links broke when LAMMPS moved from lammps.sandia.gov to lammps.org - `git grep -l sandia | xargs perl -wpi~ -e 's(http://lammps\.sandia\.gov/doc)(https://docs.lammps.org)' --` - `git grep -l sandia | xargs perl -wpi~ -e 's(http://lammps\.sandia\.gov)(https://www.lammps.org)' --` --- package/MDAnalysis/coordinates/LAMMPS.py | 12 ++++++------ package/MDAnalysis/topology/LAMMPSParser.py | 10 +++++----- .../sphinx/source/documentation_pages/overview.rst | 2 +- package/doc/sphinx/source/index.rst | 2 +- 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/package/MDAnalysis/coordinates/LAMMPS.py b/package/MDAnalysis/coordinates/LAMMPS.py index b888c1a092..a8584bb3f1 100644 --- a/package/MDAnalysis/coordinates/LAMMPS.py +++ b/package/MDAnalysis/coordinates/LAMMPS.py @@ -105,15 +105,15 @@ For further discussion follow the reports for `Issue 84`_ and `Issue 64`_. -.. _LAMMPS: http://lammps.sandia.gov/ -.. _write DCD: http://lammps.sandia.gov/doc/dump.html +.. _LAMMPS: https://www.lammps.org/ +.. _write DCD: https://docs.lammps.org/dump.html .. _CHARMM trajectory: http://www.charmm.org/documentation/c36b1/dynamc.html#%20Trajectory .. _AKMA: http://www.charmm.org/documentation/c36b1/usage.html#%20AKMA -.. _units real: http://lammps.sandia.gov/doc/units.html -.. _units command: http://lammps.sandia.gov/doc/units.html +.. _units real: https://docs.lammps.org/units.html +.. _units command: https://docs.lammps.org/units.html .. _`Issue 64`: https://github.com/MDAnalysis/mdanalysis/issues/64 .. _`Issue 84`: https://github.com/MDAnalysis/mdanalysis/issues/84 -.. _`LAMMPS dump format`: http://lammps.sandia.gov/doc/dump.html +.. _`LAMMPS dump format`: https://docs.lammps.org/dump.html Classes ------- @@ -198,7 +198,7 @@ class DCDReader(DCD.DCDReader): "Angstrom", corresponding to LAMMPS `units style`_ "**real**". See :mod:`MDAnalysis.units` for other recognized values. - .. _units style: http://lammps.sandia.gov/doc/units.html + .. _units style: https://docs.lammps.org/units.html """ format = "LAMMPS" diff --git a/package/MDAnalysis/topology/LAMMPSParser.py b/package/MDAnalysis/topology/LAMMPSParser.py index 6c3899b401..61404fbbe7 100644 --- a/package/MDAnalysis/topology/LAMMPSParser.py +++ b/package/MDAnalysis/topology/LAMMPSParser.py @@ -33,9 +33,9 @@ read from the input file. This may change in release 3.0. See :ref:`Guessers` for more information. -.. _LAMMPS: http://lammps.sandia.gov/ -.. _data: DATA file format: :http://lammps.sandia.gov/doc/2001/data_format.html -.. _dump: http://lammps.sandia.gov/doc/dump.html +.. _LAMMPS: https://www.lammps.org/ +.. _data: DATA file format: :https://docs.lammps.org/2001/data_format.html +.. _dump: https://docs.lammps.org/dump.html .. versionchanged:: 1.0.0 Deprecated :class:`LAMMPSDataConverter` has now been removed. @@ -67,7 +67,7 @@ >>> u = mda.Universe('myfile.data', atom_style='id type x y z') -.. _`atom_style`: http://lammps.sandia.gov/doc/atom_style.html +.. _`atom_style`: https://docs.lammps.org/atom_style.html Classes ------- @@ -469,7 +469,7 @@ def _parse_atoms(self, datalines, massdict=None): Lammps atoms can have lots of different formats, and even custom formats - http://lammps.sandia.gov/doc/atom_style.html + https://docs.lammps.org/atom_style.html Treated here are - atoms with 7 fields (with charge) "full" diff --git a/package/doc/sphinx/source/documentation_pages/overview.rst b/package/doc/sphinx/source/documentation_pages/overview.rst index 6fa2e91756..99b36c1708 100644 --- a/package/doc/sphinx/source/documentation_pages/overview.rst +++ b/package/doc/sphinx/source/documentation_pages/overview.rst @@ -40,7 +40,7 @@ of a protein and the radius of gyration of the backbone atoms are calculated:: .. _NumPy: https://numpy.org/ .. _CHARMM: http://www.charmm.org/ -.. _LAMMPS: http://lammps.sandia.gov/ +.. _LAMMPS: https://www.lammps.org/ .. _NAMD: http://www.ks.uiuc.edu/Research/namd/ .. _Gromacs: http://www.gromacs.org/ diff --git a/package/doc/sphinx/source/index.rst b/package/doc/sphinx/source/index.rst index adee0e6ece..243464ef13 100644 --- a/package/doc/sphinx/source/index.rst +++ b/package/doc/sphinx/source/index.rst @@ -32,7 +32,7 @@ written out in a range of formats. .. _NumPy: https://numpy.org/ .. _CHARMM: http://www.charmm.org/ .. _Amber: http://ambermd.org/ -.. _LAMMPS: http://lammps.sandia.gov/ +.. _LAMMPS: https://www.lammps.org/ .. _NAMD: http://www.ks.uiuc.edu/Research/namd/ .. _Gromacs: http://www.gromacs.org/ .. _`DL_POLY`: https://www.sc.stfc.ac.uk/software/type/computational-materials-and-molecular-science/?searchquery=dl_poly