fix links to LAMMPS docs (#5063)

Author: orbeckst

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"

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"

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