fix broken doc links

doc/src/Build_extras.rst

@@ -1964,10 +1964,10 @@ OPENMP package
    Apple offers the `Xcode package and IDE
    <https://developer.apple.com/xcode/>`_ for compiling software on
    macOS, so you have likely installed it to compile LAMMPS.  Their
-   compiler is based on `Clang <https://clang.llvm.org/>`, but while it
+   compiler is based on `Clang <https://clang.llvm.org/>`_, but while it
    is capable of processing OpenMP directives, the necessary header
    files and OpenMP runtime library are missing.  The `R developers
-   <https://www.r-project.org/>` have figured out a way to build those
+   <https://www.r-project.org/>`_ have figured out a way to build those
    in a compatible fashion. One can download them from
    `https://mac.r-project.org/openmp/
    <https://mac.r-project.org/openmp/>`_.  Simply adding those files as

doc/src/Howto_mdi.rst

@@ -63,18 +63,18 @@ The package also provides a :doc:`mdi plugin <mdi>` command, which
 enables LAMMPS to operate as an MDI driver and load an MDI engine as a
 plugin library.
 
-The package furthermore includes a `fix mdi/qm <fix_mdi_qm>` command, in
-which LAMMPS operates as an MDI driver in conjunction with a quantum
-mechanics code as an MDI engine.  The post_force() method of the
-``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to another
-code.  This command can be used to couple to an MDI engine, which is
-either a stand-alone code or a plugin library.
+The package furthermore includes a :doc:`fix mdi/qm <fix_mdi_qm>`
+command, in which LAMMPS operates as an MDI driver in conjunction with a
+quantum mechanics code as an MDI engine.  The post_force() method of the
+``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to
+another code.  This command can be used to couple to an MDI engine,
+which is either a stand-alone code or a plugin library.
 
-As explained in the `fix mdi/qm <fix_mdi_qm>` command documentation, it
-can be used to perform *ab initio* MD simulations or energy
-minimizations, or to evaluate the quantum energy and forces for a series
-of independent systems.  The ``examples/mdi`` directory has example
-input scripts for all of these use cases.
+As explained in the :doc:`fix mdi/qm <fix_mdi_qm>` command
+documentation, it can be used to perform *ab initio* MD simulations or
+energy minimizations, or to evaluate the quantum energy and forces for a
+series of independent systems.  The ``examples/mdi`` directory has
+example input scripts for all of these use cases.
 
 ----------
 

doc/src/Intro_features.rst

@@ -195,7 +195,7 @@ Multi-replica models
 * :doc:`parallel replica dynamics <prd>`
 * :doc:`temperature accelerated dynamics <tad>`
 * :doc:`parallel tempering <temper>`
-* path-integral MD: `first variant <fix_pimd>`, `second variant <fix_ipi>`
+* path-integral MD: :doc:`first variant <fix_pimd>`, :doc:`second variant <fix_ipi>`
 * multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
 
 .. _prepost:

doc/src/bond_write.rst

@@ -70,7 +70,7 @@ be specified even if the potential has a finite value at r = 0.0.
 Related commands
 """"""""""""""""
 
-:doc:`bond_style table <bond_table>`, `angle_write <angle_write>`,
+:doc:`bond_style table <bond_table>`, :doc:`angle_write <angle_write>`,
 :doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
 
 Default

doc/src/dump.rst

@@ -375,7 +375,7 @@ output with each snapshot:
    nx ny nz
 
 The value dim will be 2 or 3 for 2d or 3d simulations.  It is included
-so that post-processing tools like `OVITO <https://www.ovito.org>`,
+so that post-processing tools like `OVITO <https://www.ovito.org>`_,
 which can visualize grid-based quantities know how to draw each grid
 cell.  The grid size will match the input script parameters for
 grid(s) created by the computes or fixes which are referenced by the

doc/src/fix_nh_uef.rst

@@ -218,10 +218,11 @@ use :doc:`change_box <change_box>` before invoking the fix.
 Related commands
 """"""""""""""""
 
-:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, `fix nvt/sllod
-:doc:<fix_nvt_sllod>`, `compute temp/uef <compute_temp_uef>`,
-:doc::doc:`compute pressure/uef <compute_pressure_uef>`, `dump cfg/uef
-:doc:<dump_cfg_uef>`
+:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`,
+:doc:`fix nvt/sllod <fix_nvt_sllod>`,
+:doc:`compute temp/uef <compute_temp_uef>`,
+:doc:`compute pressure/uef <compute_pressure_uef>`,
+:doc:`dump cfg/uef <dump_cfg_uef>`
 
 Default
 """""""

doc/src/fix_shake.rst

@@ -133,9 +133,9 @@ constraint lists atom types.  All bonds connected to an atom of the
 specified type will be constrained.  The *m* constraint lists atom
 masses.  All bonds connected to atoms of the specified masses will be
 constrained (within a fudge factor of MASSDELTA specified in
-fix_shake.cpp).  The *a* constraint lists angle types.  If both bonds
-in the angle are constrained then the angle will also be constrained
-if its type is in the list.
+``src/RIGID/fix_shake.cpp``).  The *a* constraint lists angle types.  If
+both bonds in the angle are constrained then the angle will also be
+constrained if its type is in the list.
 
 For all constraints, a particular bond is only constrained if both
 atoms in the bond are in the group specified with the SHAKE fix.
@@ -205,11 +205,11 @@ LAMMPS closely follows (:ref:`Andersen (1983) <Andersen3>`).
    The *fix rattle* command modifies forces and velocities and thus
    should be defined after all other integration fixes in your input
    script.  If you define other fixes that modify velocities or forces
-   after *fix rattle* operates, then *fix rattle* will not take them into
-   account and the overall time integration will typically not satisfy
-   the RATTLE constraints.  You can check whether the constraints work
-   correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
-   to 1 and recompiling LAMMPS.
+   after *fix rattle* operates, then *fix rattle* will not take them
+   into account and the overall time integration will typically not
+   satisfy the RATTLE constraints.  You can check whether the
+   constraints work correctly by setting the value of RATTLE_DEBUG in
+   ``src/RIGID/fix_rattle.cpp`` to 1 and recompiling LAMMPS.
 
 ----------
 

doc/src/minimize.rst

@@ -49,19 +49,19 @@ and forces) by pushing the atoms off of each other.
 
    The distance that atoms can move during individual minimization steps
    can be quite large, especially at the beginning of a minimization.
-   Thus `neighbor list settings <neigh_modify>` of *every = 1* and
+   Thus :doc:`neighbor list settings <neigh_modify>` of *every = 1* and
    *delay = 0* are **required**.  This may be combined with either
    *check = no* (always update the neighbor list) or *check = yes* (only
    update the neighbor list if at least one atom has moved more than
-   half the `neighbor list skin <neighbor>` distance since the last
+   half the :doc:`neighbor list skin <neighbor>` distance since the last
    reneighboring).  Using *check = yes* is recommended since it avoids
    unneeded reneighboring steps when the system is closer to the minimum
-   and thus atoms move only small distances.  Using *check = no* may
-   be required for debugging or when coupling LAMMPS with external
-   codes that require a predictable sequence of neighbor list updates.
+   and thus atoms move only small distances.  Using *check = no* may be
+   required for debugging or when coupling LAMMPS with external codes
+   that require a predictable sequence of neighbor list updates.
 
-   If the settings are **not** *every = 1* and *delay = 0*, LAMMPS
-   will temporarily apply a `neigh_modify every 1 delay 0 check yes
+   If the settings are **not** *every = 1* and *delay = 0*, LAMMPS will
+   temporarily apply a :doc:`neigh_modify every 1 delay 0 check yes
    <neigh_modify>` setting during the minimization and restore the
    original setting at the end of the minimization.  A corresponding
    message will be printed to the screen and log file, if this happens.

doc/src/pair_ylz.rst

@@ -142,10 +142,11 @@ the :doc:`atom_style ellipsoid <atom_style>` command.
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere
-:doc:<fix_nve_asphere>`, `compute temp/asphere <compute_temp_asphere>`,
-:doc::doc:`pair_style resquared <pair_resquared>`, :doc:`pair_style
-:doc:gayberne <pair_gayberne>`
+:doc:`pair_coeff <pair_coeff>`,
+:doc:`fix nve/asphere <fix_nve_asphere>`,
+:doc:`compute temp/asphere <compute_temp_asphere>`,
+:doc:`pair_style resquared <pair_resquared>`,
+:doc:`pair_style gayberne <pair_gayberne>`
 
 Default
 """""""