From 8aad97ca4ab4cebdaf94e1c4912a27cdbb9e16d6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 Mar 2023 17:03:07 -0500 Subject: [PATCH] fix broken doc links --- doc/src/Build_extras.rst | 4 ++-- doc/src/Howto_mdi.rst | 22 +++++++++++----------- doc/src/Intro_features.rst | 2 +- doc/src/bond_write.rst | 2 +- doc/src/dump.rst | 2 +- doc/src/fix_nh_uef.rst | 9 +++++---- doc/src/fix_shake.rst | 16 ++++++++-------- doc/src/minimize.rst | 14 +++++++------- doc/src/pair_ylz.rst | 9 +++++---- 9 files changed, 41 insertions(+), 39 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index ac6a27464b..4dd8c10b3f 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1964,10 +1964,10 @@ OPENMP package Apple offers the `Xcode package and IDE `_ for compiling software on macOS, so you have likely installed it to compile LAMMPS. Their - compiler is based on `Clang `, but while it + compiler is based on `Clang `_, but while it is capable of processing OpenMP directives, the necessary header files and OpenMP runtime library are missing. The `R developers - ` have figured out a way to build those + `_ have figured out a way to build those in a compatible fashion. One can download them from `https://mac.r-project.org/openmp/ `_. Simply adding those files as diff --git a/doc/src/Howto_mdi.rst b/doc/src/Howto_mdi.rst index 0e09ff2841..7567462397 100644 --- a/doc/src/Howto_mdi.rst +++ b/doc/src/Howto_mdi.rst @@ -63,18 +63,18 @@ The package also provides a :doc:`mdi plugin ` 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 ` 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 ` +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 ` 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 ` 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. ---------- diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index 76b989ad69..d8fb2269e5 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -195,7 +195,7 @@ Multi-replica models * :doc:`parallel replica dynamics ` * :doc:`temperature accelerated dynamics ` * :doc:`parallel tempering ` -* path-integral MD: `first variant `, `second variant ` +* path-integral MD: :doc:`first variant `, :doc:`second variant ` * multi-walker collective variables with :doc:`Colvars ` and :doc:`Plumed ` .. _prepost: diff --git a/doc/src/bond_write.rst b/doc/src/bond_write.rst index 43015e25e7..bd63ebea29 100644 --- a/doc/src/bond_write.rst +++ b/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 `, `angle_write `, +:doc:`bond_style table `, :doc:`angle_write `, :doc:`bond_style `, :doc:`bond_coeff ` Default diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 01fcc2e7e1..7993ae985f 100644 --- a/doc/src/dump.rst +++ b/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 `, +so that post-processing tools like `OVITO `_, 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 diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index cf20d56ce7..922c2d515a 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -218,10 +218,11 @@ use :doc:`change_box ` before invoking the fix. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix npt `, `fix nvt/sllod -:doc:`, `compute temp/uef `, -:doc::doc:`compute pressure/uef `, `dump cfg/uef -:doc:` +:doc:`fix nvt `, :doc:`fix npt `, +:doc:`fix nvt/sllod `, +:doc:`compute temp/uef `, +:doc:`compute pressure/uef `, +:doc:`dump cfg/uef ` Default """"""" diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 32cb5a2d19..4688fcbf2a 100644 --- a/doc/src/fix_shake.rst +++ b/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) `). 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. ---------- diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index 5143cab5d5..6221d33aad 100644 --- a/doc/src/minimize.rst +++ b/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 ` of *every = 1* and + Thus :doc:`neighbor list settings ` 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 ` distance since the last + half the :doc:`neighbor list skin ` 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 ` 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. diff --git a/doc/src/pair_ylz.rst b/doc/src/pair_ylz.rst index 17cf0ca639..22a707e9cb 100644 --- a/doc/src/pair_ylz.rst +++ b/doc/src/pair_ylz.rst @@ -142,10 +142,11 @@ the :doc:`atom_style ellipsoid ` command. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`fix nve/asphere -:doc:`, `compute temp/asphere `, -:doc::doc:`pair_style resquared `, :doc:`pair_style -:doc:gayberne ` +:doc:`pair_coeff `, +:doc:`fix nve/asphere `, +:doc:`compute temp/asphere `, +:doc:`pair_style resquared `, +:doc:`pair_style gayberne ` Default """""""