Fixing remaining errors/warnings in doc build

doc/src/Commands_fix.rst

@@ -159,7 +159,6 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
-   * :doc:`pair/tracker <fix_pair_tracker>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
@@ -223,7 +222,6 @@ OPT.
    * :doc:`spring/rg <fix_spring_rg>`
    * :doc:`spring/self <fix_spring_self>`
    * :doc:`srd <fix_srd>`
-   * :doc:`store/local <fix_store_local>`
    * :doc:`store/force <fix_store_force>`
    * :doc:`store/state <fix_store_state>`
    * :doc:`tdpd/source <fix_dpd_source>`

doc/src/Howto.rst

@@ -23,6 +23,7 @@ General howto
    Howto_library
    Howto_couple
    Howto_mdi
+   Howto_bpm
    Howto_broken_bonds
 
 Settings howto

doc/src/Howto_bpm.rst

@@ -1,5 +1,5 @@
 Bonded particle models
-===============
+======================
 
 The BPM package implements bonded particle models which can be used to
 simulate mesoscale solids.  Solids are constructed as a collection of
@@ -21,7 +21,7 @@ pouring of extended, elastic bodies.
 ----------
 
 Bonds can be created using a :doc:`read data <read_data>` or
-:doc:`create bond <create_bond>` command. Alternatively, a
+:doc:`create bonds <create_bonds>` command. Alternatively, a
 :doc:`molecule <molecule>` template with bonds can be used with
 :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` to
 create solid grains.
@@ -98,7 +98,7 @@ to :doc:`fix nve/asphere <fix_nve_asphere>`.
 
 To monitor the fracture of bonds in the system, all BPM bond styles
 have the ability to record instances of bond breakage to output using
-the :doc:`dump local <dump_local>` command. Additionally, one can use
+the :doc:`dump local <dump>` command. Additionally, one can use
 :doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
 number of bonds per atom.
 
@@ -118,7 +118,7 @@ following are currently compatible with BPM bond styles:
 * :doc:`fix bond/break <fix_bond_break>`
 * :doc:`fix bond/swap <fix_bond_swap>`
 
-Note :doc:`bond_create <bond_create>` requires certain special_bonds settings.
+Note :doc:`create_bonds <create_bonds>` requires certain special_bonds settings.
 To subtract pair interactions, one will need to switch between different
 special_bonds settings in the input script. An example is found in
 examples/bpm/impact.

doc/src/Howto_broken_bonds.rst

@@ -1,10 +1,10 @@
 Broken Bonds
-===============
+============
 
 Typically, bond interactions persist for the duration of a simulation
 in LAMMPS. However, there are some exceptions that allow for bonds to
 break includung the :doc:`quartic bond style <bond_quartic>` and the
-bond styles in the :doc:`BPM package <Howto_BPM>` which contains the
+bond styles in the :doc:`BPM package <Howto_bpm>` which contains the
 :doc:`bpm/spring <bond_bpm_spring>` and
 :doc:`bpm/rotational <bond_bpm_rotational>` bond styles. In these cases,
 a bond can be broken if it is stretched beyond a user-defined threshold.
@@ -26,7 +26,7 @@ two atoms is turned on, since they are no longer bonded.
 In the BPM package, one can either turn off all pair interactions between
 bonded particles or leave them on, overlaying pair forces on top of bond
 forces. To remove pair forces, the special bond list is dynamically
-updated. More details can be found on the :doc:`Howto BPM <Howto_BPM>`
+updated. More details can be found on the :doc:`Howto BPM <Howto_bpm>`
 page.
 
 Bonds can also be broken by fixes which change bond topology, including
@@ -44,5 +44,5 @@ status of broken bonds or permanently delete them, e.g.:
    delete_bonds all stats
    delete_bonds all bond 0 remove
 
-The compute :doc:`nbonds/atom <compute_nbonds_atom>` can also be used
+The compute :doc:`nbond/atom <compute_nbond_atom>` can also be used
 to tally the current number of bonds per atom, excluding broken bonds.

doc/src/Packages_details.rst

@@ -304,7 +304,7 @@ models for mesoscale simulations of solids and fracture.  See the
 * :doc:`atom_style bpm/sphere <atom_style>`
 * :doc:`bond_style bpm/rotational <bond_bpm_rotational>`
 * :doc:`bond_style bpm/spring <bond_bpm_spring>`
-* :doc:`compute nbonds/atom <compute_nbonds_atom>`
+* :doc:`compute nbond/atom <compute_nbond_atom>`
 * :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
 * :doc:`pair_style bpm/spring <pair_bpm_spring>`
 * examples/bpm

doc/src/bond_bpm_rotational.rst

@@ -1,7 +1,7 @@
 .. index:: bond_style bpm/rotational
 
 bond_style bpm/rotational command
-==========================
+=================================
 
 Syntax
 """"""
@@ -71,7 +71,7 @@ particles which are proportional to angular bending and twisting
 displacements with stiffnesses of :math`k_b` and :math:`k_t',
 respectively.  Details on the calculations of shear displacements and
 angular displacements can be found in :ref:`(Wang) <Wang2009>` and
-:ref:`(Wang and Mora) <WangMora2009b>`.
+:ref:`(Wang and Mora) <Wang2009b>`.
 
 Bonds will break under sufficient stress. A breaking criteria is calculated
 
@@ -154,7 +154,7 @@ timesteps. At the end of each interval, all of the saved accumulated
 data is deleted to make room for new data. Individual datum may
 therefore persist anywhere between *1* to *N* timesteps depending on
 when they are saved. This data can be accessed using the *fix_ID* and a
-:doc:`dump local <dump_local>` command. To ensure all data is output,
+:doc:`dump local <dump>` command. To ensure all data is output,
 the dump frequency should correspond to the same interval of *N*
 timesteps. A dump frequency of an integer multiple of *N* can be used
 to regularly output a sample of the accumulated data.

doc/src/bond_bpm_spring.rst

@@ -1,7 +1,7 @@
 .. index:: bond_style bpm/spring
 
 bond_style bpm/spring command
-==========================
+=============================
 
 Syntax
 """"""
@@ -118,7 +118,7 @@ timesteps. At the end of each interval, all of the saved accumulated
 data is deleted to make room for new data. Individual datum may
 therefore persist anywhere between *1* to *N* timesteps depending on
 when they are saved. This data can be accessed using the *fix_ID* and a
-:doc:`dump local <dump_local>` command. To ensure all data is output,
+:doc:`dump local <dump>` command. To ensure all data is output,
 the dump frequency should correspond to the same interval of *N*
 timesteps. A dump frequency of an integer multiple of *N* can be used
 to regularly output a sample of the accumulated data.

doc/src/compute_nbond_atom.rst

@@ -1,7 +1,7 @@
 .. index:: compute nbond/atom
 
 compute nbond/atom command
-=======================
+==========================
 
 Syntax
 """"""
@@ -50,6 +50,3 @@ Default
 """""""
 
 none
-
-----------
-

doc/src/dump_modify.rst

@@ -475,7 +475,7 @@ The *fileper* keyword is documented below with the *nfile* keyword.
 The *header* keyword toggles whether the dump file will include a
 header.  Excluding a header will reduce the size of the dump file for
 data produced by :doc:`pair tracker <pair_tracker>` or
-:doc:`bpm bond styles <HowTo_bpm>` which may not require the
+:doc:`bpm bond styles <Howto_bpm>` which may not require the
 information typically written to the header.
 
 ----------

doc/src/fix.rst

@@ -365,7 +365,6 @@ accelerated styles exist.
 * :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
 * :doc:`spring/self <fix_spring_self>` - spring from each atom to its origin
 * :doc:`srd <fix_srd>` - stochastic rotation dynamics (SRD)
-* :doc:`store/local <fix_store_local>` - store local data for output
 * :doc:`store/force <fix_store_force>` - store force on each atom
 * :doc:`store/state <fix_store_state>` - store attributes for each atom
 * :doc:`tdpd/source <fix_dpd_source>` -
@@ -384,7 +383,6 @@ accelerated styles exist.
 * :doc:`ttm/grid <fix_ttm>` - two-temperature model for electronic/atomic coupling (distributed grid)
 * :doc:`ttm/mod <fix_ttm>` - enhanced two-temperature model with additional options
 * :doc:`tune/kspace <fix_tune_kspace>` - auto-tune KSpace parameters
-* :doc:`update/special/bonds <fix_update_special_bonds>` - update special bond lists for BPM bond styles that allow for bond breakage
 * :doc:`vector <fix_vector>` - accumulate a global vector every N timesteps
 * :doc:`viscosity <fix_viscosity>` - Muller-Plathe momentum exchange for viscosity calculation
 * :doc:`viscous <fix_viscous>` - viscous damping for granular simulations

doc/src/fix_nve_bpm_sphere.rst

@@ -1,7 +1,7 @@
 .. index:: fix nve/bpm/sphere
 
 fix nve/bpm/sphere command
-======================
+==========================
 
 Syntax
 """"""
@@ -38,7 +38,7 @@ ensemble.
 
 This fix differs from the :doc:`fix nve <fix_nve>` command, which
 assumes point particles and only updates their position and velocity.
-It also differs from the :doc:`fix nve/sphere <fix_nve/sphere>`
+It also differs from the :doc:`fix nve/sphere <fix_nve_sphere>`
 command which assumes finite-size spheroid particles which do not
 store a quaternion.  It thus does not update a particle's orientation
 or quaternion.

doc/src/pair_bpm_spring.rst

@@ -1,7 +1,7 @@
 .. index:: pair_style bpm/spring
 
 pair_style bpm/spring command
-=======================
+=============================
 
 Syntax
 """"""

doc/src/pair_tracker.rst

@@ -86,7 +86,7 @@ timesteps. At the end of each interval, all of the saved accumulated
 data is deleted to make room for new data. Individual datum may
 therefore persist anywhere between *1* to *N* timesteps depending on
 when they are saved. This data can be accessed using the *fix_ID* and a
-:doc:`dump local <dump_local>` command. To ensure all data is output,
+:doc:`dump local <dump>` command. To ensure all data is output,
 the dump frequency should correspond to the same interval of *N*
 timesteps. A dump frequency of an integer multiple of *N* can be used
 to regularly output a sample of the accumulated data.
@@ -178,9 +178,6 @@ This fix is part of the MISC package.  It is only enabled if LAMMPS
 was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-A corresponding :doc:`fix store_local <fix_store_local>` must be
-defined to use this pair style.
-
 This pair style is currently incompatible with granular pair styles
 that extend beyond the contact (e.g. JKR and DMT).
 

src/atom.cpp

@@ -2618,7 +2618,7 @@ length of the data area, and a short description.
      - int
      - 1
      - 1 if the particle is a body particle, 0 if not
-  * - quat
+   * - quat
      - double
      - 4
      - four quaternion components of the particles