Fixing remaining errors/warnings in doc build
This commit is contained in:
Joel Thomas Clemmer
@ -159,7 +159,6 @@ OPT.
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* :doc:`orient/fcc <fix_orient>`
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* :doc:`orient/eco <fix_orient_eco>`
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* :doc:`pafi <fix_pafi>`
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* :doc:`pair/tracker <fix_pair_tracker>`
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* :doc:`phonon <fix_phonon>`
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* :doc:`pimd <fix_pimd>`
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* :doc:`planeforce <fix_planeforce>`
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@ -223,7 +222,6 @@ OPT.
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* :doc:`spring/rg <fix_spring_rg>`
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* :doc:`spring/self <fix_spring_self>`
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* :doc:`srd <fix_srd>`
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* :doc:`store/local <fix_store_local>`
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* :doc:`store/force <fix_store_force>`
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* :doc:`store/state <fix_store_state>`
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* :doc:`tdpd/source <fix_dpd_source>`
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@ -23,6 +23,7 @@ General howto
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Howto_library
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Howto_couple
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Howto_mdi
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Howto_bpm
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Howto_broken_bonds
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Settings howto
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@ -1,5 +1,5 @@
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Bonded particle models
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===============
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======================
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The BPM package implements bonded particle models which can be used to
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simulate mesoscale solids. Solids are constructed as a collection of
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@ -21,7 +21,7 @@ pouring of extended, elastic bodies.
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----------
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Bonds can be created using a :doc:`read data <read_data>` or
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:doc:`create bond <create_bond>` command. Alternatively, a
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:doc:`create bonds <create_bonds>` command. Alternatively, a
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:doc:`molecule <molecule>` template with bonds can be used with
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:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` to
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create solid grains.
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@ -98,7 +98,7 @@ to :doc:`fix nve/asphere <fix_nve_asphere>`.
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To monitor the fracture of bonds in the system, all BPM bond styles
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have the ability to record instances of bond breakage to output using
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the :doc:`dump local <dump_local>` command. Additionally, one can use
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the :doc:`dump local <dump>` command. Additionally, one can use
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:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
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number of bonds per atom.
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@ -118,7 +118,7 @@ following are currently compatible with BPM bond styles:
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* :doc:`fix bond/break <fix_bond_break>`
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* :doc:`fix bond/swap <fix_bond_swap>`
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Note :doc:`bond_create <bond_create>` requires certain special_bonds settings.
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Note :doc:`create_bonds <create_bonds>` requires certain special_bonds settings.
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To subtract pair interactions, one will need to switch between different
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special_bonds settings in the input script. An example is found in
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examples/bpm/impact.
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@ -1,10 +1,10 @@
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Broken Bonds
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===============
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============
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Typically, bond interactions persist for the duration of a simulation
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in LAMMPS. However, there are some exceptions that allow for bonds to
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break includung the :doc:`quartic bond style <bond_quartic>` and the
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bond styles in the :doc:`BPM package <Howto_BPM>` which contains the
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bond styles in the :doc:`BPM package <Howto_bpm>` which contains the
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:doc:`bpm/spring <bond_bpm_spring>` and
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:doc:`bpm/rotational <bond_bpm_rotational>` bond styles. In these cases,
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a bond can be broken if it is stretched beyond a user-defined threshold.
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@ -26,7 +26,7 @@ two atoms is turned on, since they are no longer bonded.
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In the BPM package, one can either turn off all pair interactions between
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bonded particles or leave them on, overlaying pair forces on top of bond
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forces. To remove pair forces, the special bond list is dynamically
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updated. More details can be found on the :doc:`Howto BPM <Howto_BPM>`
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updated. More details can be found on the :doc:`Howto BPM <Howto_bpm>`
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page.
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Bonds can also be broken by fixes which change bond topology, including
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@ -44,5 +44,5 @@ status of broken bonds or permanently delete them, e.g.:
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delete_bonds all stats
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delete_bonds all bond 0 remove
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The compute :doc:`nbonds/atom <compute_nbonds_atom>` can also be used
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The compute :doc:`nbond/atom <compute_nbond_atom>` can also be used
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to tally the current number of bonds per atom, excluding broken bonds.
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@ -304,7 +304,7 @@ models for mesoscale simulations of solids and fracture. See the
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* :doc:`atom_style bpm/sphere <atom_style>`
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* :doc:`bond_style bpm/rotational <bond_bpm_rotational>`
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* :doc:`bond_style bpm/spring <bond_bpm_spring>`
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* :doc:`compute nbonds/atom <compute_nbonds_atom>`
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* :doc:`compute nbond/atom <compute_nbond_atom>`
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* :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
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* :doc:`pair_style bpm/spring <pair_bpm_spring>`
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* examples/bpm
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@ -1,7 +1,7 @@
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.. index:: bond_style bpm/rotational
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bond_style bpm/rotational command
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==========================
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=================================
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Syntax
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""""""
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@ -71,7 +71,7 @@ particles which are proportional to angular bending and twisting
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displacements with stiffnesses of :math`k_b` and :math:`k_t',
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respectively. Details on the calculations of shear displacements and
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angular displacements can be found in :ref:`(Wang) <Wang2009>` and
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:ref:`(Wang and Mora) <WangMora2009b>`.
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:ref:`(Wang and Mora) <Wang2009b>`.
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Bonds will break under sufficient stress. A breaking criteria is calculated
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@ -154,7 +154,7 @@ timesteps. At the end of each interval, all of the saved accumulated
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data is deleted to make room for new data. Individual datum may
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therefore persist anywhere between *1* to *N* timesteps depending on
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when they are saved. This data can be accessed using the *fix_ID* and a
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:doc:`dump local <dump_local>` command. To ensure all data is output,
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:doc:`dump local <dump>` command. To ensure all data is output,
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the dump frequency should correspond to the same interval of *N*
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timesteps. A dump frequency of an integer multiple of *N* can be used
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to regularly output a sample of the accumulated data.
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@ -1,7 +1,7 @@
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.. index:: bond_style bpm/spring
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bond_style bpm/spring command
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==========================
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=============================
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Syntax
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""""""
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@ -118,7 +118,7 @@ timesteps. At the end of each interval, all of the saved accumulated
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data is deleted to make room for new data. Individual datum may
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therefore persist anywhere between *1* to *N* timesteps depending on
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when they are saved. This data can be accessed using the *fix_ID* and a
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:doc:`dump local <dump_local>` command. To ensure all data is output,
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:doc:`dump local <dump>` command. To ensure all data is output,
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the dump frequency should correspond to the same interval of *N*
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timesteps. A dump frequency of an integer multiple of *N* can be used
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to regularly output a sample of the accumulated data.
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@ -1,7 +1,7 @@
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.. index:: compute nbond/atom
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compute nbond/atom command
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=======================
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==========================
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Syntax
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""""""
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@ -50,6 +50,3 @@ Default
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"""""""
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none
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----------
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@ -475,7 +475,7 @@ The *fileper* keyword is documented below with the *nfile* keyword.
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The *header* keyword toggles whether the dump file will include a
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header. Excluding a header will reduce the size of the dump file for
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data produced by :doc:`pair tracker <pair_tracker>` or
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:doc:`bpm bond styles <HowTo_bpm>` which may not require the
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:doc:`bpm bond styles <Howto_bpm>` which may not require the
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information typically written to the header.
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----------
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@ -365,7 +365,6 @@ accelerated styles exist.
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* :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
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* :doc:`spring/self <fix_spring_self>` - spring from each atom to its origin
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* :doc:`srd <fix_srd>` - stochastic rotation dynamics (SRD)
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* :doc:`store/local <fix_store_local>` - store local data for output
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* :doc:`store/force <fix_store_force>` - store force on each atom
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* :doc:`store/state <fix_store_state>` - store attributes for each atom
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* :doc:`tdpd/source <fix_dpd_source>` -
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@ -384,7 +383,6 @@ accelerated styles exist.
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* :doc:`ttm/grid <fix_ttm>` - two-temperature model for electronic/atomic coupling (distributed grid)
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* :doc:`ttm/mod <fix_ttm>` - enhanced two-temperature model with additional options
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* :doc:`tune/kspace <fix_tune_kspace>` - auto-tune KSpace parameters
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* :doc:`update/special/bonds <fix_update_special_bonds>` - update special bond lists for BPM bond styles that allow for bond breakage
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* :doc:`vector <fix_vector>` - accumulate a global vector every N timesteps
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* :doc:`viscosity <fix_viscosity>` - Muller-Plathe momentum exchange for viscosity calculation
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* :doc:`viscous <fix_viscous>` - viscous damping for granular simulations
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@ -1,7 +1,7 @@
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.. index:: fix nve/bpm/sphere
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fix nve/bpm/sphere command
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======================
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==========================
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Syntax
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""""""
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@ -38,7 +38,7 @@ ensemble.
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This fix differs from the :doc:`fix nve <fix_nve>` command, which
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assumes point particles and only updates their position and velocity.
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It also differs from the :doc:`fix nve/sphere <fix_nve/sphere>`
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It also differs from the :doc:`fix nve/sphere <fix_nve_sphere>`
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command which assumes finite-size spheroid particles which do not
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store a quaternion. It thus does not update a particle's orientation
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or quaternion.
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@ -1,7 +1,7 @@
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.. index:: pair_style bpm/spring
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pair_style bpm/spring command
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=======================
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=============================
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Syntax
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""""""
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@ -86,7 +86,7 @@ timesteps. At the end of each interval, all of the saved accumulated
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data is deleted to make room for new data. Individual datum may
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therefore persist anywhere between *1* to *N* timesteps depending on
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when they are saved. This data can be accessed using the *fix_ID* and a
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:doc:`dump local <dump_local>` command. To ensure all data is output,
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:doc:`dump local <dump>` command. To ensure all data is output,
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the dump frequency should correspond to the same interval of *N*
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timesteps. A dump frequency of an integer multiple of *N* can be used
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to regularly output a sample of the accumulated data.
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@ -178,9 +178,6 @@ This fix is part of the MISC package. It is only enabled if LAMMPS
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was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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A corresponding :doc:`fix store_local <fix_store_local>` must be
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defined to use this pair style.
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This pair style is currently incompatible with granular pair styles
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that extend beyond the contact (e.g. JKR and DMT).
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@ -2618,7 +2618,7 @@ length of the data area, and a short description.
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- int
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- 1
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- 1 if the particle is a body particle, 0 if not
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* - quat
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* - quat
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- double
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- 4
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- four quaternion components of the particles
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