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clean up and correct some documentation link issues

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This commit is contained in:
Axel Kohlmeyer
2020-01-12 10:08:14 -05:00
parent a957d1c4c2
commit a0ecf539f6
4 changed files with 33 additions and 361 deletions
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1
doc/src/bond_style.rst
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@ -100,6 +100,7 @@ accelerated styles exist.
* :doc:`nonlinear <bond_nonlinear>` - nonlinear bond
* :doc:`oxdna/fene <bond_oxdna>` - modified FENE bond suitable for DNA modeling
* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
* :doc:`quartic <bond_quartic>` - breakable quartic bond
* :doc:`table <bond_table>` - tabulated by bond length

22
doc/src/fix.rst
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@ -64,16 +64,16 @@ with new settings). This is the same as if an "unfix" command were
first performed on the old fix, except that the new fix is kept in the
same order relative to the existing fixes as the old one originally
was. Note that this operation also wipes out any additional changes
made to the old fix via the :doc:`fix\_modify <fix_modify>` command.
made to the old fix via the :doc:`fix_modify <fix_modify>` command.
The :doc:`fix modify <fix_modify>` command allows settings for some
fixes to be reset. See the doc page for individual fixes for details.
Some fixes store an internal "state" which is written to binary
restart files via the :doc:`restart <restart>` or
:doc:`write\_restart <write_restart>` commands. This allows the fix to
:doc:`write_restart <write_restart>` commands. This allows the fix to
continue on with its calculations in a restarted simulation. See the
:doc:`read\_restart <read_restart>` command for info on how to re-specify
:doc:`read_restart <read_restart>` command for info on how to re-specify
a fix in an input script that reads a restart file. See the doc pages
for individual fixes for info on which ones can be restarted.
@ -133,7 +133,7 @@ various commands explain the details.
In LAMMPS, the values generated by a fix can be used in several ways:
* Global values can be output via the :doc:`thermo\_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
* Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
Or the values can be referenced in a :doc:`variable equal <variable>` or
:doc:`variable atom <variable>` command.
* Per-atom values can be output via the :doc:`dump custom <dump>` command.
@ -257,6 +257,7 @@ accelerated styles exist.
* :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm
* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
* :doc:`nph/body <fix_nph_body>` - NPH for body particles
@ -339,15 +340,16 @@ accelerated styles exist.
* :doc:`rx <fix_rx>` -
* :doc:`saed/vtk <fix_saed_vtk>` -
* :doc:`setforce <fix_setforce>` - set the force on each atom
* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
* :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
* :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
* :doc:`smd <fix_smd>` - applied a steered MD force to a group
* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` -
* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` -
* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` -
* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` -
* :doc:`smd/adjust_dt <fix_smd_adjust_dt>` -
* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>` -
* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>` -
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
* :doc:`smd/setvel <fix_smd_setvel>` -
* :doc:`smd/wall\_surface <fix_smd_wall_surface>` -
* :doc:`smd/wall_surface <fix_smd_wall_surface>` -
* :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
* :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
* :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
@ -399,7 +401,7 @@ individual fixes tell if it is part of a package.
Related commands
""""""""""""""""
:doc:`unfix <unfix>`, :doc:`fix\_modify <fix_modify>`
:doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`
**Default:** none

33
doc/src/pair_style.rst
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@ -32,7 +32,7 @@ Description
Set the formula(s) LAMMPS uses to compute pairwise interactions. In
LAMMPS, pair potentials are defined between pairs of atoms that are
within a cutoff distance and the set of active interactions typically
changes over time. See the :doc:`bond\_style <bond_style>` command to
changes over time. See the :doc:`bond_style <bond_style>` command to
define potentials between pairs of bonded atoms, which typically
remain in place for the duration of a simulation.
@ -48,11 +48,11 @@ different pair potentials can be setup using the *hybrid* pair style.
The coefficients associated with a pair style are typically set for
each pair of atom types, and are specified by the
:doc:`pair\_coeff <pair_coeff>` command or read from a file by the
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
:doc:`pair_coeff <pair_coeff>` command or read from a file by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands.
The :doc:`pair\_modify <pair_modify>` command sets options for mixing of
The :doc:`pair_modify <pair_modify>` command sets options for mixing of
type I-J interaction coefficients and adding energy offsets or tail
corrections to Lennard-Jones potentials. Details on these options as
they pertain to individual potentials are described on the doc page
@ -70,11 +70,11 @@ cutoffs for all pairs of atom types. The distance(s) can be smaller
or larger than the dimensions of the simulation box.
Typically, the global cutoff value can be overridden for a specific
pair of atom types by the :doc:`pair\_coeff <pair_coeff>` command. The
pair of atom types by the :doc:`pair_coeff <pair_coeff>` command. The
pair style settings (including global cutoffs) can be changed by a
subsequent pair\_style command using the same style. This will reset
the cutoffs for all atom type pairs, including those previously set
explicitly by a :doc:`pair\_coeff <pair_coeff>` command. The exceptions
explicitly by a :doc:`pair_coeff <pair_coeff>` command. The exceptions
to this are that pair\_style *table* and *hybrid* settings cannot be
reset. A new pair\_style command for these styles will wipe out all
previously specified pair\_coeff values.
@ -88,7 +88,7 @@ also listed in more compact form on the :doc:`Commands pair <Commands_pair>` doc
Click on the style to display the formula it computes, any additional
arguments specified in the pair\_style command, and coefficients
specified by the associated :doc:`pair\_coeff <pair_coeff>` command.
specified by the associated :doc:`pair_coeff <pair_coeff>` command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
@ -170,6 +170,7 @@ accelerated styles exist.
* :doc:`gauss <pair_gauss>` - Gaussian potential
* :doc:`gauss/cut <pair_gauss>` - generalized Gaussian potential
* :doc:`gayberne <pair_gayberne>` - Gay-Berne ellipsoidal potential
* :doc:`granular <pair_granular>` - Generalized granular potential
* :doc:`gran/hertz/history <pair_gran>` - granular potential with Hertzian interactions
* :doc:`gran/hooke <pair_gran>` - granular potential with history effects
* :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects
@ -267,6 +268,12 @@ accelerated styles exist.
* :doc:`oxdna2/hbond <pair_oxdna2>` -
* :doc:`oxdna2/stk <pair_oxdna2>` -
* :doc:`oxdna2/xstk <pair_oxdna2>` -
* :doc:`oxrna2/coaxstk <pair_oxrna2>` -
* :doc:`oxrna2/dh <pair_oxrna2>` -
* :doc:`oxrna2/excv <pair_oxrna2>` -
* :doc:`oxrna2/hbond <pair_oxrna2>` -
* :doc:`oxrna2/stk <pair_oxrna2>` -
* :doc:`oxrna2/xstk <pair_oxrna2>` -
* :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
@ -280,7 +287,7 @@ accelerated styles exist.
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
* :doc:`smd/hertz <pair_smd_hertz>` -
* :doc:`smd/tlsph <pair_smd_tlsph>` -
* :doc:`smd/tri\_surface <pair_smd_triangulated_surface>` -
* :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
* :doc:`smd/ulsph <pair_smd_ulsph>` -
* :doc:`smtbq <pair_smtbq>` -
* :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
@ -328,8 +335,8 @@ Restrictions
This command must be used before any coefficients are set by the
:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`, or
:doc:`read\_restart <read_restart>` commands.
:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`, or
:doc:`read_restart <read_restart>` commands.
Some pair styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. The doc pages for
@ -338,9 +345,9 @@ individual pair potentials tell if it is part of a package.
Related commands
""""""""""""""""
:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`,
:doc:`pair\_modify <pair_modify>`, :doc:`kspace\_style <kspace_style>`,
:doc:`dielectric <dielectric>`, :doc:`pair\_write <pair_write>`
:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`,
:doc:`pair_modify <pair_modify>`, :doc:`kspace_style <kspace_style>`,
:doc:`dielectric <dielectric>`, :doc:`pair_write <pair_write>`
Default
"""""""