Merge branch 'collected-small-changes' into doc-styles-check

* :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

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.

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.

* :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

* :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

Related commands

""""""""""""""""

:doc:`unfix <unfix>`, :doc:`fix\_modify <fix_modify>`

:doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`

**Default:** none

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.

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

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.

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.

* :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

* :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

* :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

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

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

"""""""