Merge branch 'master' into fix-tester

   * :doc:`oxdna2/fene <bond_oxdna>`

   * :doc:`oxrna2/fene <bond_oxdna>`

   * :doc:`quartic (o) <bond_quartic>`

   * :doc:`special <bond_special>`

   * :doc:`table (o) <bond_table>`

.. _angle:

.. index:: bond_style special

bond_style special command

=================================

Syntax

""""""

.. code-block:: LAMMPS

   bond_style special

Examples

""""""""

.. code-block:: LAMMPS

   bond_style special

   bond_coeff 0.5 0.5

Description

"""""""""""

The *special* bond style can be used to create conceptual bonds which

effectively impose weightings on the pairwise Lennard Jones and/or

Coulombic interactions between selected pairs of particles in the

system.  The form of the pairwise interaction will be whatever is

computed by the :doc:`pair_style <pair_style>` command defined for the

system; this command defines the weightings for its two terms.

This command can thus be useful to apply weightings that cannot be

handled by the :doc:`special_bonds <special_bonds>` command, such as

on 1-5 or 1-6 interactions.  Or it can be used to add pairwise forces

between one or more pairs of atoms that otherwise would not be include

in the :doc:`pair_style <pair_style>` computation.

The potential for this bond style has the form

.. math::

   E =  w_{LJ} E_{LJ} + w_{Coul} E_{Coul}

The following coefficients must be defined for each bond type via the

:doc:`bond_coeff <bond_coeff>` command as in the example above, or in

the data file or restart files read by the :doc:`read_data <read_data>`

or :doc:`read_restart <read_restart>` commands:

* :math:`w_{LJ}` weight (0.0 to 1.0) on pairwise Lennard-Jones interactions

* :math:`w_{Coul}` weight (0.0 to 1.0) on pairwise Coulombic interactions

----------

Normally this bond style should be used in conjunction with one (or

more) other bond styles which compute forces between atoms directly

bonded to each other in a molecule.  This means the :doc:`bond_style

hybrid <bond_hybrid>` command should be used with bond_style special

as one of its sub-styles.

Note that the same as for any other bond style, pairs of bonded atoms

must be enumerated in the data file read by the :doc:`read_data

<read_data>` command.  Thus if this command is used to weight all 1-5

interactions in the system, all the 1-5 pairs of atoms must be listed

in the "Bonds" section of the data file.

This bond style imposes strict requirements on settings made with the

:doc:`special_bonds <special_bonds>` command.  These requirements

ensure that the new bonds created by this style do not create spurious

1-2, 1-3, or 1-4 interactions within the molecular topology.

Specifically 1-2 interactions must have weights of zero, 1-3

interactions must either have weights of unity or :doc:`special_bonds

angle yes <special_bonds>` must be used, and 1-4 interactions must

have weights of unity or :doc:`special_bonds dihedral yes <special_bonds>` 

must be used.

If this command is used to create bonded interactions between

particles that are further apart than usual (e.g. 1-5 or 1-6

interactions), this style may require an increase in the communication

cutoff via the :doc:`comm_modify cutoff <comm_modify>` command.  If

LAMMPS cannot find a partner atom in a bond, an error will be issued.

Restrictions

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

This bond style can only be used if LAMMPS was built with the

USER-MISC package.  See the :doc:`Build package <Build_package>` doc

page for more info.

This bond style requires the use of a :doc:`pair_style <pair_style>` which

computes a pairwise additive interaction and provides the ability to

compute interactions for individual pairs of atoms.  Manybody potentials

are not compatible in general, but also some other pair styles are missing

the required functionality and thus will cause an error.

This command is not compatible with long-range Coulombic interactions. If a 

`kspace_style <kspace_style>` is declared, an error will be issued.

Related commands

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

:doc:`bond_coeff <bond_coeff>`, :doc:`special_bonds <special_bonds>`

**Default:** none

   pair_style coul/long/soft 1.0 10.0 9.5

   pair_coeff * * 1.0

   pair_coeff 1 1 1.0 9.5

   pair_coeff 1 1 1.0

   pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8

   pair_coeff * * 1.0

   pair_coeff 1 1 1.0 9.5

   pair_coeff 1 1 1.0

   pair_style morse/soft 4 0.9 10.0

   pair_coeff * * 100.0 2.0 1.5 1.0

oppositely charged particles from overlapping each other. In this case, if

:math:`\lambda = 1`, a singularity may occur.  These sub-styles are suitable to

represent charges embedded in the Lennard-Jones radius of another site (for

example hydrogen atoms in several water models).

example hydrogen atoms in several water models). The :math:`\lambda` must

be defined for each pair, and *coul/cut/soft* can accept an optional cutoff as

the second coefficient.

.. note::

  if (!use_history) return 0;

  int n = 0;

  // pack buf[0] this way because other fixes unpack it

  buf[n++] = size_history + 1;

  for (int m = 0; m < size_history; m++)

    buf[n++] = history_one[i][m];

  double **extra = atom->extra;

  // skip to Nth set of extra values

  // unpack the Nth first values this way because other fixes pack them

  int m = 0;

  for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);

    for (m = 0; m < size_history; m++)

      buf[n++] = history_many[i][iwall][m];

  }

  // pack buf[0] this way because other fixes unpack it

  buf[0] = n;

  return n;

}

  double **extra = atom->extra;

  // skip to Nth set of extra values

  // unpack the Nth first values this way because other fixes pack them

  int m = 0;

  for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);