add pair style lj/sphere

doc/src/Commands_pair.rst

@@ -185,6 +185,7 @@ OPT.
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
    * :doc:`lj/relres (o) <pair_lj_relres>`
+   * :doc:`lj/sphere <pair_lj_sphere>`
    * :doc:`lj/spica (gko) <pair_spica>`
    * :doc:`lj/spica/coul/long (go) <pair_spica>`
    * :doc:`lj/spica/coul/msm (o) <pair_spica>`

doc/src/pair_lj_sphere.rst

@@ -0,0 +1,117 @@
+.. index:: pair_style lj/sphere
+
+pair_style lj/sphere command
+============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style style args
+
+* style = *lj/sphere*
+* args = list of arguments for a particular style
+
+.. parsed-literal::
+
+     *lj/sphere* args = cutoff
+       cutoff = global cutoff for Lennard Jones interactions (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lj/sphere 2.5
+   pair_coeff * * 1.0
+   pair_coeff 1 1 1.1 2.8
+
+Description
+"""""""""""
+
+The *lj/sphere* styles compute the standard 12/6 Lennard-Jones potential,
+given by
+
+.. math::
+
+   E = 4 \epsilon \left[ \left(\frac{\sigma_{ij}}{r}\right)^{12} -
+       \left(\frac{\sigma_{ij}}{r}\right)^6 \right]
+                       \qquad r < r_c
+
+:math:`r_c` is the cutoff.
+
+This is the same potential function as used by the :doc:`lj/cut
+<pair_lj>` pair style, but the :math:`\sigma_{ij}` parameter is not set
+as a per-type parameter via the :doc:`pair_coeff command <pair_coeff>`,
+but taken from the per-atom radius attribute of :doc:`atom_style sphere
+<atom_style>`.  The individual value of :math:`\sigma_{ij}` is computed
+using the mixing rule for pair coefficients as set by the
+:doc:`pair_modify mix <pair_modify>` command.
+
+Note that :math:`\sigma_{ij}` is defined in the LJ formula above as the
+zero-crossing distance for the potential, *not* as the energy minimum which
+is at :math:`2^{\frac{1}{6}} \sigma_{ij}`.
+
+Coefficients
+""""""""""""
+
+The following coefficients must be defined for each pair of atoms types via the
+:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in the data
+file or restart files read by the :doc:`read_data <read_data>` or
+:doc:`read_restart <read_restart>` commands, or by mixing as described below:
+
+* :math:`\epsilon` (energy units)
+* LJ cutoff (distance units) (optional)
+
+The last coefficient is optional.  If not specified, the global
+LJ cutoff specified in the pair_style command is used.
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, the epsilon coefficients and cutoff
+distance for the *lj/sphere* pair style can be mixed.  The default mix value
+is *geometric*.  See the "pair_modify" command for details.
+
+The *lj/sphere* pair style supports the :doc:`pair_modify <pair_modify>`
+shift option for the energy of the Lennard-Jones portion of the pair
+interaction.
+
+The *lj/sphere* pair style does *not* support the :doc:`pair_modify
+<pair_modify>` tail option for adding a long-range tail corrections to
+the energy and pressure.
+
+The *lj/sphere* pair style writes its information to :doc:`binary
+restart files <restart>`, so pair_style and pair_coeff commands do not
+need to be specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does *not* support the
+*inner*, *middle*, *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+The *lj/sphere* pair style is only enabled if LAMMPS was built with the
+EXTRA-PAIR package.  See the :doc:`Build package <Build_package>` page
+for more info.
+
+The *lj/sphere* pair style does not support the *sixthpower* mixing rule.
+
+----------
+
+Related commands
+""""""""""""""""
+
+* :doc:`pair_coeff <pair_coeff>`
+* :doc:`pair_style lj/cut <pair_lj>`
+
+Default
+"""""""
+
+none

doc/src/pair_style.rst

@@ -263,6 +263,7 @@ accelerated styles exist.
 * :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
 * :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
 * :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
+* :doc:`lj/sphere <pair_lj_sphere>` - LJ where per-atom radius is used as LJ sigma
 * :doc:`lj/spica <pair_spica>` - LJ for SPICA coarse-graining
 * :doc:`lj/spica/coul/long <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb
 * :doc:`lj/spica/coul/msm <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb via MSM