updated documentation

.. parsed-literal::

   fix ID group-ID pafi compute-ID Temp Tdamp seed overdamped <arg> com <arg>

   fix ID group-ID pafi compute-ID Temp Tdamp seed keyword values...

* ID, group-ID are documented in :doc:`fix <fix>` command

* pafi = style name of this fix command

* Tdamp = damping parameter (time units)

* seed = random number seed to use for white noise (positive integer)

* keyword = *overdamped* or *com*

* overdamped <arg> = Brownian (*arg* = 1) or Langevin (*arg* = 0) dynamics

* com <arg> =  enable (*arg* = 1) or disable (*arg* = 0) XXX

  .. parsed-literal::

       *overdamped* value = *yes* or *no* or *1* or *0*

         *yes* or *1* = Brownian (overdamped) integration in hyperplane

         *no* or *0* = Langevin integration in hyperplane (see :doc:`fix langevin <fix_langevin>`)

       *com* value = *yes" or *no* or *1* or *0*

         *yes* or *1* = Zero linear momentum (see :doc: `fix momentum <fix_momentum>`)

         *no* or *0* = Do not zero linear momentum, allowing center of mass drift

       *overdamped* value = *yes* or *no* or 1 or 0

         *yes* or 1 = Brownian (overdamped) integration in hyperplane

         *no* or 0 = Langevin integration in hyperplane

       *com* value = *yes" or *no* or 1 or 0

         *yes* or 1 = zero linear momentum, fixing center or mass (recommended)

         *no* or 0 = do not zero linear momentum, allowing center of mass drift

Examples

""""""""

This fix can be used with LAMMPS as demonstrated in examples/USER/misc/pafi,

though it is primarily intended to be coupled with the PAFI C++ code, which is developed

at `https://github.com/tomswinburne/pafi <https://github.com/tomswinburne/pafi>`.

at `https://github.com/tomswinburne/pafi <https://github.com/tomswinburne/pafi>`_.

A :doc:`compute property/atom <compute_property_atom>` must be provided with 9 fields per atom coordinate,

which are the

- x,y,z coordinates of a configuration on the reference path

- x,y,z coordinates of the path tangent (derivative of path position with path coordinate)

- x,y,z coordinates of the change in tangent (derivative of path tangent with path coordinate)

which in order are the x,y,z coordinates of a configuration on the reference path,

the x,y,z coordinates of the path tangent (derivative of path position with path coordinate)

and the x,y,z coordinates of the change in tangent (derivative of path tangent with path coordinate).

A 4-element vector is also calculated by this fix. The 4 components are the

modified projected force, its square, the expected projection of the minimum

Restart, fix_modify, output, run start/stop, minimize info

"""""""""""

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

No information about this fix is written to :doc:`binary restart files <restart>`.

None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.