# fix pafi command

## Syntax

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

-   ID, group-ID are documented in [fix](fix) command
-   pafi = style name of this fix command
-   compute-ID = ID of a [compute property/atom](compute_property_atom)
    that holds data used by this fix
-   Temp = desired temperature (temperature units)
-   Tdamp = damping parameter (time units)
-   seed = random number seed to use for white noise (positive integer)
-   keyword = *overdamped* or *com*

    ::

    :   

        *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

``` LAMMPS
compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
run 0 post no
fix hp all pafi pa 500.0 0.01 434 overdamped yes
```

## Description

Perform Brownian or Langevin integration whilst constraining the system
to lie in some hyperplane, which is expected to be the tangent plane to
some reference pathway in a solid state system. The instantaneous value
of a modified force projection is also calculated, whose time integral
can be shown to be equal to the true free energy gradient along the
minimum free energy path local to the reference pathway. A detailed
discussion of the projection technique can be found in
[(Swinburne)](Swinburne).

This fix can be used with LAMMPS as demonstrated in
examples/PACKAGES/pafi, though it is primarily intended to be coupled
with the PAFI C++ code, developed at
<https://github.com/tomswinburne/pafi>\_, which distributes multiple
LAMMPS workers in parallel to compute and collate hyperplane-constrained
averages, allowing the calculation of free energy barriers and pathways.

A [compute property/atom](compute_property_atom) must be provided with 9
fields per atom 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 free energy path tangent on the reference path tangent and the
minimum image distance between the current configuration and the
reference configuration, projected along the path tangent. This latter
value should be essentially zero.

:::: note
::: title
Note
:::

When com=yes/1, which is recommended, the provided tangent vector must
also have zero center of mass. This can be achieved by subtracting from
each coordinate of the path tangent the average x,y,z value. The PAFI
C++ code (see above) can generate these paths for use in LAMMPS.
::::

:::: note
::: title
Note
:::

When overdamped=yes/1, the Tdamp parameter should be around 5-10 times
smaller than that used in typical Langevin integration. See [fix
langevin](fix_langevin) for typical values.
::::

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

No information about this fix is written to [binary restart
files](restart). None of the [fix_modify](fix_modify) options are
relevant to this fix.

This fix produces a global vector each timestep which can be accessed by
various [output commands](Howto_output).

## Restrictions

This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS
was built with that package. See the [Build package](Build_package) page
for more info.

## Default

The option defaults are com = *yes*, overdamped = *no*

------------------------------------------------------------------------

::: {#Swinburne}
**(Swinburne)** Swinburne and Marinica, Physical Review Letters, 120, 1
(2018)
:::