lammps/doc/txt/fix_bocs.txt

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fix bocs command :h3

[Syntax:]

fix  ID group-ID bocs keyword values ... :pre

keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
  {temp} values = Tstart Tstop Tdamp
  {cgiso} values = Pstart Pstop Pdamp
  {basis set}
    {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
    {linear_spline} values = input_filename
    {cubic_spline} values = input_filename :pre
:ule

[Examples:]

fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre

fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre

thermo_modify press 1_press :pre


[Description:]

These commands incorporate a pressure correction as described by
Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
The first half of the command mimics a standard fix npt command:

fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre

The two differences are replacing {npt} with {bocs}, and replacing
{iso}/{aniso}/{etc} with {cgiso}.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: {analytic}, {linear_spline},
or {cubic_spline}.

With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file must be formatted so each line has:

Volume_i, PressureCorrection_i :pre

Note both the COMMA and the SPACE separating the volume's
value and its corresponding pressure correction. The volumes in the file
must be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atmospheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.

With the {analytic} option, the arguments are as follows:

... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre

Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
are using {units real}, {V_avg} should be in cubic angstroms, and the
coefficients should all be in atmospheres * cubic angstroms.

[Restrictions:]

As this is computing a (modified) pressure, group-ID should be {all}.

The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.

By default, LAMMPS will still report the normal value for the pressure
if the pressure is printed via a {thermo} command, or if the pressures
are written to a file every so often. In order to have LAMMPS report the
modified pressure, you must include the {thermo_modify} command given in
the examples. For the last argument in the command, you should put
XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1 ).

This fix is part of the USER-BOCS package.  It is only enabled if
LAMMPS was built with that package.  See the "Build
package"_Build_package.html doc page for more info.

[Related:]

For more details about the pressure correction and the entire BOCS software
package, visit the "BOCS package on GitHub"_bocsgithub and read the release
paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .


:link(bocsgithub,https://github.com/noid-group/BOCS)

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:link(bocs-Dunn1)
[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).

:link(bocs-Martyna)
[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).

:link(bocs-Dunn2)
[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).