fix bocs command

Syntax

fix  ID group-ID bocs keyword values ...

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

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

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

thermo_modify press 1_press

Description

These commands incorporate a pressure correction as described by Dunn and Noid in (Dunn1) to the standard MTTK barostat by Martyna et. al. in (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

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

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

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.


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

This fix writes the cumulative global energy change to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the fix continues in an uninterrupted fashion.

The fix_modify temp option is supported by this fix. You can use it to assign a temperature compute you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by this fix and by the compute should be the same.

The cumulative energy change in the system imposed by this fix is included in the thermodynamic output keywords ecouple and econserve. See the thermo_style doc page for details.

This fix computes a global scalar which can be accessed by various output commands. The scalar is the same cumulative energy change due to this fix described in the previous paragraph. The scalar value calculated by this fix is “extensive”.

This fix can ramp its target temperature over multiple runs, using the start and stop keywords of the run command. See the run command for details of how to do this.

This fix is not invoked during energy minimization.

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 doc page for more info.

Further information

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


(Dunn1) Dunn and Noid, J Chem Phys, 143, 243148 (2015).

(Martyna) Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).

(Dunn2) Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).