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
+
+compute bocsPress all pressureBocs thermo_temp
+thermo_modify press bocsPress
+fix_modify 1 press bocsPress
+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 should 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 +should 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 atomspheres. 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.
+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.
+There are three additional commands that must be supplied along with fix +bocs. They are given in the examples section. The name bocsPress can be +changed for any name of your choosing, provided it remains consistent across +all three commands. Additionally, the ID 1 in the fix_modify command must +match up with the ID specified in the original fix bocs command. Everything else +in those three commands must be unchanged. The first two commands can be +specified before the fix bocs command, but the fix_modify command must be +given after the original fix bocs command.
+The compute command tells LAMMPS to compute the pressure using the modified +barostat.
+The thermo_modify command tells LAMMPS to report the pressure from the modified +barostat instead of the default pressure, i.e. thermo_press.
+The fix_modify command tells LAMMPS to use the pressure from the modified +barostat for the fix, instead of using the default presure, i.e. thermo_press.
+Related:
+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).
+