\(\renewcommand{\AA}{\text{Å}}\)

fix set command

Syntax

fix ID group-ID set Nfreq rnflag set-args

  • ID, group-ID are documented in fix command

  • set = style name of this fix command

  • Nfreq = reset per-atom properties every this many timesteps

  • rnflag = 1 to reneighbor on next timestep, 0 to not

  • set-args = identical to args for the set command

Examples

fix 10 all set 1 0 group all i_dump v_new
fix 10 all set 1 0 group all i_dump v_turnoff

Description

Added in version 12Jun2025.

Reset one or more properties of one or more atoms once every Nfreq steps during a simulation.

If the rnflag for reneighboring is set to 1, then a reneighboring will be triggered on the next timestep (since the fix set operation occurs at the end of the current timestep). This is important to do if this command changes per-atom properties that need to be communicated to ghost atoms. If this is not the case, an rnflag setting of 0 can be used; reneighboring will only be triggered on subsequent timesteps by the usual neighbor list criteria; see the neigh_modify command.

Here are two examples where an rnflag setting of 1 are needed. If a custom per-atom property is changed and the fix property/atom command to create the property used the ghost yes keyword. Or if per-atom charges are changed, all pair styles which compute Coulombic interactions require charge values for ghost atoms. In both these examples, the re-neighboring will trigger the changes in the owned atom properties to be immediately communicated to ghost atoms.

The arguments following Nfreq and rnflag are identical to those allowed for the set command, as in the examples above and below.

Note that the group-ID setting for this command is ignored. The syntax for the set arguments allows selection of which atoms have their properties reset.

This command can only be used to reset an atom property using a per-atom variable. This option in allowed by many, but not all, of the keyword/value pairs supported by the set command. The reason for this restriction is that if a per-atom variable is not used, this command will typically not change atom properties during the simulation.

The set command can be used with similar syntax to this command to reset atom properties once before or between simulations.

Here is an example of input script commands which will output atoms into a dump file only when their x-velocity crosses a threshold value vthresh for the first time. Their position and x-velocity will then be output every step for twindow timesteps.

variable        vthresh equal 2             # threshold velocity
variable        twindow equal 10            # dump for this many steps
#
# define custom property i_dump to store timestep threshold is crossed
#
fix             2 all property/atom i_dump
set             group all i_dump -1
#
# fix set command checks for threshold crossings every step
# resets i_dump from -1 to current timestep when crossing occurs
#
variable        start atom "vx > v_vthresh && i_dump == -1"
variable        new atom ternary(v_start,step,i_dump)
fix             3 all set 1 0 group all i_dump v_new
#
# dump command with thresh which enforces twindow
#
dump            1 all custom 1 tmp.dump id x y vx i_dump
variable        dumpflag atom "i_dump >= 0 && (step-i_dump) < v_twindow"
dump_modify     1 thresh v_dumpflag == 1
#
# run the simulation
# final dump with all atom IDs which crossed threshold on which timestep
#
run             1000
write_dump      all custom tmp.dump.final id i_dump modify thresh i_dump >= 0

The tmp.dump.final file lists which atoms crossed the velocity threshold. This command will print the twindow timesteps when a specific atom ID (104 in this case) was output in the tmp.dump file:

% grep "^104 " tmp.dump

If these commands are used instead of the above, then an atom can cross the velocity threshold multiple times, and will be output for twindow timesteps each time. However the write_dump command is no longer useful.

variable        vthresh equal 2             # threshold velocity
variable        twindow equal 10            # dump for this many steps
#
# define custom property i_dump to store timestep threshold is crossed
#
fix             2 all property/atom i_dump
set             group all i_dump -1
#
# fix set command checks for threshold crossings every step
# resets i_dump from -1 to current timestep when crossing occurs
#
variable        start atom "vx > v_vthresh && i_dump == -1"
variable        turnon atom ternary(v_start,step,i_dump)
variable        stop atom "v_turnon >= 0 && (step-v_turnon) < v_twindow"
variable        turnoff atom ternary(v_stop,v_turnon,-1)
fix             3 all set 1 0 group all i_dump v_turnoff
#
# dump command with thresh which enforces twindow
#
dump            1 all custom 1 tmp.dump id x y vx i_dump
variable        dumpflag atom "i_dump >= 0 && (step-i_dump) < v_twindow"
dump_modify     1 thresh v_dumpflag == 1
#
# run the simulation
#
run             1000

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

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions

none

Default

none