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add renieigbor option to fix set

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This commit is contained in:
Steve Plimpton
2025-05-26 16:22:52 -06:00
parent f3adda8d3e
commit 6a5ed2af4b
5 changed files with 54 additions and 26 deletions
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1
doc/src/Commands_fix.rst
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@ -216,6 +216,7 @@ OPT.
* :doc:`rigid/small (o) <fix_rigid>`
* :doc:`rx (k) <fix_rx>`
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`set <fix_set>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`setforce/spin <fix_setforce>`
* :doc:`sgcmc <fix_sgcmc>`

36
doc/src/fix_set.rst
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@ -8,11 +8,12 @@ Syntax
.. code-block:: LAMMPS
fix ID group-ID set Nfreq set-args
fix ID group-ID set Nfreq rnflag set-args
* ID, group-ID are documented in :doc:`fix <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 :doc:`set <set>` command
Examples
@ -20,8 +21,8 @@ Examples
.. code-block:: LAMMPS
fix 10 all set 1 group all i_dump v_new
fix 10 all set 1 group all i_dump v_turnoff
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
"""""""""""
@ -29,11 +30,30 @@ Description
Reset one or more properties of one or more atoms once every *Nfreq*
steps during a simulation.
The args following *Nfreq* are identical to those allowed for the
:doc:`set <set>` command, as in the examples above and below.
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
:doc:`neigh_modify <neigh_modify.html>` command.
Here are two examples where an *rnflag* setting of 1 are needed. If a
custom per-atom property is changed and the :doc:`fix property/atom
<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 :doc:`set <set>` command, as in the examples above and
below.
Note that the group-ID setting for this command is ignored. The
syntax for the :doc:`set <set>` command allows selection of which
syntax for the :doc:`set <set>` arguments allows selection of which
atoms have their properties reset.
This command can only be used to reset an atom property using a
@ -68,7 +88,7 @@ be output every step for *twindow* timesteps.
#
variable start atom "vx > v_vthresh && i_dump == -1"
variable new atom ternary(v_start,step,i_dump)
fix 3 all set 1 group all i_dump v_new
fix 3 all set 1 0 group all i_dump v_new
#
# dump command with thresh which enforces twindow
#
@ -112,7 +132,7 @@ longer useful.
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 group all i_dump v_turnoff
fix 3 all set 1 0 group all i_dump v_turnoff
#
# dump command with thresh which enforces twindow
#

18
doc/src/run.rst
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@ -103,14 +103,16 @@ must be done.
.. note::
If your input script changes the system between 2 runs, then the
initial setup must be performed to ensure the change is recognized by
all parts of the code that are affected. Examples are adding a
:doc:`fix <fix>` or :doc:`dump <dump>` or :doc:`compute <compute>`, changing
a :doc:`neighbor <neigh_modify>` list parameter, or writing restart file
which can migrate atoms between processors. LAMMPS has no easy way to
check if this has happened, but it is an error to use the *pre no*
option in this case.
If your input script "changes" the system between 2 runs, then the
initial setup typically needs to be performed to ensure the change
is recognized by all parts of the code that are affected. Examples
are adding a :doc:`fix <fix>` or :doc:`dump <dump>` or
:doc:`compute <compute>`, changing a :doc:`neighbor <neigh_modify>`
list parameter, using the :doc:`set <set>` command, or writing a
restart file via the :doc:`write_restart <write_restart>` command,
which can migrate atoms between processors. LAMMPS has no easy way
to check if this has happened, but it is an error to use the *pre
no* option in these cases.
If *post* is specified as "no", the full timing summary is skipped;
only a one-line summary timing is printed.