new doc page for fix set command with example
This commit is contained in:
Steve Plimpton
@ -395,6 +395,7 @@ accelerated styles exist.
|
||||
* :doc:`rigid/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVE integration
|
||||
* :doc:`rx <fix_rx>` - solve reaction kinetic ODEs for a defined reaction set
|
||||
* :doc:`saed/vtk <fix_saed_vtk>` - time-average the intensities from :doc:`compute saed <compute_saed>`
|
||||
* :doc:`set <fix_set>` - reset an atom property via an atom-style variable every N steps
|
||||
* :doc:`setforce <fix_setforce>` - set the force on each atom
|
||||
* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
|
||||
* :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grand canonical MD/MC simulations
|
||||
|
||||
154
doc/src/fix_set.rst
Normal file
154
doc/src/fix_set.rst
Normal file
@ -0,0 +1,154 @@
|
||||
.. index:: fix set
|
||||
|
||||
fix set command
|
||||
===============
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix ID group-ID set Nfreq 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
|
||||
* set-args = identical to args for the :doc:`set <set>` command
|
||||
|
||||
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
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Reset one or more properties of one or more atoms once every *Nfreq*
|
||||
stepes 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.
|
||||
|
||||
Note that the group-ID setting for this command is ignored. The
|
||||
syntax for the :doc:`set <set>` command 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 :doc:`set <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 :doc:`set <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.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
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 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:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
% 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.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
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 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 :doc:`binary restart files
|
||||
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
|
||||
relevant to this fix. No global or per-atom quantities are stored by
|
||||
this fix for access by various :doc:`output commands <Howto_output>`.
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
:doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
As noted above,
|
||||
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`set <set>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -200,6 +200,10 @@ their properties reset. The remaining keywords specify which
|
||||
properties to reset and what the new values are. Some strings like
|
||||
*type* or *mol* can be used as a style and/or a keyword.
|
||||
|
||||
The :doc:`fix set <fix_set>` command can be used with similar syntax
|
||||
to this command to reset atom properties once every *N* steps during a
|
||||
simulation using via atom-style variables.
|
||||
|
||||
----------
|
||||
|
||||
This section describes how to select which atoms to change
|
||||
@ -658,7 +662,7 @@ Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`create_box <create_box>`, :doc:`create_atoms <create_atoms>`,
|
||||
:doc:`read_data <read_data>`
|
||||
:doc:`read_data <read_data>`, :doc:`fix set <fix_set>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
@ -37,8 +37,16 @@ FixSet::FixSet(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
|
||||
// pass remaining args to Set class
|
||||
// only keywords which use per-atom variables are currently allowed
|
||||
|
||||
// NOTE: could also allow when set style = region, since atoms may move in/out of regions
|
||||
|
||||
set->process_args(FIXSET,narg-4,&arg[4]);
|
||||
|
||||
// NOTE: not sure if either of these options for fix set are needed or could be problematic
|
||||
// could add ghost yes keyword/value to trigger
|
||||
// ghost comm, e.g. if atom types are reset
|
||||
// this could require an extract() method in Set to query what value(s) to comm
|
||||
// could add reneigh yes keyword/value to trigger
|
||||
// full reneighbor on next step, e.g. if xyz coords are reset
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -59,7 +67,7 @@ int FixSet::setmask()
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
use the Set instance to update per-atom properties
|
||||
NOTE: could return count of updated atoms from Set and use it as a fix output
|
||||
NOTE: could return count of updated atoms from Set for use as fix output
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void FixSet::end_of_step()
|
||||
|
||||
@ -999,6 +999,8 @@ void Set::topology(int keyword, Action *action)
|
||||
// separate two operations so can be called by either set or fix set command
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Set::process_angle(int &iarg, int narg, char **arg, Action *action)
|
||||
{
|
||||
if (atom->avec->angles_allow == 0)
|
||||
|
||||
Reference in New Issue
Block a user