new doc page for fix set command with example
This commit is contained in:
Steve Plimpton
@ -395,6 +395,7 @@ accelerated styles exist.
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* :doc:`rigid/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVE integration
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* :doc:`rx <fix_rx>` - solve reaction kinetic ODEs for a defined reaction set
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* :doc:`saed/vtk <fix_saed_vtk>` - time-average the intensities from :doc:`compute saed <compute_saed>`
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* :doc:`set <fix_set>` - reset an atom property via an atom-style variable every N steps
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* :doc:`setforce <fix_setforce>` - set the force on each atom
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* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
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* :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grand canonical MD/MC simulations
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154
doc/src/fix_set.rst
Normal file
154
doc/src/fix_set.rst
Normal file
@ -0,0 +1,154 @@
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.. index:: fix set
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fix set command
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===============
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Syntax
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""""""
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.. code-block:: LAMMPS
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fix ID group-ID set Nfreq set-args
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* set = style name of this fix command
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* Nfreq = reset per-atom properties every this many timesteps
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* set-args = identical to args for the :doc:`set <set>` command
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 10 all set 1 group all i_dump v_new
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fix 10 all set 1 group all i_dump v_turnoff
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Description
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"""""""""""
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Reset one or more properties of one or more atoms once every *Nfreq*
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stepes during a simulation.
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The args following *Nfreq* are identical to those allowed for the
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:doc:`set <set>` command, as in the examples above and below.
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Note that the group-ID setting for this command is ignored. The
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syntax for the :doc:`set <set>` command allows selection of which
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atoms have their properties reset.
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This command can only be used to reset an atom property using a
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per-atom variable. This option in allowed by many, but not all, of
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the keyword/value pairs supported by the :doc:`set <set>` command.
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The reason for this restriction is that if a per-atom variable is not
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used, this command will typically not change atom properties during
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the simulation.
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The :doc:`set <set>` command can be used with similar syntax to this
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command to reset atom properties once before or between simulations.
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----------
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Here is an example of input script commands which will output atoms
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into a dump file only when their x-velocity crosses a threshold value
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*vthresh* for the first time. Their position and x-velocity will then
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be output every step for *twindow* timesteps.
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.. code-block:: LAMMPS
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variable vthresh equal 2 # threshold velocity
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variable twindow equal 10 # dump for this many steps
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#
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# define custom property i_dump to store timestep threshold is crossed
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#
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fix 2 all property/atom i_dump
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set group all i_dump -1
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#
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# fix set command checks for threshold crossings every step
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# resets i_dump from -1 to current timestep when crossing occurs
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#
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variable start atom "vx > v_vthresh && i_dump == -1"
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variable new atom ternary(v_start,step,i_dump)
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fix 3 all set 1 group all i_dump v_new
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#
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# dump command with thresh which enforces twindow
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#
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dump 1 all custom 1 tmp.dump id x y vx i_dump
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variable dumpflag atom "i_dump >= 0 && (step-i_dump) < v_twindow"
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dump_modify 1 thresh v_dumpflag == 1
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#
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# run the simulation
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# final dump with all atom IDs which crossed threshold on which timestep
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#
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run 1000
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write_dump all custom tmp.dump.final id i_dump modify thresh i_dump >= 0
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The tmp.dump.final file lists which atoms crossed the velocity
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threshold. This command will print the *twindow* timesteps when a
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specific atom ID (104 in this case) was output in the tmp.dump file:
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.. code-block:: LAMMPS
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% grep "^104 " tmp.dump
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If these commands are used instead of the above, then an atom can
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cross the velocity threshold multiple times, and will be output for
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*twindow* timesteps each time. However the write_dump command is no
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longer useful.
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.. code-block:: LAMMPS
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variable vthresh equal 2 # threshold velocity
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variable twindow equal 10 # dump for this many steps
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#
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# define custom property i_dump to store timestep threshold is crossed
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#
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fix 2 all property/atom i_dump
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set group all i_dump -1
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#
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# fix set command checks for threshold crossings every step
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# resets i_dump from -1 to current timestep when crossing occurs
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#
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variable start atom "vx > v_vthresh && i_dump == -1"
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variable turnon atom ternary(v_start,step,i_dump)
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variable stop atom "v_turnon >= 0 && (step-v_turnon) < v_twindow"
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variable turnoff atom ternary(v_stop,v_turnon,-1)
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fix 3 all set 1 group all i_dump v_turnoff
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#
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# dump command with thresh which enforces twindow
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#
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dump 1 all custom 1 tmp.dump id x y vx i_dump
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variable dumpflag atom "i_dump >= 0 && (step-i_dump) < v_twindow"
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dump_modify 1 thresh v_dumpflag == 1
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#
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# run the simulation
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#
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run 1000
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files
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<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
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relevant to this fix. No global or per-atom quantities are stored by
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this fix for access by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during
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:doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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As noted above,
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Related commands
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""""""""""""""""
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:doc:`set <set>`
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Default
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"""""""
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none
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@ -200,6 +200,10 @@ their properties reset. The remaining keywords specify which
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properties to reset and what the new values are. Some strings like
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*type* or *mol* can be used as a style and/or a keyword.
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The :doc:`fix set <fix_set>` command can be used with similar syntax
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to this command to reset atom properties once every *N* steps during a
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simulation using via atom-style variables.
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----------
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This section describes how to select which atoms to change
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@ -658,7 +662,7 @@ Related commands
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""""""""""""""""
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:doc:`create_box <create_box>`, :doc:`create_atoms <create_atoms>`,
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:doc:`read_data <read_data>`
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:doc:`read_data <read_data>`, :doc:`fix set <fix_set>`
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Default
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"""""""
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@ -37,8 +37,16 @@ FixSet::FixSet(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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// pass remaining args to Set class
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// only keywords which use per-atom variables are currently allowed
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// NOTE: could also allow when set style = region, since atoms may move in/out of regions
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set->process_args(FIXSET,narg-4,&arg[4]);
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// NOTE: not sure if either of these options for fix set are needed or could be problematic
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// could add ghost yes keyword/value to trigger
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// ghost comm, e.g. if atom types are reset
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// this could require an extract() method in Set to query what value(s) to comm
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// could add reneigh yes keyword/value to trigger
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// full reneighbor on next step, e.g. if xyz coords are reset
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}
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/* ---------------------------------------------------------------------- */
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@ -59,7 +67,7 @@ int FixSet::setmask()
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/* ----------------------------------------------------------------------
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use the Set instance to update per-atom properties
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NOTE: could return count of updated atoms from Set and use it as a fix output
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NOTE: could return count of updated atoms from Set for use as fix output
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---------------------------------------------------------------------- */
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void FixSet::end_of_step()
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@ -999,6 +999,8 @@ void Set::topology(int keyword, Action *action)
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// separate two operations so can be called by either set or fix set command
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// ----------------------------------------------------------------------
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/* ---------------------------------------------------------------------- */
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void Set::process_angle(int &iarg, int narg, char **arg, Action *action)
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{
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if (atom->avec->angles_allow == 0)
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