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lammps/doc/src/fix_filter_corotate.txt
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fix_filter_corotate.txt
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix filter/corotate command :h3
[Syntax:]
fix ID group-ID filter/corotate keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
one or more constraint/value pairs are appended :l
constraint = {b} or {a} or {t} or {m} :l
{b} values = one or more bond types
{a} values = one or more angle types
{t} values = one or more atom types
{m} value = one or more mass values :pre
:ule
[Examples:]
timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3
fix cor all filter/corotate m 1.0 :pre
fix cor all filter/corotate b 4 19 a 3 5 2 :pre
[Description:]
This fix implements a corotational filter for a mollified impulse
method. In biomolecular simulations, it allows the usage of larger
timesteps for long-range electrostatic interactions. For details, see
"(Fath)"_#Fath2017.
When using "run_style respa"_run_style.html for a biomolecular
simulation with high-frequency covalent bonds, the outer time-step is
restricted to below ~ 4fs due to resonance problems. This fix filters
the outer stage of the respa and thus a larger (outer) time-step can
be used. Since in large biomolecular simulations the computation of
the long-range electrostatic contributions poses a major bottleneck,
this can significantly accelerate the simulation.
The filter computes a cluster decomposition of the molecular structure
following the criteria indicated by the options a, b, t and m. This
process is similar to the approach in "fix shake"_fix_shake.html,
however, the clusters are not kept contrained. Instead, the position
is slightly modified only for the computation of long-range forces. A
good cluster decomposition constitutes in building clusters which
contain the fastest covalent bonds inside clusters.
If the clusters are chosen suitably, the "run_style
respa"_run_style.html is stable for outer time-steps of at least 8fs.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about these fixes is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to these fixes. No global or per-atom quantities are
stored by these fixes for access by various "output
commands"_Section_howto.html#howto_15. No parameter of these fixes
can be used with the {start/stop} keywords of the "run"_run.html
command. These fixes are not invoked during "energy
minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
Currently, it does not support "molecule templates"_molecule.html.
[Related commands:]
[Default:] none
:line
:link(Fath2017)
[(Fath)] Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
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