Merge pull request #416 from lukin17/filter_corotate

"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).

 No newline at end of file

   fix_eos_table_rx

   fix_evaporate

   fix_external

   fix_filter_corotate

   fix_flow_gauss

   fix_freeze

   fix_gcmc

fix_eos_table_rx.html

fix_evaporate.html

fix_external.html

fix_filter_corotate.html

fix_flow_gauss.html

fix_freeze.html

fix_gcmc.html