lammps/doc/fix_shake.txt

"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 shake command :h3
fix shake/cuda command :h3
fix rattle command :h3

[Syntax:]

fix ID group-ID style tol iter N constraint values ... keyword value ... :pre

ID, group-ID are documented in "fix"_fix.html command :ulb,l
style = shake or rattle = style name of this fix command :l
tol = accuracy tolerance of SHAKE solution :l
iter = max # of iterations in each SHAKE solution :l
N = print SHAKE statistics every this many timesteps (0 = never) :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
zero or more keyword/value pairs may be appended :l
keyword = {mol} :l
  {mol} value = template-ID
    template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command :pre
:ule

[Examples:]

fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31
fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol
fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31
fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol :pre

[Description:]

Apply bond and angle constraints to specified bonds and angles in the
simulation by either the SHAKE or RATTLE algorithms.  This typically
enables a longer timestep.

[SHAKE vs RATTLE:]

The SHAKE algorithm was invented for schemes such as standard Verlet
timesteppnig, where only the coordinates are integrated and the
velocities are approximated as finite differences to the trajectories
("Ryckaert et al. (1977)"_#Ryckaert).  If the velocities are
integrated explicitly, as with velocity Verlet which is what LAMMPS
uses as an integration method, a second set of constraining forces is
required in order to eliminate velocity components along the bonds
("Andersen (1983)"_#Andersen).

In order to formulate individual constraints for SHAKE and RATTLE,
focus on a single molecule whose bonds are constrained.  Let Ri and Vi
be the position and velocity of atom {i} at time {n}, for
{i}=1,...,{N}, where {N} is the number of sites of our reference
molecule. The distance vector between sites {i} and {j} is given by

:c,image(Eqs/fix_rattle_rij.jpg)

The constraints can then be formulated as

:c,image(Eqs/fix_rattle_constraints.jpg)

The SHAKE algorithm satisfies the first condition, i.e. the sites at
time {n+1} will have the desired separations Dij immediately after the
coordinates are integrated.  If we also enforce the second condition,
the velocity components along the bonds will vanish.  RATTLE satisfies
both conditions.  As implemented in LAMMPS, fix rattle uses fix shake
for satisfying the coordinate constraints. Therefore the settings and
optional keywords are the same for both fixes, and all the information
below about SHAKE is also relevant for RATTLE.

[SHAKE:]

Each timestep the specified bonds and angles are reset to their
equilibrium lengths and angular values via the SHAKE algorithm
("Ryckaert et al. (1977)"_#Ryckaert).  This is done by applying an
additional constraint force so that the new positions preserve the
desired atom separations.  The equations for the additional force are
solved via an iterative method that typically converges to an accurate
solution in a few iterations.  The desired tolerance (e.g. 1.0e-4 = 1
part in 10000) and maximum # of iterations are specified as arguments.
Setting the N argument will print statistics to the screen and log
file about regarding the lengths of bonds and angles that are being
constrained.  Small delta values mean SHAKE is doing a good job.

In LAMMPS, only small clusters of atoms can be constrained.  This is
so the constraint calculation for a cluster can be performed by a
single processor, to enable good parallel performance.  A cluster is
defined as a central atom connected to others in the cluster by
constrained bonds.  LAMMPS allows for the following kinds of clusters
to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
one central atom bonded to 2 others and the angle between the 3 atoms
also constrained.  This means water molecules or CH2 or CH3 groups may
be constrained, but not all the C-C backbone bonds of a long polymer
chain.

The {b} constraint lists bond types that will be constrained.  The {t}
constraint lists atom types.  All bonds connected to an atom of the
specified type will be constrained.  The {m} constraint lists atom
masses.  All bonds connected to atoms of the specified masses will be
constrained (within a fudge factor of MASSDELTA specified in
fix_shake.cpp).  The {a} constraint lists angle types.  If both bonds
in the angle are constrained then the angle will also be constrained
if its type is in the list.

For all constraints, a particular bond is only constrained if both
atoms in the bond are in the group specified with the SHAKE fix.

The degrees-of-freedom removed by SHAKE bonds and angles are accounted
for in temperature and pressure computations.  Similarly, the SHAKE
contribution to the pressure of the system (virial) is also accounted
for.

IMPORTANT NOTE: This command works by using the current forces on
atoms to caculate an additional constraint force which when added will
leave the atoms in positions that satisfy the SHAKE constraints
(e.g. bond length) after the next time integration step.  If you
define fixes (e.g. "fix efield"_fix_efield.html) that add additional
force to the atoms after fix shake operates, then this fix will not
take them into account and the time integration will typically not
satisfy the SHAKE constraints.  The solution for this is to make sure
that fix shake is defined in your input script after any other fixes
which add or change forces (to atoms that fix shake operates on).

:line

The {mol} keyword should be used when other commands, such as "fix
deposit"_fix_deposit.html or "fix pour"_fix_pour.html, add molecules
on-the-fly during a simulation, and you wish to contrain the new
molecules via SHAKE.  You specify a {template-ID} previously defined
using the "molecule"_molecule.html command, which reads a file that
defines the molecule.  You must use the same {template-ID} that the
command adding molecules uses.  The coordinates, atom types, special
bond restrictions, and SHAKE info can be specified in the molecule
file.  See the "molecule"_molecule.html command for details.  The only
settings required to be in this file (by this command) are the SHAKE
info of atoms in the molecule.

:line

Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix.  They have been optimized to
run faster, depending on your available hardware, as discussed in
"Section_accelerate"_Section_accelerate.html of the manual.  The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.

These accelerated styles are part of the USER-CUDA package.  They are
only enabled if LAMMPS was built with that package.  See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.

You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.

See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.

:line

[RATTLE:]

The velocity constraints lead to a linear system of equations which
can be solved analytically.  The implementation of the algorithm in
LAMMPS closely follows ("Andersen (1983)"_#Andersen).
	
IMPORTANT NOTE: The fix rattle command modifies forces and velocities
and thus should be defined after all other integration fixes in your
input script.  If you define other fixes that modify velocities or
forces after fix rattle operates, then fix rattle will not take them
into account and the overall time integration will typically not
satisfy the RATTLE constraints.  You can check whether the constraints
work correctly by setting the value of RATTLE_DEBUG in
src/fix_rattle.cpp to 1 and recompiling LAMMPS.

: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:]

These fixes are part of the RIGID package.  They are only enabled if
LAMMPS was built with that package.  See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.

For computational efficiency, there can only be one shake or rattle
fix defined in a simulation.

If you use a tolerance that is too large or a max-iteration count that
is too small, the constraints will not be enforced very strongly,
which can lead to poor energy conservation.  You can test for this in
your system by running a constant NVE simulation with a particular set
of SHAKE parameters and monitoring the energy versus time.

[Related commands:] none

[Default:] none

:line 
 
:link(Ryckaert)
[(Ryckaert)] J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, 
Journal of Computational Physics, 23, 327–341 (1977).
 
:link(Andersen)
[(Andersen)] H. Andersen,
Journal of Computational Physics, 52, 24-34 (1983).