Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/src/fix_nvt_body.txt
39d713b5a307lammm-master

Last Change
Raw File

fix_nvt_body.txt
View Options

"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 nvt/body command :h3
[Syntax:]
fix ID group-ID nvt/body keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command
nvt/body = style name of this fix command
additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :ul
[Examples:]
fix 1 all nvt/body temp 300.0 300.0 100.0
fix 1 all nvt/body temp 300.0 300.0 100.0 drag 0.2 :pre
[Description:]
Perform constant NVT integration to update position, velocity,
orientation, and angular velocity each timestep for body
particles in the group using a Nose/Hoover temperature
thermostat. V is volume; T is temperature. This creates a system
trajectory consistent with the canonical ensemble.
This fix differs from the "fix nvt"_fix_nh.html command, which
assumes point particles and only updates their position and velocity.
The thermostat is applied to both the translational and rotational
degrees of freedom for the body particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
Additional parameters affecting the thermostat are specified by
keywords and values documented with the "fix nvt"_fix_nh.html
command. See, for example, discussion of the {temp} and {drag}
keywords.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/body", as if this command
had been issued:
compute fix-ID_temp group-ID temp/body :pre
See the "compute temp/body"_compute_temp_body.html command for
details. Note that the ID of the new compute is the fix-ID +
underscore + "temp", and the group for the new compute is the same as
the fix group.
Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.
Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual "compute
commands"_compute.html to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
:line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} 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, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. 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.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the state of the Nose/Hoover thermostat to "binary
restart files"_restart.html. See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The "fix_modify"_fix_modify.html {temp} option is supported by this
fix. You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used in its thermostatting
procedure.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes the same global scalar and global vector of
quantities as does the "fix nvt"_fix_nh.html command.
This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the
"run"_run.html command for details of how to do this.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY 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.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style body"_atom_style.html
command.
[Related commands:]
"fix nvt"_fix_nh.html, "fix nve_body"_fix_nve_body.html, "fix
npt_body"_fix_npt_body.html, "fix_modify"_fix_modify.html
[Default:] none
c4science · Help