Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/compute_vacf.txt
e3979f61439eefficient_neuronet

Last Change
Raw File

compute_vacf.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
compute vacf command :h3
[Syntax:]
compute ID group-ID vacf :pre
ID, group-ID are documented in "compute"_compute.html command
vacf = style name of this compute command :ul
[Examples:]
compute 1 all vacf
compute 1 upper vacf :pre
[Description:]
Define a computation that calculates the velocity auto-correlation
function (VACF), averaged over a group of atoms. Each atom's
contribution to the VACF is its current velocity vector dotted into
its initial velocity vector at the time the compute was specified.
A vector of four quantites is calculated by this compute. The first 3
elements of the vector are vx * vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial
x-component of velocity for the atom. The 4th element of the vector
is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and
averaged over atoms in the group.
The integral of the VACF versus time is proportional to the diffusion
coefficient of the diffusing atoms. This can be computed in the
following manner, using the "variable trap()"_variable.html function:
compute 2 all vacf
fix 5 all vector 1 c_2[4]
variable diff equal dt*trap(f_5)
thermo_style custom step v_diff :pre
IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a "restart file"_read_restart.html,
then you should use the same ID for this compute, as in the original
run. This is so that the created fix will also have the same ID, and
thus be initialized correctly with atom velocities from the restart
file.
[Output info:]
This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The vector values are "intensive". The vector values will be in
velocity^2 "units"_units.html.
[Restrictions:] none
[Related commands:]
"compute msd"_compute_msd.html
[Default:] none
c4science · Help