forked from lijiext/lammps
update fix wall/ees and wall/region/ees file to conform more to common formatting
also fix some typos and formatting issues
This commit is contained in:
Axel Kohlmeyer
parent
423e3b6389
commit
23925b3a57
|
|
@ -7,17 +7,17 @@
|
|||
:line
|
||||
|
||||
fix wall/ees command :h3
|
||||
|
||||
fix wall/region/ees command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID wall/ees face args ... keyword value ... :pre
|
||||
fix ID group-ID style args :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
one or more face/arg pairs may be appended :l
|
||||
face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
|
||||
args = coord epsilon sigma cutoff
|
||||
style = {wall/ees} or {wall/region/ees} :l
|
||||
args for style {wall/ees}: one or more {face parameters} groups may be appended
|
||||
face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi}
|
||||
parameters = coord epsilon sigma cutoff
|
||||
coord = position of wall = EDGE or constant or variable
|
||||
EDGE = current lo or hi edge of simulation box
|
||||
constant = number like 0.0 or -30.0 (distance units)
|
||||
|
|
@ -27,60 +27,57 @@ face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
|
|||
sigma = size factor for wall-particle interaction (distance units)
|
||||
sigma can be a variable (see below)
|
||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
|
||||
:ule
|
||||
|
||||
|
||||
|
||||
fix ID group-ID wall/region/ees region-ID epsilon sigma cutoff :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
wall/region = style name of this fix command
|
||||
region-ID = region whose boundary will act as wall
|
||||
epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
|
||||
sigma = size factor for wall-particle interaction (distance units)
|
||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul
|
||||
args for style {wall/region/ees}: {region-ID} {epsilon} {sigma} {cutoff}
|
||||
region-ID = region whose boundary will act as wall
|
||||
epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
|
||||
sigma = size factor for wall-particle interaction (distance units)
|
||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box
|
||||
fix wallhi all wall/ees xhi EDGE 1.0 1.0 2.5
|
||||
fix wallhi all wall/ees v_wiggle 23.2 1.0 1.0 2.5
|
||||
fix zwalls all wall/ees zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
|
||||
fix zwalls all wall/ees zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre
|
||||
|
||||
fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 :pre
|
||||
|
||||
|
||||
[Description:]
|
||||
|
||||
"Fix wall/ees" bounds the simulation domain on one or more of its faces with a flat
|
||||
wall that interacts with the ellipsoidal atoms in the group by generating a force
|
||||
on the atom in a direction perpendicular to the wall and a torque parallel with the wall. The energy of
|
||||
|
||||
Fix {wall/ees} bounds the simulation domain on one or more of its
|
||||
faces with a flat wall that interacts with the ellipsoidal atoms in the
|
||||
group by generating a force on the atom in a direction perpendicular to
|
||||
the wall and a torque parallel with the wall. The energy of
|
||||
wall-particle interactions E is given by:
|
||||
|
||||
|
||||
|
||||
|
||||
:c,image(Eqs/fix_wall_ees.jpg)
|
||||
|
||||
|
||||
Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here, {r} is the distance from the particle to the wall at
|
||||
position {coord}, and Rc is the {cutoff} distance at which the
|
||||
particle and wall no longer interact. Also, sigma_n is the distance between center of ellipsoid and the nearest point of its surface to the wall The energy of the wall (see the image below).
|
||||
|
||||
Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here,
|
||||
{r} is the distance from the particle to the wall at position {coord},
|
||||
and Rc is the {cutoff} distance at which the particle and wall no
|
||||
longer interact. Also, sigma_n is the distance between center of
|
||||
ellipsoid and the nearest point of its surface to the wall The energy
|
||||
of the wall (see the image below).
|
||||
|
||||
:c,image(JPG/fix_wall_ees_image.jpg)
|
||||
|
||||
|
||||
Details of using this command and specifications are the same as fix/wall command. You can also find an example in USER/ees/ under examples/ directory.
|
||||
|
||||
Details of using this command and specifications are the same as
|
||||
fix/wall command. You can also find an example in USER/ees/ under
|
||||
examples/ directory.
|
||||
|
||||
The prefactor {epsilon} can be thought of as an
|
||||
effective Hamaker constant with energy units for the strength of the
|
||||
ellipsoid-wall interaction. More specifically, the {epsilon} pre-factor
|
||||
= 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon * sigma_a * sigma_b * sigma_c, where epsilon
|
||||
is the LJ parameters for the constituent LJ
|
||||
particles and sigma_a, sigma_b, and sigma_c are radii of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number density of the
|
||||
constituent particles, in the wall and ellipsoid respectively, in units
|
||||
of 1/volume.
|
||||
|
||||
= 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon
|
||||
* sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for
|
||||
the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii
|
||||
of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number
|
||||
density of the constituent particles, in the wall and ellipsoid
|
||||
respectively, in units of 1/volume.
|
||||
|
||||
NOTE: You must insure that r is always bigger than sigma_n for
|
||||
all particles in the group, or LAMMPS will generate an error. This
|
||||
means you cannot start your simulation with particles touching the wall
|
||||
|
|
@ -88,18 +85,18 @@ position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r <
|
|||
wall (r < 0).
|
||||
|
||||
|
||||
Fix {wall/region/ees} treats the surface of the geometric region defined
|
||||
by the {region-ID} as a bounding wall which interacts with nearby
|
||||
ellipsoidal particles according to the EES potential introduced above.
|
||||
|
||||
"fix wall/region/ees" treat the surface of the geometric region defined by the {region-ID}
|
||||
as a bounding wall which interacts with nearby ellipsoidal particles according to
|
||||
the EES potential introduced above.
|
||||
|
||||
Other details of this command is the same wiht "fix wall/region"_fix_wall_region.html command.
|
||||
One may also find and exapmle of using this code in USER/ees/ under examples/ directory.
|
||||
Other details of this command are the same as for the "fix
|
||||
wall/region"_fix_wall_region.html command. One may also find an example
|
||||
of using this fix in the examples/USER/misc/ees/ directory.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making
|
||||
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.
|
||||
|
||||
This fix requires that atoms be ellipsoids as defined by the
|
||||
|
|
@ -112,11 +109,9 @@ This fix requires that atoms be ellipsoids as defined by the
|
|||
|
||||
[Default:]
|
||||
|
||||
The option defaults units = lattice, fld = no, and pbc = no.
|
||||
none
|
||||
|
||||
:line
|
||||
|
||||
:link(BabadiEjtehadi)
|
||||
[(Babadi)] Babadi and Ejtehadi, EPL, 77 (2007) 23002.
|
||||
:link(Babadi)
|
||||
[(Berardi)] Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
|
||||
|
|
|
|||
Loading…
Reference in New Issue