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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 2017-07-06 14:47:44 -04:00
parent 423e3b6389
commit 23925b3a57
1 changed files with 44 additions and 49 deletions
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doc/src/fix_wall_ees.txt
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@ -7,17 +7,17 @@
:line :line
fix wall/ees command :h3 fix wall/ees command :h3
fix wall/region/ees command :h3 fix wall/region/ees command :h3
[Syntax:] [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 ID, group-ID are documented in "fix"_fix.html command :ulb,l
one or more face/arg pairs may be appended :l style = {wall/ees} or {wall/region/ees} :l
face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l args for style {wall/ees}: one or more {face parameters} groups may be appended
args = coord epsilon sigma cutoff 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 coord = position of wall = EDGE or constant or variable
EDGE = current lo or hi edge of simulation box EDGE = current lo or hi edge of simulation box
constant = number like 0.0 or -30.0 (distance units) 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 = size factor for wall-particle interaction (distance units)
sigma can be a variable (see below) sigma can be a variable (see below)
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
:ule
args for style {wall/region/ees}: {region-ID} {epsilon} {sigma} {cutoff}
region-ID = region whose boundary will act as wall
fix ID group-ID wall/region/ees region-ID epsilon sigma cutoff :pre epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
sigma = size factor for wall-particle interaction (distance units)
ID, group-ID are documented in "fix"_fix.html command cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
wall/region = style name of this fix command :ule
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
[Examples:] [Examples:]
fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box 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 xhi EDGE 1.0 1.0 2.5
fix wallhi all wall/ees v_wiggle 23.2 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 fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 :pre
[Description:] [Description:]
 
"Fix wall/ees" bounds the simulation domain on one or more of its faces with a flat Fix {wall/ees} bounds the simulation domain on one or more of its
wall that interacts with the ellipsoidal atoms in the group by generating a force faces with a flat wall that interacts with the ellipsoidal atoms in the
on the atom in a direction perpendicular to the wall and a torque parallel with the wall.  The energy of 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: wall-particle interactions E is given by:
:c,image(Eqs/fix_wall_ees.jpg) :c,image(Eqs/fix_wall_ees.jpg)
 
  Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here,
Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here, {r} is the distance from the particle to the wall at {r} is the distance from the particle to the wall at position {coord},
position {coord}, and Rc is the {cutoff} distance at which the  and Rc is the {cutoff} distance at which the  particle and wall no
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). 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) :c,image(JPG/fix_wall_ees_image.jpg)
  Details of using this command and specifications are the same as
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. fix/wall command. You can also find an example in USER/ees/ under
  examples/ directory.
The prefactor {epsilon} can be thought of as an The prefactor {epsilon} can be thought of as an
effective Hamaker constant with energy units for the strength of the effective Hamaker constant with energy units for the strength of the
ellipsoid-wall interaction.  More specifically, the {epsilon} pre-factor 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 = 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon
is the LJ parameters for the constituent LJ * sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for
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 the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii
constituent particles, in the wall and ellipsoid respectively, in units of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number
of 1/volume. 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 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 all particles in the group, or LAMMPS will generate an error.  This
means you cannot start your simulation with particles touching the wall 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). 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} Other details of this command are the same as for the "fix
as a bounding wall which interacts with nearby ellipsoidal particles according to wall/region"_fix_wall_region.html command. One may also find an example
the EES potential introduced above. of using this fix in the examples/USER/misc/ees/ directory.
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.
[Restrictions:] [Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if LAMMPS This fix is part of the USER-MISC package. It is only enabled if
was built with that package. See the "Making LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info. LAMMPS"_Section_start.html#start_3 section for more info.
This fix requires that atoms be ellipsoids as defined by the 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:] [Default:]
The option defaults units = lattice, fld = no, and pbc = no. none
:line :line
:link(BabadiEjtehadi) :link(BabadiEjtehadi)
[(Babadi)] Babadi and Ejtehadi, EPL, 77 (2007) 23002. [(Babadi)] Babadi and Ejtehadi, EPL, 77 (2007) 23002.
:link(Babadi)
[(Berardi)] Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).