Merge pull request #560 from aershadinia/master

EES wall potential

doc/src/Eqs/fix_wall_ees.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+E = \epsilon \left[ \frac{2  \sigma_{LJ}^{12} \left(7 r^5+14 r^3 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n < r < r_c
+$$
+
+
+\end{document}

doc/src/Section_commands.txt

@@ -734,7 +734,9 @@ package"_Section_start.html#start_3.
 "smd/wall/surface"_fix_smd_wall_surface.html,
 "temp/rescale/eff"_fix_temp_rescale_eff.html,
 "ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html :tb(c=6,ea=c)
+"ttm/mod"_fix_ttm.html
+"wall/ees"_fix_wall_ees.html
+"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
 
 :line
 

doc/src/fix_wall_ees.txt

@@ -0,0 +1,117 @@
+"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 wall/ees command :h3
+fix wall/region/ees command :h3
+
+[Syntax:]
+
+fix ID group-ID style args :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+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)
+      variable = "equal-style variable"_variable.html like v_x or v_wiggle
+    epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+      epsilon can be a variable (see below)
+    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
+
+  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 :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
+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).
+
+: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.
+
+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.
+
+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
+position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r < sigma_n) or with particles on the wrong side of the
+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.
+
+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
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+This fix requires that atoms be ellipsoids as defined by the
+"atom_style ellipsoid"_atom_style.html command.
+
+[Related commands:]
+
+"fix wall"_fix_wall.html,
+"pair resquared"_pair_resquared.html
+
+[Default:]
+
+none
+
+:line
+
+:link(BabadiEjtehadi)
+[(Babadi)] Babadi and Ejtehadi, EPL, 77 (2007) 23002.

doc/src/fixes.txt

@@ -156,6 +156,7 @@ Fixes :h1
    fix_viscosity
    fix_viscous
    fix_wall
+   fix_wall_ees
    fix_wall_gran
    fix_wall_gran_region
    fix_wall_piston

doc/src/lammps.book

@@ -282,6 +282,7 @@ fix_vector.html
 fix_viscosity.html
 fix_viscous.html
 fix_wall.html
+fix_wall_ees.html
 fix_wall_gran.html
 fix_wall_gran_region.html
 fix_wall_piston.html