DOC files for USER-EES

txt doc files for fix_wall_ees and fix_wall_region_ees added.

doc/src/fix_wall_ees.txt

@@ -0,0 +1,102 @@
+"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
+
+
+[Syntax:]
+
+fix ID group-ID wall/ees face args ... keyword value ... :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
+    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
+zero or more keyword/value pairs may be appended :l
+keyword = {units} or {fld} :l
+  {units} value = {lattice} or {box}
+    {lattice} = the wall position is defined in lattice units
+    {box} = the wall position is defined in simulation box units
+  {fld} value = {yes} or {no}
+    {yes} = invoke the wall constraint to be compatible with implicit FLD
+    {no} = invoke the wall constraint in the normal way
+  {pbc} value = {yes} or {no}
+    {yes} = allow periodic boundary in a wall dimension
+    {no} = require non-perioidic boundaries in any wall dimension :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
+
+[Description:]
+ 
+Bound 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. 
+ 
+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). 
+ 
+[Restrictions:] none
+
+[Related commands:]
+
+"fix wall"_fix_wall.html,
+"pair resquared"_pair_resquared.html
+
+[Default:]
+
+The option defaults units = lattice, fld = no, and pbc = no.
+
+:line
+
+:link(BabadiEjtehadi)
+[(Babadi)] Babadi and Ejtehadi, EPL, 77 (2007) 23002.
+:link(Babadi)
+[(Berardi)] Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).

doc/src/fix_wall_region_ees.txt

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+"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/region/ees command :h3
+
+[Syntax:]
+
+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
+
+[Examples:]o
+o
+fix wall all wall/region/ees mySphere 1.0 1.0 2.5 :pre
+
+[Description:]
+
+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 "fix wall/ees"_fix_wall_ees.html.
+
+Other details of this command is the same wiht "fix wall/region"_fix_wall_region.html command. 
+
+[Restrictions:] none
+
+[Related commands:]
+
+"fix wall/lj93"_fix_wall.html,
+"fix wall/ees"_fix_wall_ees.html
+
+[Default:] none