more changes to new polygon/hedron docs and command names

"vector"_fix_vector.html,

"viscosity"_fix_viscosity.html,

"viscous"_fix_viscous.html,

"wall/body/polygon"_fix_wall_body_polygon.html,

"wall/body/polyhedron"_fix_wall_body_polyhedron.html,

"wall/colloid"_fix_wall.html,

"wall/gran"_fix_wall_gran.html,

"wall/gran/region"_fix_wall_gran_region.html,

"airebo (oi)"_pair_airebo.html,

"airebo/morse (oi)"_pair_airebo.html,

"beck (go)"_pair_beck.html,

"body"_pair_body.html,

"body/nparticle"_pair_body_nparticle.html,

"body/rounded/polygon"_pair_body_rounded/polygon.html,

"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,

"bop"_pair_bop.html,

"born (go)"_pair_born.html,

"born/coul/dsf"_pair_born.html,

This style can only be used for 3d models; see the

"boundary"_boundary.html command.  See the "pair_style

body/rounded/polygon" doc page for a diagram of a two 2d squares with

rounded circles at the vertices.  A 3d cube with rounded spheres

at the 8 vertices and 12 rounded edges would be similar.

TRUNG: What are the special cases allowed for 3d, if any?  Similar to

the N=1 (sphere) and N=2 (rod) special cases for 2d, descibed in

previous section.

rounded circles at the vertices.  A 3d cube with rounded spheres at

the 8 vertices and 12 rounded edges would be similar.  Special cases

for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be

specified.

This body style is for 3d discrete element models, as described in

"Wang"_#Wang.

[Syntax:]

pair_style body cutoff :pre

pair_style body/nparticle cutoff :pre

cutoff = global cutoff for interactions (distance units)

[Examples:]

pair_style body 3.0

pair_style body/nparticle 3.0

pair_coeff * * 1.0 1.0

pair_coeff 1 1 1.0 1.5 2.5 :pre

[Description:]

Style {body} is for use with body particles and calculates pairwise

body/body interactions as well as interactions between body and

point-particles.  See "Section 6.14"_Section_howto.html#howto_14

Style {body/nparticle} is for use with body particles and calculates

pairwise body/body interactions as well as interactions between body

and point-particles.  See "Section 6.14"_Section_howto.html#howto_14

of the manual and the "body"_body.html doc page for more details on

using body particles.

Style {body/rounded/polygon} is for use with 2d models of body

particles of style {rounded/polygon}.  It calculates pairwise

body/body interactions as well as interactions between body and point

particles (modeled as disks with a specified diameter).

See "Section 6.14"_Section_howto.html#howto_14 of the

manual and the "body"_body.html doc page for more details on using

body rounded/polygon particles.

body/body interactions which can include body particles modeled as

1-vertex circular disks with a specified diameter.  See "Section

6.14"_Section_howto.html#howto_14 of the manual and the

"body"_body.html doc page for more details on using body

rounded/polygon particles.

This pairwise interaction between rounded polygons is described in

"Fraige"_#Fraige, where a polygon does not have sharp corners, but is

their respective rounded surfaces, not by the separation of the

vertices and edges themselves.

This means that the specified cutoff in the pair_style command is

the cutoff distance, r_c, for the surface separation, \delta_n (see figure below).

This means that the specified cutoff in the pair_style command is the

cutoff distance, r_c, for the surface separation, \delta_n (see figure

below).  This is the distance at which two particles no longer

interact.  If r_c is specified as 0.0, then it is a contact-only

interaction.  I.e. the two particles must overlap in order to exert a

repulsive force on each other.  If r_c > 0.0, then the force between

two particles will be attractive for surface separations from 0 to

r_c, and repulsive once the particles overlap.

Note that unlike for other pair styles, the specified cutoff is not

the distance between the centers of two particles at which they stop

interacting.  This center-to-center distance depends on the shape and

size of the two particles and their relative orientation.  LAMMPS

takes that into account when computing the surface separation distance

and applying the r_c cutoff.

The forces between vertex-vertex, vertex-edge, and edge-edge overlaps

are given by:

:c,image(JPG/pair_body_rounded.jpg)

TRUNG: The diagram label "cohesive regions" confuses me.  Are you

saying there is some distance d for which the force is attractive,

i.e. the particles are cohesive?  I think when d > Ri + Rj, since Ri +

Rj is the surface/surface overlap discussed above?  If so, then the

discussion above about the specified cutoff is wrong?  I.e. you can

specify a large cutoff than the surface/surface overlap to get

cohesive interactions?  If so, this should be explained up above.

But an additional confusion is that the specied cutoff (Rc in diagram?)

is a single number, but depedning on the orientiation of the 2

particles they might have a suface/surface overlap at a much

smaller value of Ri + Rj.  So what is Rc then? - I added

the following paragraph to address this.

Note that F_n and F_t are functions of the surface separation

\delta_n = d - (R_i + R_j).

In this model, when (R_i + R_j) < d < (R_i + R_j) + r_c, that is,

0 < \delta_n < r_c, the cohesive region of the two surfaces overlap

and the two surfaces are attractive to each other.

Note that F_n and F_t are functions of the surface separation \delta_n

= d - (R_i + R_j).  In this model, when (R_i + R_j) < d < (R_i + R_j)

+ r_c, that is, 0 < \delta_n < r_c, the cohesive region of the two

surfaces overlap and the two surfaces are attractive to each other.

In "Fraige"_#Fraige, the tangential friction force between two

particles that are in contact is modeled differently prior to gross

that gross sliding takes place as soon as two particles are in

contact.

The following coefficients must be defined for each pair of atom types

via the "pair_coeff"_pair_coeff.html command as in the examples above,

or in the data file read by the "read_data"_read_data.html command:

k_na (energy/distance^2 units) :ul

Effectively, k_n and k_na are the slopes of the red lines in the plot

above for force versus surface separation, for \delta_n < 0 and 0 < \delta_n < r_c

respectively.  (TRUNG: is this sentence correct? - it should read delta_n,

instead of r)

TRUNG: reminder to copy any change in this file

to the pair polyhedron file as well (and vice versa)

above for force versus surface separation, for \delta_n < 0 and 0 <

\delta_n < r_c respectively.

[Mixing, shift, table, tail correction, restart, rRESPA info]:

Style {body/rounded/polygon} is for use with 3d models of body

particles of style {rounded/polyhedron}.  It calculates pairwise

body/body interactions as well as interactions between body and

point-particles (modeled as spheres with a specified diameter).

See "Section 6.14"_Section_howto.html#howto_14 of

the manual and the "body"_body.html doc page for more details on using

body rounded/polyhedron particles.

TRUNG: I think we need a paragraph here about how body/sphere

interactions are handled.  Does this pair style only do body/body but

allow for a body = sphere or rod or some other degenerate case?  Or

does this pair style allow you to model a simulation of mixed body and

point particles, where point particles are spheroids.  If so, does

this pair style do body/body and body/point, and you use one of the

other granular pair styles to do point/point?  I.e. a pair hybrid

model?  Or does everything have to be defined as bodies.  Actually

this paragraph would make more sense in the body.txt file about how to

create a model that includes non-body particles (spheres).  And in

this pair style file just a couple lines about which part of the

interactions this pair style computes.  Ditto in the pair body polygon

file. - The pair style supports body/sphere and sphere/sphere

given that all the atoms should be of body rounded/polyhedron.

I updated the above paragraph and added examples in body.txt for

specifying the special objects (i.e. spheres and rods).

body/body interactions which can include body particles modeled as

1-vertex spheres with a specified diameter.  See "Section

6.14"_Section_howto.html#howto_14 of the manual and the

"body"_body.html doc page for more details on using body

rounded/polyhedron particles.

This pairwise interaction between the rounded polyhedra is described in

"Wang"_#Wang, where a polyhedron does not have sharp corners and

is a discrete element model (DEM) which allows for multiple contact

points.

Note that when two particles interact, the effective surface of each

polyhedron particle is displaced outward from each of its vertices,

edges, and faces by half its sphere diameter.  The interaction forces

separation of their respective rounded surfaces, not by the separation

of the vertices, edges, and faces themselves.

This means that the specified cutoff in the pair_style command is

the cutoff distance, r_c, for the surface separation, \delta_n (see figure below).

This means that the specified cutoff in the pair_style command is the

cutoff distance, r_c, for the surface separation, \delta_n (see figure

below).  This is the distance at which two particles no longer

interact.  If r_c is specified as 0.0, then it is a contact-only

interaction.  I.e. the two particles must overlap in order to exert a

repulsive force on each other.  If r_c > 0.0, then the force between

two particles will be attractive for surface separations from 0 to

r_c, and repulsive once the particles overlap.

Note that unlike for other pair styles, the specified cutoff is not

the distance between the centers of two particles at which they stop

interacting.  This center-to-center distance depends on the shape and

size of the two particles and their relative orientation.  LAMMPS

takes that into account when computing the surface separation distance

and applying the r_c cutoff.

The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge,

and edge-face overlaps are given by:

k_na (energy/distance^2 units) :ul

Effectively, k_n and k_na are the slopes of the red lines in the plot

above for force versus surface separation, for \delta_n < 0 and 0 < \delta_n < r_c

respectively.  (TRUNG: is this sentence correct? - it should read delta_n,

instead of r)

above for force versus surface separation, for \delta_n < 0 and 0 <

\delta_n < r_c respectively.

[Mixing, shift, table, tail correction, restart, rRESPA info]: