From 6b9637eaa3277e134f3d717990966fe03395dfb4 Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Sat, 26 May 2018 12:34:07 -0500
Subject: [PATCH] Added doc page for pair body rounded/polyhedron and updated
related pages
---
doc/src/body.txt | 58 +++++++++++---------
doc/src/pair_body_rounded_polygon.txt | 14 +++--
doc/src/pair_body_rounded_polyhedron.txt | 67 ++++++++++++++++++++++++
3 files changed, 110 insertions(+), 29 deletions(-)
create mode 100644 doc/src/pair_body_rounded_polyhedron.txt
diff --git a/doc/src/body.txt b/doc/src/body.txt
index b76ca1090c..e936f5409c 100644
--- a/doc/src/body.txt
+++ b/doc/src/body.txt
@@ -240,34 +240,14 @@ The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html
command can be used with this body style to compute body/body
interactions.
-For output purposes via the "compute
-body/local"_compute_body_local.html and "dump local"_dump.html
-commands, this body style produces one datum for each of the N
-sub-particles in a body particle. The datum has 3 values:
-
-1 = x position of vertex
-2 = y position of vertex
-3 = z position of vertex :pre
-
-These values are the current position of the vertex within the
-simulation domain, not a displacement from the center-of-mass (COM) of
-the body particle itself. These values are calculated using the
-current COM and orientation of the body particle.
+:line
-For images created by the "dump image"_dump_image.html command, if the
-{body} keyword is set, then each body particle is drawn as a polygon
-consisting of N line segments. Note that the line segments
-are drawn between the N vertices, which does not correspond exactly to
-the physical extent of the body (because the "pair_style
-rounded/polygon"_pair_body_rounded_polygon.html defines finite-size
-spheres at those point and the line segments between the spheres are
-tangent to the spheres). The drawn diameter of each line segment is
-determined by the {bflag1} parameter for the {body} keyword. The
-{bflag2} argument is ignored.
+[Specifics of body style rounded/polyhedron:]
-The {rounded/polyhedon} body style represents body particles as
+The {rounded/polyhedron} body style represents body particles as
a polyhedron with N vertices, E edges and F faces.
Special cases for N = 1 (spheres) and N = 2 (rods) are also valid.
+This body style is for 3d discrete element models, as described in "Wang"_#Wang.
Similar to body style {rounded/polygon}, the atom_style body command for this body
style takes two additional arguments:
@@ -313,6 +293,36 @@ For triangular faces, the last index should be set to -1.
:line
+For output purposes via the "compute
+body/local"_compute_body_local.html and "dump local"_dump.html
+commands, this body style produces one datum for each of the N
+sub-particles in a body particle. The datum has 3 values:
+
+1 = x position of vertex
+2 = y position of vertex
+3 = z position of vertex :pre
+
+These values are the current position of the vertex within the
+simulation domain, not a displacement from the center-of-mass (COM) of
+the body particle itself. These values are calculated using the
+current COM and orientation of the body particle.
+
+For images created by the "dump image"_dump_image.html command, if the
+{body} keyword is set, then each body particle is drawn as a polygon
+consisting of N line segments. Note that the line segments
+are drawn between the N vertices, which does not correspond exactly to
+the physical extent of the body (because the "pair_style
+rounded/polygon"_pair_body_rounded_polygon.html defines finite-size
+spheres at those point and the line segments between the spheres are
+tangent to the spheres). The drawn diameter of each line segment is
+determined by the {bflag1} parameter for the {body} keyword. The
+{bflag2} argument is ignored.
+
+:line
+
:link(Fraige)
[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
Particuology, 6, 455 (2008).
+
+:link(Wang)
+[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011).
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index 32f698d9f7..5352f695b0 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -11,15 +11,16 @@ pair_style body/rounded/polygon command :h3
[Syntax:]
pair_style body/rounded/polygon c_n c_t mu delta_ua cutoff :pre
+
c_n = normal damping coefficient
c_t = tangential damping coefficient
mu = normal friction coefficient during gross sliding
delta_ua = multiple contact scaling factor
-cutoff = global sepration cutoff for interactions (distance units), see below for definition
+cutoff = global sepration cutoff for interactions (distance units), see below for definition :pre
[Examples:]
-pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cutoff}
+pair_style body/rounded/polygon 20.0 5.0 0.0 1.0 0.5
pair_coeff * * 100.0 1.0
pair_coeff 1 1 100.0 1.0 :pre
@@ -36,12 +37,13 @@ which is specified as an argument to the "atom-style body" command.
See the "body/rounded/polygon"_body.html doc page for more details about the body
styles LAMMPS supports. The pairwise interaction between the rounded polygons is described
in "Fraige"_#Fraige, where the polygons are rounded at the vertices and edges
-by circles of diameter a.
+by circles of diameter a. This is a version of discrete element models (DEM)
+with multiple contact points.
Because the polygons can have different rounded diameters, the cutoff specified in
the pair style command is for the surface separation between two interacting entities
(e.g. vertex-vertex, vertex-edge or edge-edge) excluding their rounded diameters,
-i.e. separation = center-center distance - (rounded diameter of i + rounded diameter of j)/2.
+i.e. separation = center-center distance - (rounded diameter of entity i + rounded diameter of entity j)/2.
The interaction forces and energies are also defined with respect to the rounded surface separation,
instead of center-center distance.
@@ -56,10 +58,12 @@ k_na (energy/distance^2) :ul
[Related commands:]
-"pair_style body"_pair_body.html
+"pair_coeff"_pair_coeff.html
[Default:] none
:link(Fraige)
[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
Particuology, 6, 455 (2008).
+
+
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt
new file mode 100644
index 0000000000..cfab0e6d15
--- /dev/null
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -0,0 +1,67 @@
+"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
+
+pair_style body/rounded/polyhedron command :h3
+
+[Syntax:]
+
+pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff :pre
+
+c_n = normal damping coefficient
+c_t = tangential damping coefficient
+mu = normal friction coefficient during gross sliding
+delta_ua = multiple contact scaling factor
+cutoff = global sepration cutoff for interactions (distance units), see below for definition :pre
+
+[Examples:]
+
+pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5
+pair_coeff * * 100.0 1.0
+pair_coeff 1 1 100.0 1.0 :pre
+
+[Description:]
+
+Style {body/rounded/polyhedron} 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.
+
+This pair style is designed for use with the "body/rounded/polyhedron" body style,
+which is specified as an argument to the "atom-style body" command.
+See the "body/rounded/polyhedron"_body.html doc page for more details about the body
+styles LAMMPS supports. The pairwise interaction between the rounded polygons is described
+in "Wang"_#Wang, where the polygons are rounded at the vertices and edges
+by circles of diameter a. This is a version of discrete element models (DEM)
+with multiple contact points.
+
+Because the polygons can have different rounded diameters, the cutoff specified in
+the pair style command is for the surface separation between two interacting entities
+(e.g. vertex-vertex, vertex-edge, vertex-face and edge-edge) excluding their rounded diameters,
+i.e. separation = center-center distance - (rounded diameter of entity i + rounded diameter of entity j)/2.
+The interaction forces and energies are also defined with respect to the rounded surface separation,
+instead of center-center distance.
+
+For style {body/rounded/polyhedron}, the following coefficients must be defined for each
+pair of atoms types via the "pair_coeff"_pair_coeff.html command as in
+the examples above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+k_n (energy/distance^2)
+k_na (energy/distance^2) :ul
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:link(Wang)
+[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011).
+
--
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