From d23788831c8833ed78b1bb603ad417e021af98d2 Mon Sep 17 00:00:00 2001
From: Trung Nguyen <ndactrung@gmail.com>
Date: Tue, 17 Jul 2018 10:54:05 -0500
Subject: [PATCH] Updated to the doc pages of body rounded/polygon and
rounded/polyhedra and the pair style: + added examples for special cases with
disks and rods for 2d, and spheres and rods for 3d, + corrected the
definition of the cutoff distance in pair style command
---
doc/src/body.txt | 38 +++++++++++++++++++-
doc/src/pair_body_rounded_polygon.txt | 45 +++++++++++++-----------
doc/src/pair_body_rounded_polyhedron.txt | 18 ++++------
3 files changed, 68 insertions(+), 33 deletions(-)
diff --git a/doc/src/body.txt b/doc/src/body.txt
index be5b3d4edf..85095f7fb6 100644
--- a/doc/src/body.txt
+++ b/doc/src/body.txt
@@ -238,7 +238,7 @@ For example, the following information would specify a square particle
whose edge length is sqrt(2) and rounded diameter is 1.0. The
orientation of the square is aligned with the xy coordinate axes which
is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
-1 1 4 0 0 0.
+1 1 4 0 0 0. Note that only Izz matters in 2D simulations.
3 1 27
4
@@ -253,6 +253,24 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
3 0
1.0 :pre
+A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends
+by circles of diameter 0.5, is specified as follows:
+
+1 1 13
+2
+1 1 1.33333 0 0 0
+-2 0 0
+2 0 0
+0.5 :pre
+
+A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
+
+1 1 10
+1
+1 1 4.5 0 0 0
+0 0 0
+3.0 :pre
+
The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html
command can be used with this body style to compute body/body
interactions. The "fix wall/body/polygon"_fix_wall_body_polygon.html
@@ -377,6 +395,24 @@ iyz = 0.667 0.667 0.667 0 0 0.
3 0 4 7
0.5 :pre
+A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends
+by circles of diameter 0.5, is specified as follows:
+
+1 1 13
+2
+0 1.33333 1.33333 0 0 0
+-2 0 0
+2 0 0
+0.5 :pre
+
+A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
+
+1 1 10
+1
+0.9 0.9 0.9 0 0 0
+0 0 0
+3.0 :pre
+
The "pair_style
body/rounded/polhedron"_pair_body_rounded_polyhedron.html command can
be used with this body style to compute body/body interactions. The
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index 588a7d6ff9..b4135a4065 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -29,9 +29,10 @@ pair_coeff 1 1 100.0 1.0 :pre
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. See "Section 6.14"_Section_howto.html#howto_14 of the
+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 particles.
+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
@@ -50,14 +51,8 @@ between two particles are defined with respect to the separation of
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 should
-be large enough to encompass the center-to-center distance between two
-particles (at any orientation) which would produce an overlap of the
-two surfaces. For example, consider two square particles with edge
-length = 1.0 and circle diameter 0.2. The maximum distance of one
-polygon's surface from its center is not sqrt(2)/2, but
-(sqrt(2)+0.1)/2. Thus the cutoff distance should be sqrt(2) + 0.1,
-since the surfaces of two particles that far apart could be touching.
+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).
The forces between vertex-vertex, vertex-edge, and edge-edge overlaps
are given by:
@@ -66,17 +61,6 @@ are given by:
:c,image(JPG/pair_body_rounded.jpg)
-In "Fraige"_#Fraige, the tangential friction force between two
-particles that are in contact is modeled differently prior to gross
-sliding (i.e. static friction) and during gross-sliding (kinetic
-friction). The latter takes place when the tangential deformation
-exceeds the Coulomb frictional limit. In the current implementation,
-however, we do not take into account frictional history, i.e. we do
-not keep track of how many time steps the two particles have been in
-contact nor calculate the tangential deformation. Instead, we assume
-that gross sliding takes place as soon as two particles are in
-contact.
-
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 +
@@ -89,6 +73,25 @@ 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?
+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
+sliding (i.e. static friction) and during gross-sliding (kinetic
+friction). The latter takes place when the tangential deformation
+exceeds the Coulomb frictional limit. In the current implementation,
+however, we do not take into account frictional history, i.e. we do
+not keep track of how many time steps the two particles have been in
+contact nor calculate the tangential deformation. Instead, we assume
+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:
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt
index 621254bd72..3f0a2403d0 100644
--- a/doc/src/pair_body_rounded_polyhedron.txt
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -29,9 +29,10 @@ pair_coeff 1 1 100.0 1.0 :pre
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. See "Section 6.14"_Section_howto.html#howto_14 of
+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 particles.
+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
@@ -47,7 +48,7 @@ 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.
-This pairwise interaction between rounded polyhedra is described in
+This pairwise interaction between the rounded polyhedra is described in
"Wang"_#Wang, where a polyhedron does not have sharp corners and
edges, but is rounded at its vertices and edges by spheres centered on
each vertex with a specified diameter. The edges if the polyhedron
@@ -57,6 +58,7 @@ in the data file read by the "read data"_read_data.html command. This
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
@@ -64,14 +66,8 @@ and energies between two particles are defined with respect to the
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 should
-be large enough to encompass the center-to-center distance between two
-particles (at any orientation) which would produce a surface-surface
-overlap. For example, consider two cubic particles with edge length =
-1.0 and sphere diameter 0.2. The maximum distance of one polygon's
-surface from its center is not sqrt(3)/2, but (sqrt(3)+0.1)/2. Thus
-the cutoff distance should be sqrt(3) + 0.1, since the surfaces of two
-particles that far apart could be touching.
+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).
The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge,
and edge-face overlaps are given by:
--
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