From dfd40c1b70c04ac3d3a8c24c4a2e0e399aa5168b Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Wed, 18 Jul 2018 10:48:29 -0600
Subject: [PATCH] more doc tweaks
---
doc/src/body.txt | 8 ++---
doc/src/lammps.book | 6 ++--
doc/src/pair_body_rounded_polygon.txt | 10 +++---
doc/src/pair_body_rounded_polyhedron.txt | 39 ++++++++++++------------
4 files changed, 33 insertions(+), 30 deletions(-)
diff --git a/doc/src/body.txt b/doc/src/body.txt
index cef40cc643..e7baf626f5 100644
--- a/doc/src/body.txt
+++ b/doc/src/body.txt
@@ -186,7 +186,7 @@ squares with rounded circles at the vertices. Special cases for N = 1
(circle) and N = 2 (rod with rounded ends) can also be specified.
One use of this body style is for 2d discrete element models, as
-described in "Fraige"_#Fraige.
+described in "Fraige"_#body-Fraige.
Similar to body style {nparticle}, the atom_style body command for
this body style takes two additional arguments:
@@ -292,7 +292,7 @@ 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.
+"Wang"_#body-Wang.
Similar to body style {rounded/polygon}, the atom_style body command
for this body style takes two additional arguments:
@@ -447,10 +447,10 @@ determined by the {bflag1} parameter for the {body} keyword. The
:line
-:link(Fraige)
+:link(body-Fraige)
[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
Particuology, 6, 455 (2008).
-:link(Wang)
+:link(body-Wang)
[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
Matter, 13, 1 (2011).
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 0764c593f7..9c0216412b 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -280,7 +280,8 @@ fix_vector.html
fix_viscosity.html
fix_viscous.html
fix_wall.html
-fix_wall_ees.html
+fix_wall_body_polygon.html
+fix_wall_body_polyhedron.html
fix_wall_gran.html
fix_wall_gran_region.html
fix_wall_piston.html
@@ -419,8 +420,9 @@ pair_agni.html
pair_airebo.html
pair_awpmd.html
pair_beck.html
-pair_body.html
+pair_body_nparticle.html
pair_body_rounded_polygon.html
+pair_body_rounded_polyhedron.html
pair_bop.html
pair_born.html
pair_brownian.html
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index caaa0746a1..9daeb08e9a 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -35,9 +35,9 @@ body/body interactions which can include body particles modeled as
rounded/polygon particles.
This pairwise interaction between rounded polygons is described in
-"Fraige"_#Fraige, where a polygon does not have sharp corners, but is
-rounded at its vertices by circles centered on each vertex with a
-specified diameter. The edges of the polygon are defined between
+"Fraige"_#pair-Fraige, where a polygon does not have sharp corners,
+but is rounded at its vertices by circles centered on each vertex with
+a specified diameter. The edges of the polygon are defined between
pairs of adjacent vertices. The circle diameter for each polygon is
specified in the data file read by the "read data"_read_data.html
command. This is a 2d discrete element model (DEM) which allows for
@@ -79,7 +79,7 @@ Note that F_n and F_t are functions of the surface separation \delta_n
+ 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
+In "Fraige"_#pair-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
@@ -129,6 +129,6 @@ for pair interactions.
[Default:] none
-:link(Fraige)
+:link(pair-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
index 4a58e0119b..dc559feaaf 100644
--- a/doc/src/pair_body_rounded_polyhedron.txt
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -34,15 +34,15 @@ body/body interactions which can include body particles modeled as
"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
-edges, but is rounded at its vertices and edges by spheres centered on
-each vertex with a specified diameter. The edges if the polyhedron
-are defined between pairs of adjacent vertices. Its faces are defined
-by a loop of edges. The sphere diameter for each polygon is specified
-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.
+This pairwise interaction between the rounded polyhedra is described
+in "Wang"_#pair-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 are defined between pairs of adjacent vertices. Its faces
+are defined by a loop of edges. The sphere diameter for each polygon
+is specified 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,
@@ -74,15 +74,16 @@ and edge-face overlaps are given by:
:c,image(JPG/pair_body_rounded.jpg)
-In "Wang"_#Wang, 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.
+In "Wang"_#pair-Wang, 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,
@@ -123,7 +124,7 @@ for pair interactions.
[Default:] none
-:link(Wang)
+:link(pair-Wang)
[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
Matter, 13, 1 (2011).
--
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