From a861dbf434c3c58789896b6acd409b91fa31b5d0 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 31 Jan 2013 21:59:03 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9362 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_howto.html | 5 +- doc/Section_howto.txt | 5 +- doc/atom_style.html | 6 +- doc/atom_style.txt | 6 +- doc/body.html | 170 +++++++++++++++++++++++++++++++---------- doc/body.txt | 158 ++++++++++++++++++++++++++++---------- 6 files changed, 261 insertions(+), 89 deletions(-) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 385c605a0e..a02cbd977b 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1032,7 +1032,7 @@ particles. The following aspects are discussed in turn:

Example input scripts for these kinds of models are in the body, colloid, dipole, ellipse, line, peri, pour, and tri directories of the -examples directory in the LAMMPS distribution. +examples directory in the LAMMPS distribution.

Atom styles
@@ -1204,6 +1204,7 @@ particles:

Attributes include the dipole moment, the angular velocity, the @@ -1368,7 +1369,7 @@ command.

Fixes that write output files
-

Sevarl fixes take various quantities as input and can write output +

Several fixes take various quantities as input and can write output files: fix ave/time, fix ave/spatial, fix ave/histo, fix ave/correlate, and fix diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 7b6759d66b..00935f3215 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1023,7 +1023,7 @@ rigid bodies composed of finite-size particles :ul Example input scripts for these kinds of models are in the body, colloid, dipole, ellipse, line, peri, pour, and tri directories of the -"examples directory"_Section_examples.html in the LAMMPS distribution. +"examples directory"_Section_example.html in the LAMMPS distribution. Atom styles :h5 @@ -1195,6 +1195,7 @@ particles: "dump custom"_dump.html "compute property/atom"_compute_property_atom.html +"dump local"_dump.html "compute body/local"_compute_body_local.html :ul Attributes include the dipole moment, the angular velocity, the @@ -1357,7 +1358,7 @@ command. Fixes that write output files :h5,link(fixoutput) -Sevarl fixes take various quantities as input and can write output +Several fixes take various quantities as input and can write output files: "fix ave/time"_fix_ave_time.html, "fix ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html, "fix ave/correlate"_fix_ave_correlate.html, and "fix diff --git a/doc/atom_style.html b/doc/atom_style.html index 30bd56155b..3673214fbc 100644 --- a/doc/atom_style.html +++ b/doc/atom_style.html @@ -18,10 +18,10 @@ 

  args = none for any style except body and hybrid
-  body args = bstyle Nmin Nmax
+  body args = bstyle bstyle-args
     bstyle = style of body particles
-    Nmin = minimum # of sub-particles in any body
-    Nmax = maximum # of sub-particles in any body
+    bstyle-args = additional arguments specific to the bstyle
+                  see the body doc page for details
   hybrid args = list of one or more sub-styles, each with their args

Examples: diff --git a/doc/atom_style.txt b/doc/atom_style.txt index 0101c49092..3ecb6027d9 100644 --- a/doc/atom_style.txt +++ b/doc/atom_style.txt @@ -16,10 +16,10 @@ style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ {electron} or {ellipsoid} or {full} or {line} or {meso} or \ {molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul args = none for any style except {body} and {hybrid} - {body} args = bstyle Nmin Nmax + {body} args = bstyle bstyle-args bstyle = style of body particles - Nmin = minimum # of sub-particles in any body - Nmax = maximum # of sub-particles in any body + bstyle-args = additional arguments specific to the bstyle + see the "body"_body.html doc page for details {hybrid} args = list of one or more sub-styles, each with their args :pre [Examples:] diff --git a/doc/body.html b/doc/body.html index 94308acb73..e5297811fe 100644 --- a/doc/body.html +++ b/doc/body.html @@ -9,58 +9,148 @@

-

body particles +

Body particles

-

Description: +

Overview:

-

This doc page is not about a specific LAMMPS input script command, but -about body particles, +

This doc page is not about a LAMMPS input script command, but about +body particles, which are generalized finite-size particles. +Individual body particles can represent complex entities, such as +surface meshes of discrete points, collections of sub-particles, +deformable objects, etc. Note that other kinds of finite-size +spherical and aspherical particles are also supported by LAMMPS, such +as spheres, ellipsoids, line segments, and triangles, but they are +simpler entities that body particles. See Section_howto +14 for a general overview of all these +particle types.

-

which are a specific kind of -atom_style supported by LAMMPS -

-

These are the body styles that LAMMPS currently supports. The name in -the first column is used as the bstyle argument for atom_style body: +

Body particles are used via the atom_style body +command. It takes a body style as an argument. The current body +styles supported by LAMMPS are as follows. The name in the first +column is used as the bstyle argument for the atom_style +body command.

-
nparticle body with N sub-particles +
nparticle rigid body with N sub-particles
-

Of course, the interactions -between pairs of bodies will need to be encoded in an appropriate pair -style. +

The body style determines what attributes are stored for each body and +thus how they can be used to compute pairwise body/body or +bond/non-body (point particle) interactions. More details of each +style are described below.

-

Body particles can represent complex entities, -such as surface meshes of discrete points, collections of -sub-particles, deformable objects, etc. +

We hope to add more styles in the future. See Section_modify +12 for details on how to add a new body +style to the code.

-

By contrast, the fix rigid command constructs rigid -bodies out of multiple particles. The particles can be point -particles or finite-size particles (spheres, ellipsoids, line -segments, triangles). The particles in each rigid body interact with -each other in the usual pairwise fashion via whatever pair style is -defined. The sum of these interactions determine the total force and -torque on each rigid body, which the fix rigid -command then time integrates. +

+ +

When to use body particles:

-

Syntax: +

You should not use body particles to model a rigid body made of +simpler particles (e.g. point, sphere, ellipsoid, line segment, +triangular particles), if the interaction between pairs of rigid +bodies is just the summation of pairwise interactions between the +simpler particles. LAMMPS already supports this kind of model via the +fix rigid command. Any of the numerous pair styles +that compute interactions between simpler particles can be used. The +fix rigid command time integrates the motion of the +rigid bodies. All of the standard LAMMPS commands for thermostatting, +adding constraints, performing output, etc will operate as expected on +the simple particles.

-
atom_style style args 
-
-