From 28fce3b01d5ca01a6605eae501b734ed75bb9fd3 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 2 Jul 2009 17:10:13 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2955 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_example.html | 1 + doc/Section_example.txt | 1 + doc/Section_history.html | 12 +++++++----- doc/Section_history.txt | 10 ++++++---- doc/Section_intro.html | 21 +++++++++++++++++---- doc/Section_intro.txt | 15 ++++++++++++++- 6 files changed, 46 insertions(+), 14 deletions(-) diff --git a/doc/Section_example.html b/doc/Section_example.html index 6e5843434c..e683efc169 100644 --- a/doc/Section_example.html +++ b/doc/Section_example.html @@ -47,6 +47,7 @@ Site. peptide dynamics of a small solvated peptide chain (5-mer) peri Peridynamics example of cylinder hit by projectile pour pouring of granular particles into a 3d box, then chute flow +reax simple example for ReaxFF force field rigid rigid bodies modeled as independent or coupled shear sideways shear applied to 2d solid, with and without a void diff --git a/doc/Section_example.txt b/doc/Section_example.txt index 60a61f6061..4db9e70784 100644 --- a/doc/Section_example.txt +++ b/doc/Section_example.txt @@ -43,6 +43,7 @@ obstacle: flow around two voids in a 2d channel peptide: dynamics of a small solvated peptide chain (5-mer) peri: Peridynamics example of cylinder hit by projectile pour: pouring of granular particles into a 3d box, then chute flow +reax: simple example for ReaxFF force field rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void :tb(s=:) diff --git a/doc/Section_history.html b/doc/Section_history.html index fb75631d1b..ffcbaf90ba 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -31,11 +31,13 @@ GranFlow for granular materials. are being worked on; some haven't been implemented because of lack of time or interest; others are just a lot of work!

- +

Diagnostics: h4 +(fix command, compute command) +

+

see the various flavors of the fix and compute commands +

Output

(dump, restart commands) @@ -208,9 +213,9 @@ commands)

Pre- and post-processing

Our group has also written and released a separate toolkit called -Pizza.py which provides tools for doing setup, analysis, +Pizza.py which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is -written in Python and is available for download from the +written in Python and is available for download from the Pizza.py WWW site.

@@ -246,10 +251,10 @@ section. However, many people use other codes or write their own tools for these tasks.

As noted above, our group has also written and released a separate -toolkit called Pizza.py which addresses some of the listed +toolkit called Pizza.py which addresses some of the listed bullets. It provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is written in -Python and is available for download from the Pizza.py WWW +Python and is available for download from the Pizza.py WWW site.

LAMMPS requires as input a list of initial atom coordinates and types, @@ -471,6 +476,14 @@ the list.

+ + + + + + + + diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index c3009d0428..4c9546b2f9 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -191,6 +191,11 @@ Integrators :h4 rRESPA hierarchical timestepping parallel tempering (replica exchange) :ul +Diagnostics: h4 +("fix"_fix.html command, "compute"_compute.html command) + + see the various flavors of the fix and compute commands + Output :h4 ("dump"_dump.html, "restart"_restart.html commands) @@ -211,7 +216,7 @@ plotting, and visualization for LAMMPS simulations. Pizza.py is written in "Python"_python and is available for download from "the Pizza.py WWW site"_pizza. -:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html) +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) :link(python,http://www.python.org) :line @@ -457,6 +462,14 @@ the list. :link(sjp,http://www.cs.sandia.gov/~sjplimp) +compute heat/flux for Green-Kubo : Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL) +region cone : Pim Schravendijk +fix reax/bonds : Aidan Thompson (Sandia) +pair born/coul/long : Ahmed Ismail (Sandia) +fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan) +fix box/relax : Aidan Thompson and David Olmsted (Sandia) +ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT) +compute cna/atom : Wan Liang (Chinese Academy of Sciences) Tersoff/ZBL potential : Dave Farrell (Northwestern U) peridynamics : Mike Parks (Sandia) fix smd for steered MD : Axel Kohlmeyer (U Penn)
compute heat/flux for Green-Kubo Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)
region cone Pim Schravendijk
fix reax/bonds Aidan Thompson (Sandia)
pair born/coul/long Ahmed Ismail (Sandia)
fix ttm Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
fix box/relax Aidan Thompson and David Olmsted (Sandia)
ReaxFF potential Aidan Thompson (Sandia) and Hansohl Cho (MIT)
compute cna/atom Wan Liang (Chinese Academy of Sciences)
Tersoff/ZBL potential Dave Farrell (Northwestern U)
peridynamics Mike Parks (Sandia)
fix smd for steered MD Axel Kohlmeyer (U Penn)