From 37fff687dc1da62785cef30282110fb7ba4e8efa Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 30 Jul 2015 13:55:51 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13795 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_python.html | 8 ++++---- doc/balance.html | 6 +++--- doc/compute_saed.html | 4 ++-- doc/compute_temp_cs.html | 5 ++++- doc/compute_temp_cs.txt | 7 +++++-- doc/compute_xrd.html | 2 +- doc/create_atoms.html | 2 +- doc/dump_image.html | 4 ++-- doc/fix_balance.html | 6 +++--- doc/neb.html | 4 ++-- doc/searchindex.js | 2 +- 11 files changed, 28 insertions(+), 22 deletions(-) diff --git a/doc/Section_python.html b/doc/Section_python.html index 9894991264..0e7318a3dc 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -860,7 +860,7 @@ variables that have to match the VMD installation on your system.

source code for individual scripts for comments about what they do.

Here are screenshots of the vizplotgui_tool.py script in action for different visualization package options. Click to see larger images:

- width="25%" height="auto" alt=""/> - width="25%" height="auto" alt=""/> - width="25%" height="auto" alt=""/> - - width="25%" height="auto" alt=""/> - width="25%" height="auto" alt=""/> - reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire simulation domain or (b) manually using selected values as shown in the 2D diagram below.

-dR_Ewald thick surface of the Ewald sphere. See the example 3D intestiety data and the intersection of a [010] zone axis in the below image.

- +atom is part of. Note that atoms that are not core or shell particles +are also included in the temperature calculation (if they are in the +specified group-ID); they contribute to the total kinetic energy in +the usual way.

A kinetic energy tensor, stored as a 6-element vector, is also calculated by this compute for use in the computation of a pressure tensor. The formula for the components of the tensor is the same as diff --git a/doc/compute_temp_cs.txt b/doc/compute_temp_cs.txt index 4e880704a4..4171a09fd5 100644 --- a/doc/compute_temp_cs.txt +++ b/doc/compute_temp_cs.txt @@ -41,7 +41,7 @@ For this compute, core and shell particles are specified by two respective group IDs, which can be defined using the "group"_group.html command. The number of atoms in the two groups must be the same and there should be one bond defined between a pair -of atoms in the two groups. +of atoms in the two groups. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), @@ -49,7 +49,10 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. Note that the velocity of each core or shell atom used in the KE calculation is the velocity of the center-of-mass (COM) of the core/shell pair the -atom is part of. +atom is part of. Note that atoms that are not core or shell particles +are also included in the temperature calculation (if they are in the +specified group-ID); they contribute to the total kinetic energy in +the usual way. A kinetic energy tensor, stored as a 6-element vector, is also calculated by this compute for use in the computation of a pressure diff --git a/doc/compute_xrd.html b/doc/compute_xrd.html index 09eef38a15..52179cf86d 100644 --- a/doc/compute_xrd.html +++ b/doc/compute_xrd.html @@ -185,7 +185,7 @@ the optional LP keyword.

reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire simulation domain or (b) manually using selected values as shown in the 2D diagram below.

- -

Here are two sample images, rendered as 1024x1024 JPEG files. Click to see the full-size images:

-
width="25%" height="auto" alt=""/> - - width="25%" height="auto" alt=""/> - width="25%" height="auto" alt=""/> - neb_combine.py script run on the dump files produced by the two example input scripts in examples/neb. Click on them to see a larger image.

- width="25%" height="auto" alt=""/> -