Author: bugman
Date: Tue Dec 23 11:07:45 2014
New Revision: 27153
URL: http://svn.gna.org/viewcvs/relax?rev=27153&view=rev
Log:
Fix for the parallax shift description in the structure.atomic_fluctuations
user function.
The parallax shift is not quite orthogonal to the distance fluctuations.
Modified:
trunk/user_functions/structure.py
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27153&r1=27152&r2=27153&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Tue Dec 23 11:07:45 2014
@@ -341,7 +341,7 @@
uf.desc[-1].add_paragraph("This is used to visualise the interatomic
fluctuations between different structures. By setting the measure argument,
different categories of fluctuations can seen:")
uf.desc[-1].add_item_list_element("'distance'", "The interatomic distance
fluctuations is the default option. The corrected sample standard deviation
(SD) is calculated for the distances between all atom pairs, resulting in a
pairwise matrix of SD values. This is frame independent and hence is
superimposition independent.")
uf.desc[-1].add_item_list_element("'angle'", "The interatomic vector angle
fluctuations. The corrected sample standard deviation (SD) is calculated for
the angles between the inter atom vectors all atom pairs to an average vector.
This also produces a pairwise matrix of SD values.")
-uf.desc[-1].add_item_list_element("'parallax shift'", "The interatomic
parallax shift fluctuations. The corrected sample standard deviation (SD) is
calculated for the parallax shift between the inter atom vectors all atom pairs
to an average vector. This also produces a pairwise matrix of SD values. The
parallax shift is calculated as the dot product of the interatomic vector and
the unit average vector, times the unit average vector. It is a frame and
superimposition dependent measure orthogonal to the interatomic distance
fluctuations. It is similar to the angle measure however, importantly, it is
independent of the distance between the two atoms.")
+uf.desc[-1].add_item_list_element("'parallax shift'", "The interatomic
parallax shift fluctuations. The corrected sample standard deviation (SD) is
calculated for the parallax shift between the inter atom vectors all atom pairs
to an average vector. This also produces a pairwise matrix of SD values. The
parallax shift is calculated as the dot product of the interatomic vector and
the unit average vector, times the unit average vector. It is a frame and
superimposition dependent measure close to orthogonal to the interatomic
distance fluctuations. It is similar to the angle measure however,
importantly, it is independent of the distance between the two atoms.")
uf.desc[-1].add_paragraph("For the output file, the currently supported
formats are:")
uf.desc[-1].add_item_list_element("'text'", "This is the default value and
will result in a single text file being created.")
uf.desc[-1].add_item_list_element("'gnuplot'", "This will create a both a text
file with the data and a script for visualising the correlation matrix using
gnuplot. The script will have the same name as the text file, however the file
extension will be changed to *.gnu.")
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