Author: bugman
Date: Mon Dec 22 10:56:15 2014
New Revision: 27152
URL: http://svn.gna.org/viewcvs/relax?rev=27152&view=rev
Log:
Improved the structure.atomic_fluctuations user function documentation.
The fluctuation categories are now better explained. And the 'parallax shift'
option is now
available in the GUI.
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=27152&r1=27151&r2=27152&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Mon Dec 22 10:56:15 2014
@@ -300,8 +300,8 @@
desc_short = "measure",
desc = "The type of fluctuation to investigate. This allows for both
interatomic distance and vector angle fluctuations to be calculated.",
wiz_element_type = "combo",
- wiz_combo_choices = ["Interatomic distance fluctuations", "Interatomic
vector angle fluctuations"],
- wiz_combo_data = ["distance", "angle"]
+ wiz_combo_choices = ["Interatomic distance fluctuations", "Interatomic
vector angle fluctuations", "Interatomic parallax shift fluctuations"],
+ wiz_combo_data = ["distance", "angle", "parallax shift"]
)
uf.add_keyarg(
name = "file",
@@ -338,10 +338,10 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This is used to visualise the interatomic
fluctuations between different structures. By setting the measure argument,
this can be set to either the fluctuations of the interatomic distances or the
fluctuations of the interatomic vector angles:")
-uf.desc[-1].add_item_list_element("'distance'", "This is the default. The
corrected sample standard deviation (SD) is calculated for the distances
between all atom pairs, resulting in a pairwise matrix of SD values.")
-uf.desc[-1].add_item_list_element("'angle'", "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 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 the length of the average
vector minus the interatomic vector. It is similar to the angle measure
however, importantly, it is independent of the distance between the two atoms.")
+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_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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