r27152 - /trunk/user_functions/structure.py -- December 22, 2014 - 10:56

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.")