[Wien] R0 to big
Martin Kroeker
martin at ruby.chemie.uni-freiburg.de
Tue Aug 2 08:47:34 CEST 2011
Maurits et al.,
as far as I can tell, the wrong R0 value appears to be creeping in from
SRC_w2web/htdocs/util/structask.pl , which gets called by SRC_w2web/lib/struct.pl
when one starts the structure editor in w2web without a case.struct
file. First, it copies the case.struct template from SRC_templates,
and then it does a loop (in line 41 of structask.pl) that sets
s_r0[$i]=0.0001
for all atoms ($i) that the user wants to enter.
Much later in struct.pl is a point where these s_r0 values (there called
s_ro) are used to set the "ro" variable that it prints to the "R0=" line
in the struct file.
(This is in SRC_w2web/lib/struct.pl starting from line 308). Here we see
a check if "Z" has been set by the user - if it is empty, the code calls
the "Element()" function that sets Z according to the atomic symbol.
More importantly, Element() then goes ahead and sets R0 to the correct
value - which it takes to be 0.0001 for light, 0.00005 for medium and
0.00001 for heavy elements.
Only if you entered the Z number yourself when preparing the struct file
in the editor, the Element() routine is never called and you end up
with the 0.0001 value for all atoms. I have not tried this yet as I am
travelling, but it should be sufficient to remove the "if $s_zz[$i]==0)"
condition in line 309 of struct.pl so that this line reads just
"&Element() ;" and Element() is called regardless of Z being already set.
Martin
--
Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de
c/o Prof.Dr. Caroline Roehr
Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg
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