Nico has released Jmol 11.3.27
This release adds two new features and fixes a few bugs.
vibrational vectors
-------------------
In labels, you can show the vibrational vector for an atom using
%v gives x, y, and z
%vx just x
%vy just y
%vz just z
And in Jmol math you can use
{atomno=3}.vibx
{atomno=3}.viby
{atomno=3}.vibz
So, for example, the following function returns the atoms in XYZ file
format translated by their vibrational vectors:
function getVectors(modelNumber, scaleFactor);
# return an XYZ file from a vibration;
var theatoms = {model=modelNumber};
var n = theatoms.size;
var s = "" + n + "\n";
s = s + "max vibration for model " + modelNumber + "\n";
for (var i = 1; i <= n; i=i+1);
s = s + theatoms[i].label("%e");
s = s + " " +(theatoms[i].x + theatoms[i].vx*scaleFactor);
s = s + " " +(theatoms[i].y + theatoms[i].vy*scaleFactor);
s = s + " " +(theatoms[i].z + theatoms[i].vz*scaleFactor);
s = s + "\n";
end for;
return s;
end function;
Then,
x = getVectors(3,0.1)
write VAR x "vib3a.xyz"
x = getVectors(3,-0.1)
write VAR x "vib3b.xyz"
---------------------------------------
bondOrder command
-----------------
Jmol 11.2 introduced the capability to save the state, and part of that
turns out to be the capability to define a bond order directly for a
specific bond. The "bondorder" command was designed to do this; now I'm
documenting it; Jmol 11.3.27 cleans up the command a bit.
select *
bondOrder single
really this is the same as
connect (*) (*) modify single
One difference is that the bondOrder command also
accepts numerical values. See
http://chemapps.stolaf.edu/jmol/docs/?ver=1.4&command=bondorder
Another difference is that if a set of bonds are chosen first, using
select bond ({10,11,12})
bondOrder 1.5
then bondOrder acts DIRECTLY on that set of bonds. No reference to atoms.
({0}) is the first bond. Use at your own risk!
-----------------------
bug fixes
--Function returns were broken. They are fixed now.
--When "var" was added in 11.3.23, write VAR x "myfile.xxx" broke; that
is fixed.
--The Jmol Application wasn't allowing multi-line pasting into the
console. Now it does.
--There was a problem with using atomlist[i] (where atomlist was some
set of atoms) more than once, as in a for loop, for example:
var theatoms = {model=3}
var n = theatoms.size;
for (var i = 1; i <= n; i=i+1);
print theatoms[i]
end for;
This should be fixed.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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