One more thing...
Could I do something like a Jmol script that somehow pulls out the
heats of formation, puts them into an array, then returns that array
or is this something that I can do in Javascript?
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***********************************************
On Oct 22, 2008, at 4:03 PM, Jeff Hansen wrote:
I've still got questions. Ok. I understand I need to do this
differently for different filetypes. If I use a Spartan .smol I can
use the following to get the zeropoint energy:
function getEnergy() {
var _jmolText = document.getElementById('jmolText');
var Energy =
jmolGetPropertyAsString("auxiliaryInfo.zeropoint",divInc); //divInc
is a variable telling which of several applets to use
// var Energy =
jmolEvaluate('getProperty("auxiliaryInfo.zeropoint")',divInc);
var text = "Energy = " + Energy + " kJ/mol\n";
var node = document.createTextNode(text);
_jmolText.appendChild(node);
}
Please note the line that is commented out. That line doesn't
work. It returns an error message.
If I use a Spartan .spartan file it reports an E_Kcal (whatever that
is) which I can also get using similar code.
If I use a .xyz file also exported from Spartan it contains a HEAT
OF FORMATION. I've copied a portion of the auxiliaryInfo below to
show this. I can't figure out how to pull that data out. This is
the file format I would probably most like to use as I can output a
multiple model .xyz file from Spartan relatively easily.
'models' ... '0' ... 'modelName' => "Profile.1
HEAT OF FORMATION = -5.07597 KCAL = -21.23787 KJ"
'fileType' => "xyz" 'modelNumberDotted' =>
"1.1" 'modelFileNumber' => "1000001"
'modelNumber' => "1" 'fileName' => "file:/Users/jeffhans/
Sites/Jmol/jmol/Models/n-butane.xyz"
So I have two questions. First, how to get the heat of formation
number out. Second, how to tell the applet which model to get the
energy of.
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***********************************************
On Oct 20, 2008, at 2:06 PM, Robert Hanson wrote:
Right -- it depends upon the file type. I would use the one the
originating program reports.
On Mon, Oct 20, 2008 at 11:58 AM, Jeff Hansen <[EMAIL PROTECTED]>
wrote:
I've gotten myself to a point where I need a little help. What I
would like to do is load a multiple model file into Jmol then pull
out
of the file the energy of each model. Here is the function I have so
far:
function getEnergy() {
var _jmolText = document.getElementById('jmolText');
var model = divInc + ".0";
var Energy =
jmolEvaluate('getProperty("auxiliaryInfo.zeropoint")',divInc);
var text = "Energy = " + Energy + " kJ/mol\n";
var node = document.createTextNode(text);
_jmolText.appendChild(node);
}
I guess I have two questions. First, this function is getting the
zero point energy, but when I look at all the auxiliary info there
are
other things that look like energy like E_KCAL or HEAT OF FORMATION.
What is there depends on the file type. So I'm asking which of these
do you think I should use? It is probably going to vary depending
on
file type because different filetypes have different one's of these.
I'm sure I'm showing my ignorance here, but I don't really understand
the differences between all of these. Second, the code above gets
one
value of the zeropoint energy. I need to get a different energy for
each model in the file. My code says which Jmol applet to get it
from, but how do I tell it which model of that file to get the energy
of?
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***********************************************
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