Laurence, one more thought on this, which I missed on first reading your
message. Jmol reading of XYZ formatted files can support unit cells and
space groups. This is an important feature of the LOAD command -- that you
can specify spacegroup and unit cell when loading data, regardless of the
file
I let you know; I'll get some of my students (if they do what I ask
which is not always true) to do something for my group web pages. The
"bigger" Wien2k community is only starting to use jmol, but I expect
there will be examples and I'll let you know if/when I run across
some.
On 5/23/09, Robert
that's what I figured. The key for you is to introduce enough slop in the
loadAtomDataTolerance parameter to get the job done. Since you don't have
the issue of disordered crystals, you can be quite generous there -- 0.5
Angstroms easily. In other situations people will need to have a much
tighter
I did not get back to you yesterday -- proposals.
The difference between the vibration positions in the xyz file and the
atom positions in SrTiO3.struct is "right", not a concern. More
explanation than you want. SrTiO3 is only cubic in an average sense at
room temperature; really it is dynamically
I've changed the tolerance for this and added more functionality. See
http://chemapps.stolaf.edu/jmol/docs/#loadproperty
Laurence, you will need to do something like:
set loadAtomDataTolerance 0.2
because your vib data don't match the struct file data more precisely than
that.
Bob
On Fri, Ma
OK, Laurence. Check out
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and associated
files. The idea is that now anyone can load vibration information from any
file format supporting that by just adding the "VIBRATION" keyword to the
load command.
The command is:
load VIBRATION "file
N.B., for the example I sent there may be a slight drift (i.e.
vibration is not about the center-of-mass). This is due to numerical
issues in the DFT which I have to work around (later).
On Thu, May 21, 2009 at 6:09 PM, Laurence Marks
wrote:
> Works nicely, although that's not the best example be
Works nicely, although that's not the best example because it will
only ever load packed! Not a problem.
On Thu, May 21, 2009 at 6:01 PM, Laurence Marks
wrote:
> Actually, SrTiO3 is very strange, goes unstable by very small amounts
> with soft vibrations (phonons).
>
> Your too quick for me, I'm
Actually, SrTiO3 is very strange, goes unstable by very small amounts
with soft vibrations (phonons).
Your too quick for me, I'm only just testing that I have the right jar
for the #jmolsript: at the end of Wien2k, so it may be a bit before I
respond sensibly to your earlier email!
On Thu, May 21
Naive comment:
If the Strontium atoms are the massive ones, wouldn't the oxygens be the
ones that move?
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first w
Oh, it's your lucky day. Try this:
function applyVibData(filename)
vibdata = load(filename)
S = vibdata.split()
myscript = ""
for (var i = 3; i <= S.size; i=i+1)
var line = S[i]
if (line.size < 35)
break
endif
# change the numbers below to match your file format
that's up at http://chemapps.stolaf.edu/jmol/docs/examples-11
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers & brand creativity professionals. Meet
the minds b
you want
jmolscript: {within(-0.1, atomno=1)}.vxy=...
there to pick up all unit cells.
OK, I have set it up so that
#jmolscript: .
will be read at the end of wien2k files. So, for example,
#jmolscript: load "" {1 1 1} PACKED
at the end of the file automatically loads a fully packed uni
The attached (if it makes it through sourceforge) may help understand
the point; the file shows the first 9 phonon modes for SrTiO3 (not
quite accurate, the calculation is still running) for a 2x2x2
replication of the cell. In terms of general code I would like to have
anyone who does this calculat
I was thinking about asking you to add the jmolscript protocol to
Wien2k; anything after the final symmetry element matrices is ignored,
so could go there. (There is no slack before.)
It looks like if I add (via code) a set of lines
#jmolscript: {atomno=1}.vxy=...
#jmolscript: {atomno=2}.vxy=...
Ah, but what you can do is this:
Within the file have the embedded command:
jmolscript: load "" { 1 1 1 } packed
This says "reload me with those parameters". Now, the problem might be that
the wien2k reader does not have that enabled. You would have to decide where
you would find room for that,
On Thu, May 21, 2009 at 8:59 AM, Laurence Marks wrote:
> I managed to load TiO.struct and set the vibrations for the Ti, and it
> is there for all equivalent sites so this works fine. (The button at
> the top is fine; the right-mouse click does not show vibrations as an
> option.)
>
> However, I c
I found an example on a web page on how to use jmolscript in a cif
(probably should be documented better). Works fine for a cif file
although it's technically wrong; the symmetry operations should be
applied to the vibrations. I'll play around with adding vibrations to
a cif file, and making an xyz
I managed to load TiO.struct and set the vibrations for the Ti, and it
is there for all equivalent sites so this works fine. (The button at
the top is fine; the right-mouse click does not show vibrations as an
option.)
However, I could not find a way to alter the number of unit cells
being shown w
The Jmol application probably does have some minor issues there. I'm not
sure if you load vibrational data by script, for example, that the vibration
button works. Most of us use the console. But should that be the case, then
a bug report should be filed so I can get to it.
If you have implemented
Laurence Marks wrote:
> When I attempted to do this it looked like this is not currently
> supported (the vibrations button was inactive)
I would say that is because the loaded file has no vibrations.
If you add the vibrations by scripting, the menus will probably not
be updated. Don't know if
Let me be a bit more specific. I have implemented vibrations using an
xyz file, but since this does not contain the crystal lattice
information cell repeats have to be done ahead of time. What I would
like to do is for a crystal (cif, Wien2k, other) add vibrations
(probably with a script) and then
Laurence,
Vibrations generally come into Jmol via file reading. Several types of file
(xyz, GAMESS, Gaussian, Spartan, CAChe, etc.) support vibrational data. The
other way you can add vibrational data is via the script
{x}.vxyz = {vx vy vz}
Where {x} is some atom description. For example
Are vibrations implimented for crystalline structures (as against
molecules)? If so, for which types. Thanks
--
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 4
I would like to use the scale factor for vibrations to demonstrate
the classical turning points of a vibration.
I am not sure how to read the documentation: "Adjusts the scale of
the vector independently of the vibration motion"
Does a scale factor of 1.0 simply scale each vector by 1.0, or is
> Hens,
>
> Miguel recently showed how XYZ files could be augmented to include force
> vectors. (I haven't tried this myself.) That is by far the most compact
> format one could use.
The 'vibration' commands will give a sinusoidal *animation* of force vectors.
To add force vectors to the atoms i
Hens,
Miguel recently showed how XYZ files could be augmented to include force
vectors. (I haven't tried this myself.) That is by far the most compact format
one could use. For the format of the animation commmand, see:
http://www.stolaf.edu/people/hansonr/jmol/docs/#.animation
(Is http://www.st
> Colleagues,
>
> To return to a familiar subject: visualization of vibrations.
> In Chime I used multipleXYZ files, written out by MOLDEN for a
> particular vibration and as calculated by Gaussian, MOPAC, etc.
> In Jmol I can still animate these mXYZ file, however the animation
> doesn't run smo
Colleagues,
To return to a familiar subject: visualization of vibrations.
In Chime I used multipleXYZ files, written out by MOLDEN for a
particular vibration and as calculated by Gaussian, MOPAC, etc.
In Jmol I can still animate these mXYZ file, however the animation
doesn't run smoothly.
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