Re: [Jmol-users] Vibrations
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 format. You might want to look into that as well. See http://chemapps.stolaf.edu/jmol/docs/#load Bob On Thu, May 21, 2009 at 7:11 AM, Laurence Marks l-ma...@northwestern.eduwrote: 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. -- 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 what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrations
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, May 22, 2009 at 2:41 PM, Robert Hanson hans...@stolaf.edu wrote:
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 filename
Jmol 11.7.37 introduces the capability to apply vibrational data from one
file to model data in another. Adding VIBRATION to the load command
instructs Jmol to load only the vibrational information from a file. The
vibrational data are applied to the currently selected set of atoms.
All standard load parameters are accepted, although many will be ignored,
however whereas the default for a normal LOAD operation is to load all
files, the default for LOAD VIBRATION is to read only the first set of
vibrational data in a multi-model file.
For each atom position and vector that is read, Jmol applies the
vibration to all selected atoms having a unit cell normalized position
within *loadAtomDataTolerance* (default 0.2) Angstroms of the position
read from the file.
If the file being loaded contains embedded Jmol script commands, those
commands will be processed after the application of the vibrational vectors.
For example,
*load myfile.struct {{5 5 1}} PACKED; select _O; load VIBRATION
vibs.xyz 3*
first loads a set of unit cells from myfile.struct, then applies only to
the oxygen atoms the third vibration set found in vibs.xyz. All oxygen atoms
in all unit cells are given vibrational vectors even though the data in
vibs.xyz might only be for one unit cell.
I'm betting this will serve your purposes nicely. I increased the default
tolerance to 0.2 Angstroms because I noticed that in the file you gave me
the O atom positions were 0.13 Angstrom off from the ones in SrTiO3.struct.
But this is now settable, so you may want to play with that.
-Bob
On Thu, May 21, 2009 at 6:20 PM, Laurence Marks
l-ma...@northwestern.eduwrote:
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
l-ma...@northwestern.edu wrote:
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
l-ma...@northwestern.edu wrote:
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, 2009 at 5:54 PM, Robert Hanson hans...@stolaf.edu
wrote:
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 what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity
professionals.
Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like
Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering to study the structure of matter.
--
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) 491-7820
email: L-marks
Re: [Jmol-users] Vibrations
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 fluctuating with soft
phonons (vibrations) being cubic only in the average structure. The
xyz file was refined (DFT) in a cubic cell and is non-symmetric, this
is right. The other SrTiO3.struct file is symmetry constrained to be
cubic, which is OK but not quite consistent with the xyz file -- there
is no need for them to be. More accurately the real (DFT) cell should
be tetragonal cell.
On 5/23/09, Robert Hanson hans...@stolaf.edu wrote:
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, May 22, 2009 at 2:41 PM, Robert Hanson hans...@stolaf.edu wrote:
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 filename
Jmol 11.7.37 introduces the capability to apply vibrational data from one
file to model data in another. Adding VIBRATION to the load command
instructs Jmol to load only the vibrational information from a file. The
vibrational data are applied to the currently selected set of atoms.
All standard load parameters are accepted, although many will be ignored,
however whereas the default for a normal LOAD operation is to load all
files, the default for LOAD VIBRATION is to read only the first set of
vibrational data in a multi-model file.
For each atom position and vector that is read, Jmol applies the
vibration to all selected atoms having a unit cell normalized position
within loadAtomDataTolerance (default 0.2) Angstroms of the position read
from the file.
If the file being loaded contains embedded Jmol script commands, those
commands will be processed after the application of the vibrational vectors.
For example,
load myfile.struct {{5 5 1}} PACKED; select _O; load VIBRATION
vibs.xyz 3
first loads a set of unit cells from myfile.struct, then applies only to
the oxygen atoms the third vibration set found in vibs.xyz. All oxygen atoms
in all unit cells are given vibrational vectors even though the data in
vibs.xyz might only be for one unit cell.
I'm betting this will serve your purposes nicely. I increased the default
tolerance to 0.2 Angstroms because I noticed that in the file you gave me
the O atom positions were 0.13 Angstrom off from the ones in SrTiO3.struct.
But this is now settable, so you may want to play with that.
-Bob
On Thu, May 21, 2009 at 6:20 PM, Laurence Marks l-ma...@northwestern.edu
wrote:
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
l-ma...@northwestern.edu wrote:
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
l-ma...@northwestern.edu wrote:
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, 2009 at 5:54 PM, Robert Hanson hans...@stolaf.edu
wrote:
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 what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity
professionals.
Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like
Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com
Re: [Jmol-users] Vibrations
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 Hanson hans...@stolaf.edu wrote:
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 tolerance. So I set the default to be on the low side -- and the
system will notify you with a warning if no atoms matched the position (a
potential problem) or a debugging message (not a problem) if more than one
did.
Since I was working on this code anyway, and it seemed like such a neat
solution, I also added the ability to add other parameters as well this way
--- occupation, partialcharge, temperature, and even atom position xyz.
There are going to be some very good applications of this. Since you already
are making .XYZ files for your vibrations, this should be just about all you
need.
I'm quite excited to see this avenue of Jmol use developing. Do show us some
cool web pages with jiggling crystals some time.
Bob
On Sat, May 23, 2009 at 8:05 AM, Laurence Marks l-ma...@northwestern.edu
wrote:
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 fluctuating with soft
phonons (vibrations) being cubic only in the average structure. The
xyz file was refined (DFT) in a cubic cell and is non-symmetric, this
is right. The other SrTiO3.struct file is symmetry constrained to be
cubic, which is OK but not quite consistent with the xyz file -- there
is no need for them to be. More accurately the real (DFT) cell should
be tetragonal cell.
On 5/23/09, Robert Hanson hans...@stolaf.edu wrote:
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, May 22, 2009 at 2:41 PM, Robert Hanson hans...@stolaf.edu
wrote:
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 filename
Jmol 11.7.37 introduces the capability to apply vibrational data from
one
file to model data in another. Adding VIBRATION to the load command
instructs Jmol to load only the vibrational information from a file. The
vibrational data are applied to the currently selected set of atoms.
All standard load parameters are accepted, although many will be
ignored,
however whereas the default for a normal LOAD operation is to load all
files, the default for LOAD VIBRATION is to read only the first set of
vibrational data in a multi-model file.
For each atom position and vector that is read, Jmol applies the
vibration to all selected atoms having a unit cell normalized position
within loadAtomDataTolerance (default 0.2) Angstroms of the position
read
from the file.
If the file being loaded contains embedded Jmol script commands, those
commands will be processed after the application of the vibrational
vectors.
For example,
load myfile.struct {{5 5 1}} PACKED; select _O; load VIBRATION
vibs.xyz 3
first loads a set of unit cells from myfile.struct, then applies only
to
the oxygen atoms the third vibration set found in vibs.xyz. All oxygen
atoms
in all unit cells are given vibrational vectors even though the data in
vibs.xyz might only be for one unit cell.
I'm betting this will serve your purposes nicely. I increased the
default
tolerance to 0.2 Angstroms because I noticed that in the file you gave
me
the O atom positions were 0.13 Angstrom off from the ones in
SrTiO3.struct.
But this is now settable, so you may want to play with that.
-Bob
On Thu, May 21, 2009 at 6:20 PM, Laurence Marks
l-ma...@northwestern.edu
wrote:
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).
[Jmol-users] Vibrations
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 display these using standard tools for repeating the unit cell etc, with the vibrations obeying the appropriate symmetry and translational operations. When I attempted to do this it looked like this is not currently supported (the vibrations button was inactive) although I might not have done it correctly and I don't think I used the console. N.B., there are some issues with the vibrations having a lower symmetry than the unit cell so strictly speaking the cell should have P1 symmetry. Walk before run; are vibrations active for crystals. N.N.B., an alternative would be to be able to add crystalline repeat information to an xyz format. -- 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) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter. -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrations
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 that can be changed, but at least you should get the vibrations working by script (e.g. from the console) -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrations
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 vibrations in an XYZ file, then that's all you need.
Just write a little Jmol script that
1) loads the Wien2k or other file with full symmetry
2) reads that xyz file into a variable using vibdata = file(yyy.xyz)
3) changes that to Jmol script format and runs it.
I think this is a few lines of Jmol script:
function applyVibData(filename)
var vibdata = load(filename)
var S = vibdata.split()
var myscript =
for (var i = 3; i = S.size; i=i+1)
var line = S[i]
# change the numbers below to match your file format -- I'm guessing
here
var x = { + (S[i])[3][45] + }
var v = { + (S[i])[48][0] + }
myscript = myscript + x= + x + ;v= + v+;{within(-2.5,x)}.vxyz =
v\n
end for
script inline @myscript
end function
Bob
On Thu, May 21, 2009 at 7:11 AM, Laurence Marks l-ma...@northwestern.eduwrote:
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 display these using standard tools
for repeating the unit cell etc, with the vibrations obeying the
appropriate symmetry and translational operations.
When I attempted to do this it looked like this is not currently
supported (the vibrations button was inactive) although I might not
have done it correctly and I don't think I used the console.
N.B., there are some issues with the vibrations having a lower
symmetry than the unit cell so strictly speaking the cell should have
P1 symmetry. Walk before run; are vibrations active for crystals.
N.N.B., an alternative would be to be able to add crystalline repeat
information to an xyz format.
--
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) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering to study the structure of matter.
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity professionals.
Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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 what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com ___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrations
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 without reloading the structure; is there a way of doing
this?
The alternative is to use embedded jmol scripting either in an xyz
file (to set the cell so, maybe {1 1 1} PACKED or similar will be
understood) or in a cif. I'll try this.
N.B., does a jmolscript: get embedded in a { } (i.e. C)?
On 5/21/09, Robert Hanson hans...@stolaf.edu wrote:
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 vibrations in an XYZ file, then that's all you need.
Just write a little Jmol script that
1) loads the Wien2k or other file with full symmetry
2) reads that xyz file into a variable using vibdata = file(yyy.xyz)
3) changes that to Jmol script format and runs it.
I think this is a few lines of Jmol script:
function applyVibData(filename)
var vibdata = load(filename)
var S = vibdata.split()
var myscript =
for (var i = 3; i = S.size; i=i+1)
var line = S[i]
# change the numbers below to match your file format -- I'm guessing
here
var x = { + (S[i])[3][45] + }
var v = { + (S[i])[48][0] + }
myscript = myscript + x= + x + ;v= + v+;{within(-2.5,x)}.vxyz =
v\n
end for
script inline @myscript
end function
Bob
On Thu, May 21, 2009 at 7:11 AM, Laurence Marks l-ma...@northwestern.edu
wrote:
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 display these using standard tools
for repeating the unit cell etc, with the vibrations obeying the
appropriate symmetry and translational operations.
When I attempted to do this it looked like this is not currently
supported (the vibrations button was inactive) although I might not
have done it correctly and I don't think I used the console.
N.B., there are some issues with the vibrations having a lower
symmetry than the unit cell so strictly speaking the cell should have
P1 symmetry. Walk before run; are vibrations active for crystals.
N.N.B., an alternative would be to be able to add crystalline repeat
information to an xyz format.
--
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) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering to study the structure of matter.
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity professionals.
Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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 what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity professionals.
Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Re: [Jmol-users] Vibrations
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 file understand translational symmetry
(probably some property, a clue with shorten my hunting.)
On Thu, May 21, 2009 at 8:59 AM, Laurence Marks
l-ma...@northwestern.edu 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 could not find a way to alter the number of unit cells
being shown without reloading the structure; is there a way of doing
this?
The alternative is to use embedded jmol scripting either in an xyz
file (to set the cell so, maybe {1 1 1} PACKED or similar will be
understood) or in a cif. I'll try this.
N.B., does a jmolscript: get embedded in a { } (i.e. C)?
On 5/21/09, Robert Hanson hans...@stolaf.edu wrote:
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 vibrations in an XYZ file, then that's all you need.
Just write a little Jmol script that
1) loads the Wien2k or other file with full symmetry
2) reads that xyz file into a variable using vibdata = file(yyy.xyz)
3) changes that to Jmol script format and runs it.
I think this is a few lines of Jmol script:
function applyVibData(filename)
var vibdata = load(filename)
var S = vibdata.split()
var myscript =
for (var i = 3; i = S.size; i=i+1)
var line = S[i]
# change the numbers below to match your file format -- I'm guessing
here
var x = { + (S[i])[3][45] + }
var v = { + (S[i])[48][0] + }
myscript = myscript + x= + x + ;v= + v+;{within(-2.5,x)}.vxyz =
v\n
end for
script inline @myscript
end function
Bob
On Thu, May 21, 2009 at 7:11 AM, Laurence Marks l-ma...@northwestern.edu
wrote:
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 display these using standard tools
for repeating the unit cell etc, with the vibrations obeying the
appropriate symmetry and translational operations.
When I attempted to do this it looked like this is not currently
supported (the vibrations button was inactive) although I might not
have done it correctly and I don't think I used the console.
N.B., there are some issues with the vibrations having a lower
symmetry than the unit cell so strictly speaking the cell should have
P1 symmetry. Walk before run; are vibrations active for crystals.
N.N.B., an alternative would be to be able to add crystalline repeat
information to an xyz format.
--
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) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering to study the structure of matter.
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity professionals.
Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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 what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity professionals.
Meet
the minds behind Google Creative Lab, Visual
Re: [Jmol-users] Vibrations
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, and then we would have to augment the reader
to look for it. How much slack does this file format have?
On Thu, May 21, 2009 at 3:23 PM, Robert Hanson hans...@stolaf.edu wrote:
On Thu, May 21, 2009 at 8:59 AM, Laurence Marks
l-ma...@northwestern.eduwrote:
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 without reloading the structure; is there a way of doing
this?
No. These are determined in the loading code and no where else. What people
do sometimes is load more than you need, then only DISPLAY the ones you
want.
The alternative is to use embedded jmol scripting either in an xyz
file (to set the cell so, maybe {1 1 1} PACKED or similar will be
understood) or in a cif. I'll try this.
Embedded scripts are run after loading, not before. It's an interesting
idea to provide some sort of load functionality within the file, but to date
we don't have that.
N.B., does a jmolscript: get embedded in a { } (i.e. C)?
There's Jmol script, Jmol math, and Jmol selection syntax. Generally @{ }
sets off math. { } sets off either coordinates or selection, depending upon
the context. What is C?
On 5/21/09, Robert Hanson hans...@stolaf.edu wrote:
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 vibrations in an XYZ file, then that's all you
need.
Just write a little Jmol script that
1) loads the Wien2k or other file with full symmetry
2) reads that xyz file into a variable using vibdata = file(yyy.xyz)
3) changes that to Jmol script format and runs it.
I think this is a few lines of Jmol script:
function applyVibData(filename)
var vibdata = load(filename)
var S = vibdata.split()
var myscript =
for (var i = 3; i = S.size; i=i+1)
var line = S[i]
# change the numbers below to match your file format -- I'm
guessing
here
var x = { + (S[i])[3][45] + }
var v = { + (S[i])[48][0] + }
myscript = myscript + x= + x + ;v= + v+;{within(-2.5,x)}.vxyz
=
v\n
end for
script inline @myscript
end function
Bob
On Thu, May 21, 2009 at 7:11 AM, Laurence Marks
l-ma...@northwestern.edu
wrote:
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 display these using standard tools
for repeating the unit cell etc, with the vibrations obeying the
appropriate symmetry and translational operations.
When I attempted to do this it looked like this is not currently
supported (the vibrations button was inactive) although I might not
have done it correctly and I don't think I used the console.
N.B., there are some issues with the vibrations having a lower
symmetry than the unit cell so strictly speaking the cell should have
P1 symmetry. Walk before run; are vibrations active for crystals.
N.N.B., an alternative would be to be able to add crystalline repeat
information to an xyz format.
--
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) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering to study the structure of matter.
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity
professionals.
Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like
Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com
___
Jmol-users mailing
Re: [Jmol-users] Vibrations
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=...
This will work so long as I reduce to P1. Fortunately I have the code
to reduce to debugged, so this is not hard (albeit not elegant). This
will enable loading with different numbers of cells and everything
should work
N.B. For your earlier email, C is c (as in gcc). It looks as
though #jmolscript: is a single line command, which is OK; I thought
it might be possible to have multiple lines with the C delinearator.
On Thu, May 21, 2009 at 3:40 PM, Robert Hanson hans...@stolaf.edu wrote:
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, and then we would have to augment the reader
to look for it. How much slack does this file format have?
On Thu, May 21, 2009 at 3:23 PM, Robert Hanson hans...@stolaf.edu wrote:
On Thu, May 21, 2009 at 8:59 AM, Laurence Marks l-ma...@northwestern.edu
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 could not find a way to alter the number of unit cells
being shown without reloading the structure; is there a way of doing
this?
No. These are determined in the loading code and no where else. What
people do sometimes is load more than you need, then only DISPLAY the ones
you want.
The alternative is to use embedded jmol scripting either in an xyz
file (to set the cell so, maybe {1 1 1} PACKED or similar will be
understood) or in a cif. I'll try this.
Embedded scripts are run after loading, not before. It's an interesting
idea to provide some sort of load functionality within the file, but to date
we don't have that.
N.B., does a jmolscript: get embedded in a { } (i.e. C)?
There's Jmol script, Jmol math, and Jmol selection syntax. Generally @{ }
sets off math. { } sets off either coordinates or selection, depending upon
the context. What is C?
On 5/21/09, Robert Hanson hans...@stolaf.edu wrote:
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 vibrations in an XYZ file, then that's all you
need.
Just write a little Jmol script that
1) loads the Wien2k or other file with full symmetry
2) reads that xyz file into a variable using vibdata = file(yyy.xyz)
3) changes that to Jmol script format and runs it.
I think this is a few lines of Jmol script:
function applyVibData(filename)
var vibdata = load(filename)
var S = vibdata.split()
var myscript =
for (var i = 3; i = S.size; i=i+1)
var line = S[i]
# change the numbers below to match your file format -- I'm
guessing
here
var x = { + (S[i])[3][45] + }
var v = { + (S[i])[48][0] + }
myscript = myscript + x= + x + ;v= +
v+;{within(-2.5,x)}.vxyz =
v\n
end for
script inline @myscript
end function
Bob
On Thu, May 21, 2009 at 7:11 AM, Laurence Marks
l-ma...@northwestern.edu
wrote:
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 display these using standard
tools
for repeating the unit cell etc, with the vibrations obeying the
appropriate symmetry and translational operations.
When I attempted to do this it looked like this is not currently
supported (the vibrations button was inactive) although I might not
have done it correctly and I don't think I used the console.
N.B., there are some issues with the vibrations having a lower
symmetry than the unit cell so strictly speaking the cell should have
P1 symmetry. Walk before run; are vibrations active for crystals.
N.N.B., an alternative would be to be able to add crystalline repeat
information to an xyz format.
--
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) 491-7820
email:
Re: [Jmol-users] Vibrations
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 calculation in the future (me, my students, others) pick how many cells they want to see etc. At the moment this has to be done at a higher level, and is user-unfriendly. -- 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) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter. STOa.v.xyz Description: Protein Databank data -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrations
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 unit cell, even
just with
load t.struct
On Thu, May 21, 2009 at 4:03 PM, Laurence Marks l-ma...@northwestern.eduwrote:
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=...
This will work so long as I reduce to P1. Fortunately I have the code
to reduce to debugged, so this is not hard (albeit not elegant). This
will enable loading with different numbers of cells and everything
should work
N.B. For your earlier email, C is c (as in gcc). It looks as
though #jmolscript: is a single line command, which is OK; I thought
it might be possible to have multiple lines with the C delinearator.
On Thu, May 21, 2009 at 3:40 PM, Robert Hanson hans...@stolaf.edu wrote:
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, and then we would have to augment the
reader
to look for it. How much slack does this file format have?
On Thu, May 21, 2009 at 3:23 PM, Robert Hanson hans...@stolaf.edu
wrote:
On Thu, May 21, 2009 at 8:59 AM, Laurence Marks
l-ma...@northwestern.edu
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 could not find a way to alter the number of unit cells
being shown without reloading the structure; is there a way of doing
this?
No. These are determined in the loading code and no where else. What
people do sometimes is load more than you need, then only DISPLAY the
ones
you want.
The alternative is to use embedded jmol scripting either in an xyz
file (to set the cell so, maybe {1 1 1} PACKED or similar will be
understood) or in a cif. I'll try this.
Embedded scripts are run after loading, not before. It's an interesting
idea to provide some sort of load functionality within the file, but to
date
we don't have that.
N.B., does a jmolscript: get embedded in a { } (i.e. C)?
There's Jmol script, Jmol math, and Jmol selection syntax. Generally @{
}
sets off math. { } sets off either coordinates or selection, depending
upon
the context. What is C?
On 5/21/09, Robert Hanson hans...@stolaf.edu wrote:
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 vibrations in an XYZ file, then that's all
you
need.
Just write a little Jmol script that
1) loads the Wien2k or other file with full symmetry
2) reads that xyz file into a variable using vibdata =
file(yyy.xyz)
3) changes that to Jmol script format and runs it.
I think this is a few lines of Jmol script:
function applyVibData(filename)
var vibdata = load(filename)
var S = vibdata.split()
var myscript =
for (var i = 3; i = S.size; i=i+1)
var line = S[i]
# change the numbers below to match your file format -- I'm
guessing
here
var x = { + (S[i])[3][45] + }
var v = { + (S[i])[48][0] + }
myscript = myscript + x= + x + ;v= +
v+;{within(-2.5,x)}.vxyz =
v\n
end for
script inline @myscript
end function
Bob
On Thu, May 21, 2009 at 7:11 AM, Laurence Marks
l-ma...@northwestern.edu
wrote:
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 display these using standard
tools
for repeating the unit cell etc, with the vibrations obeying the
appropriate symmetry and translational operations.
When I attempted to do this it looked like this is not currently
supported (the vibrations button was inactive) although I might not
have done it correctly and I don't think I used
Re: [Jmol-users] Vibrations
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 -- I'm guessing
here
var x = { + (S[i])[3][34] + }
var v = { + (S[i])[35][0] + }
var s = x= + x + ;v= + v+;{within(-0.1,x)}.vxyz = v\n
myscript = myscript + s
end for
print myscript
script inline @myscript
end function
load srtio3.struct {2 2 2} packed
applyvibdata(STOa.v.xyz)
vibration on
Once we get this worked out, we can perhaps augment the VIBRATION command to
do this sort of file loading and assignment automatically. How does that
sound?
Bob
On Thu, May 21, 2009 at 4:03 PM, Laurence Marks l-ma...@northwestern.eduwrote:
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=...
This will work so long as I reduce to P1. Fortunately I have the code
to reduce to debugged, so this is not hard (albeit not elegant). This
will enable loading with different numbers of cells and everything
should work
N.B. For your earlier email, C is c (as in gcc). It looks as
though #jmolscript: is a single line command, which is OK; I thought
it might be possible to have multiple lines with the C delinearator.
On Thu, May 21, 2009 at 3:40 PM, Robert Hanson hans...@stolaf.edu wrote:
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, and then we would have to augment the
reader
to look for it. How much slack does this file format have?
On Thu, May 21, 2009 at 3:23 PM, Robert Hanson hans...@stolaf.edu
wrote:
On Thu, May 21, 2009 at 8:59 AM, Laurence Marks
l-ma...@northwestern.edu
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 could not find a way to alter the number of unit cells
being shown without reloading the structure; is there a way of doing
this?
No. These are determined in the loading code and no where else. What
people do sometimes is load more than you need, then only DISPLAY the
ones
you want.
The alternative is to use embedded jmol scripting either in an xyz
file (to set the cell so, maybe {1 1 1} PACKED or similar will be
understood) or in a cif. I'll try this.
Embedded scripts are run after loading, not before. It's an interesting
idea to provide some sort of load functionality within the file, but to
date
we don't have that.
N.B., does a jmolscript: get embedded in a { } (i.e. C)?
There's Jmol script, Jmol math, and Jmol selection syntax. Generally @{
}
sets off math. { } sets off either coordinates or selection, depending
upon
the context. What is C?
On 5/21/09, Robert Hanson hans...@stolaf.edu wrote:
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 vibrations in an XYZ file, then that's all
you
need.
Just write a little Jmol script that
1) loads the Wien2k or other file with full symmetry
2) reads that xyz file into a variable using vibdata =
file(yyy.xyz)
3) changes that to Jmol script format and runs it.
I think this is a few lines of Jmol script:
function applyVibData(filename)
var vibdata = load(filename)
var S = vibdata.split()
var myscript =
for (var i = 3; i = S.size; i=i+1)
var line = S[i]
# change the numbers below to match your file format -- I'm
guessing
here
var x = { + (S[i])[3][45] + }
var v = { + (S[i])[48][0] + }
myscript = myscript + x= + x + ;v= +
v+;{within(-2.5,x)}.vxyz =
v\n
end for
script inline @myscript
end function
Bob
On Thu, May 21, 2009 at 7:11 AM, Laurence Marks
l-ma...@northwestern.edu
wrote:
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
Re: [Jmol-users] Vibrations
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 what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrations
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, 2009 at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: 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 what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter. -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrations
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 l-ma...@northwestern.edu wrote: 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 l-ma...@northwestern.edu wrote: 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, 2009 at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: 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 what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter. -- 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) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter. -- 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) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter. -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://www.creativitycat.com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Vibrations
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) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter. -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Vibrations
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,
{atomno=3}.vxyz = {1/2 1/2 1/2}
would set a vibration up for that atom along the unit cell diagonal. In the
very latest version I have also implemented:
{within(-0.1, atomno=3)}.vxyz = {1/2 1/2 1/2}
this would do the same thing, but also add the vibration to any atoms
(precisely, in a P1 sense) equivalent to atomno=3 in all unit cells.
So implemented is what you make of it. If you have a way of defining
vibrations, Jmol can read it -- with a little scripting.
What exactly would you like to do?
Bob
On Wed, May 20, 2009 at 2:33 PM, Laurence Marks l-ma...@northwestern.eduwrote:
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) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering to study the structure of matter.
--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables
unlimited royalty-free distribution of the report engine
for externally facing server and web deployment.
http://p.sf.net/sfu/businessobjects
___
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--
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 what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
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[Jmol-users] Vibrations in Jmol
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 each atom displaced one unit in the direction of each vector? Are the vectors scaled by the inverse square root of the atomic mass (technically needed to make the units come out right, but rarely done). Best regards, Jan -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Associate Research Professor Department of Chemistry jhjen...@kemi.ku.dk University of CopenhagenPhone: +45 35 32 02 39 Universitetsparken 5FAX: +45 35 32 02 14 2100 Copenhagen Denmark http://propka.ki.ku.dk/~jhjensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] vibrations
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. After one cycle it waits for a second before it restarts. So the animation doesn't look like a vibration. So my first question is: can this delay be avoided? I know that people are working on reading and displaying vibrations directly from Gaussian output. Can I select -scriptwise- a particular one of the 3N-6 vibrations? Will this feature be extended to MOPAC output? Hens --- This SF.Net email is sponsored by: Sybase ASE Linux Express Edition - download now for FREE LinuxWorld Reader's Choice Award Winner for best database on Linux. http://ads.osdn.com/?ad_id=5588alloc_id=12065op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrations
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.
After one cycle it waits for a second before it restarts.
The 1 second delay is intentional.
So the
animation doesn't look like a vibration.
So my first question is: can this delay be avoided?
Yes.
When you set the animation mode you can specify a delay of 0 at the
beginning and the end of the cycle.
animation mode palindrome 0 0
OR
animation mode loop 0 0
... whichever is appropriate
I know that people are working on reading and displaying vibrations
directly from Gaussian output.
Can I select -scriptwise- a particular one of the 3N-6 vibrations?
Yes, this should work today:
model {1, 2, 3, etc.}
vibration on
vibration scale 2.0
vector scale 4.0
Will this feature be extended to MOPAC output?
I suppose so ... but there are so many file formats that I have forgotten
how to distinguish between them :-)
Miguel
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Re: [Jmol-users] vibrations
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.stolaf.edu/people/hansonr/jmol/docs/examples/animation.htm working for people? Is this another case of 10pre16 not working?) To see how a simple Gaussian-like output works, try the second set of data at: http://www.stolaf.edu/people/hansonr/jmol/inline/ Bob Hens Borkent wrote: 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. After one cycle it waits for a second before it restarts. So the animation doesn't look like a vibration. So my first question is: can this delay be avoided? I know that people are working on reading and displaying vibrations directly from Gaussian output. Can I select -scriptwise- a particular one of the 3N-6 vibrations? Will this feature be extended to MOPAC output? Hens --- This SF.Net email is sponsored by: Sybase ASE Linux Express Edition - download now for FREE LinuxWorld Reader's Choice Award Winner for best database on Linux. http://ads.osdn.com/?ad_id=5588alloc_id=12065op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr Imagination is more important than knowledge. - Albert Einstein --- This SF.Net email is sponsored by: Sybase ASE Linux Express Edition - download now for FREE LinuxWorld Reader's Choice Award Winner for best database on Linux. http://ads.osdn.com/?ad_id=5588alloc_id=12065op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] vibrations
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 in an xyz file just add three floats (vectorX, vectorY, vectorZ) at the end of the atom coordinates. Separately, Jmol also supports formal charges in .xyz files. If present then it comes between the atom coordinates and the vector coordinates. So, each line of an XYZ file can have 3, 4, 6, or 7 floats 3 = x,y,z 4 = x,y,z,formalCharge 6 = x,y,z,vectorX,vectorY,vectorZ 7 = x,y,z,formalCharge,vectorX,vectorY,vectorZ Miguel --- This SF.Net email is sponsored by: Sybase ASE Linux Express Edition - download now for FREE LinuxWorld Reader's Choice Award Winner for best database on Linux. http://ads.osdn.com/?ad_idU88alloc_id065op=click ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
