Sorry for my last EMPTY mail:
Dear Robert Hassen,
Many thanks for your scripts and latest version of Jmol. Of course it is very useful & I got repeated images of the supercell.
Still I have a question:
Since newbies like me prefer GUI than *console interaction* to display supercells, Can Jmol do it via its GUI (simply by clicks)? OR console command is still a necessary?
My team is now working for an open-source GUI based on Jmol+Java, in windows platform for DFTB+ program; And we really like to have this feature in it (displaying supercells via GUI rather by using console...).
With best regards
Krishna
------------ Original Message ------------
From : "krishna Mohan Grangadhran Prasanna"<[email protected]>
To : [email protected]
Mail Subject : Re:_[Jmol-users]_Jmol visualization with Supercells
Sent : Tue, 29 Nov 2011 20:06:03 +0900
------------ Original Message ------------
From : "Robert Hanson"<[email protected]>
To : [email protected]
Mail Subject : Re: [Jmol-users] Jmol visualization with Supercells
Sent : Mon, 28 Nov 2011 22:23:07 -0600
Sorry, I missed the 2x2x2 supercell business -- just adapt the lattice {i j k} and SUPERCELL parameters to suit:
load ..... {1 1 1} supercell {2 2 2}
would be one 2x2x2 supercell.
load ..... {2 2 1} supercell {2 2 2}
would be four such supercells.
Bob
On Mon, Nov 28, 2011 at 10:20 PM, Robert Hanson <[email protected]> wrote:
On Mon, Nov 28, 2011 at 9:14 PM, krishna Mohan Grangadhran Prasanna <[email protected]> wrote:
Dear Jmol-users,
Am a newbie user of Jmol. Since I deal with extended systems in general, I wish to visualize these systems with Jmol (version 12.0).
Suppose if I have XYZ information of atoms and Lattice Vectors (ie. Cartesian components of the L.V.), can I use Jmol to plot super-cell and/or its periodic repetitions?
yes and yes
For example, if I have the below data, (like vasp’s POSCAR format), How can I use Jmol to visualize a 2x2x2 cell? Do I really want to use Jmol-script?
rather than what?
Lattice Vectors [u v w] =
4.36130393 -2.518 0.0
4.36130393 2.518 0.0
0.0 0.0 16.0540126
Geometry =
Cu .00000000 .00000000 -.02858610
Cu 2.18065197 1.25900000 -.02858610
Cu 2.18065197 -1.25900000 -.02858610
Cu 4.36130393 .00000000 -.02858610
Cu 1.45376813 .0000000 -2.05580070
Cu 3.63442009 1.2590000 -2.05580070
Cu 3.63442009 -1.2590000 -2.05580070
Cu 5.81507206 .0000000 -2.05580070
Cu 2.90753593 .00000000 -4.08264189
Cu 5.08818789 1.25900000 -4.08264189
Cu 5.08818789 -1.25900000 -4.08264189
Cu 7.26883986 .00000000 -4.08264189
C -.00134965 .00000000 3.50000000
H .51772049 -.89768008 3.86520453
H -1.03852359 .00000000 3.86458322
H .51772049 .89768008 3.86520453
H -.00021200 .00000000 2.39768919
What is the actual source of the data? It doesn't look like POSCAR data to me. Sure would be easier just to read the VASP output if you have that.
But if you can preprocess that data a bit, it should be no problem. With Jmol 12.3.8 (see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip -- which I just uploaded) you can do this using the new ZMATRIX option (I know, this is not a Z-Matrix, but the option allows for Gaussian Z-Matrix format, which includes simple Cartesian input as well:
load data 'model'
#ZMATRIX
Cu .00000000 .00000000 -.02858610
Cu 2.18065197 1.25900000 -.02858610
Cu 2.18065197 -1.25900000 -.02858610
Cu 4.36130393 .00000000 -.02858610
Cu 1.45376813 .0000000 -2.05580070
Cu 3.63442009 1.2590000 -2.05580070
Cu 3.63442009 -1.2590000 -2.05580070
Cu 5.81507206 .0000000 -2.05580070
Cu 2.90753593 .00000000 -4.08264189
Cu 5.08818789 1.25900000 -4.08264189
Cu 5.08818789 -1.25900000 -4.08264189
Cu 7.26883986 .00000000 -4.08264189
C -.00134965 .00000000 3.50000000
H .51772049 -.89768008 3.86520453
H -1.03852359 .00000000 3.86458322
H .51772049 .89768008 3.86520453
H -.00021200 .00000000 2.39768919
end 'model' {2 2 1} supercell {3 1 1} spacegroup "P1" unitcell [
4.36130393 -2.518 0.0
4.36130393 2.518 0.0
0.0 0.0 16.0540126
]
Bob Hanson
--
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
--
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
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
Jmol-users mailing list
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https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
Dear Robert Hassen,
Many thanks for your scripts and latest version of Jmol. Of course it is very useful & I got repeated images of the supercell.
Still I have a question:
Since newbies like me prefer GUI than *console interaction* to display supercells, Can Jmol do it via its GUI (simply by clicks)? OR console command is still a necessary?
My team is now working for an open-source GUI based on Jmol+Java, in windows platform for DFTB+ program; And we really like to have this feature in it (displaying supercells via GUI rather by using console...).
With best regards
Krishna
------------ Original Message ------------
From : "krishna Mohan Grangadhran Prasanna"<[email protected]>
To : [email protected]
Mail Subject : Re:_[Jmol-users]_Jmol visualization with Supercells
Sent : Tue, 29 Nov 2011 20:06:03 +0900
------------ Original Message ------------
From : "Robert Hanson"<[email protected]>
To : [email protected]
Mail Subject : Re: [Jmol-users] Jmol visualization with Supercells
Sent : Mon, 28 Nov 2011 22:23:07 -0600
Sorry, I missed the 2x2x2 supercell business -- just adapt the lattice {i j k} and SUPERCELL parameters to suit:
load ..... {1 1 1} supercell {2 2 2}
would be one 2x2x2 supercell.
load ..... {2 2 1} supercell {2 2 2}
would be four such supercells.
Bob
On Mon, Nov 28, 2011 at 10:20 PM, Robert Hanson <[email protected]> wrote:
On Mon, Nov 28, 2011 at 9:14 PM, krishna Mohan Grangadhran Prasanna <[email protected]> wrote:
Dear Jmol-users,
Am a newbie user of Jmol. Since I deal with extended systems in general, I wish to visualize these systems with Jmol (version 12.0).
Suppose if I have XYZ information of atoms and Lattice Vectors (ie. Cartesian components of the L.V.), can I use Jmol to plot super-cell and/or its periodic repetitions?
yes and yes
For example, if I have the below data, (like vasp’s POSCAR format), How can I use Jmol to visualize a 2x2x2 cell? Do I really want to use Jmol-script?
rather than what?
Lattice Vectors [u v w] =
4.36130393 -2.518 0.0
4.36130393 2.518 0.0
0.0 0.0 16.0540126
Geometry =
Cu .00000000 .00000000 -.02858610
Cu 2.18065197 1.25900000 -.02858610
Cu 2.18065197 -1.25900000 -.02858610
Cu 4.36130393 .00000000 -.02858610
Cu 1.45376813 .0000000 -2.05580070
Cu 3.63442009 1.2590000 -2.05580070
Cu 3.63442009 -1.2590000 -2.05580070
Cu 5.81507206 .0000000 -2.05580070
Cu 2.90753593 .00000000 -4.08264189
Cu 5.08818789 1.25900000 -4.08264189
Cu 5.08818789 -1.25900000 -4.08264189
Cu 7.26883986 .00000000 -4.08264189
C -.00134965 .00000000 3.50000000
H .51772049 -.89768008 3.86520453
H -1.03852359 .00000000 3.86458322
H .51772049 .89768008 3.86520453
H -.00021200 .00000000 2.39768919
What is the actual source of the data? It doesn't look like POSCAR data to me. Sure would be easier just to read the VASP output if you have that.
But if you can preprocess that data a bit, it should be no problem. With Jmol 12.3.8 (see http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip -- which I just uploaded) you can do this using the new ZMATRIX option (I know, this is not a Z-Matrix, but the option allows for Gaussian Z-Matrix format, which includes simple Cartesian input as well:
load data 'model'
#ZMATRIX
Cu .00000000 .00000000 -.02858610
Cu 2.18065197 1.25900000 -.02858610
Cu 2.18065197 -1.25900000 -.02858610
Cu 4.36130393 .00000000 -.02858610
Cu 1.45376813 .0000000 -2.05580070
Cu 3.63442009 1.2590000 -2.05580070
Cu 3.63442009 -1.2590000 -2.05580070
Cu 5.81507206 .0000000 -2.05580070
Cu 2.90753593 .00000000 -4.08264189
Cu 5.08818789 1.25900000 -4.08264189
Cu 5.08818789 -1.25900000 -4.08264189
Cu 7.26883986 .00000000 -4.08264189
C -.00134965 .00000000 3.50000000
H .51772049 -.89768008 3.86520453
H -1.03852359 .00000000 3.86458322
H .51772049 .89768008 3.86520453
H -.00021200 .00000000 2.39768919
end 'model' {2 2 1} supercell {3 1 1} spacegroup "P1" unitcell [
4.36130393 -2.518 0.0
4.36130393 2.518 0.0
0.0 0.0 16.0540126
]
Bob Hanson
--
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
--
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
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d
_______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
