[xcrysden] XCrySDen Digest, Vol 12, Issue 13
Scott Beckman
spbeckman at gmail.com
Tue Dec 23 16:47:56 CET 2008
Explain what you mean by awful results. Are the H atoms misplaced or
do the calculations not work correctly?
Surface passivation isn't as simple as the literature makes is
sound. It might not be the placement that is a problem, but other
issues in the calculation.
On Dec 23, 2008, at 9:23 AM, Hana Milani wrote:
> dear Tone,
>
> I have put time to add h-bonds to a nanowire to saturate the
> dangling bonds, but after all I didn't get to good results.
>
> I wanted to know if there's a way that I add the h-bonds via
> xcrysden and get the coordinates from xcrysden, then, I optimize
> the system!!!
>
> I have gone through doing it via hyperchem, I got to awful results.
>
> Any suggestions????
>
> From: "xcrysden-request at democritos.it" <xcrysden-
> request at democritos.it>
> To: xcrysden at democritos.it
> Sent: Tuesday, December 23, 2008 4:56:27 PM
> Subject: XCrySDen Digest, Vol 12, Issue 13
>
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> Today's Topics:
>
> 1. xcrysden for Siesta (pradeep bisht)
> 2. Re: H-passivation (Tone Kokalj)
> 3. Re: xcrysden for Siesta (Tone Kokalj)
> 4. two iso-surfaces (Rodrigo Oeiras)
> 5. Re: two iso-surfaces (lan haiping)
> 6. Re: two iso-surfaces (Robert Hanson)
> 7. Re: two iso-surfaces (Tone Kokalj)
> 8. Re: xcrysden for Siesta (Ricardo Faccio)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Dec 2008 12:58:25 +0530 (IST)
> From: pradeep bisht <psbishtphyjiwaji at yahoo.co.in>
> Subject: [xcrysden] xcrysden for Siesta
> To: xcrysden at democritos.it
> Message-ID: <306790.1298.qm at web94202.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Respected Xcrysden users,
> Can we use the xcrysden to visulize the structure in Siesta if yes
> please help me.
>
> Thanking you
> Pradeep
>
>
>
> Add more friends to your messenger and enjoy! Go to http://
> messenger.yahoo.com/invite/
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> ------------------------------
>
> Message: 2
> Date: Tue, 23 Dec 2008 08:59:53 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] H-passivation
> To: XCrySDen mailing list <xcrysden at democritos.it>
> Message-ID: <1230019193.18465.14.camel at walk.ijs.si>
> Content-Type: text/plain
>
> On Sun, 2008-12-21 at 22:13 -0800, Hana Milani wrote:
> > hello,
> >
> > I would like to know if there's a way to find the "h" coordinates
> via
> > xcrysden in passivated nanostructures.
>
> What do you mean by H-coordinates? xcrysden can visualize H bonds, and
> that's more or less all it can do in this respect (menus: Display-
> >H-bonds,
> and Modify->H-bonds Settings).
>
> Regards, Tone
> --
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 23 Dec 2008 09:09:19 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] xcrysden for Siesta
> To: psbishtphyjiwaji at yahoo.co.in, XCrySDen mailing list
> <xcrysden at democritos.it>
> Message-ID: <1230019759.18465.20.camel at walk.ijs.si>
> Content-Type: text/plain
>
> On Tue, 2008-12-23 at 12:58 +0530, pradeep bisht wrote:
> > Respected Xcrysden users,
> > Can we use the xcrysden to visulize the structure in Siesta if
> yes please help me.
>
>
> Well, I don't know Siesta, but googling "siesta xsf" will give you
> useful info. The first hit is this one:
>
> http://www.uam.es/departamentos/ciencias/fismateriac/siesta/
> Tutorials/Barcelona-2007/Postnikov-visual.pdf
>
> Regards, Tone
> --
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 23 Dec 2008 01:58:51 -0800 (PST)
> From: Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
> Subject: [xcrysden] two iso-surfaces
> To: xcrysden at democritos.it
> Message-ID: <928799.6288.qm at web55606.mail.re4.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> I can plot two iso-surfaces (with different values) at same molecule?
> regards
> oeiras
>
>
>
> Veja quais s?o os assuntos do momento no Yahoo! +Buscados
> http://br.maisbuscados.yahoo.com
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> ------------------------------
>
> Message: 5
> Date: Tue, 23 Dec 2008 20:42:31 +0800
> From: "lan haiping" <lanhaiping at gmail.com>
> Subject: Re: [xcrysden] two iso-surfaces
> To: rodrigo_oeiras at yahoo.com.br, "XCrySDen mailing list"
> <xcrysden at democritos.it>
> Message-ID:
> <c92002fa0812230442x379623fduabe42ba705b8aa6d at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> As far as i know, xcrysden cannot
> plot two isosurfaces at the same plot.
> But you may try to use vmd or other tools.
> Another way you may try is to write some scripts to combine the
> data for
> two iso-surface .
> regards,
>
>
>
> 2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
>
> > Hi,
> > I can plot two iso-surfaces (with different values) at same
> molecule?
> > regards
> > oeiras
> >
> > ------------------------------
> > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top
> 10<http://br.rd.yahoo.com/mail/taglines/mail/*http://
> br.maisbuscados.yahoo.com/>-
> > Celebridades<http://br.rd.yahoo.com/mail/taglines/mail/*http://
> br.maisbuscados.yahoo.com/celebridades/>-
> > M?sica<http://br.rd.yahoo.com/mail/taglines/mail/*http://
> br.maisbuscados.yahoo.com/m%C3%BAsica/>-
> > Esportes<http://br.rd.yahoo.com/mail/taglines/mail/*http://
> br.maisbuscados.yahoo.com/esportes/>
> >
> > _______________________________________________
> > XCrySDen mailing list
> > XCrySDen at democritos.it
> > http://www.democritos.it/mailman/listinfo/xcrysden
> >
> >
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
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> ------------------------------
>
> Message: 6
> Date: Tue, 23 Dec 2008 07:14:32 -0600
> From: "Robert Hanson" <hansonr at stolaf.edu>
> Subject: Re: [xcrysden] two iso-surfaces
> To: "XCrySDen mailing list" <xcrysden at democritos.it>
> Message-ID:
> <ba9c0bd60812230514k6223c777p1bc45942b199af66 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Jmol will draw as many isosurfaces as you want.
>
> On Tue, Dec 23, 2008 at 6:42 AM, lan haiping <lanhaiping at gmail.com>
> wrote:
> > Hi,
> > As far as i know, xcrysden cannot
> > plot two isosurfaces at the same plot.
> > But you may try to use vmd or other tools.
> > Another way you may try is to write some scripts to combine the
> data for
> > two iso-surface .
> > regards,
> >
> >
> >
> > 2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
> >>
> >> Hi,
> >> I can plot two iso-surfaces (with different values) at same
> molecule?
> >> regards
> >> oeiras
> >>
> >> ________________________________
> >> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top
> 10 -
> >> Celebridades - M?sica - Esportes
> >> _______________________________________________
> >> XCrySDen mailing list
> >> XCrySDen at democritos.it
> >> http://www.democritos.it/mailman/listinfo/xcrysden
> >>
> >
> >
> >
> > --
> > Hai-Ping Lan
> > Department of Electronics ,
> > Peking University , Bejing, 100871
> > lanhaiping at gmail.com, hplan at pku.edu.cn
> >
> > _______________________________________________
> > XCrySDen mailing list
> > XCrySDen at democritos.it
> > http://www.democritos.it/mailman/listinfo/xcrysden
> >
> >
>
>
>
> --
> 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
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 23 Dec 2008 14:22:59 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] two iso-surfaces
> To: rodrigo_oeiras at yahoo.com.br, XCrySDen mailing list
> <xcrysden at democritos.it>
> Message-ID: <1230038579.27591.9.camel at walk.ijs.si>
> Content-Type: text/plain
>
> On Tue, 2008-12-23 at 01:58 -0800, Rodrigo Oeiras wrote:
> > Hi,
> > I can plot two iso-surfaces (with different values) at same
> molecule?
>
> In general, xcrysden cannot. There is only one exception: you can
> plot +value and -value
> isosurface at once (there is a checkbutton Render +/- isovalue).
> Why? At the time I programmed it,
> I thought that more than one isosurface at once would be too much
> info and not very useful.
> Probably I was wrong.
>
> Regards, Tone
> --
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 23 Dec 2008 10:53:21 -0300
> From: "Ricardo Faccio" <rfaccio at fq.edu.uy>
> Subject: Re: [xcrysden] xcrysden for Siesta
> To: <psbishtphyjiwaji at yahoo.co.in>, "XCrySDen mailing list"
> <xcrysden at democritos.it>
> Message-ID: <004d01c96505$d1f3d6b0$0602a8c0 at ricardof>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Pradeep
> In the Postnikov's web page you can find a script called xv2xsf for
> a case.XV file and transforms it into case.XSF, that can easily be
> read by Xcrysden. This script is found with other tools in a
> collection called Sies2xsf (http://www.home.uni-osnabrueck.de/
> apostnik/download.html)
> Regards
> Ricardo
> ----------------------------------------------------------------------
> ---
> ----- Dr. Ricardo Faccio
>
> Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
> Facultad de Qu?mica, Universidad de la Rep?blica
> Av. Gral. Flores 2124, C.C. 1157
> C.P. 11800, Montevideo, Uruguay.
> E-mail: rfaccio at fq.edu.uy
> Phone: 598 2 9249859
> 598 2 9290705
> Fax: 598 2 9241906
> Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
> ----- Original Message -----
> From: pradeep bisht
> To: xcrysden at democritos.it
> Sent: Tuesday, December 23, 2008 4:28 AM
> Subject: [xcrysden] xcrysden for Siesta
>
>
> Respected Xcrysden users,
> Can we use the xcrysden to visulize the structure in Siesta
> if yes please help me.
>
> Thanking you
> Pradeep
>
>
>
> ----------------------------------------------------------------------
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