From owner-chemistry@ccl.net Tue Nov 29 11:31:00 2016 From: "Timur Madzhidov tmadzhidov^gmail.com" To: CCL Subject: CCL:G: AIM Message-Id: <-52532-161129091326-10510-IH+vapOhCu6OTPSzpaz0Xg _ server.ccl.net> X-Original-From: Timur Madzhidov Content-Type: multipart/alternative; boundary=f403045ea36a7fce1f054271305b Date: Tue, 29 Nov 2016 14:13:05 +0000 MIME-Version: 1.0 Sent to CCL by: Timur Madzhidov [tmadzhidov=gmail.com] --f403045ea36a7fce1f054271305b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable There is other very good and free code AIMAll http://aim.tkgristmill.com/. Standard version is free, professional that is good due to visualization capabilities is paid. But for getting numbers but pictures AIMAll is excellent. Best regards, Timur Madzhidov =D0=B2=D1=81, 27 =D0=BD=D0=BE=D1=8F=D0=B1. 2016 =D0=B3. =D0=B2 9:24, V=C3= =ADctor Lua=C3=B1a Cabal victor() fluor.quimica.uniovi.es : > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor= =3D=3D=3D > fluor.quimica.uniovi.es] > On Sun, Nov 27, 2016 at 08:55:09AM +0800, =E9=83=AD=E5=BB=BA=E4=B8=9C guo= jiandong13() > mails.ucas.ac.cn wrote: > > > > Dear Prof. V=C3=ADctor Lua=C3=B1a > > I am a beginner of computational chemistry. I have little > > knowledge of AIM. I did not try whether the AIM can be performed on > > Gaussuan 09. > > =C2=BFAre you asking why not using the AIM facility internal to g09? > Dont! The AIM algorithms within g09 fails in too many occasions and they > are not useful, in general. In fact, failures in the g09 aim algorithm > have always been a source of concern for the people doing QTAIM work. > > Use an independent code. The original AIMPAC from the Bader's > group is still available (1), but newer codes have improved > characteristics. Directly from Bader's students you have: aim2000 > and aimall. > > (1) > > My group, that went to study with Bader's group after we had created > independently codes to to do AIM studies on solid state problems, > published critic as an open source code. The original critic was intended > to analyse the electron density and its laplacian in solids. It was > heavily improved in critic2, also open source, that works both on > crystals and molecules and implements a special computational langage > to create new tasks not hard coded in the critic2 source. > > There are also excellent QTAIM codes by PLA. Popelier, from Manchester > University but I'm not currently sure how they can be obtained. You must > explore that if you want. Popelier has written that QCT (quantum chemistr= y > topology of topography) is a better name that QTAIM. The reason is that > QTAIM analysis can be extended to other scalar properties within the > electron density basins. > > There is also a chinese code, multiwfn, but the algorithms implemented > there prefer que quantity of doing many things to que quality of doing > them well. > > So, my advise is: do not use the g09 internal aim task! Use aimall > or critic2 to analyse the g09 WFX file that g09 produces. NOtice that > WFX improves on the WFN format that g03 (surely even previous gaussian > versions) started to produce to give AIMPAC programs the wavefunction > to explore. Most Bader's articles were done that way. > > If you need to study what is the AIM analysis you should read Bader's > book: Bader, Richard (1994). Atoms in Molecules: A Quantum Theory. USA: > Oxford University Press. ISBN 978-0-19-855865-1. > > I started to write this message without realizing that you were using the > CCL list. Maybe this is a too personal opinion for a Universal audience, > but I do not regret having strong opinions and showing them clearly. > > Enjoy, > Dr. V=C3=ADctor Lua=C3=B1a > -- > . . "De la cuna a la tumba es una escuela, por eso lo que llamas > / `' \ problemas son lecciones." > /(o)(o)\ (From the cradle to the grave life is a school, ...) > /`. \/ .'\ -- Facundo Cabral, Cuna > / '`'` \ > | \'`'`/ | "When are we ready to learn something? Motivation is the > | |'`'`| | Motivation is the most important step in education." > \/`'`'`'\/ -- adapted from Adam Steltzner, 2016 (ElPa=C3=ADs) > =3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. ! > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: ! > ! phone: +34-985-103491 <+34%20985%2010%2034%2091> fax: +34-985-103125 > <+34%20985%2010%2031%2025> ! > +--------------------------------------------+ > GroupPage: > Articles: > git-hub: > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > -- Best regards, Timur Madzhidov (sent from telephone) ***************************************************************************= *********************************** Dr. Timur I. Madzhidov (PhD in Organic Chemistry) Senior Researcher of Laboratory of Chemoinformatics and Molecular Modeling Senior Lecturer of Department of Organic Chemistry Responsible for Education at Master Program on Chemoinformatics and Molecular Modeling A.M. Butlerov Institute of Chemistry, Kazan Federal University E-mails: Timur.Madzhidov]![kpfu.ru, tmadzhidov]![gmail.com, madzhidov]![mail.ru Web-page: http://kpfu.ru/Timur.Madzhidov ***************************************************************************= *********************************** --f403045ea36a7fce1f054271305b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
There is other very good and free code AIMAll=C2=A0
http://aim.tkgristmill.com/.=C2= =A0

Standard version is free, professional that is= good due to visualization capabilities is paid. But for getting numbers bu= t pictures AIMAll is excellent.

Best regards,
= Timur Madzhidov




=D0=B2=D1=81, 27 =D0= =BD=D0=BE=D1=8F=D0=B1. 2016 =D0=B3. =D0=B2 9:24, V=C3=ADctor Lua=C3=B1a Cab= al victor()fluor.quimica.uniovi.= es <owner-chemistry]![ccl.n= et>:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor=3D= =3D=3Dfluor.quimica.uniovi.es]
On Sun, Nov 27, 2016 at 08:55:09AM +0800, =E9=83=AD=E5=BB=BA=E4=B8=9C guoji= andong13() mails.ucas.ac.cn wrote:
>
> Dear Prof. V=C3=ADctor Lua=C3=B1a
>=C2=A0 =C2=A0 =C2=A0 =C2=A0I am a beginner of computational chemistry. = I have little
> knowledge of AIM. I did not try=C2=A0 whether the AIM can be performed= on
> Gaussuan 09.

=C2=BFAre you asking why not using the AIM facility internal to g09?
Dont! The AIM algorithms within g09 fails in too many occasions and they are not useful, in general. In fact, failures in the g09 aim algorithm
have always been a source of concern for the people doing QTAIM work.

Use an independent code. The original AIMPAC from the Bader's
group is still available (1), but newer codes have improved
characteristics. Directly from Bader's students you have: aim2000
and aimall.

(1) <http://www.= chemistry.mcmaster.ca/aimpac/imagemap/imagemap.htm>

My group, that went to study with Bader's group after we had created independently codes to to do AIM studies on solid state problems,
published critic as an open source code. The original critic was intended to analyse the electron density and its laplacian in solids. It was
heavily improved in critic2, also open source, that works both on
crystals and molecules and implements a special computational langage
to create new tasks not hard coded in the critic2 source.

There are also excellent QTAIM codes by PLA. Popelier, from Manchester
University but I'm not currently sure how they can be obtained. You mus= t
explore that if you want. Popelier has written that QCT (quantum chemistry<= br class=3D"gmail_msg"> topology of topography) is a better name that QTAIM. The reason is that
QTAIM analysis can be extended to other scalar properties within the
electron density basins.

There is also a chinese code, multiwfn, but the algorithms implemented
there prefer que quantity of doing many things to que quality of doing
them well.

So, my advise is: do not use the g09 internal aim task! Use aimall
or critic2 to analyse the g09 WFX file that g09 produces. NOtice that
WFX improves on the WFN format that g03 (surely even previous gaussian
versions) started to produce to give AIMPAC programs the wavefunction
to explore. Most Bader's articles were done that way.

If you need to study what is the AIM analysis you should read Bader's book:=C2=A0 Bader, Richard (1994). Atoms in Molecules: A Quantum Theory. US= A:
Oxford University Press. ISBN 978-0-19-855865-1.

I started to write this message without realizing that you were using the CCL list. Maybe this is a too personal opinion for a Universal audience, but I do not regret having strong opinions and showing them clearly.

Enjoy,
=C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a
--
=C2=A0 =C2=A0 .=C2=A0 .=C2=A0 =C2=A0 "De la cuna a la tumba es una esc= uela, por eso lo que llamas
=C2=A0 =C2=A0/ `' \=C2=A0 =C2=A0 problemas son lecciones."
=C2=A0 /(o)(o)\=C2=A0 =C2=A0(From the cradle to the grave life is a school,= ...)
=C2=A0/`. \/ .'\=C2=A0 -- Facundo Cabral, Cuna
/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\
|=C2=A0 \'`'`/=C2=A0 | "When are we ready to learn something? = Motivation is the
|=C2=A0 |'`'`|=C2=A0 | Motivation is the most important step in edu= cation."
=C2=A0\/`'`'`'\/=C2=A0 -- adapted from Adam Steltzner, 2016 (El= Pa=C3=ADs)
=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:=C2=A0 <victor:fluor.quimica.uniovi.= es>=C2=A0 !
! phone: +34-985-103491=C2=A0 fax: +34-985-103125 !
+--------------------------------------------+
=C2=A0GroupPage: <http://azufre.quimica.uniov= i.es/>
=C2=A0Articles:=C2=A0 <http://scholar.google.com/citations?user=3DIbl1BWAAAAAJ&hl= =3Des>
=C2=A0git-hub:=C2=A0 =C2=A0<https://github.c= om/aoterodelaroza>



-=3D This is automatically added to each message by the mailing script =3D-=

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--

Best regards,
Timur Madzhidov

(sent from telephone)

************************************************************= **************************************************
Dr. Timur I. Madzhidov (PhD in Organic Chemistry)
Senior Researcher of Laboratory of Chemoinformatics and Molecular Modeling<= br> Senior Lecturer of Department of Organic Chemistry
Responsible for Education at Master Program on Chemoinformatics and Molecul= ar Modeling
A.M. Butlerov Institute of Chemistry, Kazan Federal University
E-mails: Timur.Madzhidov]![kpfu.ru= , tmadzhidov]![gmail.com, madzhidov]![mail.ru
Web-page: http://kpfu.ru/Timur.M= adzhidov
***************************************************************************= ***********************************

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