From owner-chemistry@ccl.net Mon Aug 22 04:18:00 2011
From: "Daniel Cappel daniel.cappel_._schrodinger.com" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL:G: Bromine basis sets in Jaguar
Message-Id: <-45304-110822041627-13563-vVbHBel6tzNtxpHD/CYtqA]![server.ccl.net>
X-Original-From: Daniel Cappel <daniel.cappel,schrodinger.com>
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Date: Mon, 22 Aug 2011 10:15:58 +0200
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Sent to CCL by: Daniel Cappel [daniel.cappel*o*schrodinger.com]
Hi Carlos!
You may use the LACVP basis set in Jaguar. This is 6-31G with ECPs and
does support Br. You can find more details on the basis sets in the
Jaguar manual in chapter 3.2.
Cheers, Daniel
On Fri, Aug 19, 2011 at 3:23 PM, Carlos T Nieto eneas*_*usal.es
<owner-chemistry---ccl.net> wrote:
>
> Sent to CCL by: "Carlos T Nieto" [eneas{=}usal.es]
> I've begun some theoretical reaction studies, bromine additions to
> olefines, and apparently, 6-31G as a basis sets is not available in Jaguar
> (only to Ar or Zn). The curious fact is Gaussian includes the complete
> 3rd row to this basis.
>
> Searching literature i've found that Jaguar doesnt include the lastest
> basis set enlargement (DOI: 10.1002/jcc.1058).
>
> The question is what basis set and theory do you recommend me for this
> bromine type reactions. There are bromine type additions to olefins, in
> which a bromonium type intermidiate is one of the structures to optimize.
>
> Thanks a lot.
>
>
--
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Direct Support Phone: +49 (621) 438 55173
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cell: +49 (175) 4334727
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From owner-chemistry@ccl.net Mon Aug 22 08:15:01 2011
From: "Jussi Lehtola jussi.lehtola---helsinki.fi" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: Simple implementation of ROHF
Message-Id: <-45305-110822081351-25716-itSRKv7pqo9GdqlhdUFvjQ,+,server.ccl.net>
X-Original-From: Jussi Lehtola <jussi.lehtola ~ helsinki.fi>
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Date: Mon, 22 Aug 2011 15:13:38 +0300
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Sent to CCL by: Jussi Lehtola [jussi.lehtola ~ helsinki.fi]
Hi,
I ran across the paper "ROHF theory made simple" by T. Tsuchimochi and
G. E. Scuseria [1], in which ROHF is formulated as a simple modification
to UHF theory written in the form using the total electron density and
spin density matrices. The new formulation seems to have many appealing
properties.
I would like to implement the method in my free SCF code [2], but I am
having trouble going from the molecular orbital picture to the atomic
orbital picture (mostly, eqn 17 in [1]). Maybe someone on the list
can figure out how to construct the Fock matrices in the AO basis?
[1] J. Chem. Phys. 133, 141102 (2010)
http://link.aip.org/link/doi/10.1063/1.3503173
[2] http://erkale.googlecode.com
--
--------------------------------------------------------
Mr. Jussi Lehtola, M. Sc. Doctoral Student
jussi.lehtola**helsinki.fi Department of Physics
http://www.helsinki.fi/~jzlehtol University of Helsinki
Office phone: +358 9 191 50 632 Finland
--------------------------------------------------------
Jussi Lehtola, FM Tohtorikoulutettava
jussi.lehtola**helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632
--------------------------------------------------------
From owner-chemistry@ccl.net Mon Aug 22 10:48:01 2011
From: "Tiago Silva tjlsilva%x%gmail.com" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL:G: Dynamic hyperpolarizabilities in G09
Message-Id: <-45306-110822104439-27592-6u5dFZE0AXeoDNfgL2Ieew(a)server.ccl.net>
X-Original-From: "Tiago Silva " <tjlsilva_+_gmail.com>
Date: Mon, 22 Aug 2011 10:44:36 -0400
Sent to CCL by: "Tiago Silva " [tjlsilva : gmail.com]
Hi all,
I am interested in the calculation of DFT dynamic first hyperpolarizabilities (beta) of organometallic compounds. To the best of my knowledge, G09 is able to calculate static analytical hyperpolarizabilities by dft methods by using the keyword POLAR=EnOnly, that causes the calculation of beta as the second numerical derivative of the dipole moment with respect to the electric field. The result is a nine rank tensor as it should be. The problem is when trying to obtain the dynamic properties, using finite field model with an applied electric field, no results are shown in the output if i use the same keyword. In order to obtain some results I've changed the keyword to Polar and add the SCRF keyword for the desired field. Now the problem is that i get an output file witch is no longer a nine rank tensor, but an higher order one. The root line and output are the following:
# polar cam-b3lyp/gen pseudo=read SCF=Maxcycle=1000 SCRF=(PCM,Solvent=Chloroform) CPHF=RdFreq
(...)
Frequencies= 0.000000 0.030376
Property number 1 -- Alpha(-w,w) frequency 1 0.000000:
1 2 3
1 0.100029D+04 0.259282D+02 0.203390D+02
2 0.259282D+02 0.597691D+03 0.149814D+02
3 0.203390D+02 0.149814D+02 0.348053D+03
Property number 1 -- Alpha(-w,w) frequency 2 0.030376:
1 2 3
1 0.971558D+03 0.226142D+02 0.188213D+02
2 0.226142D+02 0.532337D+03 0.119275D+02
3 0.188213D+02 0.119275D+02 0.310651D+03
Property number 5 -- Beta(-w,w,0) frequency 1 0.000000:
1
1 -0.127445D+05
2 -0.345797D+04
3 -0.250083D+03
4 -0.647000D+03
5 0.107710D+02
6 -0.408247D+01
7 -0.345797D+04
8 -0.250083D+03
9 0.110879D+03
10 0.107710D+02
11 0.138828D+02
12 0.950144D+02
13 -0.647000D+03
14 0.107710D+02
15 0.138828D+02
16 -0.408247D+01
17 0.950144D+02
18 0.401687D+02
Property number 5 -- Beta(-w,w,0) frequency 2 0.030376:
1
1 -0.124549D+05
2 -0.324227D+04
3 -0.271791D+03
4 -0.606860D+03
5 0.412051D+01
6 0.361738D+01
7 -0.361989D+04
8 -0.288536D+03
9 0.113181D+03
10 0.119902D+02
11 0.991250D+01
12 0.941839D+02
13 -0.636980D+03
14 0.157863D+02
15 0.548135D+01
16 -0.114109D+02
17 0.879670D+02
18 0.417869D+02
IF IT HAPPENS, IT MUST BE POSSIBLE.
-- THE UNNAMED LAW FROM PAUL DICKSON'S
"THE OFFICIAL RULES"
Job cpu time: 1 days 9 hours 56 minutes 11.1 seconds.
File lengths (MBytes): RWF= 2183 Int= 0 D2E= 0 Chk= 21 Scr= 1
Normal termination of Gaussian 09 at Mon Aug 1 23:24:40 2011.
Can someone explain me this results please.
Also can someone elucide me why does the polar=EnOnly does not work for dynamic hyperpolarizabilities
thanks in advance
--
Tiago Silva
From owner-chemistry@ccl.net Mon Aug 22 12:18:00 2011
From: "Jussi Lehtola jussi.lehtola()helsinki.fi" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: Simple implementation of ROHF
Message-Id: <-45307-110822091620-17414-Z++kACqIuFv0PqdvZsMcig%server.ccl.net>
X-Original-From: Jussi Lehtola <jussi.lehtola(~)helsinki.fi>
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Date: Mon, 22 Aug 2011 16:16:10 +0300
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Sent to CCL by: Jussi Lehtola [jussi.lehtola(_)helsinki.fi]
On Mon, 22 Aug 2011 15:13:38 +0300
"Jussi Lehtola jussi.lehtola---helsinki.fi" <owner-chemistry- -ccl.net>
wrote:
> Sent to CCL by: Jussi Lehtola [jussi.lehtola ~ helsinki.fi]
> Hi,
>
>
> I ran across the paper "ROHF theory made simple" by T. Tsuchimochi and
> G. E. Scuseria [1], in which ROHF is formulated as a simple
> modification to UHF theory written in the form using the total
> electron density and spin density matrices. The new formulation seems
> to have many appealing properties.
>
> I would like to implement the method in my free SCF code [2], but I am
> having trouble going from the molecular orbital picture to the atomic
> orbital picture (mostly, eqn 17 in [1]). Maybe someone on the list
> can figure out how to construct the Fock matrices in the AO basis?
Actually, this question was already answered by Scuseria; the algorithm
seems to be presented in "Constrained active space unrestricted
mean-field methods for controlling spin-contamination", J. Chem. Phys.
134, 064101 (2011).
http://link.aip.org/link/doi/10.1063/1.3549134
--
--------------------------------------------------------
Mr. Jussi Lehtola, M. Sc. Doctoral Student
jussi.lehtola- -helsinki.fi Department of Physics
http://www.helsinki.fi/~jzlehtol University of Helsinki
Office phone: +358 9 191 50 632 Finland
--------------------------------------------------------
Jussi Lehtola, FM Tohtorikoulutettava
jussi.lehtola- -helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632
--------------------------------------------------------
From owner-chemistry@ccl.net Mon Aug 22 12:52:01 2011
From: "Aniko Simon aniko*_*simbiosys.ca" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: Webinar: convert your documents into chemical structures
Message-Id: <-45308-110822123232-22240-NdxvZKHcHP3M8VOgnxItog+/-server.ccl.net>
X-Original-From: "Aniko Simon" <aniko##simbiosys.ca>
Date: Mon, 22 Aug 2011 12:32:28 -0400
Sent to CCL by: "Aniko Simon" [aniko**simbiosys.ca]
Dear Colleague,
You are invited to join us for an interactive webinar, with live demonstration of the recently released CLiDE (Chemical Literature Data Extraction) - a new office tool which can extract chemical structures embedded in PDF and Word documents, as well as in JPEG, TIFF and other image file formats. CLiDE is a productivity and convenience tool, it saves the time and trouble of copying useful, and often complex structures from an image into a chemical editor or an e-lab notebook. It is useful for your everyday work, as well as for creating chemical knowledge-bases from journal articles, patents, and web content.
CLiDE comes in 3 packages:
* Standard - a desktop utility for all chemists, processing one structure at a time
* Professional - for more intense use, extracting multiple structures from full documents
* Batch - for processing of libraries of documents to generate knowledge-bases and to digitize chemical information
The new CLiDE 5 is now available on Windows PCs, as well as on Mac and Linux operating systems (for more info see: http://www.simbiosys.com/clide/index.html )
The webinar sessions are live, and they provide you an opportunity to ask
questions and receive immediate feedback.
Dont miss out this opportunity, register now at:
http://www.simbiosys.com/products/webinar_request.html
What:
* INTERACTIVE WEBINAR with call-in teleconferencing
* CLiDE live demonstrations included in the presentation
When:
* Thursday Aug 25, 2011
* NOON: 12:00 pm - 1:00 pm EDT
Speaker:
* Dr Orr Ravitz, Applications Scientist, SimBioSys, Inc.
We are looking forward to seeing you at the webinar!
Best regards,
Aniko Simon
References:
[1]: http://www.simbiosys.com/clide/index.html
[2] http://pubs.acs.org/doi/abs/10.1021/ci800449t
From owner-chemistry@ccl.net Mon Aug 22 14:10:00 2011
From: "Francois Zielinski francois.zielinski]*[univ-rouen.fr" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL:G: AMD Opteron vs. Intel Xeon processors
Message-Id: <-45309-110822122322-12858-3u75LiEG5MHT0i7ESU46DA%a%server.ccl.net>
X-Original-From: Francois Zielinski <francois.zielinski[a]univ-rouen.fr>
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Date: Mon, 22 Aug 2011 18:23:11 +0200
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Sent to CCL by: Francois Zielinski [francois.zielinski~~univ-rouen.fr]
Adel,
First of all, your Gaussian binary would work just fine on AMD
platform, though designation might be confusing... one must not forget
that AMD were first on the 64bits x86 architecture, Intel has just
follow them up here (and hid AMD technical merits with standard names).
These Intel processors support Hyper-Threading, as such you will be
able to use them nearly as if they were 20-cores each (1 physical core
= 2 logical cores, I have not seen any performance issue with this
function on G09). In addition, regarding current architecture (next
AMD archi. coming this fall, so things might change at this time)
Intel processors exhibits general better performance than AMD for
equivalent frequency and thread number.
However, best choice may be based on your particular usage, since G09
is not parallelized for all calculations and methods. Bandwidth memory
may plea on AMD side, as well depending on specific computation cases.
The ideal solution would be to require some days of Gaussian
performance tests on both systems (or comparable), to see if the extra
cost worth it for your particular studies. Then you could disclose
your results here (if Gaussian benchmark policy permits it)) to advise
us!
The price gap between both systems bothers me, as I would have
expected more discount for the AMD one... make sure RAM memory
capacity are equivalent : you did not mention it, and it can worth a
lot. In addition, if you can wait a little, a price drop on AMD
systems is expected at the end of the year, providing new chips would
be on time. Even more, these new chips could provide price-competitive
alternatives to Intel systems.
To conclude, for now, the Intel system seems like a good deal.
Have a nice day.
François Zielinski
University of Rouen
France
Quoting "Adel El-azhary azhary*ksu.edu.sa" <owner-chemistry:ccl.net>:
>
> Sent to CCL by: "Adel El-azhary" [azhary a ksu.edu.sa]
>
> Dear CCl members,
>
> We are interested to buy a server. We have the choice between two
> systems. One has the AMD Opteron processor, 12 core, and the other
> has Intel Xeon processor, 10 core. The AMD system is cheaper by
> about 33%. Does anyone has experience which one to choose. I know
> that this question has been asked before but about a year ago and
> probably things have changed.
>
> Another related question. We have the binary code of the Gaussian
> program, the Intel EM64T-based systems version which runs on the
> Intel Xeon processor. Will this version run of the AMD Opteron system.
>
> The two processors are
> 2x AMD Opteron 6172, 12C, 2.1GHz, 12x512K L2/12M L3 Cache, 80W ACP,
> DDR3-1333MHz
>
> 2x Intel Xeon E7-4850, 10C, 2.00GHz, 24M Cache, 6.40GT/s, 130W TDP,
> Turbo, HT, DDR3-1066MHz
>
> Adel El-Azhary
> King Saud University
> Saudi Arabia>
>
>
From owner-chemistry@ccl.net Mon Aug 22 17:10:01 2011
From: "Adel El-Azhary azhary:_:KSU.EDU.SA" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: What is wrong with M06 vibrational frequencies
Message-Id: <-45310-110822154322-24858-em5pTxP4vAx7vF19ejgd+A^-^server.ccl.net>
X-Original-From: Adel El-Azhary <azhary++KSU.EDU.SA>
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Date: Mon, 22 Aug 2011 22:43:11 +0300
MIME-Version: 1.0
Sent to CCL by: Adel El-Azhary [azhary/a\KSU.EDU.SA]
Dear All,
Really thanks for all the replies I got from CCL. The answer, and the standard thing to do, is to use ultrafine grid. Using opt=(calcall,tight) might help. However, unfortunately nothing worked for my molecule. I have in fact more than one molecule. Some of these options work for some molecules, but they do not work for others.
Thanks a lot again for the replies I got from CCL.
Best regards,
Adel El-Azhary
________________________________________
> From: owner-chemistry+azhary==ksu.edu.sa=ccl.net [owner-chemistry+azhary==ksu.edu.sa=ccl.net] On Behalf Of Steve Williams willsd(_)appstate.edu [owner-chemistry=ccl.net]
Sent: Friday, August 19, 2011 5:31 PM
To: Adel El-Azhary
Subject: CCL:G: What is wrong with M06 vibrational frequencies
Sent to CCL by: Steve Williams [willsd() appstate.edu]
On 08/19/2011 07:55 AM, Gerald Knizia knizia]*[theochem.uni-stuttgart.de
wrote:
>
> Sent to CCL by: Gerald Knizia [knizia\a/theochem.uni-stuttgart.de]
> Adel El-Azhary azhary---ksu.edu.sa wrote:
>> I am not sure that anyone of you experienced this problem before or
>> knows a solution for it. I am calculating vibrational frequencies at
>> the HF, B3LYP, M06, M06L, M062x, M06HF and MP2 levels of a molecule.
>> All vibrational frequencies are real at the HF, B3LYP and MP2 levels
>> but at the M06, M06L, M062x and M06HF levels, one or more vibrational
>> frequency is imaginary.
>
> The M06 (and the other M* functionals) are basically fitted to
> death[1] on a large training set in order to give good thermochemistry
> values. They are not fitted on potential energy surfaces. While in
> general this apparently works well, you have to be wary. It's only to
> be expected that they break for some molecules and applications which
> are sufficiently different from what they are fitted for[2]. If you
> are sure that your geometries with the different methods converged to
> equivalent structures, you maybe shouldn't worry about that too much
> and simply use some other theoretical method.
>
> [1] They have over 30 fitting parameters, additionally to the choice
> of the functional form.
> [2] ...or which in general cannot be reliably represented by DFT
> methods, like dispersive interactions or strong correlations. Maybe HF
> and B3LYP anr just as wrong, but in a different way, which causes them
> to erroneously report positive PES curvature. To be absolutely sure
> about that you would need to repeat your calculation with a more
> accurate wave function method, but this might be unaffordable.
This is a good point. If these M* functionals are "broken" for anything
but thermochemistry at single points, you might be able to have
gradients and second derivatives "broken" in the same way. I think you
are using gaussian for these calculations, so (if you can afford it),
you might want to try opt=(calcall,tight) with your ultrafine grid.
This will use the M* analytic Hessian to guide the optimization at every
step. This is guaranteed to be really slow, but will take fewer steps
in the optimization. There is no need for a subsequent freq calculation
since this automatically reported on the converged geometry.
Steve Williamshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
From owner-chemistry@ccl.net Mon Aug 22 21:55:01 2011
From: "Guenter Grethe ggrethe[*]att.net" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: CINF Scholarships for Scientific Excellence - Call for Applications
Message-Id: <-45311-110822190850-29669-tf95/L6URAONwJYYxRFMTw[A]server.ccl.net>
X-Original-From: "Guenter Grethe" <ggrethe::att.net>
Date: Mon, 22 Aug 2011 19:08:46 -0400
Sent to CCL by: "Guenter Grethe" [ggrethe,+,att.net]
CINF Scholarship for Scientific Excellence Sponsored by Accelrys
The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by Accelrys is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF.
Up to two scholarships valued at $1,000 each will be presented at the 243th ACS National Meeting in San Diego CA, March 25 29, 2012. Applicants must be enrolled at a certified college or university and must present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS.
To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe*att.net, that you are applying for a scholarship. Submit your abstract at http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract for CINF Scholarship for Scientific Excellence. PACS will be open for abstract submissions on August 22, 2011, and close on October 17, 2011. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by January 31, 2012. Any questions related to applying for one of the scholarships should be directed to the same e-mail address.
Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of Accelrys-CINF Scholarship for Scientific Excellence at the poster session.
Guenter Grethe
ggrethe*att.net