From owner-chemistry@ccl.net Tue May 31 08:17:00 2011 From: "Daniele Gianni daniele.gianni(-)gmail.com" To: CCL Subject: CCL: Fw: IEEE e-Science 2011 workshop on Interoperability in Scientific Computing Message-Id: <-44795-110530163558-32442-BayH9N9Ifcuu96emNbnQCQ---server.ccl.net> X-Original-From: Daniele Gianni Content-Type: multipart/alternative; boundary=001e680f17e46bbb6f04a4843b79 Date: Mon, 30 May 2011 22:35:46 +0200 MIME-Version: 1.0 Sent to CCL by: Daniele Gianni [daniele.gianni^^gmail.com] --001e680f17e46bbb6f04a4843b79 Content-Type: text/plain; charset=ISO-8859-1 IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing ======================================================================== 5th December 2011, Stockholm, Sweden. http://www.comlab.ox.ac.uk/david.johnson/wisc11/ The seventh IEEE e-Science conference, sponsored by the IEEE Computer Society's Technical Committee for Scalable Computing (TCSC), will be held in Stockholm, Sweden from 5th - 8th December 2011. The Workshop on Interoperability in Scientific Computing will be held on the morning of Monday 5th of December, and is co-located with the main conference. Approaches to modelling take many forms. The mathematical, computational and encapsulated components of models can be diverse in terms of complexity and scale, as well as in published implementation (mathematics, source code, and executable files). Many of these systems are attempting to solve real-world problems in isolation. However the long-term scientific interest is in allowing greater access to models and their data, and to enable simulations to be combined in order to address ever more complex issues. Markup languages, metadata specifications, and ontologies for different scientific domains have emerged as pathways to greater interoperability. Domain specific modelling languages allow for a declarative development process to be achieved. Metadata specifications enable coupling while ontologies allow cross platform integration of data. The goal of this workshop is to bring together researchers from across scientific disciplines whose computational models require interoperability. This may arise through interactions between different domains, systems being modelled, connecting model repositories, or coupling models themselves, for instance in multi-scale or hybrid simulations. The outcomes of this workshop will be to better understand the nature of multidisciplinary computational modelling and data handling. Moreover we hope to identify common abstractions and cross-cutting themes in future interoperability research applied to the broader domain of scientific computing. CALL FOR PAPERS We invite submissions for high-quality papers (up to 8 pages in length) within the context of scientific computing in any of the traditional sciences (physics, chemistry, biology), engineering, or scientific/mathematical modelling applied to the social sciences and humanities. Papers should address progress, results or positions in one or more of the following areas: * Use of metadata standards for annotating scientific models and data * Curating and publishing digital models and data to online repositories * Meta-modelling and markup languages for model description * Theoretical frameworks for combining disparate models, multi-scale models * Using standardised data formats in computational models * Domain-specific ontologies for the sciences It is expected that the proceedings of the e-Science 2011 workshops will be published by the IEEE Computer Society Press, USA, and will be made available online through the IEEE Digital Library. SUBMISSION PROCESS Authors are invited to submit papers with unpublished, original work of not more than 8 pages of double column text using single spaced 10 point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines. Templates are available from here: http://www.ieee.org/web/publications/pubservices/confpub/AuthorTools/confere nceTemplates.html. Authors should submit a PDF or PostScript (level 2) file that will print on a PostScript printer. Papers conforming to the above guidelines should be submitted through the EasyChair submission system here: https://www.easychair.org/account/signin.cgi?conf=wisc11 Note, papers should NOT be submitted to the main e-Science 2011 paper submission system, as they will not be directed to the workshop organisers. It is requested that at least one author of each accepted paper attend the conference and workshop. IMPORTANT DATES Full papers due: Monday 18th July 2011 Notification of acceptance: 18th August 2011 Camera-ready: 16th September 2011 Workshop date: 5th December 2011 CHAIRS/ORGANISERS David Johnson, Steve McKeever, (University of Oxford, UK) PROGRAMME COMMITTEE David Nickerson (University of Auckland, New Zealand) Herbert Sauro (University of Washington, USA) Steve Harris (University of Oxford, UK) Jonathan Cooper (University of Oxford, UK) Rutger Vos (University of Reading, UK) Dagmar Waltemath (University of Rostock, Germany) Daniele Gianni (European Space Agency) Mike Stout (University of Nottingham, UK) --001e680f17e46bbb6f04a4843b79 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing=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=3D=3D=3D=3D=3D=3D=3D
5t= h December 2011, Stockholm, Sweden.
http://www.comlab.ox.ac.uk/david.johnson/wisc11/<= /font>


The seventh IEEE e-Science conference, sponsored by the IEEE Comput= er
Society's Technical Committee for Scalable Computing (TCSC), will= be held in
Stockholm, Sweden from 5th - 8th December 2011. The Workshop= on
Interoperability in Scientific Computing will be held on the morning of
= Monday 5th of December, and is co-located with the main conference.

= Approaches to modelling take many forms. The mathematical, computational an= d
encapsulated components of models can be diverse in terms of complexity and=
scale, as well as in published implementation (mathematics, source code= , and
executable files). Many of these systems are attempting to solve r= eal-world
problems in isolation. However the long-term scientific interest is in
a= llowing greater access to models and their data, and to enable simulations<= br>to be combined in order to address ever more complex issues. Markup
languages, metadata specifications, and ontologies for different scientific=
domains have emerged as pathways to greater interoperability. Domainspecific modelling languages allow for a declarative development process t= o
be achieved. Metadata specifications enable coupling while ontologies allow=
cross platform integration of data.

The goal of this workshop is= to bring together researchers from across
scientific disciplines whose = computational models require interoperability.
This may arise through interactions between different domains, systems bein= g
modelled, connecting model repositories, or coupling models themselves= , for
instance in multi-scale or hybrid simulations. The outcomes of thi= s workshop
will be to better understand the nature of multidisciplinary computational<= br>modelling and data handling. Moreover we hope to identify common
abst= ractions and cross-cutting themes in future interoperability research
applied to the broader domain of scientific computing.

CALL FOR PAPE= RS

We invite submissions for high-quality papers (up to 8 pages in l= ength)
within the context of scientific computing in any of the traditio= nal
sciences (physics, chemistry, biology), engineering, or
scientific/mathe= matical modelling applied to the social sciences and
humanities. Papers = should address progress, results or positions in one or
more of the foll= owing areas:

* Use of metadata standards for annotating scientific models and data* Curating and publishing digital models and data to online repositories<= br>* Meta-modelling and markup languages for model description
* Theoret= ical frameworks for combining disparate models, multi-scale models
* Using standardised data formats in computational models
* Domain-speci= fic ontologies for the sciences

It is expected that the proceedings = of the e-Science 2011 workshops will be
published by the IEEE Computer S= ociety Press, USA, and will be made
available online through the IEEE Digital Library.

SUBMISSION PROCES= S

Authors are invited to submit papers with unpublished, original wo= rk of not
more than 8 pages of double column text using single spaced 10= point size on
8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines.

Tem= plates are available from here:
http://www.ieee.org/web/publi= cations/pubservices/confpub/AuthorTools/conferenceTemplates.html.

Authors should submit a PDF or PostScript (level 2) file that will prin= t on
a PostScript printer. Papers conforming to the above guidelines sho= uld be
submitted through the EasyChair submission system here:
https:/= /www.easychair.org/account/signin.cgi?conf=3Dwisc11

Note, papers should NOT be submitted to the main e-Science 2011 papersubmission system, as they will not be directed to the workshop organiser= s.

It is requested that at least one author of each accepted paper a= ttend the
conference and workshop.

IMPORTANT DATES

Full papers due: Mon= day 18th July 2011
Notification of acceptance: 18th August 2011
Camer= a-ready: 16th September 2011
Workshop date: 5th December 2011

CHAIRS/ORGANISERS

David Johnson, Steve McKeever, (University of Oxfo= rd, UK)

PROGRAMME COMMITTEE

David Nickerson (University of Au= ckland, New Zealand)
Herbert Sauro (University of Washington, USA)
Steve Harris (University of Oxford, UK)
Jonathan Cooper (University of O= xford, UK)
Rutger Vos (University of Reading, UK)
Dagmar Waltemath (U= niversity of Rostock, Germany)
Daniele Gianni (European Space Agency) Mike Stout (University of Nottingham, UK)


=

--001e680f17e46bbb6f04a4843b79-- From owner-chemistry@ccl.net Tue May 31 08:51:00 2011 From: "Uttama Mukherjee uttamachemistry()gmail.com" To: CCL Subject: CCL:G: Counterpoise Jobs using G03 on Linux Message-Id: <-44796-110531084432-32349-aWrnx/gsYWYGuGjGFRmmFQ!A!server.ccl.net> X-Original-From: "Uttama Mukherjee" Date: Tue, 31 May 2011 08:44:26 -0400 Sent to CCL by: "Uttama Mukherjee" [uttamachemistry]_[gmail.com] Dear all, I'm trying to give a counterpoise correction job for calculating the binding energy of an ion pair. I am using G03 on linux operating system (64 bit). I have successfully done a similar type of job on windows operating system (using Gaussian03 commands i.e. the counterpoise keyword, then specifying the charge on the ion pair, on the cation and the anion and incorporating the standard orientation of the molecule previously optimized and specifying each value in the standard orientation to the corresponding fragment 1 or 2) and the job shows normal termination. But when I am using the same method on linux, an error is shown and the last line of the output says "Atoms in 0 layers/fragments were specified but there should be two". Is there some other command for input in the linux version? Or am I making some mistake in the input commands? Please help, My log file looked like this %nprocshared=2 Will use up to 2 processors via shared memory. %mem=200MW %chk=1butyldiNO2meimi+nitratedftcp.chk ----------------------------------------------------- # opt=calcfc b3lyp/6-31+g(d) counterpoise=2 scf=tight ----------------------------------------------------- 1/10=4,14=-1,18=20,26=3,38=1,62=2/1,3; 2/9=110,17=6,18=5,40=1/2; 1/10=4,14=-1,18=20,38=1,53=5172,62=2,63=200/22; 3/5=1,6=6,7=11,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4//1; 5/5=2,32=2,38=5/2; 8/6=4,10=90,11=11/1; 11/6=1,8=1,9=11,15=111,16=1/1,2,10; 10/6=1,7=6/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7/7=1,10=1,18=20,25=1,33=-1/1,2,3,16; 1/10=4,14=-1,18=20,53=4052,62=2,63=201/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4//1; 5/5=2,32=2,38=5/2; 8/6=4,10=90,11=11/1; 11/6=1,8=1,9=11,15=111,16=1/1,2,10; 10/6=1,7=6/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7/7=1,10=1,18=20,25=1,33=-1/1,2,3,16; 1/10=4,14=-1,18=20,53=3042,62=2,63=202/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4//1; 5/5=2,32=2,38=5/2; 8/6=4,10=90,11=11/1; 11/6=1,8=1,9=11,15=111,16=1/1,2,10; 10/6=1,7=6/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7/7=1,10=1,18=20,25=1,33=-1/1,2,3,16; 1/10=4,14=-1,18=20,53=2032,62=2,63=203/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4//1; 5/5=2,32=2,38=5/2; 8/6=4,10=90,11=11/1; 11/6=1,8=1,9=11,15=111,16=1/1,2,10; 10/6=1,7=6/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7/7=1,10=1,18=20,25=1,33=-1/1,2,3,16; 1/10=4,14=-1,18=20,53=1022,62=2,63=204/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4//1; 5/5=2,32=2,38=5/2; 8/6=4,10=90,11=11/1; 11/6=1,8=1,9=11,15=111,16=1/1,2,10; 10/6=1,7=6/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7/7=1,10=1,18=20,25=1,33=-1/1,2,3,16; 1/10=4,14=-1,18=20,53=5016,62=2,63=205/22; 7/9=1,25=1,44=-1/16; 1/10=4,14=-1,18=20,62=2,63=200/3(3); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99//99; 2/9=110/2; 1/14=-1,18=20,53=5173,62=2,63=100/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4/5=5,16=3/1; 5/5=2,32=2,38=5/2; 7/7=1,33=-1/1,2,3,16; 1/14=-1,18=20,53=4053,62=2,63=101/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4/5=5,16=3/1; 5/5=2,32=2,38=5/2; 7/7=1,33=-1/1,2,3,16; 1/14=-1,18=20,53=3043,62=2,63=102/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4/5=5,16=3/1; 5/5=2,32=2,38=5/2; 7/7=1,33=-1/1,2,3,16; 1/14=-1,18=20,53=2033,62=2,63=103/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4/5=5,16=3/1; 5/5=2,32=2,38=5/2; 7/7=1,33=-1/1,2,3,16; 1/14=-1,18=20,53=1024,62=2,63=104/22; 3/5=7,6=11,7=11,11=2,16=1,25=1,30=1,74=-5,82=7/1,2,3; 4/5=5,16=3/1; 5/5=2,32=2,38=5/2; 7/7=1,33=-1/1,2,3,16; 1/14=-1,18=20,53=5015,62=2,63=105/22; 7/9=1,44=-1/16; 1/14=-1,18=20,62=2,63=100/3(-28); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99/9=1/99; ----------------------------- 1butyldiNO2meimi+nitratedftcp ----------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 in supermolecule Charge = 1 Multiplicity = 1 in fragment 1. Charge = -1 Multiplicity = 1 in fragment 2. Atoms in 0 layers/fragments were specified but there should be 2. Error termination via Lnk1e in /home/gaussian/g03/l101.exe at Tue May 31 14:54:19 2011. Job cpu time: 0 days 0 hours 0 minutes 2.7 seconds. File lengths (MBytes): RWF= 8 Int= 0 D2E= 0 Chk= 1 Scr= 1 Thanks & regards, Uttama Mukherjee uttamachemistry]*[gmail.com Dept. of Chemistry, D.D.U. Gorakhpur University, Gorakhpur (U.P.) India From owner-chemistry@ccl.net Tue May 31 13:37:00 2011 From: "Tommaso Marcelli tommaso.marcelli(_)chem.polimi.it" To: CCL Subject: CCL:G: Natural Transition Orbitals (NTO) in Gaussian 09 Message-Id: <-44797-110531110929-550-a30U/1Kgv52VGUT1SV7jBQ[*]server.ccl.net> X-Original-From: "Tommaso Marcelli" Date: Tue, 31 May 2011 11:09:26 -0400 Sent to CCL by: "Tommaso Marcelli" [tommaso.marcelli__chem.polimi.it] Dear CCLers, I write to request some assistance with NTOs. I am performing TD-DFT calculations with Gaussian 09 and I would like to use the NTOs to get a qualitative picture of the electronic transitions for my system. While I can save the NTOs from the checkpoint file after the TD-DFT calculation, I can't understand how to get the lambda value for the electronic transition, i.e. the coefficient of the wavefunction for the excitation between a pair of NTOs (which should be very close to 1). I know that the Q-Chem package include this in the output, but I don't understand how to get this with Gaussian. Anybody can help me with that? Thanks a lot Tommaso tommaso.marcelli|,|chem.polimi.it Dipartimento di Chimica, Materiali ed Ingegneria Chimica "Giulio Natta" Politecnico di Milano Via Mancinelli, 7 20131 Milano (Italy) From owner-chemistry@ccl.net Tue May 31 14:12:00 2011 From: "Alex Allardyce aa : chemaxon.com" To: CCL Subject: CCL: Call for papers: ChemAxon's US UGM, Sept 27-28, 2011, San Diego, CA Message-Id: <-44798-110531121049-379-SQEuBYiW4LDn6Qq8iqMLhw++server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------040007080303040205070304" Date: Tue, 31 May 2011 18:10:33 +0200 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa]=[chemaxon.com] This is a multi-part message in MIME format. --------------040007080303040205070304 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit HI, Apologies for cross posting... We are calling for papers for ChemAxon's 2011 US User Group Meeting, to be held on Tuesday and Wednesday, September 27-28th at the Catamaran San Diego Hotel, Spa and Beach Resort in California. The meeting will feature presentations from ChemAxon users, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development. Oral abstract submission deadline is July 15th, 2011 and for poster abstracts, September 1st. To find out more visit the meeting page (http://www.chemaxon.com/events/2011-usugm/) and to submit an abstract please register (http://www.chemaxon.com/ugm.php). To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Wendy Warr and Yvonne Martin visit this page (http://www.chemaxon.com/library/ugm-presentations/). We look forward to seeing you there. BR Alex UGM Satellite meetings (September 26th afternoon and September 29th) - notice dates have changed! Patent professionals and Markush structure users - Monday September 26th afternoon Preceding the UGM we have the second US meeting of the Markush Forum, an afternoon for interested organizations to participate in the development of ChemAxon's tools for Markush structure enumeration and search. This meeting is open to users, content developers should contact us to confirm their participation. Find out more here: https://www.chemaxon.com/library/ugm-presentations/2011-eugm/#markush-forum Developer and End user training - Thursday September 29th Following the UGM will be a 2 track developer and end user Training Day. For developers we have a tutorial/code session and for end users, for the first time, we have a 2 tracks to allow focus on hands on and advanced training. The program is still under development but overview is available: Developer Training Day (http://www.chemaxon.com/events/2011-usugm/#training--developer). End user: Application Focus Training Day (http://www.chemaxon.com/events/2011-usugm/#training--application-focus). -- *Alex Allardyce* Marketing Dir. *ChemAxon**Ltd*. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Tel: +361 453 0435 Fax: +361 4532659 mailto:aa/a\chemaxon.com --------------040007080303040205070304 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit HI,

Apologies for cross posting...

We are calling for papers for ChemAxon's 2011 US User Group Meeting, to be held on Tuesday and Wednesday, September 27-28th at the Catamaran San Diego Hotel, Spa and Beach Resort in California.

The meeting will feature presentations from ChemAxon users, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development.

Oral abstract submission deadline is July 15th, 2011 and for poster abstracts, September 1st. To find out more visit the meeting page (http://www.chemaxon.com/events/2011-usugm/) and to submit an abstract please register (http://www.chemaxon.com/ugm.php).

To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Wendy Warr and Yvonne Martin visit this page (http://www.chemaxon.com/library/ugm-presentations/).

We look forward to seeing you there.

BR
Alex

UGM Satellite meetings (September 26th afternoon and September 29th)
- notice dates have changed!

Patent professionals and Markush structure users - Monday September 26th afternoon
Preceding the UGM we have the second US meeting of the Markush Forum, an afternoon for interested organizations to participate in the development of ChemAxon's tools for Markush structure enumeration and search. This meeting is open to users, content developers should contact us to confirm their participation.  Find out more here: https://www.chemaxon.com/library/ugm-presentations/2011-eugm/#markush-forum

Developer and End user training - Thursday September 29th
Following the UGM will be a 2 track developer and end user Training Day. For developers we have a tutorial/code session and for end users, for the first time, we have a 2 tracks to allow focus on hands on and advanced training. The program is still under development but overview is available: Developer Training Day (http://www.chemaxon.com/events/2011-usugm/#training--developer). End user: Application Focus Training Day (http://www.chemaxon.com/events/2011-usugm/#training--application-focus).


--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037 Hungary
http://www.chemaxon.com
Tel: +361 453 0435
Fax: +361 4532659
mailto:aa/a\chemaxon.com
--------------040007080303040205070304--