From owner-chemistry@ccl.net Thu Jul 31 01:56:00 2008 From: "laxmikanth rao lkjoshiji..yahoo.com" To: CCL Subject: CCL: mail from joshi Message-Id: <-37460-080730024056-2616-4ckjb7FqCl7d0V3mq66nUQ%server.ccl.net> X-Original-From: laxmikanth rao Content-Type: multipart/alternative; boundary="0-691403903-1217396430=:95267" Date: Wed, 30 Jul 2008 11:10:30 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: laxmikanth rao [lkjoshiji(-)yahoo.com] --0-691403903-1217396430=:95267 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear CCL friends=0Ahow to calculate the hole extraction potentials and elec= tron extraction potentials for polymers. =0APlease any suggestions=0AThanks= in advance=0AJoshi=0A=0A=0A Unlimited freedom, unlimited storage. Get= it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.= html/ --0-691403903-1217396430=:95267 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear CCL friends
=0A
 
=0A
how to calcul= ate the hole extraction potentials and electron extraction potentials for p= olymers.
=0A
 
=0A
Please any suggestions
=0A<= DIV> 
=0A
Thanks in advance
=0A
 
=0A
= Joshi
=0A
 
=0A
 

=0A=0A=0A =
Bollywood news, movie reviews, film trailers an= d more! Click here. --0-691403903-1217396430=:95267-- From owner-chemistry@ccl.net Thu Jul 31 04:23:01 2008 From: "may abdelghani may01dz*|*yahoo.fr" To: CCL Subject: CCL: Duel cords processors and parallel calculations Message-Id: <-37461-080730050644-23147-OIx7Prv3tRih/ECs50966w^-^server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1742714935-1217405187=:1283" Date: Wed, 30 Jul 2008 08:06:27 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz+*+yahoo.fr] --0-1742714935-1217405187=:1283 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable dear CCLers, In any calculations, a duel core processors, using only one core for this c= alculation, whereas the second rest inactive. I ask if it is any possibilit= y to help the tow cores of my processor to sharing a one calculation, like = what we do in the parallel calculations (both cores do a one task in the sa= me time). Thanks =C2=A0 =20 =0A=0A=0A ____________________________________________________________= _________________ =0AEnvoyez avec Yahoo! Mail. Une boite mail plus intellig= ente http://mail.yahoo.fr --0-1742714935-1217405187=:1283 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A=0A=0A
=0AEnvoy=C3=A9 avec Yahoo! Mail.Une boite mail plus intelligente. --0-1742714935-1217405187=:1283-- From owner-chemistry@ccl.net Thu Jul 31 06:29:00 2008 From: "Herbert Fruchtl herbert.fruchtl^st-andrews.ac.uk" To: CCL Subject: CCL:G: Duel cords processors and parallel calculations Message-Id: <-37462-080731062421-30836-YpK7RNyHx3aM20g4Qj8CPA[]server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 31 Jul 2008 10:54:17 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl#,#st-andrews.ac.uk] It would help to know WHAT you want to do in parallel. To use several cores at the same time, you need to 1) Write the program for parallel execution 2) Compile the program for parallel execution 3) Run it in parallel. If you have a parallel executable, i.e. 1) and 2) are taken care of, this leaves you with 3), which depends on the parallelization method (and the operating system). - If it's Gaussian, you need %NProcShared=2 in the input. - If it's another OpenMP program, you have to set the environment variable OMP_NUM_THREADS (it depends on the OS how you do that). - If it's an MPI program, you need to run it via a parallel startup program (in most implementations this is called mpirun, but the syntax may vary. RTFM!). - If it's yet another parallelization method (PVM, GA, ...), RTFM! But since anybody who can't be bothered to mention his program is using Gaussian anyway... Herbert may abdelghani may01dz*|*yahoo.fr wrote: > dear CCLers, > In any calculations, a duel core processors, using only one core for > this calculation, whereas the second rest inactive. I ask if it is any > possibility to help the tow cores of my processor to sharing a one > calculation, like what we do in the parallel calculations (both cores do > a one task in the same time). > Thanks > > > > > > > > > ------------------------------------------------------------------------ > Envoyé avec Yahoo! Mail > . > Une boite mail plus intelligente. -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Thu Jul 31 07:04:01 2008 From: "Aimee Tomlinson altomlinson::ngcsu.edu" To: CCL Subject: CCL: Gaussian memory limitations Message-Id: <-37463-080730064841-3859-D93sDSvgnmaRqVcRXGbfVA^_^server.ccl.net> X-Original-From: "Aimee Tomlinson" Date: Wed, 30 Jul 2008 06:48:37 -0400 Sent to CCL by: "Aimee Tomlinson" [altomlinson,,ngcsu.edu] I have 3GB of RAM and my machine will only let me set mem=1700MB - is there a way to use more RAM? From owner-chemistry@ccl.net Thu Jul 31 07:48:00 2008 From: "Mariusz Radon mariusz.radon-,-gmail.com" To: CCL Subject: CCL:G: Locating a broken-symmetry singlet state in Gaussian Message-Id: <-37464-080731062202-30547-xkixCz7+9YOc6dDPF7goJA**server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Thu, 31 Jul 2008 11:16:47 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon~~gmail.com] Sue L chsue2004:yahoo.com wrote: > Is it necessary to put a keyword guess=mix, in order to locate a > broken-symmetry singlet state in Gaussian? If the molecule contains a > symmetry, in which the singly occupied alpha and beta orbitals are in > different symmetry, there is no need to put that keyword? > Hi Sue, Is it enough or not, I think, it depends on particular case... You always need to check whether you really have converged to a broken-symmetry solution or not; AFAIK, even "guess=mix" keyword doesn't guarantee this. So, you need to inspect the molecular orbitals and/or value after the calculations are finished. In such a case, that alpha and beta singly occupied orbitals belong to different symmetries, a nice way to produce the broken symmetry solution might be to manually permute the relevant orbitals (e.g. "guess=alter") and (probably) to use "scf=symm". best wishes, Mariusz Radon From owner-chemistry@ccl.net Thu Jul 31 09:17:00 2008 From: "Jim Green fangzhengjuzhe##gmail.com" To: CCL Subject: CCL: termination failure when calculating the single point energy Message-Id: <-37465-080731032235-23348-rkNcuERPBErIcNgvPyaFjg:_:server.ccl.net> X-Original-From: "Jim Green" Date: Thu, 31 Jul 2008 03:22:31 -0400 Sent to CCL by: "Jim Green" [fangzhengjuzhe###gmail.com] After 129cycles , the job stopped with showing the following line:Convergence failure -- run terminated. Fllowing are the coordiatesobtained from the b3lyp/6-31+g* optimization without imaginary frequency) and methods used in caculating the single point energy No.1 N 0.242495 -1.154337 -0.000279 C -0.493856 -0.003331 -0.000307 C 2.199339 0.005971 0.000418 N 1.489904 -1.139241 0.000147 H 3.281157 0.007813 -0.000673 N 1.484761 1.144348 0.000236 N 0.232496 1.155344 -0.000536 S -2.206353 -0.082985 0.000115 H -2.360017 1.261310 0.001190 No.2 N -0.212199 -1.149311 -0.000403 C 0.504977 0.024785 0.000075 C -1.525031 1.124235 0.000009 C -2.235284 -0.110641 0.000081 N -1.443543 -1.173021 0.000164 H -2.065966 2.070024 -0.000931 H -3.312531 -0.223283 0.000801 N -0.212775 1.154543 -0.000050 S 2.225101 -0.073180 0.000041 H 2.388520 1.268380 0.000502 No3 N -1.432871 -1.116161 -0.000078 C 0.478066 0.025252 -0.000618 C -1.556660 1.082156 -0.000115 N -2.217085 -0.136704 0.001503 H -2.177607 1.973435 0.000119 N -0.194935 -1.201448 -0.001039 N -0.253537 1.144458 -0.001079 S 2.187213 -0.046630 0.000488 H 2.342768 1.297178 0.001312 The charge and multiply of them is 1,2 respectively. #p rob3lyp/6-311++g(2df,2p) sp scf=tight I have tried to increase the maxcycle,(because the DFT are RO, Icannot use QC),and change the initial guess but they all doesnot work. what should I do? From owner-chemistry@ccl.net Thu Jul 31 09:52:01 2008 From: "Dong Fang fangzhengjuzhe%a%gmail.com" To: CCL Subject: CCL: termination failure when calculating the single point energy Message-Id: <-37466-080731073413-5602-ItWG7Zx/wQL/p5x9Oqw60A.:.server.ccl.net> X-Original-From: "Dong Fang" Date: Thu, 31 Jul 2008 07:34:09 -0400 Sent to CCL by: "Dong Fang" [fangzhengjuzhe]![gmail.com] After 129cycles , the job stopped with showing the following line:Convergence failure -- run terminated. Fllowing are the coordiatesobtained from the b3lyp/6-31+g* optimization without imaginary frequency) and methods used in caculating the single point energy No.1 N 0.242495 -1.154337 -0.000279 C -0.493856 -0.003331 -0.000307 C 2.199339 0.005971 0.000418 N 1.489904 -1.139241 0.000147 H 3.281157 0.007813 -0.000673 N 1.484761 1.144348 0.000236 N 0.232496 1.155344 -0.000536 S -2.206353 -0.082985 0.000115 H -2.360017 1.261310 0.001190 No.2 N -0.212199 -1.149311 -0.000403 C 0.504977 0.024785 0.000075 C -1.525031 1.124235 0.000009 C -2.235284 -0.110641 0.000081 N -1.443543 -1.173021 0.000164 H -2.065966 2.070024 -0.000931 H -3.312531 -0.223283 0.000801 N -0.212775 1.154543 -0.000050 S 2.225101 -0.073180 0.000041 H 2.388520 1.268380 0.000502 No3 N -1.432871 -1.116161 -0.000078 C 0.478066 0.025252 -0.000618 C -1.556660 1.082156 -0.000115 N -2.217085 -0.136704 0.001503 H -2.177607 1.973435 0.000119 N -0.194935 -1.201448 -0.001039 N -0.253537 1.144458 -0.001079 S 2.187213 -0.046630 0.000488 H 2.342768 1.297178 0.001312 The charge and multiply of them is 1,2 respectively. #p rob3lyp/6-311++g(2df,2p) sp scf=tight I have tried to increase the maxcycle,(because the DFT are RO, Icannot use QC),and change the initial guess but they all doesnot work. what should I do? From owner-chemistry@ccl.net Thu Jul 31 10:27:00 2008 From: "errol lewars elewars:+:trentu.ca" To: CCL Subject: CCL: C&E News article Message-Id: <-37467-080730124622-18449-BZWyLOHRPeRRpDR5s1aEIQ()server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 30 Jul 2008 12:16:13 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars .. trentu.ca] Maybe you want "Battle of the Functionals", 2008, E. K. Wilson, C&EN, 30 June, pp 34-37 Other C&EN articles mentioning DFT are 1998 "Chemistry Nobel Goes Virtual", E. K. Wilson, 19 October, pp 12-13 1996 "Theoretical Chemistry Expands..." E. K. Wilson, 19 August, pp 35-38 1990 "Density Functional Theory Gains..." S. Borman, 9 April, p 22 E. Lewars ========== John McKelvey jmmckel * gmail.com wrote: > My apologies for this, but could someone remind me in which very > recent issue of C&E News was there an article discussing theoretical > methods, and I think DFT? > > Thanks! > > > John McKelvey From owner-chemistry@ccl.net Thu Jul 31 11:05:00 2008 From: "neeraj misra neerajmisra=-=hotmail.com" To: CCL Subject: CCL: frequency calculations Message-Id: <-37468-080731110306-856-cnNZFYUuqBtatJ7BIzaqNw||server.ccl.net> X-Original-From: "neeraj misra" Date: Thu, 31 Jul 2008 11:03:02 -0400 Sent to CCL by: "neeraj misra" [neerajmisra##hotmail.com] I SHALL BE VERY THANKFUL IF ANYONE OF THE CCLERS WHO HAVE EVER CALCULATED THE VIBRATIONAL FREQUENCIES USING THE SIESTA PACKAGE, TELL ME HOW TO GET THE FREQUENCIES USING SIESTA.I AM WORKING ON A BIOMOLECULE HAVING 22 ATOMS. THANKS IN ADVANCE From owner-chemistry@ccl.net Thu Jul 31 11:48:00 2008 From: "zhendong zhao zzhao : olemiss.edu" To: CCL Subject: CCL:G: Gaussian memory limitations Message-Id: <-37469-080731114340-29417-B3NBcWbz8mxnSOEpBNuh6w-#-server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 31 Jul 2008 10:15:21 -0500 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao~~olemiss.edu] Hi, For Gaussian running on 32bit machine, you can only request 2G memory per CPU for Gaussian. This is what I learned from Gaussian tech support. ZZ On Wed, 30 Jul 2008 06:48:37 -0400 "Aimee Tomlinson altomlinson::ngcsu.edu" wrote: > > Sent to CCL by: "Aimee Tomlinson" [altomlinson,,ngcsu.edu] > > I have 3GB of RAM and my machine will only let me set mem=1700MB - is > there a way to use more RAM? > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the %x% sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Thu Jul 31 12:36:01 2008 From: "Ol Ga eurisco1+*+pochta.ru" To: CCL Subject: CCL:G: termination failure when calculating the single point energy Message-Id: <-37470-080731123235-28043-cWVE4cEN9j8JCtwmpdnkKw*_*server.ccl.net> X-Original-From: "Ol Ga" Date: Thu, 31 Jul 2008 12:32:31 -0400 Sent to CCL by: "Ol Ga" [eurisco1 : pochta.ru] Dear Dong Fang! I have achieved the convergence (please see below the right answer) in SCF 1 very fast. The correct route seection is #p rob3lyp/6-311++g(2df,2p) sp scf=(vshift=100,tight,maxcycle=512) the archive section is 1|1|UNPC-UNK|SP|ROB3LYP|6-311++G(2df,2p)|C2H2N4S1(1+,2)|PCUSER|31-Jul- 2008|0||#P ROB3LYP/6-311++G(2DF,2P) SP SCF=(VSHIFT=100,TIGHT)||GN||1,2 |N,0,0.242495,-1.154337,-0.000279|C,0,-0.493856,-0.003331,-0.000307|C, 0,2.199339,0.005971,0.000418|N,0,1.489904,-1.139241,0.000147|H,0,3.281 157,0.007813,-0.000673|N,0,1.484761,1.144348,0.000236|N,0,0.232496,1.1 55344,-0.000536|S,0,-2.206353,-0.082985,0.000115|H,0,-2.360017,1.26131 ,0.00119||Version=IA32W-G03RevC.01|State=2-A|HF=-694.2412278|RMSD=4.49 8e-010|Dipole=0.3717363,0.2861733,0.0000715|PG=C01 [X(C2H2N4S1)]||+*+ Sincerely, Ol Ga > Sent to CCL by: "Dong Fang" [fangzhengjuzhe]![gmail.com] > After 129cycles , the job stopped with showing the following line:Convergence failure -- run terminated. > Fllowing are the coordiatesobtained from the b3lyp/6-31+g* optimization without imaginary frequency) and methods used in caculating the single point energy > No.1 > N 0.242495 -1.154337 -0.000279 > C -0.493856 -0.003331 -0.000307 > C 2.199339 0.005971 0.000418 > N 1.489904 -1.139241 0.000147 > H 3.281157 0.007813 -0.000673 > N 1.484761 1.144348 0.000236 > N 0.232496 1.155344 -0.000536 > S -2.206353 -0.082985 0.000115 > H -2.360017 1.261310 0.001190 > No.2 > N -0.212199 -1.149311 -0.000403 > C 0.504977 0.024785 0.000075 > C -1.525031 1.124235 0.000009 > C -2.235284 -0.110641 0.000081 > N -1.443543 -1.173021 0.000164 > H -2.065966 2.070024 -0.000931 > H -3.312531 -0.223283 0.000801 > N -0.212775 1.154543 -0.000050 > S 2.225101 -0.073180 0.000041 > H 2.388520 1.268380 0.000502 > No3 > N -1.432871 -1.116161 -0.000078 > C 0.478066 0.025252 -0.000618 > C -1.556660 1.082156 -0.000115 > N -2.217085 -0.136704 0.001503 > H -2.177607 1.973435 0.000119 > N -0.194935 -1.201448 -0.001039 > N -0.253537 1.144458 -0.001079 > S 2.187213 -0.046630 0.000488 > H 2.342768 1.297178 0.001312 > > The charge and multiply of them is 1,2 respectively. > > #p rob3lyp/6-311++g(2df,2p) sp scf=tight > > I have tried to increase the maxcycle,(because the DFT are RO, Icannot use QC),and change the initial guess but they all doesnot work. what should I do? > From owner-chemistry@ccl.net Thu Jul 31 14:53:01 2008 From: "John McKelvey jmmckel---gmail.com" To: CCL Subject: CCL: C&E News article Message-Id: <-37471-080731142005-14727-2hQZ+RF71l3bthYGcDRFJA(-)server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_73938_19576170.1217524563783" Date: Thu, 31 Jul 2008 13:16:03 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel:-:gmail.com] ------=_Part_73938_19576170.1217524563783 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks! Nice reminder of other articles. John On Wed, Jul 30, 2008 at 12:16 PM, errol lewars elewars:+:trentu.ca < owner-chemistry() ccl.net> wrote: > > Sent to CCL by: errol lewars [elewars .. trentu.ca] > > > Maybe you want "Battle of the Functionals", 2008, E. K. Wilson, C&EN, 30 > June, pp 34-37 > > Other C&EN articles mentioning DFT are > 1998 "Chemistry Nobel Goes Virtual", E. K. Wilson, 19 October, pp 12-13 > 1996 "Theoretical Chemistry Expands..." E. K. Wilson, 19 August, pp 35-38 > 1990 "Density Functional Theory Gains..." S. Borman, 9 April, p 22 > > E. Lewars > ========== > > > > John McKelvey jmmckel * gmail.com wrote: > > My apologies for this, but could someone remind me in which very recent >> issue of C&E News was there an article discussing theoretical methods, and I >> think DFT? >> >> Thanks! >> >> >> John McKelveyhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ------=_Part_73938_19576170.1217524563783 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Thanks!  Nice reminder of other articles.

John

On Wed, Jul 30, 2008 at 12:16 PM, errol lewars elewars:+:trentu.ca <owner-chemistry() ccl.net> wrote:

Sent to CCL by: errol lewars [elewars .. trentu.ca]


Maybe you want "Battle of the Functionals", 2008, E. K. Wilson, C&EN, 30 June, pp 34-37

Other C&EN articles mentioning DFT are
1998 "Chemistry Nobel Goes Virtual", E. K. Wilson, 19 October, pp 12-13
1996 "Theoretical Chemistry Expands..."  E. K. Wilson, 19 August, pp 35-38
1990  "Density Functional Theory Gains..." S. Borman, 9 April, p 22

E. Lewars
==========



John McKelvey jmmckel * gmail.com wrote:

My apologies for this, but could someone remind me in which very recent issue of C&E News was there an article discussing theoretical methods, and I think DFT?

Thanks!


John McKelvey



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------=_Part_73938_19576170.1217524563783-- From owner-chemistry@ccl.net Thu Jul 31 21:04:02 2008 From: "Kristin N Robinson krobinson,+,schrodinger.com" To: CCL Subject: CCL: University of Houston Workshop - Molecular Modeling and Drug Discovery Message-Id: <-37472-080731175705-7916-TgxvOZtq55jQeyuUnv6xjA ~~ server.ccl.net> X-Original-From: "Kristin N Robinson" Date: Thu, 31 Jul 2008 17:57:01 -0400 Sent to CCL by: "Kristin N Robinson" [krobinson#%#schrodinger.com] Please join us for a workshop on Molecular Modeling and Drug Discovery with the Schrodinger Suite at the University of Houston. Presenter: Carolyn McQuaw, PhD, Schrodinger Applications Scientist Date: August 12th, 2008 Time: 10:00am to 3:00pm; with an hour break for lunch on campus (Registration: 9:00am to 10:00am) Where: University of Houston, PGH, Room 200 Cost: Free! The morning session will include an overview of all of our products, including our molecular modeling tools for undergraduate education and research, as well as hands-on exercises with the Schrodinger Suite 2008. The afternoon session will be devoted to Drug Discovery and Design with the Schrodinger Suite, which will include a sample demonstration of active site identification, virtual screening, and protein docking. Please contact Kristin Robinson for more details or to reserve your seat at the workshop.
dear CCLers,
In any calcu= lations, a duel core processors, using only one core for this calculation, = whereas the second rest inactive. I ask if it is any possibility to help th= e tow cores of my processor to sharing a one calculation, like what we do i= n the parallel calculations (both cores do a one task in the same time).Thanks