From owner-chemistry@ccl.net Tue Nov 11 04:47:01 2008 From: "Luis Sim n ls428{=}cam.ac.uk" To: CCL Subject: CCL:G: laplacian density cube files Message-Id: <-38074-081111044404-21485-BuloySqvP9WxKPB7lDPiSw[a]server.ccl.net> X-Original-From: "Luis Sim n" Date: Tue, 11 Nov 2008 04:44:00 -0500 Sent to CCL by: "Luis Sim n" [ls428#,#cam.ac.uk] I have been triying to obtain cube files with the laplacian of the density using either cubegen utility or cube keyword in gaussian. When I used cubegen, I obtained an error message since Laplacian (or gradient, or divergence) keywords were not recognized. In the case of the cube keyword, I did not obtain any error message, but the output contained only the electron density in the .cube file (and the total integrated gradient norm and laplacian in the .out file). I have tried with different versions of Gaussian, either G03 or G98W, and allways observed the same result. Is there any way of obtaining a cube file of these parameters. Is there any 3rd party program able to do that? Can AIMPAC produce these cube files? Thanks: Luis From owner-chemistry@ccl.net Tue Nov 11 07:07:01 2008 From: "Naser eltaher Eltayeb nasertaha90*yahoo.co.uk" To: CCL Subject: CCL:G: Degeneracy in Molecular orbital Message-Id: <-38075-081111070511-13035-2hQZ+RF71l3bthYGcDRFJA(0)server.ccl.net> X-Original-From: "Naser eltaher Eltayeb" Date: Tue, 11 Nov 2008 07:05:08 -0500 Sent to CCL by: "Naser eltaher Eltayeb" [nasertaha90|*|yahoo.co.uk] Dear All 1-How can I know the degeneracy in molecular orbital(singlet , duplet or triblet)if the molecule has C1 symmetry, using the output from Gaussian 03. 2- what is the information I can get it from molecular orbital density.using Gaussian 03. Thank you Naser Eltaher Eltayeb From owner-chemistry@ccl.net Tue Nov 11 08:40:01 2008 From: "Wojciech Gren wjgren^gmail.com" To: CCL Subject: CCL: Reply for question regarding DlPoly free energy calcs along z-coord Message-Id: <-38076-081111055617-3243-C0Vm9+15bPTuy9HbyStPPg|*|server.ccl.net> X-Original-From: "Wojciech Gren" Date: Tue, 11 Nov 2008 05:56:13 -0500 Sent to CCL by: "Wojciech Gren" [wjgren|,|gmail.com] If you need to fix one of the atom coordinates in DlPoly, the best place is freeze subroutine, which deal with fixed atoms. The modification could be to make zero all velocities and forces in z-direction, and record the forces. We use similar method but developed it to be able also apply force to particular group of atoms and use any directions. Wojtek From owner-chemistry@ccl.net Tue Nov 11 09:18:01 2008 From: "William F. Coleman wcoleman.:.wellesley.edu" To: CCL Subject: CCL:G: Degeneracy in Molecular orbital Message-Id: <-38077-081111085710-32706-vT9UqPQ0dFwthJqJeFZvaw|a|server.ccl.net> X-Original-From: "William F. Coleman" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 11 Nov 2008 08:23:32 -0500 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman**wellesley.edu] >1-How can I know the degeneracy in molecular orbital(singlet , duplet or >triblet)if the molecule has C1 symmetry, using the output from Gaussian >03. If the symmetry is C1 then there is only one irreducible representation and it is non-degenerate, so there are no true degeneracies possible. Depending on the complexity molecule there may be "accidental degeneracies", orbitals with the same energy to several significant figures. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html From owner-chemistry@ccl.net Tue Nov 11 10:58:00 2008 From: "Ramon Crehuet rcsqtc(a)iiqab.csic.es" To: CCL Subject: CCL:G: ORCA questions Message-Id: <-38078-081111105434-4196-lph1d/9M5cpjiJA+e9QFsw++server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 11 Nov 2008 15:52:39 +0100 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc*|*iiqab.csic.es] Dear CCLers, I have a couple of questions regarding the use of ORCA. 1) Is it possible to freeze (=fix) the position of certain atoms during an optimization? 2) Is there any control on the memory available to the program? Other packages such as gaussian or gamess need the user to give the available memory for each run. This in some cases determines the algorithm to use. Is there any way to do that with ORCA? Thanks in advance, Ramon From owner-chemistry@ccl.net Tue Nov 11 11:50:01 2008 From: "John McKelvey jmmckel|-|gmail.com" To: CCL Subject: CCL:G: ORCA questions Message-Id: <-38079-081111114538-18736-IHVngzbU4JVZXOCmxO0efg(-)server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_136107_1103168.1226421925394" Date: Tue, 11 Nov 2008 11:45:25 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel++gmail.com] ------=_Part_136107_1103168.1226421925394 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Ramon, I do not know the answer to your question, but have you checked the ORCA site recently, and the latest developments, recent versions and associated documentation? John McKelvey On Tue, Nov 11, 2008 at 9:52 AM, Ramon Crehuet rcsqtc(a)iiqab.csic.es < owner-chemistry]-[ccl.net> wrote: > > Sent to CCL by: Ramon Crehuet [rcsqtc*|*iiqab.csic.es] > Dear CCLers, > I have a couple of questions regarding the use of ORCA. > 1) Is it possible to freeze (=fix) the position of certain atoms during > an optimization? > 2) Is there any control on the memory available to the program? Other > packages such as gaussian or gamess need the user to give the available > memory for each run. This in some cases determines the algorithm to use. > Is there any way to do that with ORCA? > Thanks in advance, > Ramon> > > ------=_Part_136107_1103168.1226421925394 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Ramon,

I do not know the answer to your question, but have you checked the ORCA site recently, and the latest developments, recent versions and associated documentation?

John McKelvey

On Tue, Nov 11, 2008 at 9:52 AM, Ramon Crehuet rcsqtc(a)iiqab.csic.es <owner-chemistry]-[ccl.net> wrote:

Sent to CCL by: Ramon Crehuet [rcsqtc*|*iiqab.csic.es]
Dear CCLers,
I have a couple of questions regarding the use of ORCA.
1) Is it possible to freeze (=fix) the position of certain atoms during
an optimization?
2) Is there any control on the memory available to the program? Other
packages such as gaussian or gamess need the user to give the available
memory for each run. This in some cases determines the algorithm to use.
Is there any way to do that with ORCA?
Thanks in advance,
Ramon



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------=_Part_136107_1103168.1226421925394-- From owner-chemistry@ccl.net Tue Nov 11 12:50:00 2008 From: "Janjua Ramzan Saeed janjua===nenu.edu.cn" To: CCL Subject: CCL: DOS density of states Message-Id: <-38080-081111071403-17305-tz6Za7qc5/cjkIFR/eNj/A{:}server.ccl.net> X-Original-From: "Janjua Ramzan Saeed" Date: Tue, 11 Nov 2008 07:13:57 -0500 Sent to CCL by: "Janjua Ramzan Saeed" [janjua#nenu.edu.cn] Hi Friends! Please! tell me how can we calculate DOS (density of states) by using ADF software! Thanksin anticipation! Janjua NENU China From owner-chemistry@ccl.net Tue Nov 11 14:19:00 2008 From: "Daniel Jana dfjana::gmail.com" To: CCL Subject: CCL:G: ORCA questions Message-Id: <-38081-081111134749-4117-NdxvZKHcHP3M8VOgnxItog]-[server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Nov 2008 19:47:31 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana(!)gmail.com] Hello, Ramon Crehuet rcsqtc(a)iiqab.csic.es wrote: > Sent to CCL by: Ramon Crehuet [rcsqtc*|*iiqab.csic.es] > Dear CCLers, > I have a couple of questions regarding the use of ORCA. > 1) Is it possible to freeze (=fix) the position of certain atoms during > an optimization? > Yes it is. You need to insert a group called "%geom Constraints". Check the manual in pages 86 and 87. > 2) Is there any control on the memory available to the program? Other > packages such as gaussian or gamess need the user to give the available > memory for each run. This in some cases determines the algorithm to use. > Is there any way to do that with ORCA? > I never used any option for this however MaxCore seems to be what you need. You can use it more or less like this: %mp2 MaxCore 1000 end the value comes in MB. There is an email in the orca mailing list from October last year in which Frank Neese mentions that the program isn't very strict in following the values so you should give it some extra space. Not sure if in newer versions things have changed. Best, Daniel From owner-chemistry@ccl.net Tue Nov 11 14:54:01 2008 From: "Adam Tenderholt atenderholt_._gmail.com" To: CCL Subject: CCL: DOS density of states Message-Id: <-38082-081111142539-14734-epZ1cejKVgjtd/w6xglTHw]_[server.ccl.net> X-Original-From: "Adam Tenderholt" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 11 Nov 2008 11:25:21 -0800 MIME-Version: 1.0 Sent to CCL by: "Adam Tenderholt" [atenderholt|-|gmail.com] Hi Janjua, CCL'ers, Please take a look at GaussSum2 (http://gausssum.sourceforge.net/). It should provide a nice graphical interface for calculating DOS spectra > from ADF calculations. Adam On Tue, Nov 11, 2008 at 4:13 AM, Janjua Ramzan Saeed janjua===nenu.edu.cn wrote: > > Sent to CCL by: "Janjua Ramzan Saeed" [janjua#nenu.edu.cn] > Hi Friends! > Please! tell me how can we calculate DOS (density of states) by using ADF software! > > Thanksin anticipation! > > Janjua NENU China> > > From owner-chemistry@ccl.net Tue Nov 11 15:32:01 2008 From: "Mike Towler mike_towler,,vallico.net" To: CCL Subject: CCL: Quantum Monte Carlo summer school - Italy Message-Id: <-38083-081111151631-22652-o2LRqvua0b2E4Hx9jgDl1A|*|server.ccl.net> X-Original-From: "Mike Towler" Date: Tue, 11 Nov 2008 15:16:28 -0500 Sent to CCL by: "Mike Towler" [mike_towler . vallico.net] SUMMER SCHOOL ANNOUNCEMENT "Quantum Monte Carlo and the CASINO program IV" =============================================== Sun 2nd August - Sun 9th August 2009 Towler Institute, Vallico Sotto, Tuscany, Italy http://www.vallico.net/tti/tti.html A4 POSTER FOR THE SCHOOL AVAILABLE HERE : http://www.tcm.phy.cam.ac.uk/~mdt26/poster.png The fourth international summer school in the series "Quantum Monte Carlo and the CASINO program" will take place during August 2009 at the TTI monastery in the Tuscan Apuan Alps in Italy, organized and hosted by members of Cambridge University physics department's Theory of Condensed Matter Group. The aim of the school is to give students a thorough introduction to quantum Monte Carlo as a method for performing high-quality calculations of the electronic structure of atoms, molecules, and materials. The course is designed for young quantum chemists or theoretical physicists who have no previous experience with this technique, though anyone interested is welcome to take part. The monastery is a unique venue where the community spirit and magnificent location have inspired memorable workshops in the past. It is a delightful 16th century building incorporating an ancient church, and is situated in the isolated but spectacular setting of the Tuscan mountain village of Vallico Sotto. We are fully equipped with relevant presentation and computer technology, and all accommodation is on-site. As with all events at the Institute, formal lectures are restricted to the mornings, and participants are given the freedom and space to think and to contemplate and discuss the issues at hand. In addition to hands-on exercises, a programme of healthy recreational activities will be organized in the afternoons, and it is hoped that by following this strict regime, together with breathing clean mountain air and by preparing and sampling fine Tuscan cuisine, the participant will be able to return home mentally and physically refreshed as well as better informed. Describing the complex behaviour of materials at the atomic level requires a sophisticated description of the correlated motion of the electrons. Quantum Monte Carlo (QMC) is an increasingly popular and explicitly many-body method with the unusual capability of yielding highly accurate results whilst also exhibiting a very favourable scaling of computational cost with system size. Over the last eighteen years, the Cambridge group have been researching QMC methods and we have created a powerful, general computer program - CASINO - to carry out the calculations. The school will focus both on the basic theory of QMC and on more advanced practical techniques, and will include a thorough introduction to the CASINO program. A background in density functional theory or similar is normally thought to be useful. Instructors will include the main authors of the CASINO program (Dr. Mike Towler, Dr. Neil Drummond and Dr. Pablo Lopez Rios) and possibly others. Participants would normally need to book a flight to Pisa airport from where onward transportation will be arranged (though other destinations are possible). Details of previous schools - including photographs - are available under the PUBLIC EVENTS link on the TTI web site. Interested students should email Mike Towler (mdt26 at cam.ac.uk) for registration and further details. ========================================================================== NB: TTI IS AVAILABLE FOR HOSTING EVENTS THROUGHOUT THE SUMMER - PLEASE ASK ========================================================================== From owner-chemistry@ccl.net Tue Nov 11 18:22:00 2008 From: "John McKelvey jmmckel#gmail.com" To: CCL Subject: CCL: File system for running ORCA in parallel Message-Id: <-38084-081111181753-24512-rXdqdtMnKkLZzJg9IdbP4A-.-server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_144229_22949946.1226445460623" Date: Tue, 11 Nov 2008 18:17:40 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel()gmail.com] ------=_Part_144229_22949946.1226445460623 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks, ORCA apparently does not run in parallel using NFS. Has anyone run ORCA in parallel on an SMP box, and what file system was used? I'm assuming the problem with NFS might be file locking. One question might be if NFS-V4 would be satisfactory since file locking is supposed to better.. Anyone try this? Best regards, John McKelvey ------=_Part_144229_22949946.1226445460623 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks,

ORCA apparently does not run in parallel using NFS.  Has anyone run ORCA in parallel on an SMP box, and what file system was used?

I'm assuming the problem with NFS might be file locking.  One question might be if NFS-V4 would be satisfactory since file locking is supposed to better..  Anyone try this?

Best regards,

John McKelvey
------=_Part_144229_22949946.1226445460623--