From owner-chemistry@ccl.net Thu Mar 25 00:42:00 2010 From: "YZ Lan lyzhao*o*zjnu.cn" To: CCL Subject: CCL: Implementation of Hartree-Fock response calculation Message-Id: <-41522-100325003933-9454-AYvsoL/LYXZJFtwM9modyA(a)server.ccl.net> X-Original-From: "YZ Lan" Date: Thu, 25 Mar 2010 00:39:29 -0400 Sent to CCL by: "YZ Lan" [lyzhao,+,zjnu.cn] Dear CCLers, I want to make a program for calculating the (hyper)polarizabilities based on Hartree-Fock response theory. J.Chem.Phys. v82, p3235 is a good theoretical reference. Is there a reference (not source code such as Dalton and NWChem) for implementation of Hartree-Fock response calculation? Thank you very much. Lan From owner-chemistry@ccl.net Thu Mar 25 01:48:00 2010 From: "Haibin Li lihb734[A]yahoo.com" To: CCL Subject: CCL: Applicability of Density Functional Message-Id: <-41523-100324085439-5541-fu8uzdnEUmb8r6VkqsXZhw^-^server.ccl.net> X-Original-From: "Haibin Li" Date: Wed, 24 Mar 2010 08:54:36 -0400 Sent to CCL by: "Haibin Li" [lihb734,yahoo.com] Dear CCLers: As we know, Density Funtional Theory (DFT) become more and more popular in the field of Computational Chemistry. Although the exact form of Exchange-Correlation Functional is not known, many expert have developed a wide variety of approximate functional designed to specific systerms, for example, SAOP potential was developed specifically to investigate spectropic properties. Thus, when a novice enter the fied of DFT, how can he understand which functional is suitable for the systems under his investigation? Is there any reference or deposity or database to which we can refer? Or, we should read all papers concerning the developmen of functional, benchmark test Thanks in advance for your help. From owner-chemistry@ccl.net Thu Mar 25 05:25:01 2010 From: "willsd,+,appstate.edu" To: CCL Subject: CCL: Applicability of Density Functional Message-Id: <-41524-100325050527-25032-+4ZjaptIjBvKQ6Z7i0CcvQ[#]server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 25 Mar 2010 08:33:24 GMT MIME-Version: 1.0 Sent to CCL by: [willsd##appstate.edu] I do not think of myself as a novice, but I am still VERY interested in the answer(s) to this question. Is there a resource that lists what functionals have been developed for which purpose, which basis sets are recommended for them (for those of us who are using orbital based DFT), and codes where these are implemented? Steve Williams ----- Original Message ----- > From: "Haibin Li lihb734[A]yahoo.com" Date: Thursday, March 25, 2010 2:39 am Subject: CCL: Applicability of Density Functional To: "Williams, Steve " > > Sent to CCL by: "Haibin Li" [lihb734,yahoo.com] > > Dear CCLers: > As we know, Density Funtional Theory (DFT) become more and more > popular in the field of Computational Chemistry. Although the exact > form of Exchange-Correlation Functional is not known, many expert > have developed a wide variety of approximate functional designed to > specific systerms, for example, SAOP potential was developed > specifically to investigate spectropic properties. Thus, when a > novice enter the fied of DFT, how can he understand which > functional is suitable for the systems under his investigation? Is > there any reference or deposity or database to which we can refer? > Or, we should read all papers concerning the developmen of > functional, benchmark test > Thanks in advance for your help. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the [] sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Thu Mar 25 06:00:01 2010 From: "pascal boulet pascal.boulet . univ-provence.fr" To: CCL Subject: CCL: Applicability of Density Functional Message-Id: <-41525-100325051053-26075-fRfvDcYivai6ntHibP+3VA:-:server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 25 Mar 2010 09:38:19 +0100 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet^univ-provence.fr] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello, Perhaps, you can start with this article (and references therein): J. Chem. Phys. A, 2007, 111(42), 10439-10452, Sousa et al. Pascal Haibin Li lihb734[A]yahoo.com a écrit : > Sent to CCL by: "Haibin Li" [lihb734,yahoo.com] > > Dear CCLers: > As we know, Density Funtional Theory (DFT) become more and more popular in the field of Computational Chemistry. Although the exact form of Exchange-Correlation Functional is not known, many expert have developed a wide variety of approximate functional designed to specific systerms, for example, SAOP potential was developed specifically to investigate spectropic properties. Thus, when a novice enter the fied of DFT, how can he understand which functional is suitable for the systems under his investigation? Is there any reference or deposity or database to which we can refer? Or, we should read all papers concerning the developmen of functional, benchmark test > Thanks in advance for your help.> > > - -- Dr. pascal Boulet, computational chemist Laboratoire Chimie Provence, UMR 6264 University of Aix-Marseille I Avenue Escadrille Normandie-Niemen 13397 Marseille Cedex 20 France ********** Tel. (+33) (0)491.63.71.17 Fax. (+33) (0)491.63.71.11 ********** http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkurIPYACgkQNLjdBN1V75lEnQCeKa8T7MeiyU2b/u63uSgBFOL9 AEMAoLwOMIcMVCGMH0X4t36U4jvipjsl =E1Ca -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Thu Mar 25 09:09:00 2010 From: "Marcel Swart marcel.swart_-_icrea.es" To: CCL Subject: CCL: Applicability of Density Functional Message-Id: <-41526-100325090143-26480-wXG28IjmZJke8VIBgT3TMQ{=}server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Date: Thu, 25 Mar 2010 14:01:29 +0100 Mime-Version: 1.0 (Apple Message framework v1077) Sent to CCL by: Marcel Swart [marcel.swart * icrea.es] I think there are a number of good references already available for DFT: Density functional theory for transition metals and transition metal = chemistry Chris Cramer and Don Truhlar Phys. Chem. Chem. Phys., 2009, 11, 10757=9610816 Prescription for the design and selection of density functional approximations: More constraint satisfaction with fewer fits John Perdew, Adrienn Ruzsinszky, Jianmin Tao, Viktor Staroverov, Gus = Scuseria, and Gabor Csonka J. Chem. Phys. 2005, 123, 062201 A Chemist's Guide To Density Functional Theory Wolfram Koch and Max Holthausen WIley-VCH, Weinheim, 2000 I don't think there is a database where it is stated which program has = which functional, etc. Marcel. On Mar 25, 2010, at 9:33 AM, willsd,+,appstate.edu wrote: > I do not think of myself as a novice, but I am still VERY interested = in the answer(s) to this=20 > question. Is there a resource that lists what functionals have been = developed for which=20 > purpose, which basis sets are recommended for them (for those of us = who are using=20 > orbital based DFT), and codes where these are implemented? > Steve Williams =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. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart**icrea.es marcel.swart**udg.edu web http://www.marcelswart.eu =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 From owner-chemistry@ccl.net Thu Mar 25 09:45:01 2010 From: "Thomas =?iso-8859-1?b?S2rDg8KmcmdhYXJk?= tkjaergaard^-^chem.au.dk" To: CCL Subject: CCL: Implementation of Hartree-Fock response calculation Message-Id: <-41527-100325045905-24520-yRXYU5JebpNCIX28qZrMBw#server.ccl.net> X-Original-From: Thomas =?iso-8859-1?b?S2rDg8KmcmdhYXJk?= Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 25 Mar 2010 09:22:31 +0100 MIME-Version: 1.0 Sent to CCL by: Thomas =?iso-8859-1?b?S2rDg8KmcmdhYXJk?= [tkjaergaard++chem.au.dk] not that I know of but J. chem. Phys. 97 (2) 1992 page 1174 gives a little more details, although no explicit expressions for implementation so you need to work out the commutators yourself. best regards Thomas kjaergaard Quoting "YZ Lan lyzhao*o*zjnu.cn" : > > Sent to CCL by: "YZ Lan" [lyzhao,+,zjnu.cn] > Dear CCLers, > I want to make a program for calculating the > (hyper)polarizabilities based on Hartree-Fock response theory. > J.Chem.Phys. v82, p3235 is a good theoretical reference. Is there a > reference (not source code such as Dalton and NWChem) for > implementation of Hartree-Fock response calculation? > Thank you very much. > > Lan> > > From owner-chemistry@ccl.net Thu Mar 25 10:18:00 2010 From: "Chad P Johnston chad.johnston^engr.uconn.edu" To: CCL Subject: CCL: solid/liquid interface reactions Message-Id: <-41528-100325095508-8046-USeG1b40azQofaGIUdny1Q-x-server.ccl.net> X-Original-From: "Chad P Johnston" Date: Thu, 25 Mar 2010 09:55:04 -0400 Sent to CCL by: "Chad P Johnston" [chad.johnston+/-engr.uconn.edu] Hi All, I am interested in modeling reactions at the solid/liquid interface, e.g., adsorption and redox, primarily for geochemical applications. There are a number of methods used in the literature including cluster models and periodic slabs. Many of these systems include transition metals, which I understand can complicate DFT calculations. I am wondering what opinions people have as to which approaches work best, balancing calculation efficiency with accuracy. For example, does the ONIOM model have promise here? Thanks and I look forward to an interesting discussion. Chad Johnston chad.johnston]=[engr.uconn.edu From owner-chemistry@ccl.net Thu Mar 25 10:53:01 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek .. few.vu.nl" To: CCL Subject: CCL: Implementation of Hartree-Fock response calculation Message-Id: <-41529-100325102435-32102-VhHFY1DZjbVXN/y0zzwM2A_-_server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 25 Mar 2010 15:18:22 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek#,#few.vu.nl] On Thu, Mar 25, 2010 at 5:39 AM, YZ Lan lyzhao*o*zjnu.cn wrote: > > Sent to CCL by: "YZ =A0Lan" [lyzhao,+,zjnu.cn] > Dear CCLers, > =A0 I want to make a program for calculating the (hyper)polarizabilities = based on Hartree-Fock response theory. J.Chem.Phys. v82, p3235 is a good th= eoretical reference. Is there a reference (not source code such as Dalton a= nd NWChem) for implementation of Hartree-Fock response calculation? Can you say something about the size of your system? Do you want to work in an orthogonal one particle basis? Is quadratic response enough or do you need arbitrary order? I ask because the more modern approaches for large systems are also more complicated to implement. If you just want to experiment on small systems you can write something in an afternoon if you have access to the one and two electron integrals. Regards, Ulf Ekstrom From owner-chemistry@ccl.net Thu Mar 25 13:52:00 2010 From: "Thomas Manz thomasamanz**gmail.com" To: CCL Subject: CCL: negative eigen value for virtual orbital reg Message-Id: <-41530-100322153601-825-Tb3yxJhXmiDvgMcwwE9yPw*|*server.ccl.net> X-Original-From: Thomas Manz Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 22 Mar 2010 14:34:45 -0400 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz- -gmail.com] Rajagopala Reddy, I think there are situations where slightly negative eigenvalues appear for the unoccupied orbitals. I expect this would be the case for the F atom, for example, since adding another electron would be highly favorable. Sincerely, Tom Manz On Sat, Mar 20, 2010 at 11:39 PM, Rajagopala Reddy Seelam rajagopalaseelam^^^gmail.com wrote: > > Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam(~)gmail.com] > Dear CCL members, > > Can a virtual(unoccupied) orbital have negative eigen value.Generally occ= upied > orbitals have negative eigen value and unoccupied orbitals have positive = eigen > values.If we get any negative eigen values for unoccupied orbitals was th= at > mean optimization not done correctly.Can any one of you please clarify my > doubt. > > Thank you so much > > Regards, > Rajagopala Reddy > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Mar 25 14:26:01 2010 From: "Andrew Voronkov drugdesign : yandex.ru" To: CCL Subject: CCL: question on free patents online database Message-Id: <-41531-100325135348-475-wEW770naM9eXKv/+v00s3g::server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 25 Mar 2010 20:53:34 +0300 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign*_*yandex.ru] Dear CCL users, I am curious about how Free Patents online was created. It s a very nice service, but for the last time it s almost all the time not available. I wonder where and how approximately the mine and get chemical structure-patent information. It would be nice to do something similar. Best regards, Andrew From owner-chemistry@ccl.net Thu Mar 25 17:27:01 2010 From: "Lesley Rae Rutledge lesley.rutledge-*-uleth.ca" To: CCL Subject: CCL:G: Problem with ONIOM calculations Message-Id: <-41532-100325172520-4684-JZAKDZ8elNIlZKjjCP0zdQ*_*server.ccl.net> X-Original-From: "Lesley Rae Rutledge" Date: Thu, 25 Mar 2010 17:25:17 -0400 Sent to CCL by: "Lesley Rae Rutledge" [lesley.rutledge|*|uleth.ca] Hello, I am trying to run ONIOM calculations (M06-2x/6-31G(d):AMBER) in Gaussian 09 Revision A.02 and I am having a few problems. My system has 4162 atoms, where 149 are in the QM region (1316 basis functions). I am running my calculations on 8 processors with 8GB of memory and 160 GB of disk space. In order to build my model, there are multiple stages of calculations, where I came to the stage where I wish to fix all of the low level region and optimize just the hydrogen atoms of the QM region. This calculation finished. However, the next stage was to use this system, and optimize the whole QM region (with the MM region fixed). These calculations die just before it starts the high-level calculation on the model system with the following error: Cartesian Forces: Max 0.059474500 RMS 0.000788502 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Internal Forces: Max 0.047983376 RMS 0.006291829 Search for a local minimum. Step number 1 out of a maximum of 894 All quantities printed in internal units (Hartrees-Bohrs-Radians) NRF ne Abs NRFX Error termination via Lnk1e in /opt/g09/l103.exe If I reduce the size of the MM region, I get the same error. Also, if I delete all of the MM region and just run an M06-2X/6-31G(d) calculation (on the QM part), I have no problems (goes about 35 steps in the optimization in 24 hours). We are aware that you can split up ONIOM calculations into their parts (to run separately), which I have tried to generate, yet these don't finish either. I get the following error: GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Operation on file out of range. However, this calculation does generate the three inputs for the single-point calculations on the system before it dies. The high-level calculation on the model system has all of the MM atoms present, but they appear as: Bq-#1-0.442200(Iso=1.00782504,Spin=1,GFac=2.792846) -1 -25.988729094663 -0.265707167253 -16.971277852321 Bq-#1--0.631800(Iso=15.99491464) -1 -26.778340617607 -0.824800703903 -17.146345953700 Bq-#1--0.006900(Iso=12) -1 -26.646213612701 -2.047053577460 -16.427388903608 .. If I take this partial output as input for the high-level optimization calculation on the model system, this calculation will run (but very slowly - only 2 optimization steps in 24 hours, even though the basis functions are correct for only the QM atoms being present). Therefore, my questions are: Why are my ONIOM calculations dying? Is this a memory or disk problem? How do I properly calculate the required memory (and disk) for an ONIOM calculation in Gaussian? Any help would be greatly appreciated. Thanks very much for your time, Lesley Rutledge From owner-chemistry@ccl.net Thu Mar 25 20:33:00 2010 From: "YZ Lan lyzhao-#-zjnu.cn" To: CCL Subject: CCL: Implementation of Hartree-Fock response calculation Message-Id: <-41533-100325202702-19938-uUTIwfHHz+mWAaeW8BGycg{=}server.ccl.net> X-Original-From: "YZ Lan" Date: Thu, 25 Mar 2010 20:26:59 -0400 Sent to CCL by: "YZ Lan" [lyzhao : zjnu.cn] Dear CCLers, Thank Dr. Ulf Ekstrom and Dr. Thomas kjaergaard for your help. >Can you say something about the size of your system? Do you want >to work in an orthogonal one particle basis? Is quadratic response >enough or do you need arbitrary order? >I ask because the more modern approaches for large systems are also >more complicated to implement. If you just want to experiment on >small systems you can write something in an afternoon if you have >access to the one and two electron integrals. I have finished the RHF energy calculation model for a system with about 500 GTOs. Could you give me a reference for writing something in an afternoon to implement the HF response calculation for a small system? Best regards, Lan Date:2010-03-26 ======================================================== > FromUlf_Ekstr ulfek .. few.vu.nl Date2010-03-25 23:22:10 ToLan, Youzhao Cc SubjectCCL: Implementation of Hartree-Fock response calculation Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstrm?= [ulfek#,#few.vu.nl] On Thu, Mar 25, 2010 at 5:39 AM, YZ Lan lyzhao*o*zjnu.cn wrote: > > Sent to CCL by: "YZ Lan" [lyzhao,+,zjnu.cn] > Dear CCLers, > I want to make a program for calculating the (hyper)polarizabilities based on Hartree-Fock response theory. J.Chem.Phys. v82, p3235 is a good theoretical reference. Is there a reference (not source code such as Dalton and NWChem) for implementation of Hartree-Fock response calculation? Can you say something about the size of your system? Do you want to work in an orthogonal one particle basis? Is quadratic response enough or do you need arbitrary order? I ask because the more modern approaches for large systems are also more complicated to implement. If you just want to experiment on small systems you can write something in an afternoon if you have access to the one and two electron integrals. Regards, Ulf Ekstromhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt