From owner-chemistry@ccl.net Tue Nov 23 00:29:01 2010 From: "Mikael Johansson mikael.johansson^^iki.fi" To: CCL Subject: CCL: Peterson basis sets Message-Id: <-43200-101122084307-6636-XaFf6Z8WQoRk3hqJkLYt4w-$-server.ccl.net> X-Original-From: Mikael Johansson Content-ID: Content-Type: MULTIPART/Mixed; BOUNDARY="-696237619-1555081583-1290432674=:19082" Date: Mon, 22 Nov 2010 15:42:59 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson+/-iki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---696237619-1555081583-1290432674=:19082 Content-Type: TEXT/PLAIN; CHARSET=UTF-8; FORMAT=flowed Content-Transfer-Encoding: 8BIT Content-ID: Hello Nazanin, On Mon, 22 Nov 2010, nazanin jamshidi na.jamshidi,+,gmail.com wrote: > I used pseudopotential-based augmented correlation-consistent basis sets > (aug-cc-pVDZ-PP) [...] > Therefore I don't know how can I omit relativistic effect from these basis > sets. You cannot omit relativistic effect from the ECP, they are "built-in". You have to use a non-relativistic ECP, or do an all-electron calculation without including any relativistic effects. The latest NRPP for gold that I am aware of (enlighten me, someone, if there is something newer) is by Schwerdtfeger at al, JCP 91 (1989) 1762. Take a look at: http://www.theochem.uni-stuttgart.de/pseudopotentials/index.en.html Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ ---696237619-1555081583-1290432674=:19082-- From owner-chemistry@ccl.net Tue Nov 23 08:47:00 2010 From: "Maciej Maslyk maciejmarcin.maslyk .. ceu.es" To: CCL Subject: CCL:G: Gaussian output problem Message-Id: <-43201-101123084525-30761-uKxuO21mT4w7naKs8bEBYw%%server.ccl.net> X-Original-From: "Maciej Maslyk" Date: Tue, 23 Nov 2010 08:45:23 -0500 Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] Hi everyone, could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? It looks like this in output: 9995 1 20001030 -12.655571 46.600810 32.540627 9996 1 20001030 -12.533484 47.134581 33.952118 9997 8 20001021 2.441067 -19.529269 31.331119 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 **** 8 20001021 23.735956 -43.072924 13.135294 **** 1 20001030 23.388276 -42.182008 13.115359 **** 1 20001030 22.974070 -43.624340 13.312930 Do you have any suggestions? Thanks in advance Maciek From owner-chemistry@ccl.net Tue Nov 23 10:53:00 2010 From: "Ben Roberts roberts+/-qtp.ufl.edu" To: CCL Subject: CCL:G: Gaussian output problem Message-Id: <-43202-101123104329-7205-3vaqPnbq5WNCZfQkWGszWA{=}server.ccl.net> X-Original-From: Ben Roberts Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 23 Nov 2010 10:43:09 -0500 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Ben Roberts [roberts_-_qtp.ufl.edu] Hi Maciej, On 23/11/2010, at 8:45 a.m., Maciej Maslyk maciejmarcin.maslyk .. ceu.es wrote: > > Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] > Hi everyone, > could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? > > It looks like this in output: > 9995 1 20001030 -12.655571 46.600810 32.540627 > 9996 1 20001030 -12.533484 47.134581 33.952118 > 9997 8 20001021 2.441067 -19.529269 31.331119 > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > **** 8 20001021 23.735956 -43.072924 13.135294 > **** 1 20001030 23.388276 -42.182008 13.115359 > **** 1 20001030 22.974070 -43.624340 13.312930 > > Do you have any suggestions? I've seen this before in various contexts within Gaussian. About the only thing I could suggest is to post-process your output using e.g. a Perl script. To change the field width permanently, you would need access to the Gaussian source code. Hope that helps. Ben From owner-chemistry@ccl.net Tue Nov 23 12:15:01 2010 From: "Close, David M. CLOSED _ mail.etsu.edu" To: CCL Subject: CCL:G: Gaussian output problem Message-Id: <-43203-101123111848-31344-te7fFhUSIj947bS90MeKBQ||server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 23 Nov 2010 16:18:07 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED..mail.etsu.edu] Maciej: Do you own the source code? If so, look at the print command. The program is most likely trying to print a 5 digit number in a fix field (something like I4). Much of Gaussian code is in Fortran with fixed formats. The **** just mean that you have tried to print something that doesn't fix in the space allowed. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu^^ccl.net [mailto:owner-chemistry+closed==etsu.edu^^ccl.net] On Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es Sent: Tuesday, November 23, 2010 8:45 AM To: Close, David M. Subject: CCL:G: Gaussian output problem Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] Hi everyone, could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? It looks like this in output: 9995 1 20001030 -12.655571 46.600810 32.540627 9996 1 20001030 -12.533484 47.134581 33.952118 9997 8 20001021 2.441067 -19.529269 31.331119 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 **** 8 20001021 23.735956 -43.072924 13.135294 **** 1 20001030 23.388276 -42.182008 13.115359 **** 1 20001030 22.974070 -43.624340 13.312930 Do you have any suggestions? Thanks in advance Maciekhttp://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 Tue Nov 23 12:49:00 2010 From: "Herbert Fruchtl herbert.fruchtl]^[st-andrews.ac.uk" To: CCL Subject: CCL:G: Gaussian output problem Message-Id: <-43204-101123121902-13614-kdWw+u8xlPskR7i+9T8E0g]~[server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 23 Nov 2010 17:18:26 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl%%st-andrews.ac.uk] This is a normal effect of formatted Fortran output. If you have the source code, it's straight-forward to find and fix (with the risk that other programs that analyse the output can't do that anymore). If you only have the binary executable, you are out of luck. Gaussian is really an electronic structure program, and not made for tens of thousands of atoms. If you want to do force field or semiempirical calculations, there are much more suitable programs available. Herbert Ben Roberts roberts+/-qtp.ufl.edu wrote: > Sent to CCL by: Ben Roberts [roberts_-_qtp.ufl.edu] > Hi Maciej, > > On 23/11/2010, at 8:45 a.m., Maciej Maslyk maciejmarcin.maslyk .. ceu.es wrote: > >> Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] >> Hi everyone, >> could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? >> >> It looks like this in output: >> 9995 1 20001030 -12.655571 46.600810 32.540627 >> 9996 1 20001030 -12.533484 47.134581 33.952118 >> 9997 8 20001021 2.441067 -19.529269 31.331119 >> 9998 1 20001030 2.813824 -19.307495 32.184450 >> 9999 1 20001030 1.933916 -20.325103 31.491166 >> **** 8 20001021 37.587292 -11.572024 28.812192 >> **** 1 20001030 37.333847 -11.927328 27.960694 >> **** 1 20001030 38.095189 -12.272395 29.221488 >> **** 8 20001021 23.735956 -43.072924 13.135294 >> **** 1 20001030 23.388276 -42.182008 13.115359 >> **** 1 20001030 22.974070 -43.624340 13.312930 >> >> Do you have any suggestions? > > I've seen this before in various contexts within Gaussian. About the only thing I could suggest is to post-process your output using e.g. a Perl script. To change the field width permanently, you would need access to the Gaussian source code. > > Hope that helps. > > Ben> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Tue Nov 23 13:25:01 2010 From: "Ivo Jacobs jacobs.ivo(0)gmail.com" To: CCL Subject: CCL:G: Gaussian output problem Message-Id: <-43205-101123121538-7495-wWkWeZORACMkKWilqg8T0g-$-server.ccl.net> X-Original-From: Ivo Jacobs Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 23 Nov 2010 18:15:23 +0100 MIME-Version: 1.0 Sent to CCL by: Ivo Jacobs [jacobs.ivo*|*gmail.com] Hello Maciek, I don't actually know if this will solve your problem as I have never worked with such big systems, but have you tried to use the newzmat utility to convert the checkpoint file to some other format? HTH, Ivo On 23-11-10 2:45 PM, Maciej Maslyk maciejmarcin.maslyk .. ceu.es wrote: > Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] > Hi everyone, > could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? > > It looks like this in output: > 9995 1 20001030 -12.655571 46.600810 32.540627 > 9996 1 20001030 -12.533484 47.134581 33.952118 > 9997 8 20001021 2.441067 -19.529269 31.331119 > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > **** 8 20001021 23.735956 -43.072924 13.135294 > **** 1 20001030 23.388276 -42.182008 13.115359 > **** 1 20001030 22.974070 -43.624340 13.312930 > > Do you have any suggestions? > > Thanks in advance > > Maciek> > > From owner-chemistry@ccl.net Tue Nov 23 14:00:00 2010 From: "Abrash, Sam sabrash:_:richmond.edu" To: CCL Subject: CCL:G: Gaussian output problem Message-Id: <-43206-101123130915-19766-jaRMt2Lxnfm0DFxJjsoppQ[a]server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 23 Nov 2010 13:09:02 -0500 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu] Hi, I think David is correct. However, there's a relatively easy fix (I think) unless your atom count exceeds 9999 by a lot. Just go into the output file with an editor, and replace the **** by the actual atom number. That should fix the problem of not being able to read structures (unless the program you're using for the structures has the same problem). Sam Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash^-^richmond.edu Web-page: http://www.richmond.edu/~sabrash "In 1893 Charles Hinton left Japan to become a mathematics instructor at Princeton University, where he invented a baseball-pitching machine that used gunpowder to propel the balls, like a cannon.  After several accidents, the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu^-^ccl.net [mailto:owner-chemistry+sabrash==richmond.edu^-^ccl.net] On Behalf Of Close, David M. CLOSED _ mail.etsu.edu Sent: Tuesday, November 23, 2010 11:18 AM To: Abrash, Sam Subject: CCL:G: Gaussian output problem Sent to CCL by: "Close, David M." [CLOSED..mail.etsu.edu] Maciej: Do you own the source code? If so, look at the print command. The program is most likely trying to print a 5 digit number in a fix field (something like I4). Much of Gaussian code is in Fortran with fixed formats. The **** just mean that you have tried to print something that doesn't fix in the space allowed. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu__ccl.net [mailto:owner-chemistry+closed==etsu.edu__ccl.net] On Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es Sent: Tuesday, November 23, 2010 8:45 AM To: Close, David M. Subject: CCL:G: Gaussian output problem Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] Hi everyone, could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? It looks like this in output: 9995 1 20001030 -12.655571 46.600810 32.540627 9996 1 20001030 -12.533484 47.134581 33.952118 9997 8 20001021 2.441067 -19.529269 31.331119 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 **** 8 20001021 23.735956 -43.072924 13.135294 **** 1 20001030 23.388276 -42.182008 13.115359 **** 1 20001030 22.974070 -43.624340 13.312930 Do you have any suggestions? Thanks in advance Maciekhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Tue Nov 23 14:42:00 2010 From: "Van Dam, Hubertus J HubertusJJ.vanDam++pnl.gov" To: CCL Subject: CCL: convergence failure in NWChem Message-Id: <-43207-101123142642-12459-Vn635zLIjODI6fSDeFSUIQ[-]server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 23 Nov 2010 11:26:32 -0800 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam .. pnl.gov] Hi Indu, At the moment I am running your calculation with NWChem 6.0 on 4 cores (compiled with gfortran/gcc 4.1.2). The only change I made to the input was to run the DFT module in integral direct mode. I.e. I am using for the dft block: dft direct xc m06-2x end The code calculates the frequencies with numerical differentiation for the M06-2x functional. So far I have got to the z-coordinate of atom 8 (running this calculation on only 4 cores obviously is a bit slow). Nevertheless I haven't been able to reproduce the error you were reporting. I'll continue the calculation and see what happens. Whatever the outcome I'll send you the output when the calculation is done, so at least you can compare it against your results. Best wishes, Huub On Mon, Nov 22, 2010 at 1:20 AM, Indu Kaul indu.kaul[-]iiserpune.ac.in > wrote: Sent to CCL by: "Indu Kaul" [indu.kaul+/-iiserpune.ac.in] Iam facing problem while calculating frequency for indole=pyridine dimer in m062x/aug-ccpvdz.It is terminated with an error of "error related with convergence failure"/PLease suggest me to run it normally without any error.Hereby iam attaching the input file that i have given. charge 0 geometry C 0.22595787 1.49582748 -0.22657386 C 0.70490509 2.74139529 0.25519651 C -0.22529421 3.73299280 0.61801736 C -1.57831795 3.46164427 0.49646613 C -2.03282270 2.21421528 0.01380046 C -1.14272545 1.21795122 -0.35505649 C 2.46155091 1.41243630 -0.21782550 C 2.13991638 2.66157899 0.24831676 H 0.11505573 4.69922665 0.98865952 H -2.30845051 4.22038042 0.77374897 H -3.10329081 2.03526758 -0.07457134 H -1.48965257 0.25935158 -0.73867508 H 1.25711883 -0.25912518 -0.82016671 H 3.43507226 0.96018982 -0.36942861 H 2.84168142 3.43076328 0.54891561 N 1.31687164 0.70939294 -0.50915412 C -0.07870766 -2.06710091 0.57285102 C -0.77547085 -3.13248813 1.14039988 C -0.92933762 -4.29757466 0.39420646 C -0.38206597 -4.34903917 -0.88552062 C 0.29674948 -3.23000091 -1.36353187 N 0.45016258 -2.10747409 -0.65509720 H -1.46740379 -5.15205258 0.80233152 H 0.05991841 -1.13439971 1.12314792 H -1.18552475 -3.04252550 2.14399171 H -0.47665308 -5.23694117 -1.50709884 H 0.73677294 -3.23400745 -2.36094519 end basis "ao basis" spherical C library aug-cc-pvdz N library aug-cc-pvdz H library aug-cc-pvdz end dft xc m06-2x end task dft freq 5E-mail to subscribers: CHEMISTRY ~ ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST ~ ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Nov 23 19:29:00 2010 From: "Hari Lamichhane hlamichhane1 ~~ student.gsu.edu" To: CCL Subject: CCL:G: PED calculation Message-Id: <-43208-101123153114-13273-MgaQu2d0+X5EWY+dlj/I2Q:-:server.ccl.net> X-Original-From: "Hari Lamichhane" Date: Tue, 23 Nov 2010 15:31:11 -0500 Sent to CCL by: "Hari Lamichhane" [hlamichhane1[#]student.gsu.edu] Hi all, I am wondering if there is any available software out there where one can take Gaussian03 calculated vibrational frequencies and use this output to calculate the potential energy distributions of the normal modes?