From owner-chemistry@ccl.net Fri Jan 7 01:14:00 2011 From: "M shabbir agri_chemist],[yahoo.com" To: CCL Subject: CCL: Gauss View 5 with Macintosh to make new cub Message-Id: <-43543-110107011157-18477-2BZu1+asIyv/G9iU9IfMUQ%x%server.ccl.net> X-Original-From: "M shabbir" Date: Fri, 7 Jan 2011 01:11:44 -0500 Sent to CCL by: "M shabbir" [agri_chemist]|[yahoo.com] Dear CCL Colleagues, We are using unix system for our calculations with G09. I formate the chk file using unix system and take fchk file out for opening it in GaussView 5 installed in Macintosh. Now the problem is that when I open the fchk file and go to surfaces/counter option for making cub file I could not find the option for new cube. It shows option for load a cub but not for new cube. The same fchk file I can use to make new cub on GaussView installed in Windows. Is anyone knows about the above solution? or any comment how to install properly Gauss View in Macintosh operating system so that we can make new cub files. Thanks in advance and Happy new year! Dr.M.Shabbir Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan Cell # 00818038458604 From owner-chemistry@ccl.net Fri Jan 7 03:32:00 2011 From: "Rzepa, Henry h.rzepa*o*imperial.ac.uk" To: CCL Subject: CCL:G: Gauss View 5 with Macintosh to make new cub Message-Id: <-43544-110107031411-32096-HFJhX14hVy6om0GUbdiRiw]_[server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Fri, 7 Jan 2011 08:13:52 +0000 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa:+:imperial.ac.uk] >Sent to CCL by: "M shabbir" [agri_chemist]|[yahoo.com] >Dear CCL Colleagues, >We are using unix system for our calculations with G09. I formate the chk file using unix system and >take fchk file out for opening it in GaussView 5 installed in Macintosh. > >Now the problem is that when I open the fchk file and go to surfaces/counter option for making cub >file I could not find the option for new cube. >It shows option for load a cub but not for new cube. The same fchk file I can use to make new cub on >GaussView installed in Windows. Is anyone knows about the above solution? or any comment how to >install properly Gauss View in Macintosh operating system so that we can make new cub files. A new cube is generated by cubegen, which is part of the Gaussian 09 package. so you need to install that first before installing Gaussview. You also need to have your environment variables set (Gaussian is odd because it does not use the default Mac OS X bash shell but the c shell) so that the path to cubegen is found by Gaussview. -- +44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Fri Jan 7 11:20:00 2011 From: "Jim Kress ccl_nospam=-=kressworks.com" To: CCL Subject: CCL: CUDA/Linux security hole - serious issue Message-Id: <-43545-110107104448-23376-6Mj04FZzRYxIeYJsYOQxXw-x-server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 7 Jan 2011 10:44:36 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam#%#kressworks.com] This appears to be a serious security issue that must be addressed by Nvidia. What has been their response? Have other members of the CCL noticed this serious issue and/or received support from Nvidia? Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com],[ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com],[ccl.net] On Behalf Of Alex A > Granovsky gran%x%classic.chem.msu.su > Sent: Thursday, January 06, 2011 9:17 AM > To: Kress, Jim > Subject: CCL: CUDA/Linux security hole > > > Sent to CCL by: "Alex A Granovsky" [gran(!)classic.chem.msu.su] > Dear CCLers, > > I'd ask you to draw your attention to the two recent posts on the > Firefly's QC > discussion forum: > > http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/? > C35e9ea936bHW-7675-1380-00.htm > > http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/? > C35e9ea936bHW-7676-1022+00.htm > > The reason is not the Firefly package itself, nor it is the announce of > availability of Linux/CUDA enabled Firefly version. The actual reason > is > the very important security hole we found a couple of days ago in Linux > CUDA drivers. This hole is described in two posts mentioned above, and > the only available workaround we know right now is to completely > disable > CUDA drivers on all multi-user Linux systems and clusters. > > Kind regards, > > Alex Granovsky, > Firefly Project.> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Fri Jan 7 14:43:00 2011 From: "jacqueline cawthray jcawth01===gmail.com" To: CCL Subject: CCL: Restart Oniom in G09 Message-Id: <-43546-110107144131-14477-kepWK1I8SItPhOMRcYy/YA#server.ccl.net> X-Original-From: "jacqueline cawthray" Date: Fri, 7 Jan 2011 14:41:30 -0500 Sent to CCL by: "jacqueline cawthray" [jcawth01,+,gmail.com] Hi, I wish to know if it is possible to restart an ONIOM opt job in g09 that terminated due to exceeded wall time. I have tried: # opt=restart geom=check guess=read and # opt=restart oniom(hf/3-21+g*:amber) geom=checkpoint but it terminates with : 1/14=-1,18=1000020,19=15,52=2,64=3,115=4/3(-16); 2/9=110/2; 99//99; GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Restoring state from the checkpoint file "P1-BX1-Omopt-restart.chk". FileIO operation on non-existent file. even though the chk point file is present. I would be grateful for any suggestions. Best regards JC From owner-chemistry@ccl.net Fri Jan 7 15:17:00 2011 From: "Alex A Granovsky gran/a\classic.chem.msu.su" To: CCL Subject: CCL: CUDA/Linux security hole - serious issue Message-Id: <-43547-110107145209-31276-6l8OPyqulokhrBtE7fwGfg__server.ccl.net> X-Original-From: "Alex A Granovsky" Date: Fri, 7 Jan 2011 14:52:07 -0500 Sent to CCL by: "Alex A Granovsky" [gran+/-classic.chem.msu.su] Jim, the issue is very serious as CUDA functionality is built in into every (relatively recent) version of Nvidia graphics drivers for Windows, Linux and OSX. Moreover, to install CUDA toolkit (all that is needed to exploit this bug) one does not need any special privileges so everybody having access to system with Nvidia video drivers running can do this. After toolkit installation, one just need to write simple C program which calls cudaHostAlloc() to allocate sufficiently large piece of pinned memory, and then dump all non-zero content to HDD for later examination. One can do this on a timely fashion gathering more and more information. As an example, our simplest "proof of concept" program was able to catch large fragments of files (or even entire files) being written or read by other users - emails, documents, various system logs, inputs, outputs, etc... - virtually everything one can imagine to find in the OS file cache and in the released memory of other programs. It seems the bug was here from the first days of CUDA. It does not exist under Windows (my Microsoft's contacts pointed me out that Windows forcibly zeroes any memory exported to user space so most likely this is the reason why it is not here), and I have not checked OSX as of yet. However, every owner of Nvidia graphics card running Linux and Nvidia graphics drivers should now consider switching to Nouveau driver, or even to GPUs of other vendors (or maybe to Windows OS :) ). As to Nvidia's response, it was really strange - their point was that if application does not like its data to be visible by other programs/users via this security issue, it should explicitly clear data in memory before releasing it. This is really strange and absolutely wrong idea, moreover, the contents of OS file cache, unused physical memory etc... cannot be cleared from within user programs at all. More globally, this is a question of how trustworthy are all proprietary drivers which are capable to expose memory into user space. Alex ----- Original Message ----- > From: "Jim Kress ccl_nospam=-=kressworks.com" To: "Granovsky, Alex, A. " Sent: Friday, January 07, 2011 6:44 PM Subject: CCL: CUDA/Linux security hole - serious issue > > Sent to CCL by: "Jim Kress" [ccl_nospam#%#kressworks.com] > This appears to be a serious security issue that must be addressed by > Nvidia. What has been their response? > > Have other members of the CCL noticed this serious issue and/or received > support from Nvidia? > > Jim > > > -----Original Message----- > > From: owner-chemistry+ccl_nospam==kressworks.com%x%ccl.net [mailto:owner- > > chemistry+ccl_nospam==kressworks.com%x%ccl.net] On Behalf Of Alex A > > Granovsky gran%x%classic.chem.msu.su > > Sent: Thursday, January 06, 2011 9:17 AM > > To: Kress, Jim > > Subject: CCL: CUDA/Linux security hole > > > > > > Sent to CCL by: "Alex A Granovsky" [gran(!)classic.chem.msu.su] > > Dear CCLers, > > > > I'd ask you to draw your attention to the two recent posts on the > > Firefly's QC > > discussion forum: > > > > http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/? > > C35e9ea936bHW-7675-1380-00.htm > > > > http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/? > > C35e9ea936bHW-7676-1022+00.htm > > > > The reason is not the Firefly package itself, nor it is the announce of > > availability of Linux/CUDA enabled Firefly version. The actual reason > > is > > the very important security hole we found a couple of days ago in Linux > > CUDA drivers. This hole is described in two posts mentioned above, and > > the only available workaround we know right now is to completely > > disable > > CUDA drivers on all multi-user Linux systems and clusters. > > > > Kind regards, > > > > Alex Granovsky, > > Firefly Project.> To recover the email address of the author of the message, please > > change> > > From owner-chemistry@ccl.net Fri Jan 7 15:52:00 2011 From: "Alex A. Granovsky gran+*+classic.chem.msu.su" To: CCL Subject: CCL: CUDA/Linux security hole - serious issue Message-Id: <-43548-110107135159-10970-aoybm8YKoraG/1IlD8zxMA-*-server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1" Date: Fri, 7 Jan 2011 21:54:48 +0300 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran---classic.chem.msu.su] Jim, the issue is very serious as CUDA functionality is built in into every (relatively recent) version of Nvidia graphics drivers for Windows, Linux and OSX. Moreover, to install CUDA toolkit (all that is needed to exploit this bug) one does not need any special privileges so everybody having access to system with Nvidia video drivers running can do this. After toolkit installation, one just need to write simple C program which calls cudaHostAlloc() to allocate sufficiently large piece of pinned memory, and then dump all non-zero content to HDD for later examination. One can do this on a timely fashion gathering more and more information. As an example, our simplest "proof of concept" program was able to catch large fragments of files (or even entire files) being written or read by other users - emails, documents, various system logs, inputs, outputs, etc... - virtually everything one can imagine to find in the OS file cache and in the released memory of other programs. It seems the bug was here from the first days of CUDA. It does not exist under Windows (my Microsoft's contacts pointed me out that Windows forcibly zeroes any memory exported to user space so most likely this is the reason why it is not here), and I have not checked OSX as of yet. However, every owner of Nvidia graphics card running Linux and Nvidia graphics drivers should now consider switching to Nouveau driver, or even to GPUs of other vendors (or maybe to Windows OS :) ). As to Nvidia's response, it was really strange - their point was that if application does not like its data to be visible by other programs/users via this security issue, it should explicitly clear data in memory before releasing it. This is really strange and absolutely wrong idea, moreover, the contents of OS file cache, unused physical memory etc... cannot be cleared from within user programs at all. More globally, this is a question of how trustworthy are all third-party proprietary drivers which are capable to expose memory into user space. Alex ----- Original Message ----- > From: "Jim Kress ccl_nospam=-=kressworks.com" To: "Granovsky, Alex, A. " Sent: Friday, January 07, 2011 6:44 PM Subject: CCL: CUDA/Linux security hole - serious issue > > Sent to CCL by: "Jim Kress" [ccl_nospam#%#kressworks.com] > This appears to be a serious security issue that must be addressed by > Nvidia. What has been their response? > > Have other members of the CCL noticed this serious issue and/or received > support from Nvidia? > > Jim > > > -----Original Message----- > > From: owner-chemistry+ccl_nospam==kressworks.com%x%ccl.net [mailto:owner- > > chemistry+ccl_nospam==kressworks.com%x%ccl.net] On Behalf Of Alex A > > Granovsky gran%x%classic.chem.msu.su > > Sent: Thursday, January 06, 2011 9:17 AM > > To: Kress, Jim > > Subject: CCL: CUDA/Linux security hole > > > > > > Sent to CCL by: "Alex A Granovsky" [gran(!)classic.chem.msu.su] > > Dear CCLers, > > > > I'd ask you to draw your attention to the two recent posts on the > > Firefly's QC > > discussion forum: > > > > http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/? > > C35e9ea936bHW-7675-1380-00.htm > > > > http://classic.chem.msu.su/cgi-bin/ceilidh.exe/gran/gamess/forum/? > > C35e9ea936bHW-7676-1022+00.htm > > > > The reason is not the Firefly package itself, nor it is the announce of > > availability of Linux/CUDA enabled Firefly version. The actual reason > > is > > the very important security hole we found a couple of days ago in Linux > > CUDA drivers. This hole is described in two posts mentioned above, and > > the only available workaround we know right now is to completely > > disable > > CUDA drivers on all multi-user Linux systems and clusters. > > > > Kind regards, > > > > Alex Granovsky, > > Firefly Project.> To recover the email address of the author of the message, please > > change> > > From owner-chemistry@ccl.net Fri Jan 7 16:27:00 2011 From: "dipankar roy theodip a gmail.com" To: CCL Subject: CCL:G: Restart Oniom in G09 Message-Id: <-43549-110107154348-13909-xhZUSBzW49HRM9djqi/3lg||server.ccl.net> X-Original-From: dipankar roy Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 7 Jan 2011 15:43:36 -0500 MIME-Version: 1.0 Sent to CCL by: dipankar roy [theodip : gmail.com] Hi, Use 'OPT=restart' only without 'geom=checkpoint' Please see http://www.gaussian.com/g_tech/g_ur/k_opt.htm for more information. Hope this helps. Dipankar Roy -- ----------------------------------- Dr. Dipankar Roy Research Associate Hunter College (CUNY) 695 Park Avenue New York, USA NY-10065 ----------------------------------- On Fri, Jan 7, 2011 at 2:41 PM, jacqueline cawthray jcawth01===gmail.com wrote: > > Sent to CCL by: "jacqueline  cawthray" [jcawth01,+,gmail.com] > Hi, > > I wish to know if it is possible to restart an ONIOM opt job in g09 that > terminated due to exceeded wall time. I have tried: > > # opt=restart geom=check guess=read > > and > > # opt=restart oniom(hf/3-21+g*:amber) geom=checkpoint > > but it terminates with : > > > 1/14=-1,18=1000020,19=15,52=2,64=3,115=4/3(-16); >  2/9=110/2; >  99//99; > >  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad >  Berny optimization. >  Restoring state from the checkpoint file "P1-BX1-Omopt-restart.chk". >  FileIO operation on non-existent file. > > even though the chk point file is present. > > I would be grateful for any suggestions. > > Best regards > JC>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Fri Jan 7 18:16:00 2011 From: "Olawale Lukman Olasunkanmi waleolasunkanmi+*+gmail.com" To: CCL Subject: CCL: help running MOPAC job Message-Id: <-43550-110107165540-1407-c2sqHY18CXdcLDgThnYs2w[]server.ccl.net> X-Original-From: "Olawale Lukman Olasunkanmi" Date: Fri, 7 Jan 2011 16:55:38 -0500 Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi###gmail.com] I just started using MOPAC. I made PM6 geometry optimizations for some molecules. I don't know how I can set or reset my key word. Because the calculation results I got are like: PM6 CALCULATION MOPAC2009 (Version: 10.341W) Tue Oct 31 00:08:23 2006 No. of days left = 0 FINAL HEAT OF FORMATION = 352.46208 KCAL/MOL = 1474.70135 KJ/MOL TOTAL ENERGY = -7583.93843 EV ELECTRONIC ENERGY = -86866.48561 EV POINT GROUP: C1 CORE-CORE REPULSION = 79282.54718 EV COSMO AREA = 596.98 SQUARE ANGSTROMS COSMO VOLUME = 740.30 CUBIC ANGSTROMS GRADIENT NORM = 0.95289 IONIZATION POTENTIAL = 6.498619 EV HOMO LUMO ENERGIES (EV) = -6.499 -2.063 NO. OF FILLED LEVELS = 125 MOLECULAR WEIGHT = 859.817 I like to calculate entropy, free energy, heat capacity and dipole moments also. Kindly put me through. Thanks. From owner-chemistry@ccl.net Fri Jan 7 18:50:00 2011 From: "Jacqueline Cawthray jcawth01**gmail.com" To: CCL Subject: CCL:G: Restart Oniom in G09 Message-Id: <-43551-110107181755-25103-DUxjutQWQLGgcy5ZkTtgow-$-server.ccl.net> X-Original-From: Jacqueline Cawthray Content-Type: multipart/alternative; boundary=20cf30549f616527a6049949d35a Date: Fri, 7 Jan 2011 15:17:45 -0800 MIME-Version: 1.0 Sent to CCL by: Jacqueline Cawthray [jcawth01!^!gmail.com] --20cf30549f616527a6049949d35a Content-Type: text/plain; charset=ISO-8859-1 Dr. Dipankar Roy, Thanks so much for your suggestion. However I still encounter the same problem with the job terminating due to "non-existent file". Perhaps I am missing something else? Thanks JC On Fri, Jan 7, 2011 at 12:43 PM, dipankar roy theodip a gmail.com < owner-chemistry]_[ccl.net> wrote: > > Sent to CCL by: dipankar roy [theodip : gmail.com] > Hi, > > Use 'OPT=restart' only without 'geom=checkpoint' > > Please see http://www.gaussian.com/g_tech/g_ur/k_opt.htm for more > information. > > Hope this helps. > > Dipankar Roy > -- > ----------------------------------- > Dr. Dipankar Roy > Research Associate > Hunter College (CUNY) > 695 Park Avenue > New York, USA > NY-10065 > ----------------------------------- > > On Fri, Jan 7, 2011 at 2:41 PM, jacqueline cawthray > jcawth01===gmail.com wrote: > > > > Sent to CCL by: "jacqueline cawthray" [jcawth01,+,gmail.com] > > Hi, > > > > I wish to know if it is possible to restart an ONIOM opt job in g09 that > > terminated due to exceeded wall time. I have tried: > > > > # opt=restart geom=check guess=read > > > > and > > > > # opt=restart oniom(hf/3-21+g*:amber) geom=checkpoint > > > > but it terminates with : > > > > > > 1/14=-1,18=1000020,19=15,52=2,64=3,115=4/3(-16); > > 2/9=110/2; > > 99//99; > > > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > > Berny optimization. > > Restoring state from the checkpoint file "P1-BX1-Omopt-restart.chk". > > FileIO operation on non-existent file. > > > > even though the chk point file is present. > > > > I would be grateful for any suggestions. > > > > Best regards > > JC> > > -- Jacqueline Cawthray, Ph.D. Orvig Research Group Department of Chemistry University of British Columbia 2036 Main Mall Vancouver, BC, V6T 2A3 Ph: 604-822-8632 Email: jcawth01]_[chem.ubc.ca --20cf30549f616527a6049949d35a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dr. Dipankar Roy,

Thanks so much for your suggestion. Ho= wever I still encounter the same problem with the job terminating due to &q= uot;non-existent file". Perhaps I am missing something else?

Thanks
JC

On Fri= , Jan 7, 2011 at 12:43 PM, dipankar roy theodip a gmail.com <owner-chemistry]_[ccl.net> wrote:

Sent to CCL by: dipankar roy [theodip : gmail.com]
Hi,

Use 'OPT=3Drestart' only without 'geom=3Dcheckpoint'

Please see http://www.gaussian.com/g_tech/g_ur/k_opt.htm for more info= rmation.

Hope this helps.

Dipankar Roy
--
-----------------------------------
Dr. Dipankar Roy
Research Associate
Hunter College (CUNY)
695 Park Avenue
New York, USA
NY-10065
-----------------------------------

On Fri, Jan 7, 2011 at 2:41 PM, jacqueline cawthray
jcawth01=3D=3D=3Dgmail.com <owner-chemistry-.-ccl.n= et> wrote:
>
> Sent to CCL by: "jacqueline =A0cawthray" [jcawth01,+,gmail.com]
> Hi,
>
> I wish to know if it is possible to restart an ONIOM opt job in g09 th= at
> terminated due to exceeded wall time. I have tried:
>
> # opt=3Drestart geom=3Dcheck guess=3Dread
>
> and
>
> # opt=3Drestart oniom(hf/3-21+g*:amber) geom=3Dcheckpoint
>
> but it terminates with :
>
>
> 1/14=3D-1,18=3D1000020,19=3D15,52=3D2,64=3D3,115=3D4/3(-16);
> =A02/9=3D110/2;
> =A099//99;
>
> =A0GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGra= dGrad
> =A0Berny optimization.
> =A0Restoring state from the checkpoint file "P1-BX1-Omopt-restart= .chk".
> =A0FileIO operation on non-existent file.
>
> even though the chk point file is present.
>
> I would be grateful for any suggestions.
>
> Best regards
> JC> =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>
>
>



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Jacqueline Cawthray, Ph= .D.

Orvig Research Group
Department of Chemistry
University of= British Columbia
2036 Main Mall
Vancouver, BC, V6T 2A3
Ph: 604-82= 2-8632
Email: jcawth01]_[c= hem.ubc.ca


--20cf30549f616527a6049949d35a-- From owner-chemistry@ccl.net Fri Jan 7 19:25:00 2011 From: "Decai Yu decaiyu23:-:yahoo.com" To: CCL Subject: CCL:G: eliminate Spin Contamination for CCSD and MP2 in Gaussian Message-Id: <-43552-110107184348-15705-DzBlHoqvt+P3281U3zTEAQ\a/server.ccl.net> X-Original-From: Decai Yu Content-Type: text/plain; charset=us-ascii Date: Fri, 7 Jan 2011 15:43:36 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Decai Yu [decaiyu23,yahoo.com] Dear All, I have encountered significant spin-contamination with MP2 and CCSD using Gaussian 09. Can anyone comment on how to eliminate the spin contamination using Gaussian? Your help is appreciated. Regards, Decai Yu From owner-chemistry@ccl.net Fri Jan 7 20:34:00 2011 From: "Mahmoud A. A. Ibrahim m.ibrahim : compchem.net" To: CCL Subject: CCL:G: Restart Oniom in G09 Message-Id: <-43553-110107203204-30920-A8EkbBD9/gMINN3xCPEd1g*server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 8 Jan 2011 01:31:51 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim]^[compchem.net] Dear Dipankar You have defined a wrong checkpoint file name which doesn't exist. I see you called "P1-BX1-Omopt-restart.chk". As I think, your original checkpoint file (created from the first run) is called P1-BX1-Omopt.chk So, in your opt=restart you HAVE TO call the same checkpoint file (P1-BX1-Omopt.chk NOT P1-BX1-Omopt-restart.chk). Sincerely; M. Ibrahim On Fri, Jan 7, 2011 at 11:17 PM, Jacqueline Cawthray jcawth01**gmail.com wrote: > Dr. Dipankar Roy, > Thanks so much for your suggestion. However I still encounter the same > problem with the job terminating due to "non-existent file". Perhaps I am > missing something else? > Thanks > JC > > On Fri, Jan 7, 2011 at 12:43 PM, dipankar roy theodip a gmail.com > wrote: >> >> Sent to CCL by: dipankar roy [theodip : gmail.com] >> Hi, >> >> Use 'OPT=restart' only without 'geom=checkpoint' >> >> Please see http://www.gaussian.com/g_tech/g_ur/k_opt.htm for more >> information. >> >> Hope this helps. >> >> Dipankar Roy >> -- >> ----------------------------------- >> Dr. Dipankar Roy >> Research Associate >> Hunter College (CUNY) >> 695 Park Avenue >> New York, USA >> NY-10065 >> ----------------------------------- >> >> On Fri, Jan 7, 2011 at 2:41 PM, jacqueline cawthray >> jcawth01===gmail.com wrote: >> > >> > Sent to CCL by: "jacqueline  cawthray" [jcawth01,+,gmail.com] >> > Hi, >> > >> > I wish to know if it is possible to restart an ONIOM opt job in g09 that >> > terminated due to exceeded wall time. I have tried: >> > >> > # opt=restart geom=check guess=read >> > >> > and >> > >> > # opt=restart oniom(hf/3-21+g*:amber) geom=checkpoint >> > >> > but it terminates with : >> > >> > >> > 1/14=-1,18=1000020,19=15,52=2,64=3,115=4/3(-16); >> >  2/9=110/2; >> >  99//99; >> > >> > >> >  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad >> >  Berny optimization. >> >  Restoring state from the checkpoint file "P1-BX1-Omopt-restart.chk". >> >  FileIO operation on non-existent file. >> > >> > even though the chk point file is present. >> > >> > I would be grateful for any suggestions. >> > >> > Best regards >> > JC>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message> >> >  http://www.ccl.net/cgi-bin/ccl/send_ccl_message> >> >  http://www.ccl.net/chemistry/sub_unsub.shtml> >> >  http://www.ccl.net/spammers.txt>> E-mail to subscribers: CHEMISTRY]*[ccl.net or use: >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message >> >> E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or use >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>>      http://www.ccl.net/chemistry/sub_unsub.shtml>>      http://www.ccl.net/spammers.txt>> >> > > > > -- > Jacqueline Cawthray, Ph.D. > > Orvig Research Group > Department of Chemistry > University of British Columbia > 2036 Main Mall > Vancouver, BC, V6T 2A3 > Ph: 604-822-8632 > Email: jcawth01]*[chem.ubc.ca > > > --                   Mahmoud A. A. Ibrahim                        Current Address                  7.05, School of Chemistry,               The University of Manchester,          Oxford Road, Manchester, M13 9PL,                        United Kingdom.                         Home Address                   Chemistry Department,                      Faculty of Science,                         Minia University,                            Minia 61519,                                 Egypt.                      Contact Information            Email: m.ibrahim/./compchem.net               Website: www.compchem.net                    Fax No.: +20862342601 From owner-chemistry@ccl.net Fri Jan 7 22:10:00 2011 From: "Mahmoud A. A. Ibrahim m.ibrahim|compchem.net" To: CCL Subject: CCL:G: Restart Oniom in G09 Message-Id: <-43554-110107220856-27341-trcawsLwzVETGXHz1jDzIQ(~)server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 8 Jan 2011 03:08:44 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim[#]compchem.net] Dear Dr. Dipankar Please accept my apologizes, it is addressed to you wrongly. Sincerely; M. Ibrahim On Sat, Jan 8, 2011 at 1:31 AM, Mahmoud A. A. Ibrahim m.ibrahim : compchem.net wrote: > > Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim]^[compchem.net] > Dear Dipankar > You have defined a wrong checkpoint file name which doesn't exist. > I see you called "P1-BX1-Omopt-restart.chk". > As I think, your original checkpoint file (created from the first run) > is called P1-BX1-Omopt.chk > So, in your opt=restart you HAVE TO call the same checkpoint file > (P1-BX1-Omopt.chk NOT P1-BX1-Omopt-restart.chk). > Sincerely; > M. Ibrahim > > On Fri, Jan 7, 2011 at 11:17 PM, Jacqueline Cawthray > jcawth01**gmail.com wrote: >> Dr. Dipankar Roy, >> Thanks so much for your suggestion. However I still encounter the same >> problem with the job terminating due to "non-existent file". Perhaps I am >> missing something else? >> Thanks >> JC >> >> On Fri, Jan 7, 2011 at 12:43 PM, dipankar roy theodip a gmail.com >> wrote: >>> >>> Sent to CCL by: dipankar roy [theodip : gmail.com] >>> Hi, >>> >>> Use 'OPT=restart' only without 'geom=checkpoint' >>> >>> Please see http://www.gaussian.com/g_tech/g_ur/k_opt.htm for more >>> information. >>> >>> Hope this helps. >>> >>> Dipankar Roy >>> -- >>> ----------------------------------- >>> Dr. Dipankar Roy >>> Research Associate >>> Hunter College (CUNY) >>> 695 Park Avenue >>> New York, USA >>> NY-10065 >>> ----------------------------------- >>> >>> On Fri, Jan 7, 2011 at 2:41 PM, jacqueline cawthray >>> jcawth01===gmail.com wrote: >>> > >>> > Sent to CCL by: "jacqueline  cawthray" [jcawth01,+,gmail.com] >>> > Hi, >>> > >>> > I wish to know if it is possible to restart an ONIOM opt job in g09 that >>> > terminated due to exceeded wall time. I have tried: >>> > >>> > # opt=restart geom=check guess=read >>> > >>> > and >>> > >>> > # opt=restart oniom(hf/3-21+g*:amber) geom=checkpoint >>> > >>> > but it terminates with : >>> > >>> > >>> > 1/14=-1,18=1000020,19=15,52=2,64=3,115=4/3(-16); >>> >  2/9=110/2; >>> >  99//99; >>> > >>> > >>> >  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad >>> >  Berny optimization. >>> >  Restoring state from the checkpoint file "P1-BX1-Omopt-restart.chk". >>> >  FileIO operation on non-existent file. >>> > >>> > even though the chk point file is present. >>> > >>> > I would be grateful for any suggestions. >>> > >>> > Best regards >>> > JC>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message> >>> >  http://www.ccl.net/cgi-bin/ccl/send_ccl_message> >>> >  http://www.ccl.net/chemistry/sub_unsub.shtml> >>> >  http://www.ccl.net/spammers.txt>> E-mail to subscribers: CHEMISTRY]*[ccl.net or use: >>>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message >>> >>> E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or use >>>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>>      http://www.ccl.net/chemistry/sub_unsub.shtml>>      http://www.ccl.net/spammers.txt>> >>> >> >> >> >> -- >> Jacqueline Cawthray, Ph.D. >> >> Orvig Research Group >> Department of Chemistry >> University of British Columbia >> 2036 Main Mall >> Vancouver, BC, V6T 2A3 >> Ph: 604-822-8632 >> Email: jcawth01]*[chem.ubc.ca >> >> >> > > > > -- >                   Mahmoud A. A. Ibrahim >                        Current Address >                  7.05, School of Chemistry, >               The University of Manchester, >          Oxford Road, Manchester, M13 9PL, >                        United Kingdom. > >                         Home Address >                   Chemistry Department, >                      Faculty of Science, >                         Minia University, >                            Minia 61519, >                                 Egypt. > >                      Contact Information >            Email: m.ibrahim-,-compchem.net >               Website: www.compchem.net >                    Fax No.: +20862342601>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > --                   Mahmoud A. A. Ibrahim                        Current Address                  7.05, School of Chemistry,               The University of Manchester,          Oxford Road, Manchester, M13 9PL,                        United Kingdom.                         Home Address                   Chemistry Department,                      Faculty of Science,                         Minia University,                            Minia 61519,                                 Egypt.                      Contact Information            Email: m.ibrahim,,compchem.net               Website: www.compchem.net                    Fax No.: +20862342601 From owner-chemistry@ccl.net Fri Jan 7 23:27:00 2011 From: "Victor Rosas Garcia rosas.victor]*[gmail.com" To: CCL Subject: CCL: help running MOPAC job Message-Id: <-43555-110107184324-15529-c4QkJcc6cBvL6QEQ0sYkBA|-|server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0015174c109869712004994a2e1a Date: Fri, 7 Jan 2011 17:43:12 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor~~gmail.com] --0015174c109869712004994a2e1a Content-Type: text/plain; charset=ISO-8859-1 Perhaps this pages can get you started: http://www.openmopac.net/Entropy_table.html http://www.openmopac.net/Heat_capacity_table.html Good luck with your calcs. Victor 2011/1/7 Olawale Lukman Olasunkanmi waleolasunkanmi+*+gmail.com < owner-chemistry ~~ ccl.net> > > Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi###gmail.com] > I just started using MOPAC. I made PM6 geometry optimizations for some > molecules. I don't know how I can set or reset my key word. Because the > calculation results I got are like: > > PM6 CALCULATION > MOPAC2009 (Version: > 10.341W) > Tue Oct 31 00:08:23 2006 > No. of days left = 0 > > > > > FINAL HEAT OF FORMATION = 352.46208 KCAL/MOL = 1474.70135 > KJ/MOL > > > TOTAL ENERGY = -7583.93843 EV > ELECTRONIC ENERGY = -86866.48561 EV POINT GROUP: C1 > CORE-CORE REPULSION = 79282.54718 EV > COSMO AREA = 596.98 SQUARE ANGSTROMS > COSMO VOLUME = 740.30 CUBIC ANGSTROMS > > GRADIENT NORM = 0.95289 > IONIZATION POTENTIAL = 6.498619 EV > HOMO LUMO ENERGIES (EV) = -6.499 -2.063 > NO. OF FILLED LEVELS = 125 > MOLECULAR WEIGHT = 859.817 > > I like to calculate entropy, free energy, heat capacity and dipole moments > also. > Kindly put me through. > Thanks.> > > --0015174c109869712004994a2e1a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Perhaps this pages can get you started:

http://www.openmopac.net/Entropy_table.html=
http://ww= w.openmopac.net/Heat_capacity_table.html

Good luck with your calcs.

Victor

2011/1/7 Olawale Lukman Olasunkanmi waleolasunkanmi+*+gmail.com <owner-chemistry ~~ ccl.net>

Sent to CCL by: "Olawale Lukman Olasunkanmi" [waleolasunkanmi###<= a href=3D"http://gmail.com" target=3D"_blank">gmail.com]
I just started using MOPAC. I made PM6 geometry optimizations for some mole= cules. I don't know how I can set or reset my key word. Because the cal= culation results I got are like:

=A0PM6 =A0 =A0 CALCULATION
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 MOPAC2009 (Version: 10.341W)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 Tue Oct 31 00:08:23 2006
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 No. of days left =3D =A0 0




=A0 =A0 =A0 =A0 =A0FINAL HEAT OF FORMATION =3D 352.46208 KCAL/MOL =3D =A0 = =A01474.70135 KJ/MOL


=A0 =A0 =A0 =A0 =A0TOTAL ENERGY =A0 =A0 =A0 =A0 =A0 =A0=3D =A0 =A0 =A0-758= 3.93843 EV
=A0 =A0 =A0 =A0 =A0ELECTRONIC ENERGY =A0 =A0 =A0 =3D =A0 =A0-86866.48561 E= V =A0POINT GROUP: =A0 =A0 C1
=A0 =A0 =A0 =A0 =A0CORE-CORE REPULSION =A0 =A0 =3D =A0 =A0 =A079282.54718 = EV
=A0 =A0 =A0 =A0 =A0COSMO AREA =A0 =A0 =A0 =A0 =A0 =A0 =A0=3D =A0 =A0 =A0 = =A0596.98 SQUARE ANGSTROMS
=A0 =A0 =A0 =A0 =A0COSMO VOLUME =A0 =A0 =A0 =A0 =A0 =A0=3D =A0 =A0 =A0 =A0= 740.30 CUBIC ANGSTROMS

=A0 =A0 =A0 =A0 =A0GRADIENT NORM =A0 =A0 =A0 =A0 =A0 =3D =A0 =A0 =A0 =A0 = =A00.95289
=A0 =A0 =A0 =A0 =A0IONIZATION POTENTIAL =A0 =A0=3D =A0 =A0 =A0 =A0 =A06.49= 8619 EV
=A0 =A0 =A0 =A0 =A0HOMO LUMO ENERGIES (EV) =3D =A0 =A0 =A0 =A0 -6.499 -2.0= 63
=A0 =A0 =A0 =A0 =A0NO. OF FILLED LEVELS =A0 =A0=3D =A0 =A0 =A0 =A0125
=A0 =A0 =A0 =A0 =A0MOLECULAR WEIGHT =A0 =A0 =A0 =A0=3D =A0 =A0 =A0 =A0859.= 817

I like to calculate entropy, free energy, heat capacity and dipole moments = also.
Kindly put me through.
Thanks.



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