Menu
▾
▴
cclib-devel
|
From: Noel O'B. <bao...@gm...> - 2009-06-05 08:08:38
|
(Please reply-all) We are also interested in feature requests. - Noel 2009/6/4 Manuel Melle Franco <man...@gm...>: > Dear Noel, > > New feature I am afraid > > regards > > Manuel > > ____________________________________________________________ > > Mohandas K. Gandhi often changed his mind publicly. An aide once asked > him how he could so freely contradict this week what he had said just > last week. The great man replied that it was because this week he knew > better. > > ____________________________________________________________ > > Manuel Melle-Franco, > Investigador Auxiliar do Requimte > Chemistry Department > Faculty of Sciences > University of Porto > Rua do Campo Alegre,687 > 4169-007 Porto > Portugal. > Portuguese mobile : 00351-918817917 > Portuguese work : 00351-220402526 > Spanish mobile: : 0034-651754516 > Italian mobile: : 0039-3283647205 > > --------------------------------------------------------- > > A mind all logic is like a knife all blade. It makes the hand bleed that > uses it. > Rabindranath Tagore > > --------------------------------------------------------- > > > On Thu, Jun 4, 2009 at 3:43 PM, Noel O'Boyle <bao...@gm...> wrote: >> >> Hello Manuel, >> >> Can you send us a public domain test file so we can see what the problem >> is? >> >> Are you saying that there is a bug, or are you requesting a new feature? >> >> Regards, >> Noel >> >> 2009/6/4 Manuel Melle Franco <man...@gm...>: >> > Dear Users, >> > >> > Any chance of parsing g03 output in oniom calculations in the future? >> > >> > if not, do you think is it feasible to modify the existing parser to add >> > the >> > funcionality? >> > >> > best regards >> > >> > Manu >> > ____________________________________________________________ >> > >> > Mohandas K. Gandhi often changed his mind publicly. An aide once asked >> > him how he could so freely contradict this week what he had said just >> > last week. The great man replied that it was because this week he knew >> > better. >> > >> > ____________________________________________________________ >> > >> > Manuel Melle-Franco, >> > Investigador Auxiliar do Requimte >> > Chemistry Department >> > Faculty of Sciences >> > University of Porto >> > Rua do Campo Alegre,687 >> > 4169-007 Porto >> > Portugal. >> > Portuguese mobile : 00351-918817917 >> > Portuguese work : 00351-220402526 >> > Spanish mobile: : 0034-651754516 >> > Italian mobile: : 0039-3283647205 >> > >> > --------------------------------------------------------- >> > >> > A mind all logic is like a knife all blade. It makes the hand bleed that >> > uses it. >> > Rabindranath Tagore >> > >> > --------------------------------------------------------- >> > >> > >> > ------------------------------------------------------------------------------ >> > OpenSolaris 2009.06 is a cutting edge operating system for enterprises >> > looking to deploy the next generation of Solaris that includes the >> > latest >> > innovations from Sun and the OpenSource community. Download a copy and >> > enjoy capabilities such as Networking, Storage and Virtualization. >> > Go to: http://p.sf.net/sfu/opensolaris-get >> > _______________________________________________ >> > cclib-users mailing list >> > ccl...@li... >> > https://lists.sourceforge.net/lists/listinfo/cclib-users >> > >> > > > |
|
From: Manuel M. F. <man...@gm...> - 2009-06-08 14:16:33
|
Hi all, There is this method in gaussian called Oniom which is becoming increasingly popular. Loosely speaking is a calculation where different levels of theory can be mixed, MM and different flavours of QM. Adding the parsing should not be difficult I think, although the output gets me quite puzzled still! regards Manuel ____________________________________________________________ Mohandas K. Gandhi often changed his mind publicly. An aide once asked him how he could so freely contradict this week what he had said just last week. The great man replied that it was because this week he knew better. ____________________________________________________________ Manuel Melle-Franco, Investigador Auxiliar do Requimte Chemistry Department Faculty of Sciences University of Porto Rua do Campo Alegre,687 4169-007 Porto Portugal. Portuguese mobile : 00351-918817917 Portuguese work : 00351-220402526 Spanish mobile: : 0034-651754516 Italian mobile: : 0039-3283647205 --------------------------------------------------------- A mind all logic is like a knife all blade. It makes the hand bleed that uses it. Rabindranath Tagore --------------------------------------------------------- On Fri, Jun 5, 2009 at 9:08 AM, Noel O'Boyle <bao...@gm...> wrote: > (Please reply-all) > > We are also interested in feature requests. > > - Noel > > 2009/6/4 Manuel Melle Franco <man...@gm...>: > > Dear Noel, > > > > New feature I am afraid > > > > regards > > > > Manuel > > > > ____________________________________________________________ > > > > Mohandas K. Gandhi often changed his mind publicly. An aide once asked > > him how he could so freely contradict this week what he had said just > > last week. The great man replied that it was because this week he knew > > better. > > > > ____________________________________________________________ > > > > Manuel Melle-Franco, > > Investigador Auxiliar do Requimte > > Chemistry Department > > Faculty of Sciences > > University of Porto > > Rua do Campo Alegre,687 > > 4169-007 Porto > > Portugal. > > Portuguese mobile : 00351-918817917 > > Portuguese work : 00351-220402526 > > Spanish mobile: : 0034-651754516 > > Italian mobile: : 0039-3283647205 > > > > --------------------------------------------------------- > > > > A mind all logic is like a knife all blade. It makes the hand bleed that > > uses it. > > Rabindranath Tagore > > > > --------------------------------------------------------- > > > > > > On Thu, Jun 4, 2009 at 3:43 PM, Noel O'Boyle <bao...@gm...> > wrote: > >> > >> Hello Manuel, > >> > >> Can you send us a public domain test file so we can see what the problem > >> is? > >> > >> Are you saying that there is a bug, or are you requesting a new feature? > >> > >> Regards, > >> Noel > >> > >> 2009/6/4 Manuel Melle Franco <man...@gm...>: > >> > Dear Users, > >> > > >> > Any chance of parsing g03 output in oniom calculations in the future? > >> > > >> > if not, do you think is it feasible to modify the existing parser to > add > >> > the > >> > funcionality? > >> > > >> > best regards > >> > > >> > Manu > >> > ____________________________________________________________ > >> > > >> > Mohandas K. Gandhi often changed his mind publicly. An aide once > asked > >> > him how he could so freely contradict this week what he had said just > >> > last week. The great man replied that it was because this week he > knew > >> > better. > >> > > >> > ____________________________________________________________ > >> > > >> > Manuel Melle-Franco, > >> > Investigador Auxiliar do Requimte > >> > Chemistry Department > >> > Faculty of Sciences > >> > University of Porto > >> > Rua do Campo Alegre,687 > >> > 4169-007 Porto > >> > Portugal. > >> > Portuguese mobile : 00351-918817917 > >> > Portuguese work : 00351-220402526 > >> > Spanish mobile: : 0034-651754516 > >> > Italian mobile: : 0039-3283647205 > >> > > >> > --------------------------------------------------------- > >> > > >> > A mind all logic is like a knife all blade. It makes the hand bleed > that > >> > uses it. > >> > Rabindranath Tagore > >> > > >> > --------------------------------------------------------- > >> > > >> > > >> > > ------------------------------------------------------------------------------ > >> > OpenSolaris 2009.06 is a cutting edge operating system for enterprises > >> > looking to deploy the next generation of Solaris that includes the > >> > latest > >> > innovations from Sun and the OpenSource community. Download a copy and > >> > enjoy capabilities such as Networking, Storage and Virtualization. > >> > Go to: http://p.sf.net/sfu/opensolaris-get > >> > _______________________________________________ > >> > cclib-users mailing list > >> > ccl...@li... > >> > https://lists.sourceforge.net/lists/listinfo/cclib-users > >> > > >> > > > > > > |
|
From: Noel O'B. <bao...@gm...> - 2009-06-08 14:36:17
|
Could you be more specific? Could you send a log file and say exactly what information you would like to see parsed? - Noel 2009/6/8 Manuel Melle Franco <man...@gm...>: > Hi all, > > There is this method in gaussian called Oniom which is becoming increasingly > popular. Loosely speaking is a calculation where different levels of theory > can be mixed, MM and different flavours of QM. Adding the parsing should not > be difficult I think, although the output gets me quite puzzled still! > > regards > > Manuel > > > > > ____________________________________________________________ > > Mohandas K. Gandhi often changed his mind publicly. An aide once asked > him how he could so freely contradict this week what he had said just > last week. The great man replied that it was because this week he knew > better. > > ____________________________________________________________ > > Manuel Melle-Franco, > Investigador Auxiliar do Requimte > Chemistry Department > Faculty of Sciences > University of Porto > Rua do Campo Alegre,687 > 4169-007 Porto > Portugal. > Portuguese mobile : 00351-918817917 > Portuguese work : 00351-220402526 > Spanish mobile: : 0034-651754516 > Italian mobile: : 0039-3283647205 > > --------------------------------------------------------- > > A mind all logic is like a knife all blade. It makes the hand bleed that > uses it. > Rabindranath Tagore > > --------------------------------------------------------- > > > On Fri, Jun 5, 2009 at 9:08 AM, Noel O'Boyle <bao...@gm...> wrote: >> >> (Please reply-all) >> >> We are also interested in feature requests. >> >> - Noel >> >> 2009/6/4 Manuel Melle Franco <man...@gm...>: >> > Dear Noel, >> > >> > New feature I am afraid >> > >> > regards >> > >> > Manuel >> > >> > ____________________________________________________________ >> > >> > Mohandas K. Gandhi often changed his mind publicly. An aide once asked >> > him how he could so freely contradict this week what he had said just >> > last week. The great man replied that it was because this week he knew >> > better. >> > >> > ____________________________________________________________ >> > >> > Manuel Melle-Franco, >> > Investigador Auxiliar do Requimte >> > Chemistry Department >> > Faculty of Sciences >> > University of Porto >> > Rua do Campo Alegre,687 >> > 4169-007 Porto >> > Portugal. >> > Portuguese mobile : 00351-918817917 >> > Portuguese work : 00351-220402526 >> > Spanish mobile: : 0034-651754516 >> > Italian mobile: : 0039-3283647205 >> > >> > --------------------------------------------------------- >> > >> > A mind all logic is like a knife all blade. It makes the hand bleed that >> > uses it. >> > Rabindranath Tagore >> > >> > --------------------------------------------------------- >> > >> > >> > On Thu, Jun 4, 2009 at 3:43 PM, Noel O'Boyle <bao...@gm...> >> > wrote: >> >> >> >> Hello Manuel, >> >> >> >> Can you send us a public domain test file so we can see what the >> >> problem >> >> is? >> >> >> >> Are you saying that there is a bug, or are you requesting a new >> >> feature? >> >> >> >> Regards, >> >> Noel >> >> >> >> 2009/6/4 Manuel Melle Franco <man...@gm...>: >> >> > Dear Users, >> >> > >> >> > Any chance of parsing g03 output in oniom calculations in the future? >> >> > >> >> > if not, do you think is it feasible to modify the existing parser to >> >> > add >> >> > the >> >> > funcionality? >> >> > >> >> > best regards >> >> > >> >> > Manu >> >> > ____________________________________________________________ >> >> > >> >> > Mohandas K. Gandhi often changed his mind publicly. An aide once >> >> > asked >> >> > him how he could so freely contradict this week what he had said just >> >> > last week. The great man replied that it was because this week he >> >> > knew >> >> > better. >> >> > >> >> > ____________________________________________________________ >> >> > >> >> > Manuel Melle-Franco, >> >> > Investigador Auxiliar do Requimte >> >> > Chemistry Department >> >> > Faculty of Sciences >> >> > University of Porto >> >> > Rua do Campo Alegre,687 >> >> > 4169-007 Porto >> >> > Portugal. >> >> > Portuguese mobile : 00351-918817917 >> >> > Portuguese work : 00351-220402526 >> >> > Spanish mobile: : 0034-651754516 >> >> > Italian mobile: : 0039-3283647205 >> >> > >> >> > --------------------------------------------------------- >> >> > >> >> > A mind all logic is like a knife all blade. It makes the hand bleed >> >> > that >> >> > uses it. >> >> > Rabindranath Tagore >> >> > >> >> > --------------------------------------------------------- >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------------ >> >> > OpenSolaris 2009.06 is a cutting edge operating system for >> >> > enterprises >> >> > looking to deploy the next generation of Solaris that includes the >> >> > latest >> >> > innovations from Sun and the OpenSource community. Download a copy >> >> > and >> >> > enjoy capabilities such as Networking, Storage and Virtualization. >> >> > Go to: http://p.sf.net/sfu/opensolaris-get >> >> > _______________________________________________ >> >> > cclib-users mailing list >> >> > ccl...@li... >> >> > https://lists.sourceforge.net/lists/listinfo/cclib-users >> >> > >> >> > >> > >> > > > |
|
From: Karol L. <kar...@gm...> - 2009-06-11 21:57:56
|
Hi Manuel, As far as I know, ONIOM is not implemented in an other quantum chem program that we support at the moment. That being said, parsing ONIOM-specific stuff from only Gaussian would not be very useful in general, as we aim for extracted the same data from many programs. Correct me if I'm wrong, Noel. However, if ONIOM output is not parsed by cclib, then that is a bug and we should be able to fix it. Best, Karol On Monday 08 June 2009 15:49:31 Manuel Melle Franco wrote: > Hi all, > > There is this method in gaussian called Oniom which is becoming > increasingly popular. Loosely speaking is a calculation where different > levels of theory can be mixed, MM and different flavours of QM. Adding the > parsing should not be difficult I think, although the output gets me quite > puzzled still! > > regards > > Manuel -- written by Karol Langner Fri Jun 12 00:04:04 CEST 2009 |
|
From: Manuel M. F. <man...@gm...> - 2009-06-12 06:36:51
|
On Fri, Jun 12, 2009 at 12:09 AM, Karol Langner <kar...@gm...>wrote: > Hi Manuel, > > As far as I know, ONIOM is not implemented in an other quantum chem > program > that we support at the moment. That being said, parsing ONIOM-specific > stuff > from only Gaussian would not be very useful in general, as we aim for > extracted the same data from many programs. Correct me if I'm wrong, Noel. > > However, if ONIOM output is not parsed by cclib, then that is a bug and we > should be able to fix it. Dear Karol and Noel, As far as I know only gaussian and nwchem have it. I am quite new to it and currently doing the parsing myself (fgrep mostly) but it works only in the cases I use, and it is a bit of a pain in the ass to parse. I agree with Karol, I think it might not be easy to write a general parser for oniom so that it would not be worth the effort to add it to cclib, at list at this point, maybe when more program have it, if that ever happens. best regards Manuel > > > Best, > Karol > > On Monday 08 June 2009 15:49:31 Manuel Melle Franco wrote: > > Hi all, > > > > There is this method in gaussian called Oniom which is becoming > > increasingly popular. Loosely speaking is a calculation where different > > levels of theory can be mixed, MM and different flavours of QM. Adding > the > > parsing should not be difficult I think, although the output gets me > quite > > puzzled still! > > > > regards > > > > Manuel > > -- > written by Karol Langner > Fri Jun 12 00:04:04 CEST 2009 > > |
|
From: Karol M. L. <kar...@gm...> - 2009-07-20 15:29:20
Attachments:
test370.log.bz2
test371.log.bz2
|
On Friday 12 June 2009 08:36:43 Manuel Melle Franco wrote: > On Fri, Jun 12, 2009 at 12:09 AM, Karol Langner <kar...@gm...>wrote: > > Hi Manuel, > > > > As far as I know, ONIOM is not implemented in an other quantum chem > > program > > that we support at the moment. That being said, parsing ONIOM-specific > > stuff > > from only Gaussian would not be very useful in general, as we aim for > > extracted the same data from many programs. Correct me if I'm wrong, > > Noel. > > > > However, if ONIOM output is not parsed by cclib, then that is a bug and > > we should be able to fix it. > > Dear Karol and Noel, > > As far as I know only gaussian and nwchem have it. > I am quite new to it and currently doing the parsing myself (fgrep mostly) > but it works only in the cases I use, > and it is a bit of a pain in the ass to parse. > > I agree with Karol, I think it might not be easy to write a general parser > for oniom so that it would not be worth the effort to add it to cclib, at > list at this point, maybe when more program have it, if that ever happens. > > best regards > > Manuel Manuel, I fixed the gaussian parser so that it does not fail now when parsing ONIOM calcs. Attached are two Gausian03 test files that I used for testing. Since it is not a new feature, I'm not adding them as tests or regressions. Please be aware that this does not mean that cclib now parses ONIOM output -- it does not! It merely does not crash now. Perhaps some of the parsed data can be of use, anyway. If you have output that still crashes the parser (using today's revision), please send it to us so we can make the parser more failure-proof. Cheers, Karol -- written by Karol Langner Mon Jul 20 17:23:26 CEST 2009 |
|
From: Noel O'B. <bao...@gm...> - 2009-07-20 17:46:35
|
2009/7/20 Karol M. Langner <kar...@gm...>: > On Friday 12 June 2009 08:36:43 Manuel Melle Franco wrote: >> On Fri, Jun 12, 2009 at 12:09 AM, Karol Langner > <kar...@gm...>wrote: >> > Hi Manuel, >> > >> > As far as I know, ONIOM is not implemented in an other quantum chem >> > program >> > that we support at the moment. That being said, parsing ONIOM-specific >> > stuff >> > from only Gaussian would not be very useful in general, as we aim for >> > extracted the same data from many programs. Correct me if I'm wrong, >> > Noel. >> > >> > However, if ONIOM output is not parsed by cclib, then that is a bug and >> > we should be able to fix it. >> >> Dear Karol and Noel, >> >> As far as I know only gaussian and nwchem have it. >> I am quite new to it and currently doing the parsing myself (fgrep mostly) >> but it works only in the cases I use, >> and it is a bit of a pain in the ass to parse. >> >> I agree with Karol, I think it might not be easy to write a general parser >> for oniom so that it would not be worth the effort to add it to cclib, at >> list at this point, maybe when more program have it, if that ever happens. >> >> best regards >> >> Manuel > > Manuel, > > I fixed the gaussian parser so that it does not fail now when parsing ONIOM > calcs. Attached are two Gausian03 test files that I used for testing. Since > it is not a new feature, I'm not adding them as tests or regressions. Please do add the files - this is what the regression test suite is for. :-) > Please be aware that this does not mean that cclib now parses ONIOM output -- > it does not! It merely does not crash now. Perhaps some of the parsed data > can be of use, anyway. > If you have output that still crashes the parser (using today's revision), > please send it to us so we can make the parser more failure-proof. > > Cheers, > Karol > > -- > written by Karol Langner > Mon Jul 20 17:23:26 CEST 2009 > |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X