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From: Karol M. L. <kar...@gm...> - 2011-12-15 19:28:19
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Hi Ed, Sorry for not answering sooner, I was bogged down with work. On Nov 07 2011, Edward Holland wrote: > I managed to run two fairly simple, and representative jobs over the weekend. They aren't very interesting jobs but the correctly illustrate the type of data that will need to be parsed. > The key parts are headed with "Summary of Optimized Potential Surface Scan" or "Summary of the potential surface scan". > as you will be able to see the non optimised jobs will be much simpler to parse as there is no need to store a complete set of geometry data for each step. > One complicated i can see if translating the z matrix variables given by the output into xyz coordinates as normally expected within cclib. So, could you provide the output file(s) you would liked parsed for this? With something to work, it oculd be easy to implement what you want. > Another idea i've had is a boolean that stores if a output file has terminated at an expected point, or been cut short. > I suspect this would be useful for people hoping to make their job submission scripts more intelligent. I'm afraid I don't understand this idea, and you need to explain in more detail what you mean. Best regards, Karol > On 3 Nov 2011, at 13:08, Noel O'Boyle wrote: > > > Hi Ed, > > > > Sounds like an interesting project. > > > > Regarding the scans, your're right - currently we don't support this. > > Can you provide an example? (Preferably a small test case.) Then we'll > > be able to discuss this a bit more. > > > > - Noel > > > > On 3 November 2011 12:44, Edward Holland <hol...@ca...> wrote: > >> Hi all, > >> > >> I thought before i got down to the juice of the subject i should introduce myself. I'm Ed Holland i'm currently studying for a phD under Prof Barry K Carpenter in Cardiff on physical organic chemistry. Specifically we are researching novel H transfer reactions in amine radical cations and their applications to renewable energy. I've come across your project and its something i would much like to be involved with in any way i can help. As I am primarily a chemist and my programming skills are not as advanced as i would like but i hope i can see contribute in some way! > >> > >> Now down to the real core of the message. I've been running a number of scan jobs recently and i would find it incredibly useful to automate the analysis of such jobs. Currently (as far as i can tell) cclib doesn't support this at all, having had a read through some of the code i think this would be fairly simple to implement for the Gaussian parser at least. > >> > >> Has anyone thought about doing this before? Can anyone provide examples of scan jobs from the other programs supported by cclib? Would anyone be willing to discuss the most suitable way of storing this data within the ccData type. I wouldn't want to miss out any conventions i don't know about. -- written by Karol M. Langner Thu Dec 15 20:24:17 CET 2011 |
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From: Edward H. <hol...@ca...> - 2011-11-07 13:49:25
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Hi All, I managed to run two fairly simple, and representative jobs over the weekend. They aren't very interesting jobs but the correctly illustrate the type of data that will need to be parsed. The key parts are headed with "Summary of Optimized Potential Surface Scan" or "Summary of the potential surface scan". as you will be able to see the non optimised jobs will be much simpler to parse as there is no need to store a complete set of geometry data for each step. One complicated i can see if translating the z matrix variables given by the output into xyz coordinates as normally expected within cclib. Another idea i've had is a boolean that stores if a output file has terminated at an expected point, or been cut short. I suspect this would be useful for people hoping to make their job submission scripts more intelligent. Yours Ed Holland |
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From: Edward H. <hol...@ca...> - 2011-11-04 12:33:38
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Hi Noel, Yes i can provide a series of test cases, however my cluster is pretty busy at the moment. It normally clears up somewhat over the weekend, so I should have some examples for you around Monday. Yours Ed On 3 Nov 2011, at 13:08, Noel O'Boyle wrote: > Hi Ed, > > Sounds like an interesting project. > > Regarding the scans, your're right - currently we don't support this. > Can you provide an example? (Preferably a small test case.) Then we'll > be able to discuss this a bit more. > > - Noel > > On 3 November 2011 12:44, Edward Holland <hol...@ca...> wrote: >> Hi all, >> >> I thought before i got down to the juice of the subject i should introduce myself. I'm Ed Holland i'm currently studying for a phD under Prof Barry K Carpenter in Cardiff on physical organic chemistry. Specifically we are researching novel H transfer reactions in amine radical cations and their applications to renewable energy. I've come across your project and its something i would much like to be involved with in any way i can help. As I am primarily a chemist and my programming skills are not as advanced as i would like but i hope i can see contribute in some way! >> >> Now down to the real core of the message. I've been running a number of scan jobs recently and i would find it incredibly useful to automate the analysis of such jobs. Currently (as far as i can tell) cclib doesn't support this at all, having had a read through some of the code i think this would be fairly simple to implement for the Gaussian parser at least. >> >> Has anyone thought about doing this before? Can anyone provide examples of scan jobs from the other programs supported by cclib? Would anyone be willing to discuss the most suitable way of storing this data within the ccData type. I wouldn't want to miss out any conventions i don't know about. >> >> Yours >> >> Ed Holland >> -----BEGIN PGP SIGNATURE----- >> >> iQEcBAEBAgAGBQJOsn6cAAoJEEJc9s8gBQlyhl4H+wdYnB0d/tnWrzwDT+BD343q >> O/3YpIJyN5g+/NeyVyyCm+xZ75wiGt0q/SVzX4kcJXnQ+khW93NLximdhIt+4D2d >> +585rZBzopm9I3a+voWhGigD0qgDvxsutvlwTVRTojyRCEm827mae6jt7nxhQHYe >> MEZxxvN/9+t85NVG3TUh2TSD4vzH4u2agRC+fhD3f/EBB8oKgUlAPZLksiwhy1Qk >> SsQPuAh1DmEiWJ2nrfJ0tawnEmWIFbMGkv/QW06GnxhOvDbysi89YWbBWIRpz1h+ >> FrWcY4PztyRU+jsGZzUIeY/yWUrpxzdsQbfdm6P0608C/f4erZ2aEvgiBLaP3R4= >> =I/6k >> -----END PGP SIGNATURE----- >> >> ------------------------------------------------------------------------------ >> RSA(R) Conference 2012 >> Save $700 by Nov 18 >> Register now >> http://p.sf.net/sfu/rsa-sfdev2dev1 >> _______________________________________________ >> cclib-devel mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-devel >> >> |
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From: SourceForge.net <no...@so...> - 2011-11-03 19:15:11
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Feature Requests item #3432873, was opened at 2011-11-03 08:50 Message generated for change (Comment added) made by atenderholt You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3432873&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface Improvements Group: None Status: Open Priority: 6 Private: No Submitted By: Karol Langner (langner) Assigned to: Nobody/Anonymous (nobody) Summary: CML output Initial Comment: It might be nice to be able to save parsed data in CML. ---------------------------------------------------------------------- >Comment By: Adam Tenderholt (atenderholt) Date: 2011-11-03 12:15 Message: As a script that is distributed with cclib (e.g. ccget and cda)? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3432873&group_id=161285 |
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From: SourceForge.net <no...@so...> - 2011-11-03 15:50:14
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Feature Requests item #3432873, was opened at 2011-11-03 16:50 Message generated for change (Tracker Item Submitted) made by langner You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3432873&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface Improvements Group: None Status: Open Priority: 6 Private: No Submitted By: Karol Langner (langner) Assigned to: Nobody/Anonymous (nobody) Summary: CML output Initial Comment: It might be nice to be able to save parsed data in CML. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819225&aid=3432873&group_id=161285 |
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From: Noel O'B. <bao...@gm...> - 2011-11-03 13:09:01
|
Hi Ed, Sounds like an interesting project. Regarding the scans, your're right - currently we don't support this. Can you provide an example? (Preferably a small test case.) Then we'll be able to discuss this a bit more. - Noel On 3 November 2011 12:44, Edward Holland <hol...@ca...> wrote: > Hi all, > > I thought before i got down to the juice of the subject i should introduce myself. I'm Ed Holland i'm currently studying for a phD under Prof Barry K Carpenter in Cardiff on physical organic chemistry. Specifically we are researching novel H transfer reactions in amine radical cations and their applications to renewable energy. I've come across your project and its something i would much like to be involved with in any way i can help. As I am primarily a chemist and my programming skills are not as advanced as i would like but i hope i can see contribute in some way! > > Now down to the real core of the message. I've been running a number of scan jobs recently and i would find it incredibly useful to automate the analysis of such jobs. Currently (as far as i can tell) cclib doesn't support this at all, having had a read through some of the code i think this would be fairly simple to implement for the Gaussian parser at least. > > Has anyone thought about doing this before? Can anyone provide examples of scan jobs from the other programs supported by cclib? Would anyone be willing to discuss the most suitable way of storing this data within the ccData type. I wouldn't want to miss out any conventions i don't know about. > > Yours > > Ed Holland > -----BEGIN PGP SIGNATURE----- > > iQEcBAEBAgAGBQJOsn6cAAoJEEJc9s8gBQlyhl4H+wdYnB0d/tnWrzwDT+BD343q > O/3YpIJyN5g+/NeyVyyCm+xZ75wiGt0q/SVzX4kcJXnQ+khW93NLximdhIt+4D2d > +585rZBzopm9I3a+voWhGigD0qgDvxsutvlwTVRTojyRCEm827mae6jt7nxhQHYe > MEZxxvN/9+t85NVG3TUh2TSD4vzH4u2agRC+fhD3f/EBB8oKgUlAPZLksiwhy1Qk > SsQPuAh1DmEiWJ2nrfJ0tawnEmWIFbMGkv/QW06GnxhOvDbysi89YWbBWIRpz1h+ > FrWcY4PztyRU+jsGZzUIeY/yWUrpxzdsQbfdm6P0608C/f4erZ2aEvgiBLaP3R4= > =I/6k > -----END PGP SIGNATURE----- > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > > |
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From: Edward H. <hol...@ca...> - 2011-11-03 12:09:51
|
Hi all, I thought before i got down to the juice of the subject i should introduce myself. I'm Ed Holland i'm currently studying for a phD under Prof Barry K Carpenter in Cardiff on physical organic chemistry. Specifically we are researching novel H transfer reactions in amine radical cations and their applications to renewable energy. I've come across your project and its something i would much like to be involved with in any way i can help. As I am primarily a chemist and my programming skills are not as advanced as i would like but i hope i can see contribute in some way! Now down to the real core of the message. I've been running a number of scan jobs recently and i would find it incredibly useful to automate the analysis of such jobs. Currently (as far as i can tell) cclib doesn't support this at all, having had a read through some of the code i think this would be fairly simple to implement for the Gaussian parser at least. Has anyone thought about doing this before? Can anyone provide examples of scan jobs from the other programs supported by cclib? Would anyone be willing to discuss the most suitable way of storing this data within the ccData type. I wouldn't want to miss out any conventions i don't know about. Yours Ed Holland |
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From: Noel O'B. <bao...@gm...> - 2011-09-29 10:08:13
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Hey there, A user was asking me about extracting the orbitals at k-points in PBC calculations. Any of you familiar with these types of calculations? We actually already have an example in our test data in Gaussian03/maheshkumar.log.gz. - Noel |
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From: Karol M. L. <kar...@gm...> - 2011-08-02 16:39:18
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Jeff is correct, and it took a bit of work to figure how to reasonably separate the components of cclib into two parts for main and non-free. It seems, however, that the log files might night even be OK for non-free due to these license issues. It might be easier to just discard all unittests and log files from the Debian packages. Most users don't care about them anyway. We will see, Karol On Mon, Aug 01, 2011 at 05:58:09PM -0500, Jeff Hammond wrote: > You can learn more about Debian's rules of inclusion from > <http://en.wikipedia.org/wiki/Debian_Free_Software_Guidelines>. > Gaussian log files are definitely not compliant with #1 since a > licensee cannot share them with a competitor of Gaussian (e.g. me). > If you interpret #2 and #4 to mean that one must have the source code > used to generate an output file, then this is a clear requirement that > log files cannot be included without the source of the program used to > create them, thus, output files from any non-free code must be > excluded. > > On Debian, Firefox is renamed and uses a different logo because the > Firefox logo is subject to restrictions that the Debian folks can't > accept. They are, of course, happy with the code itself though, since > it is GPL. See > http://en.wikipedia.org/wiki/Mozilla_Corporation_software_rebranded_by_the_Debian_project > for details. > > Jeff > > On Mon, Aug 1, 2011 at 2:14 PM, Noel O'Boyle <bao...@gm...> wrote: > > Non-free? Surprised to hear that. What do they require to be free? > > > > On 29 July 2011 17:56, Karol M. Langner <kar...@gm...> wrote: > >> Hi, > >> > >> I'm happy to say that cclib 1.0.1 is in the official Debian archive: > >> http://packages.debian.org/sid/cclib > >> > >> For copyright reasons, the log files (and therefore also unit tests) > >> were separated into the package cclib-data and moved to the non-free > >> section of Debian. This package isn't available yet. > >> > >> Cheers, > >> Karol > >> > >> -- > >> written by Karol M. Langner > >> Fri Jul 29 18:52:32 CEST 2011 > >> > >> ------------------------------------------------------------------------------ > >> Got Input? Slashdot Needs You. > >> Take our quick survey online. Come on, we don't ask for help often. > >> Plus, you'll get a chance to win $100 to spend on ThinkGeek. > >> http://p.sf.net/sfu/slashdot-survey > >> _______________________________________________ > >> cclib-users mailing list > >> ccl...@li... > >> https://lists.sourceforge.net/lists/listinfo/cclib-users > >> > > > > ------------------------------------------------------------------------------ > > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > > The must-attend event for mobile developers. Connect with experts. > > Get tools for creating Super Apps. See the latest technologies. > > Sessions, hands-on labs, demos & much more. Register early & save! > > http://p.sf.net/sfu/rim-blackberry-1 > > _______________________________________________ > > cclib-users mailing list > > ccl...@li... > > https://lists.sourceforge.net/lists/listinfo/cclib-users > > > > > > -- > Jeff Hammond > Argonne Leadership Computing Facility > University of Chicago Computation Institute > jha...@al... / (630) 252-5381 > http://www.linkedin.com/in/jeffhammond > https://wiki.alcf.anl.gov/index.php/User:Jhammond -- written by Karol M. Langner Tue Aug 2 18:36:48 CEST 2011 |
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From: Jeff H. <jha...@al...> - 2011-08-01 22:58:17
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You can learn more about Debian's rules of inclusion from <http://en.wikipedia.org/wiki/Debian_Free_Software_Guidelines>. Gaussian log files are definitely not compliant with #1 since a licensee cannot share them with a competitor of Gaussian (e.g. me). If you interpret #2 and #4 to mean that one must have the source code used to generate an output file, then this is a clear requirement that log files cannot be included without the source of the program used to create them, thus, output files from any non-free code must be excluded. On Debian, Firefox is renamed and uses a different logo because the Firefox logo is subject to restrictions that the Debian folks can't accept. They are, of course, happy with the code itself though, since it is GPL. See http://en.wikipedia.org/wiki/Mozilla_Corporation_software_rebranded_by_the_Debian_project for details. Jeff On Mon, Aug 1, 2011 at 2:14 PM, Noel O'Boyle <bao...@gm...> wrote: > Non-free? Surprised to hear that. What do they require to be free? > > On 29 July 2011 17:56, Karol M. Langner <kar...@gm...> wrote: >> Hi, >> >> I'm happy to say that cclib 1.0.1 is in the official Debian archive: >> http://packages.debian.org/sid/cclib >> >> For copyright reasons, the log files (and therefore also unit tests) >> were separated into the package cclib-data and moved to the non-free >> section of Debian. This package isn't available yet. >> >> Cheers, >> Karol >> >> -- >> written by Karol M. Langner >> Fri Jul 29 18:52:32 CEST 2011 >> >> ------------------------------------------------------------------------------ >> Got Input? Slashdot Needs You. >> Take our quick survey online. Come on, we don't ask for help often. >> Plus, you'll get a chance to win $100 to spend on ThinkGeek. >> http://p.sf.net/sfu/slashdot-survey >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > The must-attend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, hands-on labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rim-blackberry-1 > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jha...@al... / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/index.php/User:Jhammond |
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From: Noel O'B. <bao...@gm...> - 2011-08-01 20:43:50
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And I forgot to say, well done on getting it in! Our world-domination plan is continuing. - Noel On 1 August 2011 20:14, Noel O'Boyle <bao...@gm...> wrote: > Non-free? Surprised to hear that. What do they require to be free? > > On 29 July 2011 17:56, Karol M. Langner <kar...@gm...> wrote: >> Hi, >> >> I'm happy to say that cclib 1.0.1 is in the official Debian archive: >> http://packages.debian.org/sid/cclib >> >> For copyright reasons, the log files (and therefore also unit tests) >> were separated into the package cclib-data and moved to the non-free >> section of Debian. This package isn't available yet. >> >> Cheers, >> Karol >> >> -- >> written by Karol M. Langner >> Fri Jul 29 18:52:32 CEST 2011 >> >> ------------------------------------------------------------------------------ >> Got Input? Slashdot Needs You. >> Take our quick survey online. Come on, we don't ask for help often. >> Plus, you'll get a chance to win $100 to spend on ThinkGeek. >> http://p.sf.net/sfu/slashdot-survey >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> > |
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From: Noel O'B. <bao...@gm...> - 2011-08-01 19:14:59
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Non-free? Surprised to hear that. What do they require to be free? On 29 July 2011 17:56, Karol M. Langner <kar...@gm...> wrote: > Hi, > > I'm happy to say that cclib 1.0.1 is in the official Debian archive: > http://packages.debian.org/sid/cclib > > For copyright reasons, the log files (and therefore also unit tests) > were separated into the package cclib-data and moved to the non-free > section of Debian. This package isn't available yet. > > Cheers, > Karol > > -- > written by Karol M. Langner > Fri Jul 29 18:52:32 CEST 2011 > > ------------------------------------------------------------------------------ > Got Input? Slashdot Needs You. > Take our quick survey online. Come on, we don't ask for help often. > Plus, you'll get a chance to win $100 to spend on ThinkGeek. > http://p.sf.net/sfu/slashdot-survey > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users > |
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From: Karol M. L. <kar...@gm...> - 2011-07-29 16:56:14
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Hi, I'm happy to say that cclib 1.0.1 is in the official Debian archive: http://packages.debian.org/sid/cclib For copyright reasons, the log files (and therefore also unit tests) were separated into the package cclib-data and moved to the non-free section of Debian. This package isn't available yet. Cheers, Karol -- written by Karol M. Langner Fri Jul 29 18:52:32 CEST 2011 |
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From: Karol M. L. <kar...@gm...> - 2011-07-29 13:42:24
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Hi guys, The 1.0.1 tarball is missing test/__init__.py. is this intentional? - Karol -- written by Karol M. Langner Fri Jul 29 15:41:42 CEST 2011 |
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From: Nuno A. G. B. <nun...@is...> - 2011-07-18 18:23:35
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Dear Adam, Thanks for the update! It's always better than nothing. You could somehow upload some occasional builds (usually called "nightly" by developers but they're seldom daily or nightly for that matter) as an additional resource on sourceforge. There could be others who are interested. Best, Nuno -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- |
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From: Adam T. <ate...@gm...> - 2011-07-18 17:30:37
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Hi Nuno (and Karol), It's tough to find time to get a solid release of QMForge, but it's on my list of things to do. I have a very rough version that is built upon a relatively new version of cclib. I haven't worked out all the bugs so there might be a random crash here and there, and you should make sure that it doesn't accidentally duplicate or remove atomic basis functions added to fragments. You can find a windows binary at: http://faculty.washington.edu/adamlt82/QMForge-11Mar27.zip. I hope that helps, and please let me know if you run into any problems. Cheers, Adam On Sun, Jul 17, 2011 at 2:16 PM, Karol M. Langner <kar...@gm...> wrote: > On Sun, Jul 17, 2011 at 10:44:46PM +0200, Nuno A. G. Bandeira wrote: >> On 17-07-2011 21:39, Karol M. Langner wrote: >> > You will have to wait for Adam's input concerning that, as he is the >> > sole author. Is there any particular functionality in QMForge that you >> > need and can't find elsewhere? Cheers, Karol >> >> Well, yes! A GUI that allows to create fragments on the spot is a lot >> better and more immediate than writing input scripts don't you think ? > > Perhaps, although I do not understand fully your needs. Are you dividing > your molecules into smaller parts? > > In any case I did not mean to be sarcastic. I do not know QMForge too well > and haven't used it myself. If you describe what you need to do exactly, > we might be able to propose a different tool/GUI. > > Best regards, > Karol > > -- > written by Karol Langner > Sun Jul 17 23:12:58 CEST 2011 > > ------------------------------------------------------------------------------ > AppSumo Presents a FREE Video for the SourceForge Community by Eric > Ries, the creator of the Lean Startup Methodology on "Lean Startup > Secrets Revealed." This video shows you how to validate your ideas, > optimize your ideas and identify your business strategy. > http://p.sf.net/sfu/appsumosfdev2dev > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > |
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From: Karol M. L. <kar...@gm...> - 2011-07-17 21:17:04
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On Sun, Jul 17, 2011 at 10:44:46PM +0200, Nuno A. G. Bandeira wrote: > On 17-07-2011 21:39, Karol M. Langner wrote: > > You will have to wait for Adam's input concerning that, as he is the > > sole author. Is there any particular functionality in QMForge that you > > need and can't find elsewhere? Cheers, Karol > > Well, yes! A GUI that allows to create fragments on the spot is a lot > better and more immediate than writing input scripts don't you think ? Perhaps, although I do not understand fully your needs. Are you dividing your molecules into smaller parts? In any case I did not mean to be sarcastic. I do not know QMForge too well and haven't used it myself. If you describe what you need to do exactly, we might be able to propose a different tool/GUI. Best regards, Karol -- written by Karol Langner Sun Jul 17 23:12:58 CEST 2011 |
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From: Nuno A. G. B. <nun...@is...> - 2011-07-17 20:53:16
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You may find QMForge credited in my paper for instance : Chem. Eur. J. 2011, 17, 1988 -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- |
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From: Nuno A. G. B. <nun...@is...> - 2011-07-17 20:44:56
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On 17-07-2011 21:39, Karol M. Langner wrote: > You will have to wait for Adam's input concerning that, as he is the > sole author. Is there any particular functionality in QMForge that you > need and can't find elsewhere? Cheers, Karol Well, yes! A GUI that allows to create fragments on the spot is a lot better and more immediate than writing input scripts don't you think ? -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- |
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From: SourceForge.net <no...@so...> - 2011-07-17 20:25:53
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Bugs item #1756789, was opened at 2007-07-19 14:20 Message generated for change (Comment added) made by langner You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=1756789&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Noel O'Boyle (baoilleach) Assigned to: Karol Langner (langner) Summary: Gaussian: problem reading MO values Initial Comment: Reported by Jerome Kieffer; no test file due to IP issues. Dear CCLib developpers, I noticed a bug when reading a gaussian log file when the energy of the deepest orbital cannot fit in the formated 9 char . Maybe this is due to the 2 iodines in this molecule (di-iodophenyl) or to the Dgauss DZVP basis set used. Of course the bug occures by the python command : float("**********"), in Logfile.parse.float(), line 188 of logfileparser.py Here is an extract of the gaussian output. The electronic state is 1-A. Alpha occ. eigenvalues -- ********************-176.38175-176.37760-165.76438 Alpha occ. eigenvalues -- -165.76230-165.76225-165.76023-165.75813-165.75807 Alpha occ. eigenvalues -- -35.82446 -35.82036 -31.33591 -31.33183 -31.33009 Kind regards. -- Jérôme Kieffer (PhD) ---------------------------------------------------------------------- >Comment By: Karol Langner (langner) Date: 2011-07-17 22:25 Message: I added the log file that reproduces this (di-iodophenyl.log.gz with Gaussian09) and fixed the bug with revision 949. Now moenergies will contain numpy.nan when Gaussian print this kind of garbage. ---------------------------------------------------------------------- Comment By: Karol Langner (langner) Date: 2011-07-17 20:07 Message: I managed to reproduce this bug, which it seems is still relevant. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=1756789&group_id=161285 |
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From: Karol M. L. <kar...@gm...> - 2011-07-17 19:40:03
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On Sun, Jul 17, 2011 at 08:33:50PM +0200, Nuno A. G. Bandeira wrote: > On 17-07-2011 20:07, SourceForge.net wrote: > > Bugs item #1756789, was opened at 2007-07-19 14:20 > > Message generated for change (Comment added) made by langner > > You can respond by visiting: > > https://sourceforge.net/tracker/?func=detail&atid=819222&aid=1756789&group_id=161285 > > Any news on the update of QMForge by the way ? It's going immensely out > of date... > > Best, > Nuno You will have to wait for Adam's input concerning that, as he is the sole author. Is there any particular functionality in QMForge that you need and can't find elsewhere? Cheers, Karol -- written by Karol Langner Sun Jul 17 21:39:01 CEST 2011 |
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From: Nuno A. G. B. <nun...@is...> - 2011-07-17 19:09:16
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On 17-07-2011 20:07, SourceForge.net wrote: > Bugs item #1756789, was opened at 2007-07-19 14:20 > Message generated for change (Comment added) made by langner > You can respond by visiting: > https://sourceforge.net/tracker/?func=detail&atid=819222&aid=1756789&group_id=161285 Any news on the update of QMForge by the way ? It's going immensely out of date... Best, Nuno -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN -- |
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From: SourceForge.net <no...@so...> - 2011-07-17 18:07:10
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Bugs item #1756789, was opened at 2007-07-19 14:20 Message generated for change (Comment added) made by langner You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=1756789&group_id=161285 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Parsers Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Noel O'Boyle (baoilleach) >Assigned to: Karol Langner (langner) Summary: Gaussian: problem reading MO values Initial Comment: Reported by Jerome Kieffer; no test file due to IP issues. Dear CCLib developpers, I noticed a bug when reading a gaussian log file when the energy of the deepest orbital cannot fit in the formated 9 char . Maybe this is due to the 2 iodines in this molecule (di-iodophenyl) or to the Dgauss DZVP basis set used. Of course the bug occures by the python command : float("**********"), in Logfile.parse.float(), line 188 of logfileparser.py Here is an extract of the gaussian output. The electronic state is 1-A. Alpha occ. eigenvalues -- ********************-176.38175-176.37760-165.76438 Alpha occ. eigenvalues -- -165.76230-165.76225-165.76023-165.75813-165.75807 Alpha occ. eigenvalues -- -35.82446 -35.82036 -31.33591 -31.33183 -31.33009 Kind regards. -- Jérôme Kieffer (PhD) ---------------------------------------------------------------------- >Comment By: Karol Langner (langner) Date: 2011-07-17 20:07 Message: I managed to reproduce this bug, which it seems is still relevant. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=819222&aid=1756789&group_id=161285 |
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From: Noel O'B. <bao...@gm...> - 2011-07-11 08:26:35
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There's a long standing problem parsing ONIOM files. We (i.e. at cclib) know about it, and have a test case - we just haven't sorted it out. I'll bump this up the priority list. - Noel On 11 July 2011 08:40, Jason Alvino <jas...@ad...> wrote: > Hi, > I'm trying to use Gaussum 2.2.5 to open some ONIOM logfiles and look at the > DOS but it gives me the following error: > "Traceback (most recent call last): > File "gausssum\gausssumgui.pyc", line 404, in runscript > File "gausssum\popanalysis.pyc", line 439, in Popanalysis > AttributeError: 'ccData' object has no attribute 'nbasis'" > I am running Windows 7, using the all-in-one gausssum package and trying to > open a Gaussian 09 ONIOM calculation and generate the DOS. I can parse the > logfiles and generate the frequency spectrum and other things just fine, it > only seems to have problems generating the DOS or COOP. > Have you seen this error before? > Any help would be much appreciated (Not that I don't appreciate GaussSum > already!) > Cheers, > -Jason > -- > Jason F. Alvino > PhD Candidate (Chemistry) > School of Chemistry and Physics > University of Adelaide, AUSTRALIA 5005 > Ph: +61 8 8303 3707 > |
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From: Noel O'B. <bao...@gm...> - 2011-05-10 20:17:18
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Can you zip up the problematic log file and send it to us? Note we require a public domain log file though. If you send us one, can you confirm that you are happy to place it in the public domain? - Noel On 10 May 2011 20:59, Pavel Solntsev <pav...@gm...> wrote: > The latest version of cclib (svn). > Gaussian 09 Single point output file works just fine, but same file from > g03 doesn't. > I console i see > Traceback (most recent call last): > File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", > line 250, in fileOpen > self.open(str(filename)) > File "/usr/local/lib/python2.7/dist-packages/qmforge/qmforge.py", > line 150, in open > data = parser.parse() > File > "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py", > line 221, in parse > self.extract(inputfile, line) > File > "/usr/local/lib/python2.7/dist-packages/cclib/parser/gaussianparser.py", > line 933, in extract > temp.append(float(part[j:j+10])) > ValueError: could not convert string to float: (B2)--O > > If i change "(B2)--O" to "O" the it works too. > Unfortunately, molecule very big, so i can't do this for all orbitals :). > > Best wishes, > > PS. > > -- > Pavlo V. Solntsev > pavlo.solntsev at gmail.com > > > ------------------------------------------------------------------------------ > Achieve unprecedented app performance and reliability > What every C/C++ and Fortran developer should know. > Learn how Intel has extended the reach of its next-generation tools > to help boost performance applications - inlcuding clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > |
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