gausssum-help Mailing List for GaussSum (Page 2)
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From: Ajeet S. <aje...@gm...> - 2017-12-04 09:28:33
|
Dear Sir, For the % contribution of a group to each molecular orbital (PDOS), I follow the procedure and I have made groups.txt file. However this file was not execute by GaussSum. The error is as: cclib does not recognize groups.txt as a valid log file. For your kind perusal, I am appending the snapshot of the error a long this e-mail. Thanking you, Regrads, Ajeet Singh *Dr. Ajeet Singh*M.Sc., Ph.D., Division of Advanced Materials Science, POSTECH, South Korea e-mail: aje...@gm... Google Scholar Page: http://scholar.google.co.in/citations?user=KDGOcbAAAAAJ |
From: Noel O'B. <bao...@gm...> - 2017-12-01 11:40:11
|
Hi Victor, File size should not be a problem. Can you make sure you are running the latest version of GaussSum? If you would like me to take a look, can you send me a zipped log file? Please note that I only fix bugs for public domain log files, so I also need to know whether you are happy to place the file in the public domain. Regards, - Noel On 28 November 2017 at 19:23, Volkov, Victor <vic...@nt...> wrote: > Good evening. > > This is Dr. Victor Volkov - a researcher in Nottingham Trent. > > I experienced with a probelm with Gaussum > > "cclib has problem parsing of a log file" > > The log file is larger than 2 GB. > > Could it be a reason?. > > Thank you. > > Victor > > > DISCLAIMER: This email is intended solely for the addressee. It may > contain private and confidential information. If you are not the intended > addressee, please take no action based on it nor show a copy to anyone. In > this case, please reply to this email to highlight the error. Opinions and > information in this email that do not relate to the official business of > Nottingham Trent University shall be understood as neither given nor > endorsed by the University. Nottingham Trent University has taken steps to > ensure that this email and any attachments are virus-free, but we do advise > that the recipient should check that the email and its attachments are > actually virus free. This is in keeping with good computing practice. > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > > |
From: Volkov, V. <vic...@nt...> - 2017-11-28 19:39:38
|
Good evening. This is Dr. Victor Volkov - a researcher in Nottingham Trent. I experienced with a probelm with Gaussum "cclib has problem parsing of a log file" The log file is larger than 2 GB. Could it be a reason?. Thank you. Victor DISCLAIMER: This email is intended solely for the addressee. It may contain private and confidential information. If you are not the intended addressee, please take no action based on it nor show a copy to anyone. In this case, please reply to this email to highlight the error. Opinions and information in this email that do not relate to the official business of Nottingham Trent University shall be understood as neither given nor endorsed by the University. Nottingham Trent University has taken steps to ensure that this email and any attachments are virus-free, but we do advise that the recipient should check that the email and its attachments are actually virus free. This is in keeping with good computing practice. |
From: Otávio F. <zox...@ya...> - 2017-10-24 15:32:59
|
Hi,I have a problem with the cclib in the last Debian update.My computer is run the Debian 4.12.6-1~bpo9+1 (2017-08-27).The only message is cclib has problems parsing file.out The file.out is a gaussian03 output. Thanks ------- Otávio FugantiDoutorando em QuímicaUniversidade Federal do ParanáSetor de Ciências ExatasDepartamento de QuímicaLaboratório de Química Inorgânica AplicadaP. Box 19032, 81531-980 Curitiba PR / BrasilCelular: +55(41)91956737Comercial: +55(41)33613181Email: zox...@ya... ota...@uf... ------- |
From: Noel O'B. <bao...@gm...> - 2017-10-09 13:40:41
|
HI Adebayo, I'll have a look into it. Regards, - Noel On 9 October 2017 at 13:09, Adebayo Adeniyi <ade...@gm...> wrote: > Dear Coordinator, > > Greetings. > > i want to make use of Gausssum but I keep getting a cclib parsing error: > > "cclib has problems parsing mNO2PhMeAcid-pop.log". > Kindly assist. An example of the file that gave the error is attached. > > Thanks. > > Kind regards, > > > *Adebayo A. Adeniyi, PhD* > > Rated in 2016 by NRF (South Africa) as young promising researcher (Y2) > Participated in 2009 ATOSIM European Erasmus Mundus Master Program > Member of CSN (Nigeria), SACI (South Africa), NLA (South Africa), ISID > (USA), AAPS (USA) > BSc (Pure Chemistry), MSc (Physical Chemistry) and PhD (Physical-Inorganic > Chemistry) > Postdoctoral fellow at UFH (2014-2015), UKZN (2015-2016), UFS (2017-till > date) and Lecturer at FUOYE (Nigeria) > > Tel: +27717873258 > E-mail: a.a...@ya..., ade...@go... > Address: Department of chemistry, Faculty of Natural and Agricultural > Sciences, University of the Free State, Bloemfontein, South Africa. > > Specialization: Computational/Physical-inorganic Chemistry, Drug Design > and Electrochemistry > > Career Motto: "Everything that living things do can be understood in > terms of the jigglings and wigglings of atoms" by Richard Feynman.This > is why I take pleasure in Computational Chemistry ! > > *Psalms 111: 2 The works of the LORD are great, sought out of all them > that have pleasure therein.* > > > |
From: Adebayo A. <ade...@gm...> - 2017-10-09 12:26:00
|
Please kindly see the attachment of one of the output file given cclib parsing error. I have rename zip as txt because of the error *Adebayo A. Adeniyi, PhD* Rated in 2016 by NRF (South Africa) as young promising researcher (Y2) Participated in 2009 ATOSIM European Erasmus Mundus Master Program Member of CSN (Nigeria), SACI (South Africa), NLA (South Africa), ISID (USA), AAPS (USA) BSc (Pure Chemistry), MSc (Physical Chemistry) and PhD (Physical-Inorganic Chemistry) Postdoctoral fellow at UFH (2014-2015), UKZN (2015-2016), UFS (2017-till date) and Lecturer at FUOYE (Nigeria) Tel: +27717873258 E-mail: a.a...@ya..., ade...@go... Address: Department of chemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa. Specialization: Computational/Physical-inorganic Chemistry, Drug Design and Electrochemistry Career Motto: "Everything that living things do can be understood in terms of the jigglings and wigglings of atoms" by Richard Feynman.This is why I take pleasure in Computational Chemistry ! *Psalms 111: 2 The works of the LORD are great, sought out of all them that have pleasure therein.* On Mon, Oct 9, 2017 at 2:21 PM, Adebayo Adeniyi <ade...@gm...> wrote: > Please kindly see the attachment of one of the output file given cclib > parsing error. > > > *Adebayo A. Adeniyi, PhD* > > Rated in 2016 by NRF (South Africa) as young promising researcher (Y2) > Participated in 2009 ATOSIM European Erasmus Mundus Master Program > Member of CSN (Nigeria), SACI (South Africa), NLA (South Africa), ISID > (USA), AAPS (USA) > BSc (Pure Chemistry), MSc (Physical Chemistry) and PhD (Physical-Inorganic > Chemistry) > Postdoctoral fellow at UFH (2014-2015), UKZN (2015-2016), UFS (2017-till > date) and Lecturer at FUOYE (Nigeria) > > Tel: +27717873258 <071%20787%203258> > E-mail: a.a...@ya..., ade...@go... > Address: Department of chemistry, Faculty of Natural and Agricultural > Sciences, University of the Free State, Bloemfontein, South Africa. > > Specialization: Computational/Physical-inorganic Chemistry, Drug Design > and Electrochemistry > > Career Motto: "Everything that living things do can be understood in > terms of the jigglings and wigglings of atoms" by Richard Feynman.This > is why I take pleasure in Computational Chemistry ! > > *Psalms 111: 2 The works of the LORD are great, sought out of all them > that have pleasure therein.* > > On Mon, Oct 9, 2017 at 2:09 PM, Adebayo Adeniyi <ade...@gm...> > wrote: > >> Dear Coordinator, >> >> Greetings. >> >> i want to make use of Gausssum but I keep getting a cclib parsing error: >> >> "cclib has problems parsing mNO2PhMeAcid-pop.log". >> Kindly assist. An example of the file that gave the error is attached. >> >> Thanks. >> >> Kind regards, >> >> >> *Adebayo A. Adeniyi, PhD* >> >> Rated in 2016 by NRF (South Africa) as young promising researcher (Y2) >> Participated in 2009 ATOSIM European Erasmus Mundus Master Program >> Member of CSN (Nigeria), SACI (South Africa), NLA (South Africa), ISID >> (USA), AAPS (USA) >> BSc (Pure Chemistry), MSc (Physical Chemistry) and PhD >> (Physical-Inorganic Chemistry) >> Postdoctoral fellow at UFH (2014-2015), UKZN (2015-2016), UFS (2017-till >> date) and Lecturer at FUOYE (Nigeria) >> >> Tel: +27717873258 <071%20787%203258> >> E-mail: a.a...@ya..., ade...@go... >> Address: Department of chemistry, Faculty of Natural and Agricultural >> Sciences, University of the Free State, Bloemfontein, South Africa. >> >> Specialization: Computational/Physical-inorganic Chemistry, Drug Design >> and Electrochemistry >> >> Career Motto: "Everything that living things do can be understood in >> terms of the jigglings and wigglings of atoms" by Richard Feynman.This >> is why I take pleasure in Computational Chemistry ! >> >> *Psalms 111: 2 The works of the LORD are great, sought out of all them >> that have pleasure therein.* >> >> >> > |
From: Adebayo A. <ade...@gm...> - 2017-10-09 12:09:52
|
Dear Coordinator, Greetings. i want to make use of Gausssum but I keep getting a cclib parsing error: "cclib has problems parsing mNO2PhMeAcid-pop.log". Kindly assist. An example of the file that gave the error is attached. Thanks. Kind regards, *Adebayo A. Adeniyi, PhD* Rated in 2016 by NRF (South Africa) as young promising researcher (Y2) Participated in 2009 ATOSIM European Erasmus Mundus Master Program Member of CSN (Nigeria), SACI (South Africa), NLA (South Africa), ISID (USA), AAPS (USA) BSc (Pure Chemistry), MSc (Physical Chemistry) and PhD (Physical-Inorganic Chemistry) Postdoctoral fellow at UFH (2014-2015), UKZN (2015-2016), UFS (2017-till date) and Lecturer at FUOYE (Nigeria) Tel: +27717873258 E-mail: a.a...@ya..., ade...@go... Address: Department of chemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa. Specialization: Computational/Physical-inorganic Chemistry, Drug Design and Electrochemistry Career Motto: "Everything that living things do can be understood in terms of the jigglings and wigglings of atoms" by Richard Feynman.This is why I take pleasure in Computational Chemistry ! *Psalms 111: 2 The works of the LORD are great, sought out of all them that have pleasure therein.* |
From: Noel O'B. <bao...@gm...> - 2017-08-09 08:43:29
|
Thanks Stefano, I'll look into it. On 1 August 2017 at 17:30, Stefano Ottani <ste...@is...> wrote: > Hi, I'm afraid I found a bug in the Linux version of GaussSum 3 (file > GaussSum-3.0.1.1.tgz. > > I'm using OpenSuSE Leap42.2 and everything was fine with previous versions > of GaussSum. Now, when plotting spectra, the graphic window with the diagram > pops up, but it's vanishing small and not resizable. > > I think that the problem likely stems from replacing the grid() method by > the pack() method. > > As a fast workaround I patched the file .../GaussSum-3.0.1/gausssum/plot.py > as follows: > > 35c35,37 > < self.popup.resizable(False,False) > --- >> # self.popup.resizable(False,False) >> self.popup.resizable(True,True) >> self.popup.geometry("800x600") > > However, I'm not sure this is a good solution. Will you please look at this > problem? > > Thanks a lot for your attention and for providing such a nice and useful > program. > > Regards > > Stefano Ottani > > > -- > > ----------------------------------------------- > Stefano Ottani > Consiglio Nazionale delle Ricerche > Istituto per la Sintesi Organica e la Fotoreattivita' > Via P. Gobetti, 101 > I - 40129 Bologna (Italy) > > Phone: +39-051-6398299 > Fax: +39-051-6398349 > E-mail: ste...@is... > ----------------------------------------------- > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: Stefano O. <ste...@is...> - 2017-08-01 16:49:17
|
Hi, I'm afraid I found a bug in the Linux version of GaussSum 3 (file GaussSum-3.0.1.1.tgz. I'm using OpenSuSE Leap42.2 and everything was fine with previous versions of GaussSum. Now, when plotting spectra, the graphic window with the diagram pops up, but it's vanishing small and not resizable. I think that the problem likely stems from replacing the grid() method by the pack() method. As a fast workaround I patched the file .../GaussSum-3.0.1/gausssum/plot.py as follows: 35c35,37 < self.popup.resizable(False,False) --- > # self.popup.resizable(False,False) > self.popup.resizable(True,True) > self.popup.geometry("800x600") However, I'm not sure this is a good solution. Will you please look at this problem? Thanks a lot for your attention and for providing such a nice and useful program. Regards Stefano Ottani -- ----------------------------------------------- Stefano Ottani Consiglio Nazionale delle Ricerche Istituto per la Sintesi Organica e la Fotoreattivita' Via P. Gobetti, 101 I - 40129 Bologna (Italy) Phone: +39-051-6398299 Fax: +39-051-6398349 E-mail: ste...@is... ----------------------------------------------- |
From: Mahnaz J. s. <mj...@sh...> - 2017-07-10 12:29:56
|
Hi, I used GaussSum 3.0. I performed calculations with Gaussian 09 using the following routes: 1] #p b3lyp/gen iop(3/91=4) 2] #p b3lyp/gen gfinput iop(3/91=4,9/33=1,9/36=-1) pop=full scf=dsymm symm=loose 3] #p b3lyp/gen gfinput iop(3/91=4,3/33=1,3/36=-1) pop=full scf=dsymm symm=loose and the basis sets (downloaded from EMSL basis set exchange, https://bse.pnl.gov/bse/portal): **** Au 0 S 8 1.00 14703222.86676416 0.0037526 2262824.6780320 0.0100581 541256.94037958 0.0214627 164442.91034176 0.0419279 59155.59429110 0.0745368 24111.28878337 0.1319630 10152.24890131 0.2484028 4170.67168425 0.4678957 S 2 1.00 1707.4339431 0.5704913 708.28135147 0.4295086 S 3 1.00 243.52806941 -0.4833215 117.22573806 -0.4189882 53.38778177 -0.0976901 S 2 1.00 10.72476847 0.5023106 4.98291235 0.4976893 S 2 1.00 1.37574165 -0.7187708 0.66299967 -0.2812291 S 1 1.00 25.23167009 1.0000000 S 1 1.00 0.11066351 1.0000000 S 1 1.00 0.03911478 1.0000000 P 8 1.00 57867.45693148 0.0025583 14466.07282046 0.0069902 5096.80289128 0.0204152 2035.23445681 0.0610881 842.36068729 0.1629640 361.46395991 0.3385020 161.78689265 0.3128406 73.04451373 0.0946414 P 3 1.00 16.95126547 0.2800147 7.8956218 0.4069449 3.73415826 0.3130403 P 1 1.00 35.18821179 1.0000000 P 1 1.00 1.40958119 1.0000000 P 1 1.00 0.52307734 1.0000000 P 1 1.00 0.12434867 1.0000000 P 1 1.00 0.03469933 1.0000000 D 5 1.00 1057.31409955 0.0149745 315.34985277 0.0904567 118.76210977 0.2923335 49.52241329 0.4170518 21.54470227 0.1851834 D 2 1.00 9.19880872 -0.7782852 3.88284809 -0.2217147 D 1 1.00 1.23471691 1.0000000 D 1 1.00 0.35702456 1.0000000 F 4 1.00 86.31773515 0.0583691 27.55700975 0.2444140 9.83940823 0.4153993 3.31580164 0.2818174 F 1 1.00 0.8410348 1.0000000 **** and Cu 0 S 4 1.00 313264.6119074 0.0213057 48393.25759622 0.0691267 11479.79228103 0.2214256 3384.61235923 0.6881418 S 2 1.00 1137.39282708 0.3076302 420.02333059 0.6923697 S 2 1.00 168.05814116 -0.6283913 71.30338905 -0.3716086 S 2 1.00 23.99018809 0.4179216 10.50131154 0.5820783 S 2 1.00 1.80862431 -0.7627821 0.75612558 -0.2372178 S 1 1.00 3.8198126 1.0000000 S 1 1.00 0.10764031 1.0000000 S 1 1.00 0.04158824 1.0000000 P 4 1.00 3873.61970711 0.0070717 920.27679219 0.0439049 296.24894498 0.2123032 110.87219054 0.7367200 P 2 1.00 45.50466094 0.4364703 19.80898271 0.5635296 P 3 1.00 3.78063332 0.4637392 1.56185032 0.4139766 0.59880914 0.1222840 P 1 1.00 8.93265073 1.0000000 P 1 1.00 3.4835000 1.0000000 P 1 1.00 0.2951600 1.0000000 D 4 1.00 47.14549465 0.0312064 13.10955824 0.1604277 4.35166717 0.3654101 1.4074933 0.4429556 D 1 1.00 0.37796216 1.0000000 F 1 1.00 2.64507327 1.0000000 **** on Au, Au6 and Cu6 ( iop(3/91=4) is for relativistic calculations). route [1] is sufficient to plot DOS diagram for Cu6 using GaussSum3.0 but it is impossible for atomic gold and Aun clusters using any of the routs. I would appreciate it if you could guide me. Best regards M. Jabbarzadeh Sani. On Wed, 07/05/2017 07:34 PM, Noel O'Boyle <bao...@gm...> wrote: > Hi, > > Can you zip a single log file and resend it? Please note > that I only fix bugs for public domain log files, so are you happy to > place this file in the public domain? > > - Noel > > On 26 June 2017 at 13:57, Noel O'Boyle " target="_blank"><bao...@gm...> wrote: > > Can you provide a zipped log file that shows the problem? Please note > > that I only fix bugs for public domain log files, so are you happy to > > place this file in the public domain? > > > > On 20 June 2017 at 11:34, Mahnaz Jabarzadeh sani " target="_blank"><mj...@sh...> wrote: > >> Dear sir or madam > >> I want to plot density of states (DOS) for Au6 and Cu6. There is no problem > >> with Cu6 but for Au6 only the orbital energies are depicted from -1 to 0 > >> without any DOS diagram. I would be much grateful if you could help me. > >> Best regards > >> M. Jabbarzadeh Sani. > >> > >> ------------------------------------------------------------------------------ > >> Check out the vibrant tech community on one of the world's most > >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >> _______________________________________________ > >> Gausssum-help mailing list > >> Gau...@li... > >> https://lists.sourceforge.net/lists/listinfo/gausssum-help > >> > |
From: Noel O'B. <bao...@gm...> - 2017-07-05 15:04:20
|
Hi, Can you zip a single log file and resend it? Please note that I only fix bugs for public domain log files, so are you happy to place this file in the public domain? - Noel On 26 June 2017 at 13:57, Noel O'Boyle <bao...@gm...> wrote: > Can you provide a zipped log file that shows the problem? Please note > that I only fix bugs for public domain log files, so are you happy to > place this file in the public domain? > > On 20 June 2017 at 11:34, Mahnaz Jabarzadeh sani <mj...@sh...> wrote: >> Dear sir or madam >> I want to plot density of states (DOS) for Au6 and Cu6. There is no problem >> with Cu6 but for Au6 only the orbital energies are depicted from -1 to 0 >> without any DOS diagram. I would be much grateful if you could help me. >> Best regards >> M. Jabbarzadeh Sani. >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Gausssum-help mailing list >> Gau...@li... >> https://lists.sourceforge.net/lists/listinfo/gausssum-help >> |
From: Noel O'B. <bao...@gm...> - 2017-06-29 15:07:38
|
Hi Madison, If you don't zip them, then it uses up my web mail allowance and these files are sometimes pretty big but zip really well. Try one of the following please: 1. zipping and renaming to .txt before attaching. 2. Create a gmail account and then attach as .zip. 3. Use a different zip program, e.g. 7zip to create .7z, .gz, bz2 or whatever type of zipped file. 4. Place the file on a public webserver, even one of those super dodgy ones, and send me the link. Separately, please note that I only fix bugs for public domain log files. Please let me know if you are happy to place the file in the public domain. Regards, - Noel On 28 June 2017 at 21:00, Madison Herling <her...@sa...> wrote: > Dear Dr. O’Boyle, > > I am attempting to use GaussSum 3.0.1 to perform DOS analyses on a series of > compounds. The method I used, as per your instructions in the > documentation, was rb3lyp/6-311g+(d,p) pop=full iop(3/33=1,3/36=-1). When > trying to open the file, I get an error saying “cclib has problems parsing > [insert file name here].log”. If it helps, I am running this software on > MacOS X El Capitan. I was able to install it correctly and there are some > files I am able to open, but I can’t open any of the files important to me > at this time. I know that you request the output files to be zipped, but my > institution/email server will not let me send compressed attachments. May I > send them to you as text files? > > Best, > > Madison R. Herling > her...@sa... > > 2nd Year PhD Student > Kozlowski Research Group > Department of Chemistry > School of Arts and Sciences > University of Pennsylvania > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: Madison H. <her...@sa...> - 2017-06-28 20:00:46
|
Dear Dr. O’Boyle, I am attempting to use GaussSum 3.0.1 to perform DOS analyses on a series of compounds. The method I used, as per your instructions in the documentation, was rb3lyp/6-311g+(d,p) pop=full iop(3/33=1,3/36=-1). When trying to open the file, I get an error saying “cclib has problems parsing [insert file name here].log”. If it helps, I am running this software on MacOS X El Capitan. I was able to install it correctly and there are some files I am able to open, but I can’t open any of the files important to me at this time. I know that you request the output files to be zipped, but my institution/email server will not let me send compressed attachments. May I send them to you as text files? Best, Madison R. Herling her...@sa... <mailto:her...@sa...> 2nd Year PhD Student Kozlowski Research Group Department of Chemistry School of Arts and Sciences University of Pennsylvania |
From: Noel O'B. <bao...@gm...> - 2017-06-26 12:57:32
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Can you provide a zipped log file that shows the problem? Please note that I only fix bugs for public domain log files, so are you happy to place this file in the public domain? On 20 June 2017 at 11:34, Mahnaz Jabarzadeh sani <mj...@sh...> wrote: > Dear sir or madam > I want to plot density of states (DOS) for Au6 and Cu6. There is no problem > with Cu6 but for Au6 only the orbital energies are depicted from -1 to 0 > without any DOS diagram. I would be much grateful if you could help me. > Best regards > M. Jabbarzadeh Sani. > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: Noel O'B. <bao...@gm...> - 2017-06-26 12:57:13
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Hi Ross, Can you provide a zipped log file that shows the problem? Please note that I only fix bugs for public domain log files, so are you happy to place this file in the public domain? - Noel On 26 May 2017 at 18:50, Larsen, Ross <Ros...@nr...> wrote: > Hello, > > I have just installed GaussSum and I am trying to evaluate the PDOS from a log file that is the output from a Gaussian 09 calculation with the following input (using an optimized geometry and guess from a previous run): > > > #P b3lyp/6-31g(d) geom=check guess=check pop=full iop(3/33=1,3/36=-1) > > > When I try to open the output file I get the error message: > > > "Problems parsing the logfile: > > > cclib has problems parsing file.log. > > If you think it shouldn't, please send and email...." > > > Any suggestions on what I should do to troubleshoot this? Thanks, > > > Ross > > -- > Ross Larsen > Computational Science Center > National Renewable Energy Laboratory > (303)275-4422 | Ros...@nr... (email preferred) > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help |
From: Mahnaz J. s. <mj...@sh...> - 2017-06-20 10:50:11
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Dear sir or madam I want to plot density of states (DOS) for Au6 and Cu6. There is no problem with Cu6 but for Au6 only the orbital energies are depicted from -1 to 0 without any DOS diagram. I would be much grateful if you could help me. Best regards M. Jabbarzadeh Sani. |
From: Larsen, R. <Ros...@nr...> - 2017-05-26 18:05:43
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Hello, I have just installed GaussSum and I am trying to evaluate the PDOS from a log file that is the output from a Gaussian 09 calculation with the following input (using an optimized geometry and guess from a previous run): #P b3lyp/6-31g(d) geom=check guess=check pop=full iop(3/33=1,3/36=-1) When I try to open the output file I get the error message: "Problems parsing the logfile: cclib has problems parsing file.log. If you think it shouldn't, please send and email...." Any suggestions on what I should do to troubleshoot this? Thanks, Ross -- Ross Larsen Computational Science Center National Renewable Energy Laboratory (303)275-4422 | Ros...@nr... (email preferred) |
From: Noel O'B. <bao...@gm...> - 2017-05-12 13:48:36
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Hi Neus, There's no Admin working here, just me :-) Can you send me a zipped log file that shows the problem? Please note that I only fix bugs for log files that are in the public domain, so let me know if you are happy to place the file in the public domain. Also, please zip the file. Thanks. And please zip the file. :-) Regards, Noel On 11 May 2017 at 11:06, N.Aguilera-Porta <neu...@ua...> wrote: > Dear Admin, > > I have been analysing a bunch of molecules with GaussSum.py without a > problem. > I even used the script uvvis.py from Mr. O’Boyle, but now it fails to > execute on the molecules I did and on the new ones. > What can I do? > > > > The terminal gives the following message > > Traceback (most recent call last): > File "./uvvis.py", line 28, in <module> > log.logger.setLevel(logging.ERROR) > AttributeError: 'NoneType' object has no attribute 'logger' > > > Thank you for your advice, > > Neus > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > > |
From: N.Aguilera-Porta <neu...@ua...> - 2017-05-11 10:23:35
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Dear Admin, I have been analysing a bunch of molecules with GaussSum.py without a problem. I even used the script uvvis.py from Mr. O’Boyle, but now it fails to execute on the molecules I did and on the new ones. What can I do? The terminal gives the following message Traceback (most recent call last): File "./uvvis.py", line 28, in <module> log.logger.setLevel(logging.ERROR) AttributeError: 'NoneType' object has no attribute 'logger' Thank you for your advice, Neus |
From: Noel O'B. <bao...@gm...> - 2017-04-19 11:12:33
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It should work fine. What exactly is the problem? On 31 March 2017 at 08:56, adnan ali Khan <aak...@gm...> wrote: > Hello Dear Gausssum Developers > > Is there is 64 bit microsoft windows 7/8 latest version available of > gaussum? I downloaded latest version but it is 32 bit and not working on 64 > bit. > > -- > > Adnan Ali Khan > > M.Phil Student > > Department of Chemistry > > University of Malakand (Pakistan) > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: adnan a. K. <aak...@gm...> - 2017-03-31 07:56:41
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Hello Dear Gausssum Developers Is there is 64 bit microsoft windows 7/8 latest version available of gaussum? I downloaded latest version but it is 32 bit and not working on 64 bit. -- Adnan Ali Khan M.Phil Student Department of Chemistry University of Malakand (Pakistan) |
From: Priyanka S. <pri...@gm...> - 2017-03-06 07:56:20
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Dear Sir, how to use Gauss sum 2.2 program. and how to download this program file. How to find the % contribution of a group to each molecular orbital (PDOS) <http://gausssum.sourceforge.net/GaussSum2.2/DocBook/ch07s02.html>. How to find the nature of the overlap between different groups of atoms (COOP) <http://gausssum.sourceforge.net/GaussSum2.2/DocBook/ch07s03.html> -- Dr. Priyanka Singh Laser and Spectroscopy Lab Department of Physics Banaras Hindu University Varanasi-221005 |
From: priyanka s. <pri...@gm...> - 2017-03-03 06:21:42
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Dear sir, I am research scholar. I also working Gaussian 09 (anticancer drugs). I want how to calculate Total, Patial and overlap population density-of-states withe the help of Gauss sum program. and how to download gauss sum 2.2 . please send me link this project. and how to operate and save the file. Please help me. Thanking You Dr. Akshit Priya Jamia Millia Islamia New Delhi-110025 |
From: Anton R. <vo...@gm...> - 2017-03-02 13:48:19
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Hello, team! I have a minor trouble with COOP orbitals construction. Firstly, I though that trouble is in my calculations, but then i tried to use your example (at http://gausssum.sourceforge.net/Example/index.html ) and got the same error. I have Groups.txt file which is perfectly found by GaussSum, it can nicely visualise PDOS but cant COOP. GaussSum write me message (screenshot provided as well): *File "/.../pythin3.5/site-packages/numpy/core/fromnumeric.py", line 124, in take return take(indices, axis, out, mode) ValueError: axis(=1) out of bonds* [image: Встроенное изображение 1] I use latest macOS Sierra, Python 3.5.2, and GaussSum 3.0.1. Thank you in advance! Best regards, Anton Ruzanov |
From: Noel O'B. <bao...@gm...> - 2017-02-23 15:03:15
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Right. Try replacing the / with // in line 1158. - Noel On 23 February 2017 at 13:31, N.Aguilera-Porta <neu...@ua...> wrote: > No, not at all. > > Afterwards I manage to run it with the warning, > but now with double IOP i get a new error > without getting any analysis out of it. > > > > /usr/local/lib/python3.6/site-packages/matplotlib/__init__.py:1401: > UserWarning: This call to matplotlib.use() has no effect > because the backend has already been chosen; > matplotlib.use() must be called *before* pylab, matplotlib.pyplot, > or matplotlib.backends is imported for the first time. > > warnings.warn(_use_error_msg) > Traceback (most recent call last): > File "./uvvis.py", line 29, in <module> > data = log.parse(filename) > File > "/Applications/Execute_GaussSum/gausssum/cclib/parser/logfileparser.py", > line 247, in parse > self.extract(inputfile, line) > File > "/Applications/Execute_GaussSum/gausssum/cclib/parser/gaussianparser.py", > line 1158, in extract > mocoeffs[0][base:base + len(part) / 10, i] = temp > TypeError: slice indices must be integers or None or have an __index__ > method > > > El 23 febr 2017, a les 12:22, Noel O'Boyle <bao...@gm...> va > escriure: > > Actually, that's just a warning. Did the script do what you expected? > > On 16 February 2017 at 10:17, N.Aguilera-Porta <neu...@ua...> wrote: > > Dear Admin, > > I have been trying to execute uvvis.py script with Gausssum > > https://gist.github.com/baoilleach/5717024 (script) > > but I get this error > > python3 uvvis.py Results/ > > > /usr/local/lib/python3.6/site-packages/matplotlib/__init__.py:1401: > UserWarning: This call to matplotlib.use() has no effect > because the backend has already been chosen; > matplotlib.use() must be called *before* pylab, matplotlib.pyplot, > or matplotlib.backends is imported for the first time. > warnings.warn(_use_error_msg) > > > > Could you help me to solve it? > > Thank you in advance, > > Neus Aguilera > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > > |