gausssum-help Mailing List for GaussSum (Page 13)
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From: <ir...@ma...> - 2007-04-04 14:31:01
|
Hi, Let me thank you for making Gaussum available. I am finding it really helpful. I encountered a problem while using Gausssum for plotting PDOS from the log file of a periodic boundary condition (PBC)-DFT calculation. The error message says that "cclib has probelms parsing the log file". While searching on ccl.net I found that Noel had offered help to Fred regarding a similar problem. I was wondering if I could obtain the modified script for the same purpose? Thanks in advance. Rudra -- |
From: Noel O'B. <bao...@gm...> - 2007-02-26 09:59:48
|
Announcing the release of GaussSum 2.0.4, which is available from: http://gausssum.sf..net This is a bug fix release which allows GAMESS frequency calculations containing imaginary frequencies to be dealt with correctly (they previously failed on opening). The previous release, 2.0.3, was not announced due to problems with our hosting site, SourceForge. This was also a bug fix release which allowed GaussSum to handle frequency calculations where the frequencies did not have associated symmetries. Thanks to Dr. Charles Bradshaw for identifying both these bugs. Have fun! Noel |
From: Noel O'B. <bao...@gm...> - 2007-02-23 14:47:08
|
What operating system are you using? My guess is that you're using Linux, and that you have installed Python, but that you haven't installed Tkinter, which is the standard GUI fort python. On Debian, you can installed tkinter using "apt-get install python-tk". I will add some instructions to the website regarding this in future. Regards, Noel On 23/02/07, Jer...@un... <Jer...@un...> wrote: > Hi, I have followed all the installtion steps givne in thje web site. > When I launch "python GaussSum.py" > > I get the following output : > Traceback (most recent call last): > File "GaussSum.py", line 16, in ? > from Tkinter import * # GUI stuff > ImportError: No module named Tkinter > > > Do you known what's going on ? > regards > > -- > Jerome Golebiowski, PhD > Lab. Chemistry of Bioactive Molecules and Aromas, > Team Chemometrics and Molecular Modeling > University of Nice, parc Valrose > 06108 Nice Cedex2 France > tel : +33 (0)4 92 07 61 03 > http://www.unice.fr/lcmba > http://www.unice.fr/lcmba/golebiowski > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: <Jer...@un...> - 2007-02-23 14:22:33
|
Hi, I have followed all the installtion steps givne in thje web site. When I launch "python GaussSum.py" I get the following output : Traceback (most recent call last): File "GaussSum.py", line 16, in ? from Tkinter import * # GUI stuff ImportError: No module named Tkinter Do you known what's going on ? regards -- Jerome Golebiowski, PhD Lab. Chemistry of Bioactive Molecules and Aromas, Team Chemometrics and Molecular Modeling University of Nice, parc Valrose 06108 Nice Cedex2 France tel : +33 (0)4 92 07 61 03 http://www.unice.fr/lcmba http://www.unice.fr/lcmba/golebiowski |
From: Noel O'B. <bao...@gm...> - 2007-02-15 09:15:07
|
Dear Dr. Bradshaw, The good news is that the problem sounds easy to fix. Your GAMESS output file does not contain symmetry labels for the harmonic frequencies ('vibsyms'). Unfortunately, GaussSum expects to find these and so it doesn't know what to do. I will change the code so that it will be able to deal with files that do not contain these symmetry labels. Could you send me (direct to my email a/c please, not this list) a log file that shows these problems? This will make it easier to test whether the problem has been fixed. Regards, Noel On 14/02/07, Bradshaw, Charles F. <cbr...@mi...> wrote: > When trying to analyze the frequencies from a GAMESS Hessian run, I > receive the following errors: > > > > Starting to analyse the vibrational frequencies > Using old output folder > > ************* Doing the IR ***************** > Going to scale with a scaling factor of 1.0 > Writing scaled spectrum to IRSpectrum.txt > Log of error messages > ******************** > Traceback (most recent call last): > File "gausssum\gausssumgui.pyc", line 384, in runscript > File "gausssum\vibfreq.pyc", line 104, in Vibfreq > File "gausssum\vibfreq.pyc", line 68, in dofreqs > AttributeError: 'GAMESS' object has no attribute 'vibsyms' > > Does anyone know how to fix this problem? > > Regards, > > Dr. Charles F. Bradshaw > The MITRE Corporation > MS T630 > 7515 Colshire Drive > McLean, VA 22102-7508 > W - 703-983-5847 > Fax - 703-983-6989 > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: Bradshaw, C. F. <cbr...@mi...> - 2007-02-14 20:25:50
|
When trying to analyze the frequencies from a GAMESS Hessian run, I receive the following errors: Starting to analyse the vibrational frequencies Using old output folder ************* Doing the IR ***************** Going to scale with a scaling factor of 1.0 Writing scaled spectrum to IRSpectrum.txt Log of error messages ******************** Traceback (most recent call last): File "gausssum\gausssumgui.pyc", line 384, in runscript File "gausssum\vibfreq.pyc", line 104, in Vibfreq File "gausssum\vibfreq.pyc", line 68, in dofreqs AttributeError: 'GAMESS' object has no attribute 'vibsyms' Does anyone know how to fix this problem? Regards, Dr. Charles F. Bradshaw The MITRE Corporation MS T630 7515 Colshire Drive McLean, VA 22102-7508 W - 703-983-5847 Fax - 703-983-6989 |
From: Noel O'B. <bao...@gm...> - 2007-02-09 09:13:06
|
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From: chen x. <cx...@ho...> - 2007-02-09 08:38:04
|
Hi, this is Xiu Ying here. there's a problem with the Gausssum software. I can't open some of my output files with Gausssum, the error message said that "cclib has problems parsing ***.out". I don't know what's wrong with it. please give me some advice. Thanks a lot! XY _________________________________________________________________ 与联机的朋友进行交流,请使用 Live Messenger; http://get.live.com/messenger/overview |
From: Noel O'B. <bao...@gm...> - 2007-02-01 13:40:48
|
Hello Delwar, First of all, can you give me some more information... (1) Exactly which version of GaussSum did you install? (2) If you click on "File", "Settings", what is the location of the Gnuplot executable, and is this correct? Noel On 31/01/07, dh...@ms... <dh...@ms...> wrote: > > Dear Sir, > Prviously I used gaussssu 0.9 version. I deleted that version and install new > version. > I got the following error: > No plot was created as the gunplot excutable can not be found. > Track Back (most recent call last) > File 'gausssum/gausssummaui.pyc line 391, in run script. > > File 'gausssum/gausssummaui.pyc line 415, in in popanalysis > Attribute: 'Gaussum' object has no attribute n'basis. > > I therfore request you to help me to solve the problem. > Thank you in advance for your generous help. > With regrads, > Delwar Hossain (Ph.D) > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: <dh...@ms...> - 2007-01-31 23:48:50
|
Dear Sir, Prviously I used gaussssu 0.9 version. I deleted that version and install new version. I got the following error: No plot was created as the gunplot excutable can not be found. Track Back (most recent call last) File 'gausssum/gausssummaui.pyc line 391, in run script. File 'gausssum/gausssummaui.pyc line 415, in in popanalysis Attribute: 'Gaussum' object has no attribute n'basis. I therfore request you to help me to solve the problem. Thank you in advance for your generous help. With regrads, Delwar Hossain (Ph.D) |
From: Noel O'B. <bao...@gm...> - 2006-11-09 09:25:21
|
Dear Luca, Sorry to hear you're having trouble. I am not very familiar with Macs, so my installation instructions may need to be updated... After a quick google, it seems that there is a version of Python for Macs called MacPython http://homepages.cwi.nl/~jack/macpython/macpython-osx.html, which has a package manager which will install Numeric, Tkinter and PIL, at the click of a button. This means that you do not have to compile anything yourself. I would appreciate if you could try this, and write down every step necessary to install these. I will put these instructions on the web page and this will help other Mac users. Regards, Noel On 08/11/06, Luca Salassa <luc...@gm...> wrote: > Hi, I was trying to install GaussSum on a Mac. I'm having some > problems in installing the numerical pythonand PIL; there is some > error in the compilation, because I surely miss some package (I just > started using Mac\Linux). > > Do you have any general suggestion? or any link where I can find some info? > > Thanks a lot > > Luca Salassa > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: Luca S. <luc...@gm...> - 2006-11-08 19:59:51
|
Hi, I was trying to install GaussSum on a Mac. I'm having some problems in installing the numerical pythonand PIL; there is some error in the compilation, because I surely miss some package (I just started using Mac\Linux). Do you have any general suggestion? or any link where I can find some info? Thanks a lot Luca Salassa |
From: Noel O'B. <bao...@gm...> - 2006-11-02 14:10:23
|
Hello Wang, The question for me is, how do you simulate the UV photoelectron spectrum? If you can explain this to me, then it may be possible to do this with GaussSum. Are you sure that it is not possible to do this by creating the DOS (density of states) spectrum? Regards, Noel On 02/11/06, KeDong Wang <wa...@ma...> wrote: > Dear sir: > I'am a student of University of Science and Technology of China. In these days > ,I am trying to simulate photoelectron spectra of some molecules. As far as I > have known ,the gaussum can simulate the UV-Visible Spectrum, Vibrational > spectrum. But the question whether it can simulate the UV photoelectron spectra > baffles me! Would you like to give me some advice or some answer to resolve it! > > > Looking forward to your reply! > Thank you ! > > > yours adherent > > From a faraway country > > wangkedong > > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: KeDong W. <wa...@ma...> - 2006-11-02 14:08:08
|
Dear sir: I'am a student of University of Science and Technology of China. In these days ,I am trying to simulate photoelectron spectra of some molecules. As far as I have known ,the gaussum can simulate the UV-Visible Spectrum, Vibrational spectrum. But the question whether it can simulate the UV photoelectron spectra baffles me! Would you like to give me some advice or some answer to resolve it! Looking forward to your reply! Thank you ! yours adherent From a faraway country wangkedong |
From: KeDong W. <wa...@ma...> - 2006-11-02 14:02:36
|
Dear sir: I'am a student of University of Science and Technology of China. In these days ,I am trying to simulate photoelectron spectra of some molecules. As far as I have known ,the gaussum can simulate the UV-Visible Spectrum, Vibrational spectrum. But the question whether it can simulate the UV photoelectron spectra baffles me! Would you like to give me some advice or some answer to resolve it! Looking forward to your reply! Thank you ! yours adherent From a faraway country wangkedong |
From: Jean-Sabin Mc E. <jm...@ul...> - 2006-10-31 16:41:24
|
Hello, > What platform are you using exactly? e.g. Suse Linux 10.1 I am using Madriva 2006 (2.6.12-12mdksmp). More precisely: Linux cenoli71 2.6.12-12mdksmp #1 SMP Fri Sep 9 17:20:34 CEST 2005 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 4200+ unknown GNU/Linux > > The reason I ask is that there may be a package for PIL available for > your system. The package is sometimes called 'python-imaging'. > > If the problem is with compiling PIL, please send an email to the > python-imaging mailing list listed at > http://www.pythonware.com/products/pil/. I am trying to get to this site but it is not working (I had to download the package from somewhere else). Do you think that this website failure is temporary? Any other suggestions on where else to go? Best wishes, Jean-Sabin > > Regards, > Noel > > On 31/10/06, Jean-Sabin Mc Ewen <jm...@ul...> wrote: > > Hello, > > > > I cannot seem to be able to plot with GaussSum. If I try with the "TEST" > > button in "File", Settings", I get, in the prompt: > > > > Exception in Tkinter callback > > Traceback (most recent call last): > > File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 1345, in __call__ > > return self.func(*args) > > File "/home/jmcewen/pierre/GaussSum-2.0/gausssum/preferencesbox.py", > > line 291, in testgnuplot > > DisplayPlot(self.parent,g,"You should see the GaussSum logo > > below...drawn by Gnuplot") > > File "/home/jmcewen/pierre/GaussSum-2.0/gausssum/plot.py", line 55, in > > __init__ > > self.graph = ImageTk.PhotoImage(image) > > File "/usr/lib64/python2.4/site-packages/PIL/ImageTk.py", line 116, in > > __init__ > > self.paste(image) > > File "/usr/lib64/python2.4/site-packages/PIL/ImageTk.py", line 181, in > > paste > > import _imagingtk > > ImportError: No module named _imagingtk > > > > > > > > Thus, I am quite sure that the error is linked to the fact that the Python > > Imaging Library (PIL) was not installed properly. If I do > > > > > > python setup.py build_ext -i > > > > I get: > > > > running build_ext > > -------------------------------------------------------------------- > > PIL 1.1.5 BUILD SUMMARY > > -------------------------------------------------------------------- > > version 1.1.5 > > platform linux2 2.4.3 (#2, Sep 18 2006, 19:28:43) > > [GCC 4.1.1 20060724 (prerelease) (4.1.1-3mdk)] > > -------------------------------------------------------------------- > > *** TKINTER support not available (Tcl/Tk 8.4 libraries needed) > > *** JPEG support not available > > --- ZLIB (PNG/ZIP) support ok > > *** FREETYPE2 support not available > > -------------------------------------------------------------------- > > To add a missing option, make sure you have the required > > library, and set the corresponding ROOT variable in the > > setup.py script. > > > > To check the build, run the selftest.py script. > > > > > > > > I have concluded that the Python Imaging Library (PIL) is not working > > properly with GaussSum because TKINTER is not supported. I have > > checked if the Tcl/Tk 8.4 libraries are installed and they are! > > I modified two lines in setup.py > > > > TCL_ROOT = "/usr/lib/tcl8.4","/usr/include" > > > > and I still get the same messages as above when running > > > > python setup.py build_ext -i > > > > Could you please help? > > > > Is there something else that I am supposed to do? > > > > With many thanks, > > > > Jean-Sabin McEwen > > > > ------------------------------------------------------------------------- > > Using Tomcat but need to do more? Need to support web services, security? > > Get stuff done quickly with pre-integrated technology to make your job easier > > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > _______________________________________________ > > Gausssum-help mailing list > > Gau...@li... > > https://lists.sourceforge.net/lists/listinfo/gausssum-help > > > |
From: Noel O'B. <bao...@gm...> - 2006-10-31 16:14:11
|
What platform are you using exactly? e.g. Suse Linux 10.1 The reason I ask is that there may be a package for PIL available for your system. The package is sometimes called 'python-imaging'. If the problem is with compiling PIL, please send an email to the python-imaging mailing list listed at http://www.pythonware.com/products/pil/. Regards, Noel On 31/10/06, Jean-Sabin Mc Ewen <jm...@ul...> wrote: > Hello, > > I cannot seem to be able to plot with GaussSum. If I try with the "TEST" > button in "File", Settings", I get, in the prompt: > > Exception in Tkinter callback > Traceback (most recent call last): > File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 1345, in __call__ > return self.func(*args) > File "/home/jmcewen/pierre/GaussSum-2.0/gausssum/preferencesbox.py", > line 291, in testgnuplot > DisplayPlot(self.parent,g,"You should see the GaussSum logo > below...drawn by Gnuplot") > File "/home/jmcewen/pierre/GaussSum-2.0/gausssum/plot.py", line 55, in > __init__ > self.graph = ImageTk.PhotoImage(image) > File "/usr/lib64/python2.4/site-packages/PIL/ImageTk.py", line 116, in > __init__ > self.paste(image) > File "/usr/lib64/python2.4/site-packages/PIL/ImageTk.py", line 181, in > paste > import _imagingtk > ImportError: No module named _imagingtk > > > > Thus, I am quite sure that the error is linked to the fact that the Python > Imaging Library (PIL) was not installed properly. If I do > > > python setup.py build_ext -i > > I get: > > running build_ext > -------------------------------------------------------------------- > PIL 1.1.5 BUILD SUMMARY > -------------------------------------------------------------------- > version 1.1.5 > platform linux2 2.4.3 (#2, Sep 18 2006, 19:28:43) > [GCC 4.1.1 20060724 (prerelease) (4.1.1-3mdk)] > -------------------------------------------------------------------- > *** TKINTER support not available (Tcl/Tk 8.4 libraries needed) > *** JPEG support not available > --- ZLIB (PNG/ZIP) support ok > *** FREETYPE2 support not available > -------------------------------------------------------------------- > To add a missing option, make sure you have the required > library, and set the corresponding ROOT variable in the > setup.py script. > > To check the build, run the selftest.py script. > > > > I have concluded that the Python Imaging Library (PIL) is not working > properly with GaussSum because TKINTER is not supported. I have > checked if the Tcl/Tk 8.4 libraries are installed and they are! > I modified two lines in setup.py > > TCL_ROOT = "/usr/lib/tcl8.4","/usr/include" > > and I still get the same messages as above when running > > python setup.py build_ext -i > > Could you please help? > > Is there something else that I am supposed to do? > > With many thanks, > > Jean-Sabin McEwen > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gausssum-help mailing list > Gau...@li... > https://lists.sourceforge.net/lists/listinfo/gausssum-help > |
From: Jean-Sabin Mc E. <jm...@ul...> - 2006-10-31 15:35:05
|
Hello, I cannot seem to be able to plot with GaussSum. If I try with the "TEST" button in "File", Settings", I get, in the prompt: Exception in Tkinter callback Traceback (most recent call last): File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 1345, in __call__ return self.func(*args) File "/home/jmcewen/pierre/GaussSum-2.0/gausssum/preferencesbox.py", line 291, in testgnuplot DisplayPlot(self.parent,g,"You should see the GaussSum logo below...drawn by Gnuplot") File "/home/jmcewen/pierre/GaussSum-2.0/gausssum/plot.py", line 55, in __init__ self.graph = ImageTk.PhotoImage(image) File "/usr/lib64/python2.4/site-packages/PIL/ImageTk.py", line 116, in __init__ self.paste(image) File "/usr/lib64/python2.4/site-packages/PIL/ImageTk.py", line 181, in paste import _imagingtk ImportError: No module named _imagingtk Thus, I am quite sure that the error is linked to the fact that the Python Imaging Library (PIL) was not installed properly. If I do python setup.py build_ext -i I get: running build_ext -------------------------------------------------------------------- PIL 1.1.5 BUILD SUMMARY -------------------------------------------------------------------- version 1.1.5 platform linux2 2.4.3 (#2, Sep 18 2006, 19:28:43) [GCC 4.1.1 20060724 (prerelease) (4.1.1-3mdk)] -------------------------------------------------------------------- *** TKINTER support not available (Tcl/Tk 8.4 libraries needed) *** JPEG support not available --- ZLIB (PNG/ZIP) support ok *** FREETYPE2 support not available -------------------------------------------------------------------- To add a missing option, make sure you have the required library, and set the corresponding ROOT variable in the setup.py script. To check the build, run the selftest.py script. I have concluded that the Python Imaging Library (PIL) is not working properly with GaussSum because TKINTER is not supported. I have checked if the Tcl/Tk 8.4 libraries are installed and they are! I modified two lines in setup.py TCL_ROOT = "/usr/lib/tcl8.4","/usr/include" and I still get the same messages as above when running python setup.py build_ext -i Could you please help? Is there something else that I am supposed to do? With many thanks, Jean-Sabin McEwen |
From: Noel O'B. <bao...@gm...> - 2006-09-22 08:20:07
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From: dfa <zl_...@16...> - 2006-09-22 02:23:34
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Dear sir, My gausssum (2.0 version)software downloaded from the internet can not recognise groups.txt as a valid logfile when I used GaussSum to calculate the molecular orbital contributions again. I don't know the reason. Please help me. Thanks Sincerely yours, Wang, Ziliang |