From: Noel O'B. <bao...@gm...> - 2007-03-05 09:39:57
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Works for me. Looks great, although I'm not sure what it's doing - I'd better read the manual. :-) We're starting to plan what we want to include in cclib 0.8. Can you describe exactly what information you currently extract from the log files? (Please 'cc' everything to cclib-dev list) P.S. I'm away soon until the 17th March, so don't worry if you don't hear from me. Regards, Noel On 03/03/07, Maxim Fedorovsky <Max...@un...> wrote: > Dear Noel, > > The executable for Windows is available now. It was frozen for > Python 2.4.4, ActiveTcl 8.4.14, latest VTK 5.0.2, numpy 1.0.1, > matplotlib 0.90, Pmw 1.20, under WinXP (SP 2.0) compiled with MS VC++ > 6.0. I have tested it on several computers. Please let me know if it > does not run. > > Results for methyloxirane which can be opened are located on > http://pyvib2.sourceforge.net/material.shtml. > > > Best wishes, > Max. > |
From: Maxim F. <Max...@un...> - 2007-03-05 10:17:58
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Noel O'Boyle schrieb: > Works for me. Looks great, although I'm not sure what it's doing - I'd > better read the manual. :-) > > We're starting to plan what we want to include in cclib 0.8. Can you > describe exactly what information you currently extract from the log > files? (Please 'cc' everything to cclib-dev list) > > P.S. I'm away soon until the 17th March, so don't worry if you don't > hear from me. > > Regards, > Noel Hello ! Thanks for testing) If something appears to you to be illogical or annoying, please tell me. To see what exactly is extracted refer to the docstrings of the pyviblib.io.parsers module, http://pyvib2.sourceforge.net/doc/pydoc/pyviblib.io.parsers.html. PyVib2 uses properties (and so, new-style classes) rather than class attributes to store the information. The pyviblib.io.writers module might be also of interest for you. Apropos, I have recently implemented the support of FCHK files (parsing and vibrational analysis) in OpenBabel. With best regards, Maxim Fedorovsky. |
From: Noel O'B. <bao...@gm...> - 2007-03-05 12:58:44
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On 05/03/07, Maxim Fedorovsky <Max...@un...> wrote: > Noel O'Boyle schrieb: > > Works for me. Looks great, although I'm not sure what it's doing - I'd > > better read the manual. :-) > > > > We're starting to plan what we want to include in cclib 0.8. Can you > > describe exactly what information you currently extract from the log > > files? (Please 'cc' everything to cclib-dev list) > > > > P.S. I'm away soon until the 17th March, so don't worry if you don't > > hear from me. > > > > Regards, > > Noel > Hello ! > > To see what exactly is extracted refer to the docstrings of the > pyviblib.io.parsers module, > http://pyvib2.sourceforge.net/doc/pydoc/pyviblib.io.parsers.html. You refer to "Cartesian excursions". I wonder if this is the same as what I call "cartesian displacement vectors". > PyVib2 > uses properties (and so, new-style classes) rather than class attributes > to store the information. > The pyviblib.io.writers module might be also of interest for you. They are interesting, but it's not currently a goal of cclib to write output files, until a standard XML output file for comp chem has been developed (which I understand is currently in development by a number of interested parties). Anyway, my question is, if we extract the information that PyVib2 likes, would PyVib2 use cclib? Regards, Noel |
From: Maxim F. <Max...@un...> - 2007-03-05 13:54:29
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Noel O'Boyle schrieb: > You refer to "Cartesian excursions". I wonder if this is the same as > what I call "cartesian displacement vectors". What I mean : sum_{a=1, N; i=1, 3} m_a * Lx_{a, i}**2 = 1, where the masses are expressed in atomic units. MOLDEN, for instance, uses Lx but takes the masses in atomic mass units rather than in a.u. > > Anyway, my question is, if we extract the information that PyVib2 > likes, would PyVib2 use cclib? > > Regards, > Noel > I guess, that as for any project, an additional dependency should justify its existence. Each of the PyVib2's dependencies was chosen very carefully. For instance, take Matplotlib -- an outstanding quality of 2D rendering is a weighty argument for using the package. If there would be more *reasonable* pro's than contra's in introducing cclib -- why not ? :) With best regards, Maxim Fedorovsky. |
From: Noel O'B. <bao...@gm...> - 2007-03-05 14:17:33
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On 05/03/07, Maxim Fedorovsky <Max...@un...> wrote: > Noel O'Boyle schrieb: > > You refer to "Cartesian excursions". I wonder if this is the same as > > what I call "cartesian displacement vectors". > What I mean : sum_{a=1, N; i=1, 3} m_a * Lx_{a, i}**2 = 1, where the > masses are expressed in atomic units. > MOLDEN, for instance, uses Lx but takes the masses in atomic mass units > rather than in a.u. Hmmm...that's a very exact answer, but not a quick one to digest. I'll look into this once I get back. > > Anyway, my question is, if we extract the information that PyVib2 > > likes, would PyVib2 use cclib? > > > > Regards, > > Noel > > > I guess, that as for any project, an additional dependency should > justify its existence. Each of the PyVib2's dependencies was chosen very > carefully. For instance, take Matplotlib -- an outstanding quality of 2D > rendering is a weighty argument for using the package. If there would be > more *reasonable* pro's than contra's in introducing cclib -- why not ? :) But in fact, using cclib doesn't necessarily introduce any dependencies. You can include the relevant code directly in your project (and this is what I recommend). I do this with GaussSum, as a vendor drop-in (http://svnbook.red-bean.com/nightly/en/svn.advanced.vendorbr.html) and previously as an svn external (http://svnbook.red-bean.com/nightly/en/svn.advanced.externals.html) pointing to the latest release. >From the point of view of cclib, we would like to extract as much information as possible that is useful to people, especially people who do analyses. Noel |