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From: Nuno A. G. B. <nun...@is...> - 2008-09-22 14:36:44
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Hello, It seems that cclib is not equiped to handle periodic boundary condition runs. Is it on your to do list aytime soon ? Also the main website for cclib is down. Any reason for that ? Cheers, Nuno -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student @ IST,Lisbon -- |
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From: Noel O'B. <bao...@gm...> - 2008-09-22 14:51:18
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Hello Nuno, The cclib website is down as sourceforge have just had a major update of their web hosting system (for the first time ever!). We are going to sort this out soon but it is not a quick fix. Regarding PBC, I think it is an easy fix (although I could be wrong). I have a feeling this has been fixed in SVN or that I have a test file somewhere. Just in case, can you send us a small test file (public domain and zipped please) that I can look at...? Noel 2008/9/22 Nuno A. G. Bandeira <nun...@is...>: > Hello, > > It seems that cclib is not equiped to handle periodic boundary condition > runs. Is it on your to do list aytime soon ? > > Also the main website for cclib is down. Any reason for that ? > > Cheers, > Nuno > > -- > Nuno A. G. Bandeira, AMRSC > Graduate researcher and molecular sculptor > Inorganic and Theoretical Chemistry Group, > Faculty of Science > University of Lisbon - C8 building, Campo Grande, > 1749-016 Lisbon,Portugal > http://cqb.fc.ul.pt/intheochem/nuno.html > Doctoral student @ IST,Lisbon > -- > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > |
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From: Nuno A. G. B. <nun...@is...> - 2008-09-23 17:36:15
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> </head> <body bgcolor="#ffffff" text="#000000"> Strange error message from the cclib website<br> <p><br> </p> <p>An error has been encountered in accessing this page. </p> <p>1. <b>Server:</b> <a class="moz-txt-link-abbreviated" href="http://www.cclib.sourceforge.net">www.cclib.sourceforge.net</a><br> 2. <b>URL path:</b> /<br> 3. <b>Error notes:</b> NONE<br> 4. <b>Error type:</b> 404<br> 5. <b>Request method:</b> GET<br> 6. <b>Request query string:</b> NONE<br> 7. <b>Time:</b> 2008-09-23 17:33:12 UTC (1222191192) </p> <p><b>Reporting this problem:</b> The problem you have encountered is with a project web site hosted by SourceForge.net. <b>This issue should be reported to the SourceForge.net-hosted project</b> (not to SourceForge.net). </p> <p><i>If this is a severe or recurring/persistent problem,</i> please do one of the following, and provide the error text (numbered 1 through 7, above): </p> <ol> <li>Contact the project via their <a href="http://sourceforge.net/support/prweb-lookup.php?host=www.cclib.sourceforge.net&support=1">designated support resources</a>. </li> <li>Contact the project administrators of this project via email (see the upper right-hand corner of the <a href="http://sourceforge.net/support/prweb-lookup.php?host=www.cclib.sourceforge.net">Project Summary page</a> for their usernames) at <i>user-name</i>@users.sourceforge.net</li> </ol> <p>If you are a member of the project that maintains this web content, please refer to the <a href="https://sourceforge.net/docs/E07/">Site Documentation regarding the project web service</a> for further assistance</p> <br> <br> <pre class="moz-signature" cols="72">-- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal <a class="moz-txt-link-freetext" href="http://cqb.fc.ul.pt/intheochem/nuno.html">http://cqb.fc.ul.pt/intheochem/nuno.html</a> Doctoral student @ IST,Lisbon --</pre> </body> </html> |
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From: Adam T. <a-t...@st...> - 2008-09-23 20:20:51
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The website used to be at cclib.sourceforge.net. Unfortunately, it's now saying that we don't have permission to access the wiki subdirectory. Noel, do you know anything about this? Adam On Sep 23, 2008, at 10:35 AM, Nuno A. G. Bandeira wrote: > Strange error message from the cclib website > > An error has been encountered in accessing this page. > > 1. Server: www.cclib.sourceforge.net > 2. URL path: / > 3. Error notes: NONE > 4. Error type: 404 > 5. Request method: GET > 6. Request query string: NONE > 7. Time: 2008-09-23 17:33:12 UTC (1222191192) > > Reporting this problem: The problem you have encountered is with a > project web site hosted by SourceForge.net. This issue should be > reported to the SourceForge.net-hosted project (not to > SourceForge.net). > > If this is a severe or recurring/persistent problem, please do one > of the following, and provide the error text (numbered 1 through 7, > above): > > • Contact the project via their designated support resources. > • Contact the project administrators of this project via email (see > the upper right-hand corner of the Project Summary page for their > usernames) at use...@us... > If you are a member of the project that maintains this web content, > please refer to the Site Documentation regarding the project web > service for further assistance > > > > -- > Nuno A. G. Bandeira, AMRSC > Graduate researcher and molecular sculptor > Inorganic and Theoretical Chemistry Group, > Faculty of Science > University of Lisbon - C8 building, Campo Grande, > 1749-016 Lisbon,Portugal > http://cqb.fc.ul.pt/intheochem/nuno.html > Doctoral student @ IST,Lisbon > -- > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win > great prizes > Grand prize is a trip for two to an Open Source event anywhere in > the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel |
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From: Noel O'B. <bao...@gm...> - 2008-09-24 08:04:22
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---------- Forwarded message ---------- From: Nuno A. G. Bandeira <nun...@is...> Date: 2008/9/23 Subject: Re: [cclib-devel] Gaussian PBC To: Noel O'Boyle <bao...@gm...> Also, Mayer bond orders are twice as much as they should be in Gaussian outputs. You can confirm that with any Gaussian run. Somehow along the way cclib overmultiplies the values by two. Best, Nuno -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student @ IST,Lisbon -- |
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From: Adam T. <a-t...@st...> - 2008-09-24 20:18:26
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> Also, Mayer bond orders are twice as much as they should be in > Gaussian outputs. > You can confirm that with any Gaussian run. Somehow along the way > cclib overmultiplies the values by two. Yeah, I'm aware of this, although I'm pretty sure it's only affects restricted calculations. Can you confirm that this is your case? Adam |
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From: Noel O'B. <bao...@gm...> - 2008-09-24 08:04:48
Attachments:
neoprene.zip
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---------- Forwarded message ---------- From: Nuno A. G. Bandeira <nun...@is...> Date: 2008/9/22 Subject: Re: [cclib-devel] Gaussian PBC To: Noel O'Boyle <bao...@gm...> Hi! > > Regarding PBC, I think it is an easy fix (although I could be wrong). > I have a feeling this has been fixed in SVN or that I have a test file > somewhere. Just in case, can you send us a small test file (public > domain and zipped please) that I can look at...? > I think the problem is the coordinate read out which isn't parsed correctly. Anyway here's one example from the manual. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student @ IST,Lisbon -- |
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From: Noel O'B. <bao...@gm...> - 2008-10-04 15:18:07
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Hmmm...here's the text of an email I sent to a user back in May. It's basically the same problem and the same solution: ========== The problem is that GaussSum is confused over the number of atoms: 11 or 8? The correct answer is 8, but there are also 3 translation vectors. The avoid the error, please replace the line in gausssianparser.py that says "assert self.natom == natom" with "pass" If this works, please check all of the data carefully. It is possible that there will be some other error because I have not looked at a PBC file before this. ========== This is just a workaround, but if you could try this out, could you let me know how it goes. What sort of information do you extract from PBC calculations in general? I would like to make sure that such information is extracted correctly before releasing a fix to this. I've added neoprene.zip to our test suite, so that we will remember to fix this before the next release. Noel 2008/9/22 Nuno A. G. Bandeira <nun...@is...>: > Hi! >> >> Regarding PBC, I think it is an easy fix (although I could be wrong). >> I have a feeling this has been fixed in SVN or that I have a test file >> somewhere. Just in case, can you send us a small test file (public >> domain and zipped please) that I can look at...? >> > > I think the problem is the coordinate read out which isn't parsed correctly. > > Anyway here's one example from the manual. > > > > -- > Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor > Inorganic and Theoretical Chemistry Group, Faculty of Science University of > Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal > http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student @ IST,Lisbon > -- > > |
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