Bugs item #3419710, was opened at 2011-10-06 10:29 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3419710&group_id=23629
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: Algorithms Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Jiahao Chen (jiahao) Assigned to: Bob Hanson (hansonr) Summary: Molden reader does not accept coordinates in Angstroms Initial Comment: When reading a Molden file in 12.2.0, the code will fail with "Error reading file at line 2: [ATOMS] (ANGS) invalid coordinate unit (ANGS) in [Atoms]" In the file I have, that line in the Molden file is capitalized as [Atoms] Angs Looking in the source code, it looks like org/jmol/adapter/readers/quantum/MoldenReader is parsing lines in a case-sensitive manner for the unit "Angs" but the lines being read in are automatically capitalized (perhaps in readLine?). ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2011-10-06 13:33 Message: OK, I'll fix that in Jmol. ---------------------------------------------------------------------- Comment By: Jiahao Chen (jiahao) Date: 2011-10-06 13:03 Message: (This file was generated from Q-Chem 3.2 and opens in Molden 5.0 without problems. I could post a screenshot of Molden with this file open but it seems pointless.) ---------------------------------------------------------------------- Comment By: Jiahao Chen (jiahao) Date: 2011-10-06 13:00 Message: In fact, my experience is indeed that Molden 5.0 reads this file without any problems. Thus according to the reference implementation the spaces are not necessary. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-10-06 12:50 Message: (if you can show me that Molden reads it without a space, I will adapt Jmol to do that as well) ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-10-06 12:49 Message: Ah, I see. The file format is invalid. Please see www.cmbi.ru.nl/molden/molden_format.html There needs to be a space after the "=" in all those records: Sym= symmetry_label_1 Ene= mo_energy_1 Spin= (Alpha|Beta) Occup= mo_occupation_number_1 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2011-10-06 11:08 Message: yes, that's exactly what happened. OK that's fixed for 12.2.1 and 12.3.1, but regarding SYM=X, please send me that file directly (hans...@stolaf.edu) not broken up like that. I can't read that. ---------------------------------------------------------------------- Comment By: Jiahao Chen (jiahao) Date: 2011-10-06 10:49 Message: Attached is a sample Molden file which is failing to load correctly. After fixing Args -> ARGS in MoldenReader it continues to fail at line 1306 "Sym=X". ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3419710&group_id=23629 ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
