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[Jmol-developers] [ jmol-Bugs-3419710 ] Molden reader does not accept coordinates in Angstroms
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From: SourceForge.net <no...@so...> - 2011-10-06 17:49:55
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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 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 (ha...@st...) 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 |