Bugs item #3273118, was opened at 2011-04-03 23:21 Message generated for change (Tracker Item Submitted) made by jiahao You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3273118&group_id=40728
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: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Jiahao Chen (jiahao) Assigned to: Nobody/Anonymous (nobody) Summary: Wrong spin computed for lithium atom in XYZ -> QChem input Initial Comment: For some reason babel treats the hydrogen atom differently from the lithium atom in the xyz parser. This is what happens for lithium $ babel -ixyz li.xyz -oreport FILENAME: li.xyz FORMULA: Li MASS: 6.9410 EXACT MASS: 7.0160045 INTERATOMIC DISTANCES ... $ babel -ixyz li.xyz -oqcin $comment li.xyz $end $molecule 0 1 3 0 0 0 $end $rem $end 1 molecule converted 12 audit log messages And this is what happens for the hydrogen atom: $ babel -ixyz test.xyz -oreport FILENAME: test.xyz FORMULA: H MASS: 1.0079 EXACT MASS: 1.0078250 TOTAL SPIN: 2 INTERATOMIC DISTANCES ... $ babel -ixyz test.xyz -oqcin $comment test.xyz $end $molecule 0 2 1 0 0 0 $end $rem $end 1 molecule converted 11 audit log messages As can be seen, the Q-Chem input file for the lithium atom has the wrong multiplicity (1=singlet) instead of the expected 2. Running with ---errorlevel 5, it appears that the lithium atom XYZ input triggers OpenBabel::AssignImplicitValence but not the hydrogen atom XYZ input. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3273118&group_id=40728 ------------------------------------------------------------------------------ Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
