Bugs item #1255787, was opened at 2005-08-10 08:08 Message generated for change (Comment added) made by rkanters You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1255787&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: File Input/Output Group: None Status: Open Resolution: None Priority: 5 Submitted By: Rene Kanters (rkanters) Assigned to: Miguel (migueljmol) Summary: Spartan reader Initial Comment: I tried reading an smol file from Spartan 02 (Mac), and got the message that no atoms were present. It seems that depending on how you set up the calculation the "Standard Nuclear Orientation" part may not be present. (before or after the BEGINOUTPUT section). For instance, I did a geometry optimization of a small molecule: 'No atoms in file'. I did a transition state calculation, followed (separately) by a frequency calculation: I do have atoms.. It seems that it may be safer to use the geometry information in the ARCHIVE section since that section is always present. While the following section BEGINPROPARC, contains vibrational information, (PROP VALUE IR_INTENS), and frequencies and symmetries of the frequencies, followed by the displacement vectors, which need to be multiplied by -1.6804058339 to get the values that are reported in the BEGINVOUTPUT section, which is currently parsed. René ---------------------------------------------------------------------- >Comment By: Rene Kanters (rkanters) Date: 2006-03-15 11:13 Message: Logged In: YES user_id=905185 I think that *.spartan files are generated by older SGI versions of Spartan, but I am not sure. You can check out all the data files through svn: svn co https://svn.sourceforge.net/svnroot/jmol/trunk/Jmol-datafiles jmol- datafiles ---------------------------------------------------------------------- Comment By: Einar Coutin (einarc) Date: 2006-03-15 10:35 Message: Logged In: YES user_id=1475990 And what about *.spartan files. And where can I find the J-mol data files? Thanks... ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2006-03-15 07:32 Message: Logged In: YES user_id=905185 The CH3F.smol file was an example of a case where the Spartan smol reader fails. The sample spartan files in the Jmol-datafiles of the project load properly. This reader looks for the text "BEGINOUTPUT" followed by "Standard Nuclear Orientation (Ang", which is not always present in the smol file. Their presence is dependent on what type of calculation is done. I just did a few quick tests on H2 geometry optimizations: PM3 no IR (frequency analysis) : fails to load PM3 with freq: fails to load RHF no IR: fails to load RHF with IR: loads My message, which started this, pointed out that it may be safer to look for the 'archive' type information in the .smol file as opposed to the captured text log generated by the modules in spartan itself. ---------------------------------------------------------------------- Comment By: Einar Coutin (einarc) Date: 2006-03-14 23:26 Message: Logged In: YES user_id=1475990 Darn jmol doesnt even opens the file CH3F.smol which you attached. wth? ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2006-03-14 23:15 Message: Logged In: NO In my case jmol doesnt even reads an spartan file. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1255787&group_id=23629 ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
