I have just uploaded a rewrite of the ionic lookup table in JmolConstants. It's now merged and split into two tables, one for cations and one for anions.
In case you are worried, I did this all in Excel with very simple text-to-data splits and reorganizing. I can send the spreadsheet if anyone is worried. JmolConstants also catalogues the cations and anions separately, so it should be faster/better as well. In addition, the algorithm only returns the charge=0 value if it finds absolutely no other ion of the same type (cation or anion) in its the tables, although I realize this was not Alan's issue -- that was that we aren't reading charges out of CIF files yet. Instead, if returns either (1) the next lower charge or (2) the next higher if none lower exists. (Right now a call for -1 that is missing will return -2 if it exists; a +3 that is missing will return +2 if it exists and if not, then +4. If no charged values are in the tables, then it returns the neutral radius value. I made a note that I'm suspicious of "Sn-4". I think there is no "Sn-4" -- One reference I have lists the value shown for "Sn-3", although this must be very rare -- tin is usually +2 or +4. Perhaps someone can look that up for us? Bob Alan Hewat wrote: > Firstly, I was wrong :-) in thinking that Jmol does not have access to > different ionic radii for different valence states (thanks Angel and > Phillip). Bob's table radii.xls does indeed contain the various > valence states. But does Jmol actually use the valence states > specified in CIF files ? eg: > >_atom_type_oxidation_number >As3- -3. >Na1+ 1. > > > > For example, as Angel's table shows: > http://biomodel.uah.es/jmol/radii/jmol_radii.en.html > there should be a big difference between As-3 > http://icsd.ill.fr/icsd/index.php?action=Search&elements=as-3 > <http://icsd.ill.fr/icsd/index.php?action=Search&elements=as-3> > as in Na3As, and As+3 as in CsAs4F13 > http://icsd.ill.fr/icsd/index.php?action=Search&elements=as%2B3 > <http://icsd.ill.fr/icsd/index.php?action=Search&elements=as%2B3>I > have taken those examples because there can be no doubt about the > valence state of As, it is clearly marked in the CIF files, and these > files are freely available from the demo WWW version of ICSD. > > For CIF files, Jmol draws As-3 with much the same radius as As+3. I > suspect it is using the uncharged atom radius, so As-3 and As+3 are > drawn the same size, intermediate between Na+1 and Cs+1 > > Alan. > BTW, David Brown tells me that the best values for ionic radii are > still those of Shannon and Prewitt 1969, Acta Cryst. B25, 925-946 (for > oxides) and Shannon 1976 Acta Cryst. A32, 751-767 (for halides), so I > guess the values in Jmol are fine (I haven't checked). > > _____________________________________________________________ > Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 > +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ > _____________________________________________________________ > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
