On Tue, Jun 06, 2006 at 06:14:59PM -0500, Bob Hanson wrote: > [note: this message relates to the experimental prototype "Jmol 10.x" not > the public release Jmol 10.2. See > http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm for details.] > > > Yes, I'm yelling. WHOOPING, actually. What do you know..... > > Jmol can now display accurate, CALCULATED atomic orbitals via the > Schroedinger equation and based on > > Quantum numbers n, l, and m > Effective nuclear charge Zeff > Resolution factor (grid points per Angstrom) > > # px > isosurface delete; isosurface orbital 2 1 1 6 10 phase; > # pz > isosurface delete; isosurface orbital 2 1 0 6 10 phase; > # py > isosurface delete; isosurface orbital 2 1 -1 6 10 sign yellow violet > phase;slab 70;slab on > # dxz > isosurface delete; isosurface orbital 3 2 1 6 10 phase; > # dyz > isosurface delete; isosurface orbital 3 2 -1 6 10 phase; > # dxy > isosurface delete; isosurface orbital 3 2 -2 6 10 phase; > # dx2-y2 > isosurface delete; isosurface orbital 3 2 2 6 10 phase; > # dz2 > isosurface delete; isosurface orbital 3 2 0 6 10 phase; > # f something or other > isosurface delete; isosurface orbital 4 3 2 6 10 phase; > > limited only by your imagination and the quantum rules (oh, and you > can't go TOO high -- no check for that yet; it will crash at about n=10). > > see http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm > > It turns out that since I had already done this coding in Visual Basic > for ORBITAL.EXE, it was a fairly simple addition to isosurfaces; > > The syntax is certainly up for discussion. > Right now it is: > > isosurface orbital [n] [m] [l] [Zeff] [ResFactor] > > followed, if desired, by either: > > sign [color_neg] [color_pos] phase > > or just the word "phase" to select default colors. > > Now we need to figure out how to place these where we want them. > Right now they just go in at 0,0,0. > > Ideas? > > > Bob Hanson >
Wonderful :) then how about to add a PSI88(viewmol or molden etc.) like feature - generate on-the-fly molecular orbital surfaces ? These software can read some MO infos from gaussianXX/gamess/etc. and generate molecular orbital surfaces Molden or viewmol read gaussianXX ouput log files(or *.fchk) and parse basis set infos and molecular orbital coefficients to make MOs. I have some fortran program to make a cube like as the cubegen program but it read gaussianXX logfile instead of *.fchk. and I make some small awk/sh script to extract basis set infos and MO coefficients. http://chem.skku.ac.kr/~wkpark/chem/gmo (awk/sh script) http://chem.skku.ac.kr/~wkpark/chem/mocube.f (fortran source code to generate cube) (some utility routines are ommited. use PSI88's fast algorithm.) above awk/sh script extract following simple format and mocube.f read it to generate a cube. This format is similar to PSI88 input but it has additional basis-set infos. (from gaussian03 output with '#HF/3-21g gfinput Iop(5/33=1) pop=full' keywords) ----------------8X------8X------------------------- O 0.000000 0.000000 0.114698 H 0.000000 0.753989 -0.458790 H 0.000000 -0.753989 -0.458790 Standard basis: 3-21G (6D, 7F) O 0 # basis-set info from the gaussian log file S 3 0.3220370000D+03 0.5923939339D-01 0.4843080000D+02 0.3514999608D+00 0.1042060000D+02 0.7076579210D+00 SP 2 0.7402940000D+01 -0.4044535832D+00 0.2445861070D+00 0.1576200000D+01 0.1221561761D+01 0.8539553735D+00 SP 1 0.3736840000D+00 0.1000000000D+01 0.1000000000D+01 **** H 0 S 2 0.5447178000D+01 0.1562849787D+00 0.8245472400D+00 0.9046908767D+00 S 1 0.1831915800D+00 0.1000000000D+01 **** H 0 S 2 0.5447178000D+01 0.1562849787D+00 0.8245472400D+00 0.9046908767D+00 S 1 0.1831915800D+00 0.1000000000D+01 **** 0.983230 0.096000 0.000000 0.000000 -0.003520 -0.038330 0.000000 0.000000 0.006780 0.002570 0.007060 0.002570 0.007060 -0.228970 0.217380 0.000000 0.000000 -0.084950 0.703710 0.000000 0.000000 -0.093230 0.119480 0.017940 0.119480 0.017940 0.000000 0.000000 0.000000 0.399840 0.000000 0.000000 0.000000 0.366750 0.000000 0.236400 0.178980 -0.236400 -0.178980 -0.088120 0.081590 0.000000 0.000000 0.444180 0.403950 0.000000 0.000000 0.510760 -0.129530 -0.101080 -0.129530 -0.101080 0.000000 0.000000 0.520760 0.000000 0.000000 0.000000 0.632600 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -0.110140 0.034620 0.000000 0.000000 -0.204330 1.062460 0.000000 0.000000 -0.458600 -0.044940 -0.870750 -0.044940 -0.870750 0.000000 0.000000 0.000000 -0.300200 0.000000 0.000000 0.000000 -0.777870 0.000000 0.031560 1.193010 -0.031560 -1.193010 0.000000 0.000000 0.000000 -0.182880 0.000000 0.000000 0.000000 -0.488700 0.000000 0.971120 -0.661020 -0.971120 0.661020 0.070380 -0.095840 0.000000 0.000000 0.268530 -0.149010 0.000000 0.000000 0.322890 0.992790 -0.473940 0.992790 -0.473940 0.000000 0.000000 1.029540 0.000000 0.000000 0.000000 -0.964860 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.044250 -0.126570 0.000000 0.000000 -1.012290 -0.186720 0.000000 0.000000 1.150590 0.249800 0.100420 0.249800 0.100420 0.000000 0.000000 0.000000 -1.068090 0.000000 0.000000 0.000000 1.406690 0.000000 -0.133280 -0.524110 0.133280 0.524110 0.084200 -1.645260 0.000000 0.000000 0.154490 2.013580 0.000000 0.000000 -0.492240 -0.284290 -0.368870 -0.284290 -0.368870 and additional info here... (homo lumo etc..) ----------------------------- Regards, Won-Kyu Park _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
