From: Park Won-K. <wk...@gm...> - 2005-07-15 13:50:09
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2005/7/15, Miguel <mi...@jm...>: >=20 > > wow!! what a good job is it :) >=20 > I assume you are talking about the direct support for .cube files. > I mean the Marching cube code in the Jmol :) . one can read any cube related files from so many ab-initio QM packages and can see the Molecular orbitals and Iso surfaces > It still needs work. Vertex points are not being shared by the various > triangles that meet at the points. That is why the facets are not being > shaded properly. >=20 > Nothing is working with color/translucent. > and concerned about the rendering speed, I think It is also useful merely wireflame or dotted isosurfaces. >=20 > > I also made fix for Isovis to make a pmesh surfaces from a gaussian > > cubefile. > > and this is a example page: > > http://chemie.skku.ac.kr/~wkpark/demos/demo/sample.html >=20 > It would be helpful for me if I could download both the .pmesh files and > the .cube file >=20 > That way, I could see whether or not I was generating the same surface. >=20 > > 2005/7/15, Miguel <mi...@jm...>: > >> Richard, > >> > >> I am making good progress on the gaussian cube file surfaces ... > >> > >> It is important that we have a proper name to call these things. As I > >> understand it, the scalar field values that are output could be one of > >> several things. > >> > >> Q: What is the complete list of scalar volumetric data type values tha= t > >> can be stored in a gaussian .cube file? > >> > >> Q: Is there a way for me to automatically distinguish which data type > >> value is contained in a gaussian .cube file? > >> > > ----- > > coh optimization mo=3D8 > > Alpha MO coefficients > > -4 -6.264596 -5.253640 -4.986823 > > 91 0.138461 0.000000 0.000000 > > 77 0.000000 0.138461 0.000000 > > 73 0.000000 0.000000 0.138461 > > 8 8.000000 1.293844 0.282884 -0.016087 > > 8 8.000000 -1.293860 -0.282905 -0.016084 > > 1 1.000000 -2.005769 1.459916 0.128679 > > 1 1.000000 2.005901 -1.459753 0.128690 > > 1 8 > > <skip> > > ----- > > third line " -4" indicate that this cube file is for the Molecular > > orbital ( < 0) >=20 > OK. >=20 > > 11-th line "1 8" indicate that this cube has one and 8-th Molecular > > orbital > > (multiple cube can be possible) >=20 > Very good. >=20 > If possible, please give me a simple explanation of "1 and 8-th Molecular > orbital" > > >> Q: What other programs other than 'gaussian' can generate this type of > >> 'volumetric scalar field data'? > > > > there are so many ab-initio package like GAMESS, molpro and > > semi-emperical packages > > like MOPAC etc. can generate this type of file. >=20 > Do they all generate *exactly* the same .cube file? >=20 > Or does each of these programs have its own format? >=20 > >> > >> Please send me a few simple samples of the various field types along > >> with > >> descriptive file names. Names like 'chargeDistribution.cube' or > >> 'orbitals.cube' or 'sp3.cube' > >> > > > > this is some MO files for h2o2 generated by the "cubegen" > > http://chemie.skku.ac.kr/~wkpark/demos/demo/o2h2_1_04.cube > > http://chemie.skku.ac.kr/~wkpark/demos/demo/o2h2_1_05.cube > > http://chemie.skku.ac.kr/~wkpark/demos/demo/o2h2_1_06.cube > > http://chemie.skku.ac.kr/~wkpark/demos/demo/o2h2_1_07.cube > > http://chemie.skku.ac.kr/~wkpark/demos/demo/o2h2_1_08.cube >=20 > These are very helpful. >=20 > One of them helped me find a bug because a data point was exactly the sam= e > as the iso cutoff. >=20 > I see that the orbital numbers are '1 4' '1 5', etc. >=20 > Q: What does the '1' mean and what does the '4' mean? > first, '1' means this cube file have only one cube dataset(and only one Moecular orbital info) 4 is just a comment i think a gaussian cube file can include multiple volumetric datasets this is a example (generated by the cubegen in the gaussian03 package $ cubegen 0 mo=3DALL ts1.fchk ts1.cube -2) http://chemie.skku.ac.kr/~wkpark/demos/demo/ts1.cube.gz and this cube file have multiple Molecular orbitals -------- TS1 mo=3DALL Alpha MO coefficients -4 -6.264577 -5.254665 -4.970781 39 0.333333 0.000000 0.000000 33 0.000000 0.333333 0.000000 31 0.000000 0.000000 0.333333 8 8.000000 1.293841 -0.283929 -0.000045 8 8.000000 -1.293841 0.283929 -0.000045 1 1.000000 2.007113 1.464231 0.000361 1 1.000000 -2.007113 -1.464231 0.000361 12 1 2 3 4 5 6 7 8 9 10 11 12 volumetric datas ... ----- > Q: How do I map this to a proper name for the different surfaces? > > Q: Should the surfaces be automatically calculated when the file is > loaded, or should there be separate script commands to allow you to > construct the surface? >=20 > At first I was thinking that they should load automatically ... now I am > thinking that they should be separate commands ... more like the 'pmesh' > commands. >=20 >=20 >=20 > Miguel |