Re: [Jmol-developers] Gaussian cube files ... more questions

[Miguel <mi...@jm...>]

> 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

Good.

I am very glad that you are testing.

>> 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 bein=
g
>> shaded properly.
>>
>> Nothing is working with color/translucent.
>
> and concerned about the rendering speed,

I am also somewhat concerned about rendering speed.

Rendering performance is one of the fundamental problems that I have had
in my work with solvent-accessible-surfaces.

> I think It is also useful
> merely wireflame or dotted
> isosurfaces.

I will expose script commands to allow individual control of dotted,
wiremesh, and filled surfaces.

>> I see that the orbital numbers are '1 4' '1 5', etc.
>>
>> 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)

OK. I understand.

>  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
>
> =24 cubegen 0 mo=3DALL ts1.fchk ts1.cube -2)
>
>  http://chemie.skku.ac.kr/=7Ewkpark/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 ...
> -----

OK.

I did not know tht it could contain more than one volumetric data set.

I now realize that the interface should be different.

Reading the atoms should be different from reading the volumetric data.

Reading the volumetric data should be independent, more like the 'pmesh'
command.

That way, a user can have more control over the names of the volumetric
surfaces and the coloring/rendering of each one.


Miguel