[vtk-developers] Google Summer of Code students announced

David Lonie loniedavid at gmail.com
Wed Apr 27 10:18:53 EDT 2011


Hi Bill,

Not much has changed in computational chemistry since then -- the
codes are still mammoth fortran implementations that eat up most of
the processor time on our clusters. The algorithms and hardware have
improved, but that just means we can look at larger systems for the
same (enormous) computational expense :-)

Thanks for sharing about the chem roots of VTK. I know at least one
quantum chemistry package (SCM's ADF-GUI,
http://www.scm.com/Products/Overview/ADFGUIInfo.html) is currently
using VTK for their visualization, and I hope to involve them in this
project as well. It is also likely that Avogadro
(http://avogadro.openmolecules.net) will also be using VTK soon. So
there's a nice present and future for VTK in chemistry as well!

Dave

On Tue, Apr 26, 2011 at 3:26 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> David,
>
> Welcome. It will be great to see more computational chemistry support in
> VTK. When I joined GE Research in 1978 my first projects involved
> computational chemistry. I can't recall the names of the software, but they
> were large Fortran programs that consumed many of the CPU cycles we had at
> GE Research.
>
> An early molecular visualization appeared on this GE recruiting brochure.I
> wrote a Ray Tracer to visualize some GE polymers.
> http://marchingcubes.org/index.php/Image:CRDRecruitingBrochure.png
>
> I worked with a polymer chemist, John Bendler, and we had a pub in 1981.
> Bendler, J. T., W. E. Lorensen, and R. J. Dowe, "Computer Modeling of
> Polymer Conformations and Torsional Parameters," in American Physical
> Society General Meeting, March 1981.
>
> Part of my job was to interface with a number of molecular dynamics programs
> and visualize the results on a Tektronix storage display.
>
> So, there are some computational chemistry roots in the VTK community.
>
> Looking forward to seeing some exciting work,
>
> Bill
>
> PS: There are also some google roots. I was doing a sabbatical in 1995-1996
> in the Stanford Graphics Lab. Mark Levoy and Pat Hanrahan were my hosts. The
> internet was starting to explode. I was a big user and posted many pages on
> the Stanford site. I used the altavista search engine
> (http://en.wikipedia.org/wiki/AltaVista). There were only a couple of search
> engines then. I spent time with a young graduate student who told me about
> his work on search engines. I advised him to pick another topic since
> searching was a solved problem.
>
> The student was Larry Page.
>
> Moral: Sometimes experience is trumped by innovation.
>
>
> On Tue, Apr 26, 2011 at 2:47 PM, David Lonie <loniedavid at gmail.com> wrote:
>>
>> Hi list,
>>
>> I'm very excited to find out that my proposal was accepted! I'm a
>> computational chemistry Ph.D. student at SUNY Buffalo and I will be
>> working with Marcus to add native chemistry visualization tools to
>> VTK. This will involve several new additions across the pipeline,
>> mainly:
>>
>> * Sources that read the output of quantum mechanics calculations and
>> other standard molecule formats
>> * Filters to operate on electronic structure data, e.g. calculate
>> electron density from molecular orbital data
>> * Mappers to render molecules (ball and stick, wireframe, van der
>> Waals spheres, etc) and electronic structure
>>
>> I look forward to working on VTK, and this summer should be very
>> productive! :-)
>>
>> Dave
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