VMD-L Mailing List

From: Matt Watkins (mattwatkinsuk_at_gmail.com)
Date: Tue Nov 22 2016 - 16:31:28 CST

Hi,

the hope is to use it for fairly large systems (compared to conventional QC
softwares), so I'm just seeing what is doable.

System I tried is 192 atoms (48 Si and 144 CaF2) with double zeta plus
polarization basis - so up each atom having a D shell, and the basis set is
quite heavy with 6-7 primitive gaussians contracted per shell. I appreciate
this might be fairly heavy, total output size is 125 MB, so I can't easily
directly share. The equivalent step in CP2K costs ~20s on 8 CPU cores
(there are quite some optimizations for the form of basis set etc though),
VMD was ~800s.

I should say that at the moment I am not 'compressing' the output at all -
i.e. just directly printing all MO coefficients, so it is hard to compare
to the cost within the CP2K, where we throw away density matrix elements
below a certain threshold. I suspect I can get a 10-100x compression at
negligible cost in accuracy for visualization by truncating the output at a
given size and trimming data lengths. But I think the plugin has a
threshold?

Thanks for the rapid response, I'd be very interested in working out a way
to get this working nicely. I'll add in some 'compression' to make things
more reasonable and get back in touch,

Matt

P.S. thinking ahead, would it be plausible to get this projection working
with periodic boundary conditions, at least for orthorhombic cells?

On Tue, Nov 22, 2016 at 10:01 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> What can you tell me about the size of the basis set or the highest
> shell type it incorporates? It is possible that some aspect of your
> conversion is overwhelming a size limit in the GPU code that might be
> a very uncommon case for the other codes we've tested with. I would be
> happy to get a copy of the input files you're testing with so I can look
> at it in more detail.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Nov 22, 2016 at 09:03:38PM +0000, Matt Watkins wrote:
> > Dear all,
> > I'm interested in using [1]VMDs orbital representation for rapid
> > visualisation of molecular orbitals. I've added the ability to output
> > MOLDEN format to CP2K, and can successfully read in the orbitals (as
> > compared to cube files). But it seems that the operations putting the
> > gaussians on the grid are occurring on the CPU rather than GPU (just
> > looking at CPU usage) and the performance is not great.
> > Are there any settings to activate GPU / speed up the orbital
> rendering
> > (beyond increasing the grid size) - I've only tried through the GUI
> > interface currently.
> > I've tried VMD 1.92 and 1.93 on Windows 7. It seems to be picking up
> the
> > QUADRO card in the blurb on startup and claims full rendering modes
> > available.
> > Thanks for the great program,
> > Matt
> >
> > References
> >
> > Visible links
> > 1. http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?
> tbcode=STON2009
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>