Subject: Linear scaling QM calculations -summary-

From: "Julien MICHEL" <[email-masked]>
Date: Tue, 5 Mar 2002 10:56:52 +0100

If someone is interested by this, here is a compilation of the
links/references i received on the subject of Linear scaling algorithms for
QM calculations.

> From Andrew Horsfield :

A good overview of the theory can be found in the review article

 Stefan Goedecker, Reviews of Modern Physics 71, 1085 (1999)

For data on performance for quantum chemistry applications, the papers of
Gustavo Scuseria are useful. For example:

 J. M. Millam and G. E. Scuseria, Journal of Chemical Physics 106, 5569
(1997)
 A. Daniels and G. Scuseria, Journal of Chemical Physics 110, 1321 (1999)
 K. Nemeth and G. Scuseria, Journal of Chemical Physics 113, 6035 (2000)

> From Ed Brothers :

Our lab has developed linear sclaing Semiempirical code for modeling sizable
protiens and slovated systems at the (admittedly low) QM level.  The
relevent
refrerences are:

J Chem Phys, 1996, 104, 6643-9.
J Chem Phys, 1997, 107, 879-93

> From Cherif F. Matta

Matta, C.F.  (2001) "Theoretical reconstruction of the electron density of
large molecules from fragments determined as proper open quantum systems:
The properties of morphine, the oripavine PEO, and enkephanlins".
J. Phys. Chem. A, 105, 11088-11101.

> From Sam Abrash

This is state of the art work, and is still under development. Several
labs in the world are working on this development. One of the best is the
Berkeley group of Professor Head-Gordon.  I believe that they have linear
scaling working for Hartree-Fock, and are trying to extend it to correlated
methods.
Best regards,
Sam Abrash

> From Dr Martin Schuetz

For coupled cluster methods with linear scaling check references
on my web site
 http://www.theochem.uni-stuttgart.de/~schuetz/

> From David Gallagher

One recent publication suggests that the frontier orbitals on the hydrated
enzyme (calculated by MOPAC 2000) correlate to the active sites. See:

Effects of Hydration on the Electronic Structure of an Enzyme: Implication
for Catalytic Function,  Kazuki Ohno et al, J. Am. Chem. Soc. 2001, 123,
8161-8162

A MOPAC 2002 SCF on Crambin (641 atom protein) takes less than 3 minutes on
a 1,000 MHz Windows PC and uses only 60 MB of memory.

MOPAC 2002 with the MOZYME linear scaling algorithm handles up to 20,000
atoms,  for full geometry optimizations and reaction coordinates, and
includes the COSMO solvent field. The algorithm also scales approximately
linearly in memory usage. MOPAC 2002 is available stand-alone or as part of
CAChe software suite. As the method is fairly new, there are not many
publications on it's application to proteins around just yet. However, there
is more information at www.cachesoftware.com

> From Kris Van Alsenoy

You may want to look at the following paper :
Ab-initio geometry detreminations of proteins : 1. Crambin
J. Phys. Chem. A, vol. 102, p2246-2251 (1998)

> From Matt Challacombe

Hi Julien,

You can have a look at our web site (www.t12.lanl.gov/~mchalla), which is
woefully out of date (will bring it to the present soon). It does however
have some background papers that you may find relevant.  We have a fully
O(N)
code that is getting close to beta quality, which does the following in TRUE
O(N) for 3-D insulating systems: Orthogonalization, solution of SCF
equations, exact exchange, exchange-correlation and Coulomb sums.  It does
geometry optimization and PBCs for pure DFT.

-Matt

> From Huud Van Dam

Yes, linear scaling is possible at least for methods and in the limit of
infinitely large molecules. There is still a lot of work being done in this
field as the size of molecule at which linear scaling is "achieved"
influences
the total cost of the calculation (the sooner you reach linear scaling the
cheaper the method, unless the prefactors differ dramatically of course).

Places to start:

- The group of Prof. Martin Head-Gordon:

    http://www.cchem.berkeley.edu/~mhggrp/

- The group of Prof Peter Gill:

    http://maclaurin.chem.nott.ac.uk/

    Although their webpages aren't very clear about it they have done work
on
so called "attenuated Coulomb operators" but I am not sure what the current
concensus on that approach is.

- Then there is the Siesta program

    http://www.uam.es/departamentos/ciencias/fismateriac/siesta/

And there is a lot of material science stuff (you could do a search at
www.google.com on "order-N"). I hope these pointers are something of a
start.

Best wishes,