Biomedical subjects

Alex Sodt

Publications and source records attributed to Alex Sodt.

5 recordsLinked to original sources

PubMed2006

Linear scaling density fitting.

Two modifications of the resolution of the identity (RI)/density fitting (DF) approximations are presented. First, we apply linear scaling and J-engine techniques to speed up traditional DF. Second, we develop an algorithm that produces local, accurate fits with effort that scales linearly with system size. The fits produced are continuous, differentiable, well-defined, and do not require preset fitting domains. This metric-independent technique for producing a priori local fits is shown to be accurate and robust even for large systems. Timings are presented for linear scaling RI/DF calculations on large one-, two-, and three-dimensional carbon systems.

Algorithms↗

PubMed2006

A near linear-scaling smooth local coupled cluster algorithm for electronic structure.

We demonstrate near linear scaling of a new algorithm for computing smooth local coupled-cluster singles-doubles (LCCSD) correlation energies of quantum mechanical systems. The theory behind our approach has been described previously, [J. Subotnik and M. Head-Gordon, J. Chem. Phys. 123, 064108 (2005)], and requires appropriately multiplying standard iterative amplitude equations by a bump function, creating local amplitude equations (which are smooth according to the implicit function theorem). Here, we provide an example that this theory works in practice: we show that our algorithm leads to smooth potential energy surfaces and yields large computational savings. As an example, we apply our LCCSD approach to measure the post-MP2 correction to the energetic gap between two different alanine tetrapeptide conformations.

Algorithms↗

PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗

PubMed2005

Unrestricted perfect pairing: the simplest wave-function-based model chemistry beyond mean field.

The perfect pairing (PP) approximation from generalized valence bond theory is formulated in an unrestricted fashion for both closed- and open-shell systems using a coupled cluster ansatz. In the model chemistry proposed here, active electron pairs are correlated, but the unpaired or radical electrons remain uncorrelated, leading to a linear number of decoupled cluster amplitudes which can be solved for analytically. The alpha and beta spatial orbitals are variationally optimized independently. This minimal treatment of electron-electron correlation noticeably improves upon symmetry-breaking problems and other pathologies in Hartree-Fock (HF) theory and may be computed using the resolution of the identity approximation at only a factor of several times more effort than HF itself. PP also generally predicts improved molecular structures over HF. This compact, correlated wave function potentially provides a useful starting point for dynamical correlation corrections.

Journal Article↗

PubMed2005

Auxiliary basis expansions for large-scale electronic structure calculations.

One way to reduce the computational cost of electronic structure calculations is to use auxiliary basis expansions to approximate four-center integrals in terms of two- and three-center integrals, usually by using the variationally optimum Coulomb metric to determine the expansion coefficients. However, the long-range decay behavior of the auxiliary basis expansion coefficients has not been characterized. We find that this decay can be surprisingly slow. Numerical experiments on linear alkanes and a toy model both show that the decay can be as slow as 1/r in the distance between the auxiliary function and the fitted charge distribution. The Coulomb metric fitting equations also involve divergent matrix elements for extended systems treated with periodic boundary conditions. An attenuated Coulomb metric that is short-range can eliminate these oddities without substantially degrading calculated relative energies. The sparsity of the fit coefficients is assessed on simple hydrocarbon molecules and shows quite early onset of linear growth in the number of significant coefficients with system size using the attenuated Coulomb metric. Hence it is possible to design linear scaling auxiliary basis methods without additional approximations to treat large systems.

Alkanes↗