Biomedical subjects

Valéry Weber

Publications and source records attributed to Valéry Weber.

7 recordsLinked to original sources

PubMed2006

Parallel algorithm for the computation of the Hartree-Fock exchange matrix: gas phase and periodic parallel ONX.

In this paper we present an efficient parallelization of the ONX algorithm for linear computation of the Hartree-Fock exchange matrix [J. Chem. Phys. 106, 9708 (1997)]. The method used is based on the equal time (ET) partitioning recently introduced [J. Chem. Phys. 118, 9128 (2003)] and [J. Chem. Phys. 121, 6608 (2004)]. ET exploits the slow variation of the density matrix between self-consistent-field iterations to achieve load balance. The method is presented and some benchmark calculations are discussed for gas phase and periodic systems with up to 128 processors. The current parallel ONX code is able to deliver up to 77% overall efficiency for a cluster of 50 water molecules on 128 processors (2.56 processors per heavy atom) and up to 87% for a box of 64 water molecules (two processors per heavy atom) with periodic boundary conditions.

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PubMed2006

Energy gradients with respect to atomic positions and cell parameters for the Kohn-Sham density-functional theory at the Gamma point.

The application of theoretical methods based on density-functional theory is known to provide atomic and cell parameters in very good agreement with experimental values. Recently, construction of the exact Hartree-Fock exchange gradients with respect to atomic positions and cell parameters within the Gamma-point approximation has been introduced. In this article, the formalism is extended to the evaluation of analytical Gamma-point density-functional atomic and cell gradients. The infinite Coulomb summation is solved with an effective periodic summation of multipole tensors. While the evaluation of Coulomb and exchange-correlation gradients with respect to atomic positions are similar to those in the gas phase limit, the gradients with respect to cell parameters needs to be treated with some care. The derivative of the periodic multipole interaction tensor needs to be carefully handled in both direct and reciprocal space and the exchange-correlation energy derivative leads to a surface term that has its origin in derivatives of the integration limits that depend on the cell. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm to optimize one-dimensional and three-dimensional periodic systems at the density-functional theory and hybrid Hartree-Fock/density-functional theory levels. We also report the full relaxation of forsterite supercells at the B3LYP level of theory.

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PubMed2006

Exchange energy gradients with respect to atomic positions and cell parameters within the Hartree-Fock Gamma-point approximation.

Recently, linear scaling construction of the periodic exact Hartree-Fock exchange matrix within the Gamma-point approximation has been introduced [J. Chem. Phys. 122, 124105 (2005)]. In this article, a formalism for evaluation of analytical Hartree-Fock exchange energy gradients with respect to atomic positions and cell parameters at the Gamma-point approximation is presented. While the evaluation of exchange gradients with respect to atomic positions is similar to those in the gas phase limit, the gradients with respect to cell parameters involve the accumulation of atomic gradients multiplied by appropriate factors and a modified electron repulsion integral (ERI). This latter integral arises from use of the minimum image convention in the definition of the Gamma-point Hartree-Fock approximation. We demonstrate how this new ERI can be computed with the help of a modified vertical recurrence relation in the frame of the Obara-Saika and Head-Gordon-Pople algorithm. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm [K. Nemeth and M. Challacombe, J. Chem. Phys. 121, 2877 (2004)] to optimize periodic systems at the Hartree-Fock level of theory.

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PubMed2005

Higher-order response in O(N) by perturbed projection.

Perturbed projection for linear scaling solution of the coupled-perturbed self-consistent-field equations [V. Weber, A.M.N. Niklasson, and M. Challacombe, Phys. Rev. Lett. 92, 193002 (2004)] is extended to the computation of higher-order static response properties. Although generally applicable, perturbed projection is further developed here in the context of the self-consistent first and second electric hyperpolarizabilities at the Hartree-Fock level of theory. Nonorthogonal, density-matrix analogs of Wigner's 2n+1 rule valid for linear one-electron perturbations are given up to fourth order. Linear scaling and locality of the higher-order response densities under perturbation by a global electric field are demonstrated for three-dimensional water clusters.

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PubMed2005

Nonorthogonal density-matrix perturbation theory.

Recursive density-matrix perturbation theory [A.M.N. Niklasson and M. Challacombe, Phys. Rev. Lett. 92, 193001 (2004)] provides an efficient framework for the linear scaling computation of materials response properties [V. Weber, A.M.N. Niklasson, and M. Challacombe, Phys. Rev. Lett. 92, 193002 (2004)]. In this article, we generalize the density-matrix perturbation theory to include properties computed with a perturbation-dependent nonorthogonal basis. Such properties include analytic derivatives of the energy with respect to nuclear displacement, as well as magnetic response computed with a field-dependent basis. The theory is developed in the context of linear scaling purification methods, which are briefly reviewed.

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PubMed2004

Ab initio linear scaling response theory: electric polarizability by perturbed projection.

A linear scaling method for calculation of the static ab initio response within self-consistent field theory is developed and applied to the calculation of the static electric polarizability. The method is based on the density matrix perturbation theory [Phys. Rev. Lett. 92, 193001 (2004)]], obtaining response functions directly via a perturbative approach to spectral projection. The accuracy and efficiency of the linear scaling method is demonstrated for a series of three-dimensional water clusters at the RHF/6-31G(**) level of theory. The locality of the response under a global electric field perturbation is numerically demonstrated by the approximate exponential decay of derivative density matrix elements.

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PubMed2003

One-pot rhodium(i)-catalyzed hydroboration of alkenes: radical conjugate addition.

B-Alkylcatecholboranes, prepared by rhodium(I)-catalyzed hydroboration of alkenes, are suitable radical precursors for conjugate addition to activated olefins. This procedure proved to be particularly useful for the control of the regio- and chemoselectivity of such tandem processes. Enantioselective hydroboration has also been successfully coupled with radical chain reaction in a one-pot process.

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