Biomedical subjects

J Ulises Reveles

Publications and source records attributed to J Ulises Reveles.

3 recordsLinked to original sources

PubMed2004

Calculation of exchange-correlation potentials with auxiliary function densities.

The use of Hermite Gaussian auxiliary function densities from the variational fitting of the Coulomb potential for the calculation of exchange-correlation potentials is discussed. The basic working equations for the energy and gradient calculation are derived. The accuracy of this approximation for optimized structure parameters and bond energies are analyzed. It is shown that the quality of the approximation can be systematically improved by enlarging the auxiliary function set. Average errors of 0.5 kcal/mol are obtained with auxiliary function sets including f and g functions. The timings for a series of alkenes demonstrate a substantial performance improvement.

Journal Article↗

PubMed2004

Geometry optimization in density functional methods.

The geometry optimization in delocalized internal coordinates is discussed within the framework of the density functional theory program deMon. A new algorithm for the selection of primitive coordinates according to their contribution to the nonredundant coordinate space is presented. With this new selection algorithm the excessive increase in computational time and the deterioration of the performance of the geometry optimization for floppy molecules and systems with high average coordination numbers is avoided. A new step selection based on the Cartesian geometry change is introduced. It combines the trust radius and line search method. The structure of the new geometry optimizer is described. The influence of the SCF convergence criteria and the grid accuracy on the geometry optimization are discussed. A performance analysis of the new geometry optimizer using different start Hessian matrices, basis sets and grid accuracies is given.

Journal Article↗

PubMed2004

Efficient and reliable numerical integration of exchange-correlation energies and potentials.

An adaptive numerical integrator for the exchange-correlation energy and potential is presented. It uses the diagonal elements of the exchange-correlation potential matrix as a grid generating function. The only input parameter is the requested grid tolerance. In combination with a defined cell function the adaptive grid generation scales almost linear with the number of basis functions in a system. With the adaptive numerical integrator the self-consistent field energy error, which is due to the numerical integration of the exchange-correlation energy, converges with increasing adaptive grid size to a reference value. The performance of the adaptive numerical integration is analyzed using molecules with first, second, and third row elements. Especially for transition metal systems the adaptive numerical integrator shows considerably improved performance and reliability.

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