Biomedical subjects

Lemin Li

Publications and source records attributed to Lemin Li.

4 recordsLinked to original sources

PubMed2005

Parallelization of MRCI based on hole-particle symmetry.

The parallel implementation of multireference configuration interaction program based on the hole-particle symmetry is described. The platform to implement the parallelization is an Intel-Architectural cluster consisting of 12 nodes, each of which is equipped with two 2.4-G XEON processors, 3-GB memory, and 36-GB disk, and are connected by a Gigabit Ethernet Switch. The dependence of speedup on molecular symmetries and task granularities is discussed. Test calculations show that the scaling with the number of nodes is about 1.9 (for C1 and Cs), 1.65 (for C2v), and 1.55 (for D2h) when the number of nodes is doubled. The largest calculation performed on this cluster involves 5.6 x 10(8) CSFs.

Algorithms↗

PubMed2004

An efficient method for constructing nonorthogonal localized molecular orbitals.

A new method for constructing nonorthogonal localized molecular orbitals (NOLMOs) is presented. The set of highly localized NOLMOs is obtained by minimization of the spread functional starting from an initial set of canonical orthogonal molecular orbitals. To enhance the stability and efficiency, the centroids of the NOLMOs are constrained to be those of the corresponding orthogonal localized molecular orbitals (OLMOs), which are obtained with the Boys criterion in advance. In particular, these centroid constraints make the optimization for each NOLMO independent of the others, which is an attractive feature for application to large systems. The minimization with the constraints incorporated through the multiplier-penalty function method is stable and efficient in convergence. While exhibiting the classical bonding pattern in chemistry and sharing a spatial distribution similar to that of the corresponding OLMOs, the obtained NOLMOs are more compact than the corresponding OLMOs with about 10%-28% reduction in the value of the spread functional and devoid of the troublesome "orthogonalization tails."

Journal Article↗

PubMed2004

Numerical examination of performance of some exchange-correlation functionals for molecules containing heavy elements.

The performance of 17 exchange-correlation functionals for molecules containing heavy elements are numerically examined through four-component relativistic density DFT calculations. The examined functionals show the similar accuracy as they do for the molecules containing light elements only except for bond lengths. LDA and OP86 produce good results for bond lengths and frequencies but bad bond energies. Different functionals do not show much different performance for bond energies except LDA. BP86 and GP86 produce results with average accuracy while LYP does not perform well. Although encouraging results are obtained with functional B97GGA-1, other heavily parameterized and meta-GGA functionals do not produce impressive results.

Journal Article↗

PubMed2002

Analytical energy gradient evaluation in relativistic and nonrelativistic density functional calculations.

The expressions of analytical energy gradients in density functional theory and their implementation in programs are reported. The evaluation of analytical energy gradients can be carried out in the fully 4-component relativistic, approximate relativistic, and nonrelativistic density functional calculations under local density approximation or general gradient approximation with or without frozen core approximation using different basis sets in our programs. The translational invariance condition and the fact that the one-center terms do not contribute to the energy gradients are utilized to improve the calculation accuracy and to reduce the computational effort. The calculated results of energy gradients and optimized geometry as well as atomization energies of some molecules by the analytical gradient method are in very good agreement with results obtained by the numerical derivative method.

Journal Article↗