Ryan M. Olson

A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method(FMO)

A two‐level hierarchical scheme, generalized distributed data interface (GDDI), implemented into GAMESS is presented. Parallelization is accomplished first at the upper level by assigning computational tasks to groups. Then each group does parallelization at the lower level, by dividing its task into smaller work loads. The types of computations that can be used with this scheme are limited to those for which nearly independent tasks and subtasks can be assigned. Typical examples implemented, tested, and analyzed in this work are numeric derivatives and the fragment molecular orbital method (FMO) that is used to compute large molecules quantum mechanically by dividing them into fragments. Numeric derivatives can be used for algorithms based on them, such as geometry optimizations, saddle‐point searches, frequency analyses, etc. This new hierarchical scheme is found to be a flexible tool easily utilizing network topology and delivering excellent performance even on slow networks. In one of the typical tests, on 16 nodes the scalability of GDDI is 1.7 times better than that of the standard parallelization scheme DDI and on 128 nodes GDDI is 93 times faster than DDI (on a multihub Fast Ethernet network). FMO delivered scalability of 80–90% on 128 nodes, depending on the molecular system (water clusters and a protein). A numerical gradient calculation for a water cluster achieved a scalability of 70% on 128 nodes. It is expected that GDDI will become a preferred tool on massively parallel computers for appropriate computational tasks.

The interaction of oxygen with small gold clusters

Presented in this work are the results of a quantum chemical study of oxygen adsorption on small Aun and Aun− (n=2,3) clusters. Density functional theory (DFT), second order perturbation theory (MP2), and singles and doubles coupled cluster theory with perturbative triples [CCSD(T)] methods have been used to determine the geometry and the binding energy of oxygen to Aun. The multireference character of the wave functions has been studied using the complete active space self-consistent field method. There is considerable disagreement between the oxygen binding energies provided by CCSD(T) calculations and those obtained with DFT. The disagreement is often qualitative, with DFT predicting strong bonds where CCSD(T) predicts no bonds or structures that are bonded but have energies that exceed those of the separated components. The CCSD(T) results are consistent with experimental measurements, while DFT calculations show, at best, a qualitative agreement. Finally, the lack of a regular pattern in the size and...

A study of the reactions of molecular hydrogen with small gold clusters

This work presents a study of reactions between neutral and negatively charged Au(n) clusters (n=2,3) and molecular hydrogen. The binding energies of the first and second hydrogen molecule to the gold clusters were determined using density functional theory (DFT), second order perturbation theory (MP2) and coupled cluster (CCSD(T)) methods. It is found that molecular hydrogen easily binds to neutral Au(2) and Au(3) clusters with binding energies of 0.55 eV and 0.71 eV, respectively. The barriers to H(2) dissociation on these clusters with respect to Au(n)H(2) complexes are 1.10 eV and 0.59 eV for n=2 and 3. Although negatively charged Au(n) (-) clusters do not bind molecular hydrogen, H(2) dissociation can occur with energy barriers of 0.93 eV for Au(2) (-) and 1.39 eV for Au(3) (-). The energies of the Au(2)H(2) (-) and Au(3)H(2) (-) complexes with dissociated hydrogen molecules are lower than the energies of Au(2) (-)+H(2) and Au(3) (-)+H(2) by 0.49 eV and 0.96 eV, respectively. There is satisfactory agreement between the DFT and CCSD(T) results for binding energies, but the agreement is not as good for barrier heights.

Isomers of Au8

Using newly developed correlation consistent basis sets for gold, the relative energies for the neutral Au8 geometric isomers have been re-evaluated and the vertical ionization potentials calculated. The results using the correlation consistent basis sets show that second-order Moller-Plesset perturbation theory calculations strongly favor nonplanar Au8 structures for all basis sets that were employed. However, the general trend at the coupled cluster singles and doubles with perturbative triples level of theory is to increasingly favor planar structures as the basis set is improved. The effects of basis set and the effects of core-valence correlation are discussed.

Enabling the Efficient Use of SMP Clusters: The GAMESS/DDI Model

An important advance in cluster computing is the evolution from single processor clusters to multi-processor SMP clusters. Due to the increased complexity in the memory model on SMP clusters, new approaches are needed for applications that make use of distributed-memory paradigms. This paper presents new communications software developments that are designed to take advantage of SMP cluster hardware. Although the specific focus is on the central field of computational chemistry and materials science, as embodied in the popular electronic structure package GAMESS (General Atomic and Molecular Electronic Structure System), the impact of these new developments will be far broader in scope. Following a summary of the essential features of the distributed data interface (DDI) in the current implementation of GAMESS, the new developments for SMP clusters are described. The advantages of these new features are illustrated using timing benchmarks on several hardware platforms, using a typical computational chemistry application.

Parallel coupled perturbed CASSCF equations and analytic CASSCF second derivatives.

A parallel algorithm for solving the coupled‐perturbed MCSCF (CPMCSCF) equations and analytic nuclear second derivatives of CASSCF wave functions is presented. A parallel scheme for evaluating derivative integrals and their subsequent use in constructing other derivative quantities is described. The task of solving the CPMCSCF equations is approached using a parallelization scheme that partitions the electronic hessian matrix over all processors as opposed to simple partitioning of the 3 N solution vectors among the processors. The scalability of the current algorithm, up to 128 processors, is demonstrated. Using three test cases, results indicate that the parallelization of derivative integral evaluation through a simple scheme is highly effective regardless of the size of the basis set employed in the CASSCF energy calculation. Parallelization of the construction of the MCSCF electronic hessian during solution of the CPMCSCF equations varies quantitatively depending on the nature of the hessian itself, but is highly scalable in all cases.

The structure of the Si9H12 cluster : A coupled cluster and multi-reference perturbation theory study

Full geometry optimizations using both singles and doubles coupled cluster theory with perturbative triple excitations, CCSD(T), and second order multi-reference perturbation theory, MRMP2, have been employed to predict the structure of Si9H12, a cluster commonly used in calculations to represent the Si(100) surface. Both levels of theory predict the structure of this cluster to be symmetric (not buckled), and no evidence for a buckled (asymmetric) structure is found at either level of theory.

Reply to a comment: oxygen adsorption on Au clusters by W.T. Wallace, A.J. Leavitt, and R.J. Whetten

Abstract In response to the comment of Wallace et al., we point out that density functional theory has very serious difficulties in dealing with the oxygen molecule and that unpublished calculations with more accurate methods are in agreement with the experimental results of Salisbury et al.

Scalable correlated electronic structure theory

The approach taken in Ames to advance high-level electronic structure theory has been a combination of the development and implementation of new and novel methods with the continuing development of strategies to optimize scalable computing. This work summarizes advances on both fronts. Several new methods have been implemented under the Distributed Data Interface (DDI), most recently including analytic Hessians for both Hatree- Fock and CASSCF (complete active space self-consistent field) wavefunctions, gradients for restricted open shell second order perturbation theory, and the fragment molecular orbital method (FMO). Exciting new method developments include the FMO method and the CEEIS (Correlation Energy Extrapolation by Intrinsic Scaling) method for efficiently approaching the exact energy for atomic and molecular systems.