Toward high-performance computational chemistry: I. Scalable Fock matrix construction algorithms

Several parallel algorithms for Fock matrix construction are described. The algorithms calculate only the unique integrals, distribute the Fock and density matrices over the processors of a massively parallel computer, use blocking techniques to construct the distributed data structures, and use clustering techniques on each processor to maximize data reuse. Algorithms based on both square and row-blocked distributions of the Fock and density matrices are described and evaluated. Variants of the algorithms are discussed that use either triple-sort or canonical ordering of integrals, and dynamic or static task clustering schemes. The algorithms are shown to adapt to screening, with communication volume scaling down with computation costs. Modeling techniques are used to characterize algorithm performance. Given the characteristics of existing massively parallel computers, all the algorithms are shown to be highly efficient for problems of moderate size. The algorithms using the row-blocked data distribution are the most efficient. © 1996 by John Wiley & Sons, Inc.     

Investigating the performance of parallel eigensolvers for large processor counts

Summary Eigensolving (diagonalizing) small dense matrices threatens to become a bottleneck in the application of massively parallel computers to electronic structure methods. Because the computational cost of electronic structure methods typically scales asO(N ³) or worse, even teraflop computer systems with thousands of processors will often confront problems withN 10,000. At present, diagonalizing anN×N matrix onP processors is not efficient whenP is large compared toN. The loss of efficiency can make diagonalization a bottleneck on a massively parallel computer, even though it is typically a minor operation on conventional serial machines. This situation motivates a search for both improved methods and identification of the computer characteristics that would be most productive to improve.In this paper, we compare the performance of several parallel and serial methods for solving dense real symmetric eigensystems on a distributed memory message passing parallel computer. We focus on matrices of sizeN=200 and processor countsP=1 toP=512, with execution on the Intel Touchstone DELTA computer. The best eigensolver method is found to depend on the number of available processors. Of the methods tested, a recently developed Blocked Factored Jacobi (BFJ) method is the slowest for smallP, but the fastest for largeP. Its speed is a complicated non-monotonic function of the number of processors used. A detailed performance analysis of the BFJ method shows that: (1) the factor most responsible for limited speedup is communication startup cost; (2) with current communication costs, the maximum achievable parallel speedup is modest (one order of magnitude) compared to the best serial method; and (3) the fastest solution is often achieved by using less than the maximum number of available processors.Pacific Northwest Laboratory is operated for the U.S. Department of Energy (DOE) by Battelle Memorial Institute under contract DE-AC06-76RLO 1830     

Visual-field displacements in human beings evoked by accoustical transients.

Sixty-two of 133 subjects reported visual-field displacements when they were exposed to intense (125 dB SPL) repetitive audiofrequency transients. This phenomenon was investigated in three experiments. Frequency (100-5000 Hz) was varied in experiment I; repetition rate (0.5/s--6.0/s) was varied in experiment II; acoustical transient onset/offset time (0.2--25 ms) was examined in experiment III. The results of these three experiments indicated that the largest proportion of displacement reports and the largest perceived motion magnitudes followed stimulation in the 500- to 1000-Hz frequency range at repetition rates of about 1/s. Response differences as a function of onset/offset time were erratic. The pattern of results obtained in this study, in conjunction with the results of previous investigations of acoustical vestibular stimulation, suggests that the visual-field displacments resulted from stimulation of the receptors of the vestibular system. These experiments may account for discrepancies in reports of infrasound-evoked eye movements. Finally, it is suggested that intense sound exposure may damage the vestibular receptors with or without concomitant damage to the auditory portion of the membranous labyrinth.     

Synthesis, characterization and Stat3 inhibitory properties of the prototypical platinum(IV) anticancer drug, [PtCl3(NO2)(NH3)2] (CPA-7)

This paper describes a reinvestigation of the literature concerning the synthesis and structural characterization of the platinum(IV)-based anticancer drug known as CPA-7 and believed to be the compound fac-[PtCl3(NO2)(NH 3)2]. CPA-7 has previously been extensively investigated for its ability to control tumor cell growth by inhibition of Stat3 signaling, but very little information is available concerning its synthesis or spectroscopic properties. A reproducible synthetic route is shown to produce an active material which is characterized by IR and (1)H, (14)N, (15)N, and (195)Pt NMR spectroscopy, and single crystal X-ray crystallography. The freshly prepared drug is obtained as a single isomer which may in fact be fac- or mer-[PtCl3(NO2)(NH3)2], but recrystallization resulted in a disordered crystal containing approximately equal amounts of the two geometric isomers.     

Structure of the Be(OH)4(2-) anion

Sr[Be(OH)(4)] has been synthesised and its structure determination contains the first definitive characterisation of the discrete Be(OH)(4)(2-) anion.     

Comparison of steric effects on 31P chemical shifts in some 7-norbornyl, 7-norbornenyl and cyclohexyl phosphorus compounds

Phosphorus-31 NMR spectra were obtained on both syn and anti isomers of norbornenes with the 7-position bearing Cl₂P-, Me₂P-, Me₂(S)P- and Me₃P as substituents. Norbornanes with 7-Cl₂P- and 7-Me₂P- were also studied. Just as is true for ¹³C shifts for 7-Me in these bicyclo[2.2.1]heptane derivatives, the ³¹P shifts all fall noticeably upfield of published values for comparable cyclohexane derivatives. Consistent also with the ¹³C effect, a slight shielding of ³¹P in Me₂P- (1.1 ppm) was noted when this group was syn to the double bond of the norbornene system, relative to the value for the anti compound, suggesting the sensitivity of ³¹P to a diamagnetic effect from the double bond. However, the more space-demanding Cl₂P group when moved from the crowded anti to the less crowded syn position experienced a strong deshielding effect, as did the Me₂(S)P- and Me₃P- groups. The opposite is seen when these same groups are moved from the crowded axial to the less crowded equatorial position of cyclohexane, and a new structural influence appears to be operating in this system. A recent proposal that steric compression causes bond angles about phosphorus to increase and that this is the cause of the γ-shielding effect is not supported by published NMR and X-ray structural data for cis- and trans-1-methyl-4-tert-butyl-4-phosphorinanol. Bond angles about phosphorus are virtually identical in these isomers, yet ³¹P shifts differ by 6.9 ppm.     

Synthesis, chemistry and structures of complexes of the dioxovanadium(V) halides VO2F and VO2Cl

[VO2F(L-L)] (L-L = 2,2'-bipyridyl, 1,10-phenanthroline, Me2N(CH2)2NMe2) and [VO2F(py)2] (py = pyridine) have been prepared from the corresponding [VOF3(L-L)] or [VOF3(py)2] and O(SiMe3)2 in MeCN solution. VO2F (itself made from VOF3 and O(SiMe3)2 in MeCN) forms [Me4N][VO2F2] with [Me4N]F, but does not react with neutral N- or O-donor ligands. VO2Cl, prepared from VOCl3 and ozone, reacts with 2,2'-bipyridyl or 1,10-phenanthroline to form [VO2Cl(L-L)], with pyridine or pyridine-N-oxide (L) to produce [VO2Cl(L)2], and with OPPh3 or OAsPh3 (L') gives [VO2Cl(L')]. A second product from the OPPh3 system is the ionic [VO2(OPPh3)3][VO2Cl2] containing a trigonal bipyramidal cation. Neither VO2F nor VO2Cl form isolable complexes with MeCN, thf or MeO(CH2)2OMe, and both are reduced by P-, As-, S- or Se-donor ligands. [Ph4As][VO2X2] (X = F or Cl) react with 2,2'-bipyridyl to form [VO2X(2,2'-bipyridyl)], but similar reactions with weaker O-donor ligands fail. The complexes have been characterised by IR, multinuclear NMR (1H, 19F, 51V or 31P) and UV-visible spectroscopy. X-ray crystal structures are reported for [VO2F(py)2], [VO2Cl(L)2] (L = py or pyNO) and [VO2(OPPh3)3][VO2Cl2].     

SOME MONOCYCLIC AND SPIROCYCLIC FLUOROPHOSPHORANES CONTAINING 6- AND 7-MEMBERED RINGS

Abstract

The reaction of 2,2-dimethyl-(1,8-naphtho[c,d])-1,3,2-dioxysilenin (3) and 2,2-dimethyldibenzo-1,3,2-dioxysilepin (4) with (C₆H₅)₂PF₃ gave the expected monocyclic fluorophosphoranes. Reaction of the same siloxy compounds with PF₅ gave products which could not be purified but whose ¹⁹F nmr spectra suggested that the desired spirocyclic compounds were present in the impure products. Reaction of the siloxy compounds with C₆H₅PF₄ did not yield identifiable products. The ¹⁹F nmr spectra of the products obtained are discussed and structures are tentatively assigned.