Parallel calculations of molecular properties

Wiley interdisciplinary reviews. Computational molecular science, 2014

Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, Møller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied ...

2001

A parallel realization of the NDDO-WF technique for semi-empirical quantum-chemical calcu- lations on large molecular systems in the spd-basis is described. The technological aspects of designing scalable parallel calculations on super computers (by using MPI library) are discussed. The scaling of individual algorithms and entire package was carried out for two model systems with a number of atomic orbitals of 894 and 2014, respectively. The speedup was determined in computer experiments with the RM600 E60 and Cluster Intel PIII multi-processor systems. The eect of communication rate on the pack- age performance is discussed.

Astrophysics and space science library, 2001

2006

We report the results of intensive numerical calculations for four atomic H2+H2 energy transfer collision. A parallel computing technique based on LAM/MPI functions is used. In this algorithm, the data is distributed to the processors according to the value of the momentum quantum number J and its projection M. Most of the work is local to each processor. The topology of the data communication is a simple star. Timings are given and the scaling of the algorithm is discussed. Two different recently published potential energy surfaces for the H2-H2 system are applied. New results obtained for the state resolved excitation-deexcitation cross sections and rates valuable for astrophysical applications are presented. Finally, more sophisticated extensions of the parallel code are discussed.

The use of massively parallel computers has allowed us to carry out computational chemistry studies of gas phase and condensed phase systems. Smaller systems can be studied to a more accurate level and in greater detail than previously possible. Thus, the effect of atmospheric water crystals, on reactions aiding ozone depletion over the Antarctic, has been modelled. In addition systems that could not be studied previously are now open to investigation. We have carried out a large number of accurate calculations on the solvation of the Fluoride ion by four water molecules to obtain its thermodynamic characteristics. A project involving the controlled oxidation of hydrocarbons at relatively low temperatures involved the use of serial and parallel machines.

International Journal of Quantum Chemistry, 2009

The Theoretical Chemistry Group at Argonne National Laboratory has had a Floating Point System, Inc., Model 164 Attached Processor (FPS-164) for several months. Actual production calculations, as well as benchmark calculations, indicate that the FPS-164 is capable of performance comparable to large mainframe computers. Our experience with the FPS-164 includes the conversion of a complete system of electronic stntcture codes, including integral evaluation programs, generalized valence bond programs, integral transformation programs, and unitary group configuration interaction programs, and two classical trajectory codes. Timings of these programs at various levels of optimization along with estimates of the amount of effort required to make the necessary program modifications are discussed. (RRKM) theory, and quasiclassical trajectory theories. Thus, our group's computational requirements are similar to those of many other large quantum chemistry groups.

International Journal of Quantum Chemistry, 2002

A parallel implementation of the conventionally used NDDO (MNDO, AM1, PM3, CLUSTER-Z1) and modified NDDO-WF (CLUSTER-Z2) techniques for semiempirical quantumchemical calculations of large molecular systems in the sp-and spd-basis, respectively, is described. The atom-pair distribution of data over processors forms the basis of the parallelization. The technological aspects of designing scalable parallel calculations on supercomputers (by using ScaLAPACK and MPI libraries) are discussed. The scaling of individual algorithms and entire package was carried out for model systems with 894, 1920, and 2014 atomic orbitals. The package speedup provided by different multi-processor systems involving a cluster of the Intel PIII processors, Alpha-21264processor-built machine MBC-1000M, and CRAY-T3E, is analyzed. The effect of computer characteristics on the package performance is discussed.

Computer Physics Communications, 2001

In this paper we would discuss the increasing role played by the past and upcoming silicon technology in solving real computational applications' cases in correlated scientific fields ranging from quantum chemistry, materials science, atomic and molecular physics and bio-chemistry. Although the wide range of computational applications of computer technology in this areas does not permit to have a full rationale of its present and future role, some basic features appear to be so clearly defined that an attempt to find common numerical behaviours become now feasible to be exploited.

2010

Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik et al., Science 309, 1704] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially.

Journal of Computational Chemistry, 1996

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. 0 1996 by John Wiley & Sons, Inc. chines the potential to solve Grand Challenge-class problems in computational chemistry. In this and a companion article, we report our initial efforts to develop effective ab initio electronic structure codes for MPP computers that are capable of solving problems with 0(102-3) atoms and 0(103-4) basis functions. Problems of this scale almost automatically imply that all matrices be distributed over

Computer Physics Communications, 2000

NWChem is the software package for computational chemistry on massively parallel computing systems developed by the High Performance Computational Chemistry Group for the Environmental Molecular Sciences Laboratory. The software provides a variety of modules for quantum mechanical and classical mechanical simulation. This article describes the design and some implementation details of the overall NWChem architecture. The architecture facilitates rapid development and portability of fully distributed application modules. We also delineate some of the functionality within NWChem and show performance of a few of the modules within NWChem.

The Journal of Chemical Physics, 2008

ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II ͓J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 ͑1992͒; ͓ACES II program system, University of Florida, 1994͔ have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock ͑HF͒ self-consistent field ͑SCF͒, second-order many-body perturbation theory ͓MBPT͑2͔͒ energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples ͓CCSD͑T͔͒ energy and gradient. For SCF, MBPT͑2͒, and CCSD͑T͒, both restricted HF and unrestricted HF reference wave functions are available. For MBPT͑2͒ gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language ͑SIAL͒. The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor ͑SIP͒, interprets and executes the SIAL program. By separating the algorithmic complexity ͑in SIAL͒ from the complexities of execution on computer hardware ͑in SIP͒, a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort.

Journal of Computational Chemistry, 2015

The Journal of …, 2008