We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.

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The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

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QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

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CHARMM: the biomolecular simulation program.

We present a new local density functional, called M06-L, for main-group and transition element thermochemistry, thermochemical kinetics, and noncovalent interactions. The functional is designed to capture the main dependence of the exchange-correlation energy on local spin density, spin density gradient, and spin kinetic energy density, and it is parametrized to satisfy the uniform-electron-gas limit and to have good performance for both main-group chemistry and transition metal chemistry. The M06-L functional and 14 other functionals have been comparatively assessed against 22 energetic databases. Among the tested functionals, which include the popular B3LYP, BLYP, and BP86 functionals as well as our previous M05 functional, the M06-L functional gives the best overall performance for a combination of main-group thermochemistry, thermochemical kinetics, and organometallic, inorganometallic, biological, and noncovalent interactions. It also does very well for predicting geometries and vibrational frequencies. Because of the computational advantages of local functionals, the present functional should be very useful for many applications in chemistry, especially for simulations on moderate-sized and large systems and when long time scales must be addressed. © 2006 American Institute of Physics. DOI: 10.1063/1.2370993

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A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions.

Cloud computing has become another buzzword after Web 2.0. However, there are dozens of different definitions for cloud computing and there seems to be no consensus on what a cloud is. On the other hand, cloud computing is not a completely new concept; it has intricate connection to the relatively new but thirteen-year established grid computing paradigm, and other relevant technologies such as utility computing, cluster computing, and distributed systems in general. This paper strives to compare and contrast cloud computing with grid computing from various angles and give insights into the essential characteristics of both.

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Cloud Computing and Grid Computing 360-Degree Compared

High performance computational chemistry: An overview of NWChem a distributed parallel application

The motivation for a stable, efficient, backfill scheduler that runs in a consistent manner on multiple hardware platforms and operating systems is outlined and justified in this work. The combination of the Maui Scheduler and the Portable Batch System (PBS), are evaluated on several cluster solutions of various size, performance and communications profiles. The total job throughput is simulated in this work, with particular attention given to maximizing resource utilization and to the execution of large parallel jobs.

The portable batch scheduler and the maui scheduler on linux clusters

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.

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

The parallel performance of the NWChem version 1.2a parallel direct-SCF code has been characterized on five massively parallel supercomputers (IBM SP, Kendall Square KSR-2, CRAY T3D and T3E, and Intel Touchstone DELTA) using single-point energy calculations on seven molecules of varying size (up to 389 atoms) and composition (first-row atoms, halogens, and transition metals). The authors compare the performance using both replicated-data and distributed-data algorithms and the original McMurchie-Davidson and recently incorporated TEXAS integrals packages.

High-Performance Computational Chemistry: Hartree-Fock Electronic Structure Calculations on Massively Parallel Processors

We investigate two strategies to improve the performance of collective communications on a cluster of SMPs. In the first part of the paper, we explore the advantages and disadvantages of the commonly used strategy "optimize shared memory send and receive only". In the second part of the paper, we show a model to design collective communications on SMP clusters which can be used to improve the disadvantages of the former strategy. Several collective operations are implemented through the later process, and the experimental results show better performance than vendor supplied implementations.

Ricky A. Kendall

Papers

High performance computational chemistry: An overview of NWChem a distributed parallel application

The portable batch scheduler and the maui scheduler on linux clusters

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

High-Performance Computational Chemistry: Hartree-Fock Electronic Structure Calculations on Massively Parallel Processors

Exploring collective communications on a cluster of SMPs