Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

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

Hybrid density functionals are very successful in describing a wide range of molecular properties accurately. In large molecules and solids, however, calculating the exact (Hartree–Fock) exchange is computationally expensive, especially for systems with metallic characteristics. In the present work, we develop a new hybrid density functional based on a screened Coulomb potential for the exchange interaction which circumvents this bottleneck. The results obtained for structural and thermodynamic properties of molecules are comparable in quality to the most widely used hybrid functionals. In addition, we present results of periodic boundary condition calculations for both semiconducting and metallic single wall carbon nanotubes. Using a screened Coulomb potential for Hartree–Fock exchange enables fast and accurate hybrid calculations, even of usually difficult metallic systems. The high accuracy of the new screened Coulomb potential hybrid, combined with its computational advantages, makes it widely applicable to large molecules and periodic systems.

Hybrid functionals based on a screened Coulomb potential

A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP)

Part I: Basics. 1. Elementary concepts in density functional theory. (M. Levy). 2. Explicit density functionals for the energy by means of pade approximants to local-scaling transformations. (E.V. Ludena, R. Lopez-Boada, R. Pino). 3. Inhomogenous electron gas: transcending semiclassical Thomas-Fermi-Dirac method (N.M. March). 4. An introduction to high-precision computational methods for simple atomic and molecular systems (F.C. Sanders). 5. Density functional theory in the classical domain (J.K. Percus). Part II: Functionals and their Problems. 6. Density functional theory, the exchange hole, and the molecular bond (M. Ernzerhof, K. Burke, J.P. Perdew). 7. Nonlocal weighted density approximation to exchange, correlation and kinetic energy in density functional theory (J.A. Alonso, N.A. Cordero). 8. Generalized gradient approximations to density functional theory: comparison with exact results (C. Filippi, X. Gonze, C.J. Umrigar). 9. On degeneracy, near-degenaracy and density functional theory (A. Savin). 10. A simple method of removing spin contamination from unrestricted Kohn-Sham density functional calculations. (A.A. Ovchinnikov, C.F. Bender, J.K. Labanowski). Part III: Approaches and Methods. 11. Time-dependent density functional response theory of molecular systems: theory, computational methods, and functionals (M.E. Casida). 12. Advances in methodologies for linear-scaling density functional calculations (B.G. Johnson et al.). 13. A divide-and-conquer implementation of the linear combination of Gaussian-type orbitals density functional (LCGTO-DF) method (A. St-Amant, S. Koon Goh, R.T. Gallant). 14. The Douglas-Kroll-Hess approach to relativistic density functional theory methodological aspects and applications to metal complexes and clusters (N. Roesch, M. Mayer, V.A. Nasluzov). Part IV: Applications. 15. Adsorption complexes on oxides: density functional model cluster studies (K.M. Neyman, G. Pacchioni, N. Roesch). 16. Density functional theory as a tool in studying catalytic processes (E. Broclawik, R. Vetrivel, A. Miyamoto). 17. DFT study of nickel: towards the MD simulation of the nickel-waterinterface (P.B. Balbuena, J.M. Seminario). 18. Systematic model chemistries based on density functional theory: comparison with traditional models and with experiment (M.J. Frisch, G.W. Trucks, J.R. Cheeseman). 19. Computing transition state structures with density functional theory methods (B.S. Jursic). 20. Density functional theory as a tool for the prediction of the properties in molecules with biological and pharmacological significance (M. Belcastro et al.). 21. Density functional theory concepts and techniques for studying molecular charge distributions and related properties. (P. Geerlings, F. De Proft, J.M.L. Martin). 22. Density functional calculations of heats and reaction (P. Politzer, J.M. Wiener, J.M. Seminario). Index.

Recent developments and applications of modern density functional theory

This Review focuses on research oriented toward elucidation of the various aspects that determine adsorption of CO2 in metal–organic frameworks and its separation from gas mixtures found in industrial processes. It includes theoretical, experimental, and combined approaches able to characterize the materials, investigate the adsorption/desorption/reaction properties of the adsorbates inside such environments, screen and design new materials, and analyze additional factors such as material regenerability, stability, effects of impurities, and cost among several factors that influence the effectiveness of the separations. CO2 adsorption, separations, and membranes are reviewed followed by an analysis of the effects of stability, impurities, and process operation conditions on practical applications.

CO2 Capture and Separations Using MOFs: Computational and Experimental Studies

An introduction to density functional theory in chemistry, J.M. Seminario semilocal density functionals for exchange and correlation - theory and applications, K. Burke et al the local-scaling version of density functional theory - a practical method for rigorous calculations of many-electron systems, E.V. Ludena et al towards a practical algorithm for large molecule calculations, Z. Zhou symmetry and density-functional exchange and correlation, B.I. Dunlap development, implementation and applications of efficient methodologies for density functional calculations, B.G. Johnson DMol, a standard tool for density functional calculations - review and advances, B. Delley and P. Scherrer constrained optimization procedure for finding transition states and reaction pathways in the framework of Guassian based density functional method - the case of isomerization reactions, Y. Abashkin et al the calculation of NMR and ESR spectroscopy parameters using density functional theory, V.G. Malkin et al density functional theory and transition metal oxides, E. Broclawik density functional studies of decomposition processes of energetic molecules, P. Politzer et al density functional theory - further applications, P.B. Balbuena and J.M. Seminario.

Modern density functional theory : a tool for chemistry

Density functional theory calculations are performed to explain the electrical behavior of a π-conjugated oligo(phenylene ethynylene) resembling a resonant tunneling diode. Results of this theoretical study are compatible with the assumptions that electron transport occurs through the lowest unoccupied molecular orbital, that the conduction barrier is determined by the molecule chemical potential, and that the molecule becomes charged as the external potential increases. We are able to explain the nonlinear character of the current−voltage characteristic of the molecule and its temperature dependence. The intrinsic controlled-amplification feature of these molecules is indicated.

Theoretical Study of a Molecular Resonant Tunneling Diode

Green function and density functional theories are used to study electron transport characteristics through single molecules addressed by two metallic contacts. Each contact is modeled with one nan...

Jorge M. Seminario

Papers

Recent developments and applications of modern density functional theory

CO2 Capture and Separations Using MOFs: Computational and Experimental Studies

Modern density functional theory : a tool for chemistry

Theoretical Study of a Molecular Resonant Tunneling Diode

Electron Transport through Single Molecules: Scattering Treatment Using Density Functional and Green Function Theories