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

"Chemists familiar with conventional quantum mechanics will applaud and benefit greatly from this particularly instructive, thorough and clearly written exposition of density functional theory: its basis, concepts, terms, implementation, and performance in diverse applications. Users of DFT for structure, energy, and molecular property computations, as well as reaction mechanism studies, are guided to the optimum choices of the most effective methods. Well done!" Paul von RaguE Schleyer "A conspicuous hole in the computational chemist's library is nicely filled by this book, which provides a wide-ranging and pragmatic view of the subject.[...It] should justifiably become the favorite text on the subject for practioneers who aim to use DFT to solve chemical problems." J. F. Stanton, J. Am. Chem. Soc. "The authors' aim is to guide the chemist through basic theoretical and related technical aspects of DFT at an easy-to-understand theoretical level. They succeed admirably." P. C. H. Mitchell, Appl. Organomet. Chem. "The authors have done an excellent service to the chemical community. [...] A Chemist's Guide to Density Functional Theory is exactly what the title suggests. It should be an invaluable source of insight and knowledge for many chemists using DFT approaches to solve chemical problems." M. Kaupp, Angew. Chem.

A Chemist's Guide to Density Functional Theory

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The surface chemistry of amorphous silica. Zhuravlev model

https://web.iitd.ac.in/~arunku/files/CEL311_Y13/Adsorption%20Theory%20to%20practice_Dabrowski.pdf

Adsorption — from theory to practice

Note: Times Cited: 875 Reference EPFL-ARTICLE-206025doi:10.1021/cr0501846View record in Web of Science URL: ://WOS:000249839900009 Record created on 2015-03-03, modified on 2017-05-12

Complex Hydrides for Hydrogen Storage

The B3LYP method augmented with a damped empirical dispersion term (−f(R)C6/R6) is shown to yield structures and cohesive energies, for a representative set of molecular crystals, in excellent agreement with experimental data. Vibrational lattice modes of crystalline urea are also reported to be very close to experiment. The role of the damping function in scaling the dispersion contribution has been analyzed as well as the relevance of the BSSE in the prediction of structure and cohesive energy.

/pdf/b3lyp-augmented-with-an-empirical-dispersion-term-b3lyp-d-as-2u6eqti0sb.pdf

B3LYP augmented with an empirical dispersion term (B3LYP-D*) as applied to molecular crystals

Theoretical Study of van der Waals Complexes at Surface Sites in Comparison with the Experiment

Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments / Albert Rimola;Dominique Costa;Mariona Sodupe;Jean-François Lambert;Piero Ugliengo. In: CHEMICAL REVIEWS. ISSN 0009-2665. STAMPA. 113:6(2013), pp. 4216-4313. Original Citation: Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

/pdf/silica-surface-features-and-their-role-in-the-adsorption-of-2hhuc04ksj.pdf

Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

Realistic Models of Hydroxylated Amorphous Silica Surfaces and MCM‐41 Mesoporous Material Simulated by Large‐scale Periodic B3LYP Calculations

MOLDRAW is a simple and easy to learn molecular graphics program running on personal computers, which allows drawing and manipulation of any molecular structure. In this article the program functions and examples of its application are presented. The user-friendly interface and the simple but powerful underlying logic are the main reasons for the widespread diffusion of MOLDRAW in the crystallographic and chemical community

Piero Ugliengo

Papers

B3LYP augmented with an empirical dispersion term (B3LYP-D*) as applied to molecular crystals

Theoretical Study of van der Waals Complexes at Surface Sites in Comparison with the Experiment

Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

Realistic Models of Hydroxylated Amorphous Silica Surfaces and MCM‐41 Mesoporous Material Simulated by Large‐scale Periodic B3LYP Calculations

MOLDRAW. Molecular graphics on a personal computer