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

A modification of the nudged elastic band method for finding minimum energy paths is presented. One of the images is made to climb up along the elastic band to converge rigorously on the highest saddle point. Also, variable spring constants are used to increase the density of images near the top of the energy barrier to get an improved estimate of the reaction coordinate near the saddle point. Applications to CH4 dissociative adsorption on Ir~111! and H2 on Si~100! using plane wave based density functional theory are presented. © 2000 American Institute of Physics. @S0021-9606~00!71246-3#

/pdf/a-climbing-image-nudged-elastic-band-method-for-finding-40kp70z5oe.pdf

A climbing image nudged elastic band method for finding saddle points and minimum energy paths

Data Mining Practical Machine Learning Tools and Techniques

http://theory.cm.utexas.edu/henkelman/pubs/henkelman06_354.pdf

A fast and robust algorithm for Bader decomposition of charge density

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.

/pdf/charmm-the-biomolecular-simulation-program-4kexem0xkx.pdf

CHARMM: the biomolecular simulation program.

Although grain boundaries can serve as effective sinks for radiation-induced defects such as interstitials and vacancies, the atomistic mechanisms leading to this enhanced tolerance are still not well understood With the use of three atomistic simulation methods, we investigated defect-grain boundary interaction mechanisms in copper from picosecond to microsecond time scales We found that grain boundaries have a surprising "loading-unloading" effect Upon irradiation, interstitials are loaded into the boundary, which then acts as a source, emitting interstitials to annihilate vacancies in the bulk This unexpected recombination mechanism has a much lower energy barrier than conventional vacancy diffusion and is efficient for annihilating immobile vacancies in the nearby bulk, resulting in self-healing of the radiation-induced damage

https://science.sciencemag.org/content/sci/327/5973/1631.full.pdf

Efficient annealing of radiation damage near grain boundaries via interstitial emission.

Ceramics destined for use in hostile environments such as nuclear reactors or waste immobilization must be highly durable and especially resistant to radiation damage effects. In particular, they must not be prone to amorphization or swelling. Few ceramics meet these criteria and much work has been devoted in recent years to identifying radiation-tolerant ceramics and the characteristics that promote radiation tolerance. Here, we examine trends in radiation damage behaviour for families of compounds related by crystal structure. Specifically, we consider oxides with structures related to the fluorite crystal structure. We demonstrate that improved amorphization resistance characteristics are to be found in compounds that have a natural tendency to accommodate lattice disorder.

Radiation-induced amorphization resistance and radiation tolerance in structurally related oxides

Defect-interface interactions

http://dspace.mit.edu/bitstream/handle/1721.1/90424/beyerlein-2013-radiationdamagetol.pdf?sequence=1

Blas P. Uberuaga

Papers

A climbing image nudged elastic band method for finding saddle points and minimum energy paths

Efficient annealing of radiation damage near grain boundaries via interstitial emission.

Radiation-induced amorphization resistance and radiation tolerance in structurally related oxides

Defect-interface interactions

Radiation damage tolerant nanomaterials