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

Preface Acknowledgements Notation Part I. Overview and Background Topics: 1. Introduction 2. Overview 3. Theoretical background 4. Periodic solids and electron bands 5. Uniform electron gas and simple metals Part II. Density Functional Theory: 6. Density functional theory: foundations 7. The Kohn-Sham ansatz 8. Functionals for exchange and correlation 9. Solving the Kohn-Sham equations Part III. Important Preliminaries on Atoms: 10. Electronic structure of atoms 11. Pseudopotentials Part IV. Determination of Electronic Structure, The Three Basic Methods: 12. Plane waves and grids: basics 13. Plane waves and grids: full calculations 14. Localized orbitals: tight binding 15. Localized orbitals: full calculations 16. Augmented functions: APW, KKR, MTO 17. Augmented functions: linear methods Part V. Predicting Properties of Matter from Electronic Structure - Recent Developments: 18. Quantum molecular dynamics (QMD) 19. Response functions: photons, magnons ... 20. Excitation spectra and optical properties 21. Wannier functions 22. Polarization, localization and Berry's phases 23. Locality and linear scaling O (N) methods 24. Where to find more Appendixes References Index.

Electronic Structure: Basic Theory and Practical Methods

We have developed an efficient and reliable methodology for crystal structure prediction, merging ab initio total-energy calculations and a specifically devised evolutionary algorithm. This method allows one to predict the most stable crystal structure and a number of low-energy metastable structures for a given compound at any P-T conditions without requiring any experimental input. Extremely high (nearly 100%) success rate has been observed in a few tens of tests done so far, including ionic, covalent, metallic, and molecular structures with up to 40 atoms in the unit cell. We have been able to resolve some important problems in high-pressure crystallography and report a number of new high-pressure crystal structures (stable phases: epsilon-oxygen, new phase of sulphur, new metastable phases of carbon, sulphur and nitrogen, stable and metastable phases of CaCO3). Physical reasons for the success of this methodology are discussed.

Crystal structure prediction using ab initio evolutionary techniques: principles and applications.

Modeling hardness of polycrystalline materials and bulk metallic glasses

Phase transition in MgSiO 3 perovskite in the earth's lower mantle

We have investigated by first principles the electronic, vibrational, and structural properties of bct C4, a new form of crystalline sp{3} carbon recently found in molecular dynamics simulations of carbon nanotubes under pressure. This phase is transparent, dynamically stable at zero pressure, and more stable than graphite beyond 18.6 GPa. Coexistence of bct C4 with M carbon can explain better the x-ray diffraction pattern of a transparent and hard phase of carbon produced by the cold compression of graphite. Its structure appears to be intermediate between that of graphite and hexagonal diamond. These facts suggest that bct C4 is an accessible form of sp{3} carbon along the graphite-to-hexagonal diamond transformation path.

Body-centered tetragonal C4: a viable sp3 carbon allotrope.

CaIrO3-type MgSiO3 is the planet-forming silicate stable at pressures and temperatures beyond those of Earth9s core-mantle boundary. First-principles quasiharmonic free-energy computations show that this mineral should dissociate into CsCl-type MgO cotunnite-type SiO2 at pressures and temperatures expected to occur in the cores of the gas giants + and in terrestrial exoplanets. At ∼10 megabars and ∼10,000 kelvin, cotunnite-type SiO2 should have thermally activated electron carriers and thus electrical conductivity close to metallic values. Electrons will give a large contribution to thermal conductivity, and electronic damping will suppress radiative heat transport.

https://science.sciencemag.org/content/sci/311/5763/983.full.pdf

Dissociation of MgSiO3 in the cores of gas giants and terrestrial exoplanets.

[1] We have determined by first principles the athermal elastic constant tensor, single crystal and aggregated acoustic velocities, and anisotropy of the recently discovered post-perovskite MgSiO3 polymorph. This phase may be the most abundant mineral in the D″ region. We find that the post-perovskite phase has similar bulk modulus and larger shear modulus than perovskite at relevant pressures. This phase is remarkably anisotropic. Analyses of horizontal shear wave splittings in transversely isotropic aggregates indicate that diverse lattice preferred orientations could produce large variation in anisotropy consistent with seismic observations in D″.

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2004GL020278

Elasticity of post‐perovskite MgSiO3

We present a genetic algorithm (GA) for structural search that combines the speed of structure exploration by classical potentials with the accuracy of density functional theory (DFT) calculations in an adaptive and iterative way. This strategy increases the efficiency of the DFT-based GA by several orders of magnitude. This gain allows a considerable increase in the size and complexity of systems that can be studied by first principles. The performance of the method is illustrated by successful structure identifications of complex binary and ternary intermetallic compounds with 36 and 54 atoms per cell, respectively. The discovery of a multi-TPa Mg-silicate phase with unit cell containing up to 56 atoms is also reported. Such a phase is likely to be an essential component of terrestrial exoplanetary mantles.

https://iopscience.iop.org/article/10.1088/0953-8984/26/3/035402/pdf

Koichiro Umemoto

Papers

Phase transition in MgSiO 3 perovskite in the earth's lower mantle

Body-centered tetragonal C4: a viable sp3 carbon allotrope.

Dissociation of MgSiO3 in the cores of gas giants and terrestrial exoplanets.

Elasticity of post‐perovskite MgSiO3

An adaptive genetic algorithm for crystal structure prediction.