Hybrid finite-element/molecular-dynamics/electronic-density-functional approach to materials simulations on parallel computers

A hybrid simulation approach is developed to study chemical reactions coupled with long-range mechanical phenomena in materials. The finite-element method for continuum mechanics is coupled with the molecular dynamics method for an atomic system that embeds a cluster of atoms described quantum-mechanically with the electronic density-functional method based on real-space multigrids. The hybrid simulation approach is implemented on parallel computers using both task and spatial decompositions. Additive hybridization and unified finite-element/molecular-dynamics schemes allow scalable parallel implementation and rapid code development, respectively. A hybrid simulation of oxidation of Si(111) surface demonstrates seamless coupling of the continuum region with the classical and the quantum atomic regions.

[1]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[2]  P. Hohenberg,et al.  Inhomogeneous Electron Gas , 1964 .

[3]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[4]  Ami Marowka,et al.  The GRID: Blueprint for a New Computing Infrastructure , 2000, Parallel Distributed Comput. Pract..

[5]  H. Fischmeister,et al.  Crack propagation in b.c.c. crystals studied with a combined finite-element and atomistic model , 1991 .

[6]  Noam Bernstein,et al.  Spanning the length scales in dynamic simulation , 1998 .

[7]  Y. Nishioka,et al.  Molecular adsorption and dissociative reaction of oxygen on the Si(111)7×7 surface , 2000 .

[8]  M. A. Dokainish,et al.  Simulation of the (001) plane crack in α-iron employing a new boundary scheme , 1982 .

[9]  Rajiv K. Kalia,et al.  Scalable molecular-dynamics, visualization, and data management algorithms for materials simulations , 1989, Comput. Sci. Eng..

[10]  Anupam Madhukar,et al.  A unified atomistic and kinetic framework for growth front morphology evolution and defect initiation in strained epitaxy , 1996 .

[11]  C. Brooks Computer simulation of liquids , 1989 .

[12]  Weber,et al.  Computer simulation of local order in condensed phases of silicon. , 1985, Physical review. B, Condensed matter.

[13]  S. Mantl,et al.  Patterning method for silicides based on local oxidation , 1995 .

[14]  James R. Chelikowsky,et al.  Electronic Structure Methods for Predicting the Properties of Materials: Grids in Space , 2000 .

[15]  D. Brandt,et al.  Multi-level adaptive solutions to boundary-value problems math comptr , 1977 .

[16]  George K. Thiruvathukal,et al.  Wide-Area Implementation of the Message Passing Interface , 1998, Parallel Comput..

[17]  J. Fattebert,et al.  Towards grid-based OÑNÖ density-functional theory methods: Optimized nonorthogonal orbitals and multigrid acceleration , 2000 .

[18]  Michael B. Bever,et al.  Concise encyclopedia of advanced ceramic materials , 1991 .

[19]  Janos H. Fendler,et al.  Nanoparticles and Nanostructured Films , 1998 .

[20]  Andrew G. Glen,et al.  APPL , 2001 .

[21]  A. Oshiyama,et al.  Metastable atomic configurations for oxygen adsorption on Si (100) surfaces , 1990 .

[22]  Rajiv K. Kalia,et al.  Large-scale atomistic modeling of nanoelectronic structures , 2000 .

[23]  Martins,et al.  Efficient pseudopotentials for plane-wave calculations. , 1991, Physical review. B, Condensed matter.

[24]  William Gropp,et al.  Skjellum using mpi: portable parallel programming with the message-passing interface , 1994 .

[25]  C. Kölmel,et al.  Combining ab initio techniques with analytical potential functions for structure predictions of large systems: Method and application to crystalline silica polymorphs , 1997 .

[26]  M. Tsukada,et al.  SCANNING-TUNNELING-MICROSCOPY IMAGES OF OXYGEN ADSORPTION ON THE SI(001) SURFACE , 1997 .

[27]  William H. Press,et al.  Numerical Recipes: FORTRAN , 1988 .

[28]  U. Singh,et al.  A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .

[29]  H. Balamane,et al.  Comparative study of silicon empirical interatomic potentials. , 1992, Physical review. B, Condensed matter.

[30]  Donald G. Truhlar,et al.  Multiconfiguration molecular mechanics algorithm for potential energy surfaces of chemical reactions , 2000 .

[31]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[32]  T. Arias,et al.  Iterative minimization techniques for ab initio total energy calculations: molecular dynamics and co , 1992 .

[33]  N. Horiguchi,et al.  Patterned self‐assembly of one‐dimensional arsenic particle arrays in GaAs by controlled precipitation , 1996 .

[34]  J. Q. Broughton,et al.  Concurrent Coupling of Length Scales in Solid State Systems , 2000 .

[35]  B. M. Fulk MATH , 1992 .

[36]  Leonid V. Zhigilei,et al.  A combined molecular dynamics and finite element method technique applied to laser induced pressure wave propagation , 1999 .

[37]  Y. Saad,et al.  Finite-difference-pseudopotential method: Electronic structure calculations without a basis. , 1994, Physical review letters.

[38]  Michael Frenklach,et al.  Molecular dynamics with combined quantum and empirical potentials: C2H2 adsorption on Si(100) , 1993 .

[39]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[40]  Jian Wang,et al.  Efficient real-space solution of the Kohn–Sham equations with multiscale techniques , 1999, cond-mat/9905422.

[41]  T. Uda,et al.  BACKBOND OXIDATION OF THE SI(001) SURFACE : NARROW CHANNEL OF BARRIERLESS OXIDATION , 1998 .

[42]  J. Q. Broughton,et al.  Concurrent coupling of length scales: Methodology and application , 1999 .

[43]  R. Cook,et al.  Concepts and Applications of Finite Element Analysis , 1974 .

[44]  S. Mantl,et al.  Nanometer patterning of epitaxial CoSi2/Si(100) for ultrashort channel Schottky barrier metal–oxide–semiconductor field effect transistors , 1999 .