IMD: A Software Package for Molecular Dynamics Studies on Parallel Computers

Stadler, Jörg; Mikulla, R.; Trebin, Hans‐Rainer

doi:10.1142/s0129183197000990

Cited by 294 publications

(159 citation statements)

References 5 publications

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“…For example, we identified the ideal dimensions of the simulation box ͑9 nm base and 8 nm QW embedded in 22 nm GaAs barriers͒ as the smallest ones that minimized fluctuations in the elastic energy due to compositional disorder. The structures were relaxed ͑molecular statics implementation͒ using a parallel implementation of the IMD™ software 80 comprising optimized bond-order empirical potentials 81 with the parameters of Powell et al 82 From the relaxed atomic positions we evaluated the crystal strain energy ͑shown in Fig. 4͒ by taking the local composition under consideration and by evaluating the strain on each tetrahedron in the crystal.…”

Section: Strain-energy Calculationsmentioning

confidence: 99%

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Role of segregation in InAs/GaAs quantum dot structures capped with a GaAsSb strain-reduction layer

et al. 2009

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Please check the document version of this publication:• A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website.• The final author version and the galley proof are versions of the publication after peer review.• The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rightsCopyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal.If the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the "Taverne" license above, please follow below link for the End User Agreement: We report a combined experimental and theoretical analysis of Sb and In segregation during the epitaxial growth of InAs self-assembled quantum dot structures covered with a GaSbAs strain-reducing capping layer. Cross-sectional scanning tunneling microscopy shows strong Sb and In segregation which extends through the GaAsSb and into the GaAs matrix. We compare various existing models used to describe the exchange of group III and V atoms in semiconductors and conclude that commonly used methods that only consider segregation between two adjacent monolayers are insufficient to describe the experimental observations. We show that a three-layer model originally proposed for the SiGe system ͓D. J. Godbey and M. G. Ancona, J. Vac. Sci. Technol. A 15, 976 ͑1997͔͒ is instead capable of correctly describing the extended diffusion of both In and Sb atoms. Using atomistic modeling, we present strain maps of the quantum dot structures that show the propagation of the strain into the GaAs region is strongly affected by the shape and composition of the strain-reduction layer.

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Section: Strain-energy Calculationsmentioning

confidence: 99%

“…The structures have been relaxed using molecular statics within the IMD™ software. 80 Just like in the elastic strain calculations, the strain is directly extracted from the atomic bonds by comparing the strained lattice to an ideal unstrained one and taking the local composition into account.…”

Section: Modeling Strain In Quantum Dotsmentioning

confidence: 99%

Role of segregation in InAs/GaAs quantum dot structures capped with a GaAsSb strain-reduction layer

et al. 2009

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“…In the spatial decomposition methods 13,16,17,[35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54] (also referred to as domain decomposition or geometric methods), each processor is associated with a fixed block of space throughout the course of the simulation. During a given MD time step, the processor is responsible for calculating the forces experienced by all atoms currently residing within its own block and updating their respective positions, but atoms may move from one block (and thus one processor) to another over the course of the simulation.…”

Section: Standard Methods For Parallelizing MD Simulationsmentioning

confidence: 99%

A fast, scalable method for the parallel evaluation of distance‐limited pairwise particle interactions

2005

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Classical molecular dynamics simulations of biological macromolecules in explicitly modeled solvent typically require the evaluation of interactions between all pairs of atoms separated by no more than some distance R, with more distant interactions handled using some less expensive method. Performing such simulations for periods on the order of a millisecond is likely to require the use of massive parallelism. The extent to which such simulations can be efficiently parallelized, however, has historically been limited by the time required for interprocessor communication. This article introduces a new method for the parallel evaluation of distance-limited pairwise particle interactions that significantly reduces the amount of data transferred between processors by comparison with traditional methods. Specifically, the amount of data transferred into and out of a given processor scales as O(R 3/ 2 p Ϫ1/ 2 ), where p is the number of processors, and with constant factors that should yield a substantial performance advantage in practice.

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“…At present there are several high-quality molecular dynamics programs in the public domain, such as LAMMPS [18], DL POLY [19,20], Moldy [21], IMD [22,23], and some codes with biomolecular focus, such as NAMD [24,25] and Gromacs [26,27]. CHARMM [28] and AMBER [29] are not free but are standard and extremely powerful codes in biology.…”

Section: Molecular Dynamics Codesmentioning

confidence: 99%

Basic Molecular Dynamics

2005

Handbook of Materials Modeling

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A working definition of molecular dynamics (MD) simulation is technique by which one generates the atomic trajectories of a system of N particles by numerical integration of Newton's equation of motion, for a specific interatomic potential, with certain initial condition (IC) and boundary condition (BC).Consider, for example (see Fig. 1), a system with N atoms in a volume . We can define its internal energy: E ≡ K + U , where K is the kinetic energy,and U is the potential energy,x 3N (t) denotes the collective of 3 D coordinates x 1 (t), x 2 (t), . . . , x N (t). Note that E should be a conserved quantity, i.e., a constant of time, if the system is truly isolated.One can often treat a MD simulation like an experiment. Below is a common flowchart of an ordinary MD run:in which we fine-tune the system until it reaches the desired condition (here, temperature T and pressure P), and then perform property averages, for instance calculating the radial distribution function g(r)[1] or thermal conductivity [2]. One may also perform a non-equilibrium MD calculation, during which the system is subjected to perturbational or large external driving forces, 565 S. Yip (ed.), Handbook of Materials Modeling,

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IMD: A Software Package for Molecular Dynamics Studies on Parallel Computers

Cited by 294 publications

References 5 publications

Role of segregation in InAs/GaAs quantum dot structures capped with a GaAsSb strain-reduction layer

Role of segregation in InAs/GaAs quantum dot structures capped with a GaAsSb strain-reduction layer

A fast, scalable method for the parallel evaluation of distance‐limited pairwise particle interactions

Basic Molecular Dynamics

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