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NEMO3D User Guide for Quantum Dot Simulations

By M. Usman1, Gerhard Klimeck1

1. Electrical and Computer Engineering, Purdue University, West Lafayette, IN

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Nanoelectronics is a fascinating area of research that has significant impact on our lives helping in all sort of problems related to medicine, communications, defense, etc. Due to confinement of carriers in three dimensions, quantum dots (QDs) are ideal candidates for the design of nanoscale optoelectronic devices and quantum information processing. However efficient design of QD based devices is still a huge challenge despite significant advancements in their growth and characterization techniques. This is mainly because QD morphology such as their chemical composition, size, shape etc. significantly changes during the growth of capping layer and the post-growth annealing process. Thus modeling and simulations of QDs with realistic dimensions, atomistic resolution, and essential physical effects such as strain, piezoelectricity etc is critical to understand their electronic and optical properties. This can also provide an efficient way to explore their design space to guide experiments before actual experimentation.

Most of the commercial simulators are based on continuum models and are fundamentally limited to qualitative description of the QD properties. NEMO 3D, based on fully atomistic strain and electronic structure calculations, is a multi-scale simulator that has been compiled and tested to run on multiple cores of modern age supercomputers. Its capabilities include computation of the electronic structure within an empirical tight-binding model for quantum dots (3-D confinement), nanowires (2-D confinement), quantum wells (1-D confinement), and bulk (no confinement); strain is computed from classical valence force field method. Further details about the simulator can be found at: and the source code can be downloaded from the NEMO3D distributions group on

NEMO 3D is a large and complex simulator; and understanding of its source code requires considerable knowledge of quantum mechanics, condensed matter theory, and parallel programming. Even for just running a simple QD simulation without knowing its source code, good amount of knowledge about QD modeling, XML files, parallel programming, and Linux/Unix commands is imperative. The inputs to NEMO 3D executable are specified in an XML based input deck which contains many selectable options to set up execution and output parameters. The purpose of this user guide is to instruct a first time user about basic steps for the compilation of NEMO 3D source code on a Linux/Unix based machine, setup of an input deck for a simple QD simulation, and understanding of various output files that are generated from a typical QD simulation. It is advised that a user MUST first become fully familiar and comfortable with the simple example provided in this manual before moving on to a more complex QD device.

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Researchers should cite this work as follows:

  • M. Usman; Gerhard Klimeck (2011), "NEMO3D User Guide for Quantum Dot Simulations,"

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Tags, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.