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TOPIC: Simulation of a vibrating nanotube with an adsorbed molecule whose mass we will determine by observing the change in the vibrations, (U8). The overall scheme of the process is:

http://phony1.technion.ac.il/~phr76ja/athens15/flow2.html

In this project's first stage (just before SimPhoNy started) we made mappings from the atomistic level (own MD code) to continuum modelling, with verification and then improvement of continuum models by comparison with the MD results. We used AViz visualization to verify results.

In the next stage we (Joan Adler, Bastien Grosso and 4 others) have carried out calculations moving between the nano and the electronic scale with AViz visualization for verification and understanding at both levels. A manuscript about this stage is in Communications in Computational Physics (2015), Volume 195C pp. 1-13. One of its highlights (visualization of electron density of 3 nanotube rings) is shown on the left below, and the flowchart for the DFT-MD transformation is shown center and on the right we show audioslides from the paper.

http://phony1.technion.ac.il/~phr76ja/athens15/edsim.html http://phony1.technion.ac.il/~phr76ja/athens15/edsim5.html

A review of visualization of Electronic Density has appeared in Physics Procedia, - Joan Adler, Omri Adler, Meytal Krief, Or Cohen, Bastien Grosso, Adham Hashibon, and Valentino R. Cooper, ``Mini-review of electronic density vizualization, (201 5), Physics Procedia 68 , p. 26. In addition to review material, this manuscript's authors include Omri Adler who is analysed the nanotube width data.

The initial wrappers were in Fortran, then translated to C++; and Jeremy Rutman (experienced code developer/physicist) has translated these to python, see here, and jeremy's new link. In current aspects of this project Michael Kislev (class project) has begun modelling the nanotube supports with LAMMPS, and Omri Adler (MSc. student) is moving over to WP5 and the full NEMS simulation.

TOPIC: In a long term group project, summarised in U7, we are studying damage in diamond. We previously moved between own MD codes with classical potentials, and several tight-binding codes. We use the MD codes to prepare large samples, and tightbinding for interesting regions. In our latest paper (accepted by CiCP) we used dftb code for vacancy modelling for quantum computer sample preparation. A new project on percolation of damaged regions is being carried out by Omri Harosh (undergraduate project student) using LAMMPS and AViz. I propose wrapper preparation to move between tightbinding code(s) and LAMMPS with AViz at atomistic level. These projects are in collaboration with Amihai Silverman, who as well as co-supervising students, provides advanced systems support for the Technion SimPhoNy computers.