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,
flowchart for the DFT-MD transformation is shown center and on the right we show audioslides from the paper.
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.