Computing

Unix Training

• Getting Started With Linux
• UNIX Tutorial

MATLAB Training

Hands-on tutorials by Instructor

• MATLAB: Getting Started
• MATLAB: Sparse Matrices

Hands-on Lab tutorials by MathWorks

• MATLAB Student Center
• Rapid code iteration using cells in the Editor

Reference

• MATLAB Brief List of Commands
• MATLAB Documentation
• Some Common MATLAB Programming Pitfalls and How to Avoid Them

Books and notes

• C. Moler: Numerical Computing with MATLAB (SIAM, Philadelphia, 2004). [PDF]
• UD Crash Course on Matlab

Implementation Tools

• Running MATLAB m-files in the background under Linux
• Multithreaded MATLAB performance on multicores

MATLAB Scripts

Electron density in nanowires using equilibrium density matrix

• electron_density.m

DOS of disordered nanowire using eigenvalues and Anderson localization of eigenfunctions

• disordered_nanowire.m

Density of states using equilibrium retarded Green function

• dos_negf.m
• graphene_dos.m

Subband structure of graphene nanoribbons using tight-binding models

• 8zgnr.m (pedestrian code for 8-ZGNR only)

Quantum transport in 1D nanowires using NEGF

• qt_1d.m (code to compute the conductance and total and local density of states of a 1D nanowire, with possible potential barriers or impurities, attached to two semi-infinite electrodes)

Klein tunneling in graphene heterojunctions

• gnr_cond_recursive.m,bstruct.m, blocktosparse.m, sparsetoblock.m, h_zigzag.m, invnn.m, Self.m, (code to compute the conductance of a finite graphene nanoribbon attached to two semi-infinite graphene electrodes)

MATLAB functions

• matrix_exp.m (Exponential, or any other function with small changed in the code, of a Hermitian matrix)
• visual_graphene_H.m (For a given tight-binding Hamiltonian on the honeycomb lattice, function plots position of carbon atoms and draws blue lines to represent hoppings between them; red circles to represent on-site potential between them; and cyan lines to represent the periodic boundary conditions; it can be used to test if the tight-binding Hamiltonian of graphene is set correctly); This function calls another three function which should be placed in the same directory (or in the path): atomCoord.m, atomPosition.m, and constrainView.m
• self_energy.m (Self-energy of the semi-infinite ideal metallic lead modeled on the square tight-binding lattice - the code shows how to convert analytical formulas of the lead surface Green function into a working program)

Density functional theory using GPAW

Hands-on tutorials by CAMd at Denmark Technical University

• CAMd Summer School Tutorials
• GPAW Tutorials

Hands-on tutorials by Instructor

• Band structure of Fe
• Subbandstructure of graphene nanoribbons
• Subband structure of carbon nanotubes
• Quantum transport through single-molecule nanojunctions