Software: Theory

Initio

I have developed the Python program Initio to analyze results from and orchestrate DFT calculations. The primary goal is to use calculation data to generate experimental observables in the STM. The LDOSGenerator object in particular can generate simulated LDOS images as they would appear in STM, taking specific details of the tip into account. Initio is built on top of Pymatgen, ASE, NGLView, Plotly, and currently works with VASP. I plan to extend its compatibility to Quantum Espresso and incorporate some MathemaTB functionality in the future. More info to come. A little vernissage is shown below.

MathemaTB

MathemaTB is a quantum chemistry (tight-binding) package written in the Wolfram language, with comprehensive tools to calculate the electronic structure of all kinds of molecules, structures, and solids. Calculations can be done in 0D, 1D, 2D and 3D. It is particularly powerful in terms of orbital- and symmetry-projected local density of states and band structure plotting capabilities, as well as (molecular and crystal) orbital plotting.

MathemaTB was developed during my time as a PhD candidate at Utrecht University. During this time, I utilized Mathematica to perform electronic structure calculations of increasing complexity for various experimental papers on graphene nanoribbons and Lieb lattices.[2,3] Eventually, I decided to keep developing the assembled pieces of code into a full-blown, general-purpose tight-binding package. This has culminated in the release of MathemaTB.[1]

Regrettably, the many scientific endeavors on my career path have kept me from maintaining the package, and it can be classified as abandonware. I have still implemented non-equilibrium Green's Function technique algorithms for addressing charge transport through structures and we have published on these calculations, but have not pushed newer versions of the package for general use.

Files

MathemaTB1v1.zip (all files: version 1.1)

MathemaTB1v1.m (package only: version 1.1)

MathemaTB_tutorial.nb (tutorial notebook only: version 1.0)

old files

MathemaTB.zip (all files: version 1.0)

MathemaTB.m (package only: version 1.0)

Note:

MoleculePlot has been renamed StructurePlot for compatibility with Mathematica version 12, and has the optional argument Interact which helps in identifying atoms within a structure.

The MathemaTB paper

MathemaTB_manual.pdf

Publications

MathemaTB: A Mathematica package for tight-binding calculations. Peter H. Jacobse, Comp. Phys. Comm. 244 (2019)
Experimental Realization and Characterization of an Electronic Lieb Lattice. Marlou R. Slot, Thomas S. Gardenier, Peter H. Jacobse, Guido C. P. van Miert, Sander N. Kempkes, Stephan J. M. Zevenhuizen, Cristiane Morais Smith, Daniel Vanmaekelbergh, Ingmar Swart, Nat. Phys. 13 (2017)
Tuning Edge State Localization in Graphene Nanoribbons by In-plane Bending. Simon G. Stuij, Peter H. Jacobse, Vladimir Juričić, Cristiane Morais Smith, Phys. Rev. B 92 (2015)
Modeling the Self-Assembly of Organic Molecules in 2D Molecular Layers with Different Structures. Joost van der Lit, Jolien L. Marsman, Rik S. Koster, Peter H. Jacobse, Stephan A. den Hartog, Daniel Vanmaekelbergh, Robertus J. M. Klein Gebbink, Laura Filion, Ingmar Swart, J. Phys Chem. C 120 (2015)

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