Data management

Storage: Yakobson’s group has established the practice to archive each dataset (not part of a dedicated database) as a structured and documented directory on optical discs and additionally backed up on local storage at Rice and off-campus computing facilities. Specific guidelines can be found here.

Software packages/tools

In-house  developed

  • JELLY-MAKER: software tool for generating a UPF pseudopotential file to simulate a spherical jellium particle using the Quantum Espresso package, as described in Artyukhov et al., “A jellium model of a catalyst particle in carbon nanotube growth”, J. Chem. Phys. 146, 244701 (2017).
  • XTRANS: An electron transport package for current distribution and magnetic field in helical nanostructures. Incorporated with the tight-binding method, this package not only can compute the regular PBC structure, but also is capable of studying those systems which possess no translational symmetry but helical symmetry. It selects the appropriate symmetry to minimize the computation cost if the system is subject to both symmetries. It also involves the utility of visualizing the current distribution across the nanostructure in forms of “bond current”, with which we developed a fast and accurate procedure to compute the induced magnetic field and further the inductance.
  • EDGECOUNT: A simple software tool for determining the type of edge atoms in a honeycomb lattice. The algorithm is based on nearest neighbor counting. Whether an edge atom is of armchair or zigzag type is decided by the unique pattern of its nearest neighbors.  Ultimately, the tool in combination with density-functional theory or tight-binding method can also be helpful in correlating the properties of graphene flakes with the different armchair-to-zigzag ratios. Some usage examples can be found here.
  • BALLTRAN (Ballistic Transport Calculator)… [coming soon]

 Other software

Selected software packages and tools used in the group:

  • ATAT (Alloy Theoretical Automated Toolkit)
  • ASE (Atomic Simulation Environment)
  • CALYPSO  (Crystal  structure  AnaLYsis  by  Particle  Swarm  Optimization)
  • DFTB+ (Density Functional Based Tight Binding)
  • GAMESS (The General Atomic and Molecular Electronic Structure System)
  • LAMMPS (Large-Scale Atomic Molecular Massively Parallel Simulator)
  • LIGGGHTS (LAMMPS Improved for General Granular and Granular Heat Transfer Simulations)
  • MCCCS Towhee (The Monte Carlo for Chemical Systems)
  • Mathematica
  • PHON
  • Quantum ESPRESSO
  • Quantum Wise
  • SPPARKS (Stochastic Parallel Particle Kinetic Simulation)
  • VASP (Vienna Ab inito Simulation Package)
  • WHAM (Weighted Histogram Analysis Method)
Visualization & Tools
  • CaGe (The Chemical & abstract Graph environment)
  • Gnuplot
  • Jmol
  • OVITO (The Open VIsualization TOol)
  • QSTEM (Quantitative TEM/STEM Simulations)
  • VMD (Visual Molecular Dynamics)
  • Visit
  • XCrySDen (X-window Crystalline Structures and Densities)
  • YASARA (Yet Another Scientific Artificial Reality Application)

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