Fortran

• EDGECOUNT: A tool for characterizing graphene edge

  • This is a software tool for determining the type of edge atoms in a honeycomb lattice. The algorithm is based on nearest neighbor counting. For details, please refer to the Comput. Phys. Comm. article. Ranked #8 in the SciVerse ScienceDirect's Top 25 Hottest Articles in Chemistry for January-March 2011.

    • Examples:

    • Getting the id's of all open-edge atoms of a (8,3) carbon nanotube (tube.xyz), the other edge being H-terminated

    • edgecount tube.xyz; awk '/^AC|^ZZ/ {print $5}' edge.xyz | xargs

    • Filter out "dangling" atoms (H's in this case)

    • edgecount tube.xyz; awk 'NR>2 && $5>1 {print}' output.xyz

• TiReX: Replica exchange molecular dynamics with Tinker

  • This is a parallel implementation (MPI) of the replica-exchange molecular dynamics algorithm using Tinker 4.2 or 5.0. Ranked #14 in the SciVerse ScienceDirect's Top 25 Hottest Articles in Chemistry for July-September 2009. Here's a quick patch to (hopefully) make TiReX work with Tinker 6.2. Put the patch file where the tirex.f90 source file is and apply it: patch -b < tirex.patch.

• Formation energies of intrinsic point defects in Si: sipdef.zip

  • Small project in Fortran90 illustrating simple implementation of the steepest descent algorithm, numerical Hessian calculation, symmetric matrix diagonalization using LAPACK dsyev() driver routine, etc. You need to download the optimized EDIP Si force field. Geometries can be visualized with V_Sim.

• MURFIT: command-line tool for fitting to the Murnaghan's equation of state: murn.tar

  • This is a simple Bourne-shell script which allows you to create consistent input and run the MURN program. It is documented in Chapter 1 of The FHIMD Toolkit. User's Manual

• The Epsilon algorithm: epsilon.f90

  • This is the Fortran90 source code of Appendix A of our article T. Mishonov and E. Penev, Int. J. Mod. Phys. B 14, 3831 (2000). It demonstrates the operation of the epsilon algorithm (see also Wynn's Epsilon Method on mathworld) for finding the limit of infinite series in case where only limited number of terms are known. Ports available: C++ (S. Klenov), BASIC (R. Weaver).

Mathematica

• Graphene flakes: hexagon.nb (hexagonal flake); rndflake.nb (random flake)

  • The two Mathematica notebooks, part of the EDGECOUNT distribution: the former was used to construct all geometries of hexagonal flakes used in the examples; the latter can be used to cut out a flake with "random"-shaped edge.

• LCAO band structure with Mathematica: bands.nb

  • This is a Mathematica notebook illustrating some aspects of band structure calculations on the example of a hypothetical two-dimensional metal oxide lattice

• Calculation of elastic moduli: appendix.nb

  • This is Appendix C of my thesis. The notebook calculates the c11 bulk elastic modulus of GaAs; it can be easily customized to calculate any of the elastic moduli and to evaluate corrections according to the scaling hypothesis .

LAMMPS

• Quick minimizer: in.qmin

  • This script can take input geometry in XYZ or PDB, etc. formats and do quick minimization using either AIREBO or ReaxFF. Intended for Carbon systems. VMD (w/ TopoTools) is required. The scripts parses itself to extract an embedded VMD script, runs VMD to generate LAMMPS data file through TopoTools functionalities:

  • lammps -v p <a|r> -v f <file> < in.qmin

Miscellaneous

• Many ways to create... graphene

• LAMMPS : in.graphene.lmp This script creates n x m graphene patch (graphene.xyz):

• lammps -v n <integer> -v m <integer> < in.graphene.lmp

• and similar for graphite (AB stacking): in.graphite.lmp

• BALSAC : graphene.lat This batch file creates nearly square graphene patch of 200 atoms (graphene.xyz):

• Mathematica : graphene.m (comming soon)

• math < graphene.m

• VMD : a lazy way..., single cmdline. This should create a 1x1 nm2 graphene patch (graphene.xyz):

• tmp=$(mktemp); echo "package req nanotube; graphene -lx 1 -ly 1 -type zigzag -nlayers 1; [atomselect top all] writexyz graphene.xyz; quit" > $tmp; vmd -dispdev text -e $tmp; rm $tmp

• From paper, sugar, or just garbage ;-)

• TubeGen Online (select Crystal Cell: Planar (unrolled))

Data Sets/Project Archives

• Complete archives: input/output data, figures, custom software, scripts, documents, etc.