latgraph

Utilities for creating, converting, and manipulating files containing lattices.

This program can read and write lattices from/to different file formats and manipulate them in the process. Alternatively, new lattices can be generated. Use python latgraph.py -h to get a list of supported arguments.

Some example files are included under lattices:

• c60_ipr.w3d, c60_ipr.w2d: C60 fullerene obeying the isolated pentagon rule. Generated using CaGe.
• c60_ipr_yml: Like above but relabelled using the anticlockwise method. Contains some additional metadata.

Requirements

• Python 3
• Numpy
• Matplotlib
• PyYaml

Generating

Lattices can be generated using python latgraph.py --generate <gen>, where <gen> is the name of a supported generator. Currently, only tube is supported for generating carbon nano tubes.

All arguments specified after --generate <gen> are passed directly to the generator. Any of the base argments need to be specified before generate. Use --generate <gen> -h to get generator specific help.

Tube

This generator creates carbon nano tubes. Call it via

python latgraph.py -o tube.yml --generate tube 2,3 5

The first set of arguments (2,3, no spaces!) is the chirality of the tube. The second argument (5) is the number of unit cells along the tube. Important optional arguments are

• --bc_sh, --bc_t for boundary conditions along circumference and tube, respectively. Supported values are [o]pen and [p]eriodic, default is periodic
• --emb for the desired embedding; can be 2d or 3d.

The tube generator can also be used to create nano ribbons by specifying a 2D embedding (and open boundary conditions in this example):

python latgraph.py -o ribbon.yml --generate tube 3,3 10 --bc_ch=o --bc_t=o --emb=2d --comment="Hey a ribbon!"

Note however that the size of the ribbon must be set via the cirality and the number of tube(!) unit cells, not the number of hexagons.

Supported Formats

Formats are deduced from file suffixes, see brackets below.

• writegraph3d [.w3d], writegraph2d [.w2d]
  • Adjacency graph
  • 3D/2D positions
  • No hopping strengths (defaults to 1)
  • No information about time
  • No metadata
• YAML [.yml/.yaml]
  • Adjacency graph
  • 3D/2D positions
  • Hopping strengths
  • Number of time slices
  • Name, comment metadata

Relabelling

Graphs can be relabelled to change the order of sites. For this, use the arguments -l file -m method to select a file to determine the labels from and a method. The file must be consistent with the main input file but may have a different embedding (e.g. 2D vs. 3D). Supported methods are

• innermost: Start at the site clostest to the centre. Then move to the neighbour of the current site which is closest the the centre and has not been visited yet; repeat.
• anticlockwise: Like 'innermost' but always move around the centre in anti-clockwise order.

Depending on the label file, the program can get stuck and will abort in that case.

Plotting

Graphs can be drawn as 3D or 2D meshes. Use -p to plot the main graph and -P to plot the label graph. In addition, the adjacency matrix can be plotted using the argument -a. All plots show the state after relabelling if a labelfile was specified.