Related Tools

odatse_neighborlist

This tool generates a neighborhood-list file from the mesh file.

When you install ODAT-SE via pip command, odatse_neighborlist is also installed under the bin. A python script src/odatse_neighborlist.py is also available.

Usage

Pass a path to the mesh file as an argument. The filename of the generated neighborhood-list file is specified by -o option.

$ odatse_neighborlist -o neighborlist.txt MeshData.txt

Or

$ python3 src/odatse_neighborlist.py -o MeshData.txt

The following command-line options are available.

• -o output or --output output

  • The filename of output (default: neighborlist.txt)

• -u "unit1 unit2..." or --unit "unit1 unit2..."

  • Length scale for each dimension of coordinate (default: 1.0 for all dims)

    • Put values splitted by whitespaces and quote the whole

      • e.g.) -u "1.0 0.5"

  • Each dimension of coordinate is divided by the corresponding unit.

• -r radius or --radius radius

  • A pair of nodes where the Euclidean distance is less than radius is considered a neighborhood (default: 1.0)

  • Distances are calculated in the space after coordinates are divided by -u

• -q or --quiet

  • Do not show a progress bar

  • Showing a progress bar requires tqdm python package

• --allow-selfloop

  • Include \(i\) in the neighborhoods of \(i\) itself

• --check-allpairs

  • Calculate distances of all pairs

  • This is for debug

MPI parallelization is available.