Related Tools

odatse_neighborlist

This tool generates a neighborhood-list file from the mesh file for Monte Carlo search in discrete spaces.

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 neighborlist.txt 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

    • Example: -u "2.0 1.0 3.0" (For 3D space, apply scale 2.0 for x-axis, 1.0 for y-axis, and 3.0 for z-axis)

  • 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 Parallel Computation

MPI parallelization is available to speed up calculations. For example, when using the mpirun command:

$ mpirun -np 4 odatse_neighborlist -o neighborlist.txt MeshData.txt

The -np 4 part specifies the number of processes to use. Adjust according to the number of cores available.

Depending on your environment, you may need to use mpiexec or other commands, or execute MPI programs through a job scheduler. In those cases, please modify the command to suit your environment.