1.3. 3D Orthogonal Grid Generation

This is very similar to the previous 2D Orthogonal Grid tutorial. We use the two partitioners again (KBA and Parmetis).

To run the code, simply type: jupyter nbconvert --to python --execute <basename>.ipynb.

To convert it to a python file (named <basename>.py), simply type: jupyter nbconvert --to python <basename>.ipynb

To run the python file from the terminal, using N processes, simply type: mpiexec -n <N> python <basename>.py

[ ]:

import os
import sys

sys.path.append("../../..")

from pyopensn.mesh import OrthogonalMeshGenerator, KBAGraphPartitioner, PETScGraphPartitioner
from pyopensn.context import UseColor, Finalize

UseColor(False)

1.3.1. List of Nodes

First, we create a list of nodes that are evenly spaced from -L/2 to +L/2.

[ ]:

length = 2.
n_cells = 10
dx = length / n_cells
nodes = [-length/2 + i * dx for i in range(n_cells + 1)]

1.3.2. Mesh and KBA Partition

We use the OrthogonalMeshGenerator and pass the list of nodes per dimension.

The domain will be partitioned using the KBAGraphPartitioner into 8 subdomains and the locations of the plane cuts along x, y, and z need to be specified.

[ ]:

meshgen = OrthogonalMeshGenerator(
    node_sets=[nodes, nodes, nodes],
    partitioner=KBAGraphPartitioner(
        nx=2,
        ny=2,
        nz=2,
        xcuts=[0.0],
        ycuts=[0.0],
        zcuts=[0.0],
    ),
)
grid = meshgen.Execute()

1.3.3. Material IDs

When using the in-house OrthogonalMeshGenerator, no material IDs are assigned. The user needs to assign material IDs to all cells. Here, we have a homogeneous domain, so we assign a material ID with value 0 for each cell in the spatial domain.

[ ]:

grid.SetUniformBlockID(0)

1.3.4. Export the mesh

We export to vtu format. The resulting mesh partition is shown below below1

[ ]:

grid.ExportToPVTU("ortho_3D_KBA")

1.3.5. Mesh (again) and Parmetis partition

Now, we partition the mesh using the Parmetis partitioner, accessed through PETScGraphPartitioner.

[ ]:

meshgen2 = OrthogonalMeshGenerator(
    node_sets=[nodes, nodes, nodes],
    partitioner=PETScGraphPartitioner(type='parmetis'),
)
grid2 = meshgen2.Execute()
grid2.SetUniformBlockID(0)

1.3.6. Export the mesh

On such a simple regular mesh, both partitioners are giving the same result. The Parmetis partition is shown below below2

[ ]:

grid2.ExportToPVTU("ortho_3D_Parmetis")

1.3.7. Finalize (for Jupyter Notebook only)

In Python script mode, PyOpenSn automatically handles environment termination. However, this automatic finalization does not occur when running in a Jupyter notebook, so explicit finalization of the environment at the end of the notebook is required. Do not call the finalization in Python script mode, or in console mode.

Note that PyOpenSn’s finalization must be called before MPI’s finalization.

[ ]:

from IPython import get_ipython

def finalize_env():
    Finalize()
    MPI.Finalize()

ipython_instance = get_ipython()
if ipython_instance is not None:
    ipython_instance.events.register("post_execute", finalize_env)