Visualizing dislocation evolution

Dislocation evolution can be visualized in several ways:

Interactive matplotlib visualization module

Module VisualizeNetwork can be used to visualize the evolution of the dislocation network during a simulation through a matplotlib window, e.g.

from pyexadis_base import VisualizeNetwork

vis = VisualizeNetwork()

sim = SimulateNetwork(
    ...,
    vis=vis, plot_freq=10
)

Important

Interactive plotting of the dislocation network through matplotlib module can induce a significant overhead to the simulation run time.

Note

The interactive visualization window will not display when using the performance driver SimulateNetworkPerf from pyexadis, as this driver is intended for production runs in HPC environments.

Visualizing .data output files

Simulation drivers SimulateNetwork and SimulateNetworkPerf from pyexadis regularly output the dislocation network in .data files (with frequency defined by write_freq) during a simulation run. There are several ways the .data dislocation configurations can be visualized:

• VisIt: the VisIt visualization software supports .data files.

Note

Some users have reported issues with animations in the latest versions of VisIt.

• Ovito Pro: you will need to use a custom file reader, following this thread.

Note

This requires Ovito Pro, and will not work with Ovito Basic.

• ParaView: .data files can be converted to .vtk files for visualization in ParaView using functions from pyexadis_utils.py. Here is an example of an OpenDiS script to convert .data files in batch:

import os, glob
import pyexadis
from pyexadis_utils import read_paradis, write_vtk
pyexadis.initialize()

output_path = '/path/to/opendis/simulation/output'
for f in glob.glob(output_path+'/*.data'):
    N = read_paradis(f)
    write_vtk(N, os.path.splitext(f)[0]+'.vtk')