Simulations with spatial grids in 3D can be visualized via scatter plots. The grid may have irregular spacing such that each of the x, y, z dimensions is itself a 3-dimensional array. This can be visualized in Matlab or Python by reshaping the 3D arrays to a vector in the plotting command.

Scatter plots are one way to visualize 3D data in Matlab.

scatter3(x(:), y(:), z(:))

Python Matplotlib has several 3D visualization methods. Matplotlib scatter() also requires 1D vectors, which can be obtained at O(0) cost by the Numpy ndarray ravel method.

from matplotlib.pyplot import figure, show

ax = figure().gca()
ax.scatter(x.ravel(), y.ravel(), z.ravel())
show()