Add visualisation

[samwaseda]

Currently there's only 2D projections in pyiron, while most of the calculations are for 3D. @jan-janssen and I talked about the following possibilities:

• plotly (example in the next comment)
• PyVista (already part of dependencies)
• paraview

[samwaseda]

import plotly.graph_objects as go
data = go.Isosurface(
    x=x_mesh.reshape(-1, 3)[:, 0],
    y=x_mesh.reshape(-1, 3)[:, 1],
    z=x_mesh.reshape(-1, 3)[:, 2],
    value=values,
    isomin=0,
    isomax=0.5,
    surface_fill=0.5,
    # opacity=0.5,
    surface_count=5, # number of isosurfaces, 2 by default: only min and max
    # colorbar_nticks=3, # colorbar ticks correspond to isosurface values
    caps=dict(x_show=False, y_show=False, z_show=False),
    colorscale="Turbo"
)
fig = go.Figure(data=data)
fig = go.Figure(data=fig.data + gb.structure.plot3d(mode='plotly', particle_size=10).data)
fig.update_scenes(aspectmode='data')
# fig.layout.scene.camera.projection.type = 'orthographic'
# fig.show()
fig.update_layout(autosize=True, height=600) # remove height=800
# fig.show(renderer="browser")  # remove display(fig)

[samwaseda]

Being implemented here