WIP: make a script for plotting Fermi surfaces

src/fermi_surfaces.md

 # Periodic table of Fermi surfaces
 
 Data taken from the [Fermi surface database](https://www.phys.ufl.edu/fermisurface/), © 2000 Tat-Sang Choy, CC-BY.
+
+```python
+import json
+import itertools
+
+import numpy as np
+from plotly import graph_objects as go
+
+with open('code/fermi_surfaces.json') as f:
+    fermi_surface_data = json.load(f)
+```
+
+```python
+palette = [
+    '#1f77b4',  # muted blue
+    '#ff7f0e',  # safety orange
+    '#2ca02c',  # cooked asparagus green
+    '#d62728',  # brick red
+    '#9467bd',  # muted purple
+    '#8c564b',  # chestnut brown
+    '#e377c2',  # raspberry yogurt pink
+    '#7f7f7f',  # middle gray
+    '#bcbd22',  # curry yellow-green
+    '#17becf'   # blue-teal
+]
+
+
+def element_to_traces(data):
+    brillouin_zone = data['brillouin_zone']
+    coords, indices = brillouin_zone['coords'], np.array(brillouin_zone['indices'])
+    fermi_surfaces = data['fermi_surfaces']
+    coords = np.array(3*[np.nan] + coords).reshape(-1, 3)
+    x, y, z = coords[indices + 1].T
+    bz_contour = go.Scatter3d(
+        x=x, y=y, z=z,
+        mode='lines',
+        hoverinfo='none',
+    )
+    surfaces = []
+    for zone, surface in fermi_surfaces.items():
+        x, y, z = np.array(surface['coords']).reshape(-1, 3).T
+        i, j, k = np.array(surface['indices']).T
+        surfaces.append(go.Mesh3d(
+            x=x, y=y, z=z, i=i, j=j, k=k,
+            color=palette[int(zone) % len(palette)],
+            opacity=.8,
+            hoverinfo='name',
+            name=f'Band {zone}',
+        ))
+
+    return [bz_contour] + surfaces
+
+```
+
+```python
+elements_data = {name: element_to_traces(data) for name, data in fermi_surface_data.items()}
+
+index = itertools.count()
+trace_indices = [
+    [i for i, j in zip(index, traces)]
+    for traces in elements_data.values()
+]
+```
+
+```python
+    frames=[
+        go.Frame(
+            data=traces,
+            name=name,
+        )
+        for name, traces, _
+        in zip(elements_data, elements_data.values(), range(5))
+    ],
+
+```
+
+```python
+fig = go.Figure(
+    layout=go.Layout(
+        scene=go.layout.Scene(
+            xaxis=go.layout.scene.XAxis(
+                color='rgba(0,0,0,0)',
+                backgroundcolor='rgba(0,0,0,0)',
+            ),
+            yaxis=go.layout.scene.YAxis(
+                color='rgba(0,0,0,0)',
+                backgroundcolor='rgba(0,0,0,0)',
+            ),
+            zaxis=go.layout.scene.ZAxis(
+                color='rgba(0,0,0,0)',
+                backgroundcolor='rgba(0,0,0,0)',
+            ),
+        )
+    )
+)
+
+for element, traces in fig.data[len(trace_indices[0]):]:
+    trace.visible = False
+
+fig.layout.updatemenus = [
+    {
+        'sliders': [
+            go.layout.Slider(
+                steps=[
+                    dict(
+                    
+                )
+                ],
+            ),
+        ],
+        'direction': 'left',
+        'pad': {'r': 10, 't': 87},
+        'showactive': False,
+        'type': 'sli',
+        'x': 0.55,
+        'xanchor': 'right',
+        'y': 0,
+        'yanchor': 'top'
+    }
+]
+
+fig
+```
+
+```python
+
+```
+
+```python
+# Imports
+import numpy as np
+import plotly.graph_objs as go
+import ipywidgets as widgets
+import time
+init_notebook_mode()
+
+# Compute surface data
+x = np.linspace(-10,10,201)
+y = np.linspace(-10,10,201)
+X,Y = np.meshgrid(x,y)
+
+z_bath = X+Y
+z_tnm = np.zeros((10,201,201),dtype=float)
+
+for t in range(10):
+    tsunami = t*np.sin(X+t/10*np.pi)
+    z_tnm[t] = tsunami
+
+# Create FigureWidget and add surface trace
+#fig = go.Figure()
+#surface = fig.add_surface(z=z_bath,name='bath')
+
+# ----- change part ------ 
+bath = go.Surface(z=z_bath)
+fig = go.Figure(data=[bath,bath])
+
+# Set axis ranges to fixed values to keep them from retting during animation
+fig.layout.scene.zaxis.range = [-10, 10]
+fig.layout.scene.yaxis.range = [0, 150]
+fig.layout.scene.xaxis.range = [0, 150]
+#surface.cmin = -10
+#surface.cmax = 10
+
+frames = []
+for i in range(10):
+    frames.append(go.Frame(data=[{'type': 'surface', 'z': z_tnm[i], 'name':'tsunami'}]))
+
+fig.frames = frames
+
+fig.layout.updatemenus = [
+    {
+        'buttons': [
+            {
+                'args': [None, {'frame': {'duration': 500, 'redraw': False},
+                         'fromcurrent': True, 'transition': {'duration': 300}}],
+                'label': 'Play',
+                'method': 'animate'
+            },
+            {
+                'args': [[None], {'frame': {'duration': 0, 'redraw': False}, 'mode': 'immediate',
+                'transition': {'duration': 0}}],
+                'label': 'Pause',
+                'method': 'animate'
+            }
+        ],
+        'direction': 'left',
+        'pad': {'r': 10, 't': 87},
+        'showactive': False,
+        'type': 'buttons',
+        'x': 0.55,
+        'xanchor': 'right',
+        'y': 0,
+        'yanchor': 'top'
+    }
+]
+
+fig
+```
+
+```python
+%
+```
+
+```python
+
+```