Trying to replicate your movie and slider examples

[chipbrock]

I'm brand new at this. Trying to create animated and interactive graphics in a JupyterBook for a classroom text that I'm writing. I found your examples of the Fermi-Dirac distribution in your nice Medium article of last year.

I can easily recreate the static diagram but when I try to create either the movie or the slider example I get errors. I've pasted in the two projects at the end of the first one (is that the right thing to do?) I'm working in Jupyter Lab, but my eventual target is JupyterBook. I'd appreciate some pointers.

BTW I know that making it work in a notebook is not how to make it work interactively in JupyterBook. If you have suggestions there, that would be very much appreciated!

I'm working on an M1 MacBook pro in, like I said, Jupyter Lab.

Python 3.8.8 (default, Apr 13 2021, 12:59:45) 
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin

Thanks in advance for your help and advice on web-embedding?

Here are the code and results:

Movie:

After the lines:

mpl.rcParams['xtick.major.size'] = 10
mpl.rcParams['xtick.major.width'] = 2
mpl.rcParams['ytick.major.size'] = 10
mpl.rcParams['ytick.major.width'] = 2

in the static program, I insert

# Change matplotlib backend
%matplotlib notebook


# Create figure and add axes
fig = plt.figure(figsize=(6, 4))
ax = fig.add_subplot(111)

and so on

through to the end of your movie example code. It produces errors:

Javascript Error: Can't find variable: IPython

NameError                                 Traceback (most recent call last)
<ipython-input-1-a0c46868fd22> in <module>
     76 
     77 # Create animation
---> 78 ani = FuncAnimation(fig, animate, frames=range(len(T)), interval=500, repeat=True)
     79 
     80 # Ensure the entire plot is visible

NameError: name 'FuncAnimation' is not defined

Sliders

In the same way, at the same point, I add the lines from the example:

fig = plt.figure(figsize=(6, 4.5))

# Create main axis
ax = fig.add_subplot(111)
fig.subplots_adjust(bottom=0.2, top=0.75)

and it produces a static picture of the plot with sliders (probably a slice of the animated gif from your article?) and errors

NameError                                 Traceback (most recent call last)
<ipython-input-1-560d20080917> in <module>
     72 plt.show()
     73 
---> 74 Slider.on_changed(func)

NameError: name 'func' is not defined

Here are the complete cells for both

Movie

# Import packages
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np

# Fermi-Dirac Distribution
def fermi(E: float, E_f: float, T: float) -> float:
    k_b = 8.617 * (10**-5) # eV/K
    return 1/(np.exp((E - E_f)/(k_b * T)) + 1)

# General plot parameters
mpl.rcParams['font.family'] = 'Avenir'
mpl.rcParams['font.size'] = 18
mpl.rcParams['axes.linewidth'] = 2
mpl.rcParams['axes.spines.top'] = False
mpl.rcParams['axes.spines.right'] = False
mpl.rcParams['xtick.major.size'] = 10
mpl.rcParams['xtick.major.width'] = 2
mpl.rcParams['ytick.major.size'] = 10
mpl.rcParams['ytick.major.width'] = 2

# Change matplotlib backend
%matplotlib notebook


# Create figure and add axes
fig = plt.figure(figsize=(6, 4))
ax = fig.add_subplot(111)

# Temperature values
T = np.linspace(100, 1000, 10)

# Get colors from coolwarm colormap
colors = plt.get_cmap('coolwarm', 10)

# Plot F-D data
for i in range(len(T)):
    x = np.linspace(0, 1, 100)
    y = fermi(x, 0.5, T[i])
    ax.plot(x, y, color=colors(i), linewidth=2.5)
    
# Add legend
labels = ['100 K', '200 K', '300 K', '400 K', '500 K', '600 K', 
          '700 K', '800 K', '900 K', '1000 K']
ax.legend(labels, bbox_to_anchor=(1.05, -0.1), loc='lower left', 
          frameon=False, labelspacing=0.2)

# Create figure and add axes
fig = plt.figure(figsize=(6, 4))
ax = fig.add_subplot(111)

# Get colors from coolwarm colormap
colors = plt.get_cmap('coolwarm', 10)

# Temperature values
T = np.linspace(100, 1000, 10)

# Create variable reference to plot
f_d, = ax.plot([], [], linewidth=2.5)

# Add text annotation and create variable reference
temp = ax.text(1, 1, '', ha='right', va='top', fontsize=24)

# Set axes labels
ax.set_xlabel('Energy (eV)')
ax.set_ylabel('Fraction')

# Animation function
def animate(i):
    x = np.linspace(0, 1, 100)
    y = fermi(x, 0.5, T[i])
    f_d.set_data(x, y)
    f_d.set_color(colors(i))
    temp.set_text(str(int(T[i])) + ' K')
    temp.set_color(colors(i))

# Create animation
ani = FuncAnimation(fig, animate, frames=range(len(T)), interval=500, repeat=True)

# Ensure the entire plot is visible
fig.tight_layout()

# Save and show animation
ani.save('AnimatedPlot.gif', writer='imagemagick', fps=2)
plt.show()

Sliders

# Import packages
%matplotlib inline

import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
from matplotlib.widgets import Slider
import numpy as np
import networkx as nx
from matplotlib.animation import FuncAnimation, PillowWriter 

# Fermi-Dirac Distribution
def fermi(E: float, E_f: float, T: float) -> float:
    k_b = 8.617 * (10**-5) # eV/K
    return 1/(np.exp((E - E_f)/(k_b * T)) + 1)

# General plot parameters
mpl.rcParams['font.family'] = 'Avenir'
mpl.rcParams['font.size'] = 18

mpl.rcParams['axes.linewidth'] = 2
mpl.rcParams['axes.spines.top'] = False
mpl.rcParams['axes.spines.right'] = False

mpl.rcParams['xtick.major.size'] = 10
mpl.rcParams['xtick.major.width'] = 2
mpl.rcParams['ytick.major.size'] = 10
mpl.rcParams['ytick.major.width'] = 2


fig = plt.figure(figsize=(6, 4.5))

# Create main axis
ax = fig.add_subplot(111)
fig.subplots_adjust(bottom=0.2, top=0.75)

# Create axes for sliders
ax_Ef = fig.add_axes([0.3, 0.85, 0.4, 0.05])
ax_Ef.spines['top'].set_visible(True)
ax_Ef.spines['right'].set_visible(True)

ax_T = fig.add_axes([0.3, 0.92, 0.4, 0.05])
ax_T.spines['top'].set_visible(True)
ax_T.spines['right'].set_visible(True)

# Create sliders
s_Ef = Slider(ax=ax_Ef, label='Fermi Energy ', valmin=0, valmax=1.0, valinit=0.5, valfmt=' %1.1f eV', facecolor='#cc7000')
s_T = Slider(ax=ax_T, label='Temperature ', valmin=100, valmax=1000, valinit=300, valfmt=' %i K', facecolor='#cc7000')

# Plot default data
x = np.linspace(-0, 1, 100)
Ef_0 = 0.5
T_0 = 300
y = fermi(x, Ef_0, T_0)
f_d, = ax.plot(x, y, linewidth=2.5)


# Update values
def update(val):
    Ef = s_Ef.val
    T = s_T.val
    f_d.set_data(x, fermi(x, Ef, T))
    fig.canvas.draw_idle()

s_Ef.on_changed(update)
s_T.on_changed(update)
    
# Set axis labels
ax.set_xlabel('Energy (eV)')
ax.set_ylabel('Fraction')

plt.show()

Slider.on_changed(func)