PlotBand

A Python script for simulating UV/Vis spectra

There are a number of tools for simulating UV/Vis spectra (such as GaussSum), but sometimes you might want to use a quantum chemistry code that isn't supported (or something else exotic). PlotBand is a simple Python3 script that uses matplotlib (and numpy) to generate a UV/Vis spectrum using only excitation energies and oscillator strengths. Using matplotlib means the script is easily hackable for producing publication-ready graphics. If you find the script useful, or find any problems, then please let us know.

PlotBand

import sys

# Check for numpy and matplotlib, try to exit gracefully if not found

import imp

try:

imp.find_module('numpy')

foundnp = True

except ImportError:

foundnp = False

try:

imp.find_module('matplotlib')

foundplot = True

except ImportError:

foundplot = False

if not foundnp:

print("Numpy is required. Exiting")

sys.exit()

if not foundplot:

print("Matplotlib is required. Exiting")

sys.exit()

import numpy as np

import matplotlib.pyplot as plt

# Adjust the following three variables to change which area of the spectrum is plotted and number of points used

# in plotting the curves

start=200

finish=380

points=300

# A sqrt(2) * standard deviation of 0.4 eV is 3099.6 nm. 0.1 eV is 12398.4 nm. 0.2 eV is 6199.2 nm.

stdev = 12398.4

# For Lorentzians, gamma is half bandwidth at half peak height (nm)

gamma = 12.5

# Excitation energies in nm

bands = [330,328,328,308,290,290,288,283,276,270,268]

# Oscillator strengths (dimensionless)

f = [7.90e-7,0.00,7.16e-4,1.02e-2,1.38e-6,2.94e-7,0.00,8.86e-4,1.54e-5,1.25e-2,9.31e-3]

# Basic check that we have the same number of bands and oscillator strengths

if len(bands) != len(f):

print('Number of bands does not match the number of oscillator strengths.')

sys.exit()

# Information on producing spectral curves (Gaussian and Lorentzian) is adapted from:

# P. J. Stephens, N. Harada, Chirality 22, 229 (2010).

# Gaussian curves are often a better fit for UV/Vis.

def gaussBand(x, band, strength, stdev):

"Produces a Gaussian curve"

bandshape = 1.3062974e8 * (strength / (1e7/stdev)) * np.exp(-(((1.0/x)-(1.0/band))/(1.0/stdev))**2)

return bandshape

def lorentzBand(x, band, strength, stdev, gamma):

"Produces a Lorentzian curve"

bandshape = 1.3062974e8 * (strength / (1e7/stdev)) * ((gamma**2)/((x - band)**2 + gamma**2))

return bandshape

x = np.linspace(start,finish,points)

composite = 0

for count,peak in enumerate(bands):

thispeak = gaussBand(x, peak, f[count], stdev)

# thispeak = lorentzBand(x, peak, f[count], stdev, gamma)

composite += thispeak

fig, ax = plt.subplots()

ax.plot(x,composite)

plt.xlabel('$\lambda$ / nm')

plt.ylabel('$\epsilon$ / L mol$^{-1}$ cm$^{-1}$')

plt.show()

If the script doesn't generate anything, it may be that you don't have a matplotlib backend that is capable of interactive plotting. In that case you could try substituting the line plt.show() with plt.savefig('foo.png').

The resulting image should look like this:

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