Let us now dive into nuclear physics and remind ourselves briefly about some basic features about binding energies. A basic quantity which can be measured for the ground states of nuclei is the atomic mass \( M(N, Z) \) of the neutral atom with atomic mass number \( A \) and charge \( Z \). The number of neutrons is \( N \). There are indeed several sophisticated experiments worldwide which allow us to measure this quantity to high precision (parts per million even).
Atomic masses are usually tabulated in terms of the mass excess defined by $$ \Delta M(N, Z) = M(N, Z) - uA, $$ where \( u \) is the Atomic Mass Unit $$ u = M(^{12}\mathrm{C})/12 = 931.4940954(57) \hspace{0.1cm} \mathrm{MeV}/c^2. $$
In the 2016 mass evaluation of by W.J.Huang, G.Audi, M.Wang, F.G.Kondev, S.Naimi and X.Xu there are data on masses and decays of 3437 nuclei.
The nuclear binding energy is defined as the energy required to break up a given nucleus into its constituent parts of \( N \) neutrons and \( Z \) protons. In terms of the atomic masses \( M(N, Z) \) the binding energy is defined by $$ BE(N, Z) = ZM_H c^2 + Nm_n c^2 - M(N, Z)c^2 , $$ where \( M_H \) is the mass of the hydrogen atom and \( m_n \) is the mass of the neutron. In terms of the mass excess the binding energy is given by $$ BE(N, Z) = Z\Delta_H c^2 + N\Delta_n c^2 -\Delta(N, Z)c^2 , $$ where \( \Delta_H c^2 = 7.2890 \) MeV and \( \Delta_n c^2 = 8.0713 \) MeV.
A popular and physically intuitive model which can be used to parametrize the experimental binding energies as function of \( A \), is the so-called liquid drop model. The ansatz is based on the following expression $$ BE(N,Z) = a_1A-a_2A^{2/3}-a_3\frac{Z^2}{A^{1/3}}-a_4\frac{(N-Z)^2}{A}, $$
where \( A \) stands for the number of nucleons and the $a_i$s are parameters which are determined by a fit to the experimental data.
Let us start with reading and organizing our data. We start with the compilation of masses and binding energies from 2016. After having downloaded this file to our own computer, we are now ready to read the file and start structuring our data.
We start with preparing folders for storing our calculations and the data file over masses and binding energies. We import also various modules that we will find useful in order to present various Machine Learning methods. Here we focus mainly on the functionality of scikit-learn.
# Common imports
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import sklearn.linear_model as skl
from sklearn.model_selection import train_test_split
from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_error
import os
# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "DataFiles/"
if not os.path.exists(PROJECT_ROOT_DIR):
os.mkdir(PROJECT_ROOT_DIR)
if not os.path.exists(FIGURE_ID):
os.makedirs(FIGURE_ID)
if not os.path.exists(DATA_ID):
os.makedirs(DATA_ID)
def image_path(fig_id):
return os.path.join(FIGURE_ID, fig_id)
def data_path(dat_id):
return os.path.join(DATA_ID, dat_id)
def save_fig(fig_id):
plt.savefig(image_path(fig_id) + ".png", format='png')
infile = open(data_path("MassEval2016.dat"),'r')
Before we proceed, we define also a function for making our plots. You can obviously avoid this and simply set up various matplotlib commands every time you need them. You may however find it convenient to collect all such commands in one function and simply call this function.
from pylab import plt, mpl
plt.style.use('seaborn')
mpl.rcParams['font.family'] = 'serif'
def MakePlot(x,y, styles, labels, axlabels):
plt.figure(figsize=(10,6))
for i in range(len(x)):
plt.plot(x[i], y[i], styles[i], label = labels[i])
plt.xlabel(axlabels[0])
plt.ylabel(axlabels[1])
plt.legend(loc=0)
Our next step is to read the data on experimental binding energies and reorganize them as functions of the mass number \( A \), the number of protons \( Z \) and neutrons \( N \) using pandas. Before we do this it is always useful (unless you have a binary file or other types of compressed data) to actually open the file and simply take a look at it!
In particular, the program that outputs the final nuclear masses is written in Fortran with a specific format. It means that we need to figure out the format and which columns contain the data we are interested in. Pandas comes with a function that reads formatted output. After having admired the file, we are now ready to start massaging it with pandas. The file begins with some basic format information.
"""
This is taken from the data file of the mass 2016 evaluation.
All files are 3436 lines long with 124 character per line.
Headers are 39 lines long.
col 1 : Fortran character control: 1 = page feed 0 = line feed
format : a1,i3,i5,i5,i5,1x,a3,a4,1x,f13.5,f11.5,f11.3,f9.3,1x,a2,f11.3,f9.3,1x,i3,1x,f12.5,f11.5
These formats are reflected in the pandas widths variable below, see the statement
widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
Pandas has also a variable header, with length 39 in this case.
"""
The data we are interested in are in columns 2, 3, 4 and 11, giving us the number of neutrons, protons, mass numbers and binding energies, respectively. We add also for the sake of completeness the element name. The data are in fixed-width formatted lines and we will covert them into the pandas DataFrame structure.
# Read the experimental data with Pandas
Masses = pd.read_fwf(infile, usecols=(2,3,4,6,11),
names=('N', 'Z', 'A', 'Element', 'Ebinding'),
widths=(1,3,5,5,5,1,3,4,1,13,11,11,9,1,2,11,9,1,3,1,12,11,1),
header=39,
index_col=False)
# Extrapolated values are indicated by '#' in place of the decimal place, so
# the Ebinding column won't be numeric. Coerce to float and drop these entries.
Masses['Ebinding'] = pd.to_numeric(Masses['Ebinding'], errors='coerce')
Masses = Masses.dropna()
# Convert from keV to MeV.
Masses['Ebinding'] /= 1000
# Group the DataFrame by nucleon number, A.
Masses = Masses.groupby('A')
# Find the rows of the grouped DataFrame with the maximum binding energy.
Masses = Masses.apply(lambda t: t[t.Ebinding==t.Ebinding.max()])
We have now read in the data, grouped them according to the variables we are interested in. We see how easy it is to reorganize the data using pandas. If we were to do these operations in C/C++ or Fortran, we would have had to write various functions/subroutines which perform the above reorganizations for us. Having reorganized the data, we can now start to make some simple fits using both the functionalities in numpy and Scikit-Learn afterwards.
Now we define five variables which contain the number of nucleons \( A \), the number of protons \( Z \) and the number of neutrons \( N \), the element name and finally the energies themselves.
A = Masses['A']
Z = Masses['Z']
N = Masses['N']
Element = Masses['Element']
Energies = Masses['Ebinding']
print(Masses)
The next step, and we will define this mathematically later, is to set up the so-called design matrix. We will throughout call this matrix \( \boldsymbol{X} \). It has dimensionality \( p\times n \), where \( n \) is the number of data points and \( p \) are the so-called predictors. In our case here they are given by the number of polynomials in \( A \) we wish to include in the fit.
# Now we set up the design matrix X
X = np.zeros((len(A),5))
X[:,0] = 1
X[:,1] = A
X[:,2] = A**(2.0/3.0)
X[:,3] = A**(-1.0/3.0)
X[:,4] = A**(-1.0)
With scikitlearn we are now ready to use linear regression and fit our data.
clf = skl.LinearRegression().fit(X, Energies)
fity = clf.predict(X)
Pretty simple! Now we can print measures of how our fit is doing, the coefficients from the fits and plot the final fit together with our data.
# The mean squared error
print("Mean squared error: %.2f" % mean_squared_error(Energies, fity))
# Explained variance score: 1 is perfect prediction
print('Variance score: %.2f' % r2_score(Energies, fity))
# Mean absolute error
print('Mean absolute error: %.2f' % mean_absolute_error(Energies, fity))
print(clf.coef_, clf.intercept_)
Masses['Eapprox'] = fity
# Generate a plot comparing the experimental with the fitted values values.
fig, ax = plt.subplots()
ax.set_xlabel(r'$A = N + Z$')
ax.set_ylabel(r'$E_\mathrm{bind}\,/\mathrm{MeV}$')
ax.plot(Masses['A'], Masses['Ebinding'], alpha=0.7, lw=2,
label='Ame2016')
ax.plot(Masses['A'], Masses['Eapprox'], alpha=0.7, lw=2, c='m',
label='Fit')
ax.legend()
save_fig("Masses2016")
plt.show()