MM220: Computational Lab

Amrita Bhattacharya

March 25, 2019

1 Introduction to python -II: Plotting and Differentiation

1.1 Locating, adding, and importing libraries
Python has strong in built libraries for numerical and scientific operations such as Numpy, Scipy,
Sympy etc. Locate your libraries and add path of the libraries in your preamble (if required).

Listing 1: locate

locate numpy
locate scipy

Add the following in your preamble (if required), depending upon your search result to the path of
the libraries;

Listing 2: path

#!/usr/bin/python
#!/usr/share/pyshared/
#!/usr/share/pyshared/scipy

Import the libraries, depending on their need;

Listing 3: Import

import matplotlib.pyplot as plt;

import numpy as np;
import scipy.optimize as opt;

1.2 Plotting
Hereforth, we will use the in built library of python called matplotlib for plotting.

1
 Listing 4: harmonics

import matplotlib.pyplot as plt;

import numpy as np;

def func_duo(x):
return np.sin(x) , np.cos(x)

def comp_func(x, a, b):

return a*np.sin(x) + b*np.cos(x)

xdata = np.linspace(-np.pi, np.pi, 300)

sin, cos = func_duo(xdata)
y_comp = comp_func(xdata, 2, 1)

plt.plot(xdata, sin, ".", label="sin");

plt.plot(xdata, cos, ".", label="cos");
plt.plot(xdata, y_comp, ".", label="Data");
plt.xlabel("x")
plt.ylabel("y")
plt.legend(( 'sin(x)', 'cos(x)','harmonics(x)'))
plt.savefig('harmonics.png')
plt.show();

The output of the given program should be as follows;

sin(x)
2 cos(x)
harmonics(x)

0
y

−1

−2

−3 −2 −1 0 1 2 3
x

Figure 1: Plot of the harmonics.

2
 Listing 5: polyfit

import matplotlib.pyplot as plt;

import numpy as np;
import scipy.optimize as opt;

# This is the function we are trying to fit to the data.

def func(x, a, b, c):
return a * np.exp(-b * x) + c

# Generate some data

xdata = np.linspace(0, 4, 50)
y = func(xdata, 2.5, 1.3, 0.5)
y_noise = 0.2 * np.random.normal(size=xdata.size)
ydata = y + y_noise

# Plot the actual data

plt.plot(xdata, ydata, ".", label="Data");

# The actual curve fitting happens here

p1 = np.polyfit(xdata,ydata,1)
p2 = np.polyfit(xdata,ydata,2)
p3 = np.polyfit(xdata,ydata,3)
plt.plot(xdata, np.polyval(p1,xdata), 'r-')
plt.plot(xdata, np.polyval(p2,xdata), 'b-')
plt.plot(xdata, np.polyval(p3,xdata), 'g-')
# Show the graph
plt.xlabel("x")
plt.ylabel("y")
plt.legend(('data', 'p_1', 'p_2', 'p_3'))
plt.savefig("polyfit.png")
plt.show();

data
p_1
3.0
p_2
p_3
2.5

2.0
y

1.5

1.0

0.5

0.0
0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0
x

Figure 2: Plot showing the polynomial fit for the function.

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1.3 Numerical Differentiation

Listing 6: Numerical

import matplotlib.pyplot as plt;

import numpy as np;
import scipy.optimize as opt;
from scipy.misc import derivative
import sympy

########## Definition of the functions #############

def func(x):
fn1 = 4*x**2 +2
fn2 = np.sin(x)
return fn1, fn2

####### Numerical derivative of the functions ######

def nd_func(x):
h = 1e-5
ndfn1 = (func(x+h)[0]-func(x-h)[0])/(2*h)
ndfn2 = (func(x+h)[1]-func(x-h)[1])/(2*h)
return ndfn1, ndfn2

######## x corresponding to min of f(x) ###################

x = np.linspace(-6, 6)

fn1, fn2 = func(x)

ndfn1, ndfn2 = nd_func(x)

set = zip(x, fn1, ndfn1)

for i in range(len(set)):
if set[i][1] == min(fn1):
print set[i][0], set[i][1]

######### plotting ###################

x = np.linspace(-6, 6)
plt.plot(x,func(x)[0])
plt.xlabel("x")
plt.ylabel("y")
plt.plot(x,nd_func(x)[0])
plt.legend(('fn(x)', 'd_fn(x)'))
plt.savefig('num_diff_fx.eps')
plt.show()

x = np.linspace(-2*np.pi,2*np.pi)
plt.plot(x,func(x)[1])
plt.xlabel("x")
plt.ylabel("y")
plt.plot(x,nd_func(x)[1])
plt.legend(('sin(x)', 'cos(x)'))
plt.savefig('num_diff_harmonics.eps')
plt.show()

4
 150

125

100

75

50
y

25

−25
fn(x)
−50 d_fn(x)

−6 −4 −2 0 2 4 6
x

Figure 3: Numerical differentiation of function

1.00

0.75

0.50

0.25

0.00
y

−0.25

−0.50

−0.75
sin(x)
−1.00 cos(x)

−6 −4 −2 0 2 4 6
x

Figure 4: Numerical differentiation of harmonics.

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1.4 Symbolic Differentiation

Listing 7: Symbolic

import matplotlib.pyplot as plt;

import numpy as np;
import scipy.optimize as opt;
from scipy.misc import derivative
import sympy

#################### Symbolic derivative of the functions ############

def diff_func(x):
x = sympy.symbols('x')
fn1 = 4*x**2 +2
fn2 = 50*sympy.sin(x)
dfn1 = sympy.diff(fn1, x)
dfn2 = sympy.diff(fn2, x)
return fn1, dfn1, fn2, dfn2

x = sympy.symbols('x')
fn1, dfn1, fn2, dfn2 = diff_func(x)

print fn1, dfn1, fn2, dfn2

print diff_func(x)[0], diff_func(x)[1], diff_func(x)[2], diff_func(x)[3]

##################### plotting the functions ##########################

fx1=[]
diffx1=[]
fx2=[]
diffx2=[]
for i in np.linspace(-6,6):
x = sympy.symbols('x')
fx1.append(fn1.evalf(subs={x: i}))
diffx1.append(dfn1.evalf(subs={x: i}))
fx2.append(fn2.evalf(subs={x: i}))
diffx2.append(dfn2.evalf(subs={x: i}))

x = np.linspace(-6,6)
plt.plot(x,fx1)
plt.plot(x,diffx1)
plt.xlabel("x")
plt.ylabel("y")
plt.plot(x,fx2)
plt.plot(x,diffx2)
plt.legend(('fx1', 'dfx1', 'fx2', 'dfx2'))
plt.savefig('sym_diff.png')
plt.show()

6
 150 fx1
dfx1
125 fx2
dfx2
100

75

50
y
25

−25

−50
−6 −4 −2 0 2 4 6
x

Figure 5: Symbolic differentiation.

2 Assignments
(i) Write a program that does the following:
(a) creates a function, f (x) = aex + be−x that takes the parameters a = 2, 4 and b = 3, 6
(b) plots the function for −6 < x < 6.
(c) fits the function with polynomials of the order two, three and four.
(ii) The Lennard-Jones (LJ) model is used to model the inter atomic force/ potential between two
atoms. It consists of a steep repulsive term, and smooth attractive term. The 12-6 LJ potential is
given by the following equation:

   
B A
V(r) = − (1)
r12 r6
Say,
A = 1.024 × 10−23 (J nm6 )
B = 1.582 × 10−26 (J nm12 )
The force between the atom is given by F(r) = − dVdr . At equilibrium separation, the potential between
the two atoms is minimum, which implies the force is equal to zero, i.e. F(r) = 0.
Write a program that does the following:
(a) plots the LJ potential V(r) as a function of r (in nm) varying in range 0.3 6 r 6 0.8.
(b) plots the force F(r) between the atoms as a function of r.
(c) calculates the equilibrium separation r0 between the atoms for which the force is minimum.

Hints: It is easier if you divide A and B by the Boltzmann’s constant, 1.381 × 10−23 JK−1 so as to
measure V(r) in units of K.