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Indian Institute of Technology Gandhinagar: PH 509: Computational Physics

The document describes modeling disease dynamics using the SIR model of epidemiology. It presents: 1) The SIR differential equations and shows two equations are sufficient by normalizing populations. 2) Numerical solutions using odeint and Runge-Kutta methods for S(t), I(t), R(t) with λ < μ and λ > μ. 3) A plot of asymptotic recovered population R(∞) versus infection rate λ/recovery rate μ, showing it levels off at higher λ/μ ratios.

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Jitendra Gurjar
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Download as PDF, TXT or read online on Scribd
34 views

Indian Institute of Technology Gandhinagar: PH 509: Computational Physics

The document describes modeling disease dynamics using the SIR model of epidemiology. It presents: 1) The SIR differential equations and shows two equations are sufficient by normalizing populations. 2) Numerical solutions using odeint and Runge-Kutta methods for S(t), I(t), R(t) with λ < μ and λ > μ. 3) A plot of asymptotic recovered population R(∞) versus infection rate λ/recovery rate μ, showing it levels off at higher λ/μ ratios.

Uploaded by

Jitendra Gurjar
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Indian Institute of Technology Gandhinagar

PH 509: Computational Physics

Assignment - 3

Due date: 31st Aug

Name: Akash Arya,Uday sigh,Jitendra Gurjar Roll number: 16510006,16510092,16510034

1 Problem
DISEASE DYNAMICS(SIR Model)

A famous for disease model is the SIR model.Here population is divided into Susceptible,Infected
and Recovered(S,I,R) groups with total population S+I+R=N,constant.Infection spreads when
susceptible and infected are in contact,at a rate .Infected people recover at a rate .The equations
governing these are

dS
= S I
dt

dI
=SI I
dt

dS
=I
dt

(a) Show that only two equations (say S,I) are sufficient to describe the dyanamics,when normalized
S
by N.Write equations for s = N and i = NI ,what is r ?

(b)With initial conditions s(0)=0.99,i(0)=0.01,solve the system using RK4 and odeint for the fol-
lowing conditions (plot s(t),i(t),r(t) v/s t) (i) < say = 0.8, = 1.0 (ii) > say = 1.2, = 1.0


(c)Set = 1,vary = 0.1 10 in steps of o.1.Plot r() v/s

1.1 ODEint Method


1.2 Program
import s c i p y . i n t e g r a t e a s s p i
import numpy a s np
import p ylab a s p l

Lambda=1.2
mu=1.0
TS=1.0
ND=70.0
s 0 =0.99
i 0 =0.01
INPUT = ( s0 , i 0 , 0 . 0 )

def d i f f e q s ( INP , t ) :

1
The main s e t o f e q u a t i o n s
( dS dt , d I d t , dR dt)=np . z e r o s ( ( 3 ) )
V = INP
dS dt = Lambda V [ 0 ] V [ 1 ]
d I d t = Lambda V [ 0 ] V [ 1 ] mu V [ 1 ]
dR dt = muV [ 1 ]
return ( dS dt , d I d t , dR dt ) # For o d e i n t

t s t a r t = 0 . 0 ; t e n d = ND; t i n c = TS
t s t e p = np . a r a n g e ( t s t a r t , t e n d+t i n c , t i n c )
RES = s p i . o d e i n t ( d i f f e q s , INPUT, t s t e p )

print RES

p l . p l o t (RES [ : , 0 ] , -g , l a b e l=s(t) )
p l . p l o t (RES [ : , 2 ] , -k , l a b e l=r(t) )
p l . p l o t (RES [ : , 1 ] , -b , l a b e l=i(t) )
p l . l e g e n d ( l o c =0)
p l . t i t l e ( Disease Dynamics . py )
p l . x l a b e l ( Time )
p l . y l a b e l ( s(t),r(t) and i(t) )
p l . yli m ( [ 0 . 0 , 1 . 0 ] )
pl . grid ()
p l . show ( )

1.3 Results
for = 0.8, = 1.0

2
for = 1.2, = 1.0

2 Runge Kutta Method


2.1 Program
import s c i p y a s sp
import numpy a s np
import p ylab a s p l

Lambda=0.8
mu=1.0
s 0 =0.99
i 0 =0.01
r 0 =0.0
h =0.001
P= [ ]
Q= [ ]
R= [ ]
time=np . a r a n g e ( 0 , 1 0 0 , h )

def f 1 ( S , I , R, t ) :
return LambdaS I
def f 2 ( S , I , R, t ) :
return LambdaS Imu I
def f 3 ( S , I , R, t ) :
return mu I

f o r t in time :
k0=h f 1 ( t , s0 , i 0 , r 0 )
l 0=h f 2 ( t , s0 , i 0 , r 0 )
m0=h f 3 ( t , s0 , i 0 , r 0 )
k1=h f 1 ( ( t+h / 2 . 0 ) , ( s 0+k0 / 2 . 0 ) , ( i 0+l 0 / 2 . 0 ) , ( r 0+m0 / 2 . 0 ) )
l 1=h f 2 ( ( t+h / 2 . 0 ) , ( s 0+k0 / 2 . 0 ) , ( i 0+l 0 / 2 . 0 ) , ( r 0+m0 / 2 . 0 ) )
m1=h f 3 ( ( t+h / 2 . 0 ) , ( s 0+k0 / 2 . 0 ) , ( i 0+l 0 / 2 . 0 ) , ( r 0+m0 / 2 . 0 ) )
k2=h f 1 ( ( t+h / 2 . 0 ) , ( s 0+k1 / 2 . 0 ) , ( i 0+l 1 / 2 . 0 ) , ( r 0+m1 / 2 . 0 ) )
l 2=h f 2 ( ( t+h / 2 . 0 ) , ( s 0+k1 / 2 . 0 ) , ( i 0+l 1 / 2 . 0 ) , ( r 0+m1 / 2 . 0 ) )
m2=h f 3 ( ( t+h / 2 . 0 ) , ( s 0+k1 / 2 . 0 ) , ( i 0+l 1 / 2 . 0 ) , ( r 0+m1 / 2 . 0 ) )
k3=h f 1 ( ( t+h ) , ( s 0+k2 ) , ( i 0+l 2 ) , ( r 0+m2) )
l 3=h f 2 ( ( t+h ) , ( s 0+k2 ) , ( i 0+l 2 ) , ( r 0+m2) )
m3=h f 3 ( ( t+h ) , ( s 0+k2 ) , ( i 0+l 2 ) , ( r 0+m2) )
s 0=s 0 +(h / 6 . 0 ) ( k0 + ( 2 . 0 k1 ) + ( 2 . 0 k2 ) + k3 )

3
i 0=i 0 +(h / 6 . 0 ) ( l 0 + ( 2 . 0 l 1 ) + ( 2 . 0 l 2 ) + l 3 )
r 0=r 0 +(h / 6 . 0 ) ( m0 + ( 2 . 0 m1) + ( 2 . 0 m2) + m3)

P . append ( s 0 )
Q. append ( i 0 )
R. append ( r 0 )

pl . subplot (2 ,2 ,1)
p l . p l o t ( time , P , l a b e l=s0 )
pl . grid ()
pl . subplot (2 ,2 ,2)
p l . p l o t ( time , Q, l a b e l=i0 )
pl . grid ()
pl . subplot (2 ,2 ,3)
p l . p l o t ( time , R, l a b e l=r0 )
pl . grid ()
p l . show ( )

2.2 Results
for = 0.8, = 1.0

4
for = 1.2, = 1.0

(C) when we increases the value of time and we plot r with respect to different values of / this will
be constant at higher values.

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