ans =
Main Content
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Hello :-) I am interested in reading the book "The finite element method for solid and structural mechanics" online with somebody who is also interested in studying the finite element method particularly its mathematical aspect. I enjoy discussing the book instead of reading it alone. Please if you were interested email me at: student.z.k@hotmail.com Thank you!
An attractor is called strange if it has a fractal structure, that is if it has non-integer Hausdorff dimension. This is often the case when the dynamics on it are chaotic, but strange nonchaotic attractors also exist. If a strange attractor is chaotic, exhibiting sensitive dependence on initial conditions, then any two arbitrarily close alternative initial points on the attractor, after any of various numbers of iterations, will lead to points that are arbitrarily far apart (subject to the confines of the attractor), and after any of various other numbers of iterations will lead to points that are arbitrarily close together. Thus a dynamic system with a chaotic attractor is locally unstable yet globally stable: once some sequences have entered the attractor, nearby points diverge from one another but never depart from the attractor.
The term strange attractor was coined by David Ruelle and Floris Takens to describe the attractor resulting from a series of bifurcations of a system describing fluid flow. Strange attractors are often differentiable in a few directions, but some are like a Cantor dust, and therefore not differentiable. Strange attractors may also be found in the presence of noise, where they may be shown to support invariant random probability measures of Sinai–Ruelle–Bowen type.
Lorenz
% Lorenz Attractor Parameters
sigma = 10;
beta = 8/3;
rho = 28;
% Lorenz system of differential equations
f = @(t, a) [-sigma*a(1) + sigma*a(2);
rho*a(1) - a(2) - a(1)*a(3);
-beta*a(3) + a(1)*a(2)];
% Time span
tspan = [0 100];
% Initial conditions
a0 = [1 1 1];
% Solve the system using ode45
[t, a] = ode45(f, tspan, a0);
% Plot using scatter3 with time-based color mapping
figure;
scatter3(a(:,1), a(:,2), a(:,3), 5, t, 'filled'); % 5 is the marker size
title('Lorenz Attractor');
xlabel('x(t)');
ylabel('y(t)');
zlabel('z(t)');
grid on;
colorbar; % Add a colorbar to indicate the time mapping
view(3); % Set the view to 3D
Sprott
% Define the parameters
a = 2.07;
b = 1.79;
% Define the system of differential equations
dynamics = @(t, X) [ ...
X(2) + a * X(1) * X(2) + X(1) * X(3); % dx/dt
1 - b * X(1)^2 + X(2) * X(3); % dy/dt
X(1) - X(1)^2 - X(2)^2 % dz/dt
];
% Initial conditions
X0 = [0.63; 0.47; -0.54];
% Time span
tspan = [0 100];
% Solve the system using ode45
[t, X] = ode45(dynamics, tspan, X0);
% Plot the results with color gradient
figure;
colormap(jet); % Set the colormap
c = linspace(1, 10, length(t)); % Color data based on time
% Create a 3D line plot with color based on time
for i = 1:length(t)-1
plot3(X(i:i+1,1), X(i:i+1,2), X(i:i+1,3), 'Color', [0 0.5 0.9]*c(i)/10, 'LineWidth', 1.5);
hold on;
end
% Set plot properties
title('Sprott Attractor');
xlabel('x(t)');
ylabel('y(t)');
zlabel('z(t)');
grid on;
colorbar; % Add a colorbar to indicate the time mapping
view(3); % Set the view to 3D
hold off;
Rössler
% Define the parameters
a = 0.2;
b = 0.2;
c = 5.7;
% Define the system of differential equations
dynamics = @(t, X) [ ...
-(X(2) + X(3)); % dx/dt
X(1) + a * X(2); % dy/dt
b + X(3) * (X(1) - c) % dz/dt
];
% Initial conditions
X0 = [10.0; 0.00; 10.0];
% Time span
tspan = [0 100];
% Solve the system using ode45
[t, X] = ode45(dynamics, tspan, X0);
% Plot the results
figure;
scatter3(X(:,1), X(:,2), X(:,3), 5, t, 'filled');
title('Rössler Attractor');
xlabel('x(t)');
ylabel('y(t)');
zlabel('z(t)');
grid on;
colorbar; % Add a colorbar to indicate the time mapping
view(3); % Set the view to 3D
Rabinovich-Fabrikant
%% Parameters for Rabinovich-Fabrikant Attractor
alpha = 0.14;
gamma = 0.10;
dt = 0.01;
num_steps = 5000;
% Initial conditions
x0 = -1;
y0 = 0;
z0 = 0.5;
% Preallocate arrays for performance
x = zeros(1, num_steps);
y = zeros(1, num_steps);
z = zeros(1, num_steps);
% Set initial values
x(1) = x0;
y(1) = y0;
z(1) = z0;
% Generate the attractor
for i = 1:num_steps-1
x(i+1) = x(i) + dt * (y(i)*(z(i) - 1 + x(i)^2) + gamma*x(i));
y(i+1) = y(i) + dt * (x(i)*(3*z(i) + 1 - x(i)^2) + gamma*y(i));
z(i+1) = z(i) + dt * (-2*z(i)*(alpha + x(i)*y(i)));
end
% Create a time vector for color mapping
t = linspace(0, 100, num_steps);
% Plot using scatter3
figure;
scatter3(x, y, z, 5, t, 'filled'); % 5 is the marker size
title('Rabinovich-Fabrikant Attractor');
xlabel('x(t)');
ylabel('y(t)');
zlabel('z(t)');
grid on;
colorbar; % Add a colorbar to indicate the time mapping
view(3); % Set the view to 3D
References
A library of runnable PDEs. See the equations! Modify the parameters! Visualize the resulting system in your browser! Convenient, fast, and instructive.
This project discusses predator-prey system, particularly the Lotka-Volterra equations,which model the interaction between two sprecies: prey and predators. Let's solve the Lotka-Volterra equations numerically and visualize the results.% Define parameters
% Define parameters
alpha = 1.0; % Prey birth rate
beta = 0.1; % Predator success rate
gamma = 1.5; % Predator death rate
delta = 0.075; % Predator reproduction rate
% Define the symbolic variables
syms R W
% Define the equations
eq1 = alpha * R - beta * R * W == 0;
eq2 = delta * R * W - gamma * W == 0;
% Solve the equations
equilibriumPoints = solve([eq1, eq2], [R, W]);
% Extract the equilibrium point values
Req = double(equilibriumPoints.R);
Weq = double(equilibriumPoints.W);
% Display the equilibrium points
equilibriumPointsValues = [Req, Weq]
% Solve the differential equations using ode45
lotkaVolterra = @(t,Y)[alpha*Y(1)-beta*Y(1)*Y(2);
delta*Y(1)*Y(2)-gamma*Y(2)];
% Initial conditions
R0 = 40;
W0 = 9;
Y0 = [R0, W0];
tspan = [0, 100];
% Solve the differential equations
[t, Y] = ode45(lotkaVolterra, tspan, Y0);
% Extract the populations
R = Y(:, 1);
W = Y(:, 2);
% Plot the results
figure;
subplot(2,1,1);
plot(t, R, 'r', 'LineWidth', 1.5);
hold on;
plot(t, W, 'b', 'LineWidth', 1.5);
xlabel('Time (months)');
ylabel('Population');
legend('R', 'W');
grid on;
subplot(2,1,2);
plot(R, W, 'k', 'LineWidth', 1.5);
xlabel('R');
ylabel('W');
grid on;
hold on;
plot(Req, Weq, 'ro', 'MarkerSize', 8, 'MarkerFaceColor', 'r');
legend('Phase Trajectory', 'Equilibrium Point');
Now, we need to handle a modified version of the Lotka-Volterra equations. These modified equations incorporate logistic growth fot the prey population.
These equations are:
% Define parameters
alpha = 1.0;
K = 100; % Carrying Capacity of the prey population
beta = 0.1;
gamma = 1.5;
delta = 0.075;
% Define the symbolic variables
syms R W
% Define the equations
eq1 = alpha*R*(1 - R/K) - beta*R*W == 0;
eq2 = delta*R*W - gamma*W == 0;
% Solve the equations
equilibriumPoints = solve([eq1, eq2], [R, W]);
% Extract the equilibrium point values
Req = double(equilibriumPoints.R);
Weq = double(equilibriumPoints.W);
% Display the equilibrium points
equilibriumPointsValues = [Req, Weq]
% Solve the differential equations using ode45
modified_lv = @(t,Y)[alpha*Y(1)*(1-Y(1)/K)-beta*Y(1)*Y(2);
delta*Y(1)*Y(2)-gamma*Y(2)];
% Initial conditions
R0 = 40;
W0 = 9;
Y0 = [R0, W0];
tspan = [0, 100];
% Solve the differential equations
[t, Y] = ode45(modified_lv, tspan, Y0);
% Extract the populations
R = Y(:, 1);
W = Y(:, 2);
% Plot the results
figure;
subplot(2,1,1);
plot(t, R, 'r', 'LineWidth', 1.5);
hold on;
plot(t, W, 'b', 'LineWidth', 1.5);
xlabel('Time (months)');
ylabel('Population');
legend('R', 'W');
grid on;
subplot(2,1,2);
plot(R, W, 'k', 'LineWidth', 1.5);
xlabel('R');
ylabel('W');
grid on;
hold on;
plot(Req, Weq, 'ro', 'MarkerSize', 8, 'MarkerFaceColor', 'r');
legend('Phase Trajectory', 'Equilibrium Point');
Does your company or organization require that all your Word Documents and Excel workbooks be labeled with a Microsoft Azure Information Protection label or else they can't be saved? These are the labels that are right below the tool ribbon that apply a category label such as "Public", "Business Use", or "Highly Restricted". If so, you can either
- Create and save a "template file" with the desired label and then call copyfile to make a copy of that file and then write your results to the new copy, or
- If using Windows you can create and/or open the file using ActiveX and then apply the desired label from your MATLAB program's code.
For #1 you can do
copyfile(templateFileName, newDataFileName);
writematrix(myData, newDataFileName);
If the template has the AIP label applied to it, then the copy will also inherit the same label.
For #2, here is a demo for how to apply the code using ActiveX.
% Test to set the Microsoft Azure Information Protection label on an Excel workbook.
% Reference support article:
% https://www.mathworks.com/matlabcentral/answers/1901140-why-does-azure-information-protection-popup-pause-the-matlab-script-when-i-use-actxserver?s_tid=ta_ans_results
clc; % Clear the command window.
close all; % Close all figures (except those of imtool.)
clear; % Erase all existing variables. Or clearvars if you want.
workspace; % Make sure the workspace panel is showing.
format compact;
% Define your workbook file name.
excelFullFileName = fullfile(pwd, '\testAIP.xlsx');
% Make sure it exists. Open Excel as an ActiveX server if it does.
if isfile(excelFullFileName)
% If the workbook exists, launch Excel as an ActiveX server.
Excel = actxserver('Excel.Application');
Excel.visible = true; % Make the server visible.
fprintf('Excel opened successfully.\n');
fprintf('Your workbook file exists:\n"%s".\nAbout to try to open it.\n', excelFullFileName);
% Open up the existing workbook named in the variable fullFileName.
Excel.Workbooks.Open(excelFullFileName);
fprintf('Excel opened file successfully.\n');
else
% File does not exist. Alert the user.
warningMessage = sprintf('File does not exist:\n\n"%s"\n', excelFullFileName);
fprintf('%s\n', warningMessage);
errordlg(warningMessage);
return;
end
% If we get here, the workbook file exists and has been opened by Excel.
% Ask Excel for the Microsoft Azure Information Protection (AIP) label of the workbook we just opened.
label = Excel.ActiveWorkbook.SensitivityLabel.GetLabel
% See if there is a label already. If not, these will be null:
existingLabelID = label.LabelId
existingLabelName = label.LabelName
% Create a label.
label = Excel.ActiveWorkbook.SensitivityLabel.CreateLabelInfo
label.LabelId = "a518e53f-798e-43aa-978d-c3fda1f3a682";
label.LabelName = "Business Use";
% Assign the label to the workbook.
fprintf('Setting Microsoft Azure Information Protection to "Business Use", GUID of a518e53f-798e-43aa-978d-c3fda1f3a682\n');
Excel.ActiveWorkbook.SensitivityLabel.SetLabel(label, label);
% Save this workbook with the new AIP setting we just created.
Excel.ActiveWorkbook.Save;
% Shut down Excel.
Excel.ActiveWorkbook.Close;
Excel.Quit;
% Excel is now closed down. Delete the variable from the MATLAB workspace.
clear Excel;
% Now check to see if the AIP label has been set
% by opening up the file in Excel and looking at the AIP banner.
winopen(excelFullFileName)
Note that there is a line in there that gets an AIP label from the existing workbook, if there is one at all. If there is not one, you can set one. But to determine what the proper LabelId (that crazy long hexadecimal number) should be, you will probably need to open an existing document that already has the label that you want set (applied to it) and then read that label with this line:
label = Excel.ActiveWorkbook.SensitivityLabel.GetLabel
This stems purely from some play on my part. Suppose I asked you to work with the sequence formed as 2*n*F_n + 1, where F_n is the n'th Fibonacci number? Part of me would not be surprised to find there is nothing simple we could do. But, then it costs nothing to try, to see where MATLAB can take me in an explorative sense.
n = sym(0:100).';
Fn = fibonacci(n);
Sn = 2*n.*Fn + 1;
Sn(1:10) % A few elements
For kicks, I tried asking ChatGPT. Giving it nothing more than the first 20 members of thse sequence as integers, it decided this is a Perrin sequence, and gave me a recurrence relation, but one that is in fact incorrect. Good effort from the Ai, but a fail in the end.
Is there anything I can do? Try null! (Look carefully at the array generated by Toeplitz. It is at least a pretty way to generate the matrix I needed.)
X = toeplitz(Sn,[1,zeros(1,4)]);
rank(X(5:end,:))
Hmm. So there is no linear combination of those columns that yields all zeros, since the resulting matrix was full rank.
X = toeplitz(Sn,[1,zeros(1,5)]);
rank(X(6:end,:))
But if I take it one step further, we see the above matrix is now rank deficient. What does that tell me? It says there is some simple linear combination of the columns of X(6:end,:) that always yields zero. The previous test tells me there is no shorter constant coefficient recurrence releation, using fewer terms.
null(X(6:end,:))
Let me explain what those coefficients tell me. In fact, they yield a very nice recurrence relation for the sequence S_n, not unlike the original Fibonacci sequence it was based upon.
S(n+1) = 3*S(n) - S_(n-1) - 3*S(n-2) + S(n-3) + S(n-4)
where the first 5 members of that sequence are given as [1 3 5 13 25]. So a 6 term linear constant coefficient recurrence relation. If it reminds you of the generating relation for the Fibonacci sequence, that is good, because it should. (Remember I started the sequence at n==0, IF you decide to test it out.) We can test it out, like this:
SfunM = memoize(@(N) Sfun(N));
SfunM(25)
2*25*fibonacci(sym(25)) + 1
And indeed, it works as expected.
function Sn = Sfun(n)
switch n
case 0
Sn = 1;
case 1
Sn = 3;
case 2
Sn = 5;
case 3
Sn = 13;
case 4
Sn = 25;
otherwise
Sn = Sfun(n-5) + Sfun(n-4) - 3*Sfun(n-3) - Sfun(n-2) +3*Sfun(n-1);
end
end
A beauty of this, is I started from nothing but a sequence of integers, derived from an expression where I had no rational expectation of finding a formula, and out drops something pretty. I might call this explorational mathematics.
The next step of course is to go in the other direction. That is, given the derived recurrence relation, if I substitute the formula for S_n in terms of the Fibonacci numbers, can I prove it is valid in general? (Yes.) After all, without some proof, it may fail for n larger than 100. (I'm not sure how much I can cram into a single discussion, so I'll stop at this point for now. If I see interest in the ideas here, I can proceed further. For example, what was I doing with that sequence in the first place? And of course, can I prove the relation is valid? Can I do so using MATLAB?)
(I'll be honest, starting from scratch, I'm not sure it would have been obvious to find that relation, so null was hugely useful here.)
hello i found the following tools helpful to write matlab programs. copilot.microsoft.com chatgpt.com/gpts gemini.google.com and ai.meta.com. thanks a lot and best wishes.
Hi everyone,
I've recently joined a forest protection team in Greece, where we use drones for various tasks. This has sparked my interest in drone programming, and I'd like to learn more about it. Can anyone recommend any beginner-friendly courses or programs that teach drone programming?
I'm particularly interested in courses that focus on practical applications and might align with the work we do in forest protection. Any suggestions or guidance would be greatly appreciated!
Thank you!
I have picked the title but don't know which direction to take it. Looking for any and all inspiration. I took the project as it sounded interesting when reading into it, but I'm a satellite novice, and my degree is in electronics.
"What are your favorite features or functionalities in MATLAB, and how have they positively impacted your projects or research? Any tips or tricks to share?
Check out the LLMs with MATLAB project on File Exchange to access Large Language Models from MATLAB.
Along with the latest support for GPT-4o mini, you can use LLMs with MATLAB to generate images, categorize data, and provide semantic analyis.
Gabriel's horn is a shape with the paradoxical property that it has infinite surface area, but a finite volume.
Gabriel’s horn is formed by taking the graph of 
with the domain 
and rotating it in three dimensions about the 
axis.
with the domain and rotating it in three dimensions about the axis.There is a standard formula for calculating the volume of this shape, for a general function 
.Wwe will just state that the volume of the 
solid between a and b is:
.Wwe will just state that the volume of the solid between a and b is:
The surface area of the solid is given by:
One other thing we need to consider is that we are trying to find the value of these integrals between 1 and ∞. An integral with a limit of infinity is called an improper integral and we can't evaluate it simply by plugging the value infinity into the normal equation for a definite integral. Instead, we must first calculate the definite integral up to some finite limit b and then calculate the limit of the result as b tends to ∞:
Volume
We can calculate the horn's volume using the volume integral above, so
The total volume of this infinitely long trumpet isπ.
Surface Area
To determine the surface area, we first need the function’s derivative:
Now plug it into the surface area formula and we have:
This is an improper integral and it's hard to evaluate, but since in our interval 
So, we have :
Now,we evaluate this last integral
So the surface are is infinite.
% Define the function for Gabriel's Horn
gabriels_horn = @(x) 1 ./ x;
% Create a range of x values
x = linspace(1, 40, 4000); % Increase the number of points for better accuracy
y = gabriels_horn(x);
% Create the meshgrid
theta = linspace(0, 2 * pi, 6000); % Increase theta points for a smoother surface
[X, T] = meshgrid(x, theta);
Y = gabriels_horn(X) .* cos(T);
Z = gabriels_horn(X) .* sin(T);
% Plot the surface of Gabriel's Horn
figure('Position', [200, 100, 1200, 900]);
surf(X, Y, Z, 'EdgeColor', 'none', 'FaceAlpha', 0.9);
hold on;
% Plot the central axis
plot3(x, zeros(size(x)), zeros(size(x)), 'r', 'LineWidth', 2);
% Set labels
xlabel('x');
ylabel('y');
zlabel('z');
% Adjust colormap and axis properties
colormap('gray');
shading interp; % Smooth shading
% Adjust the view
view(3);
axis tight;
grid on;
% Add formulas as text annotations
dim1 = [0.4 0.7 0.3 0.2];
annotation('textbox',dim1,'String',{'$$V = \pi \int_{1}^{a} \left( \frac{1}{x} \right)^2 dx = \pi \left( 1 - \frac{1}{a} \right)$$', ...
'', ... % Add an empty line for larger gap
'$$\lim_{a \to \infty} V = \lim_{a \to \infty} \pi \left( 1 - \frac{1}{a} \right) = \pi$$'}, ...
'Interpreter','latex','FontSize',12, 'EdgeColor','none', 'FitBoxToText', 'on');
dim2 = [0.4 0.5 0.3 0.2];
annotation('textbox',dim2,'String',{'$$A = 2\pi \int_{1}^{a} \frac{1}{x} \sqrt{1 + \left( -\frac{1}{x^2} \right)^2} dx > 2\pi \int_{1}^{a} \frac{dx}{x} = 2\pi \ln(a)$$', ...
'', ... % Add an empty line for larger gap
'$$\lim_{a \to \infty} A \geq \lim_{a \to \infty} 2\pi \ln(a) = \infty$$'}, ...
'Interpreter','latex','FontSize',12, 'EdgeColor','none', 'FitBoxToText', 'on');
% Add Gabriel's Horn label
dim3 = [0.3 0.9 0.3 0.1];
annotation('textbox',dim3,'String','Gabriel''s Horn', ...
'Interpreter','latex','FontSize',14, 'EdgeColor','none', 'HorizontalAlignment', 'center');
hold off
daspect([3.5 1 1]) % daspect([x y z])
view(-27, 15)
lightangle(-50,0)
lighting('gouraud')
The properties of this figure were first studied by Italian physicist and mathematician Evangelista Torricelli in the 17th century.
Acknowledgment
I would like to express my sincere gratitude to all those who have supported and inspired me throughout this project.
First and foremost, I would like to thank the mathematician and my esteemed colleague, Stavros Tsalapatis, for inspiring me with the fascinating subject of Gabriel's Horn.
I am also deeply thankful to Mr. @Star Strider for his invaluable assistance in completing the final code.
References:
When it comes to MOS tube burnout, it is usually because it is not working in the SOA workspace, and there is also a case where the MOS tube is overcurrent.
For example, the maximum allowable current of the PMOS transistor in this circuit is 50A, and the maximum current reaches 80+ at the moment when the MOS transistor is turned on, then the current is very large.
At this time, the PMOS is over-specified, and we can see on the SOA curve that it is not working in the SOA range, which will cause the PMOS to be damaged.
So what if you choose a higher current PMOS? Of course you can, but the cost will be higher.
We can choose to adjust the peripheral resistance or capacitor to make the PMOS turn on more slowly, so that the current can be lowered.
For example, when adjusting R1, R2, and the jumper capacitance between gs, when Cgs is adjusted to 1uF, The Ids are only 40A max, which is fine in terms of current, and meets the 80% derating.
(50 amps * 0.8 = 40 amps).
Next, let’s look at the power, from the SOA curve, the opening time of the MOS tube is about 1ms, and the maximum power at this time is 280W.
The normal thermal resistance of the chip is 50°C/W, and the maximum junction temperature can be 302°F.
Assuming the ambient temperature is 77°F, then the instantaneous power that 1ms can withstand is about 357W.
The actual power of PMOS here is 280W, which does not exceed the limit, which means that it works normally in the SOA area.
Therefore, when the current impact of the MOS transistor is large at the moment of turning, the Cgs capacitance can be adjusted appropriately to make the PMOS Working in the SOA area, you can avoid the problem of MOS corruption.
Hello everyone, i hope you all are in good health. i need to ask you about the help about where i should start to get indulge in matlab. I am an electrical engineer but having experience of construction field. I am new here. Please do help me. I shall be waiting forward to hear from you. I shall be grateful to you. Need recommendations and suggestions from experienced members. Thank you.
I recently wrote up a document which addresses the solution of ordinary and partial differential equations in Matlab (with some Python examples thrown in for those who are interested). For ODEs, both initial and boundary value problems are addressed. For PDEs, it addresses parabolic and elliptic equations. The emphasis is on finite difference approaches and built-in functions are discussed when available. Theory is kept to a minimum. I also provide a discussion of strategies for checking the results, because I think many students are too quick to trust their solutions. For anyone interested, the document can be found at https://blanchard.neep.wisc.edu/SolvingDifferentialEquationsWithMatlab.pdf
Kindly link me to the Channel Modeling Group.
I read and compreheneded a paper on channel modeling "An Adaptive Geometry-Based Stochastic Model for Non-Isotropic MIMO Mobile-to-Mobile Channels" except the graphical results obtained from the MATLAB codes. I have tried to replicate the same graphs but to no avail from my codes. And I am really interested in the topic, i have even written to the authors of the paper but as usual, there is no reply from them. Kindly assist if possible.
Hi, I'm looking for sites where I can find coding & algorithms problems and their solutions. I'm doing this workshop in college and I'll need some problems to go over with the students and explain how Matlab works by solving the problems with them and then reviewing and going over different solution options. Does anyone know a website like that? I've tried looking in the Matlab Cody By Mathworks, but didn't exactly find what I'm looking for. Thanks in advance.
What do you think about the NVIDIA's achivement of becoming the top giant of manufacturing chips, especially for AI world?
We are modeling the introduction of a novel pathogen into a completely susceptible population. In the cells below, I have provided you with the Matlab code for a simple stochastic SIR model, implemented using the "GillespieSSA" function
Simulating the stochastic model 100 times for 
Since γ is 0.4 per day, 
per day
per day% Define the parameters
beta = 0.36;
gamma = 0.4;
n_sims = 100;
tf = 100; % Time frame changed to 100
% Calculate R0
R0 = beta / gamma
% Initial state values
initial_state_values = [1000000; 1; 0; 0]; % S, I, R, cum_inc
% Define the propensities and state change matrix
a = @(state) [beta * state(1) * state(2) / 1000000, gamma * state(2)];
nu = [-1, 0; 1, -1; 0, 1; 0, 0];
% Define the Gillespie algorithm function
function [t_values, state_values] = gillespie_ssa(initial_state, a, nu, tf)
t = 0;
state = initial_state(:); % Ensure state is a column vector
t_values = t;
state_values = state';
while t < tf
rates = a(state);
rate_sum = sum(rates);
if rate_sum == 0
break;
end
tau = -log(rand) / rate_sum;
t = t + tau;
r = rand * rate_sum;
cum_sum_rates = cumsum(rates);
reaction_index = find(cum_sum_rates >= r, 1);
state = state + nu(:, reaction_index);
% Update cumulative incidence if infection occurred
if reaction_index == 1
state(4) = state(4) + 1; % Increment cumulative incidence
end
t_values = [t_values; t];
state_values = [state_values; state'];
end
end
% Function to simulate the stochastic model multiple times and plot results
function simulate_stoch_model(beta, gamma, n_sims, tf, initial_state_values, R0, plot_type)
% Define the propensities and state change matrix
a = @(state) [beta * state(1) * state(2) / 1000000, gamma * state(2)];
nu = [-1, 0; 1, -1; 0, 1; 0, 0];
% Set random seed for reproducibility
rng(11);
% Initialize plot
figure;
hold on;
for i = 1:n_sims
[t, output] = gillespie_ssa(initial_state_values, a, nu, tf);
% Check if the simulation had only one step and re-run if necessary
while length(t) == 1
[t, output] = gillespie_ssa(initial_state_values, a, nu, tf);
end
if strcmp(plot_type, 'cumulative_incidence')
plot(t, output(:, 4), 'LineWidth', 2, 'Color', rand(1, 3));
elseif strcmp(plot_type, 'prevalence')
plot(t, output(:, 2), 'LineWidth', 2, 'Color', rand(1, 3));
end
end
xlabel('Time (days)');
if strcmp(plot_type, 'cumulative_incidence')
ylabel('Cumulative Incidence');
ylim([0 inf]);
elseif strcmp(plot_type, 'prevalence')
ylabel('Prevalence of Infection');
ylim([0 50]);
end
title(['Stochastic model output for R0 = ', num2str(R0)]);
subtitle([num2str(n_sims), ' simulations']);
xlim([0 tf]);
grid on;
hold off;
end
% Simulate the model 100 times and plot cumulative incidence
simulate_stoch_model(beta, gamma, n_sims, tf, initial_state_values, R0, 'cumulative_incidence');
% Simulate the model 100 times and plot prevalence
simulate_stoch_model(beta, gamma, n_sims, tf, initial_state_values, R0, 'prevalence');
Base case:
Suppose you need to do a computation many times. We are going to assume that this computation cannot be vectorized. The simplest case is to use a for loop:
number_of_elements = 1e6;
test_fcn = @(x) sqrt(x) / x;
tic
for i = 1:number_of_elements
x(i) = test_fcn(i);
end
t_forward = toc;
disp(t_forward + " seconds")
Preallocation:
This can easily be sped up by preallocating the variable that houses results:
tic
x = zeros(number_of_elements, 1);
for i = 1:number_of_elements
x(i) = test_fcn(i);
end
t_forward_prealloc = toc;
disp(t_forward_prealloc + " seconds")
In this example, preallocation speeds up the loop by a factor of about three to four (running in R2024a). Comment below if you get dramatically different results.
disp(sprintf("%.1f", t_forward / t_forward_prealloc))
Run it in reverse:
Is there a way to skip the explicit preallocation and still be fast? Indeed, there is.
clear x
tic
for i = number_of_elements:-1:1
x(i) = test_fcn(i);
end
t_backward = toc;
disp(t_backward + " seconds")
By running the loop backwards, the preallocation is implicitly performed during the first iteration and the loop runs in about the same time (within statistical noise):
disp(sprintf("%.2f", t_forward_prealloc / t_backward))
Do you get similar results when running this code? Let us know your thoughts in the comments below.
Beneficial side effect:
Have you ever had to use a for loop to delete elements from a vector? If so, keeping track of index offsets can be tricky, as deleting any element shifts all those that come after. By running the for loop in reverse, you don't need to worry about index offsets while deleting elements.
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