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haugboelhaugboel
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ADD 2025 SIR exercise files
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‎module1/Makefile

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CXX := g++
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OPT=-O1 -Wall
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CXXFLAGS := $(OPT) -Wall -Wno-unused-const-variable -std=c++17 -march=native
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default: SIR # SIR_python
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#INC := $(shell python3 -m pybind11 --includes) $(shell python3-config --ldflags)
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SIR: SIR.cpp
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$(CXX) SIR.cpp -o SIR $(CXXFLAGS)
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#SIR_python: SIR_python.cpp
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# $(CXX) SIR_python.cpp -o SIR_python$(shell python3-config --extension-suffix) -fPIC -shared $(CXXFLAGS) $(INC)
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clean:
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rm -f SIR SIR_python
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# rm -f SIR_python$(shell python3-config --extension-suffix)

‎module1/SIR.cpp

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#include <iostream>
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#include <fstream>
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#include <vector>
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// Function to take a step in the SIR model
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// state: vector of S, I, R
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// beta: infection rate
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// gamma: recovery rate
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// dt: time step
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std::vector<float> take_step(std::vector<float> state, float beta, float gamma, float dt){
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//todo: implement the SIR model
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return new_state;
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}
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//======================================================================================================
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//======================== Main function ===============================================================
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//======================================================================================================
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int main(int argc, char* argv[]){
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// define the parameters
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// TODO: Define the parameters of the SIR model
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// TODO: implement the SIR model
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// TODO: Save the results to a file
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}

‎module1/SIR_python.cpp

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#include <iostream>
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#include <fstream>
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#include <vector>
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#include <pybind11/stl.h>
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#include <pybind11/pybind11.h>
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#include <pybind11/numpy.h>
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// Function to take a step in the SIR model
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// state: vector of S, I, R
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// beta: infection rate
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// gamma: recovery rate
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// dt: time step
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std::vector<float> take_step(std::vector<float> state, float beta, float gamma, float dt){
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//todo: implement the SIR model
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return new_state;
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}
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// Function simulating num_steps of the SIR model, saving the state every return_every steps and returning the results
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// S0: initial number of susceptible individuals
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// I0: initial number of infected individuals
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// R0: initial number of recovered individuals
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// beta: infection rate
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// gamma: recovery rate
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// dt: time step
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// num_steps: number of steps to simulate
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// return_every: save the state every return_every steps
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pybind11::array integrate_system(float S0, float I0, float R0, float beta, float gamma, float dt, int num_steps, int return_every){
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std::vector<std::vector<float>> results;
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// TODO: implement the SIR model
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return pybind11::cast(results);
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}
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PYBIND11_MODULE(SIR_python, m) {
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m.doc() = "This is a Python binding for the SIR model";
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m.def("integrate_system", &integrate_system);
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}

‎module1/Unknown_SIR_data.csv

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,S,I,R
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0.0,1006.3962321148992,1.0070910683435152,7.674741286043622e-05
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2.0408163265306123,1014.5530989172524,1.4228372519638564,0.17801879976726537
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4.081632653061225,1000.7690545258415,2.0649559812501175,0.4357831476990105
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6.122448979591837,996.1175035857603,2.826917534720307,0.8026813201190486
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8.16326530612245,1011.9294971598068,4.0801534860520015,1.3148981972730154
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10.204081632653061,974.391662965824,5.692035241042004,2.0098514363818563
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12.244897959183675,987.2580209977217,8.127084233861519,3.077002361340375
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14.285714285714286,997.1921555652444,11.1411402004285,4.460492394260581
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16.3265306122449,982.5264642273422,16.178692639617495,6.640116313279181
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18.367346938775512,985.5391134693785,22.438734952694826,9.302401673285305
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20.408163265306122,950.3929592274865,30.9867062109544,13.453561212371968
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22.448979591836736,943.6768450787737,43.1172181507687,18.902994501944676
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24.48979591836735,923.9712883457852,58.55787164713293,26.461358749920777
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26.53061224489796,889.3736903686494,78.3870367496892,36.42799336312908
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28.571428571428573,829.7717726263381,103.99688813928137,50.47456378959229
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30.612244897959183,803.6038006158797,134.86301821185936,67.78296315480418
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32.6530612244898,739.4531398609986,170.07930310542255,89.57453306868761
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34.69387755102041,662.6057572102866,207.0584204365696,120.4683551291235
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36.734693877551024,588.7107715185717,251.76602405172594,155.82715996942417
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38.775510204081634,528.0945273414742,284.48622084623474,196.03112205363107
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40.816326530612244,453.6387542336385,311.49392179639165,238.62917703193912
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42.85714285714286,379.64101876152733,324.6956212073424,295.3771886609074
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44.89795918367347,328.7240024764717,335.86960613328057,336.9380611019739
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46.93877551020408,276.6226521708966,342.9129552547733,386.64888732108915
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48.9795918367347,230.46604078409402,332.5172677294927,436.2620642180145
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51.02040816326531,198.41886797255233,312.985461763179,482.2774728413838
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53.06122448979592,172.31113754951818,295.36931154816244,536.5337246723285
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55.10204081632653,147.10640197410112,280.47647356374284,591.4279411760413
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57.142857142857146,130.2172301299589,257.34236499547103,614.2528711129506
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59.183673469387756,114.13385455729035,232.85793225104177,655.9244771150093
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61.224489795918366,102.4047733203167,208.066233857558,694.3136177899195
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63.26530612244898,91.79101179657,189.2152289525042,715.0072780394455
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65.3061224489796,84.84614462227702,170.5458134975131,746.7161144614075
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67.34693877551021,77.56253691742647,154.62995852816593,772.2091496683425
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69.38775510204081,73.30534380238566,135.99961469908644,776.27645565576
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71.42857142857143,67.34601887552232,122.52869734263317,814.7301940332044
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73.46938775510205,64.31334481761729,110.21573349736046,836.4965234263399
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75.51020408163265,61.66582472302947,96.03826238406376,842.6057280125577
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77.55102040816327,58.97457490297767,86.49580546030899,848.9915046223448
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79.59183673469389,56.07920007819682,75.9703698400598,849.5257527067243
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81.63265306122449,53.29737876865533,67.02012369361692,875.3995783493236
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83.6734693877551,52.78529217886916,59.541480121267504,881.0482364490581
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85.71428571428572,50.91742018377428,51.66658726016318,920.9086552034577
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87.75510204081633,49.98086105684715,46.26699373748106,906.5765503440235
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89.79591836734694,47.580613323137655,40.5184260065114,906.9232321517168
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91.83673469387756,47.18889650978118,36.03883717711462,912.0509520982456
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93.87755102040816,46.55568568499699,31.46335647347164,928.7371564916173
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95.91836734693878,45.78250532061345,27.796278245398238,931.6387069680544
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97.9591836734694,46.018787328504715,24.222348556744723,944.5588773050516
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100.0,44.70104560362663,21.48687578031168,942.6100942732352

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