Make clang-tidy a little happier

.gitignore

@@ -110,3 +110,6 @@ fabric.properties
 
 # Android studio 3.1+ serialized cache file
 .idea/caches/build_file_checksums.ser
+
+/run
+*.jl

DLASystem.cpp

@@ -4,96 +4,43 @@
 
 #include "DLASystem.h"
 
-#include <utility>
+using std::cout;
+using std::endl;
 
 // this function gets called every step,
 //   if there is an active particle then it gets moved,
 //   if not then add a particle
-bool DLASystem::Update() {
+void DLASystem::update() {
+    this->frame++;
+
     if (lastParticleIsActive == 1) {
         moveLastParticle();
-    } else if (numParticles < endNum) {
+    } else if (this->particleList.size() < (size_t) endNum) {
         addParticleOnAddCircle();
         setParticleActive();
     } else {
-        return false;
+        this->running = false;
     }
-
-    return true;
-}
-
-
-void DLASystem::clearParticles() {
-    // delete particles and the particle list
-    for (int i = 0; i < numParticles; i++) {
-        delete particleList[i];
-    }
-    particleList.clear();
-    numParticles = 0;
-}
-
-// remove any existing particles and setup initial condition
-void DLASystem::Reset() {
-    // stop running
-    running = 0;
-
-    clearParticles();
-
-    lastParticleIsActive = 0;
-
-    // set the grid to zero
-    for (int i = 0; i < gridSize; i++) {
-        for (int j = 0; j < gridSize; j++) {
-            grid[i][j] = 0;
-        }
-    }
-
-    // setup initial condition and parameters
-    addCircle = 10;
-    killCircle = 2.0 * addCircle;
-    clusterRadius = 0.0;
-    // add a single particle at the origin
-    double pos[] = {0.0, 0.0};
-    addParticle(pos);
-
-    // set the view
-    int InitialViewSize = 40;
-    setViewSize(InitialViewSize);
-
 }
 
 // set the value of a grid cell for a particular position
 // note the position has the initial particle at (0,0)
 // but this corresponds to the middle of the grid array ie grid[ halfGrid ][ halfGrid ]
-void DLASystem::setGrid(double pos[], int val) {
+void DLASystem::setGrid(std::array<double, 2> pos, int val) {
-    int halfGrid = gridSize / 2;
+    *index_grid(pos) = val;
-    grid[(int) (pos[0] + halfGrid)][(int) (pos[1] + halfGrid)] = val;
 }
 
 // read the grid cell for a given position
-int DLASystem::readGrid(double pos[]) {
+int DLASystem::readGrid(std::array<double, 2> pos) {
-    int halfGrid = gridSize / 2;
+    return *index_grid(pos);
-    return grid[(int) (pos[0] + halfGrid)][(int) (pos[1] + halfGrid)];
-}
-
-// check if the cluster is big enough and we should stop:
-// to be safe, we need the killCircle to be at least 2 less than the edge of the grid
-int DLASystem::checkStop() {
-    if (killCircle + 2 >= gridSize / 2) {
-        pauseRunning();
-        cout << "STOP" << endl;
-//        glutPostRedisplay(); // update display
-        return 1;
-    } else return 0;
 }
 
 // add a particle to the system at a specific position
-void DLASystem::addParticle(double pos[]) {
+void DLASystem::addParticle(std::array<double, 2> pos) {
     // create a new particle
-    Particle *p = new Particle(pos);
+    auto *p = new Particle(pos);
     // push_back means "add this to the end of the list"
     particleList.push_back(p);
-    numParticles++;
 
     // pos coordinates should be -gridSize/2 < x < gridSize/2
     setGrid(pos, 1);
@@ -103,20 +50,19 @@ void DLASystem::addParticle(double pos[]) {
 // if we hit an occupied site then we do nothing except print a message
 // (this should never happen)
 void DLASystem::addParticleOnAddCircle() {
-    double pos[2];
     double theta = rgen.random01() * 2 * M_PI;
-    pos[0] = ceil(addCircle * cos(theta));
+    std::array<double, 2> pos{ceil(addCircle * cos(theta)), ceil(addCircle * sin(theta))};
-    pos[1] = ceil(addCircle * sin(theta));
+    if (readGrid(pos) == 0) {
-    if (readGrid(pos) == 0)
         addParticle(pos);
-    else
+    } else {
         cout << "FAIL " << pos[0] << " " << pos[1] << endl;
     }
+}
 
 // send back the position of a neighbour of a given grid cell
 // NOTE: there is no check that the neighbour is inside the grid,
 // this has to be done separately...
-void DLASystem::setPosNeighbour(double setpos[], double pos[], int val) {
+void DLASystem::setPosNeighbour(std::array<double, 2> &setpos, const std::array<double, 2> pos, int val) {
     switch (val) {
         case 0:
             setpos[0] = pos[0] + 1.0;
@@ -137,95 +83,68 @@ void DLASystem::setPosNeighbour(double setpos[], double pos[], int val) {
     }
 }
 
-// if the view is smaller than the kill circle then increase the view area (zoom out)
-void DLASystem::updateViewSize() {
-    double mult = 1.2;
-    if (viewSize < 2.0 * killCircle) {
-        setViewSize(viewSize * mult);
-    }
-}
-
-// set the view to be the size of the add circle (ie zoom in on the cluster)
-void DLASystem::viewAddCircle() {
-    setViewSize(2.0 * addCircle);  // factor of 2 is to go from radius to diameter
-}
-
 // when we add a particle to the cluster, we should update the cluster radius
 // and the sizes of the addCircle and the killCircle
-void DLASystem::updateClusterRadius(double pos[]) {
+void DLASystem::updateClusterRadius(std::array<double, 2> pos) {
-
+    double newRadius = distanceFromOrigin(pos);
-    double rr = distanceFromOrigin(pos);
+    if (newRadius > clusterRadius) {
-    if (rr > clusterRadius) {
+        clusterRadius = newRadius;
-        clusterRadius = rr;
         // this is how big addCircle is supposed to be:
         //   either 20% more than cluster radius, or at least 5 bigger.
         double check = clusterRadius * addRatio;
-        if (check < clusterRadius + 5)
+        if (check < clusterRadius + 5) {
             check = clusterRadius + 5;
+        }
+
         // if it is smaller then update everything...
         if (addCircle < check) {
             addCircle = check;
             killCircle = killRatio * addCircle;
-            updateViewSize();
         }
-        checkStop();
+
+        if (killCircle + 2 >= gridSize / 2) {
+            std::cerr << "Early Exit" << endl;
+            this->running = false;
+        }
     }
 }
 
 // make a random move of the last particle in the particleList
 void DLASystem::moveLastParticle() {
-    int rr = rgen.randomInt(4);  // pick a random number in the range 0-3, which direction do we hop?
+    int direction = rgen.randomInt(4);  // pick a random number in the range 0-3, which direction do we hop?
-    double newpos[2];
+    std::array<double, 2> newpos{};
 
-    Particle *lastP = particleList[numParticles - 1];
+    Particle *lastP = particleList[this->particleList.size() - 1];
 
-    setPosNeighbour(newpos, lastP->pos, rr);
+    setPosNeighbour(newpos, lastP->pos, direction);
 
     if (distanceFromOrigin(newpos) > killCircle) {
-        //cout << "#deleting particle" << endl;
         setGrid(lastP->pos, 0);
         particleList.pop_back();  // remove particle from particleList
-        numParticles--;
         setParticleInactive();
-    }
+    } else if (readGrid(newpos) == 0) {
-        // check if destination is empty
-    else if (readGrid(newpos) == 0) {
         setGrid(lastP->pos, 0);  // set the old grid site to empty
         // update the position
-        particleList[numParticles - 1]->pos[0] = newpos[0];
+        particleList[this->particleList.size() - 1]->pos[0] = newpos[0];
-        particleList[numParticles - 1]->pos[1] = newpos[1];
+        particleList[this->particleList.size() - 1]->pos[1] = newpos[1];
         setGrid(lastP->pos, 1);  // set the new grid site to be occupied
 
         // check if we stick
-        if (checkStick()) {
+        if (checkStick() && this->rgen.random01() <= this->stickProbability) {
-            this->csv_out << newpos[0] << "," << newpos[1] << "\n";
+            this->csv_out << frame << "," << lastP->pos[0] << "," << lastP->pos[1] << endl;
-            this->csv_out.flush();
-
-            //cout << "stick" << endl;
             setParticleInactive();  // make the particle inactive (stuck)
             updateClusterRadius(lastP->pos);  // update the cluster radius, addCircle, etc.
-
-            if (numParticles % 100 == 0 && logfile.is_open()) {
-                logfile << numParticles << " " << clusterRadius << endl;
         }
     }
-    } else {
-        // if we get to here then we are trying to move to an occupied site
-        // (this should never happen as long as the sticking probability is 1.0)
-        cout << "reject " << rr << endl;
-        cout << lastP->pos[0] << " " << lastP->pos[1] << endl;
-        //cout << newpos[0] << " " << newpos[1] << " " << (int)newpos[0] << endl;
-        //printOccupied();
-    }
 }
 
 // check if the last particle should stick (to a neighbour)
 int DLASystem::checkStick() {
-    Particle *lastP = particleList[numParticles - 1];
+    Particle *lastP = particleList[this->particleList.size() - 1];
     int result = 0;
     // loop over neighbours
     for (int i = 0; i < 4; i++) {
-        double checkpos[2];
+        std::array<double, 2> checkpos{};
         setPosNeighbour(checkpos, lastP->pos, i);
         // if the neighbour is occupied...
         if (readGrid(checkpos) == 1)
@@ -236,42 +155,44 @@ int DLASystem::checkStick() {
 
 
 // constructor
-DLASystem::DLASystem(ofstream out_file) {
+DLASystem::DLASystem(Config config)
-    cout << "creating system, gridSize " << gridSize << endl;
+        : stickProbability(config.stickProbability),
-    numParticles = 0;
+          grid(gridSize * gridSize),
-    endNum = 1000;
+          csv_out(std::move(config.csv)),
-    csv_out = std::move(out_file);
+          endNum(config.maxParticles),
+          frame(0),
+          running(false),
+          lastParticleIsActive(false) {
+    cout << "GridSize: " << gridSize << endl;
+    rgen.setSeed(config.seed);
 
-    // allocate memory for the grid, remember to free the memory in destructor
+    /*
-    grid = new int *[gridSize];
+     * Handle grid data structure.
-    for (int i = 0; i < gridSize; i++) {
+     * */
-        grid[i] = new int[gridSize];
+    // Add particle to the centre of the grid to start
-    }
+    std::array<double, 2> pos{0.0, 0.0};
-    slowNotFast = 0;
+    addParticle(pos);
-    running = true;
 
-    // reset initial parameters
+    // Make sure to include the central location in our csv.
-    Reset();
+    this->csv_out << 0 << "," << 0 << "," << 0 << std::endl;
 
+    /*
+     * System behaviour parameters
+     * */
     addRatio = 1.2;   // how much bigger the addCircle should be, compared to cluster radius
     killRatio = 1.7;   // how much bigger is the killCircle, compared to the addCircle
-
+    addCircle = 10;
-    // this opens a logfile, if we want to...
+    killCircle = 2.0 * addCircle;
-    //logfile.open("opfile.txt");
+    clusterRadius = 0.0;
 }
 
 // destructor
 DLASystem::~DLASystem() {
-    // strictly we should not print inside the destructor but never mind...
-    cout << "deleting system" << endl;
     // delete the particles
-    clearParticles();
+    particleList.clear();
-    // delete the grid
-    for (int i = 0; i < gridSize; i++)
-        delete[] grid[i];
-    delete[] grid;
 
-    if (this->csv_out.is_open()) {
+    if (csv_out.is_open()) {
-        this->csv_out.close();
+        csv_out.flush();
+        csv_out.close();
     }
 }

DLASystem.h

@@ -2,12 +2,12 @@
 
 #include <iostream>
 #include <fstream>
-#include <stdio.h>
+#include <cstdio>
 #include <vector>
 
 #define _USE_MATH_DEFINES
 
-#include <math.h>
+#include <cmath>
 #include <random>
 #include <string>
 #include <sstream>
@@ -15,17 +15,21 @@
 #include "Particle.h"
 #include "rnd.h"
 
-using namespace std;
+class Config {
+public:
+    int seed;
+    double stickProbability;
+    std::ofstream csv;
+    int maxParticles;
 
+    Config(int argc, char **argv);
+};
 
 class DLASystem {
-public:
+private:
+    // these are private variables and functions that the user will not see
     // list of particles
-    vector<Particle *> particleList;
+    std::vector<Particle *> particleList;
-    int numParticles;
-
-    // delete particles and clear the particle list
-    void clearParticles();
 
     // size of cluster
     double clusterRadius;
@@ -33,21 +37,17 @@ public:
     double addCircle;
     double killCircle;
 
-    ofstream csv_out;
+    double stickProbability;
 
     // size of grid
     static const int gridSize = 1600;
-    int **grid;  // this will be a 2d array that stores whether each site is occupied
+    std::vector<int> grid;
-
-    // the window draws only part of the grid, viewSize controls how much...
-    double viewSize;
-    double drawScale;
 
     // random number generator, class name is rnd, instance is rgen
     rnd rgen;
 
     // output file (not used at the moment)
-    ofstream logfile;
+    std::ofstream csv_out;
 
     // number of particles at which the simulation will stop
     // (the value is set in constructor)
@@ -57,77 +57,52 @@ public:
     double addRatio;    // how much bigger the addCircle should be, compared to cluster radius
     double killRatio;   // how much bigger is the killCircle, compared to the addCircle
 
+    int frame;
 
+    int *index_grid(std::array<double, 2> pos) {
+        int halfGrid = gridSize / 2;
+        int i = (int) (pos[0] + halfGrid);
+        int j = (int) (pos[1] + halfGrid);
+
+        int ij = i * gridSize + j;
+        return &grid[ij];
+    }
 public:
     // these are public variables and functions
 
     // update the system: if there is an active particle then move it,
     // else create a new particle (on the adding circle)
-    bool Update();
+    void update();
-
-    // draw particles as squares
-    void DrawSquares();
 
     // is the simulation running (1) or paused (0) ?
-    int running;
+    bool running;
-
-    // slowNotFast is +1 for slow running, 0 for fast
-    int slowNotFast;
 
     // lastParticleIsActive is +1 if there is an active particle in the system, otherwise 0
     int lastParticleIsActive;
 
     // constructor
-    DLASystem(ofstream output);
+    explicit DLASystem(Config config);
 
     // destructor
     ~DLASystem();
 
-    // delete all particles and reset
-    void Reset();
-
     // this sets the seed for the random numbers
     void setSeed(int s) { rgen.setSeed(s); }
 
-    // check whether we should stop (eg the cluster has reached the edge of the grid)
+    void setRunning() { running = true; }
-    int checkStop();
 
-    // stop/start the algorithm
+    void pauseRunning() { running = false; }
-    void setRunning() { if (checkStop() == 0) running = 1; }
-
-    void pauseRunning() { running = 0; }
-
-    // set whether it runs fast or slow
-    void setSlow() { slowNotFast = 1; }
-
-    void setFast() { slowNotFast = 0; }
-
-    void setSuperFast() { slowNotFast = -1; }
-
-    // set which part of the grid is visible on the screen
-    // basically the screen shows co-ordinates -vv < x < vv
-    // where vv is the input value
-    void setViewSize(double vv) {
-        viewSize = vv;
-        drawScale = 2.0 / viewSize;
-    }
-
-    // if the killcircle is almost as big as the view then increase the view
-    void updateViewSize();
-
-    // set the view to be the approx size of the addCircle
-    void viewAddCircle();
 
     // if pos is outside the cluster radius then set clusterRadius to be the distance to pos.
-    void updateClusterRadius(double pos[]);
+    void updateClusterRadius(std::array<double, 2> pos);
 
     // set and read grid entries associated with a given position
-    void setGrid(double pos[], int val);
+    void setGrid(std::array<double, 2> pos, int val);
 
-    int readGrid(double pos[]);
+    int readGrid(std::array<double, 2> pos);
 
     // return the distance of a given point from the origin
-    double distanceFromOrigin(double pos[]) {
+    double distanceFromOrigin(std::array<double, 2> pos) {
         return sqrt(pos[0] * pos[0] + pos[1] * pos[1]);
     }
 
@@ -137,14 +112,14 @@ public:
     void setParticleInactive() { lastParticleIsActive = 0; }
 
     // add a particle at pos
-    void addParticle(double pos[]);
+    void addParticle(std::array<double, 2> pos);
 
     // add a particle at a random point on the addCircle
     void addParticleOnAddCircle();
 
     // assign setpos to the position of a neighbour of pos
     // which neighbour we look at is determined by val (=0,1,2,3)
-    void setPosNeighbour(double setpos[], double pos[], int val);
+    void setPosNeighbour(std::array<double, 2> &setpos, std::array<double, 2> pos, int val);
 
     // this attempts to move the last particle in the List to a random neighbour
     // if the neighbour is occupied then nothing happens

Makefile

@@ -14,7 +14,7 @@ CXXFLAGS = -Wall -Wextra -g -O0 -std=c++20 -stdlib=libc++
 
 IFLAGS = -I/usr/local/include -I/usr/include
 
-LFLAGS = -L/usr/local/lib -lm -framework OpenGL -framework GLUT	
+LFLAGS = -L/usr/local/lib -lm
 
 # ------------------------------------------
 # FOR GENERIC MAKEFILE:

Particle.h

@@ -1,22 +1,14 @@
 #pragma once
+#include <array>
 
 class Particle {
 public:
     static const int dim = 2;  // we are in two dimensions
-    double *pos;  // pointer to an array of size dim, to store the position
+    std::array<double, dim> pos{};
 
-    // default constructor
+    // constructor, with a specified initial pos
-    Particle() {
+    explicit Particle(std::array<double, dim> pos) {
-        pos = new double[dim];
+        this->pos[0] = pos[0];
+        this->pos[1] = pos[1];
     }
-
-    // constructor, with a specified initial position
-    Particle(double set_pos[]) {
-        pos = new double[dim];
-        for (int d = 0; d < dim; d++)
-            pos[d] = set_pos[d];
-    }
-
-    // destructor
-    ~Particle() { delete[] pos; }
 };

harness.bash

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+parallel "../run {1} {2} {3}" ::: $(seq 0 10) ::: $(seq 0 0.05 1) ::: $(seq 2000 1000 10000)

mainDLA.cpp

@@ -1,43 +1,58 @@
 #include <iostream>
 #include <vector>
+#include <cmath>
+#include <string>
 
 #include "DLASystem.h"
 
-using namespace std;
+using std::cout;
+using std::endl;
 
-// functions which are needed for openGL go into a namespace so that we can identify them
+/*
-namespace drawFuncs {
+ * In a proper project I would write a better argument parser, don't care here, just exit with an error if it is wrong.
-    void handleKeypress(unsigned char key, int x, int y);
+ * */
+Config::Config(int argc, char **argv) {
+    if (argc != 4) {
+        exit(1);
+    } else {
+        this->seed = std::stoi(argv[1]);
+        this->stickProbability = std::stod(argv[2]);
+        this->maxParticles = std::stoi(argv[3]);
 
-    void display(void);
+        if (stickProbability <= 0 || stickProbability > 1) {
-
+            exit(1);
-    void update(int val);
-
-    void introMessage();
         }
 
-// this is a global pointer, which is how we access the system itself
+        std::stringstream str;
-DLASystem *sys;
+        // Ensure the output file name contains all information required to replicate data
+        str << "./out-" << seed << '-' << stickProbability << "-" << maxParticles << ".csv";
+        std::ofstream csv_out(str.str());
+        this->csv = std::move(csv_out);
+
+        // Add headers to csv output
+        this->csv << "frame" << "," << "x" << "," << "y" << std::endl;
+
+        cout <<
+             "seed: " << seed << ", " <<
+             "stickProbability: " << stickProbability << ", " <<
+             "maxParticles: " << maxParticles <<
+             endl;
+    }
+}
 
 int main(int argc, char **argv) {
-    const auto seed = std::stoi(argv[1]);
+    Config config(argc, argv);
-    char buffer[20];
-    snprintf(buffer, 20, "seed-%i.csv", seed);
-    const auto p1 = std::chrono::system_clock::now();
-    std::ofstream myfile;
-    myfile.open(buffer);
 
-    // create the system
+    // Create the system
-    sys = new DLASystem(std::move(myfile));
+    auto *sys = new DLASystem(std::move(config));
+    sys->setRunning();
 
-    // this is the seed for the random numbers
+    /*
-    cout << "setting seed " << seed << endl;
+     * NOTE: We run at max speed as rendering is handled by a different engine so we don't need to care.
-    sys->setSeed(seed);
+     * */
-
+    while (sys->running) {
-    while (sys->Update()) {
+        sys->update();
     }
 
-    cout << sys->numParticles;
-
     return 0;
 }

seed-2.csv

@@ -1,999 +0,0 @@
-0,-1
--1,0
--1,1
-0,-2
-0,-3
--1,-2
-1,-1
-0,1
--1,-3
-0,2
-0,3
-0,4
--1,3
-1,-3
-1,3
-2,-1
--1,4
-2,-3
--2,4
-2,-4
-0,-4
--3,4
-3,-4
--4,4
--1,-1
-0,-5
-0,5
--4,5
-4,-4
-2,3
--5,4
-0,-6
-2,4
-1,5
-3,4
--5,5
-3,3
-3,5
-5,-4
-2,-5
-5,-3
-0,-7
-6,-4
-5,-2
-1,-7
-7,-4
-4,5
-7,-5
-6,-2
-0,-8
-3,6
--4,6
-0,6
--2,-3
--1,-6
-4,3
--1,-8
--4,7
--2,-4
--5,3
--4,8
--1,-9
-3,7
-3,8
-4,6
-8,-5
--4,9
-4,2
-5,6
-7,-2
-7,-6
--6,3
--1,-10
--5,9
--1,-11
--3,8
--2,-11
-5,3
--5,10
-9,-5
--5,11
--3,-3
-10,-5
-8,-2
--5,12
--2,-9
-4,8
-10,-6
--1,-12
--3,-11
-11,-6
-12,-6
--3,-12
--6,2
--4,-3
--7,3
-0,-12
-2,8
-6,6
--5,8
--7,4
--6,10
-1,-12
-5,8
-12,-5
--2,-6
-4,9
--4,-11
-2,-12
-2,9
--6,12
-2,-6
--6,9
--3,-6
-12,-4
--5,-11
-4,-5
-7,6
-11,-4
--2,-12
--1,-13
--8,3
--7,12
--5,-10
-12,-7
-2,-13
--7,13
--6,13
-1,8
--9,3
--10,3
-6,8
-12,-3
-6,9
--6,5
-13,-7
-6,10
--10,2
--5,13
-8,6
--6,8
-11,-7
--7,8
-8,-6
--6,14
--10,4
--8,13
-6,11
--11,3
-2,-11
--5,14
-5,11
-14,-7
-3,-11
-12,-2
--6,1
--12,3
-14,-8
-2,-14
-15,-8
--12,4
--2,-13
-6,12
-15,-9
-15,-7
--4,14
-9,6
-13,-4
--4,15
--3,15
-13,-2
-14,-9
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