Implement configs (#18)

* made progress on octree class; working on building the octree class

* finished implementing octree class and members/functions; need to fix segmentation fault in testing

* update testing and previous implementation; debug octree implementation and makefile configuration

* add inclusion of <memory> to octree files

* add tests for body implementation; slightly edit body.cpp implementation

* Implement config file functionality.

* Fix everything

* Add yaml-cpp install to workflows

* Debug

---------

Co-authored-by: jdinovi <[email protected]>

.github/workflows/coverage.yml

@@ -11,6 +11,11 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v3
+
+    - name: Install requirements
+      run: |
+        sudo apt-get update -q
+        sudo apt-get install libyaml-cpp-dev -y
 
     - name: Evaluate coverage
       run: |

.github/workflows/test.yml

@@ -12,6 +12,11 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v3
 
+    - name: Install requirements
+      run: |
+        sudo apt-get update -q
+        sudo apt-get install libyaml-cpp-dev -y
+
     - name: Run tests
       run: |
         result=$(make test)

Makefile

@@ -1,5 +1,6 @@
 CXX = g++
 CXXFLAGS = -std=c++17 -Wall --coverage
+LDFLAGS = -lyaml-cpp
 SRC_DIR = src
 INC_DIR = include
 OBJ_DIR = obj
@@ -22,15 +23,15 @@ INC_DIRS = -I $(INC_DIR)
 
 # Linking step for src files
 $(BIN_DIR)/$(TARGET): $(OBJS)
-	$(CXX) $(CXXFLAGS) -o $@ $^
+	$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
 
 # Compiling step for src files
 $(OBJ_DIR)/%.o: $(SRC_DIR)/%.cpp
 	$(CXX) $(CXXFLAGS) $(INC_DIRS) -c -o $@ $<
 
 # Linking step for test files
 $(BIN_DIR)/$(TEST_TARGET): $(filter-out $(OBJ_DIR)/simulation.o, $(OBJS)) $(TEST_OBJS)
-	$(CXX) $(CXXFLAGS) -o $@ $^
+	$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
 
 # Compiling step for test files
 $(TEST_OBJ_DIR)/%.o: $(TEST_DIR)/%.cpp

configs/default.yaml

@@ -0,0 +1,29 @@
+global:
+  nParticles: 1000
+mass:
+  dist: constant
+  val: 100000000
+x:
+  dist: uniform
+  min: 0
+  max: 4
+y:
+  dist: uniform
+  min: -2
+  max: 4
+z:
+  dist: uniform
+  min: 1
+  max: 10
+vx:
+  dist: uniform
+  min: 0
+  max: 4
+vy:
+  dist: normal
+  mu: -2
+  sigma: 4
+vz:
+  dist: uniform
+  min: -10
+  max: 10

include/environment.h

@@ -1,37 +1,40 @@
 #pragma once
 #include <vector>
 #include <array>
-#include <memory>
+#include <map>
+#include <memory> // Include for smart pointers
+#include "particle.h"
 
-#include "./particle.h"
 
 template <typename T>
-class GravitationalEnvironment{
-
-    public:
-        // Constructors
-        // GravitationalEnvironment(const std::vector<std::shared_ptr<T>>& particlePtrs, const bool log);
-        GravitationalEnvironment(const std::vector<std::shared_ptr<T>>& particlePtrs, const bool log, std::string logFilePrefix="run");
+class GravitationalEnvironment {
+public:
+    // Constructors
+    GravitationalEnvironment(const std::vector<std::shared_ptr<T>>& particlePtrs, const bool log, std::string logFilePrefix = "run");
+    GravitationalEnvironment(const std::string configFileName, const bool log, std::string logFilePrefix = "run");
 
-        // Define member functions
-        std::vector<std::array<double, 3>> getForces(const double timestep);
-        void updateAll(const std::vector<std::array<double, 3>>& forces, const double timestep);
-        void step(const double timestep);
-        void simulate(const double duration, const double timestep);
-        std::string getStepLog() const;
-        std::string getLogHeader() const;
-        void reset();
+    // Define member functions
+    void loadParticlesFromConfig(std::string configFileName);
+    std::vector<std::array<double, 3>> getForces(const double timestep);
+    void updateAll(const std::vector<std::array<double, 3>>& forces, const double timestep);
+    void step(const double timestep);
+    void simulate(const double duration, const double timestep);
+    std::string getStepLog() const;
+    std::string getLogHeader() const;
+    void reset();
 
-        // Instantiation of the physical members
-        std::vector<std::shared_ptr<T>> particlePtrs; // Changed to std::shared_ptr
-        bool log;
-        double time;
-        int nParticles;
-        std::string logFileName;
+    // Instantiation of the physical members
+    std::vector<std::shared_ptr<T>> particlePtrs; // Changed to std::shared_ptr
+    bool log;
+    double time;
+    int nParticles; // This should be calculated in the constructor.
+    std::string logFileName;
+
+private:
+    // Instantiation of the physical members
+    std::string logFilePrefix;
 };
 
 // Helper functions
 int getLargestLabelNumber(const std::vector<std::string>& filenames, const std::string logFilePrefix);
-
-
-typedef GravitationalEnvironment<Particle> ParticleEnvironment;
+std::map<std::string, std::map<std::string, std::string>> loadConfig(const std::string& fileName);

include/octree.h

@@ -0,0 +1,40 @@
+#pragma once
+
+#include <vector>
+#include <memory>
+
+#include "body.h"
+
+template <typename T>
+class Octree {
+    public:
+
+        // Octree constructor
+        Octree(std::array<float, 2>& xCoords, std::array<float, 2>& yCoords, std::array<float, 2>& zCoords);
+
+        // Member functions
+        void clear();
+        void insert(std::shared_ptr<T> objPtr);
+        void build(std::vector<std::shared_ptr<T>>& objPtrs);
+
+        // Members
+        std::vector<std::shared_ptr<T>> objPtrs;
+        std::array<float, 3> centerOfMass;
+        float* totalMass;
+
+        // Dimensions of the current octant
+        std::array<float, 2> xCoords;
+        std::array<float, 2> yCoords;
+        std::array<float, 2> zCoords;
+
+        // Octree children --> 0-7 based on 2D convention in postive z, and then 2D convention in negative z, observing from above        
+        Octree<T>* child0;
+        Octree<T>* child1;
+        Octree<T>* child2;
+        Octree<T>* child3;
+        Octree<T>* child4;
+        Octree<T>* child5;
+        Octree<T>* child6;
+        Octree<T>* child7;
+
+};

include/statistics.h

@@ -0,0 +1,18 @@
+#pragma once
+#include <vector>
+#include <random>
+
+// Assuming you have the random device and generator declared somewhere
+extern std::random_device rd;
+extern std::mt19937 GENERATOR;
+
+// Distribution template used to sample from random distributions
+template <typename Distribution>
+std::vector<double> sampleFromDistribution(size_t n, Distribution& distribution) {
+    // Generate samples
+    std::vector<double> samples(n);
+    for (size_t i = 0; i < n; ++i) {
+        samples[i] = distribution(GENERATOR);
+    }
+    return samples;
+}

src/body.cpp

@@ -12,4 +12,4 @@ float DENSITY = 4E3;
 
 // Constructor definition
 Body::Body(const std::array<double, 3>* initial_position, const std::array<double, 3>* initial_velocity, double mass, float radius)
-    : Particle(initial_position, initial_velocity, mass), radius(radius == 0 ? pow(3 * mass / (4 * M_PI * DENSITY), 1/3) : radius) {};
+    : Particle(initial_position, initial_velocity, mass), radius((radius == 0) ? pow(3 * mass / (4 * M_PI * DENSITY), 1./3.) : radius) {};