Add atoms generation methods

src/md/Atom.cpp

@@ -0,0 +1,23 @@
+/**
+ * @file Atom.cpp
+ * @author jun <jun@firmwarejun.net>
+ * @brief Atom definitions
+ * @version 0.1
+ * @date 2023-08-05
+ *
+ * Copyright (c) 2023 jun <https://git.firmwarejun.net/jun/MolecularDynamics2>
+ *
+ */
+
+#include <iostream>
+
+#include "Atom.hpp"
+
+void printAtom(Atom atom) {
+  std::cout << "Atom(" << atom.x << ", " << atom.y << ", " << atom.z << ")" << std::endl;
+}
+
+void printAtoms(std::vector<Atom> atoms) {
+  for (auto atom : atoms)
+    printAtom(atom);
+}

src/md/Atom.hpp

@@ -0,0 +1,42 @@
+/**
+ * @file Atom.hpp
+ * @author jun <jun@firmwarejun.net>
+ * @brief Atom declarations
+ * @version 0.1
+ * @date 2023-07-25
+ *
+ * Copyright (c) 2023 jun <https://git.firmwarejun.net/jun/MolecularDynamics2>
+ *
+ */
+
+#pragma once
+
+#include <vector>
+
+/**
+ * @brief Atom class
+ *
+ */
+class Atom {
+public:
+  double x, y, z;    ///< Positions
+  double vx, vy, vz; ///< Velocities
+  double m;          ///< Mass
+
+  Atom(double x, double y, double z) : x(x), y(y), z(z), vx(0), vy(0), vz(0), m(1) {
+  }
+};
+
+/**
+ * @brief Print an atom
+ *
+ * @param atom
+ */
+void printAtom(Atom atom);
+
+/**
+ * @brief Print atoms
+ *
+ * @param atoms
+ */
+void printAtoms(std::vector<Atom> atoms);

src/md/AtomsGenerator.cpp

@@ -0,0 +1,46 @@
+/**
+ * @file AtomsGenerator.cpp
+ * @author jun <jun@firmwarejun.net>
+ * @brief AtomsGenerator definitions
+ * @version 0.1
+ * @date 2023-08-05
+ *
+ * Copyright (c) 2023 jun <https://git.firmwarejun.net/jun/MolecularDynamics2>
+ *
+ */
+
+#include <stdexcept>
+
+#include "AtomsGenerator.hpp"
+
+std::vector<Atom> generateFCCAtoms(double latticeConstant, std::size_t numberOfCells) {
+  // Check for invalid lattice constants
+  if (latticeConstant <= 0)
+    throw std::invalid_argument("Lattice constant must be positive");
+
+  std::vector<Atom> atoms;
+
+  // Generate atoms in FCC lattice
+  for (std::size_t i = 0; i < numberOfCells; i++)
+    for (std::size_t j = 0; j < numberOfCells; j++)
+      for (std::size_t k = 0; k < numberOfCells; k++) {
+        atoms.push_back(Atom(i * latticeConstant, j * latticeConstant, k * latticeConstant));
+        atoms.push_back(
+            Atom((i + 0.5) * latticeConstant, (j + 0.5) * latticeConstant, k * latticeConstant));
+        atoms.push_back(
+            Atom((i + 0.5) * latticeConstant, j * latticeConstant, (k + 0.5) * latticeConstant));
+        atoms.push_back(
+            Atom(i * latticeConstant, (j + 0.5) * latticeConstant, (k + 0.5) * latticeConstant));
+      }
+
+  // Use std::move to move the vector to the caller
+  return std::move(atoms);
+}
+
+void offsetAtoms(std::vector<Atom> &atoms, double x, double y, double z) {
+  for (auto &atom : atoms) {
+    atom.x += x;
+    atom.y += y;
+    atom.z += z;
+  }
+}

src/md/AtomsGenerator.hpp

@@ -0,0 +1,39 @@
+/**
+ * @file AtomsGenerator.hpp
+ * @author jun <jun@firmwarejun.net>
+ * @brief AtomsGenerator declarations
+ * @version 0.1
+ * @date 2023-08-05
+ *
+ * Copyright (c) 2023 jun <https://git.firmwarejun.net/jun/MolecularDynamics2>
+ *
+ */
+
+#pragma once
+
+#include <vector>
+
+#include "Atom.hpp"
+
+/**
+ * @brief Generate atoms in FCC lattice
+ *
+ * @param latticeConstant
+ * @param numberOfCells
+ * @return std::vector<Atom>
+ */
+std::vector<Atom> generateFCCAtoms(double latticeConstant, std::size_t numberOfCells);
+
+/**
+ * Utilitary functions
+ */
+
+/**
+ * @brief Move atoms according to the given offset
+ *
+ * @param atoms
+ * @param x
+ * @param y
+ * @param z
+ */
+void offsetAtoms(std::vector<Atom> &atoms, double x, double y, double z);

src/md/CMakeLists.txt

@@ -3,4 +3,7 @@
 project(md)
 
 add_library(md
-  MolecularDynamics.cpp)
+  MolecularDynamics.cpp
+  Atom.cpp
+  AtomsGenerator.cpp
+  System.cpp)

src/md/Potentials.hpp

@@ -0,0 +1,18 @@
+/**
+ * @file Potentials.hpp
+ * @author jun <jun@firmwarejun.net>
+ * @brief Potentials declarations
+ * @version 0.1
+ * @date 2023-07-25
+ *
+ * Copyright (c) 2023 jun <https://git.firmwarejun.net/jun/MolecularDynamics2>
+ *
+ */
+
+#pragma once
+
+class Potential {
+public:
+  virtual double potential(double r) = 0;
+  virtual double force(double r)     = 0;
+};

src/md/System.cpp

@@ -0,0 +1,33 @@
+/**
+ * @file System.cpp
+ * @author jun <jun@firmwarejun.net>
+ * @brief System definitions
+ * @version 0.1
+ * @date 2023-08-05
+ *
+ * Copyright (c) 2023 jun <https://git.firmwarejun.net/jun/MolecularDynamics2>
+ *
+ */
+
+#include <iostream>
+
+#include "System.hpp"
+
+System::System(double timeDelta) : timeDelta(timeDelta) {
+}
+
+void System::initForceTable() {
+}
+
+void System::addAtom(Atom atom) {
+  this->atoms.push_back(atom);
+}
+
+void System::addAtom(std::vector<Atom> atoms) {
+  this->atoms.insert(this->atoms.end(), atoms.begin(), atoms.end());
+}
+
+void System::printAtoms() {
+  for (auto atom : this->atoms)
+    printAtom(atom);
+}

src/md/System.hpp

@@ -0,0 +1,62 @@
+/**
+ * @file System.hpp
+ * @author jun <jun@firmwarejun.net>
+ * @brief System declarations
+ * @version 0.1
+ * @date 2023-07-25
+ *
+ * Copyright (c) 2023 jun <https://git.firmwarejun.net/jun/MolecularDynamics2>
+ *
+ */
+
+#pragma once
+
+#include <vector>
+
+#include "Atom.hpp"
+
+class System {
+private:
+  std::vector<Atom> atoms;    ///< Atoms in the system
+  std::vector<Atom> atomsOld; ///< Atoms in the system in the previous step
+
+  double timeDelta = 0; ///< Time delta between steps
+
+  /**
+   * @brief Initialize the force table
+   *
+   */
+  void initForceTable();
+
+  /**
+   * @brief Initialize the potential table
+   *
+   */
+  void initPotentialTable();
+
+public:
+  explicit System(double timeDelta);
+
+  void step();
+  void stepFirst();
+
+  /**
+   * @brief Add an atom to the system
+   *
+   * @param atom
+   */
+  void addAtom(Atom atom);
+
+  /**
+   * @brief Add a vector of atoms to the system
+   *
+   * @param atoms
+   */
+  void addAtom(std::vector<Atom> atoms);
+
+  /**
+   * @brief Print atoms
+   *
+   */
+  void printAtoms();
+};