Add pair potential and tests

src/CMakeLists.txt

@@ -1,16 +1,17 @@
 project(${CMAKE_PROJECT_NAME}_lib CUDA CXX)
 
 set(HEADER_FILES
-    ./test.h
+    particle.hpp
+    simulation.hpp
+    box.hpp
+    pair_potentials.hpp
 )
 set(SOURCE_FILES
-    ./test.cpp
+    pair_potentials.cpp
 )
 
 # The library contains header and source files.
-add_library(${CMAKE_PROJECT_NAME}_lib
+add_library(${CMAKE_PROJECT_NAME}_lib 
+    ${HEADER_FILES} 
     ${SOURCE_FILES}
-    ${HEADER_FILES}
 )
-
-target_include_directories(${CMAKE_PROJECT_NAME}_lib PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})

src/box.hpp

@@ -0,0 +1,22 @@
+#ifndef BOX_H
+#define BOX_H
+
+/**
+ * Struct representing the simulation box.
+ * Currently the simulation box is always assumed to be perfectly rectangular.
+ * This code does not support shearing the box. This functionality may be added
+ * in later.
+ */
+template <typename T> struct Box {
+  T xlo;
+  T xhi;
+  T ylo;
+  T yhi;
+  T zlo;
+  T zhi;
+  bool x_is_periodic;
+  bool y_is_periodic;
+  bool z_is_periodic;
+};
+
+#endif

src/pair_potentials.cpp

@@ -0,0 +1,33 @@
+#include "potentials.hpp"
+#include <cmath>
+
+/**
+ * Calculate the Lennard-Jones energy and force for the current particle pair
+ * described by displacement vector r
+ */
+ForceAndEnergy LennardJones::calc_force_and_energy(Vec3<real> r) {
+  real rmagsq = r.squared_norm2();
+  if (rmagsq < this->m_rcutoffsq && rmagsq > 0.0) {
+    real inv_rmag = 1 / std::sqrt(rmagsq);
+
+    // Pre-Compute the terms (doing this saves on multiple devisions/pow
+    // function call)
+    real sigma_r = m_sigma / inv_rmag;
+    real sigma_r5 = sigma_r * sigma_r * sigma_r * sigma_r * sigma_r;
+    real sigma_r6 = sigma_r5 * sigma_r;
+    real sigma_r11 = sigma_r5 * sigma_r5 * sigma_r;
+    real sigma_r12 = sigma_r6 * sigma_r6;
+
+    // Get the energy
+    real energy = 4.0 * m_epsilon * (sigma_r12 - sigma_r6);
+
+    // Get the force vector
+    real force_mag = 4.0 * m_epsilon * (6.0 * sigma_r5 - 12.0 * sigma_r11);
+    Vec3<real> force = r.scale(force_mag * inv_rmag);
+
+    return {energy, force};
+
+  } else {
+    return ForceAndEnergy::zero();
+  }
+};

src/pair_potentials.hpp

@@ -0,0 +1,41 @@
+#ifndef POTENTIALS_H
+#define POTENTIALS_H
+
+#include "precision.hpp"
+#include "vec3.h"
+
+/**
+ * Result struct for the Pair Potential
+ */
+struct ForceAndEnergy {
+  real energy;
+  Vec3<real> force;
+
+  inline static ForceAndEnergy zero() { return {0.0, {0.0, 0.0, 0.0}}; };
+};
+
+/**
+ * Abstract implementation of a Pair Potential.
+ * Pair potentials are potentials which depend solely on the distance
+ * between two particles. These do not include multi-body potentials such as
+ * EAM
+ *
+ */
+struct PairPotential {
+  real m_rcutoffsq;
+
+  /**
+   * Calculate the force and energy for a specific atom pair based on a
+   * displacement vector r.
+   */
+  virtual ForceAndEnergy calc_force_and_energy(Vec3<real> r) = 0;
+};
+
+struct LennardJones : PairPotential {
+  real m_epsilon;
+  real m_sigma;
+
+  ForceAndEnergy calc_force_and_energy(Vec3<real> r);
+};
+
+#endif

src/particle.hpp

@@ -0,0 +1,18 @@
+#ifndef PARTICLE_H
+#define PARTICLE_H
+
+#include "vec3.h"
+
+/**
+ * Class representing a single molecular dynamics particle.
+ * This class is only used on the host side of the code and is converted
+ * to the device arrays.
+ */
+template <typename T = float> struct Particle {
+  Vec3<T> pos;
+  Vec3<T> vel;
+  Vec3<T> force;
+  T mass;
+};
+
+#endif

src/precision.hpp

@@ -0,0 +1,15 @@
+#ifndef PRECISION_H
+#define PRECISION_H
+
+#ifdef USE_FLOATS
+
+/*
+ * If macro USE_FLOATS is set then the default type will be floating point
+ * precision. Otherwise we use double precision by default
+ */
+typedef float real;
+#else
+typedef double real;
+#endif
+
+#endif

src/simulation.hpp

@@ -0,0 +1,17 @@
+#ifndef SIMULATION_H
+#define SIMULATION_H
+
+#include "box.hpp"
+#include "particle.hpp"
+#include <vector>
+
+template <typename T> class Simulation {
+  // Simulation State variables
+  T timestep;
+  Box<T> box;
+
+  // Host Data
+  std::vector<Particle<T>> particles;
+};
+
+#endif

src/test.cpp

@@ -1,4 +0,0 @@
-#include "test.h"
-#include <iostream>
-
-void test_hello() { std::cout << "Hello!"; }

src/test.h

@@ -1,2 +0,0 @@
-#include <iostream>
-void test_hello();