Update CMakeFiles, add initial pair potential implementation and tests

.gitignore

@@ -1,5 +1,7 @@
 # Builds
 build/
+Debug/
+Testing/
 
 # Google Tests
 tests/lib/
@@ -7,3 +9,6 @@ tests/lib/
 # Jet Brains
 .idea/
 cmake-build-debug/
+
+# Cache dir
+.cache

CMakeLists.txt

@@ -1,32 +1,47 @@
 cmake_minimum_required(VERSION 3.9)
-project(MyProject LANGUAGES CUDA CXX)
+set(NAME "cudaCAC")
+project(${NAME} LANGUAGES CUDA CXX)
 
+enable_testing()
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+# Default settings 
 add_compile_options(-Wall -Wextra -Wpedantic)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CUDA_ARCHITECTURES 61)
 set(CUDA_SEPARABLE_COMPILATION ON)
 
+# Add Vec3  as a dependency
+include(FetchContent)
+FetchContent_Declare(Vec3
+    GIT_REPOSITORY https://www.alexselimov.com/git/aselimov/Vec3.git
+)
 
+FetchContent_GetProperties(Vec3)
+if(NOT Vec3_POPULATED)
+    FetchContent_MakeAvailable(Vec3)
+    include_directories(${Vec3_SOURCE_DIR})
+endif()
 
 include_directories(src)
 include_directories(kernels)
 include_directories(/usr/local/cuda-12.8/include)
 
-
 add_subdirectory(src)
 add_subdirectory(kernels)
 add_subdirectory(tests)
 
-add_executable(${CMAKE_PROJECT_NAME}_run main.cpp)
+add_executable(${NAME} main.cpp)
-
+install(DIRECTORY src/ DESTINATION src/)
 
 
 target_link_libraries(
-    ${CMAKE_PROJECT_NAME}_run 
+    ${NAME} 
     PRIVATE
-    ${CMAKE_PROJECT_NAME}_lib 
+    ${NAME}_lib 
-    ${CMAKE_PROJECT_NAME}_cuda_lib 
+    ${NAME}_cuda_lib 
+    
     ${CUDA_LIBRARIES}
 )
 

kernels/CMakeLists.txt

@@ -1,4 +1,4 @@
-project(${CMAKE_PROJECT_NAME}_cuda_lib CUDA CXX)
+project(${NAME}_cuda_lib CUDA CXX)
 
 set(HEADER_FILES
     hello_world.h
@@ -8,11 +8,9 @@ set(SOURCE_FILES
 )
 
 # The library contains header and source files.
-add_library(${CMAKE_PROJECT_NAME}_cuda_lib STATIC
+add_library(${NAME}_cuda_lib STATIC
     ${SOURCE_FILES}
     ${HEADER_FILES}
 )
 
-if(CMAKE_COMPILER_IS_GNUCXX)
+target_compile_options(${CMAKE_PROJECT_NAME}_cuda_lib PRIVATE -Wno-gnu-line-marker -Wno-pedantic)
-  target_compile_options(${CMAKE_PROJECT_NAME}_cuda_lib PRIVATE -Wno-gnu-line-marker)
-endif()

main.cpp

@@ -1,10 +1,10 @@
-#include "hello_world.h"
+#include "particle.hpp"
+#include "vec3.h"
 #include <iostream>
 
 int main() {
-  std::cout << "Starting CUDA example..." << std::endl; // Using endl to flush
+  Particle<float> test = {
-  check_cuda();
+      {0.0, 0.0, 0.0}, {0.0, 0.0, 0.0}, {0.0, 0.0, 0.0}, 10};
-  launch_hello_cuda();
+  std::cout << test.pos.x << " " << test.pos.y << " " << test.pos.z;
-  std::cout << "Ending CUDA example" << std::endl; // Using endl to flush
   return 0;
 }

src/CMakeLists.txt

@@ -1,16 +1,17 @@
-project(${CMAKE_PROJECT_NAME}_lib CUDA CXX)
+project(${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(${CMAKE_PROJECT_NAME}_lib
+add_library(${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 "pair_potentials.hpp"
+#include <cmath>
+
+PairPotential::~PairPotential() {};
+/**
+ * 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_r6 = sigma_r * sigma_r * sigma_r * sigma_r * sigma_r * 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 *
+                     (12.0 * sigma_r12 * inv_rmag - 6.0 * sigma_r6 * inv_rmag);
+    Vec3<real> force = r.scale(force_mag * inv_rmag);
+
+    return {energy, force};
+
+  } else {
+    return ForceAndEnergy::zero();
+  }
+};

src/pair_potentials.hpp

@@ -0,0 +1,49 @@
+#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;
+
+  PairPotential(real rcutoff) : m_rcutoffsq(rcutoff * rcutoff) {};
+  virtual ~PairPotential() = 0;
+
+  /**
+   * 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;
+
+  LennardJones(real sigma, real epsilon, real rcutoff)
+      : PairPotential(rcutoff), m_epsilon(epsilon), m_sigma(sigma) {};
+
+  ForceAndEnergy calc_force_and_energy(Vec3<real> r);
+
+  ~LennardJones() {};
+};
+
+#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();

tests/unit_tests/CMakeLists.txt

@@ -1,8 +1,9 @@
 include_directories(${gtest_SOURCE_DIR}/include ${gtest_SOURCE_DIR})
 
-add_executable(Unit_Tests_run
+add_executable(${NAME}_tests
-    test_example.cpp
+    test_potential.cpp
 )
 
-target_link_libraries(Unit_Tests_run gtest gtest_main)
+target_link_libraries(${NAME}_tests gtest gtest_main)
-target_link_libraries(Unit_Tests_run ${CMAKE_PROJECT_NAME}_lib)
+target_link_libraries(${NAME}_tests ${CMAKE_PROJECT_NAME}_lib)
+add_test(NAME ${NAME}Tests COMMAND ${CMAKE_BINARY_DIR}/tests/unit_tests/${NAME}_tests)

tests/unit_tests/test_potential.cpp

@@ -0,0 +1,174 @@
+#include "pair_potentials.hpp"
+#include "precision.hpp"
+#include "gtest/gtest.h"
+#include <cmath>
+
+class LennardJonesTest : public ::testing::Test {
+protected:
+  void SetUp() override {
+    // Default parameters
+    sigma = 1.0;
+    epsilon = 1.0;
+    r_cutoff = 2.5;
+
+    // Create default LennardJones object
+    lj = new LennardJones(sigma, epsilon, r_cutoff);
+  }
+
+  void TearDown() override { delete lj; }
+
+  real sigma;
+  real epsilon;
+  real r_cutoff;
+  LennardJones *lj;
+
+  // Helper function to compare Vec3 values with tolerance
+  void expect_vec3_near(const Vec3<real> &expected, const Vec3<real> &actual,
+                        real tolerance) {
+    EXPECT_NEAR(expected.x, actual.x, tolerance);
+    EXPECT_NEAR(expected.y, actual.y, tolerance);
+    EXPECT_NEAR(expected.z, actual.z, tolerance);
+  }
+};
+
+TEST_F(LennardJonesTest, ZeroDistance) {
+  // At zero distance, the calculation should return zero force and energy
+  Vec3<real> r = {0.0, 0.0, 0.0};
+  auto result = lj->calc_force_and_energy(r);
+
+  EXPECT_EQ(0.0, result.energy);
+  expect_vec3_near({0.0, 0.0, 0.0}, result.force, 1e-10);
+}
+
+TEST_F(LennardJonesTest, BeyondCutoff) {
+  // Distance beyond cutoff should return zero force and energy
+  Vec3<real> r = {3.0, 0.0, 0.0}; // 3.0 > r_cutoff (2.5)
+  auto result = lj->calc_force_and_energy(r);
+
+  EXPECT_EQ(0.0, result.energy);
+  expect_vec3_near({0.0, 0.0, 0.0}, result.force, 1e-10);
+}
+
+TEST_F(LennardJonesTest, AtMinimum) {
+  // The LJ potential has a minimum at r = 2^(1/6) * sigma
+  real min_dist = std::pow(2.0, 1.0 / 6.0) * sigma;
+  Vec3<real> r = {min_dist, 0.0, 0.0};
+  auto result = lj->calc_force_and_energy(r);
+
+  // At minimum, force should be close to zero
+  EXPECT_NEAR(-epsilon, result.energy, 1e-10);
+  expect_vec3_near({0.0, 0.0, 0.0}, result.force, 1e-10);
+}
+
+TEST_F(LennardJonesTest, AtEquilibrium) {
+  // At r = sigma, the energy should be zero and force should be repulsive
+  Vec3<real> r = {sigma, 0.0, 0.0};
+  auto result = lj->calc_force_and_energy(r);
+
+  EXPECT_NEAR(0.0, result.energy, 1e-10);
+  EXPECT_GT(result.force.x,
+            0.0); // Force should be repulsive (positive x-direction)
+  EXPECT_NEAR(0.0, result.force.y, 1e-10);
+  EXPECT_NEAR(0.0, result.force.z, 1e-10);
+}
+
+TEST_F(LennardJonesTest, RepulsiveRegion) {
+  // Test in the repulsive region (r < sigma)
+  Vec3<real> r = {0.8 * sigma, 0.0, 0.0};
+  auto result = lj->calc_force_and_energy(r);
+
+  // Energy should be positive and force should be repulsive
+  EXPECT_GT(result.energy, 0.0);
+  EXPECT_GT(result.force.x, 0.0); // Force should be repulsive
+}
+
+TEST_F(LennardJonesTest, AttractiveRegion) {
+  // Test in the attractive region (sigma < r < r_min)
+  Vec3<real> r = {1.5 * sigma, 0.0, 0.0};
+  auto result = lj->calc_force_and_energy(r);
+
+  // Energy should be negative and force should be attractive
+  EXPECT_LT(result.energy, 0.0);
+  EXPECT_LT(result.force.x,
+            0.0); // Force should be attractive (negative x-direction)
+}
+
+TEST_F(LennardJonesTest, ArbitraryDirection) {
+  // Test with a vector in an arbitrary direction
+  Vec3<real> r = {1.0, 1.0, 1.0};
+  auto result = lj->calc_force_and_energy(r);
+
+  // The force should be in the same direction as r but opposite sign
+  // (attractive region)
+  real r_mag = std::sqrt(r.squared_norm2());
+
+  // Calculate expected force direction (should be along -r)
+  Vec3<real> normalized_r = r.scale(1.0 / r_mag);
+  real force_dot_r = result.force.x * normalized_r.x +
+                     result.force.y * normalized_r.y +
+                     result.force.z * normalized_r.z;
+
+  // In this case, we're at r = sqrt(3) * sigma which is in attractive region
+  EXPECT_LT(force_dot_r, 0.0); // Force should be attractive
+
+  // Force should be symmetric in all dimensions for this vector
+  EXPECT_NEAR(result.force.x, result.force.y, 1e-10);
+  EXPECT_NEAR(result.force.y, result.force.z, 1e-10);
+}
+
+TEST_F(LennardJonesTest, ParameterVariation) {
+  // Test with different parameter values
+  real new_sigma = 2.0;
+  real new_epsilon = 0.5;
+  real new_r_cutoff = 5.0;
+
+  LennardJones lj2(new_sigma, new_epsilon, new_r_cutoff);
+
+  Vec3<real> r = {2.0, 0.0, 0.0};
+  auto result1 = lj->calc_force_and_energy(r);
+  auto result2 = lj2.calc_force_and_energy(r);
+
+  // Results should be different with different parameters
+  EXPECT_NE(result1.energy, result2.energy);
+  EXPECT_NE(result1.force.x, result2.force.x);
+}
+
+TEST_F(LennardJonesTest, ExactValueCheck) {
+  // Test with pre-calculated values for a specific case
+  LennardJones lj_exact(1.0, 1.0, 3.0);
+  Vec3<real> r = {1.5, 0.0, 0.0};
+  auto result = lj_exact.calc_force_and_energy(r);
+
+  // Pre-calculated values (you may need to adjust these based on your specific
+  // implementation)
+  real expected_energy =
+      4.0 * (std::pow(1.0 / 1.5, 12) - std::pow(1.0 / 1.5, 6));
+  real expected_force =
+      24.0 * (std::pow(1.0 / 1.5, 6) - 2.0 * std::pow(1.0 / 1.5, 12)) / 1.5;
+
+  EXPECT_NEAR(expected_energy, result.energy, 1e-10);
+  EXPECT_NEAR(-expected_force, result.force.x,
+              1e-10); // Negative because force is attractive
+  EXPECT_NEAR(0.0, result.force.y, 1e-10);
+  EXPECT_NEAR(0.0, result.force.z, 1e-10);
+}
+
+TEST_F(LennardJonesTest, NearCutoff) {
+  // Test behavior just inside and just outside the cutoff
+  real inside_cutoff = r_cutoff - 0.01;
+  real outside_cutoff = r_cutoff + 0.01;
+
+  Vec3<real> r_inside = {inside_cutoff, 0.0, 0.0};
+  Vec3<real> r_outside = {outside_cutoff, 0.0, 0.0};
+
+  auto result_inside = lj->calc_force_and_energy(r_inside);
+  auto result_outside = lj->calc_force_and_energy(r_outside);
+
+  // Inside should have non-zero values
+  EXPECT_NE(0.0, result_inside.energy);
+  EXPECT_NE(0.0, result_inside.force.x);
+
+  // Outside should be zero
+  EXPECT_EQ(0.0, result_outside.energy);
+  expect_vec3_near({0.0, 0.0, 0.0}, result_outside.force, 1e-10);
+}