.gitignore

@@ -1,8 +1,5 @@
 # Builds
 build/
-Debug/
-Testing/
-compile_commands.json
 
 # Google Tests
 tests/lib/
@@ -10,7 +7,3 @@ tests/lib/
 # Jet Brains
 .idea/
 cmake-build-debug/
-
-# Cache dir
-.cache
-

CMakeLists.txt

@@ -1,63 +1,23 @@
 cmake_minimum_required(VERSION 3.9)
-set(NAME "cudaCAC")
+project(MyProject)
-project(${NAME} LANGUAGES CUDA CXX)
-
-enable_testing()
-set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
-
-# Default settings 
-add_compile_options(-Wall -Wextra -Wpedantic)
-
-add_compile_options($<$<COMPILE_LANGUAGE:CUDA>:-Wno-pedantic>)
-
-# Add pedantic just for 
 
 set(CMAKE_CXX_STANDARD 17)
 
-# Cuda Settings
+set(SOURCE_FILES main.cpp)
-set(CMAKE_CUDA_ARCHITECTURES 61)
+add_executable(${CMAKE_PROJECT_NAME}_run ${SOURCE_FILES})
-set(CUDA_SEPARABLE_COMPILATION ON)
-# Cuda settings to get correct compile_commands.json
-set(CMAKE_CUDA_USE_RESPONSE_FILE_FOR_INCLUDES 0)
-set(CMAKE_CUDA_USE_RESPONSE_FILE_FOR_LIBRARIES 0)
-set(CMAKE_CUDA_USE_RESPONSE_FILE_FOR_OBJECTS 0)
 
-# 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(/usr/local/cuda-12.8/include)
 include_directories(src)
-include_directories(kernels)
 
 add_subdirectory(src)
-add_subdirectory(kernels)
 add_subdirectory(tests)
 
-add_executable(${NAME} main.cpp)
+target_link_libraries(${CMAKE_PROJECT_NAME}_run ${CMAKE_PROJECT_NAME}_lib)
-install(DIRECTORY src/ DESTINATION src/)
-
-target_link_libraries(
-    ${NAME} 
-    PRIVATE
-    ${NAME}_lib 
-    ${NAME}_cuda_lib 
-    ${CUDA_LIBRARIES}
-)
 
 # Doxygen Build
-option(BUILD_DOC "Build Documentation" OFF)
+option(BUILD_DOC "Build Documentation" ON)
 
 find_package(Doxygen)
-if(DOXYGEN_FOUND AND BUILD_DOC)
+if(DOXYGEN_FOUND)
     set(BUILD_DOC_DIR ${CMAKE_SOURCE_DIR}/build/docs)
     if(NOT EXISTS ${BUILD_DOC_DIR})
         file(MAKE_DIRECTORY ${BUILD_DOC_DIR})
@@ -73,6 +33,6 @@ if(DOXYGEN_FOUND AND BUILD_DOC)
             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
             COMMENT "Generating API documentation with Doxygen"
             VERBATIM)
-else(DOXYGEN_FOUND AND BUILD_DOC)
+else(DOXYGEN_FOUND)
     message("Doxygen needs to be installed to generate the documentation.")
-endif(DOXYGEN_FOUND AND BUILD_DOC)
+endif(DOXYGEN_FOUND)

README.md

@@ -6,7 +6,75 @@ following components:
 
 - Directory Structure
 - Make Build (CMake)
-- CUDA integration
 - Unit Test Framework (Google Test)
 - API Documentation (Doxygen)
 
+Feel free to fork this repository and tailor it to suit you.
+
+## Procedure
+1. Download Bash script to create new C++ projects 
+    ```bash
+    curl -O https://raw.githubusercontent.com/TimothyHelton/cpp_project_template/master/new_cpp_project.sh
+    chmod u+x new_cpp_project.sh
+    ```
+1. Create new C++ project
+    ```bash
+    ./new_cpp_project.sh NewProjectName
+    ```
+1. In the project top level **CMakeLists.txt**:
+    1. Line 2: Change the variable **MyProject** to the name of your project.
+        ```cmake
+        project(NewProject)
+        ```
+        - This variable will be used in a couple of different places.
+            - MyProject_run: will be the main executable name
+            - MyProject_lib: will be the project library name
+    1. Line 4: Set the version of C++ to use.  For example, let's set up the
+    NewProject to use C++ 11.
+        ```cmake
+        set(CMAKE_CXX_STANDARD 11)
+        ```
+1. Update project name and description in the `Doxyfile` located in the `docs`
+directory.
+    1. Update line `PROJECT_NAME`
+        1. This name will appear on each documentation page.
+    1. Update line `PROJECT_NUMBER`
+        1. This is the version number of your project.
+    1. Update line `PROJECT_BRIEF`
+        1. Any text entered here will also appear on each documentation page.
+        Try not to make this one too long.
+1. Reload the top CMake file.
+
+## CLION IDE Specific Instructions
+I started using an IDE from [JET Brains](https://www.jetbrains.com/) tailored
+for Python called [PyCharm](https://www.jetbrains.com/pycharm/) and thought
+it helped me write better code.
+I'd been wanting to learn C++ and decided to give JET Brains C/C++ IDE called
+[CLion](https://www.jetbrains.com/clion/) a try.
+The code completion, interactive suggestions, debugger, introspection tools,
+and built-in test execution are very handy.
+There are a couple extra details to set when using this IDE.
+
+1. The IDE allows you to mark directories with their desired purpose.
+To mark a directory right click on the directory name in the `Project` window
+and select `Mark Directory as` from the drop-down menu.
+    1. Mark the `src` directory as `Project Sources and Headers`
+    1. Mark the `tests/lib/googletest` directory as  `Library Files`
+1. Setup the `Run/Debug Configuration` by selecting `Edit Configurations...`
+from the pull-down menu from the run button (green triangle) in the upper right
+corner.
+    1. Update Doxygen Build to execute the unit test suite.
+        1. Select Doxygen from the Application menu on the left.
+        1. Choose the **executable** for Doxygen to be `Unit_Tests_run`.
+    1. Create a `Google Test` configuration
+        1. In the upper left corner select the plus symbol.
+        1. Chose `Google Test` from the drop-down menu.
+        1. Set **Name** to `Unit Tests`.
+        1. Set **Target** to `Unit_Tests_run`.
+
+## Wrap Up
+That should be all it takes to start writing code.
+If you find any issues or bugs with this repository please file an issue on
+[GitHub](https://github.com/TimothyHelton/cpp_project_template/issues).
+
+Hope you find this template useful and enjoy learning C++!

create_project.sh

@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+
+# Exit if name argument is not given
+if [ -z "$*" ]; then
+    echo "A project name argument must be provided."
+    exit 0
+fi
+
+NAME=$1
+
+
+################################################################################
+
+
+# Clone template repository
+git clone https://github.com/TimothyHelton/cpp_project_template
+
+# Create bare repository
+git --bare init ${NAME}
+
+# Push template master branch to bare repository
+cd cpp_project_template
+git push ../${NAME} +master:master
+
+# Convert bare repository into a normal repository
+cd ../${NAME}
+mkdir .git
+mv * .git
+git config --local --bool core.bare false
+git reset --hard
+
+# Clean Up
+rm -rf ../cpp_project_template ../create_project.sh

kernels/CMakeLists.txt

@@ -1,14 +0,0 @@
-project(${NAME}_cuda_lib CUDA CXX)
-
-set(HEADER_FILES
-    pair_potentials.cuh
-)
-set(SOURCE_FILES
-)
-
-# The library contains header and source files.
-add_library(${NAME}_cuda_lib INTERFACE
-    ${SOURCE_FILES}
-    ${HEADER_FILES}
-)
-

kernels/pair_potentials.cuh

@@ -1,91 +0,0 @@
-#ifndef POTENTIALS_H
-#define POTENTIALS_H
-
-#include "precision.hpp"
-#include "vec3.h"
-
-#ifdef __CUDACC__
-#define CUDA_CALLABLE __host__ __device__
-#else
-#define CUDA_CALLABLE
-#endif
-
-/**
- * Result struct for the Pair Potential
- */
-struct ForceAndEnergy {
-  real energy;
-  Vec3<real> force;
-
-  CUDA_CALLABLE 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) {};
-#ifdef __CUDACC__
-  CUDA_CALLABLE ~PairPotential();
-#else
-  virtual ~PairPotential() = 0;
-#endif
-
-  /**
-   * Calculate the force and energy for a specific atom pair based on a
-   * displacement vector r.
-   */
-  CUDA_CALLABLE virtual ForceAndEnergy calc_force_and_energy(Vec3<real> r) = 0;
-};
-
-/**
- * Calculate the Lennard-Jones energy and force for the current particle pair
- * described by displacement vector r
- */
-struct LennardJones : PairPotential {
-  real m_epsilon;
-  real m_sigma;
-
-  CUDA_CALLABLE LennardJones(real sigma, real epsilon, real rcutoff)
-      : PairPotential(rcutoff), m_epsilon(epsilon), m_sigma(sigma) {};
-
-  CUDA_CALLABLE ForceAndEnergy 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();
-    }
-  };
-
-  CUDA_CALLABLE ~LennardJones(){};
-};
-
-PairPotential::~PairPotential() {};
-#endif

main.cpp

@@ -1,9 +1,3 @@
-#include "particle.hpp"
-#include "vec3.h"
-#include <iostream>
-
 int main() {
-  Particle test = {{0.0, 0.0, 0.0}, {0.0, 0.0, 0.0}, {0.0, 0.0, 0.0}, 10};
-  std::cout << test.pos.x << " " << test.pos.y << " " << test.pos.z;
   return 0;
-}
+}

new_cpp_project.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+# Exit if name argument is not given
+if [ -z "$*" ]; then
+    echo "A project name argument must be provided."
+    exit 0
+fi
+
+NAME=$1
+
+
+################################################################################
+
+
+# Download latest version of the build file
+curl -O https://raw.githubusercontent.com/TimothyHelton/cpp_project_template/master/create_project.sh
+chmod u+x create_project.sh
+
+# Create Project
+./create_project.sh ${NAME}

src/CMakeLists.txt

@@ -1,16 +1,17 @@
-project(${NAME}_lib CUDA CXX)
+project(${CMAKE_PROJECT_NAME}_lib)
 
 set(HEADER_FILES
-    particle.hpp
-    simulation.hpp
-    box.hpp
-
 )
 set(SOURCE_FILES
 )
 
-# The library contains header and source files.
+if (EXISTS ${SOURCE_FILES})
-add_library(${NAME}_lib INTERFACE
+    # The library contains header and source files.
-    ${HEADER_FILES} 
+    add_library(${CMAKE_PROJECT_NAME}_lib STATIC
-    ${SOURCE_FILES}
+        ${SOURCE_FILES}
-)
+        ${HEADER_FILES}
+    )
+else()
+    # The library only contains header files.
+    add_library(${CMAKE_PROJECT_NAME}_lib INTERFACE)
+endif()

src/box.hpp

@@ -1,23 +0,0 @@
-#ifndef BOX_H
-#define BOX_H
-
-#include "precision.hpp"
-/**
- * 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.
- */
-struct Box {
-  real xlo;
-  real xhi;
-  real ylo;
-  real yhi;
-  real zlo;
-  real zhi;
-  bool x_is_periodic;
-  bool y_is_periodic;
-  bool z_is_periodic;
-};
-
-#endif

src/particle.hpp

@@ -1,19 +0,0 @@
-#ifndef PARTICLE_H
-#define PARTICLE_H
-
-#include "precision.hpp"
-#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.
- */
-struct Particle {
-  Vec3<real> pos;
-  Vec3<real> vel;
-  Vec3<real> force;
-  real mass;
-};
-
-#endif

src/precision.hpp

@@ -1,15 +0,0 @@
-#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

@@ -1,18 +0,0 @@
-#ifndef SIMULATION_H
-#define SIMULATION_H
-
-#include "box.hpp"
-#include "particle.hpp"
-#include "precision.hpp"
-#include <vector>
-
-class Simulation {
-  // Simulation State variables
-  real timestep;
-  Box box;
-
-  // Host Data
-  std::vector<Particle> particles;
-};
-
-#endif

tests/CMakeLists.txt

@@ -10,5 +10,4 @@ if(NOT EXISTS ${GOOGLETEST_DIR})
 endif()
 
 add_subdirectory(lib/googletest)
-add_subdirectory(unit_tests)
+add_subdirectory(unit_tests)
-add_subdirectory(cuda_unit_tests)

tests/cuda_unit_tests/CMakeLists.txt

@@ -1,9 +0,0 @@
-include_directories(${gtest_SOURCE_DIR}/include ${gtest_SOURCE_DIR})
-
-add_executable(${NAME}_cuda_tests
-    test_potential.cu
-)
-
-target_link_libraries(${NAME}_cuda_tests gtest gtest_main)
-target_link_libraries(${NAME}_cuda_tests ${CMAKE_PROJECT_NAME}_cuda_lib)
-add_test(NAME ${NAME}CudaTests COMMAND ${CMAKE_BINARY_DIR}/tests/unit_tests/${NAME}_tests)

tests/cuda_unit_tests/test_potential.cu

@@ -1,316 +0,0 @@
-#include "pair_potentials.cuh"
-#include "precision.hpp"
-#include "gtest/gtest.h"
-#include <cmath>
-#include <cuda_runtime.h>
-
-// Structure to hold test results from device
-struct TestResults {
-  bool zero_distance_pass;
-  bool beyond_cutoff_pass;
-  bool at_minimum_pass;
-  bool at_equilibrium_pass;
-  bool repulsive_region_pass;
-  bool attractive_region_pass;
-  bool arbitrary_direction_pass;
-  bool parameter_variation_pass;
-  bool exact_value_check_pass;
-  bool near_cutoff_pass;
-
-  // Additional result data for exact checks
-  real energy_values[10];
-  Vec3<real> force_values[10];
-};
-
-// Check if two Vec3 values are close within tolerance
-__device__ bool vec3_near(const Vec3<real> &a, const Vec3<real> &b,
-                          real tolerance) {
-  return (fabs(a.x - b.x) < tolerance) && (fabs(a.y - b.y) < tolerance) &&
-         (fabs(a.z - b.z) < tolerance);
-}
-
-// Device kernel to run all tests
-__global__ void lennard_jones_test_kernel(TestResults *results) {
-  // Default parameters
-  real sigma = 1.0;
-  real epsilon = 1.0;
-  real r_cutoff = 2.5;
-  real tolerance = 1e-10;
-
-  // Create LennardJones object on device
-  LennardJones lj(sigma, epsilon, r_cutoff);
-
-  // Zero Distance Test
-  {
-    Vec3<real> r = {0.0, 0.0, 0.0};
-    auto result = lj.calc_force_and_energy(r);
-    results->energy_values[0] = result.energy;
-    results->force_values[0] = result.force;
-    results->zero_distance_pass =
-        (result.energy == 0.0) &&
-        vec3_near(Vec3<real>{0.0, 0.0, 0.0}, result.force, tolerance);
-  }
-
-  // Beyond Cutoff Test
-  {
-    Vec3<real> r = {3.0, 0.0, 0.0};
-    auto result = lj.calc_force_and_energy(r);
-    results->energy_values[1] = result.energy;
-    results->force_values[1] = result.force;
-    results->beyond_cutoff_pass =
-        (result.energy == 0.0) &&
-        vec3_near(Vec3<real>{0.0, 0.0, 0.0}, result.force, tolerance);
-  }
-
-  // At Minimum Test
-  {
-    real min_dist = 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);
-    results->energy_values[2] = result.energy;
-    results->force_values[2] = result.force;
-    results->at_minimum_pass =
-        (fabs(result.energy + epsilon) < tolerance) &&
-        vec3_near(Vec3<real>{0.0, 0.0, 0.0}, result.force, tolerance);
-  }
-
-  // At Equilibrium Test
-  {
-    Vec3<real> r = {sigma, 0.0, 0.0};
-    auto result = lj.calc_force_and_energy(r);
-    results->energy_values[3] = result.energy;
-    results->force_values[3] = result.force;
-    results->at_equilibrium_pass = (fabs(result.energy) < tolerance) &&
-                                   (result.force.x > 0.0) &&
-                                   (fabs(result.force.y) < tolerance) &&
-                                   (fabs(result.force.z) < tolerance);
-  }
-
-  // Repulsive Region Test
-  {
-    Vec3<real> r = {0.8 * sigma, 0.0, 0.0};
-    auto result = lj.calc_force_and_energy(r);
-    results->energy_values[4] = result.energy;
-    results->force_values[4] = result.force;
-    results->repulsive_region_pass =
-        (result.energy > 0.0) && (result.force.x > 0.0);
-  }
-
-  // Attractive Region Test
-  {
-    Vec3<real> r = {1.5 * sigma, 0.0, 0.0};
-    auto result = lj.calc_force_and_energy(r);
-    results->energy_values[5] = result.energy;
-    results->force_values[5] = result.force;
-    results->attractive_region_pass =
-        (result.energy < 0.0) && (result.force.x < 0.0);
-  }
-
-  // Arbitrary Direction Test
-  {
-    Vec3<real> r = {1.0, 1.0, 1.0};
-    auto result = lj.calc_force_and_energy(r);
-    results->energy_values[6] = result.energy;
-    results->force_values[6] = result.force;
-
-    real r_mag = sqrt(r.squared_norm2());
-    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;
-
-    results->arbitrary_direction_pass =
-        (force_dot_r < 0.0) &&
-        (fabs(result.force.x - result.force.y) < tolerance) &&
-        (fabs(result.force.y - result.force.z) < tolerance);
-  }
-
-  // Parameter Variation Test
-  {
-    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->energy_values[7] = result2.energy;
-    results->force_values[7] = result2.force;
-
-    results->parameter_variation_pass = (result1.energy != result2.energy) &&
-                                        (result1.force.x != result2.force.x);
-  }
-
-  // Exact Value Check Test
-  {
-    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);
-
-    results->energy_values[8] = result.energy;
-    results->force_values[8] = result.force;
-
-    real expected_energy = 4.0 * (pow(1.0 / 1.5, 12) - pow(1.0 / 1.5, 6));
-    real expected_force =
-        24.0 * (pow(1.0 / 1.5, 6) - 2.0 * pow(1.0 / 1.5, 12)) / 1.5;
-
-    results->exact_value_check_pass =
-        (fabs(result.energy - expected_energy) < tolerance) &&
-        (fabs(result.force.x + expected_force) < tolerance) &&
-        (fabs(result.force.y) < tolerance) &&
-        (fabs(result.force.z) < tolerance);
-  }
-
-  // Near Cutoff Test
-  {
-    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);
-
-    results->energy_values[9] = result_inside.energy;
-    results->force_values[9] = result_inside.force;
-
-    results->near_cutoff_pass =
-        (result_inside.energy != 0.0) && (result_inside.force.x != 0.0) &&
-        (result_outside.energy == 0.0) &&
-        vec3_near(Vec3<real>{0.0, 0.0, 0.0}, result_outside.force, tolerance);
-  }
-}
-
-// Helper class for CUDA error checking
-class CudaErrorCheck {
-public:
-  static void checkAndThrow(cudaError_t err, const char *msg) {
-    if (err != cudaSuccess) {
-      std::string error_message =
-          std::string(msg) + ": " + cudaGetErrorString(err);
-      throw std::runtime_error(error_message);
-    }
-  }
-};
-
-// Google Test wrapper that runs the device tests
-class LennardJonesCudaTest : public ::testing::Test {
-protected:
-  void SetUp() override {
-    // Allocate device memory for results
-    CudaErrorCheck::checkAndThrow(
-        cudaMalloc(&d_results, sizeof(TestResults)),
-        "Failed to allocate device memory for test results");
-  }
-
-  void TearDown() override {
-    if (d_results) {
-      cudaFree(d_results);
-      d_results = nullptr;
-    }
-  }
-
-  // Helper function to run tests on device and get results
-  TestResults runDeviceTests() {
-    TestResults h_results;
-
-    // Clear device memory
-    CudaErrorCheck::checkAndThrow(cudaMemset(d_results, 0, sizeof(TestResults)),
-                                  "Failed to clear device memory");
-
-    // Run kernel with a single thread
-    lennard_jones_test_kernel<<<1, 1>>>(d_results);
-
-    // Check for kernel launch errors
-    CudaErrorCheck::checkAndThrow(cudaGetLastError(), "Kernel launch failed");
-
-    // Wait for kernel to complete
-    CudaErrorCheck::checkAndThrow(cudaDeviceSynchronize(),
-                                  "Kernel execution failed");
-
-    // Copy results back to host
-    CudaErrorCheck::checkAndThrow(cudaMemcpy(&h_results, d_results,
-                                             sizeof(TestResults),
-                                             cudaMemcpyDeviceToHost),
-                                  "Failed to copy results from device");
-
-    return h_results;
-  }
-
-  TestResults *d_results = nullptr;
-};
-
-// Define the actual test cases
-TEST_F(LennardJonesCudaTest, DeviceZeroDistance) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.zero_distance_pass)
-      << "Zero distance test failed on device. Energy: "
-      << results.energy_values[0] << ", Force: (" << results.force_values[0].x
-      << ", " << results.force_values[0].y << ", " << results.force_values[0].z
-      << ")";
-}
-
-TEST_F(LennardJonesCudaTest, DeviceBeyondCutoff) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.beyond_cutoff_pass)
-      << "Beyond cutoff test failed on device. Energy: "
-      << results.energy_values[1];
-}
-
-TEST_F(LennardJonesCudaTest, DeviceAtMinimum) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.at_minimum_pass)
-      << "At minimum test failed on device. Energy: "
-      << results.energy_values[2];
-}
-
-TEST_F(LennardJonesCudaTest, DeviceAtEquilibrium) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.at_equilibrium_pass)
-      << "At equilibrium test failed on device. Energy: "
-      << results.energy_values[3] << ", Force x: " << results.force_values[3].x;
-}
-
-TEST_F(LennardJonesCudaTest, DeviceRepulsiveRegion) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.repulsive_region_pass)
-      << "Repulsive region test failed on device. Energy: "
-      << results.energy_values[4] << ", Force x: " << results.force_values[4].x;
-}
-
-TEST_F(LennardJonesCudaTest, DeviceAttractiveRegion) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.attractive_region_pass)
-      << "Attractive region test failed on device. Energy: "
-      << results.energy_values[5] << ", Force x: " << results.force_values[5].x;
-}
-
-TEST_F(LennardJonesCudaTest, DeviceArbitraryDirection) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.arbitrary_direction_pass)
-      << "Arbitrary direction test failed on device.";
-}
-
-TEST_F(LennardJonesCudaTest, DeviceParameterVariation) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.parameter_variation_pass)
-      << "Parameter variation test failed on device.";
-}
-
-TEST_F(LennardJonesCudaTest, DeviceExactValueCheck) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.exact_value_check_pass)
-      << "Exact value check test failed on device. Energy: "
-      << results.energy_values[8] << ", Force x: " << results.force_values[8].x;
-}
-
-TEST_F(LennardJonesCudaTest, DeviceNearCutoff) {
-  auto results = runDeviceTests();
-  EXPECT_TRUE(results.near_cutoff_pass)
-      << "Near cutoff test failed on device. Inside energy: "
-      << results.energy_values[9];
-}

tests/unit_tests/CMakeLists.txt

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

tests/unit_tests/test_potential.cpp

@@ -1,174 +0,0 @@
-#include "pair_potentials.cuh"
-#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);
-}