Assignment4

.github/workflows/ci.yml

@@ -2,51 +2,61 @@ name: CI Pipeline
 
 on:
   push:
-    branches: [ "main", "Assignment3" ]
+    branches: [ "main", "Assignment*" ]
   pull_request:
-    branches: [ "main", "Assignment3" ]
+    branches: [ "main", "Assignment*" ]
 
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Dependencies
-      run: sudo apt install libxerces-c-dev
+      - name: Install Dependencies
+        run: sudo apt install libxerces-c-dev
 
-    - name: Create build directory
-      run: mkdir -p ${{github.workspace}}/build
+      - name: Create build directory
+        run: mkdir -p ${{github.workspace}}/build
 
-    - name: CMake Configure
-      run: cmake -D CMAKE_CXX_FLAGS="-fsanitize=address" -B ${{github.workspace}}/build ${{github.workspace}}
+      - name: CMake Configure
+        run: cmake -D CMAKE_CXX_FLAGS="-fsanitize=address" -B ${{github.workspace}}/build ${{github.workspace}}
 
-    - name: Build
-      run: cmake --build ${{github.workspace}}/build
-
-    - name: Save build environment
-      uses: actions/upload-artifact@v4
-      with:
-        name: built
-        path: ${{github.workspace}}/build
+      - name: Build
+        run: cmake --build ${{github.workspace}}/build
 
   test:
     needs: build
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install Dependencies
+        run: sudo apt install libxerces-c-dev
+
+      - name: Create build directory
+        run: mkdir -p ${{github.workspace}}/build
+
+      - name: CMake Configure
+        run: cmake -B ${{github.workspace}}/build ${{github.workspace}}
+
+      - name: Build
+        run: cmake --build ${{github.workspace}}/build
+
+      - name: Set execute permissions for tests
+        run: chmod +x ${{ github.workspace }}/build/MolSimTests ${{ github.workspace }}/build/MolSimBenchmark
+
+      - name: Check current location
+        run: pwd
 
-    - name: Reload build environment
-      uses: actions/download-artifact@v4
-      with:
-        name: built
-        path: ${{github.workspace}}/build
+      - name: list files
+        run: ls -l ${{ github.workspace }}
 
-    - name: Set execute permissions for tests
-      run: chmod +x ${{github.workspace}}/build/MolSimTests ${{github.workspace}}/build/MolSimBenchmark
+      - name: list files in build directory
+        run: ls -l ${{ github.workspace }}/build
 
-    - name: Tests
-      working-directory: ${{github.workspace}}/build
-      run: ctest -V -R '.*Test'
+      - name: Tests
+        working-directory: ${{ github.workspace }}/build
+        run: ctest -V -R '.*Test'

CMakeLists.txt

@@ -10,143 +10,166 @@ project(PSEMolDyn_GroupC VERSION 0.0.1)
 set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug;Release;RelWithDebInfo;MinSizeRel")
 
 # set Release as the default build type if it is not yet set.
-if(NOT CMAKE_BUILD_TYPE)
+if (NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE "Release" CACHE STRING
             "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE)
-endif(NOT CMAKE_BUILD_TYPE)
+endif (NOT CMAKE_BUILD_TYPE)
 
 # ----------------------------------------Adding Libraries-------------------------------------------------
 # Fetch spdlog from GitHub
 FetchContent_Declare(
         spdlog
         GIT_REPOSITORY https://github.com/gabime/spdlog
-        GIT_TAG        v1.x
+        GIT_TAG v1.x
 )
 FetchContent_MakeAvailable(spdlog)
 
 FetchContent_Declare(
-    cxxopts
-    GIT_REPOSITORY https://github.com/jarro2783/cxxopts
-    GIT_TAG        master
+        cxxopts
+        GIT_REPOSITORY https://github.com/jarro2783/cxxopts
+        GIT_TAG master
 )
 FetchContent_MakeAvailable(cxxopts)
 
 FetchContent_Declare(
         gtest
         GIT_REPOSITORY https://github.com/google/googletest.git
-        GIT_TAG        main
+        GIT_TAG main
 )
 FetchContent_MakeAvailable(gtest)
 
 FetchContent_Declare(
         benchmark
         GIT_REPOSITORY https://github.com/google/benchmark
-        GIT_TAG        main
+        GIT_TAG main
 )
 FetchContent_MakeAvailable(benchmark)
 
 find_package(OpenMP)
 if (OPENMP_FOUND)
-    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-    set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
-endif()
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+endif ()
+
 # ------------------------------------------------------------------------------------------------------------
 
 # collect all cpp files
 file(GLOB_RECURSE MY_SRC
     "${CMAKE_CURRENT_SOURCE_DIR}/src/*.cpp"
     "${CMAKE_CURRENT_SOURCE_DIR}/src/*.h"
+    "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/*.cpp"
+    "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/*.h"
+    "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/input_schema.cxx"
 )
 
 file(GLOB_RECURSE TEST_SOURCES
-    "${CMAKE_CURRENT_SOURCE_DIR}/tests/**/*.cpp"
-    "${CMAKE_CURRENT_SOURCE_DIR}/tests/**/*.h"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/*.cpp"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/objects/*.cpp"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/calculators/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/tests/**/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/tests/**/*.h"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/objects/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/calculators/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/boundaries/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/utils/*.h"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/utils/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/input_schema.cxx"
 )
 
 file(GLOB_RECURSE BENCHMARK_SOURCES
-    "${CMAKE_CURRENT_SOURCE_DIR}/benchmark/*.cpp"
-    "${CMAKE_CURRENT_SOURCE_DIR}/benchmark/*.h"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/objects/*.cpp"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/objects/*.h"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/*.cpp"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/*.h"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/calculators/*.cpp"
-    "${CMAKE_CURRENT_SOURCE_DIR}/src/calculators/*.h"
+        "${CMAKE_CURRENT_SOURCE_DIR}/benchmark/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/benchmark/*.h"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/objects/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/objects/*.h"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/*.h"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/calculators/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/calculators/*.h"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/utils/*.h"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/utils/*.cpp"
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/io/in/input_schema.cxx"
 )
 
 #------------------------------------------LOGGING---------------------------------------------------------
-# get the log level from the command line
-set(log_level "INFO" CACHE STRING "Log level")
+# check if the log level is defined in the environment
+if (DEFINED ENV{LOG_LEVEL})
+    set(log_level $ENV{LOG_LEVEL})
+else ()
+    set(log_level "INFO")
+endif ()
 
 # define the valid log levels
 set(valid_log_levels "TRACE" "DEBUG" "INFO" "WARN" "ERROR" "CRITICAL" "OFF")
 
 # check if the log level is valid
-if(NOT log_level IN_LIST valid_log_levels)
+if (NOT log_level IN_LIST valid_log_levels)
     message(FATAL_ERROR "Invalid log level: ${log_level}. Valid log levels are: ${valid_log_levels}")
-endif()
+endif ()
 
 # define the SPDLOG_ACTIVE_LEVEL macro
 add_compile_definitions(SPDLOG_ACTIVE_LEVEL=${log_level})
 add_compile_definitions(LOG_LEVEL="${log_level}")
 message(STATUS "Log level: ${log_level}")
 #-----------------------------------------------------------------------------------------------------------
 # create make target
-add_executable(MolSim ${MY_SRC})
-add_executable(MolSimTests ${TEST_SOURCES})
+add_executable(MolSim ${MY_SRC}
+        tests/io/in/XMLReaderTest.cpp)
+add_executable(MolSimTests ${TEST_SOURCES}
+        tests/io/in/XMLReaderTest.cpp)
 add_executable(MolSimBenchmark ${BENCHMARK_SOURCES})
 
 # set cxx standard. You may raise this if you want.
 target_compile_features(MolSim
         PRIVATE
-            cxx_std_17
+        cxx_std_17
 )
 
 target_include_directories(MolSim
         PUBLIC
-            ${CMAKE_CURRENT_SOURCE_DIR}/libs/libxsd
+        ${CMAKE_CURRENT_SOURCE_DIR}/libs/libxsd
         PRIVATE
-            ${CMAKE_CURRENT_SOURCE_DIR}/src
+        ${CMAKE_CURRENT_SOURCE_DIR}/src
 )
 
-target_include_directories(MolSimTests 
-    PRIVATE
+target_include_directories(MolSimTests
+        PRIVATE
         ${CMAKE_CURRENT_SOURCE_DIR}/tests
+        ${CMAKE_CURRENT_SOURCE_DIR}/src
+        ${CMAKE_CURRENT_SOURCE_DIR}/libs/libxsd
 )
 
-target_include_directories(MolSimBenchmark 
-    PRIVATE
+target_include_directories(MolSimBenchmark
+        PRIVATE
         ${CMAKE_CURRENT_SOURCE_DIR}/benchmark
+        ${CMAKE_CURRENT_SOURCE_DIR}/src
+        ${CMAKE_CURRENT_SOURCE_DIR}/libs/libxsd
 )
 
 target_link_libraries(MolSim
         # stuff that is used in headers and source files
         PUBLIC
-            xerces-c
+        xerces-c
         PRIVATE
-            spdlog::spdlog $<$<BOOL:${MINGW}>:ws2_32>
-            gtest
-            gtest_main
-            cxxopts
+        spdlog::spdlog $<$<BOOL:${MINGW}>:ws2_32>
+        gtest
+        gtest_main
+        cxxopts
 )
 
 target_link_libraries(MolSimTests
-         PRIVATE
-            gtest 
-            gtest_main
-            spdlog::spdlog $<$<BOOL:${MINGW}>:ws2_32>
+        PRIVATE
+        xerces-c
+        gtest
+        gtest_main
+        spdlog::spdlog $<$<BOOL:${MINGW}>:ws2_32>
 )
 
 target_link_libraries(MolSimBenchmark
-        PRIVATE 
-            benchmark
-            spdlog::spdlog $<$<BOOL:${MINGW}>:ws2_32>
-            gtest
-            gtest_main
+        PRIVATE
+        xerces-c
+        benchmark
+        spdlog::spdlog $<$<BOOL:${MINGW}>:ws2_32>
+        gtest
+        gtest_main
 )
 
 add_test(NAME MolSimTests COMMAND MolSimTests)
@@ -155,10 +178,10 @@ add_test(NAME MolSimTests COMMAND MolSimTests)
 # depending on the compiler different flags are used
 target_compile_options(MolSim
         PRIVATE
-            $<$<CXX_COMPILER_ID:Clang>:-Wall -fopenmp>
+        $<$<CXX_COMPILER_ID:Clang>:-Wall -fopenmp>
 )
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/modules)
 
 include(doxygen)
-include(CTest)
+include(CTest)

README.md

@@ -20,10 +20,16 @@ In order to build and run this code, you need the following tools installed on y
 
 2. Build the code:
 
-   `cmake -Dlog_level={WANTED_LOG_LEVEL} ..`
+   `cmake ..`
+
+   The default log level is `INFO`.
+
+   If you wish to set the log level manually, run:
+   `LOG_LEVEL={WANTED_LOG_LEVEL} cmake ..`
 
    Valid log levels are: `TRACE`, `DEBUG`, `INFO`, `WARN`, `ERROR`, `CRITICAL`, `OFF`.
 
+
 3. Make:
 
    `make -j $(nproc)`
@@ -34,12 +40,13 @@ In order to build and run this code, you need the following tools installed on y
 
 4. Run the code:
 
-   `./MolSim {INPUT} {DELTA_T} {END_TIME} {OUTPUT_WRITER} {CALCULATOR}`
+   `./MolSim {INPUT} {DELTA_T} {END_TIME} {OUTPUT_WRITER} {CALCULATOR} {BOUNDARIES}`
 
-   Example calls: 
-      - `./MolSim --help`
-      - `./MolSim --input=../resources/input-sun.txt --delta_t=0.014 --end_time=1000 --output=vtk --calculator=sv`
-      - `./MolSim --input=../resources/input-cuboid.txt --delta_t=0.0002 --end_time=5 --output=vtk --calculator=lj`
+   Example calls:
+   - `./MolSim --help`
+   - `./MolSim --input=../resources/input-sun.txt --delta_t=0.014 --end_time=1000 --output=vtk --calculator=sv`
+   - `./MolSim --input=../resources/input-cuboid.txt --delta_t=0.0002 --end_time=5 --output=vtk --calculator=lj`
+   - `./MolSim --input=../resources/input-cuboid.xml --output=vtk --calculator=lj`
 
 5. Available options for arguments:
 
@@ -56,9 +63,9 @@ In order to build and run this code, you need the following tools installed on y
    `{CALCULATOR}`: The calculator to use. Available options are sv, lj or dummy.
 
 6. If you wish to execute the tests:
-      - `./MolSimTests`
-      or
-      - `ctest -V -R '.*Test'`
+   - `./MolSimTests`
+     or
+   - `ctest -V -R '.*Test'`
 
 7. If you wish to execute the benchmarks:
-      - `./MolSimBenchmark`
+   - `./MolSimBenchmark`

benchmark/CalculatorLJBenchmark.cpp

@@ -2,6 +2,7 @@
 #include "../src/calculators/LJCalculator.h"
 #include "../src/objects/ParticleContainer.h"
 #include "../src/io/in/FileReader.h"
+#include "../src/io/in/TXTReader.h"
 #include "benchmark/benchmark.h"
 #include <memory>
 
@@ -11,8 +12,11 @@ static void BM_LJCalculator(benchmark::State& state) {
                             state.range(0) == 2 ? 0.001 :
                             state.range(0) == 3 ? 0.0005 : 5;
     const double end_time = 5.0;
-    std::unique_ptr<calculators::Calculator> calculator = std::make_unique<calculators::LJCalculator>(1, 5, 5.31608);
-    ParticleContainer particleContainer = FileReader::readFile("../resources/input-cuboid.txt");
+    std::unique_ptr<calculators::Calculator> calculator = std::make_unique<calculators::LJCalculator>(5.31608);
+
+    fileReaders::TXTReader fileReader = fileReaders::TXTReader();
+    SimulationDataContainer simulationDataContainer = fileReader.readFile("../resources/input-cuboid.txt");
+    ParticleContainer particleContainer = *simulationDataContainer.getParticleContainer();
 
     for (auto _ : state) {
         double current_time = 0;