jkr11 · jkr11 · Jan 31, 2025 · Jan 31, 2025 · Jan 31, 2025 · Jan 31, 2025
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -18,8 +18,6 @@ elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     add_compile_options(-xHost -ipo -qopenmp -O3 -fp-model fast=2)
 endif ()
 
-#add_compile_options(-xHost -O3 -fp-model fast=2)
-
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules")
 include(googletest)
 include(doxygen)

diff --git a/README.md b/README.md
@@ -8,6 +8,7 @@ Final Assignment
 - Cmake 3.28.3
 - Doxygen 1.9.8 (`sudo apt install doxygen`)
 - Libxerces (`sudo apt install libxerces-c-dev`)
+
 ## Build
 
 ### Configuration
@@ -33,12 +34,15 @@ Final Assignment
   cmake -S . -B build -DBUILD_TESTS=ON 
 ```
 
-To build with Intel's C++ compiler (```icx```/```icpx```), set the following options (currently this is on the [`coolmuc_test`](https://github.com/jkr11/MolSim/tree/coolmuc_test) branch, but it works locally)
+To build with Intel's C++ compiler (```icx```/```icpx```), set the following options (currently this is on the [
+`coolmuc_test`](https://github.com/jkr11/MolSim/tree/coolmuc_test) branch, but it works locally)
 
 ```bash
   cmake -S . -B build -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx
 ```
-for other compilers add the necessary compiler id to the options. 
+
+for other compilers add the necessary compiler id to the options.
+
 ```bash
   cd build/tests
   make -j $(nproc)
@@ -79,6 +83,7 @@ Using the build script in `/script/`
 - Please note that `$BUILD` and `$INPUT` are only available if the scripts are executed via source.
 
 ### CMake Options
+
 ```console
   - ENABLE_BENCHMARK : enables benchmark mode with no printing of info and writing to files
   - BUILD_TESTS : enables and builds the tests/ directory in the build directory
@@ -100,13 +105,34 @@ Using the build script in `/script/`
   ```
 
 - Output is located in `./output/<current_time>`
-- Checkpoints as an input have to be explicitely stated in the input ```.xml``` file. I would recommend putting
-  checkpoint into `/input/`.
-    - Example:
+- Checkpoints as an input have to be explicitely stated in the input ```.xml``` file. In order to verify against the
+  checkpoint schema, all checkpoint files must point to the valid schema. As this location is hardcoded, all checkpoints
+  work out of the box if they are in the `/input/` directory. If they are somewhere else, you have to adjust the schema
+  path in the header of the checkpoint file.
+
+- A quick example for checkpointing in Assignment 4 task 3: (in `build/src`)
+
+```bash
+  ./MolSim -f ../../input/week43checkpoint.xml -c ../../input/<name_of_your_choice.xml>
+  ..... This eventually writes the checkpoint after running ----------
+```
+
+the add the following to week43.xml:
 
 ```xml
 
-<checkpoint>../input/checkpoint.xml/</checkpoint>
+<checkpoint>
+    <name>../../input/
+        <name_of_your_choice.xml>
+    </name>
+    ...
+</checkpoint>
+```
+
+and run
+
+```bash
+  ./MolSim -f ../../input/week43.xml
 ```
 
 - `--step_size` is relative to the passed simulation time and not the number of iterations

diff --git a/input/week43periodic.xml b/input/week43periodic.xml
@@ -43,7 +43,7 @@
         <t_end>40</t_end>
         <twoD>true</twoD>
         <checkpoint>
-            <name>../scripts/output/test.xml</name>
+            <name>../input/testcheckpointdelete.xml</name>
             <is_membrane>false</is_membrane>
             <domain>
                 <x>0</x>

diff --git a/src/calc/VerletIntegrator.h b/src/calc/VerletIntegrator.h
@@ -37,7 +37,7 @@ class VerletIntegrator {
    */
   double current_time_;
   /**
-   * Parallelization strategy used
+   * Parallelisation strategy used, default is 3 so no parallelisation
    */
   ParallelStrategy strategy_ = ParallelStrategy::STRATEGY_3;
 

diff --git a/src/defs/Generators/MembraneGenerator.h b/src/defs/Generators/MembraneGenerator.h
@@ -6,7 +6,6 @@
 #define MEMBRANEGENERATOR_H
 #pragma once
 #include "ParticleGenerator.h"
-#include "utils/SpdWrapper.h"
 
 /**
  * @brief Generates Particles to a container in the shape of a cuboid [dim1,

diff --git a/src/defs/Particle.cpp b/src/defs/Particle.cpp
@@ -7,7 +7,6 @@
 
 #include "Particle.h"
 
-#include "debug/debug_print.h"
 #include "utils/ArrayUtils.h"
 #include "utils/SpdWrapper.h"
 

diff --git a/src/defs/Thermostat.h b/src/defs/Thermostat.h
@@ -10,7 +10,7 @@
 #include "containers/ParticleContainer.h"
 
 /**
- * adjusts the temperature of the system at a given periodic frequency
+ * @brief adjusts the temperature of the system at a given periodic frequency
  */
 class Thermostat {
  private:

diff --git a/src/defs/containers/DirectSumContainer.cpp b/src/defs/containers/DirectSumContainer.cpp
@@ -27,8 +27,6 @@ DirectSumContainer::DirectSumContainer(const std::vector<Particle>& particles)
   }
 }
 
-// DirectSumContainer::~DirectSumContainer();
-
 void DirectSumContainer::addParticle(const Particle& p) {
   particles_.push_back(p);
 }

diff --git a/src/defs/containers/LinkedCellsContainer.cpp b/src/defs/containers/LinkedCellsContainer.cpp
@@ -421,14 +421,13 @@ void LinkedCellsContainer::computeInteractiveForcesForceBuffer(
 
   // for some reason parallelising this makes it slower, no matter which
   // approach is used
-  // #pragma omp parallel for collapse(2)
   for (size_t j = 0; j < particle_count_; j++) {
     for (int i = 1; i < num_threads; i++) {
-      // #pragma omp critical
-      { force_buffers[0][j] = force_buffers[0][j] + force_buffers[i][j]; }
+      {
+        force_buffers[0][j] = force_buffers[0][j] + force_buffers[i][j];
+      }
     }
   }
-  // #pragma omp barrier
 
 #pragma omp parallel for
   for (size_t i = 0; i < particles_.size(); ++i) {
@@ -685,10 +684,6 @@ void LinkedCellsContainer::applyReflectiveBoundary(const size_t dimension) {
                                 pos);  // if both of them are so small that
       // they would trigger the boundary, the
       // simulation itself is already broken
-      // SpdWrapper::get()->info(
-      //     "double dist: {} at [{}, {}, {}] adn v=[{}, {}, {}]",
-      //     double_dist_to_boundary, p->getX()[0], p->getX()[1], p->getX()[2],
-      //     p->getV()[0], p->getV()[1], p->getV()[2]);
       if (double_dist_to_boundary < sigma_factor * p->getSigma()) {
         const double force =
             LennardJones::simpleForce(*p, double_dist_to_boundary);
@@ -707,11 +702,6 @@ void LinkedCellsContainer::applyReflectiveBoundary(const size_t dimension) {
             "Applied Force=[{}, {}, {}] to Particle at [{}, {}, {}]",
             p->getF()[0], p->getF()[1], p->getF()[2], p->getX()[0],
             p->getX()[1], p->getX()[2]);
-
-        // SpdWrapper::get()->info(
-        //     "Applied Force=[{}, {}, {}] to Particle at [{}, {}, {}]",
-        //     p->getF()[0], p->getF()[1], p->getF()[2], p->getX()[0],
-        //     p->getX()[1], p->getX()[2]);
       }
     }
   }
@@ -772,10 +762,6 @@ void LinkedCellsContainer::applyPeriodicBoundary(const size_t dimension) {
       const auto adjacent_cell_index =
           cellCoordToIndex(adjacent_cell_coordinates);
 
-      // // account for the dimension that is checked
-      // particle_distance_offset[problematic_dimension] =
-      //     domain[problematic_dimension];
-
       // iterate over all pairs and calculate force
 
       for (const auto &p : cells_[cell_index]) {

diff --git a/tests/CLArgumentParserTest.cpp b/tests/CLArgumentParserTest.cpp
@@ -6,7 +6,7 @@
 
 #include "../src/io/CLArgumentParser.h"
 
-/*
+/**
  * @brief Parse example CLI arguments correctly
  */
 TEST(CLArgumentParser, parse) {

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
@@ -19,7 +19,8 @@ if (BUILD_TESTS)
             XmlReaderTest.cpp
             TruncatedLennardJones.cpp
             IndexForceTest.cpp
-            SingularGravityTest.cpp)
+            SingularGravityTest.cpp
+            MixingTest.cpp)
 
     target_link_libraries(MolSimTest MolSimLib GTest::gtest_main)
     include(GoogleTest)

diff --git a/tests/CheckpointTest.cpp b/tests/CheckpointTest.cpp
@@ -82,7 +82,7 @@ TEST(Checkpoint, cuboid) {
   }
 }
 
-/*
+/**
  * Test whether membranes (and especially the particle neighbours) are correctly
  * translated into a checkpoint
  */
@@ -117,7 +117,6 @@ TEST(Checkpoint, membrane) {
   char arg01[] = "MolSim";
   char arg11[] = "-f";
   char arg21[] = "../../tests/checkpoint_output_membrane_test.xml";
-  // char arg31[] = "-c";
   char* argv1[] = {arg01, arg11, arg21};
   auto [name1, step1, write_checkpoint1] = CLArgumentParser::parse(3, argv1);
 

diff --git a/tests/DirectSumContainerTest.cpp b/tests/DirectSumContainerTest.cpp
@@ -5,7 +5,7 @@
 #include "../src/defs/containers/DirectSumContainer.cpp"
 #include "testUtil.h"
 
-/*
+/**
  * Add particle changes internal vector length
  */
 TEST(DirectSumContainer, addParticleAndSize) {
@@ -20,7 +20,7 @@ TEST(DirectSumContainer, addParticleAndSize) {
       << "ParticleContainer particle count not matching after addParticle.";
 }
 
-/*
+/**
  * singleIterator iterates over each distinct particle exactly once
  */
 TEST(DirectSumContainer, singleIterator) {
@@ -42,7 +42,7 @@ TEST(DirectSumContainer, singleIterator) {
   EXPECT_VECTOR_EQ(vec, {p1, p2, p3});
 }
 
-/*
+/**
  * pair_iterator iterates over each distinct pair of particles exactly once
  */
 TEST(DirectSumContainer, pair_iterator) {

diff --git a/tests/IndexForceTest.cpp b/tests/IndexForceTest.cpp
@@ -10,7 +10,7 @@
 #include "debug/debug_print.h"
 #include "testUtil.h"
 
-/*
+/**
  * TruncatedLennardJones with distance >= sigma * c
  */
 TEST(IndexForce, single_index) {

diff --git a/tests/LennardJonesTest.cpp b/tests/LennardJonesTest.cpp
@@ -32,20 +32,6 @@ TEST(LennardJones, directionalForce2) {
              "Directional force wrong", 1e-5);
 }
 
-/*
- * LennardJones directional force, arbitrary example 3
- */
-/* removed because this never happens in an actual simulation
-TEST(LennardJones, directionalForce3) {
-  Particle p({0, 0, 0}, {0, 0, 0}, 0, 0, 0);
-  Particle q({0, 0, 0}, {0, 0, 0}, 0, 0, 0);
-  LennardJones lj;
-
-  dvec3 f = lj.directionalForce(p, q);
-  DVEC3_NEAR(f, {0.0, 0.0, 0.0}, "Directional force wrong", 1e-5);
-}
-*/
-
 /*
  * LennardJones directional force, arbitrary example 4
  */

diff --git a/tests/LinkedCellsContainerTest.cpp b/tests/LinkedCellsContainerTest.cpp
@@ -309,7 +309,7 @@ TEST(LinkedCellsContainer, pairIterator) {
       << "Pair count does not match reference implementation";
 }
 
-/*
+/**
  * boundaryIterator(...) goes over all particles in boundary
  */
 TEST(LinkedCellsContainer, boundaryIterator) {
@@ -374,7 +374,7 @@ TEST(LinkedCellsContainer, haloIterator) {
 }
 
 /**
- * @brief Tests if the C18 strategy is equal
+ * @brief Tests if the C18 strategy is equal to the standard pair iterator
  */
 TEST(LinkedCellsContainer, C18Strategy) {
   LinkedCellsConfig config = {.domain = {20, 20, 20},
@@ -425,7 +425,6 @@ TEST(LinkedCellsContainer, C18Strategy) {
     for (const auto& force : forces2) {
       f = f + force->directionalForce(p, q);
     }
-    // InfoVec("In PI: ", f);
     p.addF(f);
     q.subF(f);
   });
@@ -439,6 +438,9 @@ TEST(LinkedCellsContainer, C18Strategy) {
   }
 }
 
+/**
+ * Checks if Force Buffer calculates the same result as the standard pair iterator
+ */
 TEST(LinkedCellsContainer, ForceBufferIteration) {
   LinkedCellsConfig config = {.domain = {20, 20, 20},
                               .cutoff_radius = 3,
@@ -474,7 +476,6 @@ TEST(LinkedCellsContainer, ForceBufferIteration) {
     for (const auto& force : forces) {
       f = f + force->directionalForce(p, q);
     }
-    // InfoVec("In PI: ", f);
     p.addF(f);
     q.subF(f);
   });

diff --git a/tests/MembraneTest.cpp b/tests/MembraneTest.cpp
@@ -128,7 +128,6 @@ TEST(Membrane, LC3x3) {
   for (Particle& p : particles) {
     SpdWrapper::get()->info("Neighbours: {}", p.getNeighbours().size());
     for (const auto& [fst, snd] : p.getNeighbours()) {
-      // check for expired pointer (legacy from weak_ptr impl, maybe we go back
       ASSERT_TRUE(snd);
     }
   }
@@ -158,7 +157,11 @@ TEST(Membrane, LC3x3) {
   }
 }
 
-TEST(Membrane, LC4x4) {
+/**
+ * Tests various properties of the membrane structure on 4x4 particles using
+ * id's, also tests harmonic Force
+ */
+TEST(Membrane, LC4x4Harmonic) {
   constexpr LinkedCellsConfig linked_cells_config = {
       .domain = {20, 20, 20},
       .cutoff_radius = 4.0,
@@ -176,19 +179,8 @@ TEST(Membrane, LC4x4) {
   std::vector<Particle> particles;
 
   std::vector<std::unique_ptr<SingularForce>> singular_forces;
-  // singular_forces.push_back(std::make_unique<SingularGravity>(-0.001, 2));
   singular_forces.push_back(std::make_unique<HarmonicForce>(300, 2.2));
 
-  // std::vector<std::unique_ptr<InteractiveForce>> interactive_forces;
-  // interactive_forces.push_back(std::make_unique<TruncatedLennardJones>());
-
-  // std::vector<std::unique_ptr<IndexForce>> index_forces;
-  // IndexForceConfig index_force_config = {
-  //    .ids = {5},
-  //    .end_time = 15,
-  //    .force_values = {0, 0, 0.8},
-  // };
-  // index_forces.push_back(std::make_unique<IndexForce>());
   std::cout << "global id counter " << std::endl;
   MembraneGenerator membrane_generator({0, 0, 0}, {4, 4, 1}, 2.5, 1.0,
                                        {0, 0, 0}, 0.0, 1.0, 1.0, 1, true, {});

diff --git a/tests/MixingTest.cpp b/tests/MixingTest.cpp
@@ -9,7 +9,7 @@
 #include "../src/forces/TruncatedLennardJones.h"
 
 
-/*
+/**
  * LennardJones directional force, mixing 1
  */
 TEST(LennardJones, mixing) {
@@ -22,7 +22,7 @@ TEST(LennardJones, mixing) {
              "Directional force wrong", 1e-5);
 }
 
-/*
+/**
  * TruncatedLennardJones directional force, mixing 1
  */
 TEST(TruncatedLennardJones, mixing1) {

diff --git a/tests/ThermostatTest.cpp b/tests/ThermostatTest.cpp
@@ -245,7 +245,7 @@ TEST(Thermostat, heating) {
   EXPECT_NEAR(thermostat->getTemperature(*container), 10, 1e-6);
 }
 
-/*
+/**
  * this test the gradual thermostat, so when deltaT is set. In this case its 2.0
  * as specified, so we would expect that it converges after at 3k iterations (a
  * lot earlier actually but this is good enough) if n_thermostat is 100
@@ -319,8 +319,6 @@ TEST(Thermostat, gradual) {
       double temp = thermostat->getTemperature(*container);
       std::cout << "Temperature " << temp << std::endl;
       thermostat->setTemperature(*container);
-      // EXPECT_NEAR(thermostat->getTemperature(*container),
-      //             temp + thermostat->delta_temp, thermostat->delta_temp);
     }
   }
-Original file line number
+Diff line change
@@ Expand Up @@
       }
     }
-    // DirectSumContainer::~DirectSumContainer();
     void DirectSumContainer::addParticle(const Particle& p) {
       particles_.push_back(p);
     }
@@ Expand Down @@