Merge pull request #99 from ManuelLerchner/98-refactoring

General Refactoring and Fixes
ManuelLerchner · Jan 22, 2024 · ed8bd05 · ed8bd05
2 parents 24b2840 + 7ec61bd
commit ed8bd05
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Showing 31 changed files with 884 additions and 125 deletions.
diff --git a/benchmarks/contest1.cpp b/benchmarks/contest1.cpp
@@ -27,16 +27,19 @@ void execute2DRectBenchmark() {
         LinkedCellsContainer::BoundaryCondition::OUTFLOW,    LinkedCellsContainer::BoundaryCondition::OUTFLOW};
 
     // Settings for the Cuboid spawner of task 2
-    CuboidSpawner spawner1({0.6, 2.0, 0.5}, {250, 20, 1}, 1.2, 1.0, {0.0, 0.0, 0.0}, static_cast<int>(0), 1.0, 1.2, false, false, 40);
-    CuboidSpawner spawner2({0.6, 27.0, 0.5}, {250, 20, 1}, 1.2, 2.0, {0.0, 0.0, 0.0}, static_cast<int>(1), 1.0, 1.1, false, false, 40);
+    CuboidSpawner spawner1({0.6, 2.0, 0.5}, {250, 20, 1}, 1.2, 1.0, {0.0, 0.0, 0.0}, static_cast<int>(0), 1.0, 1.2, LockState::UNLOCKED,
+                           ThirdDimension::DISABLED, 40);
+    CuboidSpawner spawner2({0.6, 27.0, 0.5}, {250, 20, 1}, 1.2, 2.0, {0.0, 0.0, 0.0}, static_cast<int>(1), 1.0, 1.1, LockState::UNLOCKED,
+                           ThirdDimension::DISABLED, 40);
 
     std::vector<std::shared_ptr<PairwiseForceSource>> pairwise_forces;
     std::vector<std::shared_ptr<SimpleForceSource>> simple_force_sources;
     pairwise_forces.push_back(std::make_shared<LennardJonesForce>());
     simple_force_sources.push_back(std::make_shared<GlobalDownwardsGravity>(12.44));
 
     // Set the thermostat:
-    std::shared_ptr<Thermostat> thermostat = std::make_shared<AbsoluteThermostat>(40, std::numeric_limits<double>::infinity(), false);
+    std::shared_ptr<Thermostat> thermostat =
+        std::make_shared<AbsoluteThermostat>(40, std::numeric_limits<double>::infinity(), ThirdDimension::DISABLED);
     std::vector<std::shared_ptr<SimulationInterceptor>> simulation_interceptors;
     simulation_interceptors.push_back(std::make_shared<ThermostatInterceptor>(thermostat, 1000));
 

diff --git a/input/membrane/membrane_periodic.xml b/input/membrane/membrane_periodic.xml
@@ -38,7 +38,8 @@
             <GlobalDownwardsGravity g="0.001" />
         </forces>
         <interceptors>
-            <FrameWriter output_format="vtu" fps="60" video_length_s="30" />
+            <FrameWriter output_format="vtu" fps="24" video_length_s="30" />
+            <FrameWriter output_format="chkpt" fps="10" video_length_s="1" />
         </interceptors>
     </settings>
 

diff --git a/src/io/input/xml/XMLFileReader.cpp b/src/io/input/xml/XMLFileReader.cpp
@@ -11,6 +11,7 @@
 #include "io/output/chkpt/CheckPointWriter.h"
 #include "io/xml_schemas/xsd_type_adaptors/XSDToInternalTypeAdapter.h"
 #include "simulation/Simulation.h"
+#include "utils/Enums.h"
 
 std::string trim(const std::string& str) {
     // skip whitespace and newlines
@@ -138,12 +139,13 @@ std::tuple<std::vector<Particle>, SimulationParams> prepareParticles(std::filesy
     auto settings = config.settings();
     auto particle_sources = config.particle_source();
 
+    ThirdDimension third_dimension = settings.third_dimension() ? ThirdDimension::ENABLED : ThirdDimension::DISABLED;
+
     std::vector<Particle> particles;
 
     auto container_type = XSDToInternalTypeAdapter::convertToParticleContainer(settings.particle_container());
 
-    auto interceptors =
-        XSDToInternalTypeAdapter::convertToSimulationInterceptors(settings.interceptors(), settings.third_dimension(), container_type);
+    auto interceptors = XSDToInternalTypeAdapter::convertToSimulationInterceptors(settings.interceptors(), third_dimension, container_type);
 
     auto forces = XSDToInternalTypeAdapter::convertToForces(settings.forces(), container_type);
 
@@ -199,7 +201,7 @@ std::tuple<std::vector<Particle>, SimulationParams> prepareParticles(std::filesy
     if (load_in_spawners) {
         // Spawn particles specified in the XML file
         for (auto cuboid_spawner : particle_sources.cuboid_spawner()) {
-            auto spawner = XSDToInternalTypeAdapter::convertToCuboidSpawner(cuboid_spawner, settings.third_dimension());
+            auto spawner = XSDToInternalTypeAdapter::convertToCuboidSpawner(cuboid_spawner, third_dimension);
             int num_spawned = spawner.spawnParticles(particles);
             Logger::logger->info("Spawned {} particles from cuboid spawner", num_spawned);
         }
@@ -214,19 +216,19 @@ std::tuple<std::vector<Particle>, SimulationParams> prepareParticles(std::filesy
                 }
             }
 
-            auto spawner = XSDToInternalTypeAdapter::convertToSoftBodyCuboidSpawner(soft_body_cuboid_spawner, settings.third_dimension());
+            auto spawner = XSDToInternalTypeAdapter::convertToSoftBodyCuboidSpawner(soft_body_cuboid_spawner, third_dimension);
             int num_spawned = spawner.spawnParticles(particles);
             Logger::logger->info("Spawned {} particles from soft body cuboid spawner", num_spawned);
         }
 
         for (auto sphere_spawner : particle_sources.sphere_spawner()) {
-            auto spawner = XSDToInternalTypeAdapter::convertToSphereSpawner(sphere_spawner, settings.third_dimension());
+            auto spawner = XSDToInternalTypeAdapter::convertToSphereSpawner(sphere_spawner, third_dimension);
             int num_spawned = spawner.spawnParticles(particles);
             Logger::logger->info("Spawned {} particles from sphere spawner", num_spawned);
         }
 
         for (auto single_particle_spawner : particle_sources.single_particle_spawner()) {
-            auto spawner = XSDToInternalTypeAdapter::convertToSingleParticleSpawner(single_particle_spawner, settings.third_dimension());
+            auto spawner = XSDToInternalTypeAdapter::convertToSingleParticleSpawner(single_particle_spawner, third_dimension);
             int num_spawned = spawner.spawnParticles(particles);
             Logger::logger->info("Spawned {} particles from single particle spawner", num_spawned);
         }