MolSim PSEMolDyn_GroupG

Code for the practical course PSE: Molecular Dynamics by group G.

Members:
Alexandra Marquardt
Matteo Wohlrapp
Michael Borisov
Group Id: G

Link to the repository: https://github.com/SecTedd/PSEMolDyn_GroupG
Branch: master
Commit Id: #

Video:

1. Video
   membrane.avi is the simulation of the membrane (task 1)
   

2. Video
   RT3d.avi shows the Rayleigh-Taylor instability in 3D (task 3)
   The video doesn't show the full length of the simulation run
   

3. Video
   nano_scale_flow.avi shows the default nano-scale flow simulation until t = 50 (task 4)
   

Input

All input files from assignment 5 can be found in the /input/ folder

Build and run

Build without Doxygen

1. Navigate into the build folder: cd build
2. Run cmake .. to create the makefile. We use gcc 11.3.0 as compiler.
3. Run make to generate the executable and tests.

Build with Doxygen

1. Navigate into the build folder: cd build
2. Run cmake -D BUILD_DOC=ON .. to create the makefile. We use gcc 11.3.0 as the compiler.
3. Run make to generate the executable and tests and make doc_doxygen to generate the documentation.

Run

After building the project you can run the executable

1. Familiarize yourself with the provided .xml file located in the /input/ folder and the .xsd file located in the /xsd/ folder.
   XML-Files are used to specify different parameters.
   
2. Create a new XML-File or use one of the provided ones and specify all the input parameters that are needed.
   
3. Navigate into the build folder: cd build
4. The application can be run from the console. Run ./MolSim -h to print the help text.
   The -f option automatically distinguishes between different input files, such as xml, cuboid, sphere etc.
   
5. The application also allows you to enter an interactive menu where you can read in multiple files, start the simulation multiple times, etc. Run ./MolSim -m to enter the menu, a help message is shown.
   The -f option automatically distinguishes between different input files, such as xml, cuboid, sphere etc.
   
6. The generated VTK-Files can be found at the path you specified in the xml.
   
7. Warning the contents of the output folders will be overwritten if you run the simulation multiple times with the same output folder path!
   

Checkpoints

When running the program with the flag -c the program creates a checkpoint in the checkpoints folder, which has the PSEMOLDYN_GROUPG folder as its parent directory. If the checkpoint folder does not exist, you need to create it manually as a direct child of the parent directory. After writing a checkpoint file, you can read it with the -f command or include the path in the filename bracket in a XML file for the configuration. The exact syntax can be found at src/xsd/Simulation.xsd

CSV-Output

When specifying a csvWriteFrequency greater than 0, the program writes .csv files in the /csv/directory.
This directory must exist on the same level as the /src/folder and needs to be created if it's not there. Otherwise no csv output will be written.

Run tests

1. Navigate into the build folder: cd build
2. Run ctest to execute all unit tests.
3. The result of the unit tests are printed to the console.

Logging

For logging we use spdlog.
The logs are written to files which can be found in the /logs/ folder or to the console (see ./MolSim -h). The logs are separated into logic and memory logs.
Logic logs are used to log events in the program flow. Within the logic logs, there is the distinction between input, output and simulation.
Memory logs on the other hand document the construction and destruction of objects and therefore help to detect and prevent memory leaks.

Contest 2 (Parallel)

Ran with OMP_NUM_THREADS=28 on cm2_tiny and 1 benchmark iteration
GCC:

• 2D 38 sec; 2,61 * 10^6 MUPS
  
• 3D 1381 sec; 723787 MUPS
  ICPX:
  
• 2D: 42 sec; 2,38 * 10^6 MUPS
  
• 3D: 1534 sec; 651890 MUPS
  

Structure:

./
├── CMakeLists.txt
├── Doxyfile
├── README.md
├── build
├── checkpoints
├── cmake
│   └── modules
│       ├── doxygen.cmake
│       ├── googletest.cmake
│       └── spdlog.cmake
├── csv
├── input
│   ├── Benchmark.xml
│   ├── Membrane.xml
│   ├── Nano-scale-flow.xml
│   ├── RayleighTaylorBig2D.xml
│   ├── RayleighTaylorBig3D.xml
│   ├── Simulation.xml
│   ├── SimulationState.xml
│   ├── eingabe-cuboid.txt
│   ├── eingabe-sonne.txt
│   └── eingabe-sphere.txt
├── libs
├── plots
├── src
│   ├── ConsoleMenu.cpp
│   ├── ConsoleMenu.h
│   ├── MolSim.cpp
│   ├── inputReader
│   │   ├── CuboidInputReader.cpp
│   │   ├── CuboidInputReader.h
│   │   ├── FileReader.cpp
│   │   ├── FileReader.h
│   │   ├── InputFacade.cpp
│   │   ├── InputFacade.h
│   │   ├── InputReader.cpp
│   │   ├── InputReader.h
│   │   ├── SphereInputReader.cpp
│   │   ├── SphereInputReader.h
│   │   ├── XMLInputReader.cpp
│   │   └── XMLInputReader.h
│   ├── model
│   │   ├── Cuboid.cpp
│   │   ├── Cuboid.h
│   │   ├── DirectSumParticleContainer.cpp
│   │   ├── DirectSumParticleContainer.h
│   │   ├── LinkedCellParticleContainer.cpp
│   │   ├── LinkedCellParticleContainer.h
│   │   ├── Particle.cpp
│   │   ├── Particle.h
│   │   ├── ParticleCell.cpp
│   │   ├── ParticleCell.h
│   │   ├── ParticleContainer.h
│   │   ├── ProgramParameters.cpp
│   │   ├── ProgramParameters.h
│   │   ├── Sphere.cpp
│   │   └── Sphere.h
│   ├── outputWriter
│   │   ├── CSVWriter.cpp
│   │   ├── CSVWriter.h
│   │   ├── CheckpointWriter.cpp
│   │   ├── CheckpointWriter.h
│   │   ├── OutputFacade.cpp
│   │   ├── OutputFacade.h
│   │   ├── VTKWriter.cpp
│   │   ├── VTKWriter.h
│   │   ├── XYZWriter.cpp
│   │   ├── XYZWriter.h
│   │   ├── vtk-unstructured.cpp
│   │   ├── vtk-unstructured.h
│   │   └── vtk-unstructured.xsd
│   ├── simulation
│   │   ├── DVProfileCalculator.cpp
│   │   ├── DVProfileCalculator.h
│   │   ├── InterParticleForce.cpp
│   │   ├── InterParticleForce.h
│   │   ├── InterParticleGravitationalForce.cpp
│   │   ├── InterParticleGravitationalForce.h
│   │   ├── LennardJonesForce.cpp
│   │   ├── LennardJonesForce.h
│   │   ├── LennardJonesForceHarmonic.cpp
│   │   ├── LennardJonesForceHarmonic.h
│   │   ├── Simulation.cpp
│   │   ├── Simulation.h
│   │   ├── SingleParticleForce.cpp
│   │   ├── SingleParticleForce.h
│   │   ├── SingleParticleGravitationalForce.cpp
│   │   ├── SingleParticleGravitationalForce.h
│   │   ├── TemporalSingleParticleForce.cpp
│   │   ├── TemporalSingleParticleForce.h
│   │   ├── Thermostat.cpp
│   │   └── Thermostat.h
│   ├── utils
│   │   ├── ArrayUtils.h
│   │   ├── File.h
│   │   ├── Input.h
│   │   ├── Logger.h
│   │   ├── MaxwellBoltzmannDistribution.h
│   │   ├── PContainer.h
│   │   └── ParticleGenerator.h
│   └── xsd
│       ├── Simulation.cxx
│       ├── Simulation.hxx
│       ├── Simulation.xsd
│       ├── SimulationState.cxx
│       ├── SimulationState.hxx
│       └── SimulationState.xsd
└── tests
    ├── CSVWriter_test.cc
    ├── Checkpoints_test.cc
    ├── CuboidInputReader_test.cc
    ├── DVCalculator_test.cc
    ├── DirectSumParticleContainer_test.cc
    ├── GetNeighbours_test.cc
    ├── LennardJonesForce_test.cc
    ├── LinkedCellParticleContainer_test.cc
    ├── Membrane_test.cc
    ├── Parallelization_test.cc
    ├── ParticleCell_test.cc
    ├── SigmaEpsilon_test.cc
    ├── Simulation.xml
    ├── SimulationState.xml
    ├── SingleParticleGravitationalForce_test.cc
    ├── SphereInputReader_test.cc
    ├── StationaryParticles_test.cc
    ├── Thermostat_test.cc
    ├── XMLInputReader_test.cc
    ├── checkpoints
    ├── csv
    ├── eingabe-cuboid.txt
    ├── eingabe-sphere.txt
    └── main.cc