Group E: Scientific Computing Molekulardynamik

Welcome to our Molecular Simulation Project! :)

This project is part of the practical course "Scientific Computing (PSE) Molekulardynamik" at TUM during the winter semester 2024/25.

Build Instructions

To generate the build files use cmake:

mkdir build
cd build
cmake ..

To build the project run make (in the directory with the generated build files):

make

The build target is called MolSim.

Usage

After building, you can run the simulation with the following commands:

./MolSim <input_file> <output_format>
./MolSim -h | --help

Arguments:

• input_file XML or TXT file with input parameters important for the simulation.
• output_format Output format: either 'XYZ' or 'VTK'

Flags

• -h, --help Show this help message and exit
• -f Delete all contents of the output folder before writing
• -b Benchmark the simulation (output_format and output_folder optional)

Logging Instructions

If no log level is set, the default log level used is info.
The log level must be configured before compiling the code. To set the desired log level, run in the build directory:

cmake -DSPDLOG_LEVEL=<desired level>

Available log levels are:

• trace Extreamly fine grained information
• debug Debug information
• info General information
• warn Potential issues
• error Occuring errors
• critical Servere issues
• off Disables logging

Doxygen Instructions

To generate Doxygen documentation for this project, run in the build directory:

make doc_doxygen

If you want to disable creating the Doxygen target (e.g., if Doxygen is not installed), run in the build directory:

cmake -DENABLE_DOXYGEN=OFF ..

Parallelization Instructions

The simulation can also be run using one of two parallelization strategies. To enable parallelization, the program must be compiled with the OpenMP flag:

cmake .. -DCMAKE_CXX_FLAGS="-fopenmp"

The parallelization strategy can be selected via the XML configuration file as follows:

    <parameters>
        [...]
        <parallel_strategy>STRATEGY</parallel_strategy>
    </parameters>

Where STRATEGY can be one of the following options:

• CELL_LOCK Locks the linked cells in a way that allows the force calculation to be performed in parallel.
• SPATIAL_DECOMPOSITION Divides the simulation space so that the force calculation can be performed in parallel.
• NONE No parallelization.