This repository contains the code written for the Molecular Dynamics Lab (IN0012) during WS24/25 at TUM.

We recommend using the following compilers:

• GCC (GNU Compiler Collection) version 11.1 or later
• Clang version 14.0.0 or later

Building this project will require the following tools:

• CMake: Version 3.10 or later. We recommend installing CMake from the official website, or using your package manager.

• Xerces-C++ XML Parser: We recommend installing and building the most recent version from the official website, or using your package manager.

Build the project

$ mkdir build
$ cd build
$ cmake ..

Compile and run the executable

$ make
$ ./MolSim

The MolSim application now supports using an XML input file for configuring simulation parameters. This XML file allows users to define the simulation setup in a structured way, making it easier to manage complex configuration.

The XML input file provides the following parameters:

• end_time: The total time for which the simulation should run.
• time_delta: The time increment between simulation steps.
• output_path: The base name for output files (including filepath).
• write_frequency: Specifies how often to write output files (e.g., every N iterations).
• r_cutoff_radius: Specifies the distance, from which the force set to 0.
• domain_size: size of the inner area including the boundary of the domain.

These parameters are defined in the XML file and are loaded when running the simulation.

Users can override the parameters defined in the XML file using command line arguments. The command line arguments available are as follows.

This simulator supports different multithreading policies in order to greatly speed up computation. These are passed via the command line arguments:

We utilize OpenMP and offer two powerful strategies:

To run the MolSim program with an XML input file and additional command line arguments:

./MolSim -i ../input/input_file.xml -e 100.0 -d 0.01 -o ../output/simulation_output -t 5

In this example:

• -i ../input_file.xml is the XML file that provides the base configuration for the simulation.
• -e 100.0 overrides the end_time specified in the XML file to run the simulation for 100.0 units of time.
• -d 0.01 overrides the delta_time specified in the XML file to set the time increment to 0.01.
• -o ../output/simulation_output overrides the output_path specified in the XML file to set the output file path.
• -t 5 overrides the write_frequence specified in the XML file to set the write frequency to write a file every 5 iterations.

Here is an example of an XML input file:

<?xml version="1.0" encoding="UTF-8"?>
<MolSim>
    <simulation_parameters>
        <end_time>5</end_time>
        <delta_time>0.005</delta_time>
        <output_basename>../output/MD_vtk</output_basename>
        <write_frequency>10</write_frequency>
        <r_cutoff_radius>3.0</r_cutoff_radius>
        <gravity>-12.44</gravity>
        <enable_brownian>true</enable_brownian>
        <domain_size>
            <x>180.0</x>
            <y>90.0</y>
            <z>0.0</z>
        </domain_size>
    </simulation_parameters>
    <thermostats>
        <initial_temp>40</initial_temp>
        <target_temp>40</target_temp>
        <delta_temp>0.0005</delta_temp>
        <is_gradual>true</is_gradual>
        <n_thermostats>1000</n_thermostats>
    <thermostats>
    <boundary_conditions>
        <left>Outflow</left>
        <right>Outflow</right>
        <top>Outflow</top>
        <bottom>Outflow</bottom>
        <front>Reflecting</front>
        <back>Reflecting</back>
    </boundary_conditions>
    <discs>
        <disc>
            <center>
                <x>60.0</x>
                <y>25.0</y>
                <z>0.0</z>
            </center>
            <initial_velocity>
                <x>0.0</x>
                <y>-10.0</y>
                <z>0.0</z>
            </initial_velocity>
            <radius>15</radius>
            <mesh_width>1.1225</mesh_width>
            <mass>1.0</mass>
            <epsilon>5.0</epsilon>
            <sigma>1.0</sigma>
        </disc>
    </discs>
    <cuboids>
        <cuboid>
            <coordinate>
                <x>0.0</x>
                <y>0.0</y>
                <z>0.0</z>
            </coordinate>
            <dimensions>
                <x>3</x>
                <y>3</y>
                <z>3</z>
            </dimensions>
            <mesh_width>1.0</mesh_width>
            <mass>1.0</mass>
            <epsilon>5.0</epsilon>
            <sigma>1.0</sigma>
            <initial_velocity>
                <x>0.0</x>
                <y>0.0</y>
                <z>0.0</z>
            </initial_velocity>
        </cuboid>
    </cuboids>
    <particles>
        <particle>
            <position>
                <x>0.0</x>
                <y>0.0</y>
                <z>0.0</z>
            </position>
            <velocity>
                <x>0.0</x>
                <y>0.0</y>
                <z>0.0</z>
            </velocity>
            <mass>1.0</mass>
        </particle>
    </particles>
</MolSim>

• The XML file is parsed first, and all defined parameters are loaded. If command line arguments are provided, they take precedence over the values in the XML file.
• Using an XML input file makes it easier to manage and reuse complex configurations, especially when working with multiple simulations or running parameter sweeps.

./scripts/cleanup.sh

Deletes all files in the output directory. Use this to clear generated files or results from previous runs.

./scripts/format.sh

Formats all .cpp and .h files in src using clang-format.

• dev-<sheet number>: For specific work sheets handed out during the course; should be merged into master branch by deadline.
• dev-<sheet number/task number>: For specific tasks on a work sheet; should be merged into specific work sheet branch throughout the week.
• dev-<feature-name>: For specific features under development.
• dev-fix-<bug name>: For fixing bugs that occur during the project.
• dev-misc: For miscellaneous updates like documentation, configuration, or small fixes.

• Bangrui Wu
• Sebastian John
• Ivan Lomakov

• Manish Kumar Mishra
• Samuel Newcome