klaramozna/PSEMolDyn_GroupD

MolSim

Bachelor Practical course:
PSE Molecular Dynamics: Developing a Molecular Dynamics Simulation

Team Members

• Rodrigo Felix Forno
• Klára Možná
• Rayen Manai

Table of Contents

• MolSim
  • Team Members
  • Table of Contents
  • Introduction
  • Features
  • Requirements
  • Getting Started
  • Usage
    • Command Line Usage:
      • Optional arguments:
  • Checkpoints:
    • Tests:
  • Documentation:
    • Build Doxygen Documentation

Introduction

Features

Particle Representation: Implementation of particle representations.
Force Calculation: Algorithms for computing inter-particle forces.
Output and Visualization: Output formats and tools for visualizing simulation results.

Requirements

• C++ compiler: sudo apt-get install g++
• Cmake: sudo apt-get install cmake
• Make: sudo apt-get install make
• Xerces-C library: sudo apt-get install libxerces-c-dev
• Boost program options: sudo apt-get install libboost-program-options-dev
• Boost test environment: sudo apt-get install libboost-test-dev
• Pkg-config: sudo apt-get install pkg-config

Getting Started

1. clone the repository: git clone https://github.com/klaramozna/PSEMolDyn_GroupD
2. Navigate to the Project Directory: cd PSEMolDyn_GroupD
3. Create Build Directory and navigate to it: mkdir build && cd build
4. Configure with CMake: cmake ..
5. Compile the Project: make

Usage

Command Line Usage:

run the program with: ./src/MolSim -p <input_file_path>

Optional arguments:

• -h , --help: produces help message
• -e, --t_end: specifies end time of simulation(default: 1000)
• -s, --delta_t: specifies the step size between iterations(default: 0.014)
• -l, --log_level: specifies the log level [0: trace, 1: debug, 2: info, 3: warning, 4: error, 5: critical, 6: off] (default: 2)
• -f,--force: Select between force calculation engines lennard or grav (default: lennard)
• -t, --testing: enable testing mode (to benchmark)
• -m,--input_mode: Select between modes of input cuboid or particle (default: cuboid)

Checkpoints:

Checkpoints are crucial in molecular dynamics, like simulating a falling drop in liquid. They save system states, aiding equilibration and data integrity.

• -c , --store_checkpoint: Enter checkpoint filename to store
• -x , --load_checkpoint: Enter checkpoint filename to load

Tests:

This project is well-tested using Google Test.
To run the tests locally switch to the build directory and run ctest
Per default running cmake .. will fetch the google test libray and compile the tests (which results in longer building times), if you want to not compile the tests you can run cmake -DBUILD_GTESTS=OFF ..

Documentation:

This project is well-documented using Doxygen.
The documentation is at the following Link: Project Documentation
To generate it locally, follow these steps:

Build Doxygen Documentation

• Create Build Directory and navigate to it: mkdir build && cd build
• Configure with CMake and enable the Doxygen documentation generation option: cmake -DBUILD_DOXYGEN=ON ..
• Compile the Project: make doc_doxygen