The repository contains my version of the Microscopic Simulation project given by Michel Masella at CHPS master, UVSQ.

The code is written in zig. Please make sure you have the 0.12.0 release version of the compiler in order to build this project.

$ zig build -Doptimize=ReleaseSafe

The executable is named simulation and located in zig-out/bin directory.

$ ./simulation [option] input_position_file [input_speed_file] [output_file]
options:
    -h, --help
            Display this help and exit

    -d, --delta-t <TIME>
            Choose delta t value (default: 1 fs)

    -t, --total-iterations <TIME>
            Number of iterations to do (default: 100)

    -s, --save-step <N>
            Save positions every N step (default: 10)

    -m, --thermostat-step <N>
            Frequency to update the temperature using Beredsen thermostat (default: 1)

The input files must be formatted as follow

first line
mass x y z
    .
    .
    .

For reference, please look at particule.xyz file.

During execution, statistics about the simulated system are printed (Energies, Temperature, Sum of forces...). A color scheme is present to differentiate abnormal values from satisfying ones. At this end, a summary of the density observed during the simulation is printed (exam question).

Finally, the program outputs the system in a PDB format (default file: test.pdb) on a regular basis. This file can then be used to visualize the simulation with vmd for instance.

All the guidelines and tips to have a working simulation code were given by Michel Masella