A simple Molecular Dynamics project, including the LJ soft fluid model and TIP-4P water model
- Git clone the simpleMD project
- Inside simpleMD, type: 'conda env create -f environment.yml'
- next: 'conda activate simpleMD'
- now run: 'python main.py' to start the Flask server
- Go into main.py
- Change the Settings object to the settings you prefer:
- N -> dimensionality of the space - keep this one 3
- density -> density of the system in dimensionless units
- temperature -> temperature of the system in dimensionless units
- step_limit -> the amount of timesteps
- step_avg -> the interval of steps after you which a properties are evaluated and a summary is printed
- step_adjust_temp -> the interval of steps after which the particle velocities are scaled down to the right temperature
- step_equilibrium -> currently not used
- show_progress -> prints out the progress of the calculation
- show_summary -> prints out the summary of the properties of the system
- Choose a system:
- gas_particles: a Lennard-Jones soft fluid simulation
- TIP4P: a TIP-4P simulation of water molecules
- And Integrator & Interaction Method:
- gas_particles is compatible with both LeapFrog and VerletVelocity Intergrator and pair_by_pair & cell_division Interaction methods
- TIP4P is currently only working with LeapFrogIntegrator and pair_by_pair interaction method
- Add a Reporter, if you would want to visualize the results afterwards
- args for the reporter are: Reporter object, amount of steps after which to report, the model(either "LJ" or "TIP4P) and the output file location
- Run main.py