# Examples

List simulation examples (mostly in order of increasing complexity).

The simulations in the examples are very short to ensure fast execution; however, you might want to make them longer.

When testing is performed, the files generated by the example scripts are removed, so rename or move if you want to keep any such files.

## Basic

- [minimal.py](minimal.py) : Minimal example simulating a single component Lennard-Jones (LJ) system using the NVT integrator.

## Atomistic models

- [bcc_lattice.py](bcc_lattice.py) : How to set up other initial structures (bcc lattice of LJ particles).
- [D2.py](D2.py) : Simulating a 2D system (Lennard-Jones particle in a hexagonal lattice).
- [D4.py](D4.py) : Simulating a 4D system
- [D8.py](D8.py) : Simulating a 8D system (harmonic repulsions)
- [kablj.py](kablj.py) : Simulating the Kob-Andersen binary LJ mixture. Also showing how to apply a temperature ramp for cooling.
- [tethered_particles.py](tethered_particles.py) : Simulation of tethered particles.
- [poiseuille.py](poiseuille.py) : Simulation of a nano-scale Poiseuille flow in a slit-pore.
- [yukawa.py](yukawa.py) : Example of implementing a user-defined potential, exemplified by the Yukawa potential.
- [hydrocorr.py](hydrocorr.py) : Calculation of the hydrodynamic correlation function for a LJ liquid

## Molecular models

- [ASD.py](ASD.py) : ASymmetric Dumbbells (toy model of toluene).
- [LJchain.py](LJchain.py) : LJ chains (coarse grained polymer model).
- [generic_molecules.py](generic_molecules.py): Simulation of a linear molecule with bond, angle, and dihedral potentials
- [molecules_polydisperse.py](molecules_polydisperse.py): Mixture of different types for molecules, here linear molecules of different length.

## Integrators

- [minimal_NPT.py](minimal_NPT.py) : Minimal example simulating a single component Lennard-Jones (LJ) system using the NPT integrators.

## Post-processing

Examples of postprocessing existing gamdpy/rumd3 data. 
These scripts require the output produced with minimal.py or a rumd3 TrajectoryFile.

- [calc_rdf_from_h5.py](calc_rdf_from_h5.py) : Read a simulation saved as h5 and calculate the RDF.
- [calc_rdf_from_rumd3.py](calc_rdf_from_rumd3.py) : Read a simulation saved as "TrajectoryFiles" from rumd3 and calculate the RDF.
- [calc_sq_from_h5.py](calc_sq_from_h5.py) : Read a simulation saved as h5 and calculate the structure factor S(q).

The following examples of data analysis scripts need a filename as a commandline argument, e.g. "python3 analyze_structure.py filename". 

- [analyze_structure.py](analyze_structure.py) Calculates rdf (radial distribution function) for configurations in filename.h5, and stores it in filename_rdf.pdf and filename_rdf.pkl (a pickle file with the computed data).
- [analyze_dynamics.py](analyze_dynamics.py) Calculates several dynamical properties (mean squared displacement, non-Gaussian parameter, and incoherent intermediate scattering function) from the trajectory stored in filename.h5. Resulting data is stored in filename_dynamics.pkl and plotted in filename_dynamics.pdf.
- [analyze_thermodynamics.py](analyze_thermodynamics.py) Calculates thermodynamical properties. Results plotted in filename_thermodynamics.pdf.

## Runtime analysis

- [thermodynamics.py](thermodynamics.py) : Calculate thermodynamic properties.
- [isochore.py](isochore.py) : Performing several simulations (an isochore) in one script.
- [isomorph.py](isomorph.py) : An isomorph is traced out using the gamma method. The script demonstrates the possibility of keeping the output of the simulation in memory (storage='memory'), useful when a lot of short simulations are performed.
- [structure_factor.py](structure_factor.py) : Calculate the structure factor of a Lennard-Jones system and plot it.
- [consistency_NPT.py](consistency_NPT.py) Calcuate several thermodynamic quantities (dP/dT|<sub>V</sub>, $\beta$<sub>P</sub>, c<sub>V</sub>, c<sub>P</sub>, K<sub>T</sub>) and check consistency of NVT and NPT fluctuations. 
- [widoms_particle_insertion.py](widoms_particle_insertion.py) Widom's particle insertion method for calculating the chemical potential.
- [evaluator_inverse_powerlaw.py](evaluator_inverse_powerlaw.py) Simulate a Lennard-Jones system and evaluate the inverse power law potential.
- [evaluator_einstein_crystal.py](evaluator_einstein_crystal.py) Simulate a Lennard-Jones crystal and evaluate the harmonic tether potential.

## Miscellaneous

- [write_to_lammps.py](write_to_lammps.py) : Write a dump file in LAMMPS format. Can be open by external tools like OVITO or VMD.
- [minimal_cpu.py](minimal_cpu.py) : Like minimal.py but running on the cpu using numba CUDA simulator.
- [xy_model.py](xy_model.py) : The classical XY model of rotators on a 2D square lattice
- [rubber_cube.py](rubber_cube.py): A rubber cube modeled as particles connected by springs