# System¶

A System contains all the data about the physical system we are simulating. It contains four types of data:

• A list of Particles, which are physical objects with a position, a velocity, a mass and a name;
• A list of Molecules containing information about how the particles are bounded together;
• An UnitCell, i.e. the bounding box of the simulation.
• Interactions, sometimes called a force field.

## Particles¶

Particles are the basic building blocks of a system. They can be atoms or more complex: coarse-grained sites, dummy atoms, anisotropic particles …

They have a name, a mass, a position, a velocity, and most importantly a particle kind, defined by the name of the particle. All particles with the same name share the same kind: all H are the same, as well as all C, etc.

## Molecules¶

When particles are bonded together, they form molecules. A Molecule contains the list of its bonds; molecules make for the molecular part in molecular simulation.

## Unit cells¶

Lumol knows about three types of unit cells:

• Infinite cells do not have any boundaries and can be used to simulate systems in vacuum;
• Orthorhombic cells have up to three independent lengths whereas all angles of the cell are set to 90°;
• Triclinic cells have 6 independent parameters: 3 lengths and 3 angles.

Orthorhombic and Triclinic cells are used in combination with periodic boundary conditions to simulate infinite systems.

## Interactions¶

Interactions are potentials acting on or between particles. Lumol provides functions for various potential types:

• Non-bonding pair potentials;
• Bonds potentials in molecules;
• Angles potentials in molecules;
• Dihedral angles potentials in molecules;
• Long-ranges coulombic potentials (Ewald and Wolf methods);
• Arbitrary external potential applying on the whole system at once.