Representations of a simulated system
Algorithm to compute physical properties of a System
The basic building block for a topology. A
The system composition contains the number of particles of each kind in the system, as well as the number of molecules of each molecule type.
This is a cache for energy computation.
An helper struct to evaluate energy components of a system.
A Molecule associate some particles bonded together.
A molecule hash allow to identify a molecule from its atoms and bonds, and to know wether two molecules are the same without checking each atom and bond.
An iterator over all the molecules in a
A mutable iterator over all the molecules in a
An analog to [
An analog to [
The Particle type hold basic data about a particle in the system. It is self contained, so that it will be easy to send data between parallels processes.
A particle kind. Particles with the same name will have the same kind. This is used for faster potential lookup.
An analog of a pointer to
An analog of a mutable pointer to
A reference to a
A mutable reference to a
An analog to
A Trajectory is a file containing one or more successive simulation steps.
Error type for Chemfiles.
The shape of a cell determine how we will be able to compute the periodic boundaries condition.
The number of degrees of freedom simulated in a given system
Possible modes when opening a
Get the mass of the element with the given atomic
Read a the first molecule from the file at