Module lumol::sys

Representations of a simulated system

Modules

compute

Algorithm to compute physical properties of a System

Structs

Angle	An Angle formed by the particles at indexes i, j and k
Bond	A Bond between the particles at indexes i and j
BondDistances	The BondDistances bitflag encode the topological distance between two particles in the molecule, i.e. the number of bonds between the particles. Two particles can have multiple bond path lionking them (in the case of cyclic molecules), which is why a bit flag is used instead of a single distance value.
Bonding	The basic building block for a topology. A Bonding contains data about the connectivity (bonds, angles, dihedrals) between particles in a single molecule.
Composition	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.
Configuration	The Configuration contains the physical data of the system:
Dihedral	A Dihedral angle formed by the particles at indexes i, j, k and m
EnergyCache	This is a cache for energy computation.
EnergyEvaluator	An helper struct to evaluate energy components of a system.
Interactions	The Interaction type hold all data about the potentials in the system.
Molecule	A Molecule associate some particles bonded together.
MoleculeHash	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.
MoleculeIter	An iterator over all the molecules in a Configuration
MoleculeIterMut	A mutable iterator over all the molecules in a Configuration
MoleculeRef	An analog to [&Molecule] using particles stored elsewhere (in a system or an Molecule).
MoleculeRefMut	An analog to [&mut Molecule] using particles stored elsewhere (in a system or an Molecule).
Particle	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.
ParticleKind	A particle kind. Particles with the same name will have the same kind. This is used for faster potential lookup.
ParticlePtr	An analog of a pointer to Particle with struct of array layout.
ParticlePtrMut	An analog of a mutable pointer to Particle with struct of array layout.
ParticleRef	A reference to a Particle with struct of array layout.
ParticleRefMut	A mutable reference to a Particle with struct of array layout.
ParticleSlice	A slice of Particle inside a ParticleVec .
ParticleSliceMut	A mutable slice of Particle inside a ParticleVec .
ParticleVec	An analog to Vec<Particle> with Struct of Array (SoA) layout
Permutation	The Permutation struct contains the old and new particle index in a Configuration after the particles where moved due to a new bond being added
System	The System type hold all the data about a simulated system.
Trajectory	A Trajectory is a file containing one or more successive simulation steps.
TrajectoryBuilder	A Trajectory builder, to set some options before opening a trajectory.
TrajectoryError	Error type for Chemfiles.
UnitCell	An UnitCell defines the system physical boundaries.

Enums

CellShape	The shape of a cell determine how we will be able to compute the periodic boundaries condition.
DegreesOfFreedom	The number of degrees of freedom simulated in a given system
OpenMode	Possible modes when opening a Trajectory.

Functions

get_atomic_mass	Get the mass of the element with the given atomic name
read_molecule	Read a the first molecule from the file at path. If no bond information exists in the file, bonds are guessed.