[]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.

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

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

Possible error when reading and writing to trajectories

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.