Crate lumol

Lumol is a classical molecular simulation engine that provides a solid base for developing new algorithms and methods.

Using Lumol, you can customize the behavior of all the algorithms in a simulation (from force fields to barostats and Monte Carlo moves).

Lumol goals are to be:

• Easy to extend: the code is modular, object-oriented, well documented, well tested, open-source and readable;
• Easy to use: the user interface is nice, with human-oriented input files;
• Stable: it will never crash on a good input, and provides helpful error messages.

Modules

consts	Useful physical constants, expressed in the internal unit system.
energy	Interaction potentials for energy and forces computations
input	This module provide a way to build a Lumol simulation using input files.
sim	Type and algorithms for simulations
sys	Representations of a simulated system
types	This module provides complexe numbers; 3D vectors and matrix; and multidimensional arrays for use in all other modules.
units	This module allow to convert from and to the internal unit system.

Structs

Angle	An Angle formed by the particles at indexes i, j and k
Array2	Two dimensional tensors, based on ndarray.
Array3	Three dimensional tensors, based on ndarray
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.
BornMayerHuggins	Born-Mayer-Huggins potential.
Buckingham	Buckingham potential.
Complex	Complex number, with double precision real and imaginary parts.
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:
CosineHarmonic	Cosine harmonic potential.
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.
Ewald	Ewald summation for coulombic interactions.
Gaussian	Gaussian potential.
Harmonic	Harmonic potential.
Interactions	The Interaction type hold all data about the potentials in the system.
LennardJones	Lennard-Jones potential.
Matrix3	A 3x3 square matrix type.
Mie	Mie potential.
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).
Morse	Morse potential
NullPotential	No-op potential.
PairInteraction	A non-bonded interaction between two particle.
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
RestrictionInfo	Restriction information attached to a pair of Particles in a System.
SharedEwald	Thread-sade wrapper around Ewald implementing CoulombicPotential.
System	The System type hold all the data about a simulated system.
TableComputation	Computation of a potential using tabulated values.
Torsion	Torsion potential.
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.
Vector3D	A 3-dimensional vector type
Wolf	Wolf summation for coulombic interactions.

Enums

BondPath	Shortest bond path between two particles in a system
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.
PairRestriction	Possible restrictions on the pair interactions.

Statics

VERSION

The full version of the crate, containing git state if available

Traits

AnglePotential	Marker trait for potentials that can be used for molecular angles.
BondPotential	Marker trait for potentials that can be used for molecular bonds.
Computation	Alternative energy and forces computation.
CoulombicPotential	Electrostatic potential solver.
DihedralPotential	Marker trait for potentials that can be used for molecular dihedral angles.
GlobalCache	Energetic cache for global potentials.
GlobalPotential	A potential acting on the whole System at once.
PairPotential	Marker trait for potentials that can be used for non-bonded two body interactions.
Potential	A potential for force and energy computations.

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.