[−]Module lumol::sys
Representations of a simulated system
Modules
compute | Algorithm to compute physical properties of a System |
Structs
Angle | An |
Bond | A |
BondDistances | The |
Bonding | The basic building block for a topology. A |
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 |
Dihedral | A |
EnergyCache | This is a cache for energy computation. |
EnergyEvaluator | An helper struct to evaluate energy components of a system. |
Interactions | The |
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 |
MoleculeIterMut | A mutable iterator over all the molecules in a |
MoleculeRef | An analog to [ |
MoleculeRefMut | An analog to [ |
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
|
ParticlePtrMut | An analog of a mutable pointer to
|
ParticleRef | A reference to a
|
ParticleRefMut | A mutable reference to a
|
ParticleSlice | A slice of
|
ParticleSliceMut | A mutable slice of
|
ParticleVec | An analog to |
Permutation | The |
System | The |
Trajectory | A Trajectory is a file containing one or more successive simulation steps. |
TrajectoryBuilder | A |
TrajectoryError | Error type for Chemfiles. |
UnitCell | An |
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 |
Functions
get_atomic_mass | Get the mass of the element with the given atomic |
read_molecule | Read a the first molecule from the file at |