Struct AtomSet 

pub struct AtomSet {
    pub atom_types: Vec<AtomTypeDesc>,
    pub positions: Vec<[f64; 3]>,
    pub velocities: Vec<[f64; 3]>,
    pub forces: Vec<[f64; 3]>,
    pub type_indices: Vec<usize>,
    pub box_size: f64,
}

A typed atom set that groups atoms by species.

Supports heterogeneous systems with multiple atom types, per-atom charges, and retrieval of all positions / velocities by type.

Fields

atom_types: Vec<AtomTypeDesc>

Registered atom type descriptors.

positions: Vec<[f64; 3]>

Per-atom position [x, y, z].

velocities: Vec<[f64; 3]>

Per-atom velocity [vx, vy, vz].

forces: Vec<[f64; 3]>

Per-atom force (accumulated each step) [fx, fy, fz].

type_indices: Vec<usize>

Per-atom type index (into atom_types).

box_size: f64

Simulation box size (cubic).

Implementations

impl AtomSet

pub fn new(box_size: f64) -> Self

Create an empty AtomSet with the given box size.

pub fn register_type(&mut self, desc: AtomTypeDesc) -> usize

Register an atom type and return its index.

pub fn add_atom(&mut self, position: [f64; 3], type_idx: usize) -> usize

Add an atom at position with the given type index. Returns atom index.

pub fn len(&self) -> usize

Number of atoms.

pub fn is_empty(&self) -> bool

Whether the atom set is empty.

pub fn mass(&self, i: usize) -> f64

Mass of atom i.

pub fn charge(&self, i: usize) -> f64

Charge of atom i.

pub fn positions_of_type(&self, type_idx: usize) -> Vec<[f64; 3]>

Return all positions of atoms with type index type_idx.

pub fn net_charge(&self) -> f64

Net charge of the system (sum of all partial charges).

pub fn kinetic_energy(&self) -> f64

Total kinetic energy.

pub fn temperature(&self) -> f64

Temperature from equipartition (reduced units k_B = 1).

Trait Implementations

impl Clone for AtomSet

fn clone(&self) -> AtomSet

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for AtomSet

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for AtomSet

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for AtomSet

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.