Struct Snapshot 

pub struct Snapshot {

    pub time: f64,
    pub atom_posits: Vec<Vec3>,
    pub atom_velocities: Vec<Vec3>,
    pub water_o_posits: Vec<Vec3>,
    pub water_h0_posits: Vec<Vec3>,
    pub water_h1_posits: Vec<Vec3>,
    pub water_velocities: Vec<Vec3>,
    pub energy_kinetic: f32,
    pub energy_potential: f32,
    pub energy_potential_between_mols: Vec<f32>,
    pub energy_potential_nonbonded: f32,
    pub energy_potential_bonded: f32,
    pub hydrogen_bonds: Vec<HydrogenBond>,
    pub temperature: f32,
    pub pressure: f32,
}

This stores the positions and velocities of all atoms in the system, and the total energy. It represents the output of the simulation. A set of these can be used to play it back over time. We save load and save this to disk in the __ format.

Fields

time: f64

atom_posits: Vec<Vec3>

atom_velocities: Vec<Vec3>

water_o_posits: Vec<Vec3>

water_h0_posits: Vec<Vec3>

water_h1_posits: Vec<Vec3>

water_velocities: Vec<Vec3>

Single velocity per water molecule, as it’s rigid.

energy_kinetic: f32

energy_potential: f32

energy_potential_between_mols: Vec<f32>

Used to track which molecule each atom is associated with in our flattened structures. This is the potential energy between every pair of molecules.

energy_potential_nonbonded: f32

Energy from non-bonded interactions only. A simple proxy for molecule-molecule potential energy, although includes energy within the molecule as well.

energy_potential_bonded: f32

E.g. energy in covalent bonds, as modelled as oscillators.

hydrogen_bonds: Vec<HydrogenBond>

Optionally added as a post-processing step.

temperature: f32

Instantaneous temperature in Kelvin.

pressure: f32

Instantaneous pressure in Bar.

Implementations

impl Snapshot

pub fn populate_hydrogen_bonds(&mut self, atoms: &[AtomDynamics])

The element indices must match the atom posits.

pub fn to_dcd(&self, cell: &SimBox, write_water: bool) -> DcdFrame

pub fn from_dcd(dcd: &DcdTrajectory) -> Vec<Self>

Note: Most of our fields are not available in the DCD format, so we leave them empty, using the Default impl.

impl Snapshot

pub fn make_mol2( &self, atoms_: &[AtomGeneric], bonds: &[BondGeneric], ) -> Result<Mol2>

pub fn make_mmcif( &self, atoms_: &[AtomGeneric], bonds: &[BondGeneric], ) -> Result<MmCif>

impl Snapshot

pub fn to_bytes(&self) -> Vec<u8>

E.g. for saving to file. Saves all items as 32-bit floating point.

pub fn from_bytes(bytes: &[u8]) -> Result<Self>

Trait Implementations

impl Clone for Snapshot

fn clone(&self) -> Snapshot

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Snapshot

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

Formats the value using the given formatter.

impl Default for Snapshot

fn default() -> Snapshot

Returns the “default value” for a type.