Struct Snapshot 

pub struct Snapshot {
    pub time: f64,
    pub atom_posits: Vec<Vec3>,
    pub atom_velocities: Option<Vec<Vec3>>,
    pub energy_data: Option<SnapshotEnergyData>,
    pub water_o_posits: Vec<Vec3>,
    pub water_h0_posits: Vec<Vec3>,
    pub water_h1_posits: Vec<Vec3>,
    pub water_velocities: Option<Vec<Vec3>>,
}

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: Option<Vec<Vec3>>

energy_data: Option<SnapshotEnergyData>

water_o_posits: Vec<Vec3>

water_h0_posits: Vec<Vec3>

water_h1_posits: Vec<Vec3>

water_velocities: Option<Vec<Vec3>>

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

Implementations

impl Snapshot

pub fn new(state: &MdState) -> Self

Initialize with position data only. We construct these with positions only, then augment with velocity and energy data as required.

pub fn update_with_velocities(&mut self, state: &MdState)

pub fn update_with_energy( &mut self, state: &MdState, pressure: f32, temperature: f32, )

pub fn unflatten( &self, mol_start_indices: &[usize], ) -> Result<Vec<Vec<(Vec3, Vec3)>>>

Unflatten positions and velocities into a per-molecule basis. mol_start_indices may be taken directly from MdState. Inner: (Posit, Vel). Does not unflatten the solvent, which is placed after all non-solvent molecules in the flat arrays.

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>

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.