Struct MdState 

pub struct MdState {

    pub cfg: MdConfig,
    pub atoms: Vec<AtomDynamics>,
    pub water: Vec<WaterMol>,
    pub adjacency_list: Vec<Vec<usize>>,
    pub time: f64,
    pub step_count: usize,
    pub snapshots: Vec<Snapshot>,
    pub cell: SimBox,
    pub neighbors_nb: NeighborsNb,
    pub water_pme_sites_forces: Vec<[Vec3; 3]>,
    pub kinetic_energy: f64,
    pub potential_energy: f64,
    pub neighbor_rebuild_count: usize,
    pub computation_time: ComputationTimeSums,
    /* private fields */
}

Fields

cfg: MdConfig

atoms: Vec<AtomDynamics>

water: Vec<WaterMol>

adjacency_list: Vec<Vec<usize>>

time: f64

Current simulation time, in picoseconds.

step_count: usize

snapshots: Vec<Snapshot>

These are the snapshots we keep in memory, accumulating.

cell: SimBox

neighbors_nb: NeighborsNb

water_pme_sites_forces: Vec<[Vec3; 3]>

kinetic_energy: f64

kcal/mol

potential_energy: f64

neighbor_rebuild_count: usize

computation_time: ComputationTimeSums

Implementations

impl MdState

pub fn apply_angle_bending_forces(&mut self)

This maintains bond angles between sets of three atoms as they should be from hybridization. It reflects this hybridization, steric clashes, and partial double-bond character. This identifies deviations from the ideal angle, calculates restoring torque, and applies forces based on this to push the atoms back into their ideal positions in the molecule.

Valence angles, which are the angle formed by two adjacent bonds ba et bc in a same molecule; a valence angle tends to maintain constant the anglê abc. A valence angle is thus concerned by the positions of three atoms.

impl MdState

pub fn step(&mut self, dev: &ComputationDevice, dt: f32)

Perform one integration step. This is the entry point for running the simulation. One step of length dt is in picoseconds (10^-12), with typical values of 0.001, or 0.002ps (1 or 2fs). This method orchestrates the dynamics at each time step. Uses a Verlet Velocity base, with different thermostat approaches depending on configuration.

impl MdState

pub fn apply_nonbonded_forces(&mut self, dev: &ComputationDevice)

Run the appropriate force-computation function to get force on non-water atoms, force on water atoms, and virial sum for the barostat. Uses GPU if available.

Applies Coulomb and Van der Waals (Lennard-Jones) forces on non-water atoms, in place. We use the MD-standard [S]PME approach to handle approximated Coulomb forces. This function applies forces from non-water, and water sources.

impl MdState

pub fn pack_atoms(&mut self)

impl MdState

pub fn zero_linear_momentum_atoms(&mut self)

Remove center-of-mass drift for “atoms” only (exclude water).

pub fn zero_angular_momentum_atoms(&mut self)

Remove rigid-body rotation for “atoms” only (exclude water). Computes ω from I ω = L about the atoms’ COM, then sets v’ = v - ω × (r - r_cm).

impl MdState

pub fn minimize_energy(&mut self, dev: &ComputationDevice, max_iters: usize)

Relaxes the molecules. Use this at the start of the simulation to control kinetic energy that arrises from differences between atom positions, and bonded parameters. It can also be called externally. It also stabilizes the water molecules, so that their hydrogen bond structure is correct at initialization.

Uses flexible bonds to hydrogen. (Not Shake/Rattle constraints)

impl MdState

pub fn new( dev: &ComputationDevice, cfg: &MdConfig, mols: &[MolDynamics], param_set: &FfParamSet, ) -> Result<Self, ParamError>

pub fn computation_time(&self) -> Result<ComputationTime>

pub fn save_snapshots_to_file(&mut self, path: &Path)

Trait Implementations

impl Default for MdState

fn default() -> MdState

Returns the “default value” for a type.

impl Display for MdState

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

Formats the value using the given formatter.