Struct MdState 

pub struct MdState {
    pub cfg: MdConfig,
    pub atoms: Vec<AtomDynamics>,
    pub adjacency_list: Vec<Vec<usize>>,
    pub force_field_params: ForceFieldParamsIndexed,
    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,
    /* private fields */
}

Fields

cfg: MdConfig

atoms: Vec<AtomDynamics>

adjacency_list: Vec<Vec<usize>>

force_field_params: ForceFieldParamsIndexed

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

Implementations

impl MdState

pub fn apply_bond_stretching_forces(&mut self)

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.

pub fn apply_dihedral_forces(&mut self, improper: bool)

This maintains dihedral angles. (i.e. the angle between four atoms in a sequence). This models effects such as σ-bond overlap (e.g. staggered conformations), π-conjugation, which locks certain dihedrals near 0 or τ, and steric hindrance. (Bulky groups clashing).

This applies both “proper” linear dihedral angles, and “improper”, hub-and-spoke dihedrals. These two angles are calculated in the same way, but the covalent-bond arrangement of the 4 atoms differs.

pub fn shake_hydrogens(&mut self)

Part of our SHAKE + RATTLE algorithms for fixed hydrogens.

pub fn rattle_hydrogens(&mut self, mol_i: usize)

Part of our SHAKE + RATTLE algorithms for fixed hydrogens.

impl MdState

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

One Velocity-Verlet step (leap-frog style) 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.

impl MdState

pub fn build_neighbors_if_needed(&mut self)

Call during each step; determines if we need to rebuild neighbors, and does so A/R. todo: Run on GPU?

pub fn rebuild_dy_water_inv(&mut self)

This inverts our neighbor set between water and dynamic atoms.

impl MdState

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

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

impl MdState

pub fn water_vv_first_half_and_drift(&mut self, dt: f32, dt_half: f32)

Verlet velocity integration for water, part 1. Forces for this step must be pre-calculated. Accepts as mutable to allow projecting M/EP force onto the other atoms.

In addition to the VV half-kick and drift, it handles force projection from M/EP, and applying SETTLE to main each molecul’s rigid geometry.

pub fn water_vv_second_half(&mut self, dt_half: f32)

Velocity-Verlet integration for water, part 2. Forces (as .accel) must be computed prior to this step.

impl MdState

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

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.