Struct SimBox 

pub struct SimBox { /* private fields */ }

Simulation box: triclinic cell with origin and per-axis PBC mask

Implementations

impl SimBox

pub fn new( h: ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>, origin: ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>, pbc: [bool; 3], ) -> Result<SimBox, BoxError>

Construct from triclinic cell matrix H, origin O, and per-axis PBC flags

pub fn try_new( h: ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>, origin: ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>, pbc: [bool; 3], ) -> Result<SimBox, BoxError>

pub fn cube( a: f64, origin: ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>, pbc: [bool; 3], ) -> Result<SimBox, BoxError>

Factory: cubic box with edge length a and origin O

pub fn ortho( lengths: ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>, origin: ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>, pbc: [bool; 3], ) -> Result<SimBox, BoxError>

Factory: ortho box with lengths (ax, ay, az) and origin O

pub fn free( points: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, padding: f64, ) -> Result<SimBox, BoxError>

Create a non-periodic (free-boundary) box enclosing all points.

Computes the axis-aligned bounding box of points and adds padding on each side. The resulting box has pbc = [false, false, false].

padding should be >= the neighbor cutoff distance so that all particles sit well inside the box for correct cell assignment.

Errors

Returns BoxError if padding is non-positive or the resulting box is degenerate.

Panics

Panics if padding <= 0.

pub fn h_view(&self) -> ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>

View of the cell matrix

pub fn inv_view(&self) -> ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>

View of the inverse cell matrix

pub fn origin_view(&self) -> ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>

View of the origin

pub fn pbc_view(&self) -> ArrayBase<ViewRepr<&bool>, Dim<[usize; 1]>>

View of the PBC flags

pub fn pbc(&self) -> [bool; 3]

Per-axis PBC flags

pub fn volume(&self) -> f64

Cell volume (|det(H)|)

pub fn tilts(&self) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Off-diagonal tilts [xy, xz, yz] of the cell matrix

pub fn lengths(&self) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Lattice vector lengths

pub fn nearest_plane_distance( &self, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Nearest plane distance (half the box size along each axis) For triclinic boxes, this is the perpendicular distance to each face

pub fn kind(&self) -> &BoxKind

pub fn lattice( &self, index: usize, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Lattice vector by index (0,1,2) — columns of H

pub fn make_fractional( &self, r: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Convert Cartesian coordinates to fractional coordinates [0, 1)

pub fn make_fractional_fast( &self, r: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Fractional coordinates with ortho fast-path

pub fn make_fractional_fast_arr( &self, r: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, ) -> [f64; 3]

Fractional coordinates returned as [F; 3] (zero-alloc hot path).

Equivalent to make_fractional_fast but avoids the Array1<F> heap allocation by returning a stack array. Use in tight inner loops (neighbor-list cell assignment, etc.).

pub fn make_cartesian( &self, frac: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Convert fractional coordinates to Cartesian coordinates

pub fn shortest_vector( &self, r1: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, r2: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Minimum image displacement vector from r1 to r2 (r2 - r1)

pub fn shortest_vector_fast( &self, a: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, b: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 1]>>

Shortest vector with ortho fast-path

pub fn shortest_vector_fast_arr( &self, a: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, b: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, ) -> [f64; 3]

Shortest vector returned as [F; 3] (zero-alloc hot path).

Equivalent to shortest_vector_fast but avoids the Array1<F> heap allocation by returning a stack array. Use inside neighbor-list pair loops where called O(N·k) times per build.

pub fn shortest_vector_raw(&self, a: [f64; 3], b: [f64; 3]) -> [f64; 3]

Shortest vector from raw [F; 3] inputs, returning [F; 3].

Both inputs and output are stack arrays — no ArrayView indexing. Called from neighbor-list inner loops where positions are stored in a flat [F; 3] slab instead of an Array2<F>.

pub fn calc_distance2( &self, a: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, b: ArrayBase<ViewRepr<&f64>, Dim<[usize; 1]>>, ) -> f64

Calculate squared distance using MIC.

pub fn to_frac( &self, xyz: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>

Convert Cartesian points to fractional coordinates (N×3)

pub fn to_cart( &self, frac: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>

Convert fractional coordinates to Cartesian points (N×3)

pub fn isin( &self, xyz: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, ) -> ArrayBase<OwnedRepr<bool>, Dim<[usize; 1]>>

Check if points lie within [0,1) in fractional space.

pub fn delta_out( &self, xyzu1: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, xyzu2: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, out: &mut ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>, minimum_image: bool, )

Batched displacement vectors row-wise (N×3). Writes result into out to avoid allocation.

pub fn delta( &self, xyzu1: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, xyzu2: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, minimum_image: bool, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>

Batched displacement vectors row-wise (N×3)

pub fn wrap( &self, xyz: ArrayBase<ViewRepr<&f64>, Dim<[usize; 2]>>, ) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>

Wrap Cartesian points into the unit cell according to PBC

pub fn get_corners(&self) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>

Trait Implementations

impl Clone for SimBox

fn clone(&self) -> SimBox

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for SimBox

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

Formats the value using the given formatter.

impl Region for SimBox

fn bounds(&self) -> ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>

Returns the axis-aligned bounding box of the region.

fn contains( &self, points: &ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>, ) -> ArrayBase<OwnedRepr<bool>, Dim<[usize; 1]>>

Batched containment test for a set of 3D points.

fn contains_point(&self, point: &[f64; 3]) -> bool

Single-point containment test.