Struct gchemol_lattice::Lattice

pub struct Lattice { /* private fields */ }

Periodic 3D lattice

Implementations

impl Lattice

pub fn replicate( &self, ra: impl Iterator<Item = isize> + Clone, rb: impl Iterator<Item = isize> + Clone, rc: impl Iterator<Item = isize> + Clone ) -> impl Iterator<Item = Vector3f>

Create a supercell along three cell directions.

impl Lattice

pub fn new<T: Into<Vector3f> + Copy>(tvs: [T; 3]) -> Self

Construct Lattice from three lattice vectors.

pub fn from_matrix<T: Into<Matrix3f>>(tvs: T) -> Self

Construct Lattice from lattice matrix (3x3).

pub fn from_params(a: f64, b: f64, c: f64, alpha: f64, beta: f64, gamma: f64) -> Self

Construct lattice from lattice parameters Unit cell angles in degrees, lengths in Angstrom

pub fn widths(&self) -> [f64; 3]

Return the perpendicular widths of the cell along three directions. i.e. the distance between opposite faces of the unit cell

pub fn volume(&self) -> f64

Return the volume of the unit cell the cache will be updated if necessary

pub fn set_origin<T: Into<Vector3f>>(&mut self, loc: T)

Set cell origin in Cartesian coordinates

pub fn lengths(&self) -> [f64; 3]

Lattice length parameters: a, b, c

pub fn angles(&self) -> [f64; 3]

Lattice angle parameters in degrees

pub fn scale_by(&mut self, v: f64)

Scale Lattice by a positive constant v

pub fn scale_by_a(&mut self, v: f64)

Scale Lattice in a direction by a positive constant v

pub fn scale_by_b(&mut self, v: f64)

Scale Lattice in b direction by a positive constant v

pub fn scale_by_c(&mut self, v: f64)

Scale Lattice in c direction by a positive constant v

pub fn origin(&self) -> Vector3f

Get cell origin in Cartesian coordinates

pub fn to_frac<T: Into<Vector3f>>(&self, p: T) -> Vector3f

Returns the fractional coordinates given cartesian coordinates.

pub fn to_cart<T: Into<Vector3f>>(&self, p: T) -> Vector3f

Returns the cartesian coordinates given fractional coordinates.

pub fn vector_a(&self) -> Vector3f

Lattice vector a

pub fn vector_b(&self) -> Vector3f

Lattice vector b

pub fn vector_c(&self) -> Vector3f

Lattice vector c

pub fn vectors(&self) -> [Vector3f; 3]

Three lattice vectors.

pub fn matrix(&self) -> Matrix3f

Lattice vectors

pub fn inv_matrix(&self) -> Matrix3f

inverse of lattice matrix

pub fn is_orthorhombic(&self) -> bool

Check if lattice is orthorhombic

pub fn wrap<T: Into<Vector3f>>(&self, vec: T) -> Vector3f

Wrap a point in cartesian coordinates into unit cell, obeying the periodic boundary conditions. Returns cartesian coordinates.

pub fn wrap_frac<T: Into<Vector3f>>(&self, f: T) -> Vector3f

Wrap a point in fractional coordinates into unit cell, obeying the periodic boundary conditions. Returns fractional coordinates.

pub fn distance<T: Into<Vector3f>>(&self, pi: T, pj: T) -> f64

Return the shortest distance between pi (point i) and the periodic images of pj (point j) under the minimum image convention

Parameters

• pi, pj: Cartesian coordinates of point i and point j

pub fn apply_mic<T: Into<[f64; 3]>>(&self, p: T) -> Vector3f

Return the shortest vector obeying the minimum image convention.

Trait Implementations

impl Clone for Lattice

fn clone(&self) -> Lattice

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Lattice

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

Formats the value using the given formatter.

impl Default for Lattice

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for Lattice

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for Lattice

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>where __S: Serializer,

Serialize this value into the given Serde serializer.

impl Copy for Lattice