Struct gchemol::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 = Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>>

Create a supercell along three cell directions.

impl Lattice

pub fn new<T>(tvs: [T; 3]) -> Latticewhere
T: Into<Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>> + Copy,

Construct Lattice from three lattice vectors.

pub fn from_matrix<T>(tvs: T) -> Latticewhere
T: Into<Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<nalgebra::::base::dimension::U3::{constant#0}>, ArrayStorage<f64, 3, 3>>>,

Construct Lattice from lattice matrix (3x3).

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

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>(&mut self, loc: T)where
T: Into<Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>>,

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

pub fn origin(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>

Get cell origin in Cartesian coordinates

pub fn to_frac<T>(
&self,
p: T
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>where
T: Into<Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>>,

Returns the fractional coordinates given cartesian coordinates.

pub fn to_cart<T>(
&self,
p: T
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>where
T: Into<Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>>,

Returns the cartesian coordinates given fractional coordinates.

pub fn vector_a(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>

Lattice vector a

pub fn vector_b(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>

Lattice vector b

pub fn vector_c(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>

Lattice vector c

pub fn vectors(
&self
) -> [Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>; 3]

Three lattice vectors.

pub fn matrix(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<nalgebra::::base::dimension::U3::{constant#0}>, ArrayStorage<f64, 3, 3>>

Lattice vectors

pub fn inv_matrix(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<nalgebra::::base::dimension::U3::{constant#0}>, ArrayStorage<f64, 3, 3>>

inverse of lattice matrix

pub fn is_orthorhombic(&self) -> bool

Check if lattice is orthorhombic

pub fn wrap<T>(
&self,
vec: T
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>where
T: Into<Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>>,

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

pub fn wrap_frac<T>(
&self,
f: T
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>where
T: Into<Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>>,

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

pub fn distance<T>(&self, pi: T, pj: T) -> f64where
T: Into<Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>>,

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>(
&self,
p: T
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>where
T: Into<[f64; 3]>,

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<(), Error>

Formats the value using the given formatter.

impl Default for Lattice

fn default() -> Lattice

Returns the “default value” for a type.

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

fn deserialize<__D>(
__deserializer: __D
) -> Result<Lattice, <__D as Deserializer<'de>>::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 as Serializer>::Ok, <__S as Serializer>::Error>where
__S: Serializer,

Serialize this value into the given Serde serializer.

impl Copy for Lattice