Struct gchemol::Lattice

pub struct Lattice { /* fields omitted */ }

Periodic 3D lattice

Methods

impl Lattice

pub fn replicate(
    &self,
    ra: impl Clone + Iterator<Item = isize>,
    rb: impl Clone + Iterator<Item = isize>,
    rc: impl Clone + Iterator<Item = isize>
) -> impl Iterator<Item = Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>

Create a supercell along three cell directions.

impl Lattice

pub fn new<T>(tvs: [T; 3]) -> Lattice where
    T: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>> + Copy, 

Construct Lattice from three lattice vectors.

pub fn from_matrix<T>(tvs: T) -> Lattice where
    T: Into<Matrix<f64, U3, U3, <DefaultAllocator as Allocator<f64, U3, U3>>::Buffer>>, 

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, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>, 

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, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>

Get cell origin in Cartesian coordinates

pub fn to_frac<T>(
    &self,
    p: T
) -> Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer> where
    T: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>, 

Returns the fractional coordinates given cartesian coordinates.

pub fn to_cart<T>(
    &self,
    p: T
) -> Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer> where
    T: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>, 

Returns the cartesian coordinates given fractional coordinates.

pub fn vector_a(
    &self
) -> Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>

Lattice vector a

pub fn vector_b(
    &self
) -> Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>

Lattice vector b

pub fn vector_c(
    &self
) -> Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>

Lattice vector c

pub fn vectors(
    &self
) -> [Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>; 3]

Three lattice vectors.

pub fn matrix(
    &self
) -> Matrix<f64, U3, U3, <DefaultAllocator as Allocator<f64, U3, U3>>::Buffer>

Lattice vectors

pub fn is_orthorhombic(&self) -> bool

Check if lattice is orthorhombic

pub fn wrap<T>(
    &self,
    vec: T
) -> Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer> where
    T: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>, 

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, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer> where
    T: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>, 

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) -> f64 where
    T: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>, 

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, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer> 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 Copy for Lattice

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.