Struct gchemol_core::Lattice

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<3>, Const<1>, ArrayStorage<f64, 3, 1>>>

Create a supercell along three cell directions.

impl Lattice

pub fn new<T>(tvs: [T; 3]) -> Lattice
where T: Into<Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>> + Copy,

Construct Lattice from three lattice vectors.

pub fn from_matrix<T>(tvs: T) -> Lattice
where T: Into<Matrix<f64, Const<3>, Const<3>, 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<3>, 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 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) -> Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>

Get cell origin in Cartesian coordinates

pub fn to_frac<T>( &self, p: T ) -> Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>
where T: Into<Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>>,

Returns the fractional coordinates given cartesian coordinates.

pub fn to_cart<T>( &self, p: T ) -> Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>
where T: Into<Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>>,

Returns the cartesian coordinates given fractional coordinates.

pub fn vector_a( &self ) -> Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>

Lattice vector a

pub fn vector_b( &self ) -> Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>

Lattice vector b

pub fn vector_c( &self ) -> Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>

Lattice vector c

pub fn vectors( &self ) -> [Matrix<f64, Const<3>, Const<1>, ArrayStorage<f64, 3, 1>>; 3]

Three lattice vectors.

pub fn matrix(&self) -> Matrix<f64, Const<3>, Const<3>, ArrayStorage<f64, 3, 3>>

Lattice vectors

pub fn inv_matrix( &self ) -> Matrix<f64, Const<3>, Const<3>, 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<3>, Const<1>, ArrayStorage<f64, 3, 1>>
where T: Into<Matrix<f64, Const<3>, 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<3>, Const<1>, ArrayStorage<f64, 3, 1>>
where T: Into<Matrix<f64, Const<3>, 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) -> f64
where T: Into<Matrix<f64, Const<3>, 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<3>, 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. Read more

1.0.0 · source§

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

Performs copy-assignment from source. Read more

impl Debug for Lattice

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

Formats the value using the given formatter. Read more

impl Default for Lattice

fn default() -> Lattice

Returns the “default value” for a type. Read more

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. Read more

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. Read more

impl Copy for Lattice

Auto Trait Implementations§

impl UnwindSafe for Lattice

Blanket Implementations§

impl<T> Any for T
where T: 'static + ?Sized,

fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

impl<T> Borrow<T> for T
where T: ?Sized,

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

impl<T> BorrowMut<T> for T
where T: ?Sized,

fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

impl<T> Configure for T
where T: Default + DeserializeOwned + Serialize,

fn print_toml(&self)

👎Deprecated: plan to be removed

Print current configuration in toml format.

fn from_json(s: &str) -> Result<Self, Error>

Deserialize an instance of type T from a string of JSON text.

fn from_toml(s: &str) -> Result<Self, Error>

Deserialize an instance of type T from a string of TOML text.

fn to_json(&self) -> Result<String, Error>

Serialize it to a JSON string.

fn to_toml(&self) -> Result<String, Error>

Serialize self to a TOML string.

impl<T> From<T> for T

fn from(t: T) -> T

Returns the argument unchanged.

impl<T, U> Into for T
where U: From<T>,

fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

impl<T> Pointable for T

const ALIGN: usize = _

The alignment of pointer.

type Init = T

The type for initializers.

unsafe fn init(init: <T as Pointable>::Init) -> usize

Initializes a with the given initializer. Read more

unsafe fn deref<'a>(ptr: usize) -> &'a T

Dereferences the given pointer. Read more

unsafe fn deref_mut<'a>(ptr: usize) -> &'a mut T

Mutably dereferences the given pointer. Read more

unsafe fn drop(ptr: usize)

Drops the object pointed to by the given pointer. Read more

impl<T> Same for T

type Output = T

Should always be Self

impl<SS, SP> SupersetOf<SS> for SP
where SS: SubsetOf<SP>,

fn to_subset(&self) -> Option<SS>

The inverse inclusion map: attempts to construct self from the equivalent element of its superset. Read more

fn is_in_subset(&self) -> bool

Checks if self is actually part of its subset T (and can be converted to it).

fn to_subset_unchecked(&self) -> SS

Use with care! Same as self.to_subset but without any property checks. Always succeeds.

fn from_subset(element: &SS) -> SP

The inclusion map: converts self to the equivalent element of its superset.

impl<T> ToOwned for T
where T: Clone,

type Owned = T

The resulting type after obtaining ownership.

fn to_owned(&self) -> T

Creates owned data from borrowed data, usually by cloning. Read more

fn clone_into(&self, target: &mut T)

Uses borrowed data to replace owned data, usually by cloning. Read more

impl<T, U> TryFrom for T
where U: Into<T>,

type Error = Infallible

The type returned in the event of a conversion error.

fn try_from(value: U) -> Result<T, <T as TryFrom>::Error>

Performs the conversion.

impl<T, U> TryInto for T
where U: TryFrom<T>,

type Error = >::Error

The type returned in the event of a conversion error.

fn try_into(self) -> Result<U, >::Error>

Performs the conversion.

impl<V, T> VZip<V> for T
where V: MultiLane<T>,

fn vzip(self) -> V