Lattice

gchemol

Struct Lattice 

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pub struct Lattice { /* private fields */ }
Expand description

Periodic 3D lattice

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impl Lattice

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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.

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impl Lattice

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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.

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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).

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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

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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

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pub fn volume(&self) -> f64

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

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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

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

Lattice length parameters: a, b, c

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

Lattice angle parameters in degrees

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

Scale Lattice by a positive constant v

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

Scale Lattice in a direction by a positive constant v

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

Scale Lattice in b direction by a positive constant v

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

Scale Lattice in c direction by a positive constant v

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

Get cell origin in Cartesian coordinates

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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.

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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.

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

Lattice vector a

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

Lattice vector b

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

Lattice vector c

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

Three lattice vectors.

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

Lattice vectors

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

inverse of lattice matrix

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pub fn is_orthorhombic(&self) -> bool

Check if lattice is orthorhombic

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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.

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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.

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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
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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.

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impl Clone for Lattice

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fn clone(&self) -> Lattice

Returns a duplicate of the value. Read more
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fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source. Read more
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impl Debug for Lattice

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

Formats the value using the given formatter. Read more
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impl Default for Lattice

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fn default() -> Lattice

Returns the “default value” for a type. Read more
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impl<'de> Deserialize<'de> for Lattice

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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
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impl Serialize for Lattice

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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
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impl Copy for Lattice

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

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more
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impl<T> Borrow<T> for T
where T: ?Sized,

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fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more
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impl<T> BorrowMut<T> for T
where T: ?Sized,

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

Mutably borrows from an owned value. Read more
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impl<T> CloneToUninit for T
where T: Clone,

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unsafe fn clone_to_uninit(&self, dest: *mut u8)

🔬This is a nightly-only experimental API. (clone_to_uninit)
Performs copy-assignment from self to dest. Read more
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impl<T> Configure for T
where T: Default + DeserializeOwned + Serialize,

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fn print_toml(&self)

👎Deprecated: plan to be removed
Print current configuration in toml format.
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fn from_json(s: &str) -> Result<Self, Error>

Deserialize an instance of type T from a string of JSON text.
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fn from_toml(s: &str) -> Result<Self, Error>

Deserialize an instance of type T from a string of TOML text.
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fn to_json(&self) -> Result<String, Error>

Serialize it to a JSON string.
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fn to_toml(&self) -> Result<String, Error>

Serialize self to a TOML string.
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impl<T> From<T> for T

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fn from(t: T) -> T

Returns the argument unchanged.

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

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fn into(self) -> U

Calls U::from(self).

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

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impl<T> IntoEither for T

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fn into_either(self, into_left: bool) -> Either<Self, Self>

Converts self into a Left variant of Either<Self, Self> if into_left is true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more
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fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
where F: FnOnce(&Self) -> bool,

Converts self into a Left variant of Either<Self, Self> if into_left(&self) returns true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more
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impl<T> Pointable for T

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const ALIGN: usize

The alignment of pointer.
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type Init = T

The type for initializers.
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unsafe fn init(init: <T as Pointable>::Init) -> usize

Initializes a with the given initializer. Read more
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unsafe fn deref<'a>(ptr: usize) -> &'a T

Dereferences the given pointer. Read more
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unsafe fn deref_mut<'a>(ptr: usize) -> &'a mut T

Mutably dereferences the given pointer. Read more
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unsafe fn drop(ptr: usize)

Drops the object pointed to by the given pointer. Read more
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impl<T> Same for T

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type Output = T

Should always be Self
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impl<SS, SP> SupersetOf<SS> for SP
where SS: SubsetOf<SP>,

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

The inverse inclusion map: attempts to construct self from the equivalent element of its superset. Read more
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fn is_in_subset(&self) -> bool

Checks if self is actually part of its subset T (and can be converted to it).
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fn to_subset_unchecked(&self) -> SS

Use with care! Same as self.to_subset but without any property checks. Always succeeds.
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fn from_subset(element: &SS) -> SP

The inclusion map: converts self to the equivalent element of its superset.
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impl<T> ToOwned for T
where T: Clone,

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type Owned = T

The resulting type after obtaining ownership.
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fn to_owned(&self) -> T

Creates owned data from borrowed data, usually by cloning. Read more
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fn clone_into(&self, target: &mut T)

Uses borrowed data to replace owned data, usually by cloning. Read more
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impl<T, U> TryFrom<U> for T
where U: Into<T>,

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type Error = Infallible

The type returned in the event of a conversion error.
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fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

Performs the conversion.
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impl<T, U> TryInto<U> for T
where U: TryFrom<T>,

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type Error = <U as TryFrom<T>>::Error

The type returned in the event of a conversion error.
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fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

Performs the conversion.
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impl<V, T> VZip<V> for T
where V: MultiLane<T>,

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fn vzip(self) -> V

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impl<T> DeserializeOwned for T
where T: for<'de> Deserialize<'de>,