Struct gchemol_lattice::Lattice

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pub struct Lattice { /* private fields */ }

Expand description

Periodic 3D lattice

Implementations

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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 = Vector3f>

Create a supercell along three cell directions.

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impl Lattice

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

Construct Lattice from three lattice vectors.

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

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
) -> Self

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

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

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pub fn origin(&self) -> Vector3f

Get cell origin in Cartesian coordinates

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

Returns the fractional coordinates given cartesian coordinates.

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

Returns the cartesian coordinates given fractional coordinates.

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pub fn vector_a(&self) -> Vector3f

Lattice vector a

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pub fn vector_b(&self) -> Vector3f

Lattice vector b

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pub fn vector_c(&self) -> Vector3f

Lattice vector c

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

Three lattice vectors.

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pub fn matrix(&self) -> Matrix3f

Lattice vectors

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pub fn inv_matrix(&self) -> Matrix3f

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

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

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: 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

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

Return the shortest vector obeying the minimum image convention.

Trait Implementations

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impl Clone for Lattice

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fn clone(&self) -> Lattice

Returns a copy 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

Formats the value using the given formatter. Read more

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impl Default for Lattice

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fn default() -> Self

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<Self, D::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::Ok, S::Error> where
S: Serializer,

Serialize this value into the given Serde serializer. Read more

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impl Copy for Lattice

Auto Trait Implementations

impl RefUnwindSafe for Lattice

impl Send for Lattice

impl Sync for Lattice

impl Unpin for Lattice

impl UnwindSafe for Lattice

Blanket Implementations

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

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pub 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,

const: unstable · source

pub 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,

const: unstable · source

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

Mutably borrows from an owned value. Read more

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impl<T> From<T> for T

const: unstable · source

pub fn from(t: T) -> T

Returns the argument unchanged.

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

const: unstable · source

pub 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

pub const ALIGN: usize

The alignment of pointer.

type Init = T

The type for initializers.

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

Initializes a with the given initializer. Read more

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

Dereferences the given pointer. Read more

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

Mutably dereferences the given pointer. Read more

pub unsafe fn drop(ptr: usize)

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

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impl<T> Same<T> for T

type Output = T

Should always be Self

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

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

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

pub fn is_in_subset(&self) -> bool

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

pub fn to_subset_unchecked(&self) -> SS

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

pub 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,

type Owned = T

The resulting type after obtaining ownership.

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pub fn to_owned(&self) -> T

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

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

🔬 This is a nightly-only experimental API. (toowned_clone_into)

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

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

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source

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

Performs the conversion.

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

type Error = >::Error

The type returned in the event of a conversion error.

const: unstable · source

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

Performs the conversion.

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Struct gchemol_lattice::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>

impl Lattice

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

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

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

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

pub fn volume(&self) -> f64

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

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

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

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

pub fn origin(&self) -> Vector3f

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

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

pub fn vector_a(&self) -> Vector3f

pub fn vector_b(&self) -> Vector3f

pub fn vector_c(&self) -> Vector3f

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

pub fn matrix(&self) -> Matrix3f

pub fn inv_matrix(&self) -> Matrix3f

pub fn is_orthorhombic(&self) -> bool

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

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

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

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

Trait Implementations

impl Clone for Lattice

fn clone(&self) -> Lattice

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

impl Debug for Lattice

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

impl Default for Lattice

fn default() -> Self

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

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

impl Serialize for Lattice

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

impl Copy for Lattice

Auto Trait Implementations

impl RefUnwindSafe for Lattice

impl Send for Lattice

impl Sync for Lattice

impl Unpin for Lattice

impl UnwindSafe for Lattice

Blanket Implementations

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

pub fn type_id(&self) -> TypeId

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

pub fn borrow(&self) -> &T

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

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

impl<T> From<T> for T

pub fn from(t: T) -> T

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

pub fn into(self) -> U

impl<T> Pointable for T

pub const ALIGN: usize

type Init = T

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

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

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

pub unsafe fn drop(ptr: usize)

impl<T> Same<T> for T

type Output = T

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

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

pub fn is_in_subset(&self) -> bool

pub fn to_subset_unchecked(&self) -> SS

pub fn from_subset(element: &SS) -> SP

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

type Owned = T

pub fn to_owned(&self) -> T

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

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

type Error = Infallible

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

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

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>

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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