Struct gchemol_core::Lattice
source · pub struct Lattice { /* private fields */ }
Expand description
Periodic 3D lattice
Implementations§
source§impl Lattice
impl Lattice
sourcepub 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>>>
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.
source§impl Lattice
impl Lattice
sourcepub 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,
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.
sourcepub 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>>>,
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).
sourcepub fn from_params(
a: f64,
b: f64,
c: f64,
alpha: f64,
beta: f64,
gamma: f64
) -> Lattice
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
sourcepub fn widths(&self) -> [f64; 3]
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
sourcepub fn volume(&self) -> f64
pub fn volume(&self) -> f64
Return the volume of the unit cell the cache will be updated if necessary
sourcepub 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>>>,
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
sourcepub fn scale_by_a(&mut self, v: f64)
pub fn scale_by_a(&mut self, v: f64)
Scale Lattice in a
direction by a positive constant v
sourcepub fn scale_by_b(&mut self, v: f64)
pub fn scale_by_b(&mut self, v: f64)
Scale Lattice in b
direction by a positive constant v
sourcepub fn scale_by_c(&mut self, v: f64)
pub fn scale_by_c(&mut self, v: f64)
Scale Lattice in c
direction by a positive constant v
sourcepub fn origin(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>
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
sourcepub 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>>>,
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.
sourcepub 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>>>,
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.
sourcepub fn vector_a(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>
pub fn vector_a( &self ) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>
Lattice vector a
sourcepub fn vector_b(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>
pub fn vector_b( &self ) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>
Lattice vector b
sourcepub fn vector_c(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>
pub fn vector_c( &self ) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>
Lattice vector c
sourcepub fn vectors(
&self
) -> [Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>; 3]
pub fn vectors( &self ) -> [Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<1>, ArrayStorage<f64, 3, 1>>; 3]
Three lattice vectors.
sourcepub fn matrix(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<nalgebra::::base::dimension::U3::{constant#0}>, ArrayStorage<f64, 3, 3>>
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
sourcepub fn inv_matrix(
&self
) -> Matrix<f64, Const<nalgebra::::base::dimension::U3::{constant#0}>, Const<nalgebra::::base::dimension::U3::{constant#0}>, ArrayStorage<f64, 3, 3>>
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
sourcepub fn is_orthorhombic(&self) -> bool
pub fn is_orthorhombic(&self) -> bool
Check if lattice is orthorhombic
sourcepub 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>>>,
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.
sourcepub 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>>>,
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.
sourcepub 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>>>,
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
Trait Implementations§
source§impl<'de> Deserialize<'de> for Lattice
impl<'de> Deserialize<'de> for Lattice
source§fn deserialize<__D>(
__deserializer: __D
) -> Result<Lattice, <__D as Deserializer<'de>>::Error>where
__D: Deserializer<'de>,
fn deserialize<__D>( __deserializer: __D ) -> Result<Lattice, <__D as Deserializer<'de>>::Error>where __D: Deserializer<'de>,
source§impl Serialize for Lattice
impl Serialize for Lattice
source§fn serialize<__S>(
&self,
__serializer: __S
) -> Result<<__S as Serializer>::Ok, <__S as Serializer>::Error>where
__S: Serializer,
fn serialize<__S>( &self, __serializer: __S ) -> Result<<__S as Serializer>::Ok, <__S as Serializer>::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§
source§impl<T> Configure for Twhere
T: Default + DeserializeOwned + Serialize,
impl<T> Configure for Twhere T: Default + DeserializeOwned + Serialize,
source§fn print_toml(&self)
fn print_toml(&self)
source§fn from_json(s: &str) -> Result<Self, Error>
fn from_json(s: &str) -> Result<Self, Error>
§impl<T> Pointable for T
impl<T> Pointable for T
§impl<SS, SP> SupersetOf<SS> for SPwhere
SS: SubsetOf<SP>,
impl<SS, SP> SupersetOf<SS> for SPwhere SS: SubsetOf<SP>,
§fn to_subset(&self) -> Option<SS>
fn to_subset(&self) -> Option<SS>
self
from the equivalent element of its
superset. Read more§fn is_in_subset(&self) -> bool
fn is_in_subset(&self) -> bool
self
is actually part of its subset T
(and can be converted to it).§fn to_subset_unchecked(&self) -> SS
fn to_subset_unchecked(&self) -> SS
self.to_subset
but without any property checks. Always succeeds.§fn from_subset(element: &SS) -> SP
fn from_subset(element: &SS) -> SP
self
to the equivalent element of its superset.