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//! Supercells and origin shifts (Task 1.7).
use crate::limits::{Limits, check_supercell};
use crate::spatial::{FractionalGrid, perpendicular_widths};
use crate::{Error, Lattice, Site, Structure, StructureBuilder};
impl Structure {
/// Builds an `na x nb x nc` supercell as a P1 structure.
///
/// # Errors
///
/// Returns [`Error::InvalidInput`] for zero repeats, or
/// [`Error::LimitExceeded`] when the estimate exceeds the hard limit.
pub fn supercell(&self, na: u32, nb: u32, nc: u32) -> Result<Self, Error> {
self.supercell_with_limits(na, nb, nc, &Limits::default())
}
/// Builds an `na x nb x nc` supercell with an explicit limits profile.
///
/// # Errors
///
/// Returns [`Error::InvalidInput`] for zero repeats, or
/// [`Error::LimitExceeded`] when the estimate exceeds the profile's hard
/// limit.
pub fn supercell_with_limits(
&self,
na: u32,
nb: u32,
nc: u32,
limits: &Limits,
) -> Result<Self, Error> {
if na == 0 || nb == 0 || nc == 0 {
return Err(Error::InvalidInput(
"supercell repeats must be positive".to_owned(),
));
}
self.supercell_matrix_with_limits(
[
[f64::from(na), 0.0, 0.0],
[0.0, f64::from(nb), 0.0],
[0.0, 0.0, f64::from(nc)],
],
limits,
)
}
/// Builds a supercell from a positive integer transformation matrix.
///
/// Rows of `p` are the new vectors in units of the old ones.
///
/// # Errors
///
/// Returns [`Error::InvalidInput`] for non-integer, singular or negative
/// determinant matrices, or [`Error::LimitExceeded`] for a refused size.
pub fn supercell_matrix(&self, p: [[f64; 3]; 3]) -> Result<Self, Error> {
self.supercell_matrix_with_limits(p, &Limits::default())
}
/// Builds a supercell with an explicit limits profile.
///
/// # Errors
///
/// Returns [`Error::InvalidInput`] for non-integer, singular or negative
/// determinant matrices, or [`Error::LimitExceeded`] for a refused size.
pub fn supercell_matrix_with_limits(
&self,
p: [[f64; 3]; 3],
limits: &Limits,
) -> Result<Self, Error> {
for value in p.iter().flatten() {
if !value.is_finite() || (value - value.round()).abs() > 1e-9 {
return Err(Error::InvalidInput(
"supercell matrix must contain integers".to_owned(),
));
}
}
let expanded = if self.is_p1() {
None
} else {
Some(self.as_p1()?)
};
let source = expanded.as_ref().unwrap_or(self);
let verdict = check_supercell(limits, source.sites().len() as u64, p)?;
if verdict.refused() {
return Err(Error::LimitExceeded(verdict));
}
let lattice = source.lattice().transform(p)?;
let inverse = Lattice::new(p)?.inverse();
let max_inverse = inverse
.iter()
.flatten()
.map(|value| value.abs())
.fold(0.0, f64::max);
let range = (max_inverse * 4.0).ceil() as i64 + 2;
let widths = perpendicular_widths(&lattice)?;
let mut grid = FractionalGrid::new(widths, 1e-6);
let mut sites: Vec<Site> = Vec::new();
for site in source.sites() {
for i in -range..=range {
for j in -range..=range {
for k in -range..=range {
let candidate = [
site.frac()[0] + i as f64,
site.frac()[1] + j as f64,
site.frac()[2] + k as f64,
];
let frac = multiply_row(candidate, inverse);
if !frac.iter().all(|value| (-1e-9..1.0).contains(value)) {
continue;
}
let mut duplicate = false;
grid.for_each_candidate(site.element(), frac, |existing_index| {
let Some(existing) = sites.get(existing_index) else {
return true;
};
if lattice.distance(existing.frac(), frac) <= 1e-6 {
duplicate = true;
return false;
}
true
});
if duplicate {
continue;
}
let index = sites.len();
sites.push(site.clone().with_frac(frac)?);
grid.insert(site.element(), frac, index);
}
}
}
}
let mut builder = StructureBuilder::new(source.name(), lattice);
for site in sites {
builder = builder.site(site);
}
for (key, value) in source.metadata() {
builder = builder.metadata(key.clone(), value.clone());
}
builder.build()
}
/// Shifts the origin by a fractional vector and rewraps the sites.
///
/// # Errors
///
/// Returns [`Error::InvalidInput`] for non-finite shifts.
pub fn origin_shift(&self, delta: [f64; 3]) -> Result<Self, Error> {
if !delta.iter().all(|value| value.is_finite()) {
return Err(Error::InvalidInput(
"origin shift must be finite".to_owned(),
));
}
let mut builder = StructureBuilder::new(self.name(), *self.lattice());
for site in self.sites() {
let frac = [
site.frac()[0] + delta[0],
site.frac()[1] + delta[1],
site.frac()[2] + delta[2],
];
builder = builder.site(site.clone().with_frac(Lattice::wrap(frac))?);
}
for (key, value) in self.metadata() {
builder = builder.metadata(key.clone(), value.clone());
}
builder.build()
}
}
fn multiply_row(vector: [f64; 3], matrix: [[f64; 3]; 3]) -> [f64; 3] {
let [x, y, z] = vector;
let [[a, b, c], [d, e, f], [g, h, i]] = matrix;
[
x * a + y * d + z * g,
x * b + y * e + z * h,
x * c + y * f + z * i,
]
}