ak_core/geometry/
structure.rs

1use crate::geometry::{AtomicNumber, Cell, Pbc, StructureView};
2
3#[derive(Clone)]
4pub struct Structure {
5    pub positions: Vec<[f64; 3]>,
6    pub numbers: Vec<AtomicNumber>,
7    pub cell: Cell,
8    pub pbc: Pbc,
9}
10
11impl Structure {
12    pub fn new(
13        positions: Vec<[f64; 3]>,
14        numbers: Vec<i32>,
15        cell: [[f64; 3]; 3],
16        pbc: [bool; 3],
17    ) -> Self {
18        assert_eq!(positions.len(), numbers.len());
19
20        let atomic_numbers = numbers
21            .iter()
22            .map(|z| AtomicNumber::new(*z).expect("Atomic number was not in [1, 110]"))
23            .collect();
24
25        Self {
26            positions,
27            numbers: atomic_numbers,
28            cell: { Cell::new(cell) },
29            pbc: { Pbc::new(pbc) },
30        }
31    }
32
33    pub fn view(&self) -> StructureView<'_> {
34        StructureView {
35            positions: &self.positions,
36            numbers: &self.numbers,
37            cell: self.cell,
38            pbc: self.pbc,
39        }
40    }
41
42    pub fn from_xyz_reader<R: std::io::BufRead>(r: R) -> Self {
43        crate::io::read_xyz(r)
44    }
45
46    pub fn from_xyz_file<P: AsRef<std::path::Path>>(path: P) -> Self {
47        let f = std::fs::File::open(path).unwrap();
48        let r = std::io::BufReader::new(f);
49        Self::from_xyz_reader(r)
50    }
51}
52
53#[cfg(test)]
54mod test {
55    use crate::Structure;
56
57    fn test_structure() -> Structure {
58        let positions = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]].to_vec();
59        let numbers = [1, 1].to_vec();
60        let cell = [[10.0, 0.0, 0.0], [0.0, 10.0, 0.0], [0.0, 0.0, 10.0]];
61        let pbc = [false, false, false];
62        Structure::new(positions.clone(), numbers.clone(), cell, pbc)
63    }
64
65    #[test]
66    fn test_positions() {
67        let structure = test_structure();
68        let positions = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]].to_vec();
69        assert_eq!(structure.positions, positions)
70    }
71
72    #[test]
73    fn test_view() {
74        let structure = test_structure();
75        let view = structure.view();
76        let positions = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]].to_vec();
77        assert_eq!(view.positions, positions)
78    }
79}
ak_core/geometry/structure.rs

ak_core/geometry/
structure.rs
