qsym2/auxiliary/
template_molecules.rs

1//! Template molecules for testing purposes.
2
3use crate::auxiliary::atom::{Atom, AtomKind, ElementMap};
4use crate::auxiliary::molecule::Molecule;
5use nalgebra::Point3;
6
7#[must_use]
8pub(crate) fn gen_twisted_h8(theta: f64) -> Molecule {
9    let emap = ElementMap::new();
10    let (atomic_number, atomic_mass) = emap.get("H").expect("Unable to retrieve element.");
11    let atoms: [Atom; 8] = [
12        Atom {
13            kind: AtomKind::Ordinary,
14            atomic_number: *atomic_number,
15            atomic_symbol: "H".to_owned(),
16            atomic_mass: *atomic_mass,
17            coordinates: Point3::new(0.0, 0.0, 0.0),
18            threshold: 1e-7,
19        },
20        Atom {
21            kind: AtomKind::Ordinary,
22            atomic_number: *atomic_number,
23            atomic_symbol: "H".to_owned(),
24            atomic_mass: *atomic_mass,
25            coordinates: Point3::new(1.0, 0.0, 0.0),
26            threshold: 1e-7,
27        },
28        Atom {
29            kind: AtomKind::Ordinary,
30            atomic_number: *atomic_number,
31            atomic_symbol: "H".to_owned(),
32            atomic_mass: *atomic_mass,
33            coordinates: Point3::new(1.0, 1.0, 0.0),
34            threshold: 1e-7,
35        },
36        Atom {
37            kind: AtomKind::Ordinary,
38            atomic_number: *atomic_number,
39            atomic_symbol: "H".to_owned(),
40            atomic_mass: *atomic_mass,
41            coordinates: Point3::new(0.0, 1.0, 0.0),
42            threshold: 1e-7,
43        },
44        Atom {
45            kind: AtomKind::Ordinary,
46            atomic_number: *atomic_number,
47            atomic_symbol: "H".to_owned(),
48            atomic_mass: *atomic_mass,
49            coordinates: Point3::new(
50                1.0 / (2.0_f64.sqrt()) * (5.0 * std::f64::consts::FRAC_PI_4 + theta).cos() + 0.5,
51                1.0 / (2.0_f64.sqrt()) * (5.0 * std::f64::consts::FRAC_PI_4 + theta).sin() + 0.5,
52                2.0,
53            ),
54            threshold: 1e-7,
55        },
56        Atom {
57            kind: AtomKind::Ordinary,
58            atomic_number: *atomic_number,
59            atomic_symbol: "H".to_owned(),
60            atomic_mass: *atomic_mass,
61            coordinates: Point3::new(
62                1.0 / (2.0_f64.sqrt()) * (7.0 * std::f64::consts::FRAC_PI_4 + theta).cos() + 0.5,
63                1.0 / (2.0_f64.sqrt()) * (7.0 * std::f64::consts::FRAC_PI_4 + theta).sin() + 0.5,
64                2.0,
65            ),
66            threshold: 1e-7,
67        },
68        Atom {
69            kind: AtomKind::Ordinary,
70            atomic_number: *atomic_number,
71            atomic_symbol: "H".to_owned(),
72            atomic_mass: *atomic_mass,
73            coordinates: Point3::new(
74                1.0 / (2.0_f64.sqrt()) * (1.0 * std::f64::consts::FRAC_PI_4 + theta).cos() + 0.5,
75                1.0 / (2.0_f64.sqrt()) * (1.0 * std::f64::consts::FRAC_PI_4 + theta).sin() + 0.5,
76                2.0,
77            ),
78            threshold: 1e-7,
79        },
80        Atom {
81            kind: AtomKind::Ordinary,
82            atomic_number: *atomic_number,
83            atomic_symbol: "H".to_owned(),
84            atomic_mass: *atomic_mass,
85            coordinates: Point3::new(
86                1.0 / (2.0_f64.sqrt()) * (3.0 * std::f64::consts::FRAC_PI_4 + theta).cos() + 0.5,
87                1.0 / (2.0_f64.sqrt()) * (3.0 * std::f64::consts::FRAC_PI_4 + theta).sin() + 0.5,
88                2.0,
89            ),
90            threshold: 1e-7,
91        },
92    ];
93    Molecule::from_atoms(&atoms, 1e-7)
94}
95
96#[must_use]
97pub(crate) fn gen_arbitrary_half_sandwich(n: u32) -> Molecule {
98    let emap = ElementMap::new();
99    let mut atoms: Vec<Atom> = vec![];
100    let (h_atomic_number, h_atomic_mass) = emap.get("H").expect("Unable to retrieve element.");
101    let (c_atomic_number, c_atomic_mass) = emap.get("C").expect("Unable to retrieve element.");
102    let (v_atomic_number, v_atomic_mass) = emap.get("V").expect("Unable to retrieve element.");
103    atoms.push(Atom {
104        kind: AtomKind::Ordinary,
105        atomic_number: *v_atomic_number,
106        atomic_symbol: "V".to_owned(),
107        atomic_mass: *v_atomic_mass,
108        coordinates: Point3::new(0.0, 0.0, 1.0 + 0.1 * (f64::from(n))),
109        threshold: 1e-7,
110    });
111    for i in 0..n {
112        atoms.push(Atom {
113            kind: AtomKind::Ordinary,
114            atomic_number: *c_atomic_number,
115            atomic_symbol: "C".to_owned(),
116            atomic_mass: *c_atomic_mass,
117            coordinates: Point3::new(
118                1.0 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
119                1.0 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
120                0.0,
121            ),
122            threshold: 1e-7,
123        });
124        atoms.push(Atom {
125            kind: AtomKind::Ordinary,
126            atomic_number: *h_atomic_number,
127            atomic_symbol: "H".to_owned(),
128            atomic_mass: *h_atomic_mass,
129            coordinates: Point3::new(
130                1.5 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
131                1.5 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
132                0.0,
133            ),
134            threshold: 1e-7,
135        });
136    }
137    Molecule::from_atoms(&atoms, 1e-7)
138}
139
140#[must_use]
141pub(crate) fn gen_arbitrary_eclipsed_sandwich(n: u32) -> Molecule {
142    let emap = ElementMap::new();
143    let mut atoms: Vec<Atom> = vec![];
144    let (h_atomic_number, h_atomic_mass) = emap.get("H").expect("Unable to retrieve element.");
145    let (c_atomic_number, c_atomic_mass) = emap.get("C").expect("Unable to retrieve element.");
146    let (m_atomic_number, m_atomic_mass) = emap.get("Co").expect("Unable to retrieve element.");
147    atoms.push(Atom {
148        kind: AtomKind::Ordinary,
149        atomic_number: *m_atomic_number,
150        atomic_symbol: "Co".to_owned(),
151        atomic_mass: *m_atomic_mass,
152        coordinates: Point3::new(0.0, 0.0, 0.0),
153        threshold: 1e-7,
154    });
155    for i in 0..n {
156        atoms.push(Atom {
157            kind: AtomKind::Ordinary,
158            atomic_number: *c_atomic_number,
159            atomic_symbol: "C".to_owned(),
160            atomic_mass: *c_atomic_mass,
161            coordinates: Point3::new(
162                1.0 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
163                1.0 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
164                -1.0 - 0.1 * (f64::from(n)),
165            ),
166            threshold: 1e-7,
167        });
168        atoms.push(Atom {
169            kind: AtomKind::Ordinary,
170            atomic_number: *h_atomic_number,
171            atomic_symbol: "H".to_owned(),
172            atomic_mass: *h_atomic_mass,
173            coordinates: Point3::new(
174                1.5 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
175                1.5 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
176                -1.0 - 0.1 * (f64::from(n)),
177            ),
178            threshold: 1e-7,
179        });
180        atoms.push(Atom {
181            kind: AtomKind::Ordinary,
182            atomic_number: *c_atomic_number,
183            atomic_symbol: "C".to_owned(),
184            atomic_mass: *c_atomic_mass,
185            coordinates: Point3::new(
186                1.0 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
187                1.0 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
188                1.0 + 0.1 * (f64::from(n)),
189            ),
190            threshold: 1e-7,
191        });
192        atoms.push(Atom {
193            kind: AtomKind::Ordinary,
194            atomic_number: *h_atomic_number,
195            atomic_symbol: "H".to_owned(),
196            atomic_mass: *h_atomic_mass,
197            coordinates: Point3::new(
198                1.5 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
199                1.5 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
200                1.0 + 0.1 * (f64::from(n)),
201            ),
202            threshold: 1e-7,
203        });
204    }
205    Molecule::from_atoms(&atoms, 1e-7)
206}
207
208#[must_use]
209pub fn gen_arbitrary_twisted_sandwich(n: u32, frac: f64) -> Molecule {
210    let emap = ElementMap::new();
211    let mut atoms: Vec<Atom> = vec![];
212    let (h_atomic_number, h_atomic_mass) = emap.get("H").expect("Unable to retrieve element.");
213    let (c_atomic_number, c_atomic_mass) = emap.get("C").expect("Unable to retrieve element.");
214    let (m_atomic_number, m_atomic_mass) = emap.get("Co").expect("Unable to retrieve element.");
215    atoms.push(Atom {
216        kind: AtomKind::Ordinary,
217        atomic_number: *m_atomic_number,
218        atomic_symbol: "Co".to_owned(),
219        atomic_mass: *m_atomic_mass,
220        coordinates: Point3::new(0.0, 0.0, 0.0),
221        threshold: 1e-7,
222    });
223    for i in 0..n {
224        atoms.push(Atom {
225            kind: AtomKind::Ordinary,
226            atomic_number: *c_atomic_number,
227            atomic_symbol: "C".to_owned(),
228            atomic_mass: *c_atomic_mass,
229            coordinates: Point3::new(
230                1.0 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
231                1.0 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
232                -1.0 - 0.1 * (f64::from(n)),
233            ),
234            threshold: 1e-7,
235        });
236        atoms.push(Atom {
237            kind: AtomKind::Ordinary,
238            atomic_number: *h_atomic_number,
239            atomic_symbol: "H".to_owned(),
240            atomic_mass: *h_atomic_mass,
241            coordinates: Point3::new(
242                1.5 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
243                1.5 * ((f64::from(i)) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
244                -1.0 - 0.1 * (f64::from(n)),
245            ),
246            threshold: 1e-7,
247        });
248        atoms.push(Atom {
249            kind: AtomKind::Ordinary,
250            atomic_number: *c_atomic_number,
251            atomic_symbol: "C".to_owned(),
252            atomic_mass: *c_atomic_mass,
253            coordinates: Point3::new(
254                1.0 * ((f64::from(i) + frac) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
255                1.0 * ((f64::from(i) + frac) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
256                1.0 + 0.1 * (f64::from(n)),
257            ),
258            threshold: 1e-7,
259        });
260        atoms.push(Atom {
261            kind: AtomKind::Ordinary,
262            atomic_number: *h_atomic_number,
263            atomic_symbol: "H".to_owned(),
264            atomic_mass: *h_atomic_mass,
265            coordinates: Point3::new(
266                1.5 * ((f64::from(i) + frac) * 2.0 * std::f64::consts::PI / (f64::from(n))).cos(),
267                1.5 * ((f64::from(i) + frac) * 2.0 * std::f64::consts::PI / (f64::from(n))).sin(),
268                1.0 + 0.1 * (f64::from(n)),
269            ),
270            threshold: 1e-7,
271        });
272    }
273    Molecule::from_atoms(&atoms, 1e-7)
274}
qsym2/auxiliary/template_molecules.rs

qsym2/auxiliary/
template_molecules.rs
