gosh-model 0.2.1

Chemical model for gosh
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134

// [[file:../models.note::178e12ff][178e12ff]]
use super::*;

use std::collections::{HashMap, HashSet};

use ::edip::EdipParameters;
use gchemol::neighbors::Neighborhood;
use vecfx::*;
// 178e12ff ends here

// [[file:../models.note::6e669f3b][6e669f3b]]
#[derive(Clone, Debug, Default)]
pub struct Edip {
    virial: f64,
    // for create neighbors
    nh: Neighborhood,
}

impl Edip {
    fn update_nh(&mut self, mol: &Molecule) {
        self.nh = Neighborhood::new();
        // use atom index (0-based) for node index
        self.nh.update(mol.positions().enumerate());
        if let Some(lat) = mol.get_lattice() {
            self.nh.set_lattice(lat.matrix().into());
        }
    }
}

impl ChemicalModel for Edip {
    fn compute(&mut self, mol: &Molecule) -> Result<Computed> {
        const search_radius: f64 = 4.0;

        // only works for silicon
        let not_silicon = mol.symbols().any(|x| x != "Si");
        if not_silicon {
            bail!("EDIP potential model only works for Silicon");
        }

        self.update_nh(mol);
        let n = mol.natoms();
        let positions = mol.positions().collect_vec();
        let mut neighbors = vec![];
        let mut distances = HashMap::new();
        // FIXME: rewrite for periodic system
        let lat = mol.get_lattice();
        for i in 0..n {
            let mut connected = HashSet::new();
            for x in self.nh.neighbors(i, search_radius) {
                // FIXME: avoid recompute pair distance in edip crate
                let j = x.node;
                let pi: Vector3f = positions[i].into();
                let pj: Vector3f = positions[j].into();
                let d = if let Some(image) = x.image {
                    // translation periodic image
                    let t = lat.unwrap().to_cart(image);
                    pj + t - pi
                } else {
                    pj - pi
                };
                distances.insert((i, j), d.into());
                connected.insert(j);
            }

            neighbors.push(connected);
        }

        let params = EdipParameters::silicon();
        let mut forces = vec![[0.0; 3]; n];
        let (energy, virial) = ::edip::compute_forces(&mut forces, &neighbors, &distances, &params);

        let mut computed = Computed::default();
        computed.set_energy(energy);
        computed.set_forces(forces);

        // FIXME: could be removed
        self.virial = virial;

        Ok(computed)
    }
}
// 6e669f3b ends here

// [[file:../models.note::28122508][28122508]]
#[test]
fn test_edip() -> Result<()> {
    use gchemol::prelude::*;
    use gchemol::Molecule;
    use vecfx::*;

    let f = "./tests/files/si10.xyz";
    let mol = Molecule::from_file(f)?;

    let mut model = Edip::default();
    let computed = model.compute(&mol)?;
    let f = computed.get_forces().unwrap();
    let f_norm = f.as_flat().as_vector_slice().norm();
    assert!(dbg!(f_norm) <= 0.005);
    let energy = computed.get_energy().unwrap();
    approx::assert_relative_eq!(energy, -39.57630354331939, epsilon = 1e-5);
    approx::assert_relative_eq!(model.virial, 0.00224989660978845, epsilon = 1e-5);

    let f = "./tests/files/si5.xyz";
    let mol = Molecule::from_file(f)?;
    let computed = model.compute(&mol)?;
    let energy = computed.get_energy().unwrap();
    approx::assert_relative_eq!(energy, -14.566606, epsilon = 1e-5);
    // FIXME: refactor
    let virial = model.virial;
    approx::assert_relative_eq!(virial, -3.643552, epsilon = 1e-5);

    let f = computed.get_forces().unwrap();
    #[rustfmt::skip]
    let f_expected = [ -0.19701000,  -0.62522600,   0.02948000,
                       -0.23330600,   0.43698600,   0.42511400,
                        0.43297600,   0.18333500,  -0.44864300,
                       -1.75669300,   0.50149400,  -1.48879300,
                        1.75403300,  -0.49658900,   1.48284200];
    approx::assert_relative_eq!(
        f.as_flat().as_vector_slice(),
        f_expected.as_vector_slice(),
        epsilon = 1E-5,
    );

    // for silicon crystal
    let mol = Molecule::from_file("./tests/files/si-3x3x3.cif")?;
    let computed = model.compute(&mol)?;
    let energy = computed.get_energy().unwrap();
    let f = computed.get_forces().unwrap();
    dbg!(f.as_flat().as_vector_slice().norm());

    Ok(())
}
// 28122508 ends here