sci-form 0.15.2

High-performance 3D molecular conformer generation using ETKDG distance geometry
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
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156

//! Integration tests for E10: Constant Potential Method

#[cfg(feature = "experimental-cpm")]
mod cpm_tests {
    use sci_form::beta::cpm::*;

    fn water() -> (Vec<u8>, Vec<[f64; 3]>) {
        (
            vec![8, 1, 1],
            vec![[0.0, 0.0, 0.0], [0.757, 0.586, 0.0], [-0.757, 0.586, 0.0]],
        )
    }

    fn ethanol() -> (Vec<u8>, Vec<[f64; 3]>) {
        (
            vec![6, 6, 8, 1, 1, 1, 1, 1, 1],
            vec![
                [0.0, 0.0, 0.0],
                [1.52, 0.0, 0.0],
                [2.14, 1.21, 0.0],
                [-0.36, 1.03, 0.0],
                [-0.36, -0.52, 0.89],
                [-0.36, -0.52, -0.89],
                [1.88, -0.52, 0.89],
                [1.88, -0.52, -0.89],
                [3.10, 1.21, 0.0],
            ],
        )
    }

    #[test]
    fn test_cpm_converges() {
        let (el, pos) = water();
        let result = compute_cpm_charges(&el, &pos, &CpmConfig::default());
        assert!(result.converged);
    }

    #[test]
    fn test_cpm_nonzero_charge() {
        let (el, pos) = water();
        // At non-neutral potential, total charge should deviate from zero
        let r1 = compute_cpm_charges(
            &el,
            &pos,
            &CpmConfig {
                mu_ev: -3.0,
                ..Default::default()
            },
        );
        let r2 = compute_cpm_charges(
            &el,
            &pos,
            &CpmConfig {
                mu_ev: -6.0,
                ..Default::default()
            },
        );
        assert!(
            (r1.total_charge - r2.total_charge).abs() > 0.01,
            "Different μ should give different Q"
        );
    }

    #[test]
    fn test_cpm_charge_increases_with_mu() {
        let (el, pos) = ethanol();
        let r_low = compute_cpm_charges(
            &el,
            &pos,
            &CpmConfig {
                mu_ev: -5.5,
                ..Default::default()
            },
        );
        let r_high = compute_cpm_charges(
            &el,
            &pos,
            &CpmConfig {
                mu_ev: -3.5,
                ..Default::default()
            },
        );
        assert!(r_high.total_charge > r_low.total_charge);
    }

    #[test]
    fn test_cpm_grand_potential_finite() {
        let (el, pos) = water();
        let result = compute_cpm_charges(&el, &pos, &CpmConfig::default());
        assert!(result.grand_potential.is_finite());
        assert!(result.electrostatic_energy.is_finite());
    }

    #[test]
    fn test_cpm_surface_scan() {
        let (el, pos) = water();
        let surface = compute_cpm_surface(&el, &pos, -5.5, -3.5, 10, 78.5);
        assert_eq!(surface.mu_values.len(), 10);
        assert_eq!(surface.total_charge.len(), 10);
        assert_eq!(surface.capacitance.len(), 10);
    }

    #[test]
    fn test_cpm_surface_charge_monotonic() {
        let (el, pos) = ethanol();
        let surface = compute_cpm_surface(&el, &pos, -5.5, -3.5, 20, 78.5);
        // Q should generally increase with μ
        let first = surface.total_charge[0];
        let last = *surface.total_charge.last().unwrap();
        assert!(
            last > first,
            "Q should increase: first={}, last={}",
            first,
            last
        );
    }

    #[test]
    fn test_cpm_surface_capacitance_positive() {
        let (el, pos) = water();
        let surface = compute_cpm_surface(&el, &pos, -5.0, -4.0, 15, 78.5);
        let positive_count = surface.capacitance.iter().filter(|&&c| c > 0.0).count();
        assert!(
            positive_count > surface.capacitance.len() / 2,
            "Most capacitance values should be positive"
        );
    }

    #[test]
    fn test_cpm_dielectric_effect() {
        let (el, pos) = water();
        let r_water = compute_cpm_charges(
            &el,
            &pos,
            &CpmConfig {
                dielectric: 78.5,
                mu_ev: -4.0,
                ..Default::default()
            },
        );
        let r_vacuum = compute_cpm_charges(
            &el,
            &pos,
            &CpmConfig {
                dielectric: 1.0,
                mu_ev: -4.0,
                ..Default::default()
            },
        );
        // In vacuum (ε=1), Coulomb coupling is stronger → different charge distribution
        assert!(
            (r_water.total_charge - r_vacuum.total_charge).abs() > 0.001,
            "Dielectric should affect charges"
        );
    }
}