conspire/physics/molecular/single_chain/efrc/
mod.rs

1#[cfg(test)]
2mod test;
3
4use crate::{
5    math::{Scalar, Tensor, TensorArray, random_uniform, random_x2_normal},
6    mechanics::CurrentCoordinate,
7    physics::{
8        BOLTZMANN_CONSTANT,
9        molecular::single_chain::{
10            Configuration, Ensemble, Extensible, Isometric, Isotensional, Legendre, MonteCarlo,
11            SingleChain, SingleChainError, Thermodynamics,
12        },
13    },
14};
15use std::f64::consts::TAU;
16
17/// The extensible freely-rotating chain model.
18#[derive(Clone, Debug)]
19pub struct ExtensibleFreelyRotatingChain {
20    /// The link angle $`\theta_b`$.
21    pub link_angle: Scalar,
22    /// The link length $`\ell_b`$.
23    pub link_length: Scalar,
24    /// The link stiffness $`k_b`$.
25    pub link_stiffness: Scalar,
26    /// The number of links $`N_b`$.
27    pub number_of_links: u8,
28    /// The thermodynamic ensemble.
29    pub ensemble: Ensemble,
30}
31
32impl ExtensibleFreelyRotatingChain {
33    fn nondimensional_link_stiffness(&self) -> Scalar {
34        self.link_stiffness * self.link_length().powi(2) / BOLTZMANN_CONSTANT / self.temperature()
35    }
36}
37
38impl SingleChain for ExtensibleFreelyRotatingChain {
39    fn link_length(&self) -> Scalar {
40        self.link_length
41    }
42    fn number_of_links(&self) -> u8 {
43        self.number_of_links
44    }
45}
46
47impl Extensible for ExtensibleFreelyRotatingChain {}
48
49impl Thermodynamics for ExtensibleFreelyRotatingChain {
50    fn ensemble(&self) -> Ensemble {
51        self.ensemble
52    }
53}
54
55impl Isometric for ExtensibleFreelyRotatingChain {
56    fn nondimensional_helmholtz_free_energy(
57        &self,
58        _nondimensional_extension: Scalar,
59    ) -> Result<Scalar, SingleChainError> {
60        unimplemented!()
61    }
62    fn nondimensional_force(
63        &self,
64        _nondimensional_extension: Scalar,
65    ) -> Result<Scalar, SingleChainError> {
66        unimplemented!()
67    }
68    fn nondimensional_stiffness(
69        &self,
70        _nondimensional_extension: Scalar,
71    ) -> Result<Scalar, SingleChainError> {
72        unimplemented!()
73    }
74    fn nondimensional_spherical_distribution(
75        &self,
76        _nondimensional_extension: Scalar,
77    ) -> Result<Scalar, SingleChainError> {
78        unimplemented!()
79    }
80}
81
82impl Isotensional for ExtensibleFreelyRotatingChain {
83    fn nondimensional_gibbs_free_energy_per_link(
84        &self,
85        _nondimensional_force: Scalar,
86    ) -> Result<Scalar, SingleChainError> {
87        unimplemented!()
88    }
89    fn nondimensional_extension(
90        &self,
91        _nondimensional_force: Scalar,
92    ) -> Result<Scalar, SingleChainError> {
93        unimplemented!()
94    }
95    fn nondimensional_compliance(
96        &self,
97        _nondimensional_force: Scalar,
98    ) -> Result<Scalar, SingleChainError> {
99        unimplemented!()
100    }
101}
102
103impl Legendre for ExtensibleFreelyRotatingChain {
104    fn nondimensional_spherical_distribution(
105        &self,
106        _nondimensional_extension: Scalar,
107    ) -> Result<Scalar, SingleChainError> {
108        unimplemented!()
109    }
110}
111
112impl MonteCarlo for ExtensibleFreelyRotatingChain {
113    fn random_configuration(&self) -> Configuration {
114        let std = 1.0 / self.nondimensional_link_stiffness().sqrt();
115        let cos_theta = 2.0 * random_uniform() - 1.0;
116        let sin_theta = (1.0 - cos_theta * cos_theta).sqrt();
117        let phi = TAU * random_uniform();
118        let (sin_phi, cos_phi) = phi.sin_cos();
119        const AY: CurrentCoordinate = CurrentCoordinate::const_from([0.0, 1.0, 0.0]);
120        const AZ: CurrentCoordinate = CurrentCoordinate::const_from([0.0, 0.0, 1.0]);
121        let mut a = AY;
122        let mut b =
123            CurrentCoordinate::const_from([sin_theta * cos_phi, sin_theta * sin_phi, cos_theta]);
124        let mut position = CurrentCoordinate::zero();
125        let (sin_theta, cos_theta) = self.link_angle.sin_cos();
126        (0..self.number_of_links())
127            .map(|link| {
128                if link > 0 {
129                    a = if b[1].abs() < 0.9 { AY } else { AZ };
130                    let u = a.cross(&b).normalized();
131                    let v = b.cross(&u);
132                    let phi = TAU * random_uniform();
133                    let (sin_phi, cos_phi) = phi.sin_cos();
134                    b = &b * cos_theta + (&u * cos_phi + &v * sin_phi) * sin_theta;
135                }
136                position += &b * random_x2_normal(1.0, std);
137                position.clone()
138            })
139            .collect()
140    }
141}
conspire/physics/molecular/single_chain/efrc/mod.rs

conspire/physics/molecular/single_chain/efrc/
mod.rs
