polymers 0.3.7

Polymers Modeling Library
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
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198

#[cfg(feature = "extern")]
pub mod ex;

#[cfg(feature = "python")]
pub mod py;

mod test;

/// The square-well freely-jointed chain (SWFJC) model thermodynamics in the isotensional ensemble approximated using a Legendre transformation.
pub mod legendre;

use std::f64::consts::PI;
use crate::physics::
{
    PLANCK_CONSTANT,
    BOLTZMANN_CONSTANT
};
use crate::physics::single_chain::ZERO;

/// The structure of the thermodynamics of the SWFJC model in the isotensional ensemble.
pub struct SWFJC
{
    /// The mass of each hinge in the chain in units of kg/mol.
    pub hinge_mass: f64,

    /// The length of each link in the chain in units of nm.
    pub link_length: f64,

    /// The number of links in the chain.
    pub number_of_links: u8,

    /// The width of the well in units of nm.
    pub well_width: f64,

    /// The thermodynamic functions of the model in the isotensional ensemble approximated using a Legendre transformation.
    pub legendre: legendre::SWFJC
}

/// The expected end-to-end length as a function of the applied force and temperature, parameterized by the number of links, link length, and well width.
pub fn end_to_end_length(number_of_links: &u8, link_length: &f64, well_width: &f64, force: &f64, temperature: &f64) -> f64
{
    let nondimensional_well_parameter = 1.0 + well_width/link_length;
    let nondimensional_force = force*link_length/BOLTZMANN_CONSTANT/temperature;
    (*number_of_links as f64)*link_length*((nondimensional_well_parameter.powi(2)*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.sinh())/(nondimensional_well_parameter*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).cosh() - (nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.cosh() + nondimensional_force.sinh()) - 3.0/nondimensional_force)
}

/// The expected end-to-end length per link as a function of the applied force and temperature, parameterized by the link length and well width.
pub fn end_to_end_length_per_link(link_length: &f64, well_width: &f64, force: &f64, temperature: &f64) -> f64
{
    let nondimensional_well_parameter = 1.0 + well_width/link_length;
    let nondimensional_force = force*link_length/BOLTZMANN_CONSTANT/temperature;
    link_length*((nondimensional_well_parameter.powi(2)*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.sinh())/(nondimensional_well_parameter*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).cosh() - (nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.cosh() + nondimensional_force.sinh()) - 3.0/nondimensional_force)
}

/// The expected nondimensional end-to-end length as a function of the applied nondimensional force, parameterized by the number of links, link length, and well width.
pub fn nondimensional_end_to_end_length(number_of_links: &u8, link_length: &f64, well_width: &f64, nondimensional_force: &f64) -> f64
{
    let nondimensional_well_parameter = 1.0 + well_width/link_length;
    (*number_of_links as f64)*((nondimensional_well_parameter.powi(2)*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.sinh())/(nondimensional_well_parameter*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).cosh() - (nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.cosh() + nondimensional_force.sinh()) - 3.0/nondimensional_force)
}

/// The expected nondimensional end-to-end length per link as a function of the applied nondimensional force, parameterized by the link length and well width.
pub fn nondimensional_end_to_end_length_per_link(link_length: &f64, well_width: &f64, nondimensional_force: &f64) -> f64
{
    let nondimensional_well_parameter = 1.0 + well_width/link_length;
    (nondimensional_well_parameter.powi(2)*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.sinh())/(nondimensional_well_parameter*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).cosh() - (nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.cosh() + nondimensional_force.sinh()) - 3.0/nondimensional_force
}

/// The Gibbs free energy as a function of the applied force and temperature, parameterized by the number of links, link length, hinge mass, and well width.
pub fn gibbs_free_energy(number_of_links: &u8, link_length: &f64, hinge_mass: &f64, well_width: &f64, force: &f64, temperature: &f64) -> f64
{
    let nondimensional_well_parameter = 1.0 + well_width/link_length;
    let nondimensional_force = force*link_length/BOLTZMANN_CONSTANT/temperature;
    (*number_of_links as f64)*BOLTZMANN_CONSTANT*temperature*((3.0*nondimensional_force.ln() - (nondimensional_well_parameter*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).cosh() - (nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.cosh() + nondimensional_force.sinh()).ln()) - (8.0*PI.powi(2)*hinge_mass*link_length.powi(2)*BOLTZMANN_CONSTANT*temperature/PLANCK_CONSTANT.powi(2)).ln())
}

/// The Gibbs free energy per link as a function of the applied force and temperature, parameterized by the link length, hinge mass, and well width.
pub fn gibbs_free_energy_per_link(link_length: &f64, hinge_mass: &f64, well_width: &f64, force: &f64, temperature: &f64) -> f64
{
    let nondimensional_well_parameter = 1.0 + well_width/link_length;
    let nondimensional_force = force*link_length/BOLTZMANN_CONSTANT/temperature;
    BOLTZMANN_CONSTANT*temperature*((3.0*nondimensional_force.ln() - (nondimensional_well_parameter*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).cosh() - (nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.cosh() + nondimensional_force.sinh()).ln()) - (8.0*PI.powi(2)*hinge_mass*link_length.powi(2)*BOLTZMANN_CONSTANT*temperature/PLANCK_CONSTANT.powi(2)).ln())
}

/// The relative Gibbs free energy as a function of the applied force and temperature, parameterized by the number of links, link length, and well width.
pub fn relative_gibbs_free_energy(number_of_links: &u8, link_length: &f64, well_width: &f64, force: &f64, temperature: &f64) -> f64
{
    gibbs_free_energy(number_of_links, link_length, &1.0, well_width, force, temperature) - gibbs_free_energy(number_of_links, link_length, &1.0, well_width, &(ZERO*BOLTZMANN_CONSTANT*temperature/link_length), temperature)
}

/// The relative Gibbs free energy per link as a function of the applied force and temperature, parameterized by the link length and well width.
pub fn relative_gibbs_free_energy_per_link(link_length: &f64, well_width: &f64,force: &f64, temperature: &f64) -> f64
{
    gibbs_free_energy_per_link(link_length, &1.0, well_width, force, temperature) - gibbs_free_energy_per_link(link_length, &1.0, well_width, &(ZERO*BOLTZMANN_CONSTANT*temperature/link_length), temperature)
}

/// The nondimensional Gibbs free energy as a function of the applied nondimensional force and temperature, parameterized by the number of links, link length, hinge mass, and well width.
pub fn nondimensional_gibbs_free_energy(number_of_links: &u8, link_length: &f64, hinge_mass: &f64, well_width: &f64, nondimensional_force: &f64, temperature: &f64) -> f64
{
    let nondimensional_well_parameter = 1.0 + well_width/link_length;
    (*number_of_links as f64)*((3.0*nondimensional_force.ln() - (nondimensional_well_parameter*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).cosh() - (nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.cosh() + nondimensional_force.sinh()).ln()) - (8.0*PI.powi(2)*hinge_mass*link_length.powi(2)*BOLTZMANN_CONSTANT*temperature/PLANCK_CONSTANT.powi(2)).ln())
}

/// The nondimensional Gibbs free energy per link as a function of the applied nondimensional force and temperature, parameterized by the link length, hinge mass, and well width.
pub fn nondimensional_gibbs_free_energy_per_link(link_length: &f64, hinge_mass: &f64, well_width: &f64, nondimensional_force: &f64, temperature: &f64) -> f64
{
    let nondimensional_well_parameter = 1.0 + well_width/link_length;
    3.0*nondimensional_force.ln() - (nondimensional_well_parameter*nondimensional_force*(nondimensional_well_parameter*nondimensional_force).cosh() - (nondimensional_well_parameter*nondimensional_force).sinh() - nondimensional_force*nondimensional_force.cosh() + nondimensional_force.sinh()).ln() - (8.0*PI.powi(2)*hinge_mass*link_length.powi(2)*BOLTZMANN_CONSTANT*temperature/PLANCK_CONSTANT.powi(2)).ln()
}

/// The nondimensional relative Gibbs free energy as a function of the applied nondimensional force, parameterized by the number of links, link length, and well width.
pub fn nondimensional_relative_gibbs_free_energy(number_of_links: &u8, link_length: &f64, well_width: &f64, nondimensional_force: &f64) -> f64
{
    nondimensional_gibbs_free_energy(number_of_links, link_length, &1.0, well_width, nondimensional_force, &300.0) - nondimensional_gibbs_free_energy(number_of_links, link_length, &1.0, well_width, &ZERO, &300.0)
}

/// The nondimensional relative Gibbs free energy per link as a function of the applied nondimensional force, parameterized by the link length and well width.
pub fn nondimensional_relative_gibbs_free_energy_per_link(link_length: &f64, well_width: &f64, nondimensional_force: &f64) -> f64
{
    nondimensional_gibbs_free_energy_per_link(link_length, &1.0, well_width, nondimensional_force, &300.0) - nondimensional_gibbs_free_energy_per_link(link_length, &1.0, well_width, &ZERO, &300.0)
}

/// The implemented functionality of the thermodynamics of the SWFJC model in the isotensional ensemble.
impl SWFJC
{
    /// Initializes and returns an instance of the thermodynamics of the SWFJC model in the isotensional ensemble.
    pub fn init(number_of_links: u8, link_length: f64, hinge_mass: f64, well_width: f64) -> Self
    {
        SWFJC
        {
            hinge_mass,
            link_length,
            number_of_links,
            well_width,
            legendre: self::legendre::SWFJC::init(number_of_links, link_length, hinge_mass, well_width)
        }
    }
    /// The expected end-to-end length as a function of the applied force and temperature.
    pub fn end_to_end_length(&self, force: &f64, temperature: &f64) -> f64
    {
        end_to_end_length(&self.number_of_links, &self.link_length, &self.well_width, force, temperature)
    }
    /// The expected end-to-end length per link as a function of the applied force and temperature.
    pub fn end_to_end_length_per_link(&self, force: &f64, temperature: &f64) -> f64
    {
        end_to_end_length_per_link(&self.link_length, &self.well_width, force, temperature)
    }
    /// The expected nondimensional end-to-end length as a function of the applied nondimensional force.
    pub fn nondimensional_end_to_end_length(&self, nondimensional_force: &f64) -> f64
    {
        nondimensional_end_to_end_length(&self.number_of_links, &self.link_length, &self.well_width, nondimensional_force)
    }
    /// The expected nondimensional end-to-end length per link as a function of the applied nondimensional force.
    pub fn nondimensional_end_to_end_length_per_link(&self, nondimensional_force: &f64) -> f64
    {
        nondimensional_end_to_end_length_per_link(&self.link_length, &self.well_width, nondimensional_force)
    }
    /// The Gibbs free energy as a function of the applied force and temperature.
    pub fn gibbs_free_energy(&self, force: &f64, temperature: &f64) -> f64
    {
        gibbs_free_energy(&self.number_of_links, &self.link_length, &self.hinge_mass, &self.well_width, force, temperature)
    }
    /// The Gibbs free energy per link as a function of the applied force and temperature.
    pub fn gibbs_free_energy_per_link(&self, force: &f64, temperature: &f64) -> f64
    {
        gibbs_free_energy_per_link(&self.link_length, &self.hinge_mass, &self.well_width, force, temperature)
    }
    /// The relative Gibbs free energy as a function of the applied force and temperature.
    pub fn relative_gibbs_free_energy(&self, force: &f64, temperature: &f64) -> f64
    {
        relative_gibbs_free_energy(&self.number_of_links, &self.link_length, &self.well_width, force, temperature)
    }
    /// The relative Gibbs free energy per link as a function of the applied force and temperature.
    pub fn relative_gibbs_free_energy_per_link(&self, force: &f64, temperature: &f64) -> f64
    {
        relative_gibbs_free_energy_per_link(&self.link_length, &self.well_width, force, temperature)
    }
    /// The nondimensional Gibbs free energy as a function of the applied nondimensional force and temperature.
    pub fn nondimensional_gibbs_free_energy(&self, nondimensional_force: &f64, temperature: &f64) -> f64
    {
        nondimensional_gibbs_free_energy(&self.number_of_links, &self.link_length, &self.hinge_mass, &self.well_width, nondimensional_force, temperature)
    }
    /// The nondimensional Gibbs free energy per link as a function of the applied nondimensional force and temperature.
    pub fn nondimensional_gibbs_free_energy_per_link(&self, nondimensional_force: &f64, temperature: &f64) -> f64
    {
        nondimensional_gibbs_free_energy_per_link(&self.link_length, &self.hinge_mass, &self.well_width, nondimensional_force, temperature)
    }
    /// The nondimensional relative Gibbs free energy as a function of the applied nondimensional force.
    pub fn nondimensional_relative_gibbs_free_energy(&self, nondimensional_force: &f64) -> f64
    {
        nondimensional_relative_gibbs_free_energy(&self.number_of_links, &self.link_length, &self.well_width, nondimensional_force)
    }
    /// The nondimensional relative Gibbs free energy per link as a function of the applied nondimensional force.
    pub fn nondimensional_relative_gibbs_free_energy_per_link(&self, nondimensional_force: &f64) -> f64
    {
        nondimensional_relative_gibbs_free_energy_per_link(&self.link_length, &self.well_width, nondimensional_force)
    }
}