Merge pull request #78 from sandialabs/dev

documentation, public/private changes
sandialabs · Jan 5, 2023 · 9ac5840 · 9ac5840
2 parents 0ccc672 + 68d5b10
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diff --git a/rust/Cargo.toml b/rust/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "polymers"
-version = "0.0.3"
+version = "0.0.4"
 edition = "2021"
 description = "Polymers Modeling Library"
 license = "BSD-3-Clause"

diff --git a/rust/README.md b/rust/README.md
@@ -7,25 +7,14 @@
 ## Installation
 
 [![Crates.io](https://img.shields.io/crates/v/polymers?logo=rust&logoColor=000000&label=Crates.io&color=32592f)](https://crates.io/crates/polymers)
-[![Anaconda](https://img.shields.io/conda/v/mrbuche/polymers.svg?logo=anaconda&color=3EB049&label=Anaconda)](https://anaconda.org/mrbuche/polymers)
-[![Docker Hub](https://img.shields.io/docker/v/mrbuche/polymers?color=0db7ed&label=Docker%20Hub&logo=docker&logoColor=0db7ed)](https://hub.docker.com/r/mrbuche/polymers)
-[![GitHub](https://img.shields.io/badge/GitHub-latest-6e5494?logo=github)](https://github.com/sandialabs/Polymers/pkgs/container/polymers)
 
-```shell
-cargo install polymers
-```
-
-```shell
-conda install --channel mrbuche polymers
-```
-
-```shell
-docker pull mrbuche/polymers
-```
+The library can be used in an existing Rust project by adding the `polymers` crate as a dependency in Cargo.toml,
 
-```shell
-docker pull ghcr.io/sandialabs/polymers
+```toml
+[dependencies]
+polymers = "*"
 ```
+The asterisk `*` represents the latest version of the crate, but should be changed to a specific version for stability.
 
 ## Citation
 

diff --git a/rust/src/lib.rs b/rust/src/lib.rs
@@ -1 +1,4 @@
+#![doc = include_str!("../README.md")]
+
+/// Models for polymer physics.
 pub mod physics;
diff --git a/rust/src/physics/mod.rs b/rust/src/physics/mod.rs
@@ -1,3 +1,8 @@
+/// Single-chain models for polymer physics.
 pub mod single_chain;
-static BOLTZMANN_CONSTANT: f64 = 8.314462618;
-static PLANCK_CONSTANT: f64 = 1.0;
+
+/// The Boltzmann constant in units of J/(mol⋅K).
+pub static BOLTZMANN_CONSTANT: f64 = 8.314462618;
+
+/// The Planck constant in units of J⋅ns/mol.
+pub static PLANCK_CONSTANT: f64 = 0.06350779923502961;
diff --git a/rust/src/physics/single_chain/efjc/mod.rs b/rust/src/physics/single_chain/efjc/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 pub mod thermodynamics;
 pub struct EFJC
 {

diff --git a/...sics/single_chain/efjc/thermodynamics/isotensional/asymptotic/alternative/legendre/mod.rs b/...sics/single_chain/efjc/thermodynamics/isotensional/asymptotic/alternative/legendre/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 use crate::physics::
 {
     PLANCK_CONSTANT,
@@ -12,8 +12,7 @@ pub struct EFJC
     pub link_length: f64,
     pub number_of_links: u8,
     pub link_stiffness: f64,
-    pub number_of_links_f64: f64,
-    pub contour_length: f64,
+    number_of_links_f64: f64
 }
 impl EFJC
 {
@@ -25,8 +24,7 @@ impl EFJC
             link_length,
             number_of_links,
             link_stiffness,
-            number_of_links_f64: number_of_links as f64,
-            contour_length: (number_of_links as f64)*link_length,
+            number_of_links_f64: number_of_links as f64
         }
     }
     pub fn helmholtz_free_energy(&self, force: &f64, temperature: &f64) -> f64

diff --git a/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/alternative/mod.rs b/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/alternative/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 pub mod legendre;
 use crate::physics::
 {
@@ -13,8 +13,7 @@ pub struct EFJC
     pub link_length: f64,
     pub number_of_links: u8,
     pub link_stiffness: f64,
-    pub number_of_links_f64: f64,
-    pub contour_length: f64,
+    number_of_links_f64: f64,
     pub legendre: self::legendre::EFJC
 }
 impl EFJC
@@ -28,7 +27,6 @@ impl EFJC
             number_of_links,
             link_stiffness,
             number_of_links_f64: number_of_links as f64,
-            contour_length: (number_of_links as f64)*link_length,
             legendre: self::legendre::EFJC::init(number_of_links, link_length, hinge_mass, link_stiffness)
         }
     }

diff --git a/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/legendre/mod.rs b/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/legendre/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 use crate::physics::
 {
     PLANCK_CONSTANT,
@@ -12,8 +12,7 @@ pub struct EFJC
     pub link_length: f64,
     pub number_of_links: u8,
     pub link_stiffness: f64,
-    pub number_of_links_f64: f64,
-    pub contour_length: f64
+    number_of_links_f64: f64
 }
 impl EFJC
 {
@@ -25,8 +24,7 @@ impl EFJC
             link_length,
             number_of_links,
             link_stiffness,
-            number_of_links_f64: number_of_links as f64,
-            contour_length: (number_of_links as f64)*link_length
+            number_of_links_f64: number_of_links as f64
         }
     }
     pub fn helmholtz_free_energy(&self, force: &f64, temperature: &f64) -> f64

diff --git a/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/mod.rs b/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 pub mod alternative;
 pub mod reduced;
 pub mod legendre;
@@ -15,8 +15,7 @@ pub struct EFJC
     pub link_length: f64,
     pub number_of_links: u8,
     pub link_stiffness: f64,
-    pub number_of_links_f64: f64,
-    pub contour_length: f64,
+    number_of_links_f64: f64,
     pub alternative: self::alternative::EFJC,
     pub reduced: self::reduced::EFJC,
     pub legendre: self::legendre::EFJC
@@ -32,7 +31,6 @@ impl EFJC
             number_of_links,
             link_stiffness,
             number_of_links_f64: number_of_links as f64,
-            contour_length: (number_of_links as f64)*link_length,
             alternative: self::alternative::EFJC::init(number_of_links, link_length, hinge_mass, link_stiffness),
             reduced: self::reduced::EFJC::init(number_of_links, link_length, hinge_mass, link_stiffness),
             legendre: self::legendre::EFJC::init(number_of_links, link_length, hinge_mass, link_stiffness)

diff --git a/.../physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/reduced/legendre/mod.rs b/.../physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/reduced/legendre/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 use crate::physics::
 {
     PLANCK_CONSTANT,
@@ -12,8 +12,7 @@ pub struct EFJC
     pub link_length: f64,
     pub number_of_links: u8,
     pub link_stiffness: f64,
-    pub number_of_links_f64: f64,
-    pub contour_length: f64,
+    number_of_links_f64: f64
 }
 impl EFJC
 {
@@ -25,8 +24,7 @@ impl EFJC
             link_length,
             number_of_links,
             link_stiffness,
-            number_of_links_f64: number_of_links as f64,
-            contour_length: (number_of_links as f64)*link_length,
+            number_of_links_f64: number_of_links as f64
         }
     }
     pub fn helmholtz_free_energy(&self, force: &f64, temperature: &f64) -> f64

diff --git a/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/reduced/mod.rs b/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/reduced/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 pub mod legendre;
 use crate::physics::
 {
@@ -13,8 +13,7 @@ pub struct EFJC
     pub link_length: f64,
     pub number_of_links: u8,
     pub link_stiffness: f64,
-    pub number_of_links_f64: f64,
-    pub contour_length: f64,
+    number_of_links_f64: f64,
     pub legendre: self::legendre::EFJC
 }
 impl EFJC
@@ -28,7 +27,6 @@ impl EFJC
             number_of_links,
             link_stiffness,
             number_of_links_f64: number_of_links as f64,
-            contour_length: (number_of_links as f64)*link_length,
             legendre: self::legendre::EFJC::init(number_of_links, link_length, hinge_mass, link_stiffness)
         }
     }

diff --git a/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/legendre/mod.rs b/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/legendre/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 use crate::physics::
 {
     PLANCK_CONSTANT,
@@ -13,8 +13,7 @@ pub struct EFJC
     pub link_length: f64,
     pub number_of_links: u8,
     pub link_stiffness: f64,
-    pub number_of_links_f64: f64,
-    pub contour_length: f64,
+    number_of_links_f64: f64
 }
 impl EFJC
 {
@@ -26,8 +25,7 @@ impl EFJC
             link_length,
             number_of_links,
             link_stiffness,
-            number_of_links_f64: number_of_links as f64,
-            contour_length: (number_of_links as f64)*link_length,
+            number_of_links_f64: number_of_links as f64
 
         }
     }

diff --git a/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/mod.rs b/rust/src/physics/single_chain/efjc/thermodynamics/isotensional/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 pub mod asymptotic;
 pub mod legendre;
 use crate::physics::
@@ -15,8 +15,7 @@ pub struct EFJC
     pub link_length: f64,
     pub number_of_links: u8,
     pub link_stiffness: f64,
-    pub number_of_links_f64: f64,
-    pub contour_length: f64,
+    number_of_links_f64: f64,
     pub asymptotic: self::asymptotic::EFJC,
     pub legendre: self::legendre::EFJC
 }
@@ -31,7 +30,6 @@ impl EFJC
             number_of_links,
             link_stiffness,
             number_of_links_f64: number_of_links as f64,
-            contour_length: (number_of_links as f64)*link_length,
             asymptotic: self::asymptotic::EFJC::init(number_of_links, link_length, hinge_mass, link_stiffness),
             legendre: self::legendre::EFJC::init(number_of_links, link_length, hinge_mass, link_stiffness)
         }

diff --git a/rust/src/physics/single_chain/efjc/thermodynamics/mod.rs b/rust/src/physics/single_chain/efjc/thermodynamics/mod.rs
@@ -1,4 +1,4 @@
-pub mod test;
+mod test;
 pub mod isotensional;
 pub struct EFJC
 {
@@ -22,15 +22,15 @@ impl EFJC
         }
     }
 }
-pub fn erf(x: &f64) -> f64
+fn erf(x: &f64) -> f64
 {
     1.0 - erfc(x)
 }
-pub fn erfc(x: &f64) -> f64
+fn erfc(x: &f64) -> f64
 {
     erfcx(x)/(x.powi(2)).exp()
 }
-pub fn erfcx(x: &f64) -> f64
+fn erfcx(x: &f64) -> f64
 {
     if x >= &0.0
     {

diff --git a/rust/src/physics/single_chain/fjc/mod.rs b/rust/src/physics/single_chain/fjc/mod.rs
@@ -1,14 +1,28 @@
-pub mod test;
+mod test;
+
+/// The thermodynamics of the FJC model.
 pub mod thermodynamics;
+
+/// The structure of the FJC model.
 pub struct FJC
 {
+    /// 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 thermodynamic functions of the model.
     pub thermodynamics: thermodynamics::FJC
 }
+
+/// The implemented functionality of the FJC model.
 impl FJC
 {
+    /// Initializes and returns an instance of the FJC model.
     pub fn init(number_of_links: u8, link_length: f64, hinge_mass: f64) -> FJC
     {
         FJC