Skip to content

Commit 3feb915

Browse files
mrbuchemrbuche
authored
Merge pull request #179 from sandialabs/wlc-isometric
WLC isometric
2 parents ca9840f + 92d5dc5 commit 3feb915

File tree

60 files changed

+10470
-160
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

60 files changed

+10470
-160
lines changed

‎Cargo.toml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
[package]
22
name = "polymers"
3-
version = "0.3.3"
3+
version = "0.3.4"
44
edition = "2021"
55
description = "Polymers Modeling Library"
66
license = "BSD-3-Clause"

‎Project.toml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
name = "Polymers"
22
uuid = "8aef037c-a721-4e8a-9d81-eb7093daef2c"
33
authors = ["mrbuche <[email protected]>"]
4-
version = "0.3.3"
4+
version = "0.3.4"
55

66
[deps]
77
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

‎docs/source/physics/single_chain.rst‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@ Single-chain models for polymer physics
99
EFJC <single_chain/efjc>
1010
SWFJC <single_chain/swfjc>
1111
uFJC <single_chain/ufjc>
12+
WLC <single_chain/wlc>
1213

1314
.. automodule:: polymers.physics.single_chain
1415
:members:

‎docs/source/physics/single_chain/wlc.rst‎

Lines changed: 15 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,15 @@
1+
WLC model
2+
=========
3+
4+
.. toctree::
5+
:maxdepth: 1
6+
7+
Thermodynamics <wlc/thermodynamics>
8+
9+
.. autoclass:: polymers.physics.single_chain.fjc::WLC(number_of_links, link_length, hinge_mass, persistance_length)
10+
11+
.. autoattribute:: number_of_links
12+
.. autoattribute:: link_length
13+
.. autoattribute:: hinge_mass
14+
.. autoattribute:: persistance_length
15+
.. autoattribute:: thermodynamics

‎docs/source/physics/single_chain/wlc/thermodynamics.rst‎

Lines changed: 15 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,15 @@
1+
WLC model thermodynamics
2+
========================
3+
4+
.. toctree::
5+
:maxdepth: 1
6+
7+
Isometric <thermodynamics/isometric>
8+
9+
.. autoclass:: polymers.physics.single_chain.wlc.thermodynamics::WLC(number_of_links, link_length, hinge_mass, persistance_length)
10+
11+
.. autoattribute:: number_of_links
12+
.. autoattribute:: link_length
13+
.. autoattribute:: hinge_mass
14+
.. autoattribute:: persistance_length
15+
.. autoattribute:: isometric

‎docs/source/physics/single_chain/wlc/thermodynamics/isometric.rst‎

Lines changed: 36 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,36 @@
1+
WLC model thermodynamics (isometric)
2+
====================================
3+
4+
.. toctree::
5+
:maxdepth: 1
6+
7+
Legendre <isometric/legendre>
8+
9+
.. autoclass:: polymers.physics.single_chain.wlc.thermodynamics.isometric::WLC(number_of_links, link_length, hinge_mass, persistance_length)
10+
11+
.. autoattribute:: number_of_links
12+
.. autoattribute:: link_length
13+
.. autoattribute:: hinge_mass
14+
.. autoattribute:: persistance_length
15+
.. autoattribute:: legendre
16+
.. automethod:: force(end_to_end_length, temperature)
17+
.. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
18+
.. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
19+
.. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
20+
.. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
21+
.. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
22+
.. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
23+
.. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
24+
.. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
25+
.. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)
26+
.. automethod:: equilibrium_distribution(end_to_end_length)
27+
.. automethod:: nondimensional_equilibrium_distribution(nondimensional_end_to_end_length_per_link)
28+
.. automethod:: equilibrium_radial_distribution(end_to_end_length)
29+
.. automethod:: nondimensional_equilibrium_radial_distribution(nondimensional_end_to_end_length_per_link)
30+
31+
.. raw::
32+
html
33+
34+
<hr>
35+
36+
.. footbibliography::

‎docs/source/physics/single_chain/wlc/thermodynamics/isometric/legendre.rst‎

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,17 @@
1+
WLC model thermodynamics (isometric/legendre)
2+
=============================================
3+
4+
.. autoclass:: polymers.physics.single_chain.wlc.thermodynamics.isometric.legendre::WLC(number_of_links, link_length, hinge_mass, persistance_length)
5+
6+
.. autoattribute:: number_of_links
7+
.. autoattribute:: link_length
8+
.. autoattribute:: hinge_mass
9+
.. autoattribute:: persistance_length
10+
.. automethod:: gibbs_free_energy(end_to_end_length, temperature)
11+
.. automethod:: gibbs_free_energy_per_link(end_to_end_length, temperature)
12+
.. automethod:: relative_gibbs_free_energy(end_to_end_length, temperature)
13+
.. automethod:: relative_gibbs_free_energy_per_link(end_to_end_length, temperature)
14+
.. automethod:: nondimensional_gibbs_free_energy(nondimensional_end_to_end_length_per_link, temperature)
15+
.. automethod:: nondimensional_gibbs_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
16+
.. automethod:: nondimensional_relative_gibbs_free_energy(nondimensional_end_to_end_length_per_link)
17+
.. automethod:: nondimensional_relative_gibbs_free_energy_per_link(nondimensional_end_to_end_length_per_link)

‎docs/src/physics/single_chain.md‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
55
* [Extensible freely-jointed chain (EFJC) model](../efjc)
66
* [Square-well freely-jointed chain (SWFJC) model](../swfjc)
77
* [Arbitrary link potential freely-jointed chain (uFJC) model](../ufjc)
8+
* [Worm-like chain (WLC) model](../wlc)
89

910
```@autodocs
1011
Modules = [Polymers.Physics.SingleChain]

‎docs/src/physics/single_chain/wlc.md‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
# Worm-like chain (WLC) model
2+
3+
* [WLC model thermodynamics](../../thermodynamics)
4+
5+
```@autodocs
6+
Modules = [Polymers.Physics.SingleChain.WLC]
7+
```

‎docs/src/physics/single_chain/wlc/thermodynamics.md‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
# WLC model thermodynamics
2+
3+
* [WLC model thermodynamics (isometric)](../../../isometric)
4+
5+
```@autodocs
6+
Modules = [Polymers.Physics.SingleChain.WLC.Thermodynamics]
7+
```

0 commit comments

Comments
 (0)