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Merge pull request #178 from sandialabs/ufjc-isometric-legendre
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uFJC isometric legendre
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@mrbuche
mrbuche authored Apr 27, 2023
2 parents 81f62b1 + dcbb55b commit ca9840f
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2 changes: 1 addition & 1 deletion Cargo.toml
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[package]
name = "polymers"
version = "0.3.2"
version = "0.3.3"
edition = "2021"
description = "Polymers Modeling Library"
license = "BSD-3-Clause"
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2 changes: 1 addition & 1 deletion Project.toml
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name = "Polymers"
uuid = "8aef037c-a721-4e8a-9d81-eb7093daef2c"
authors = ["mrbuche <[email protected]>"]
version = "0.3.2"
version = "0.3.3"

[deps]
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
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1 change: 0 additions & 1 deletion conftest.py
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import pytest
from re import sub
from sys import stdout
from subprocess import run


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2 changes: 0 additions & 2 deletions docs/source/physics/single_chain/efjc/thermodynamics/isometric.rst
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Expand Up @@ -5,7 +5,6 @@ EFJC model thermodynamics (isometric)
:maxdepth: 1

Asymptotic <isometric/asymptotic>
Legendre <isometric/legendre>

.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)

Expand All @@ -14,4 +13,3 @@ EFJC model thermodynamics (isometric)
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: asymptotic
.. autoattribute:: legendre
2 changes: 2 additions & 0 deletions docs/source/physics/single_chain/ufjc/lennard_jones/thermodynamics.rst
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Expand Up @@ -4,6 +4,7 @@ Lennard-Jones-FJC model thermodynamics
.. toctree::
:maxdepth: 1

Isometric <thermodynamics/isometric>
Isotensional <thermodynamics/isotensional>

.. autoclass:: polymers.physics.single_chain.ufjc.lennard_jones.thermodynamics::LENNARDJONESFJC(number_of_links, link_length, hinge_mass, link_stiffness)
Expand All @@ -12,4 +13,5 @@ Lennard-Jones-FJC model thermodynamics
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: isometric
.. autoattribute:: isotensional
15 changes: 15 additions & 0 deletions docs/source/physics/single_chain/ufjc/lennard_jones/thermodynamics/isometric.rst
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Lennard-Jones-FJC model thermodynamics (isometric)
==================================================

.. toctree::
:maxdepth: 1

Asymptotic <isometric/asymptotic>

.. autoclass:: polymers.physics.single_chain.ufjc.lennard_jones.thermodynamics.isometric::LENNARDJONESFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: asymptotic
17 changes: 17 additions & 0 deletions ...physics/single_chain/ufjc/lennard_jones/thermodynamics/isometric/asymptotic.rst
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Lennard-Jones-FJC model thermodynamics (isometric/asymptotic)
=============================================================

.. toctree::
:maxdepth: 1

Reduced <asymptotic/reduced>
Legendre <asymptotic/legendre>

.. autoclass:: polymers.physics.single_chain.ufjc.lennard_jones.thermodynamics.isometric.asymptotic::LENNARDJONESFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: reduced
.. autoattribute:: legendre
19 changes: 19 additions & 0 deletions ...ingle_chain/ufjc/lennard_jones/thermodynamics/isometric/asymptotic/legendre.rst
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Lennard-Jones-FJC model thermodynamics (isometric/asymptotic/legendre)
======================================================================

.. autoclass:: polymers.physics.single_chain.ufjc.lennard_jones.thermodynamics.isometric.asymptotic.legendre::LENNARDJONESFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. automethod:: force(end_to_end_length, temperature)
.. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
.. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
.. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)
15 changes: 15 additions & 0 deletions ...single_chain/ufjc/lennard_jones/thermodynamics/isometric/asymptotic/reduced.rst
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Lennard-Jones-FJC model thermodynamics (isometric/asymptotic/reduced)
=====================================================================

.. toctree::
:maxdepth: 1

Legendre <reduced/legendre>

.. autoclass:: polymers.physics.single_chain.ufjc.lennard_jones.thermodynamics.isometric.asymptotic.reduced::LENNARDJONESFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: legendre
19 changes: 19 additions & 0 deletions ...ain/ufjc/lennard_jones/thermodynamics/isometric/asymptotic/reduced/legendre.rst
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Lennard-Jones-FJC model thermodynamics (isometric/asymptotic/reduced/legendre)
==============================================================================

.. autoclass:: polymers.physics.single_chain.ufjc.lennard_jones.thermodynamics.isometric.asymptotic.reduced.legendre::LENNARDJONESFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. automethod:: force(end_to_end_length, temperature)
.. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
.. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
.. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)
2 changes: 2 additions & 0 deletions docs/source/physics/single_chain/ufjc/log_squared/thermodynamics.rst
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Expand Up @@ -4,6 +4,7 @@ Log-squared-FJC model thermodynamics
.. toctree::
:maxdepth: 1

Isometric <thermodynamics/isometric>
Isotensional <thermodynamics/isotensional>

.. autoclass:: polymers.physics.single_chain.ufjc.log_squared.thermodynamics::LOGSQUAREDFJC(number_of_links, link_length, hinge_mass, link_stiffness)
Expand All @@ -12,4 +13,5 @@ Log-squared-FJC model thermodynamics
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: isometric
.. autoattribute:: isotensional
15 changes: 15 additions & 0 deletions docs/source/physics/single_chain/ufjc/log_squared/thermodynamics/isometric.rst
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Log-squared-FJC model thermodynamics (isometric)
================================================

.. toctree::
:maxdepth: 1

Asymptotic <isometric/asymptotic>

.. autoclass:: polymers.physics.single_chain.ufjc.log_squared.thermodynamics.isometric::LOGSQUAREDFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: asymptotic
17 changes: 17 additions & 0 deletions ...e/physics/single_chain/ufjc/log_squared/thermodynamics/isometric/asymptotic.rst
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Log-squared-FJC model thermodynamics (isometric/asymptotic)
===========================================================

.. toctree::
:maxdepth: 1

Reduced <asymptotic/reduced>
Legendre <asymptotic/legendre>

.. autoclass:: polymers.physics.single_chain.ufjc.log_squared.thermodynamics.isometric.asymptotic::LOGSQUAREDFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: reduced
.. autoattribute:: legendre
6 changes: 3 additions & 3 deletions ...fjc/thermodynamics/isometric/legendre.rst → ...ynamics/isometric/asymptotic/legendre.rst
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EFJC model thermodynamics (isometric/legendre)
==============================================
Log-squared-FJC model thermodynamics (isometric/asymptotic/legendre)
====================================================================

.. autoclass:: polymers.physics.single_chain.efjc.thermodynamics.isometric.legendre::EFJC(number_of_links, link_length, hinge_mass, link_stiffness)
.. autoclass:: polymers.physics.single_chain.ufjc.log_squared.thermodynamics.isometric.asymptotic.legendre::LOGSQUAREDFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
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15 changes: 15 additions & 0 deletions ...s/single_chain/ufjc/log_squared/thermodynamics/isometric/asymptotic/reduced.rst
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Log-squared-FJC model thermodynamics (isometric/asymptotic/reduced)
===================================================================

.. toctree::
:maxdepth: 1

Legendre <reduced/legendre>

.. autoclass:: polymers.physics.single_chain.ufjc.log_squared.thermodynamics.isometric.asymptotic.reduced::LOGSQUAREDFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: legendre
19 changes: 19 additions & 0 deletions ...chain/ufjc/log_squared/thermodynamics/isometric/asymptotic/reduced/legendre.rst
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Log-squared-FJC model thermodynamics (isometric/asymptotic/reduced/legendre)
============================================================================

.. autoclass:: polymers.physics.single_chain.ufjc.log_squared.thermodynamics.isometric.asymptotic.reduced.legendre::LOGSQUAREDFJC(number_of_links, link_length, hinge_mass, link_stiffness)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. automethod:: force(end_to_end_length, temperature)
.. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
.. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
.. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)
2 changes: 2 additions & 0 deletions docs/source/physics/single_chain/ufjc/morse/thermodynamics.rst
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Expand Up @@ -4,6 +4,7 @@ Morse-FJC model thermodynamics
.. toctree::
:maxdepth: 1

Isometric <thermodynamics/isometric>
Isotensional <thermodynamics/isotensional>

.. autoclass:: polymers.physics.single_chain.ufjc.morse.thermodynamics::MORSEFJC(number_of_links, link_length, hinge_mass, link_stiffness, link_energy)
Expand All @@ -13,4 +14,5 @@ Morse-FJC model thermodynamics
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: link_energy
.. autoattribute:: isometric
.. autoattribute:: isotensional
16 changes: 16 additions & 0 deletions docs/source/physics/single_chain/ufjc/morse/thermodynamics/isometric.rst
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Morse-FJC model thermodynamics (isometric)
==========================================

.. toctree::
:maxdepth: 1

Asymptotic <isometric/asymptotic>

.. autoclass:: polymers.physics.single_chain.ufjc.morse.thermodynamics.isometric::MORSEFJC(number_of_links, link_length, hinge_mass, link_stiffness, link_energy)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: link_energy
.. autoattribute:: asymptotic
18 changes: 18 additions & 0 deletions .../source/physics/single_chain/ufjc/morse/thermodynamics/isometric/asymptotic.rst
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Morse-FJC model thermodynamics (isometric/asymptotic)
=====================================================

.. toctree::
:maxdepth: 1

Reduced <asymptotic/reduced>
Legendre <asymptotic/legendre>

.. autoclass:: polymers.physics.single_chain.ufjc.morse.thermodynamics.isometric.asymptotic::MORSEFJC(number_of_links, link_length, hinge_mass, link_stiffness, link_energy)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: link_energy
.. autoattribute:: reduced
.. autoattribute:: legendre
20 changes: 20 additions & 0 deletions ...hysics/single_chain/ufjc/morse/thermodynamics/isometric/asymptotic/legendre.rst
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Morse-FJC model thermodynamics (isometric/asymptotic/legendre)
==============================================================

.. autoclass:: polymers.physics.single_chain.ufjc.morse.thermodynamics.isometric.asymptotic.legendre::MORSEFJC(number_of_links, link_length, hinge_mass, link_stiffness, link_energy)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: link_energy
.. automethod:: force(end_to_end_length, temperature)
.. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
.. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
.. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)
16 changes: 16 additions & 0 deletions ...physics/single_chain/ufjc/morse/thermodynamics/isometric/asymptotic/reduced.rst
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Morse-FJC model thermodynamics (isometric/asymptotic/reduced)
=============================================================

.. toctree::
:maxdepth: 1

Legendre <reduced/legendre>

.. autoclass:: polymers.physics.single_chain.ufjc.morse.thermodynamics.isometric.asymptotic.reduced::MORSEFJC(number_of_links, link_length, hinge_mass, link_stiffness, link_energy)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: link_energy
.. autoattribute:: legendre
20 changes: 20 additions & 0 deletions ...ingle_chain/ufjc/morse/thermodynamics/isometric/asymptotic/reduced/legendre.rst
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Morse-FJC model thermodynamics (isometric/asymptotic/reduced/legendre)
======================================================================

.. autoclass:: polymers.physics.single_chain.ufjc.morse.thermodynamics.isometric.asymptotic.reduced.legendre::MORSEFJC(number_of_links, link_length, hinge_mass, link_stiffness, link_energy)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
.. autoattribute:: hinge_mass
.. autoattribute:: link_stiffness
.. autoattribute:: link_energy
.. automethod:: force(end_to_end_length, temperature)
.. automethod:: nondimensional_force(nondimensional_end_to_end_length_per_link)
.. automethod:: helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy(end_to_end_length, temperature)
.. automethod:: relative_helmholtz_free_energy_per_link(end_to_end_length, temperature)
.. automethod:: nondimensional_helmholtz_free_energy(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link, temperature)
.. automethod:: nondimensional_relative_helmholtz_free_energy(nondimensional_end_to_end_length_per_link)
.. automethod:: nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_end_to_end_length_per_link)
1 change: 0 additions & 1 deletion docs/src/physics/single_chain/efjc/thermodynamics/isometric.md
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# EFJC model thermodynamics (isometric)

* [EFJC model thermodynamics (isometric/asymptotic)](../../../../asymptotic)
* [EFJC model thermodynamics (isometric/legendre)](../../../../legendre)

```@autodocs
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5 changes: 0 additions & 5 deletions docs/src/physics/single_chain/efjc/thermodynamics/isometric/legendre.md
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1 change: 1 addition & 0 deletions docs/src/physics/single_chain/ufjc/lennard_jones/thermodynamics.md
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# Lennard-Jones-FJC model thermodynamics

* [Lennard-Jones-FJC model thermodynamics (isometric)](../../../../isometric)
* [Lennard-Jones-FJC model thermodynamics (isotensional)](../../../../isotensional)

```@autodocs
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7 changes: 7 additions & 0 deletions docs/src/physics/single_chain/ufjc/lennard_jones/thermodynamics/isometric.md
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# Lennard-Jones-FJC model thermodynamics (isometric)

* [Lennard-Jones-FJC model thermodynamics (isometric/asymptotic)](../../../../../asymptotic)

```@autodocs
Modules = [Polymers.Physics.SingleChain.Ufjc.LennardJones.Thermodynamics.Isometric]
```
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# Lennard-Jones-FJC model thermodynamics (isometric/asymptotic)

* [Lennard-Jones-FJC model thermodynamics (isometric/asymptotic/reduced)](../../../../../../reduced)
* [Lennard-Jones-FJC model thermodynamics (isometric/asymptotic/legendre)](../../../../../../legendre)

```@autodocs
Modules = [Polymers.Physics.SingleChain.Ufjc.LennardJones.Thermodynamics.Isometric.Asymptotic]
```
5 changes: 5 additions & 0 deletions ...single_chain/ufjc/lennard_jones/thermodynamics/isometric/asymptotic/legendre.md
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# Lennard-Jones-FJC model thermodynamics (isometric/asymptotic/legendre)

```@autodocs
Modules = [Polymers.Physics.SingleChain.Ufjc.LennardJones.Thermodynamics.Isometric.Asymptotic.Legendre]
```
7 changes: 7 additions & 0 deletions .../single_chain/ufjc/lennard_jones/thermodynamics/isometric/asymptotic/reduced.md
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# Lennard-Jones-FJC model thermodynamics (isometric/asymptotic/reduced)

* [Lennard-Jones-FJC model thermodynamics (isometric/asymptotic/reduced/legendre)](../../../../../../../legendre)

```@autodocs
Modules = [Polymers.Physics.SingleChain.Ufjc.LennardJones.Thermodynamics.Isometric.Asymptotic.Reduced]
```
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Registration pull request created: JuliaRegistries/General/82466

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.3.3 -m "<description of version>" ca9840f4c5880724c44d13d8eac7a14793a0827d
git push origin v0.3.3

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