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Merge pull request #162 from sandialabs/dev
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julia tests and related bug fixes
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@mrbuche
mrbuche authored Mar 1, 2023
2 parents e786f99 + 8d0e59b commit 4011c9b
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2 changes: 1 addition & 1 deletion Cargo.toml
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@@ -1,6 +1,6 @@
[package]
name = "polymers"
version = "0.1.1"
version = "0.1.2"
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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@@ -1,7 +1,7 @@
name = "Polymers"
uuid = "8aef037c-a721-4e8a-9d81-eb7093daef2c"
authors = ["mrbuche <mrbuche@sandia.gov>"]
version = "0.1.1"
version = "0.1.2"

[deps]
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
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2 changes: 1 addition & 1 deletion src/physics/single_chain/efjc/thermodynamics/isotensional/asymptotic/alternative/ex.rs
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Expand Up @@ -34,7 +34,7 @@ pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_a
super::relative_gibbs_free_energy(&number_of_links, &link_length, &link_stiffness, &force, &temperature)
}
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_relative_gibbs_free_energy_per_link(link_length: f64, force: f64, link_stiffness: f64, temperature: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_relative_gibbs_free_energy_per_link(link_length: f64, link_stiffness: f64, force: f64, temperature: f64) -> f64
{
super::relative_gibbs_free_energy_per_link(&link_length, &link_stiffness, &force, &temperature)
}
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16 changes: 8 additions & 8 deletions ...ysics/single_chain/efjc/thermodynamics/isotensional/asymptotic/alternative/legendre/ex.rs
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@@ -1,40 +1,40 @@
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_helmholtz_free_energy(number_of_links: u8, link_length: f64, hinge_mass: f64, link_stiffness: f64, force: f64, temperature: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_legendre_helmholtz_free_energy(number_of_links: u8, link_length: f64, hinge_mass: f64, link_stiffness: f64, force: f64, temperature: f64) -> f64
{
super::helmholtz_free_energy(&number_of_links, &link_length, &hinge_mass, &link_stiffness, &force, &temperature)
}
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_helmholtz_free_energy_per_link(link_length: f64, hinge_mass: f64, link_stiffness: f64, force: f64, temperature: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_legendre_helmholtz_free_energy_per_link(link_length: f64, hinge_mass: f64, link_stiffness: f64, force: f64, temperature: f64) -> f64
{
super::helmholtz_free_energy_per_link(&link_length, &hinge_mass, &link_stiffness, &force, &temperature)
}
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_relative_helmholtz_free_energy(number_of_links: u8, link_length: f64, link_stiffness: f64, force: f64, temperature: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_legendre_relative_helmholtz_free_energy(number_of_links: u8, link_length: f64, link_stiffness: f64, force: f64, temperature: f64) -> f64
{
super::relative_helmholtz_free_energy(&number_of_links, &link_length, &link_stiffness, &force, &temperature)
}
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_relative_helmholtz_free_energy_per_link(link_length: f64, force: f64, link_stiffness: f64, temperature: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_legendre_relative_helmholtz_free_energy_per_link(link_length: f64, link_stiffness: f64, force: f64, temperature: f64) -> f64
{
super::relative_helmholtz_free_energy_per_link(&link_length, &link_stiffness, &force, &temperature)
}
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_nondimensional_helmholtz_free_energy(number_of_links: u8, link_length: f64, hinge_mass: f64, nondimensional_link_stiffness: f64, nondimensional_force: f64, temperature: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_legendre_nondimensional_helmholtz_free_energy(number_of_links: u8, link_length: f64, hinge_mass: f64, nondimensional_link_stiffness: f64, nondimensional_force: f64, temperature: f64) -> f64
{
super::nondimensional_helmholtz_free_energy(&number_of_links, &link_length, &hinge_mass, &nondimensional_link_stiffness, &nondimensional_force, &temperature)
}
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_nondimensional_helmholtz_free_energy_per_link(link_length: f64, hinge_mass: f64, nondimensional_link_stiffness: f64, nondimensional_force: f64, temperature: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_legendre_nondimensional_helmholtz_free_energy_per_link(link_length: f64, hinge_mass: f64, nondimensional_link_stiffness: f64, nondimensional_force: f64, temperature: f64) -> f64
{
super::nondimensional_helmholtz_free_energy_per_link(&link_length, &hinge_mass, &nondimensional_link_stiffness, &nondimensional_force, &temperature)
}
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_nondimensional_relative_helmholtz_free_energy(number_of_links: u8, nondimensional_link_stiffness: f64, nondimensional_force: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_legendre_nondimensional_relative_helmholtz_free_energy(number_of_links: u8, nondimensional_link_stiffness: f64, nondimensional_force: f64) -> f64
{
super::nondimensional_relative_helmholtz_free_energy(&number_of_links, &nondimensional_link_stiffness, &nondimensional_force)
}
#[no_mangle]
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_link_stiffness: f64, nondimensional_force: f64) -> f64
pub extern fn physics_single_chain_efjc_thermodynamics_isotensional_asymptotic_alternative_legendre_nondimensional_relative_helmholtz_free_energy_per_link(nondimensional_link_stiffness: f64, nondimensional_force: f64) -> f64
{
super::nondimensional_relative_helmholtz_free_energy_per_link(&nondimensional_link_stiffness, &nondimensional_force)
}
56 changes: 45 additions & 11 deletions ...sics/single_chain/efjc/thermodynamics/isotensional/asymptotic/alternative/legendre/mod.jl
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Expand Up @@ -29,6 +29,38 @@ struct EFJC
The stiffness of each link in the chain ``k_0`` in units of J/(mol⋅nm^2).
"""
link_stiffness::Float64
"""
The Helmholtz free energy ``\\psi`` as a function of the applied force ``f`` and temperature ``T``.
"""
helmholtz_free_energy::Function
"""
The Helmholtz free energy per link ``\\psi/N_b`` as a function of the applied force ``f`` and temperature ``T``.
"""
helmholtz_free_energy_per_link::Function
"""
The relative helmholtz free energy ``\\Delta\\psi\\equiv\\psi(f,T)-\\psi(0,T)`` as a function of the applied force ``f`` and temperature ``T``.
"""
relative_helmholtz_free_energy::Function
"""
The relative helmholtz free energy per link ``\\Delta\\psi/N_b`` as a function of the applied force ``f`` and temperature ``T``.
"""
relative_helmholtz_free_energy_per_link::Function
"""
The nondimensional helmholtz free energy ``N_b\\vartheta=\\beta\\psi`` as a function of the applied nondimensional force ``\\eta`` and temperature ``T``.
"""
nondimensional_helmholtz_free_energy::Function
"""
The nondimensional helmholtz free energy per link ``\\vartheta\\equiv\\beta\\psi/N_b`` as a function of the applied nondimensional force ``\\eta`` and temperature ``T``.
"""
nondimensional_helmholtz_free_energy_per_link::Function
"""
The nondimensional relative helmholtz free energy ``N_b\\Delta\\vartheta=\\beta\\Delta\\psi`` as a function of the applied nondimensional force ``\\eta``.
"""
nondimensional_relative_helmholtz_free_energy::Function
"""
The nondimensional relative helmholtz free energy per link ``\\Delta\\vartheta\\equiv\\beta\\Delta\\psi/N_b`` as a function of the applied nondimensional force ``\\eta``.
"""
nondimensional_relative_helmholtz_free_energy_per_link::Function
end

"""
Expand Down Expand Up @@ -294,7 +326,6 @@ function nondimensional_relative_helmholtz_free_energy(
nondimensional_force_i,
),
number_of_links,
link_length,
nondimensional_link_stiffness,
nondimensional_force,
)
Expand Down Expand Up @@ -337,6 +368,7 @@ function EFJC(
hinge_mass::Float64,
link_stiffness::Float64,
)
BOLTZMANN_CONSTANT::Float64 = 8.314462618
return EFJC(
number_of_links,
link_length,
Expand All @@ -352,8 +384,8 @@ function EFJC(
),
(force, temperature) -> helmholtz_free_energy_per_link(
link_length,
link_stiffness,
hinge_mass,
link_stiffness,
force,
temperature,
),
Expand Down Expand Up @@ -386,15 +418,17 @@ function EFJC(
nondimensional_force,
temperature,
),
nondimensional_force -> nondimensional_relative_helmholtz_free_energy(
number_of_links,
link_stiffness * link_length^2 / BOLTZMANN_CONSTANT / temperature,
nondimensional_force,
),
nondimensional_force -> nondimensional_relative_helmholtz_free_energy_per_link(
link_stiffness * link_length^2 / BOLTZMANN_CONSTANT / temperature,
nondimensional_force,
),
(nondimensional_force, temperature) ->
nondimensional_relative_helmholtz_free_energy(
number_of_links,
link_stiffness * link_length^2 / BOLTZMANN_CONSTANT / temperature,
nondimensional_force,
),
(nondimensional_force, temperature) ->
nondimensional_relative_helmholtz_free_energy_per_link(
link_stiffness * link_length^2 / BOLTZMANN_CONSTANT / temperature,
nondimensional_force,
),
)
end

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7 comments on commit 4011c9b

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@mrbuche mrbuche commented on 4011c9b Mar 1, 2023

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@JuliaRegistrator register branch=main

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@mrbuche mrbuche commented on 4011c9b Mar 1, 2023

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Registration pull request created: JuliaRegistries/General/78772

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 v0.1.2 -m "<description of version>" 4011c9ba0e70d090aa4a9c50677c3cb316363926
git push origin v0.1.2

Also, note the warning: Version 0.1.2 skips over 0.1.1
This can be safely ignored. However, if you want to fix this you can do so. Call register() again after making the fix. This will update the Pull request.

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@mrbuche mrbuche commented on 4011c9b Mar 1, 2023

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Registration pull request updated: JuliaRegistries/General/78772

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 v0.1.2 -m "<description of version>" 4011c9ba0e70d090aa4a9c50677c3cb316363926
git push origin v0.1.2

Also, note the warning: Version 0.1.2 skips over 0.1.1
This can be safely ignored. However, if you want to fix this you can do so. Call register() again after making the fix. This will update the Pull request.

@mrbuche
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@mrbuche mrbuche commented on 4011c9b Mar 1, 2023

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Registration pull request updated: JuliaRegistries/General/78772

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 v0.1.2 -m "<description of version>" 4011c9ba0e70d090aa4a9c50677c3cb316363926
git push origin v0.1.2

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