From 18f1b34f55542833ac050e61922a270917418cca Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Sun, 5 Jan 2025 02:17:57 +0000 Subject: [PATCH] build based on 97d4ac4 --- dev/.documenter-siteinfo.json | 2 +- dev/formats/input/index.html | 2 +- dev/formats/output/index.html | 2 +- dev/index.html | 2 +- dev/intern/base/index.html | 2 +- dev/intern/bem/index.html | 2 +- dev/intern/format/index.html | 2 +- dev/intern/radon/index.html | 2 +- dev/intern/rjasanow/index.html | 2 +- dev/intern/testmodel/index.html | 2 +- dev/lib/constants/index.html | 2 +- dev/lib/electrostatics/index.html | 2 +- dev/lib/models/index.html | 2 +- dev/lib/quadrature/index.html | 2 +- dev/lib/solvers/index.html | 2 +- dev/lib/util/index.html | 2 +- 16 files changed, 16 insertions(+), 16 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 3ebdaf96..e6f19d03 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2025-01-04T02:09:14","documenter_version":"1.8.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2025-01-05T02:17:52","documenter_version":"1.8.0"}} \ No newline at end of file diff --git a/dev/formats/input/index.html b/dev/formats/input/index.html index 0395ea06..405d5b80 100644 --- a/dev/formats/input/index.html +++ b/dev/formats/input/index.html @@ -32,4 +32,4 @@ )

Reads a surface model from the given STL file.

Note

This file type does not support charge models! Hence, the charge list of the returning Model object is empty and has to be set separately.

Specification

https://fabbers.com/tech/STL_Format

Return type

Model{T, Triangle{T}}

Alias

readstl(
     fname::String,
          ::Type{T}=Float64
-)

Reads the model using a file name rather than an IOStream object.

source +)

Reads the model using a file name rather than an IOStream object.

source diff --git a/dev/formats/output/index.html b/dev/formats/output/index.html index ac4374e7..d8d08958 100644 --- a/dev/formats/output/index.html +++ b/dev/formats/output/index.html @@ -42,4 +42,4 @@ )

Creates a XML3D-specific XML file from a given collection of nodes, representing the latter as point cloud.

Specification

https://github.com/xml3d/xml3d.js/wiki/External-resources

Return type

Void

Alias

writexml3d_xml(
     fname::String,
     nodes::Vector{Vector{T}}
-)

Creates the XML file by name rather than IOStream object.

source +)

Creates the XML file by name rather than IOStream object.

source diff --git a/dev/index.html b/dev/index.html index 5f2ca92a..3390672b 100644 --- a/dev/index.html +++ b/dev/index.html @@ -30,4 +30,4 @@ school = {Johannes Gutenberg University Mainz}, address = {Mainz, Germany}, doi = {10.25358/openscience-5689} -}

References

+}

References

diff --git a/dev/intern/base/index.html b/dev/intern/base/index.html index 88236f34..0b14d3d4 100644 --- a/dev/intern/base/index.html +++ b/dev/intern/base/index.html @@ -66,4 +66,4 @@ 3-element Vector{Int64}: 1 2 - 3source
NESSie.vertexnormals — Function
vertexnormals(model::Model{T, Triangle{T}})

Returns a vector containing the normal vectors of the given model's triangles.

Return type

Vector{Vector{T}}

source
+ 3source
NESSie.vertexnormals — Function
vertexnormals(model::Model{T, Triangle{T}})

Returns a vector containing the normal vectors of the given model's triangles.

Return type

Vector{Vector{T}}

source
diff --git a/dev/intern/bem/index.html b/dev/intern/bem/index.html index 9df07e72..e3e6043e 100644 --- a/dev/intern/bem/index.html +++ b/dev/intern/bem/index.html @@ -32,4 +32,4 @@ Vy ::InteractionMatrix{T} # single-layer Yukawa Ky ::InteractionMatrix{T} # double-layer Yukawa params::Option{T} # system constants -end

Implicit representation of the nonlocal BEM system matrix.

Special constructors

source +end

Implicit representation of the nonlocal BEM system matrix.

Special constructors

source diff --git a/dev/intern/format/index.html b/dev/intern/format/index.html index 98402255..b913ed58 100644 --- a/dev/intern/format/index.html +++ b/dev/intern/format/index.html @@ -31,4 +31,4 @@ n ::Int, nodes ::Vector{Vector{T}}, ::Type{T}=Float64 -)

Reads the first n elements from the given OFF file.

Return type

Vector{Triangle{T}}

source +)

Reads the first n elements from the given OFF file.

Return type

Vector{Triangle{T}}

source diff --git a/dev/intern/radon/index.html b/dev/intern/radon/index.html index 6696a9e1..7a2d1671 100644 --- a/dev/intern/radon/index.html +++ b/dev/intern/radon/index.html @@ -31,4 +31,4 @@ normal::AbstractVector{T} )

Computes the normal derivative of the regular part of the Yukawa potential, that is, Yukawa minus Laplace:

\[\frac{∂}{∂n} \frac{1}{4π} \frac{e^{-\frac{|x - ξ|}{Λ}} - 1}{|x-ξ|} = \frac{1}{4π} \frac{1 - (1 + Λ^{-1} |x - ξ|)e^{-\frac{|x - ξ|}{Λ}}}{|x-ξ|²} -\frac{(x - ξ) ⋅ n}{|x - ξ|}\]

Note

The result is premultiplied by 4π.

Arguments

Return type

T

source +\frac{(x - ξ) ⋅ n}{|x - ξ|}\]

Note

The result is premultiplied by 4π.

Arguments

Return type

T

source diff --git a/dev/intern/rjasanow/index.html b/dev/intern/rjasanow/index.html index b439c8f1..ddcf9e47 100644 --- a/dev/intern/rjasanow/index.html +++ b/dev/intern/rjasanow/index.html @@ -30,4 +30,4 @@ d ::T )

Computes the Laplace potential (or its normal derivative) of the triangle with the given height h at the observation point ξ (projected onto the surface element plane) and the sines of the angles $φ₁$ and $φ₂$ between h and the triangle sides extending from ξ [Rja90].

Note

The result is premultiplied by 4π.

Arguments

Return type

T

source
NESSie.Rjasanow._logterm — Function
_logterm(χ2::T, sinφ::T)

Utility function to compute

\[\frac {\sqrt{1 - χ² \sin²(φ)} + \sqrt{1 - χ² \sin(φ)}} -{\sqrt{1 - χ² \sin²(φ)} - \sqrt{1 - χ² \sin(φ)}}\]

Return type

T

source
NESSie.Rjasanow._projectξ! — Function
_projectξ!(ξ::AbstractVector{T}, elem::Triangle{T}, dist::T)

Projects ξ onto the surface element plane, overriding its previous coordinates.

Return type

Vector{T}

source
+{\sqrt{1 - χ² \sin²(φ)} - \sqrt{1 - χ² \sin(φ)}}\]

Return type

T

source
NESSie.Rjasanow._projectξ! — Function
_projectξ!(ξ::AbstractVector{T}, elem::Triangle{T}, dist::T)

Projects ξ onto the surface element plane, overriding its previous coordinates.

Return type

Vector{T}

source
diff --git a/dev/intern/testmodel/index.html b/dev/intern/testmodel/index.html index 164b7579..65ce33bd 100644 --- a/dev/intern/testmodel/index.html +++ b/dev/intern/testmodel/index.html @@ -22,4 +22,4 @@ )

Precomputes the modified spherical Bessel function of the first kind $iₙ(r)$ for $n=-1, 0, ..., \texttt{maxn}$ and returns a generic function to access the values. $iₙ(r)$ is defined as

\[iₙ(r) = \sqrt{\frac{π}{2r}} I_{n+0.5}(r),\]

where $I_ν$ is the modified Bessel function of the first kind [Xie16].

Return type

(generic function)

(n::Int) -> iₙ(r)   # return type: T
source
NESSie.TestModel.spherical_besselk — Function
spherical_besselk(
     maxn::Int,
     r   ::T
-)

Precomputes the modified spherical Bessel function of the second kind $kₙ(r)$ for $n=-1, 0, ..., \texttt{maxn}$ and returns a generic function to access the values. $kₙ(r)$ is defined as

\[kₙ(r) = \sqrt{\frac{π}{2r}} K_{n+0.5}(r),\]

where $K_ν$ is the modified Bessel function of the second kind [Xie16].

Return type

(generic function)

(n::Int) -> kₙ(r)   # return type: T
source
+)

Precomputes the modified spherical Bessel function of the second kind $kₙ(r)$ for $n=-1, 0, ..., \texttt{maxn}$ and returns a generic function to access the values. $kₙ(r)$ is defined as

\[kₙ(r) = \sqrt{\frac{π}{2r}} K_{n+0.5}(r),\]

where $K_ν$ is the modified Bessel function of the second kind [Xie16].

Return type

(generic function)

(n::Int) -> kₙ(r)   # return type: T
source diff --git a/dev/lib/constants/index.html b/dev/lib/constants/index.html index 4489ae85..3b8244e5 100644 --- a/dev/lib/constants/index.html +++ b/dev/lib/constants/index.html @@ -5,4 +5,4 @@ ε∞::T # large-scale (bulk) solvent response λ ::T # correlation length scale [λ] = Å end

System parameters

source
NESSie.defaultopt — Function
defaultopt(T::Type{Float64} = Float64)
-defaultopt(T::Type{Float32})

Default system parameters

Return type

Option{T}

Default values

  • $ε_Ω = 2$
  • $ε_Σ = 78$
  • $ε_∞ = 1.8$
  • $λ = 20 Å$
source
+defaultopt(T::Type{Float32})

Default system parameters

Return type

Option{T}

Default values

source diff --git a/dev/lib/electrostatics/index.html b/dev/lib/electrostatics/index.html index 4c357d91..19627e4d 100644 --- a/dev/lib/electrostatics/index.html +++ b/dev/lib/electrostatics/index.html @@ -47,4 +47,4 @@ )

Computes the exterior local or nonlocal electrostatic potential $φ_Σ$ for the given observation point $ξ$.

Unit

$V = \frac{C}{F}$

Return type

T

Warning

This function does not verify whether ξ is located outside of the sphere!

source
function φΣ(
     ξ    ::Vector{T},
     model::NonlocalXieModel1{T}
-)

Computes the exterior nonlocal electrostatic potential $φ_Σ$ for the given observation point $ξ$.

Unit

$V = \frac{C}{F}$

Return type

T

Warning

This function does not verify whether ξ is located outside of the sphere!

source

Energies

NESSie.BEM.rfenergy — Function
rfenergy(::BEMResult{T})

Computes the local or nonlocal reaction field energy W* as

\[W^* = ∫φ^* ρ \quad dΩ\]

where $φ^*$ is the reaction field and $ρ$ is the corresponding charge distribution.

Unit

$\frac{kJ}{mol}$

Return type

T

source
+)

Computes the exterior nonlocal electrostatic potential $φ_Σ$ for the given observation point $ξ$.

Unit

$V = \frac{C}{F}$

Return type

T

Warning

This function does not verify whether ξ is located outside of the sphere!

source

Energies

NESSie.BEM.rfenergy — Function
rfenergy(::BEMResult{T})

Computes the local or nonlocal reaction field energy W* as

\[W^* = ∫φ^* ρ \quad dΩ\]

where $φ^*$ is the reaction field and $ρ$ is the corresponding charge distribution.

Unit

$\frac{kJ}{mol}$

Return type

T

source
diff --git a/dev/lib/models/index.html b/dev/lib/models/index.html index 9da12f7d..49faf85d 100644 --- a/dev/lib/models/index.html +++ b/dev/lib/models/index.html @@ -62,4 +62,4 @@ end

Representation of the first nonlocal Poisson dielectric model described in [Xie16]. This model comprises a full XieModel and the coefficients $A_{in}$ with $i = 1, 2, 3$ (cf. Eqs. (20a-c)) for each point charge in the model, which are used in the computation of the electrostatic potentials.

Note

This type does not provide a trivial constructor.

Constructor

NonlocalXieModel1(
     model::XieModel{T},
     len  ::Int
-)

The model is created solely from the given XieModel and the number of terms to be used to approximate the original infinite sum (Eq. 18). The coefficient vectors are computed automatically via coefficients.

source +)

The model is created solely from the given XieModel and the number of terms to be used to approximate the original infinite sum (Eq. 18). The coefficient vectors are computed automatically via coefficients.

source diff --git a/dev/lib/quadrature/index.html b/dev/lib/quadrature/index.html index 3ab823d2..0f4b9a18 100644 --- a/dev/lib/quadrature/index.html +++ b/dev/lib/quadrature/index.html @@ -56,4 +56,4 @@ elements::AbstractVector{Triangle{T}}, Ξ ::AbstractVector{Vector{T}}, yukawa ::T -)

Computes the regular part of the single or double layer Yukawa potential (that is, Yukawa minus Laplace) using a seven-point Radon cubature [Rad48] for a given list of triangles and observation points Ξ.

The first version of this function uses a vector as destination dest, where each element represents the dot product of the corresponding coefficient matrix row and the fvals vector.

Note

The result is premultiplied by 4π.

Arguments

Return type

Void

source +)

Computes the regular part of the single or double layer Yukawa potential (that is, Yukawa minus Laplace) using a seven-point Radon cubature [Rad48] for a given list of triangles and observation points Ξ.

The first version of this function uses a vector as destination dest, where each element represents the dot product of the corresponding coefficient matrix row and the fvals vector.

Note

The result is premultiplied by 4π.

Arguments

Return type

Void

source diff --git a/dev/lib/solvers/index.html b/dev/lib/solvers/index.html index a80e6dea..51ed3aff 100644 --- a/dev/lib/solvers/index.html +++ b/dev/lib/solvers/index.html @@ -12,4 +12,4 @@ w ::SubArray{T,1} # [γ₀ext(Ψ)](ξ) ∀ ξ ∈ Ξ; premultiplied by 4π⋅ε0 umol ::Vector{T} # [γ₀int(φ*mol)](ξ) ∀ ξ ∈ Ξ; premultiplied by 4π⋅ε0 qmol ::Vector{T} # [γ₁int(φ*mol)](ξ) ∀ ξ ∈ Ξ; premultiplied by 4π⋅ε0 -end

Result data of the nonlocal solving process to be used for potential computation and post-processing, with Ξ being the list of observation points, that is, the set of triangle centroids.

source
NESSie.BEM.solve — Function
solve(::Type{<: LocalityType}, ::Model{T, Triangle{T}})

Computes the full local or nonlocal cauchy data on the surface of the given biomolecule.

Return type

LocalBEMResult{T, Triangle{T}} or NonlocalBEMResult{T, Triangle{T}}

Supported keyword arguments

  • method::Symbol = :gmres Solver implementation to be used (supported arguments: :gmres and :blas)
Note

The :blas method uses an explicit representation for the BEM systems and requires a substantial amount of memory that might easily exceed the available resources on your machine (the memory demands scale quadratically with the number of surface elements). The :gmres method, on the other hand, uses implicit system representations, which provide a small memory footprint even for large systems (the memory demands scale only linearly with the number of surface elements). This comes at the cost of additional computation time, which might exceed several hours, depending on the system size. If possible, we recommend the use of our CUDA- accelerated solvers from the CuNESSie.jl package instead.

source
+end

Result data of the nonlocal solving process to be used for potential computation and post-processing, with Ξ being the list of observation points, that is, the set of triangle centroids.

source
NESSie.BEM.solve — Function
solve(::Type{<: LocalityType}, ::Model{T, Triangle{T}})

Computes the full local or nonlocal cauchy data on the surface of the given biomolecule.

Return type

LocalBEMResult{T, Triangle{T}} or NonlocalBEMResult{T, Triangle{T}}

Supported keyword arguments

  • method::Symbol = :gmres Solver implementation to be used (supported arguments: :gmres and :blas)
Note

The :blas method uses an explicit representation for the BEM systems and requires a substantial amount of memory that might easily exceed the available resources on your machine (the memory demands scale quadratically with the number of surface elements). The :gmres method, on the other hand, uses implicit system representations, which provide a small memory footprint even for large systems (the memory demands scale only linearly with the number of surface elements). This comes at the cost of additional computation time, which might exceed several hours, depending on the system size. If possible, we recommend the use of our CUDA- accelerated solvers from the CuNESSie.jl package instead.

source
diff --git a/dev/lib/util/index.html b/dev/lib/util/index.html index 52da0e44..480c127b 100644 --- a/dev/lib/util/index.html +++ b/dev/lib/util/index.html @@ -18,4 +18,4 @@ for ξ in Ξ ... end -endsource +endsource