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Commit b0e2c506 authored by s.zitz's avatar s.zitz
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Merge branch 'GPU_Usage' into 'master' 

First version update with performance studies and simpler function calls.

See merge request !5
parents a8fc113e 0b2b86ef
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.gitlab-ci.yml
View file @ b0e2c506
image: julia:1.4 # image comes from Docker hub
image: julia:1.5 # image comes from Docker hub
before_script:
# workaround for https://github.com/JuliaDocs/Documenter.jl/issues/686
......
CHANGELOG.md
View file @ b0e2c506
......@@ -5,8 +5,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
- Performance test for all functions.
- A clearer and simpler GPU integration.
<!--- ## [1.0.0] - 2017-06-20
<!-- ## [1.0.0] - 2017-06-20
### Added
- New visual identity by [@tylerfortune8](https://github.com/tylerfortune8).
- Version navigation.
......@@ -122,13 +124,41 @@ notable changes.
## [0.0.3] - 2014-08-09
### Added
- "Why should I care?" section mentioning The Changelog podcast.
--->
## [0.0.2] - 2020-09-02
## [0.0.2] - 2014-07-10
### Added
- Explanation of the recommended reverse chronological release ordering.
--->
- Better documentation for the computation of the capillary pressure.
- Theory part in most of the docstrings.
- Performance tests for the computation of the capillary pressure, see [pressure.jl](test/pressure.jl).
- New collision kernels `BGKwithBuickGreatedStream!` and `BGKwithGuoStream!`, Buick and Guo use different force corrections.
- Performance tests for the collision kernels, `BGKwithGuoStream!` is the slowest option, further details see [collision.jl](test/collisions.jl).
- The gradient of the pressure is now calculated with a circular padded array and is called `h∇p!`.
- Performance tests for all available forces, `slippage!`, `thermalfluctuations!`, `h∇p!` and `inclinedplane!`, see [forcing.jl](test/forcing.jl)
### Changed
- Computation of pressure is now mostly vectorized, see [pressure.jl](src/pressure.jl).
- Collision kernels moved from looping to vectorization with broadcasting, for details see [collision.jl](src/collision.jl).
- The default collision operation was renamed to `BGKandStream!` and has now a flag to use the weigthing function correction.
- Vectorization of equilibrium calculation in function `equilibrium!`, see [equilibrium!.jl](src/equilibria.jl).
- structs are no longer exported, to initialize them use `JuThinFilm.name` with the name of the struct.
- Docstrings of all functions have been updated accordingly.
### Removed
- Calculation of the disjoining pressure with `Pi_cuda` has been removed, GPU functionality needs further testing.
- Kernels have been removed such `kernel_laplacianperiodic!`, `kernel_gradientperiodic!` and `kernel_pressure!` are no longer existing.
- `kernel_equilibrium!` has been removed in favor of a `equilibrium!` GPU version.
- `velocitysquare` for cumoments has been removed.
- `filmpressure!` in favor of `h∇p!`, see [forcing.jl](src/forcing.jl).
## [0.0.1] - 2020-08-18
### Added
- This CHANGELOG file to document upcoming changes
- README now contains a link to the CHANGELOGs
- Full working relaxing droplet simulation on a patterned substrate see [relaxwithpatch.jl](scripts/relaxwithpatch.jl)
\ No newline at end of file
Manifest.toml
View file @ b0e2c506
......@@ -41,9 +41,9 @@ version = "0.5.10"
[[Bzip2_jll]]
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......@@ -75,10 +75,10 @@ uuid = "aafaddc9-749c-510e-ac4f-586e18779b91"
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......@@ -100,15 +100,15 @@ version = "0.7.0"
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......@@ -124,9 +124,9 @@ version = "0.3.0"
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......@@ -174,10 +174,10 @@ uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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......@@ -216,9 +216,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
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......@@ -249,9 +249,9 @@ uuid = "90fa49ef-747e-5e6f-a989-263ba693cf1a"
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......@@ -279,9 +279,9 @@ version = "0.2.0"
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......@@ -334,9 +334,9 @@ version = "5.1.0"
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[[Graphics]]
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......@@ -358,9 +358,9 @@ version = "0.3.1"
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......@@ -370,9 +370,9 @@ version = "0.3.5"
[[ImageCore]]
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version = "0.8.16"
[[ImageDistances]]
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......@@ -388,9 +388,9 @@ version = "0.6.15"
[[ImageMetadata]]
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git-tree-sha1 = "5c2c78dc11343d83320e790379e0f58de3aa1b7e"
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[[ImageMorphology]]
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......@@ -412,9 +412,9 @@ version = "0.2.3"
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version = "0.8.6"
[[Images]]
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......@@ -479,9 +479,9 @@ version = "1.0.0"
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......@@ -490,10 +490,10 @@ uuid = "7d188eb4-7ad8-530c-ae41-71a32a6d4692"
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[[JuMP]]
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......@@ -556,9 +556,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
[[MathOptInterface]]
deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "JSON", "JSONSchema", "LinearAlgebra", "MutableArithmetics", "OrderedCollections", "SparseArrays", "Test", "Unicode"]
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......@@ -574,30 +574,24 @@ version = "1.0.2"
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......@@ -617,9 +611,9 @@ uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
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......@@ -628,9 +622,9 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
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[[OrderedCollections]]
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......@@ -654,12 +648,6 @@ version = "1.0.10"
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[[Pluto]]
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[[PooledArrays]]
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......@@ -689,9 +677,9 @@ uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439"
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......@@ -701,15 +689,15 @@ version = "0.2.0"
[[Requires]]
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......@@ -781,9 +769,15 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
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[[TableTraits]]
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......@@ -845,6 +839,6 @@ version = "0.9.2"
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version = "1.2.11+16"
Project.toml
View file @ b0e2c506
......@@ -4,6 +4,7 @@ authors = ["Zitzeronion <s.zitz@fz-juelich.de>"]
version = "0.1.0"
[deps]
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
......@@ -15,7 +16,6 @@ LazySets = "b4f0291d-fe17-52bc-9479-3d1a343d9043"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
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Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
......
notebooks/droplets_and_patterns.jl
View file @ b0e2c506
......@@ -74,8 +74,8 @@ begin
hd_var = "height"
polygon = triangle
shape = @name triangle
contrast = -10.0 # [5, 10, 15, 20, -10]
vol = 30 # [20, 25, 30]
contrast = 20.0 # [5, 10, 15, 20, -10]
vol = 20 # [20, 25, 30]
end
# ╔═╡ 508d3c22-e772-11ea-3b00-03c64a90ecd2
......@@ -115,7 +115,7 @@ begin
end
# ╔═╡ ed7cdbbc-e783-11ea-0675-23b30b549382
md"And the surface area of the droplet"
md"And the surface area of the droplet excluding the base area"
# ╔═╡ fd0136e6-e783-11ea-38fa-71130320f53b
begin
......@@ -131,7 +131,7 @@ begin
plot!(trianglesurf, label="triangle", lw=2)
plot!(ellipsesurf, label="ellipse", lw=2)
plot!(circlesurf, label="circle", lw=2)
plot!(xlims = (0, 4000))
plot!(xlims = (0, 2000))
end
# ╔═╡ e91776a2-e77b-11ea-2b1b-efec77ae5aa4
......@@ -161,8 +161,8 @@ end
# ╔═╡ Cell order:
# ╠═fbec2be8-e775-11ea-3b9d-a95eac0bb6b7
# ╠═15c6d3ec-e776-11ea-271b-7d32a12e86d5
# ╠═da280ffa-e77e-11ea-30d5-65eb4b74d8c7
# ╠═15c6d3ec-e776-11ea-271b-7d32a12e86d5
# ╟─e84a8518-e39e-11ea-1cd9-59bd95e672bf
# ╠═40854412-e76f-11ea-01aa-379d8e332c43
# ╟─2aabe662-e771-11ea-37c9-0f1ca548971f
......
scripts/relaxwithpatch.jl
View file @ b0e2c506
......@@ -47,7 +47,7 @@ anim = @animate for t in 1:parameters.mt
# Relevant for plotting and animation generation
# cuts[:,1] .= mom.height[:,center[2]]
# cuts[:,2] .= mom.height[center[1],:]
l = @layout [a b; c{0.2h} d{0.2h}]
l = @layout [a b; c{0.2h}; d{0.2h}]
p1 = Plots.surface(mom.height, c=:viridis)
p2 = plot(P, fill=:blue)
p2 = contourf!(mom.height, aspect_ratio=1, c=:viridis)
......
src/JuThinFilm.jl
View file @ b0e2c506
module JuThinFilm
using CUDA, Revise, Parameters, Random, Images, LazySets, LinearAlgebra, Pluto
using CUDA, Revise, Parameters, Random, Images, LazySets, LinearAlgebra
include("structs.jl")
include("initialstates.jl")
......@@ -12,19 +12,18 @@ include("forcing.jl")
include("runsimulation.jl")
include("measurements.jl")
# Export structs
export params, lattice, culattice, velocity, cuvelocity, force, cuforce, moments, cumoments, pressurestats, collisionparams, distributions, cudistributions
export default_moments, default_cumoments, default_velocity, default_cuvelocity, default_force, default_cuforce
# Export generators for structs
export default_moments, default_cumoments, default_velocity, default_cuvelocity, default_force, default_cuforce, default_distribution
# Defined initial fluid states
export flatsurface, sinewaves, singledroplet
# As well as initial substrate states
export ellipsepattern
export ellipsepattern, trianglepattern, boxpattern
# Export functions
export Π, Pi_cuda, Δ!, kernel_laplacianperiodic!, kernel_gradientperiodic!, kernel_pressure!
export equilibrium!, kernel_equilibrium!, velsquare
export Π, Δ!, capillarypressure!
export equilibrium!
export macroscopicmoments!
export collidestreamBGK_periodic!, collidestreamBGK_periodicGUO!
export slippage!, thermalflutuations!, filmpressure!, constantforce!, sumforces!
export BGKandStream!, BGKwithBuickGreatedStream!, BGKwithGuoStream!
export slippage!, thermalfluctuations!, h∇p!, inclinedplane!, sumforces!
# Put everything together to get a full simulation
export runsimulation, runrealsimulation
......
src/calcmoments.jl
View file @ b0e2c506
"""
macroscopicmoments(mom, dists)
Computes the first few moments, `height`, `velocity.x` & `velocity.y` of the post collision distribution.
Computes the macroscopic moments `height` and `velocity` from the post collision distribution `fout`.
In case of using `BGKwithBuickGreatedStream` or `BGKwithGuoStream` add the sum of all forces to the moment calculation.
# Theory
The macroscopic moments, `density` (ρ) and `velocity` can be obtained as moments of the distribution function.
Density ρ reduces in the shallow water case to the `height` (h) of the film and is given by the zeroth moment.
On the other hand the velocity vector in 2d `(u,v)` is given by both the first and the second moment.
They are calculated according to
`` h = \\sum_{\\alpha} f_{\\alpha} .``
Velocities are thus given by
`` v_i = \\frac{1}{h}\\sum_{\\alpha} c_{\\alpha}^i f_{\\alpha},``
where the subscript `i` indicated the two components `(x,y)`.
To be efficient the height is computed simply using **Julia**s `sum!` function.
For the velocities I decided to do a little index shifting to use `sum` as well.
One can add a force as input as well, if so a Guo like force correction is applied.
# Examples
```jldoctest
julia> using JuThinFilm
julia> dists = distributions{Float64}(para=params(lx=5,ly=5));
julia> dists = default_distribution(Float64, 5, 5);
julia> mom = default_moments(Float64, 5, 5); mom.height
5×5 Array{Float64,2}:
......@@ -30,7 +50,7 @@ julia> mom.height # height is now the sum of fout.
0.1 0.1 0.1 0.1 0.1
0.1 0.1 0.1 0.1 0.1
julia> dists = cudistributions{Float32}(para=params{Float32}(lx=5,ly=5)); dists.fout[:, :, 1] .= 0.1f0; # Works similar on the GPU.
julia> dists = JuThinFilm.cudistributions{Float32}(para=JuThinFilm.params{Float32}(lx=5,ly=5)); dists.fout[:, :, 1] .= 0.1f0; # Works similar on the GPU.
julia> mom = default_cumoments(Float32, 5, 5); mom.height
5×5 CUDA.CuArray{Float32,2}:
......@@ -56,8 +76,20 @@ julia> mom.height
See also: [`distributions`](@ref), [`moments`](@ref), [`default_moments`](@ref)
"""
function macroscopicmoments!(mom::Moment, dists::Distribution)
mom.height .= sum(dists.fout, dims=3)[:,:,1]
function macroscopicmoments!(mom::moments, dists::Distribution)
sum!(mom.height, dists.fout)
mom.velocity.x = permutedims(sum(permutedims(dists.fout, [3,1,2]) .* [0; 1; 0; -1; 0; 1; -1; -1; 1;], dims=1),[2,3,1])[:, : ,1]
mom.velocity.y = permutedims(sum(permutedims(dists.fout, [3,1,2]) .* [0; 0; 1; 0; -1; 1; 1; -1; -1;], dims=1),[2,3,1])[:, : ,1]
# Normalize with height
mom.velocity.x ./= mom.height
mom.velocity.y ./= mom.height
return nothing
end
function macroscopicmoments!(mom::cumoments, dists::Distribution)
sum!(mom.height, dists.fout)
mom.velocity.x .= dists.fout[:,:,2] .- dists.fout[:,:,4] .+ dists.fout[:,:,6] .- dists.fout[:,:,7] .- dists.fout[:,:,8] .+ dists.fout[:,:,9] # This is not as easy as thought
mom.velocity.y .= dists.fout[:,:,3] .- dists.fout[:,:,5] .+ dists.fout[:,:,6] .+ dists.fout[:,:,7] .- dists.fout[:,:,8] .- dists.fout[:,:,9]
......@@ -68,8 +100,20 @@ function macroscopicmoments!(mom::Moment, dists::Distribution)
return nothing
end
function macroscopicmoments!(mom::Moment, dists::Distribution, F::Force)
mom.height .= sum(dists.fout, dims=3)[:,:,1]
function macroscopicmoments!(mom::moments, dists::Distribution, F::Force)
sum!(mom.height, dists.fout)
mom.velocity.x = permutedims(sum(permutedims(dists.fout, [3,1,2]) .* [0; 1; 0; -1; 0; 1; -1; -1; 1;], dims=1),[2,3,1])[:, : ,1] .+ F.x ./ 2
mom.velocity.y = permutedims(sum(permutedims(dists.fout, [3,1,2]) .* [0; 0; 1; 0; -1; 1; 1; -1; -1;], dims=1),[2,3,1])[:, : ,1] .+ F.y ./ 2
# Normalize with height
mom.velocity.x ./= mom.height
mom.velocity.y ./= mom.height
return nothing
end
function macroscopicmoments!(mom::cumoments, dists::Distribution, F::Force)
sum!(mom.height, dists.fout)
mom.velocity.x .= dists.fout[:,:,2] .- dists.fout[:,:,4] .+ dists.fout[:,:,6] .- dists.fout[:,:,7] .- dists.fout[:,:,8] .+ dists.fout[:,:,9] .+ F.x ./ 2
mom.velocity.y .= dists.fout[:,:,3] .- dists.fout[:,:,5] .+ dists.fout[:,:,6] .+ dists.fout[:,:,7] .- dists.fout[:,:,8] .- dists.fout[:,:,9] .+ F.y ./ 2
......@@ -78,4 +122,4 @@ function macroscopicmoments!(mom::Moment, dists::Distribution, F::Force)
mom.velocity.y ./= mom.height
return nothing
end
\ No newline at end of file
end
src/collisions.jl
View file @ b0e2c506
This diff is collapsed.
src/equilibria.jl
View file @ b0e2c506
"""
equilibrium!(dists, mom, lat, parameters, T)
equilibrium!(dists, mom, lat, parameters)
Computes the equilibrium distribution `dists.feq` of a given macroscopic state `mom`.
# Arguments
- `dists::distributions`: container for the three distribution functions.
- `mom::moments`: struct that contains a macroscopic state, e.g. height and velocity.
- `lat::lattice`: struct that stores the lattice velocities `ci` and weights `wi`.
- `parameters::param`: struct that stores lattice size and gravitational acceleration.
- `T::AbstractFloat`: numerical accuracy.
# Examples
```jldoctest
julia> using JuThinFilm
julia> dists = JuThinFilm.distributions{Float64}(para = params(lx=5, ly=5));
julia> mom = JuThinFilm.default_moments(Float64, 5, 5);
# Theory
julia> lat = lattice{Float64}(); par = params{Float64}(lx=5, ly=5);
One of the reasons why the lattice Boltzmann method became so widely spread is due to its simple assumptions.
Among them is that any system simulated with lattice Boltzmann is a system close to equilibrium.
For an ideal gas one knows that the momentum distribution is given by a maxwellian distribution with temperature T,
julia> equilibrium!(dists, mom, lat, par, Float64)
`` f^{eq} = \\