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Deprecate VoronoiFVM.Physics callbacks without data argument #122

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Sep 9, 2024
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Deprecate VoronoiFVM.Physics callbacks without data argument #122

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ec79998
Deprecate VoronoiFVM.Physics callbacks without `data` argument
pjaap Sep 5, 2024
c8377f4
Add entry in changelog
pjaap Sep 9, 2024
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6 changes: 3 additions & 3 deletions docs/src/changes.md
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@@ -1,13 +1,13 @@
# Changes
## upcoming release
- [`VoronoiFVM.Physics`](@ref) callbacks (`flux`, `storage`, etc.) without `data` argument are now deprecated

## v1.24.0 August 20, 2024
- Bernoulli function using expm1 (thanks @tcaduser !)

## v1.23.0 August 2, 2024
- Add `integrate(sys,solution)` method

## v1.23.0 August 2, 2024
- Add `integrate(sys,solution)` method

## v1.22.0 July 17, 2024
- Multithreaded assembly

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10 changes: 5 additions & 5 deletions examples/Example001_Solvers.jl
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Expand Up @@ -28,25 +28,25 @@ function main(; n = 10, Plotter = nothing, assembly = :edgwwise, kwargs...)

eps = 1.0e-2

function reaction(f, u, node)
function reaction(f, u, node, data)
f[1] = u[1]^2
end

function flux(f, u, edge)
function flux(f, u, edge, data)
f[1] = eps * (u[1, 1]^2 - u[1, 2]^2)
end

function source(f, node)
function source(f, node, data)
x1 = node[1] - 0.5
x2 = node[2] - 0.5
f[1] = exp(-20.0 * (x1^2 + x2^2))
end

function storage(f, u, node)
function storage(f, u, node, data)
f[1] = u[1]
end

function bcondition(f, u, node)
function bcondition(f, u, node, data)
boundary_dirichlet!(f,
u,
node;
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14 changes: 7 additions & 7 deletions examples/Example002_EdgeReaction.jl
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Expand Up @@ -46,18 +46,18 @@ function main(; nref = 0, dim = 2, Plotter = nothing, verbose = "and", case = :c
i1 = 6
end

function storage!(y, u, node)
function storage!(y, u, node, data)
y[1] = u[1]
end

function flux!(y, u, edge)
function flux!(y, u, edge, data)
y[1] = u[1, 1] - u[1, 2]
end

# Three ways to give a constant reaction term. As a consequence,
# these need to yield the same solution.
# 1: classical node reaction, multiplied by control volume size
function reaction!(y, u, node)
function reaction!(y, u, node, data)
y[1] = -1
end

Expand All @@ -76,7 +76,7 @@ function main(; nref = 0, dim = 2, Plotter = nothing, verbose = "and", case = :c
#
# τ=1/h v= s*h/2d = σ*h^2/2d
#
function edgereaction!(y, u, edge)
function edgereaction!(y, u, edge, data)
h = meas(edge)
y[1] = -1 * h^2 / (2 * dim)
end
Expand All @@ -88,14 +88,14 @@ function main(; nref = 0, dim = 2, Plotter = nothing, verbose = "and", case = :c
# we had before
ϕ = grid[Coordinates][1, :]

function edgereaction2!(y, u, edge)
function edgereaction2!(y, u, edge, data)
ϕK = ϕ[edge.node[1]]
ϕL = ϕ[edge.node[2]]
y[1] = -(ϕK - ϕL) * (ϕK - ϕL) / 2
end

if case == :compare_max
function bcondition!(y, u, node)
function bcondition!(y, u, node, data)
boundary_dirichlet!(y, u, node; species = 1, region = 1, value = 0)
boundary_dirichlet!(y, u, node; species = 1, region = 2, value = 0)
boundary_dirichlet!(y, u, node; species = 1, region = 3, value = 0)
Expand Down Expand Up @@ -130,7 +130,7 @@ function main(; nref = 0, dim = 2, Plotter = nothing, verbose = "and", case = :c
end

if case == :compare_flux
function bcondition2!(y, u, node)
function bcondition2!(y, u, node, data)
boundary_dirichlet!(y, u, node; species = 1, region = i1, value = 0)
end

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8 changes: 4 additions & 4 deletions examples/Example101_Laplace1D.jl
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Expand Up @@ -96,13 +96,13 @@ function main()

## Flux function which describes the flux
## between neighboring control volumes
function flux!(f, u, edge)
function flux!(f, u, edge, data)
f[1] = u[1, 1] - u[1, 2]
end

function bcond!(args...)
boundary_dirichlet!(args...; region = 1, value = 0)
boundary_dirichlet!(args...; region = 2, value = 1)
function bcond!(f, u, node, data)
boundary_dirichlet!(f, u, node; region = 1, value = 0)
boundary_dirichlet!(f, u, node; region = 2, value = 1)
end

## Create a one dimensional discretization grid
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6 changes: 3 additions & 3 deletions examples/Example105_NonlinearPoisson1D.jl
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Expand Up @@ -38,12 +38,12 @@ function main(; n = 10, Plotter = nothing, verbose = false, unknown_storage = :s

## Flux function which describes the flux
## between neighboring control volumes
function flux!(f, u, edge)
function flux!(f, u, edge, data)
f[1] = ϵ * (u[1, 1] - u[1, 2])
end

## Source term
function source!(f, node)
function source!(f, node, data)
if node[1] <= 0.5
f[1] = 1
else
Expand All @@ -52,7 +52,7 @@ function main(; n = 10, Plotter = nothing, verbose = false, unknown_storage = :s
end

## Reaction term
function reaction!(f, u, node)
function reaction!(f, u, node, data)
f[1] = exp(u[1]) - exp(-u[1])
end

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4 changes: 2 additions & 2 deletions examples/Example106_NonlinearDiffusion1D.jl
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Expand Up @@ -44,12 +44,12 @@ function main(; n = 20, m = 2, Plotter = nothing, verbose = false,

## Flux function which describes the flux
## between neighboring control volumes
function flux!(f, u, edge)
function flux!(f, u, edge, data)
f[1] = u[1, 1]^m - u[1, 2]^m
end

## Storage term
function storage!(f, u, node)
function storage!(f, u, node, data)
f[1] = u[1]
end

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4 changes: 2 additions & 2 deletions examples/Example107_NonlinearStorage1D.jl
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Expand Up @@ -40,7 +40,7 @@ function main(; n = 20, m = 2.0, Plotter = nothing, verbose = false,

## Flux function which describes the flux
## between neighboring control volumes
function flux!(f, u, edge)
function flux!(f, u, edge, data)
f[1] = u[1, 1] - u[1, 2]
end

Expand All @@ -49,7 +49,7 @@ function main(; n = 20, m = 2.0, Plotter = nothing, verbose = false,
## Storage term
## This needs to be regularized as its derivative
## at 0 is infinity
function storage!(f, u, node)
function storage!(f, u, node, data)
f[1] = (ϵ + u[1])^(1.0 / m)
end

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4 changes: 2 additions & 2 deletions examples/Example108_OrdinaryDiffEq1D.jl
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Expand Up @@ -44,12 +44,12 @@ function main(; n = 20, m = 2, Plotter = nothing, verbose = false,

## Flux function which describes the flux
## between neighboring control volumes
function flux!(f, u, edge)
function flux!(f, u, edg, data)
f[1] = u[1, 1]^m - u[1, 2]^m
end

## Storage term
function storage!(f, u, node)
function storage!(f, u, node, data)
f[1] = u[1]
end

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8 changes: 4 additions & 4 deletions examples/Example110_ReactionDiffusion1D_TwoSpecies.jl
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Expand Up @@ -29,20 +29,20 @@ function main(; n = 100, Plotter = nothing, verbose = false, unknown_storage = :
eps::Vector{Float64} = [1.0, 1.0]

physics = VoronoiFVM.Physics(
; reaction = function (f, u, node)
; reaction = function (f, u, node, data)
f[1] = u[1] * u[2]
f[2] = -u[1] * u[2]
end,
flux = function (f, u, edge)
flux = function (f, u, edge, data)
nspecies = 2
f[1] = eps[1] * (u[1, 1] - u[1, 2]) *
(0.01 + u[2, 1] + u[2, 2])
f[2] = eps[2] * (u[2, 1] - u[2, 2]) *
(0.01 + u[1, 1] + u[1, 2])
end, source = function (f, node)
end, source = function (f, node, data)
f[1] = 1.0e-4 * (0.01 + node[1])
f[2] = 1.0e-4 * (0.01 + 1.0 - node[1])
end, storage = function (f, u, node)
end, storage = function (f, u, node, data)
f[1] = u[1]
f[2] = u[2]
end)
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10 changes: 5 additions & 5 deletions examples/Example115_HeterogeneousCatalysis1D.jl
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Expand Up @@ -77,19 +77,19 @@ function main(; n = 10, Plotter = nothing, verbose = false, tend = 1,
## Diffusion flux for species A and B
D_A = 1.0
D_B = 1.0e-2
function flux!(f, u, edge)
function flux!(f, u, edge, data)
f[iA] = D_A * (u[iA, 1] - u[iA, 2])
f[iB] = D_B * (u[iB, 1] - u[iB, 2])
end

## Storage term of species A and B
function storage!(f, u, node)
function storage!(f, u, node, data)
f[iA] = u[iA]
f[iB] = u[iB]
end

## Source term for species a around 0.5
function source!(f, node)
function source!(f, node, data)
x1 = node[1] - 0.5
f[iA] = exp(-100 * x1^2)
end
Expand All @@ -110,7 +110,7 @@ function main(; n = 10, Plotter = nothing, verbose = false, tend = 1,
R_AC(u_A, u_C) = kp_AC * u_A * (1 - u_C) - km_AC * u_C
R_BC(u_B, u_C) = kp_BC * u_B * (1 - u_C) - km_BC * u_C

function breaction!(f, u, node)
function breaction!(f, u, node, data)
if node.region == 1
f[iA] = S * R_AC(u[iA], u[iC])
f[iB] = S * R_BC(u[iB], u[iC])
Expand All @@ -119,7 +119,7 @@ function main(; n = 10, Plotter = nothing, verbose = false, tend = 1,
end

## This is for the term \partial_t u_C at the boundary
function bstorage!(f, u, node)
function bstorage!(f, u, node, data)
if node.region == 1
f[iC] = u[iC]
end
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12 changes: 6 additions & 6 deletions examples/Example120_ThreeRegions1D.jl
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Expand Up @@ -31,7 +31,7 @@ function main(; n = 30, Plotter = nothing, plot_grid = false, verbose = false,
eps = [1, 1, 1]
k = [1, 1, 1]

function reaction(f, u, node)
function reaction(f, u, node, data)
if node.region == 1
f[1] = k[1] * u[1]
f[2] = -k[1] * u[1]
Expand All @@ -43,7 +43,7 @@ function main(; n = 30, Plotter = nothing, plot_grid = false, verbose = false,
end
end

function source(f, node)
function source(f, node, data)
if node.region == 1
f[1] = 1.0e-4 * (3.0 - node[1])
end
Expand All @@ -54,20 +54,20 @@ function main(; n = 30, Plotter = nothing, plot_grid = false, verbose = false,
## write into the result also where
## the corresponding species has not been enabled
## Species information is used to prevent the assembly.
flux = function (f, u, edge)
flux = function (f, u, edge, data)
for i = 1:3
f[i] = eps[i] * (u[i, 1] - u[i, 2])
end
end

storage = function (f, u, node)
storage = function (f, u, node, data)
f .= u
end
else
## This is the "old" way:
## Write into result only where
## the corresponding species has been enabled
flux = function (f, u, edge)
flux = function (f, u, edge, data)
if edge.region == 1
f[1] = eps[1] * (u[1, 1] - u[1, 2])
f[2] = eps[2] * (u[2, 1] - u[2, 2])
Expand All @@ -79,7 +79,7 @@ function main(; n = 30, Plotter = nothing, plot_grid = false, verbose = false,
end
end

storage = function (f, u, node)
storage = function (f, u, node, data)
if node.region == 1
f[1] = u[1]
f[2] = u[2]
Expand Down
6 changes: 3 additions & 3 deletions examples/Example121_PoissonPointCharge1D.jl
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Expand Up @@ -40,16 +40,16 @@ function main(; nref = 0, Plotter = nothing, verbose = false, unknown_storage =

Q::Float64 = 0.0

function flux!(f, u, edge)
function flux!(f, u, edge, data)
f[1] = u[1, 1] - u[1, 2]
end
function storage!(f, u, node)
function storage!(f, u, node, data)
f[1] = u[1]
end

## Define boundary reaction defining charge
## Note that the term is written on the left hand side, therefore the - sign
function breaction!(f, u, node)
function breaction!(f, u, node, data)
if node.region == 3
f[1] = -Q
end
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6 changes: 3 additions & 3 deletions examples/Example125_TestFunctions1D.jl
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Expand Up @@ -19,13 +19,13 @@ function main(; n = 100, Plotter = nothing, verbose = false, unknown_storage = :
eps::Vector{Float64} = [1, 1.0e-1]

physics = VoronoiFVM.Physics(
; reaction = function (f, u, node)
; reaction = function (f, u, node, data)
f[1] = 10 * (u[1] - u[2])
f[2] = 10 * (u[2] - u[1])
end, flux = function (f, u, edge)
end, flux = function (f, u, edge, data)
f[1] = eps[1] * (u[1, 1] - u[1, 2])
f[2] = eps[2] * (u[2, 1] - u[2, 2])
end, storage = function (f, u, node)
end, storage = function (f, u, node, data)
f[1] = u[1]
f[2] = u[2]
end)
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2 changes: 1 addition & 1 deletion examples/Example201_Laplace2D.jl
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Expand Up @@ -14,7 +14,7 @@ import Metis

## Flux function which describes the flux
## between neighboring control volumes
function g!(f, u, edge)
function g!(f, u, edge, data)
f[1] = u[1, 1] - u[1, 2]
end

Expand Down
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