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Remove data deprecation #125

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Sep 10, 2024
Merged

Remove data deprecation #125

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02eea67
Import changelog entry from v1
pjaap Sep 9, 2024
aa34e05
Remove deprecated Physics callbacks without data argument
pjaap Sep 9, 2024
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4 changes: 3 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,14 +12,16 @@
solve!(solution,inival, system::VoronoiFVM.AbstractSystem; kwargs...)
````
- History is now a field of the solution but not system, to be accessed with ``history(sol)``, both for stationary and transient solutions
- [`VoronoiFVM.Physics`](@ref) callbacks (`flux`, `storage`, etc.) need a provided `data` argument

### Added
- Introduced ``SystemState`` which contains entries (matrix, residuals) which before were
part of ``System``
- Introduced `solve!(state::SystemState)` method
- Stationary solutions are now subtypes of AbstractNoTimeSolution
- Changelog now in package root

## upcoming release
## v1.25.0, Sept 9, 2024
- [`VoronoiFVM.Physics`](@ref) callbacks (`flux`, `storage`, etc.) without `data` argument are now deprecated

## v1.24.0 August 20, 2024
Expand Down
95 changes: 17 additions & 78 deletions src/vfvm_physics.jl
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Expand Up @@ -60,14 +60,6 @@ function nofunc_generic_sparsity(sys)
end


#
# Dummy data type that represents data or not
# We need this for the `data` deprecation phase
#
@kwdef mutable struct MaybeData
isdata=false
end

##########################################################
"""
````
Expand Down Expand Up @@ -200,7 +192,6 @@ end
##########################################################

isdata(::Nothing) = false
isdata(d::MaybeData) = d.isdata
isdata(::Any) = true

"""
Expand All @@ -224,7 +215,7 @@ Physics(;num_species=0,
Constructor for physics data. For the meaning of the optional keyword arguments, see [`VoronoiFVM.System(grid::ExtendableGrid; kwargs...)`](@ref).
"""
function Physics(; num_species = 0,
data = MaybeData(isdata=false),
data = nothing,
flux::Function = nofunc,
reaction::Function = nofunc,
edgereaction::Function = nofunc,
Expand All @@ -239,30 +230,6 @@ function Physics(; num_species = 0,
generic::Function = nofunc_generic,
generic_sparsity::Function = nofunc_generic_sparsity,
kwargs...)
if !isdata(data)
# deprecation check: callbacks without a `data` argument are not supported in future versions
callbacks = [flux, reaction, edgereaction, storage, source, bflux, breaction, bsource, bstorage, boutflow]
callbacks_seem_fine = true
for f in callbacks
# ignore dummy functions
if !(f in [nofunc, default_storage, nosrc])
# check whether the callbacks have a method with 3 or 4 arguments, respectively
nn = nothing
if ( f in [flux, reaction, edgereaction, storage, bflux, breaction, bstorage, boutflow] && applicable(f,nn,nn,nn) ) ||
( f in [source, bsource] && applicable(f,nn,nn) )
@warn "using VoronoiFVM.Physics callback $(nameof(f)) without a `data` argument is now deprecated"
callbacks_seem_fine = false
end
end
end

# it looks like all callbacks can be called with a `data` argument ⇒ enable a dummy data attribute
if callbacks_seem_fine
data.isdata = true
end

end

return Physics(flux,
storage,
reaction,
Expand Down Expand Up @@ -376,36 +343,18 @@ function ResEvaluator(physics, data, symb::Symbol, uproto::Vector{Tv}, geom, nsp

# source functions need special handling here
if symb == :source || symb == :bsource
if isdata(physics.data)
fwrap = function (y)
y .= 0
func(rhs(geom, y), geom, data)
nothing
end
else
fwrap = function (y)
y .= 0
func(rhs(geom, y), geom)
nothing
end
fwrap = function (y)
y .= 0
func(rhs(geom, y), geom, data)
nothing
end
else # Normal functions wihth u as parameter
if isdata(physics.data)
fwrap = function (y, u)
y .= 0
## for ii in .. uu[geom.speclist[ii]]=u[ii]
func(rhs(geom, y), unknowns(geom, u), geom, data)
## for ii in .. y[ii]=y[geom.speclist[ii]]
nothing
end
else
fwrap = function (y, u)
y .= 0
## for ii in .. uu[geom.speclist[ii]]=u[ii]
func(rhs(geom, y), unknowns(geom, u), geom)
## for ii in .. y[ii]=y[geom.speclist[ii]]
nothing
end
fwrap = function (y, u)
y .= 0
## for ii in .. uu[geom.speclist[ii]]=u[ii]
func(rhs(geom, y), unknowns(geom, u), geom, data)
## for ii in .. y[ii]=y[geom.speclist[ii]]
nothing
end
end
isnontrivial = (func != nofunc)
Expand Down Expand Up @@ -478,22 +427,12 @@ Constructor for ResJEvaluator
function ResJacEvaluator(physics, data, symb::Symbol, uproto::Vector{Tv}, geom, nspec) where {Tv}
func = getproperty(physics, symb)

if isdata(physics.data)
fwrap = function (y, u)
y .= 0
## for ii in .. uu[geom.speclist[ii]]=u[ii]
func(rhs(geom, y), unknowns(geom, u), geom, data)
## for ii in .. y[ii]=y[geom.speclist[ii]]
nothing
end
else
fwrap = function (y, u)
y .= 0
## for ii in .. uu[geom.speclist[ii]]=u[ii]
func(rhs(geom, y), unknowns(geom, u), geom)
## for ii in .. y[ii]=y[geom.speclist[ii]]
nothing
end
fwrap = function (y, u)
y .= 0
## for ii in .. uu[geom.speclist[ii]]=u[ii]
func(rhs(geom, y), unknowns(geom, u), geom, data)
## for ii in .. y[ii]=y[geom.speclist[ii]]
nothing
end

isnontrivial = (func != nofunc)
Expand Down
18 changes: 3 additions & 15 deletions src/vfvm_postprocess.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -23,10 +23,6 @@ function integrate(system::AbstractSystem{Tv, Tc, Ti, Tm}, F::Function, U::Abstr

if boundary
bnode = BNode(system)
bnodeparams = (bnode,)
if isdata(data)
bnodeparams = (bnode, data)
end
#!!! bnode.time=time
#!!! bnode.embedparam=embedparam

Expand All @@ -38,17 +34,13 @@ function integrate(system::AbstractSystem{Tv, Tc, Ti, Tm}, F::Function, U::Abstr
for ibnode in noderange(system.boundary_assembly_data, item)
_fill!(bnode, system.boundary_assembly_data, ibnode, item)
res .= zero(Tv)
@views F(rhs(bnode, res), unknowns(bnode, U[:, bnode.index]), bnodeparams...)
@views F(rhs(bnode, res), unknowns(bnode, U[:, bnode.index]), bnode, data)
asm_res(idof, ispec) = integral[ispec, bnode.region] += bnode.fac * res[ispec]
assemble_res(bnode, system, asm_res)
end
end
else
node = Node(system)
nodeparams = (node,)
if isdata(data)
nodeparams = (node, data)
end
#!!! node.time=time
#!!! node.embedparam=embedparam
cellregions = grid[CellRegions]
Expand All @@ -58,7 +50,7 @@ function integrate(system::AbstractSystem{Tv, Tc, Ti, Tm}, F::Function, U::Abstr
for inode in noderange(system.assembly_data, item)
_fill!(node, system.assembly_data, inode, item)
res .= zero(Tv)
@views F(rhs(node, res), unknowns(node, U[:, node.index]), nodeparams...)
@views F(rhs(node, res), unknowns(node, U[:, node.index]), node, data)
asm_res(idof, ispec) = integral[ispec, node.region] += node.fac * res[ispec]
assemble_res(node, system, asm_res)
end
Expand Down Expand Up @@ -104,10 +96,6 @@ function edgeintegrate(system::AbstractSystem{Tv, Tc, Ti, Tm}, F::Function, U::A
error("missing implementation of boundary edge integrals")
else
edge = Edge(system)
edgeparams = (edge,)
if isdata(data)
edgeparams = (edge, data)
end
cellregions = grid[CellRegions]
ncellregions = maximum(cellregions)
integral = zeros(Tu, nspecies, ncellregions)
Expand All @@ -117,7 +105,7 @@ function edgeintegrate(system::AbstractSystem{Tv, Tc, Ti, Tm}, F::Function, U::A
@views UKL[1:nspecies] .= U[:, edge.node[1]]
@views UKL[(nspecies + 1):(2 * nspecies)] .= U[:, edge.node[2]]
res .= zero(Tv)
@views F(rhs(edge, res), unknowns(edge, UKL), edgeparams...)
@views F(rhs(edge, res), unknowns(edge, UKL), edge, data)
function asm_res(idofK, idofL, ispec)
h = meas(edge)
# This corresponds to the multiplication with the diamond volume.
Expand Down
6 changes: 1 addition & 5 deletions src/vfvm_system.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -975,11 +975,7 @@ function _initialize_dirichlet!(U::AbstractMatrix, system::AbstractSystem{Tv, Tc

# set up bnode
bnode = BNode(system, time, λ, params)
bnodeparams = (bnode,)
data = system.physics.data
if isdata(data)
bnodeparams = (bnode, data)
end

# setup unknowns to be passed
UK = zeros(Tv, num_species(system) + length(params))
Expand All @@ -999,7 +995,7 @@ function _initialize_dirichlet!(U::AbstractMatrix, system::AbstractSystem{Tv, Tc
bnode.dirichlet_value .= Inf
# set up solution vector, call boundary reaction
@views UK[1:nspecies] .= U[:, bnode.index]
system.physics.breaction(y, u, bnodeparams...)
system.physics.breaction(y, u, bnode, data)

# Check for Dirichlet bc
for ispec = 1:nspecies
Expand Down
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