further documentation work

docs/make.jl

@@ -19,7 +19,7 @@ function make(; with_examples = true,
 
     pages = [
         "Home" => "index.md",
-        "changes.md",
+        "Changelog" => "changes.md",
         "method.md",
         "API Documentation" => [
             "system.md",

docs/src/internal.md

@@ -102,3 +102,9 @@ eval_jacobian!
 mass_matrix
 prepare_diffeq!
 ```
+
+## Misc tools
+```@docs
+VoronoiFVM.doolittle_ludecomp!
+VoronoiFVM.doolittle_lusolve!
+```

docs/src/physics.md

@@ -5,8 +5,34 @@
 VoronoiFVM.AbstractPhysics
 VoronoiFVM.Physics
 VoronoiFVM.Physics(;kwargs...)
+
 Base.show(io::IO,physics::VoronoiFVM.AbstractPhysics)
 ```
+## Handling boundary conditions
+Boundary conditions are handled in the  `bcondition` callback passed to the system constructor.
+For being called in this callback, the following  functions are available
+
+```@docs
+boundary_dirichlet!(y,u,bnode::AbstractGeometryItem,ispec,ireg,val)
+boundary_dirichlet!(y,u,bnode::AbstractGeometryItem;kwargs...)
+boundary_neumann!(y,u,bnode::AbstractGeometryItem,ispec,ireg,val)
+boundary_neumann!(y,u,bnode::AbstractGeometryItem;kwargs...)
+boundary_robin!(y,u,bnode::AbstractGeometryItem,ispec,ireg,fac,val)
+boundary_robin!(y,u,bnode::AbstractGeometryItem;kwargs...)
+ramp
+```
+
+### Outflow boundary conditions
+These are characterized by the `boutflow` physics callback and 
+and the `outflowboundaries` keyword argument in the system
+resp. physics constructor. See also the 
+[corresponding notebook](https://j-fu.github.io/VoronoiFVM.jl/dev/nbhtml/outflow/)
+
+```@docs
+hasoutflownode
+isoutflownode
+outflownode
+```
 
 ## Edge and node data
 ```@docs

docs/src/system.md

@@ -38,33 +38,6 @@ VoronoiFVM.is_bulk_species
 ```
 
 
-## Handling boundary conditions
-Boundary conditions are handled in the  `bcondition` callback passed to the system constructor.
-For being called in this callback, the following  functions are available
-
-```@docs
-boundary_dirichlet!(y,u,bnode,ispec,ireg,val)
-boundary_dirichlet!(y,u,bnode;kwargs...)
-boundary_neumann!(y,u,bnode,ispec,ireg,val)
-boundary_neumann!(y,u,bnode;kwargs...)
-boundary_robin!(y,u,bnode,ispec,ireg,fac,val)
-boundary_robin!(y,u,bnode;kwargs...)
-ramp
-```
-
-### Outflow boundary conditions
-These are characterized by the `boutflow` physics callback and 
-and the `outflowboundaries` keyword argument in the system
-resp. physics constructor. See also the 
-[corresponding notebook](https://j-fu.github.io/VoronoiFVM.jl/dev/nbhtml/outflow/)
-
-```@docs
-hasoutflownode
-isoutflownode
-outflownode
-```
-
-
 ## Allocation warnings
 
 The code checks for allocations in the assembly loop. 
@@ -137,7 +110,7 @@ VoronoiFVM.System{Tv,Ti, Tm, TSpecMat<:AbstractMatrix, TSolArray<:AbstractMatrix
 
 ## Legacy API
 ```@docs
-boundary_dirichlet!(system::VoronoiFVM.AbstractSystem, ispec, ibc, v)
+boundary_dirichlet!(system::VoronoiFVM.AbstractSystem{Tv}, ispec, ibc, v) where {Tv}
 boundary_dirichlet!(system::VoronoiFVM.AbstractSystem; kwargs...)
 boundary_neumann!(system::VoronoiFVM.AbstractSystem, ispec, ibc, v)
 boundary_neumann!(system::VoronoiFVM.AbstractSystem; kwargs...)

src/VoronoiFVM.jl

@@ -58,6 +58,17 @@ using Compat: @compat
 
 
 
+"""
+   $(TYPEDEF)
+
+Abstract type for geometry items (node,bnode,edge, bedge)
+"""
+abstract type AbstractGeometryItem{Tc <: Number, Tp <: Number, Ti <: Integer} end
+export AbstractGeometryItem
+
+abstract type AbstractSolutionArray{T,N} <: AbstractArray{T,N} end
+export AbstractSolutionArray
+
 include("vfvm_physics.jl")
 @compat public Physics
 
@@ -66,7 +77,6 @@ export fbernoulli
 export fbernoulli_pm
 export inplace_linsolve!
 
-abstract type AbstractSolutionArray{T,N} <: AbstractArray{T,N} end
 
 include("vfvm_history.jl")
 export NewtonSolverHistory, TransientSolverHistory, details

src/vfvm_geometryitems.jl

@@ -1,10 +1,3 @@
-"""
-   $(TYPEDEF)
-
-Abstract type for geometry items (node,bnode,edge, bedge)
-"""
-abstract type AbstractGeometryItem{Tc <: Number, Tp <: Number, Ti <: Integer} end
-
 """
     time(edge_or_node)
 

src/vfvm_physics.jl

@@ -482,3 +482,87 @@ isnontrivial(e::AbstractEvaluator) = e.isnontrivial
 function diffusion_flux(D::T) where {T}
     (y, u, args...) -> y[1] = D(u[1, 1] + u[1, 2]) * (u[1, 1] - u[1, 2])
 end
+
+"""
+     boundary_dirichlet!(y,u,bnode,ispec,ireg,val)
+
+Set Dirichlet boundary condition for species ispec at boundary ibc.
+"""
+function boundary_dirichlet!(y, u, bnode::AbstractGeometryItem, ispec, ireg, val; penalty = bnode.Dirichlet)
+    if bnode.region == ireg
+        y[ispec] += penalty * (u[ispec] - val)
+        # just for call during initialization, so we can convert from dual number
+        bnode.dirichlet_value[ispec] = value(val)
+    end
+    nothing
+end
+
+"""
+     boundary_dirichlet!(y,u,bnode; kwargs...)
+
+Keyword argument version:
+- `species`: species number. Default: 1
+- `region`: boundary region number. By default, all boundary regions.
+- `value`: value 
+"""
+function boundary_dirichlet!(y, u, bnode::AbstractGeometryItem; species = 1, region = bnode.region, value = 0, penalty = bnode.Dirichlet)
+    boundary_dirichlet!(y, u, bnode, species, region, value; penalty)
+end
+
+"""
+       ramp(t; kwargs...)
+Ramp function for specifying time dependent boundary conditions
+
+Keyword arguments:
+- `dt`: Tuple: start and end time of ramp. Default: `(0,0.1)`
+- `du`: Tuple: values at start and end time. Default: `(0,0)`
+"""
+function ramp(t; dt = (0, 0.1), du = (0, 0))
+    (t, ubegin, uend, tbegin, tend) = promote(Float64(t), du[1], du[2], dt[1], dt[2])
+    if t < tbegin
+        return ubegin
+    elseif t < tend
+        return ubegin + (uend - ubegin) * (t - tbegin) / (tend - tbegin)
+    else
+        return uend
+    end
+end
+
+
+"""
+     boundary_neumann!(y,u,bnode,ispec,ireg,val)
+
+Set Neumann boundary condition for species ispec at boundary ibc.
+"""
+boundary_neumann!(y, u, bnode::AbstractGeometryItem, ispec, ireg, val) = bnode.region == ireg ? y[ispec] -= val : nothing
+
+"""
+     boundary_neumann!(y,u,bnode, args...; kwargs...)
+Keyword argument version:
+- `species`: species number. Default: 1
+- `region`: boundary region number. By default, all boundary regions.
+- `value`: value
+"""
+function boundary_neumann!(y, u, bnode::AbstractGeometryItem, args...; species = 1, region = bnode.region, value = 0)
+    boundary_neumann!(y, u, bnode, species, region, value)
+end
+
+
+"""
+     boundary_robin!(y,u,bnode,ispec,ireg,fac,val)
+
+Set Robin boundary condition for species ispec at boundary ibc.
+"""
+boundary_robin!(y, u, bnode::AbstractGeometryItem, ispec, ireg, fac, val) = bnode.region == ireg ? y[ispec] += fac * u[ispec] - val : nothing
+
+"""
+     boundary_robin!(y,u,bnode, args...; kwargs...)
+Keyword argument version:
+- `species`: species number. Default: 1
+- `region`: boundary region number. By default, all boundary regions.
+- `factor`: factor
+- `value`: value
+"""
+function boundary_robin!(y, u, bnode::AbstractGeometryItem, args...; species = 1, region = bnode.region, factor = 0, value = 0)
+    boundary_robin!(y, u, bnode, species, region, factor, value)
+end

src/vfvm_system.jl

@@ -806,6 +806,7 @@ end
 
 """
       boundary_dirichlet!(system; kwargs...)
+
 Keyword argument version:
 - `species`: species number
 - `region`: region number
@@ -818,49 +819,6 @@ function boundary_dirichlet!(system::AbstractSystem; species = 1, region = 1, va
     boundary_dirichlet!(system, species, region, value)
 end
 
-"""
-     boundary_dirichlet!(y,u,bnode,ispec,ireg,val)
-
-Set Dirichlet boundary condition for species ispec at boundary ibc.
-"""
-function boundary_dirichlet!(y, u, bnode, ispec, ireg, val; penalty = bnode.Dirichlet)
-    if bnode.region == ireg
-        y[ispec] += penalty * (u[ispec] - val)
-        # just for call during initialization, so we can convert from dual number
-        bnode.dirichlet_value[ispec] = value(val)
-    end
-    nothing
-end
-
-"""
-     boundary_dirichlet!(y,u,bnode, args...; kwargs...)
-Keyword argument version:
-- `species`: species number. Default: 1
-- `region`: boundary region number. By default, all boundary regions.
-- `value`: value
-"""
-function boundary_dirichlet!(y, u, bnode, args...; species = 1, region = bnode.region, value = 0, penalty = bnode.Dirichlet)
-    boundary_dirichlet!(y, u, bnode, species, region, value; penalty)
-end
-
-"""
-       ramp(t; kwargs...)
-Ramp function for specifying time dependent boundary conditions
-
-Keyword arguments:
-- `dt`: Tuple: start and end time of ramp. Default: `(0,0.1)`
-- `du`: Tuple: values at start and end time. Default: `(0,0)`
-"""
-function ramp(t; dt = (0, 0.1), du = (0, 0))
-    (t, ubegin, uend, tbegin, tend) = promote(Float64(t), du[1], du[2], dt[1], dt[2])
-    if t < tbegin
-        return ubegin
-    elseif t < tend
-        return ubegin + (uend - ubegin) * (t - tbegin) / (tend - tbegin)
-    else
-        return uend
-    end
-end
 
 ##################################################################
 """
@@ -889,23 +847,6 @@ Keyword argument version:
 """
 boundary_neumann!(system::AbstractSystem; species = 0, region = 0, value = 0) = boundary_neumann!(system, species, region, value)
 
-"""
-     boundary_neumann!(y,u,bnode,ispec,ireg,val)
-
-Set Neumann boundary condition for species ispec at boundary ibc.
-"""
-boundary_neumann!(y, u, bnode, ispec, ireg, val) = bnode.region == ireg ? y[ispec] -= val : nothing
-
-"""
-     boundary_neumann!(y,u,bnode, args...; kwargs...)
-Keyword argument version:
-- `species`: species number. Default: 1
-- `region`: boundary region number. By default, all boundary regions.
-- `value`: value
-"""
-function boundary_neumann!(y, u, bnode, args...; species = 1, region = bnode.region, value = 0)
-    boundary_neumann!(y, u, bnode, species, region, value)
-end
 
 ##################################################################
 """
@@ -938,24 +879,6 @@ function boundary_robin!(system::AbstractSystem; species = 0, region = 0, factor
     boundary_robin!(system, species, region, factor, value)
 end
 
-"""
-     boundary_robin!(y,u,bnode,ispec,ireg,fac,val)
-
-Set Robin boundary condition for species ispec at boundary ibc.
-"""
-boundary_robin!(y, u, bnode, ispec, ireg, fac, val) = bnode.region == ireg ? y[ispec] += fac * u[ispec] - val : nothing
-
-"""
-     boundary_robin!(y,u,bnode, args...; kwargs...)
-Keyword argument version:
-- `species`: species number. Default: 1
-- `region`: boundary region number. By default, all boundary regions.
-- `factor`: factor
-- `value`: value
-"""
-function boundary_robin!(y, u, bnode, args...; species = 1, region = bnode.region, factor = 0, value = 0)
-    boundary_robin!(y, u, bnode, species, region, factor, value)
-end
 
 ##################################################################
 """