fixed some things in the documentation

WIAS-PDELib · Aug 29, 2024 · 945f0d4 · 945f0d4 · chmerdon · Aug 30, 2024
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diff --git a/docs/make.jl b/docs/make.jl
@@ -43,11 +43,11 @@ function make_all(; with_examples::Bool = true)
         modules=[ExtendableFEMBase],
         sitename="ExtendableFEMBase.jl",
         authors="Christian Merdon",
-        repo = "github.com/chmerdon/ExtendableFEMBase.jl",
-        clean = false,
-        format = Documenter.HTML(size_threshold = 250000),
+        repo = "https://github.com/chmerdon/ExtendableFEMBase.jl",
+        clean = true,
+        format = Documenter.HTML(size_threshold = 250000, mathengine = MathJax3()),
         checkdocs = :all,
-        warnonly = true,
+        warnonly = false,
         doctest = true,
         pages = [
             "Home" => "index.md",
@@ -76,7 +76,7 @@ function make_all(; with_examples::Bool = true)
 
 end
 
-make_all(; with_examples = true)
+make_all(; with_examples = false)
 
 deploydocs(
     repo = "github.com/chmerdon/ExtendableFEMBase.jl",

diff --git a/docs/src/functionoperators.md b/docs/src/functionoperators.md
@@ -36,6 +36,13 @@ used to dispatch different evaluations of finite element basis functions.
     can be build from the ones available (e.g. the deviator).
 
 
+```@autodocs
+Modules = [ExtendableFEMBase]
+Pages = ["functionoperators.jl"]
+Order   = [:type, :function]
+```
+
+
 ## ReconstructionOperators
 
 There are special operators that allow to evaluate a primitive operator of some discrete
@@ -59,9 +66,4 @@ as well as for the P2-bubble (H1P2B) finite element type in two dimensions.
 
 ## Operator Pairs (experimental)
 
-Two function operators can be put into an OperatorPair so that one can provide effectively two operators in each argument of an assembly pattern. However, the user should make sure that both operators can be evaluated together reasonably (meaning both should be well-defined on the element geometries and the finite element space where the argument will be evaluated, and the action of the operator has to operate with coressponding input and result fields). This feature is still experimental and might have issues in some cases. OperatorTriple for a combination of three operators is also available.
-
-```@docs
-OperatorPair
-OperatorTriple
-```
+Two function operators can be put into an OperatorPair so that one can provide effectively two operators in each argument of an assembly pattern. However, the user should make sure that both operators can be evaluated together reasonably (meaning both should be well-defined on the element geometries and the finite element space where the argument will be evaluated, and the action of the operator has to operate with coressponding input and result fields). This feature is still experimental and might have issues in some cases. OperatorTriple for a combination of three operators is also available.
diff --git a/docs/src/interpolations.md b/docs/src/interpolations.md
@@ -39,6 +39,7 @@ Usually, Plotters need nodal values, so there is a gengeric function that evalua
 nodevalues!
 nodevalues
 nodevalues_view
+nodevalues_subset!
 ```
 
 ## Lazy Interpolation
@@ -48,4 +49,14 @@ works in all cases (but is not very efficient as it involves a PointeEvaluator a
 
 ```@docs
 lazy_interpolate!
-```
+```
+
+
+## Displace Mesh
+
+Nodal values (e.g. of a FEVector that discretizes a displacement) can be used to displace the mesh.
+
+```@docs
+displace_mesh!
+displace_mesh
+```
diff --git a/docs/src/quadrature.md b/docs/src/quadrature.md
@@ -12,4 +12,13 @@ Quadrature rules consist of points (coordinates of evaluation points with respec
 Modules = [ExtendableFEMBase]
 Pages = ["quadrature.jl"]
 Order   = [:type, :function]
+```
+
+
+#### Accumulating Vector (not relevant for users, but for completeness)
+
+Internally a global integration uses an accumulating vector and calls the cell-wise integration.
+
+```@docs
+AccumulatingVector
 ```
diff --git a/src/accumvector.jl b/src/accumvector.jl
@@ -1,21 +1,21 @@
 ###########################
 ### ACCUMULATING VECTOR ###
 ###########################
-#
-# used to store coefficients for FESpaces and can have several blocks of different FESpaces
-# acts like an AbstractArray{T,1}
 
 """
 $(TYPEDEF)
 
-block of an FEVector that carries coefficients for an associated FESpace and can be assigned as an AbstractArray (getindex, setindex, size, length)
+vector that is acting as an AbstractArray{T, 2} and 
+automatically accumulates all values from the second dimension
+
+AV[k,j] += s for any j results in AV.entries[k] += s
 """
 struct AccumulatingVector{T} <: AbstractArray{T, 2}
 	entries::Array{T, 1}
 	size2::Int
 end
 
-# AV[k,j] += s for any j results in entries[k] += s
+# 
 
 # overload stuff for AbstractArray{T,2} behaviour
 Base.getindex(AV::AccumulatingVector, i::Int, j) = AV.entries[i]

diff --git a/src/finiteelements.jl b/src/finiteelements.jl
@@ -8,6 +8,11 @@
 #######################################################################################################
 #######################################################################################################
 
+"""
+$(TYPEDEF)
+
+root type for finite element types
+"""
 abstract type AbstractFiniteElement end
 
 

diff --git a/src/interpolations.jl b/src/interpolations.jl
@@ -384,8 +384,8 @@ function nodevalues_subset!(
 Evaluates the finite element function with the coefficient vector source (interpreted as a coefficient vector for the FESpace FE)
 and the specified FunctionOperator at the specified list of nodes of the grid and writes the values in that order into target.
 Node values for nodes that are not part of the specified regions (default = all regions) are set to zero.
-Discontinuous (continuous = false) quantities are evaluated in all neighbouring cells of each node and then averaged. Continuous
-(continuous = true) quantities are only evaluated once at each node.
+Discontinuous (continuous = false) quantities are evaluated in all neighbouring cells (in the specified regions)
+of each node and then averaged. Continuous (continuous = true) quantities are only evaluated once at each node.
 """
 function nodevalues_subset!(target::AbstractArray{T, 2},
 	source::AbstractArray{T, 1},
@@ -1057,6 +1057,13 @@ function displace_mesh!(xgrid::ExtendableGrid, source::FEVectorBlock; magnify =
 end
 
 
+"""
+````
+function displace_mesh(xgrid::ExtendableGrid, source::FEVectorBlock; magnify = 1)
+````
+Returns a new grid by adding the displacement field in source (expects a vector-valued finite element)
+to the coordinates of the provided xgrid times a magnify value.
+"""
 function displace_mesh(xgrid::ExtendableGrid, source::FEVectorBlock; kwargs...)
 	xgrid_displaced = deepcopy(xgrid)
 	displace_mesh!(xgrid_displaced, source; kwargs...)