Merge pull request #376 from gridap/release-0.14

Major refactoring associated with the skeleton and multi-field

Author: fverdugo

.travis.yml

@@ -9,8 +9,8 @@ language: julia
 os:
   - linux
 julia:
-  - 1.0
-  - 1.4
+  - 1.3
+  - 1.5
 notifications:
   email:
     on_success: never

NEWS.md

@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 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).
 
+## [0.14.0] - Unreleased
+
+### Changed
+ - Table struct has been generalized such that data and ptrs arrays can be of an arbitrary type extending AbstractArray. Since PR [#310](https://github.com/gridap/Gridap.jl/pull/310/)
+ - `interpolate, interpolate!, interpolate_dirichlet...` switched argument order to function first style. For instance `interpolate(u, V)` instead of `interpolate(V, u)`
 
 ## [0.13.4] - 2020-08-23
 
@@ -69,13 +74,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Possibility to have 0 order in `DISC` directions of a `CDLagrangianRefFE`. Since PR [#308](https://github.com/gridap/Gridap.jl/pull/308).
   - Added setindex! method for Reindexed. Since PR [#309](https://github.com/gridap/Gridap.jl/pull/309).
 
+
 ### Changed
 
   - Changed the interfaces of `ReferenceFE` and `NodalReferenceFE` in relation of DOF ownership. Now function `get_face_own_dofs` and related ones are parametrized by a `Conformity` object. Since PR [#311](https://github.com/gridap/Gridap.jl/pull/311).
   - The constructors `GenericRefFE`, `GenericNodalCartesianRefFE`, and `compute_conforming_cell_dofs` take an extra argument of type `Conformity`. Since PR [#311](https://github.com/gridap/Gridap.jl/pull/311).
   - Renamed `PDiscRefFE` -> `DiscRefFE` struct keeping the name for constructor. Since PR [#293](https://github.com/gridap/Gridap.jl/pull/293).
   - One of the `GradConformingFESpace` methods now more general `ConformingFESpace`. Since PR [#293](https://github.com/gridap/Gridap.jl/pull/293).
   - `DivConformingFESpace` and `CurlConformingFESpace` constructors eliminated. Since PR [#293](https://github.com/gridap/Gridap.jl/pull/293).
+  - Extend table to support arbitrary vector types. Since PR [#310](https://github.com/gridap/Gridap.jl/pull/310).
 
 ### Fixed
 

Project.toml

@@ -1,11 +1,12 @@
 name = "Gridap"
 uuid = "56d4f2e9-7ea1-5844-9cf6-b9c51ca7ce8e"
 authors = ["Santiago Badia <santiago.badia@monash.edu>", "Francesc Verdugo <fverdugo@cimne.upc.edu>"]
-version = "0.13.4"
+version = "0.14.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
+BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
@@ -26,6 +27,7 @@ WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 [compat]
 AbstractTrees = "0.3.3"
 BSON = "0.2.5"
+BlockArrays = "0.12.12"
 Combinatorics = "1.0.0"
 DocStringExtensions = "0.8.1"
 FastGaussQuadrature = "0.4.2"
@@ -39,7 +41,7 @@ NLsolve = "4.3.0"
 QuadGK = "2.3.1"
 StaticArrays = "0.12.1"
 WriteVTK = "1.7"
-julia = "1.0"
+julia = "1.3"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

bench/FieldsBenchs/FieldApplyBenchs.jl

@@ -18,13 +18,13 @@ function bench1(n)
   v = 3.0
   d = 2
   f = MockField{d}(v)
-  g = apply_kernel_to_field(bcast(+),f,v)
+  g = operate_fields(+,f,v)
   cg = field_cache(g,x)
   @time repeat(n,evaluate!,cg,g,x)
   ∇g = gradient(g)
   ∇cg = field_cache(∇g,x)
   @time repeat(n,evaluate!,∇cg,∇g,x)
-  h = apply_kernel_to_field(bcast(+),f,f)
+  h = operate_fields(+,f,f)
   ch = field_cache(h,x)
   @time repeat(n,evaluate!,ch,h,x)
 end

bench/FieldsBenchs/FieldArraysBenchs.jl

@@ -33,7 +33,7 @@ function bench1(n)
   afx = evaluate(af,ax)
   cafx = array_cache(afx)
   @time loop(afx,cafx)
-  ag = apply_to_field_array(bcast(+),af,af)
+  ag = operate_arrays_of_fields(+,af,af)
   cag = array_cache(ag)
   @time loop(ag,cag)
   agx = evaluate(ag,ax)
@@ -58,7 +58,7 @@ function bench2(n)
   afx = evaluate(af,ax)
   cafx = array_cache(afx)
   @time loop(afx,cafx)
-  _ag = apply_to_field_array(bcast(+),af,af)
+  _ag = operate_arrays_of_fields(+,af,af)
   ag = gradient(_ag)
   cag = array_cache(ag)
   @time loop(ag,cag)
@@ -85,7 +85,7 @@ function bench2a(n)
   afx = evaluate(af,ax)
   cafx = array_cache(afx)
   @time loop(afx,cafx)
-  _ag = apply_to_field_array(bcast(+),af,av)
+  _ag = operate_arrays_of_fields(+,af,av)
   ag = gradient(_ag)
   cag = array_cache(ag)
   @time loop(ag,cag)
@@ -115,7 +115,7 @@ function bench3(n)
   afx = evaluate(af,ax)
   cafx = array_cache(afx)
   @time loop(afx,cafx)
-  ag = apply_to_field_array(bcast(+),af,aw)
+  ag = operate_arrays_of_fields(+,af,aw)
   cag = array_cache(ag)
   @time loop(ag,cag)
   agx = evaluate(ag,ax)

bench/FieldsBenchs/FieldOperationsBenchs.jl

@@ -37,20 +37,20 @@ function bench1(n)
   aba = Fill(ba,l)
   abb = Fill(bb,l)
 
-  ag_ff = field_array_operation(inner,afa,afb)
+  ag_ff = operate_arrays_of_fields(inner,afa,afb)
   agx_ff = evaluate(ag_ff,ax)
   cagx_ff = array_cache(agx_ff)
   @time loop(agx_ff,cagx_ff)
 
-  ag_bf = field_array_operation(inner,aba,afb)
+  ag_bf = operate_arrays_of_fields(inner,aba,afb)
   agx_bf = evaluate(ag_bf,ax)
   cagx_bf = array_cache(agx_bf)
   @time loop(agx_bf,cagx_bf)
 
-  ag_bb = field_array_operation(inner,aba,abb)
-  agx_bb = evaluate(ag_bb,ax)
-  cagx_bb = array_cache(agx_bb)
-  @time loop(agx_bb,cagx_bb)
+  #ag_bb = operate_arrays_of_fields(inner,aba,abb)
+  #agx_bb = evaluate(ag_bb,ax)
+  #cagx_bb = array_cache(agx_bb)
+  #@time loop(agx_bb,cagx_bb)
 
 end
 

bench/FieldsBenchs/IntegrateBenchs.jl

@@ -79,13 +79,13 @@ function bench3(n)
   ar = Fill(r,l)
   ab = attachmap(ar,aϕ)
 
-  fmass = field_array_operation(inner,ab,ab)
+  fmass = operate_arrays_of_fields(inner,ab,ab)
   mmass = integrate(fmass,ax,aw,aj)
 
   cmmass = array_cache(mmass)
   @time loop(mmass,cmmass)
 
-  fstif = field_array_operation(inner,∇(ab),∇(ab))
+  fstif = operate_arrays_of_fields(inner,∇(ab),∇(ab))
   mstif = integrate(fstif,ax,aw,aj)
 
   cmstif = array_cache(mstif)

docs/src/Geometry.md

@@ -340,19 +340,6 @@ RestrictedDiscreteModel
 
 ## CellFields
 
-### CellFieldLike interface
-```@docs
-CellFieldLike
-get_array(cf::CellFieldLike)
-get_cell_map(cf::CellFieldLike)
-similar_object(cf::CellFieldLike,array::AbstractArray)
-similar_object(cf1::CellFieldLike,cf2::CellFieldLike,array::AbstractArray)
-gradient(cf::CellFieldLike)
-grad2curl(cf::CellFieldLike)
-test_cell_field_like
-evaluate(cf::CellFieldLike,x)
-length(cf::CellFieldLike)
-```
 ### CellField interface
 
 ```@docs

src/Algebra/LinearSolvers.jl

@@ -11,10 +11,18 @@ struct AffineOperator{A<:AbstractMatrix,B<:AbstractVector} <: NonlinearOperator
 end
 
 """
+    get_matrix(operator)
+
+Return the matrix corresponding to the assembled left hand side of the operator.
+This matrix incorporates all boundary conditions and constraints.
 """
 get_matrix(op::AffineOperator) = op.matrix
 
 """
+    get_vector(operator)
+
+Return the vector corresponding to the assembled right hand side of the operator.
+This vector includes all boundary conditions and constraints.
 """
 get_vector(op::AffineOperator) = op.vector
 

src/Arrays/Arrays.jl

@@ -12,13 +12,28 @@ module Arrays
 
 using Gridap.Helpers
 using Gridap.Inference
+using Gridap.Algebra
 
 using DocStringExtensions
 using Test
 using FillArrays
 using Base: @propagate_inbounds
 using LinearAlgebra
 using ForwardDiff
+using BlockArrays
+
+export BlockArrayCoo
+export BlockVectorCoo
+export BlockMatrixCoo
+export is_zero_block
+export is_nonzero_block
+export enumerateblocks
+export eachblockindex
+export VectorOfBlockArrayCoo
+export VectorOfBlockVectorCoo
+export VectorOfBlockMatrixCoo
+export zeros_like
+export TwoLevelBlockedUnitRange
 
 export array_cache
 export getindex!
@@ -37,6 +52,7 @@ export CachedArray
 export CachedMatrix
 export CachedVector
 export setsize!
+export setaxes!
 
 export CompressedArray
 export LocalToGlobalArray
@@ -52,6 +68,8 @@ export test_kernel
 export bcast
 export elem
 export contract
+export MulKernel
+export MulAddKernel
 export kernel_return_type
 export kernel_return_types
 export kernel_testitem
@@ -103,8 +121,12 @@ import Base: IndexStyle
 import Gridap.Io: to_dict
 import Gridap.Io: from_dict
 
+import Gridap.Algebra: scale_entries!
+
 include("Interface.jl")
 
+include("BlockArraysCoo.jl")
+
 include("CachedArrays.jl")
 
 include("Kernels.jl")
@@ -131,6 +153,8 @@ include("ArrayPairs.jl")
 
 include("AppendedArrays.jl")
 
+include("VectorsOfBlockArrayCoo.jl")
+
 include("Autodiff.jl")
 
 end # module