Primitive struct optimization (#66)

* Use Enum for FileTypes; dispatch on FileType values

* Work around derive type construction for BATS, reordering

* Reduce allocations for lowercase check

* Add type annotations

* Int32 -> Int64 parameters

* Add anisotropy benchmark

* Bump minor version

Project.toml

@@ -1,7 +1,7 @@
 name = "Batsrus"
 uuid = "e74ebddf-6ac1-4047-a0e5-c32c99e57753"
 authors = ["Hongyang Zhou <[email protected]>"]
-version = "0.6.9"
+version = "0.7.0"
 
 [deps]
 FortranFiles = "c58ffaec-ab22-586d-bfc5-781a99fd0b10"

benchmark/benchmarks.jl

@@ -9,8 +9,7 @@ println()
 
 directory = artifact"testdata"
 files = ("1d__raw_2_t25.60000_n00000258.out", "z=0_raw_1_t25.60000_n00000258.out",
-   "bx0_mhd_6_t00000100_n00000352.out")
-
+   "z=0_fluid_region0_0_t00001640_n00010142.out")
 
 const SUITE = BenchmarkGroup()
 
@@ -25,4 +24,4 @@ SUITE["read"]["Extract B"] = @benchmarkable Batsrus.getvar($bd, "B")
 SUITE["read"]["Binary structured"] = @benchmarkable load($file)
 
 file = joinpath(directory, files[3])
-SUITE["read"]["Binary unstructured"] = @benchmarkable load($file)
+SUITE["read"]["Anisotropy"] = @benchmarkable bd["Anisotropy1"]

docs/examples/visualization/demo_animate_2d.md

@@ -190,9 +190,8 @@ function get_vector(bd, var, plotrange, plotinterval)
    X, Y = eachslice(x, dims=3)
    X, Y = vec(X), vec(Y)
    varstream = split(var, ";")
-   wnames = lowercase.(bd.head.wnames)
-   var1_ = findfirst(x->x==lowercase(varstream[1]), wnames)
-   var2_ = findfirst(x->x==lowercase(varstream[2]), wnames)
+   var1_ = findfirst(x->lowercase(x)==lowercase(varstream[1]), bd.head.wnames)
+   var2_ = findfirst(x->lowercase(x)==lowercase(varstream[2]), bd.head.wnames)
    # Create grid values first.
    xi = range(Float64(plotrange[1]), stop=Float64(plotrange[2]), step=plotinterval)
    yi = range(Float64(plotrange[3]), stop=Float64(plotrange[4]), step=plotinterval)

docs/src/man/manual.md

@@ -71,10 +71,12 @@ Here is a full list of predefined derived quantities:
 | Bmag                  | Magnetic field magnitude         | Bx, By, Bz        |
 | Emag                  | Electric field magnitude         | Ex, Ey, Ez        |
 | Umag                  | Velocity magnitude               | Ux, Uy, Uz        |
+| Uemag                 | Electron Velocity magnitude      | UxS0, UyS0, UzS0  |
+| Uimag                 | Ion Velocity magnitude           | UxS1, UyS1, UzS1  |
 | B                     | Magnetic field vector            | Bx, By, Bz        |
 | E                     | Electric field vector            | Ex, Ey, Ez        |
 | U                     | Velocity vector                  | Ux, Uy, Uz        |
-| Anisotropy            | Pressure/Temperature anisotropy  | B, P tensor       |
+| Anisotropy[0-1]       | Pressure/Temperature anisotropy  | B, P tensor       |
 
 ## Output format conversion
 

examples/vdf.jl

@@ -587,9 +587,9 @@ function HF_velocity()
    y = data.x[:,:,:,2]
    z = data.x[:,:,:,3]
 
-   ux_ = findfirst(x->x=="uxs1", lowercase.(data.head.wnames))
-   uy_ = findfirst(x->x=="uys1", lowercase.(data.head.wnames))
-   uz_ = findfirst(x->x=="uzs1", lowercase.(data.head.wnames))
+   ux_ = findfirst(x->lowercase(x)=="uxs1", data.head.wnames)
+   uy_ = findfirst(x->lowercase(x)=="uys1", data.head.wnames)
+   uz_ = findfirst(x->lowercase(x)=="uzs1", data.head.wnames)
 
    Ux = @view data.w[:,:,:,ux_]
    Uy = @view data.w[:,:,:,uy_]

ext/BatsrusMakieExt/typerecipe.jl

@@ -1,7 +1,7 @@
 # Type conversion from Batsrus to Makie
 
 "Conversion for 1D plots"
-function Makie.convert_arguments(P::Makie.PointBased, bd::BATLData, var::String)
+function Makie.convert_arguments(P::Makie.PointBased, bd::BATS, var::String)
    var_ = findindex(bd, var)
    if hasunit(bd)
       unitx = getunit(bd, bd.head.variables[1])
@@ -17,7 +17,7 @@ function Makie.convert_arguments(P::Makie.PointBased, bd::BATLData, var::String)
 end
 
 "Conversion for 2D plots."
-function Makie.convert_arguments(P::Makie.GridBased, bd::BATLData, var::String;
+function Makie.convert_arguments(P::Makie.GridBased, bd::BATS, var::String;
    plotrange=[-Inf,Inf,-Inf,Inf], plotinterval=0.1)
    x, y, w = interp2d(bd, var, plotrange, plotinterval)
 

src/Batsrus.jl

@@ -10,54 +10,13 @@ using Interpolations: cubic_spline_interpolation, BSpline, Linear, scale, interp
 import NaturalNeighbours as NN
 using StaticArrays: SVector, @SMatrix, SA
 
-export BATLData,
+export BATS,
    load, readlogdata, readtecdata, showhead, # io
    getvar, cutdata, subvolume, subsurface, # select
    Batl, convertTECtoVTU, convertIDLtoVTK, readhead, readtree, getConnectivity, # vtk
    interp1d, interp2d, slice1d, get_var_range, squeeze, get_range # plot/utility
 
-"Type for the file information."
-struct FileList
-   "filename"
-   name::String
-   "file type"
-   type::Symbol
-   "directory"
-   dir::String
-   "file size"
-   bytes::Int
-   "number of snapshots"
-   npictinfiles::Int
-   "length of meta data"
-   lenhead::Int
-end
-
-struct BATLHead
-   ndim::Int32
-   headline::SubString{String}
-   it::Int32
-   time::Float32
-   gencoord::Bool
-   neqpar::Int32
-   nw::Int32
-   nx::Vector{Int32}
-   eqpar::Vector{Float32}
-   variables::Vector{SubString{String}}
-   wnames::Vector{SubString{String}}
-end
-
-"Primary Batsrus data storage type."
-struct BATLData{dim, T<:AbstractFloat, U}
-   "header information"
-   head::BATLHead
-   "grid"
-   x::U
-   "variables"
-   w::U
-   "file information"
-   list::FileList
-end
-
+include("type.jl")
 include("unit/UnitfulBatsrus.jl")
 using .UnitfulBatsrus