Merge branch 'main' into threaded-macro-gpu

.zenodo.json

@@ -20,7 +20,7 @@
             "orcid": "0000-0001-6083-7038"
         },
         {
-            "affiliation": "Applied and Computational Mathematics, RWTH Aachen University, Germany",
+            "affiliation": "High-Performance Scientific Computing, University of Augsburg, Germany",
             "name": "Schlottke-Lakemper, Michael",
             "orcid": "0000-0002-3195-2536"
         },

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to
-[Michael Schlottke-Lakemper](mailto:m.schlottke-lakemper@acom.rwth-aachen.de),
+[Michael Schlottke-Lakemper](mailto:michael.schlottke-lakemper@uni-a.de),
 [Sven Berger](mailto:[email protected]),
 or any other of the principal developers responsible for enforcement listed in
 [AUTHORS.md](AUTHORS.md).
@@ -128,4 +128,4 @@ enforcement ladder](https://github.com/mozilla/diversity).
 
 For answers to common questions about this code of conduct, see the FAQ at
 https://www.contributor-covenant.org/faq. Translations are available at
-https://www.contributor-covenant.org/translations.
+https://www.contributor-covenant.org/translations.

Project.toml

@@ -45,6 +45,6 @@ SciMLBase = "1, 2"
 StaticArrays = "1"
 StrideArrays = "0.1"
 TimerOutputs = "0.5"
-TrixiBase = "0.1"
+TrixiBase = "0.1.3"
 WriteVTK = "1"
 julia = "1.9"

README.md

@@ -129,7 +129,7 @@ with the help of TrixiParticles.jl, please cite it as
 ## Authors
 Erik Faulhaber (University of Cologne) and Niklas Neher (HLRS) implemented the foundations
 for TrixiParticles.jl and are principal developers along with Sven Berger (hereon).
-The project was started by Michael Schlottke-Lakemper (RWTH Aachen University/HLRS)
+The project was started by Michael Schlottke-Lakemper (University of Augsburg)
 and Gregor Gassner (University of Cologne), who provide scientific direction and technical advice.
 The full list of contributors can be found in [AUTHORS.md](AUTHORS.md).
 

examples/n_body/n_body_benchmark_trixi.jl

@@ -108,7 +108,7 @@ end
 filename = tempname()
 open(filename, "w") do f
     redirect_stderr(f) do
-        TrixiParticles.TimerOutputs.disable_debug_timings(TrixiParticles)
+        TrixiParticles.disable_debug_timings()
     end
 end
 
@@ -124,6 +124,6 @@ end
 # Enable timers again
 open(filename, "w") do f
     redirect_stderr(f) do
-        TrixiParticles.TimerOutputs.enable_debug_timings(TrixiParticles)
+        TrixiParticles.enable_debug_timings()
     end
 end

examples/n_body/n_body_solar_system.jl

@@ -49,7 +49,7 @@ callbacks = CallbackSet(info_callback, saving_callback)
 filename = tempname()
 open(filename, "w") do f
     redirect_stderr(f) do
-        TrixiParticles.TimerOutputs.disable_debug_timings(TrixiParticles)
+        TrixiParticles.disable_debug_timings()
     end
 end
 
@@ -63,6 +63,6 @@ sol = solve(ode, SymplecticEuler(),
 # Enable timers again
 open(filename, "w") do f
     redirect_stderr(f) do
-        TrixiParticles.TimerOutputs.enable_debug_timings(TrixiParticles)
+        TrixiParticles.enable_debug_timings()
     end
 end

examples/postprocessing/interpolation_plane.jl

@@ -96,3 +96,25 @@ plot_3d = Plots.plot(scatter_3d, xlabel="X", ylabel="Y", zlabel="Z",
 
 combined_plot = Plots.plot(plot1, plot2, plot3, plot_3d, layout=(2, 2),
                            size=(1000, 1500), margin=3mm)
+
+# If we want to save planes at regular intervals, we can use the postprocessing callback.
+function save_interpolated_plane(v, u, t, system)
+    # Size of the patch to be interpolated
+    interpolation_start = [0.0, 0.0]
+    interpolation_end = [tank_size[1], tank_size[2]]
+
+    # The resolution the plane is interpolated to. In this case twice the original resolution.
+    resolution = 0.5 * fluid_particle_spacing
+
+    file_id = ceil(Int, t * 10000)
+    interpolate_plane_2d_vtk(interpolation_start, interpolation_end, resolution,
+                             semi, system, v, u, filename="plane_$file_id.vti")
+    return nothing
+end
+
+save_interpolation_cb = PostprocessCallback(; dt=0.1, write_file_interval=0,
+                                            save_interpolated_plane)
+
+trixi_include(@__MODULE__,
+              joinpath(examples_dir(), "fluid", "dam_break_2d.jl"), tspan=(0.0, 0.2),
+              extra_callback=save_interpolation_cb, fluid_particle_spacing=0.01)

src/TrixiParticles.jl

@@ -23,7 +23,8 @@ using SciMLBase: CallbackSet, DiscreteCallback, DynamicalODEProblem, u_modified!
 using StaticArrays: @SMatrix, SMatrix, setindex
 using StrideArrays: PtrArray, StaticInt
 using TimerOutputs: TimerOutput, TimerOutputs, print_timer, reset_timer!
-using TrixiBase: trixi_include
+using TrixiBase: trixi_include, @trixi_timeit, timer, timeit_debug_enabled,
+                 disable_debug_timings, enable_debug_timings
 @reexport using PointNeighbors: TrivialNeighborhoodSearch, GridNeighborhoodSearch
 using PointNeighbors: PointNeighbors, for_particle_neighbor
 using WriteVTK: vtk_grid, MeshCell, VTKCellTypes, paraview_collection, vtk_save

src/callbacks/post_process.jl

@@ -73,6 +73,7 @@ struct PostprocessCallback{I, F}
     append_timestamp    :: Bool
     write_csv           :: Bool
     write_json          :: Bool
+    git_hash            :: Ref{String}
 end
 
 function PostprocessCallback(; interval::Integer=0, dt=0.0, exclude_boundary=true,
@@ -94,7 +95,8 @@ function PostprocessCallback(; interval::Integer=0, dt=0.0, exclude_boundary=tru
     post_callback = PostprocessCallback(interval, write_file_interval,
                                         Dict{String, Vector{Any}}(), Float64[],
                                         exclude_boundary, funcs, filename, output_directory,
-                                        append_timestamp, write_csv, write_json)
+                                        append_timestamp, write_csv, write_json,
+                                        Ref("UnknownVersion"))
     if dt > 0
         # Add a `tstop` every `dt`, and save the final solution
         return PeriodicCallback(post_callback, dt,
@@ -209,9 +211,12 @@ function initialize_postprocess_callback!(cb, u, t, integrator)
 end
 
 function initialize_postprocess_callback!(cb::PostprocessCallback, u, t, integrator)
+    cb.git_hash[] = compute_git_hash()
+
     # Apply the callback
     cb(integrator)
-    return nothing
+
+    return cb
 end
 
 # `condition` with interval
@@ -281,7 +286,7 @@ function write_postprocess_callback(pp::PostprocessCallback)
     mkpath(pp.output_directory)
 
     data = Dict{String, Any}()
-    write_meta_data!(data)
+    write_meta_data!(data, pp.git_hash[])
     prepare_series_data!(data, pp)
 
     time_stamp = ""
@@ -331,9 +336,9 @@ function create_series_dict(values, times, system_name="")
                 "time" => times)
 end
 
-function write_meta_data!(data)
+function write_meta_data!(data, git_hash)
     meta_data = Dict("solver_name" => "TrixiParticles.jl",
-                     "solver_version" => get_git_hash(),
+                     "solver_version" => git_hash,
                      "julia_version" => string(VERSION))
 
     data["meta"] = meta_data

src/callbacks/solution_saving.jl

@@ -77,6 +77,7 @@ mutable struct SolutionSavingCallback{I, CQ}
     max_coordinates       :: Float64
     custom_quantities     :: CQ
     latest_saved_iter     :: Int
+    git_hash              :: Ref{String}
 end
 
 function SolutionSavingCallback(; interval::Integer=0, dt=0.0,
@@ -102,7 +103,7 @@ function SolutionSavingCallback(; interval::Integer=0, dt=0.0,
                                                save_initial_solution, save_final_solution,
                                                write_meta_data, verbose, output_directory,
                                                prefix, max_coordinates, custom_quantities,
-                                               -1)
+                                               -1, Ref("UnknownVersion"))
 
     if length(save_times) > 0
         # See the large comment below for an explanation why we use `finalize` here
@@ -131,6 +132,7 @@ end
 function initialize_save_cb!(solution_callback::SolutionSavingCallback, u, t, integrator)
     # Reset `latest_saved_iter`
     solution_callback.latest_saved_iter = -1
+    solution_callback.git_hash[] = compute_git_hash()
 
     # Save initial solution
     if solution_callback.save_initial_solution
@@ -156,7 +158,7 @@ end
 
 # `affect!`
 function (solution_callback::SolutionSavingCallback)(integrator)
-    (; interval, output_directory, custom_quantities, write_meta_data,
+    (; interval, output_directory, custom_quantities, write_meta_data, git_hash,
     verbose, prefix, latest_saved_iter, max_coordinates) = solution_callback
 
     vu_ode = integrator.u
@@ -178,12 +180,10 @@ function (solution_callback::SolutionSavingCallback)(integrator)
         println("Writing solution to $output_directory at t = $(integrator.t)")
     end
 
-    @trixi_timeit timer() "save solution" trixi2vtk(vu_ode, semi, integrator.t; iter=iter,
-                                                    output_directory=output_directory,
-                                                    prefix=prefix,
-                                                    write_meta_data=write_meta_data,
-                                                    max_coordinates=max_coordinates,
-                                                    custom_quantities...)
+    @trixi_timeit timer() "save solution" trixi2vtk(vu_ode, semi, integrator.t;
+                                                    iter, output_directory, prefix,
+                                                    write_meta_data, git_hash=git_hash[],
+                                                    max_coordinates, custom_quantities...)
 
     # Tell OrdinaryDiffEq that `u` has not been modified
     u_modified!(integrator, false)

src/general/general.jl

@@ -6,6 +6,5 @@ include("corrections.jl")
 include("smoothing_kernels.jl")
 include("initial_condition.jl")
 include("interpolation.jl")
-include("file_system.jl")
 include("custom_quantities.jl")
 include("neighborhood_search.jl")

src/util.jl

@@ -26,48 +26,6 @@ function print_startup_message()
     println(s)
 end
 
-# Enable debug timings `@trixi_timeit timer() "name" stuff...`.
-# This allows us to disable timings completely by executing
-# `TimerOutputs.disable_debug_timings(TrixiParticles)`
-# and to enable them again by executing
-# `TimerOutputs.enable_debug_timings(TrixiParticles)`
-timeit_debug_enabled() = true
-
-# Store main timer for global timing of functions
-const main_timer = TimerOutput()
-
-# Always call timer() to hide implementation details
-timer() = main_timer
-
-#     @trixi_timeit timer() "some label" expression
-#
-# Basically the same as a special case of `@timeit_debug` from
-# [TimerOutputs.jl](https://github.com/KristofferC/TimerOutputs.jl),
-# but without `try ... finally ... end` block. Thus, it's not exception-safe,
-# but it also avoids some related performance problems. Since we do not use
-# exception handling in TrixiParticles, that's not really an issue.
-#
-# Copied from [Trixi.jl](https://github.com/trixi-framework/Trixi.jl).
-macro trixi_timeit(timer_output, label, expr)
-    timeit_block = quote
-        if timeit_debug_enabled()
-            local to = $(esc(timer_output))
-            local enabled = to.enabled
-            if enabled
-                local accumulated_data = $(TimerOutputs.push!)(to, $(esc(label)))
-            end
-            local b0 = $(TimerOutputs.gc_bytes)()
-            local t0 = $(TimerOutputs.time_ns)()
-        end
-        local val = $(esc(expr))
-        if timeit_debug_enabled() && enabled
-            $(TimerOutputs.do_accumulate!)(accumulated_data, t0, b0)
-            $(TimerOutputs.pop!)(to)
-        end
-        val
-    end
-end
-
 """
     @threaded system for ... end
 
@@ -223,3 +181,21 @@ end
 function type2string(type)
     return string(nameof(typeof(type)))
 end
+
+function compute_git_hash()
+    pkg_directory = pkgdir(@__MODULE__)
+    git_directory = joinpath(pkg_directory, ".git")
+
+    # Check if the .git directory exists
+    if !isdir(git_directory)
+        return "UnknownVersion"
+    end
+
+    try
+        git_cmd = Cmd(`git describe --tags --always --first-parent --dirty`,
+                      dir=pkg_directory)
+        return string(readchomp(git_cmd))
+    catch e
+        return "UnknownVersion"
+    end
+end