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Implement EllipsisNotation where useful #189

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merged 5 commits into from
Sep 21, 2020
Merged

Implement EllipsisNotation where useful #189

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ba01871
Implement EllipsisNotation where useful
efaulhaber Sep 19, 2020
7eadd5c
Fix ba01871
efaulhaber Sep 19, 2020
611b956
Check for AbstractHyperbolicDiffusionEquations
efaulhaber Sep 20, 2020
9c6047b
Hide not more than 3 dimensions in the EllipsisNotation
efaulhaber Sep 20, 2020
1d4a5ae
Use EllipsisNotation only for DG nodes
efaulhaber Sep 21, 2020
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1 change: 1 addition & 0 deletions Project.toml
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Expand Up @@ -4,6 +4,7 @@ authors = ["Michael Schlottke-Lakemper <mschlott@math.uni-koeln.de>", "Gregor Ga
version = "0.2.5-pre"

[deps]
EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
LinearMaps = "7a12625a-238d-50fd-b39a-03d52299707e"
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1 change: 1 addition & 0 deletions src/Trixi.jl
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Expand Up @@ -20,6 +20,7 @@ using Printf: @printf, @sprintf, println
using Profile: clear_malloc_data
using Random: seed!

using EllipsisNotation
using HDF5: h5open, attrs
using StaticArrays: @MVector, @SVector, MVector, MMatrix, MArray, SVector, SMatrix, SArray
using TimerOutputs: @notimeit, @timeit, TimerOutput, print_timer, reset_timer!
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24 changes: 3 additions & 21 deletions src/io/io.jl
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Expand Up @@ -38,13 +38,7 @@ function load_restart_file!(dg::AbstractDg, restart_filename)

# Read variable
println("Reading variables_$v ($name)...")
if ndims(dg) == 2
dg.elements.u[v, :, :, :] = read(file["variables_$v"])
elseif ndims(dg) == 3
dg.elements.u[v, :, :, :, :] = read(file["variables_$v"])
else
error("Unsupported number of spatial dimensions: ", ndims(dg))
end
dg.elements.u[v, .., :] = read(file["variables_$v"])
end
end

Expand Down Expand Up @@ -88,13 +82,7 @@ function save_restart_file(dg::AbstractDg, mesh::TreeMesh, time, dt, timestep)
# Store each variable of the solution
for v in 1:nvariables(dg)
# Convert to 1D array
if ndims(dg) == 2
file["variables_$v"] = vec(data[v, :, :, :])
elseif ndims(dg) == 3
file["variables_$v"] = vec(data[v, :, :, :, :])
else
error("Unsupported number of spatial dimensions: ", ndims(dg))
end
file["variables_$v"] = vec(data[v, .., :])

# Add variable name as attribute
var = file["variables_$v"]
Expand Down Expand Up @@ -168,13 +156,7 @@ function save_solution_file(dg::AbstractDg, mesh::TreeMesh, time, dt, timestep,
# Store each variable of the solution
for v in 1:nvariables(dg)
# Convert to 1D array
if ndims(dg) == 2
file["variables_$v"] = vec(data[v, :, :, :])
elseif ndims(dg) == 3
file["variables_$v"] = vec(data[v, :, :, :, :])
else
error("Unsupported number of spatial dimensions: ", ndims(dg))
end
file["variables_$v"] = vec(data[v, .., :])

# Add variable name as attribute
var = file["variables_$v"]
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16 changes: 3 additions & 13 deletions src/run.jl
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Expand Up @@ -309,18 +309,8 @@ function run_simulation(mesh, solver, time_parameters, time_integration_function
end

# Check steady-state integration residual
if solver.equations isa HyperbolicDiffusionEquations2D
if maximum(abs, view(solver.elements.u_t, 1, :, :, :)) <= solver.equations.resid_tol
println()
println("-"^80)
println(" Steady state tolerance of ",solver.equations.resid_tol," reached at time ",time)
println("-"^80)
println()
finalstep = true
end
end
if solver.equations isa HyperbolicDiffusionEquations3D
if maximum(abs, view(solver.elements.u_t, 1, :, :, :, :)) <= solver.equations.resid_tol
if solver.equations isa AbstractHyperbolicDiffusionEquations
if maximum(abs, view(solver.elements.u_t, 1, .., :)) <= solver.equations.resid_tol
println()
println("-"^80)
println(" Steady state tolerance of ",solver.equations.resid_tol," reached at time ",time)
Expand Down Expand Up @@ -592,7 +582,7 @@ function compute_jacobian_dg(parameters_file; verbose=false, parameters...)
res_m = vec(dg.elements.u_t) |> copy
# restore linearisation state
dg.elements.u[idx] = u0[idx]
# central second order finite difference
# central second order finite difference
J[:,idx] = (res_p - res_m) / (2 * epsilon)
end

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28 changes: 6 additions & 22 deletions src/timedisc/timedisc_euler_gravity.jl
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Expand Up @@ -101,18 +101,10 @@ function update_gravity!(solver, u_euler, gravity_parameters)
end

# this is an absolute tolerance check
if ndims(solver) == 2
if maximum(abs, @views solver.elements.u_t[1, :, :, :]) <= solver.equations.resid_tol
# println(" Gravity solution tolerance ", solver.equations.resid_tol,
# " reached in iterations ",iteration)
finalstep = true
end
else
if maximum(abs, @views solver.elements.u_t[1, :, :, :, :]) <= solver.equations.resid_tol
# println(" Gravity solution tolerance ", solver.equations.resid_tol,
# " reached in iterations ",iteration)
finalstep = true
end
if maximum(abs, @views solver.elements.u_t[1, .., :]) <= solver.equations.resid_tol
# println(" Gravity solution tolerance ", solver.equations.resid_tol,
# " reached in iterations ",iteration)
finalstep = true
end
end

Expand All @@ -134,11 +126,7 @@ function timestep_gravity_2N!(solver::AbstractSolver, t, dt, u_euler, gravity_pa

# put in gravity source term proportional to Euler density
# OBS! subtract off the background density ρ_0 (spatial mean value)
if ndims(solver) == 2
@views @. solver.elements.u_t[1,:,:,:] += grav_scale*(u_euler[1,:,:,:] - rho0)
else
@views @. solver.elements.u_t[1,:,:,:,:] += grav_scale*(u_euler[1,:,:,:,:] - rho0)
end
@views @. solver.elements.u_t[1, .., :] += grav_scale * (u_euler[1, .., :] - rho0)

# now take the RK step
@timeit timer() "Runge-Kutta step" begin
Expand Down Expand Up @@ -178,11 +166,7 @@ function timestep_gravity_3Sstar!(solver::AbstractSolver, t, dt, u_euler, gravit
# Source term: Jeans instability OR coupling convergence test OR blast wave
# put in gravity source term proportional to Euler density
# OBS! subtract off the background density ρ_0 around which the Jeans instability is perturbed
if ndims(solver) == 2
@views @. solver.elements.u_t[1,:,:,:] += grav_scale*(u_euler[1,:,:,:] - rho0)
else
@views @. solver.elements.u_t[1,:,:,:,:] += grav_scale*(u_euler[1,:,:,:,:] - rho0)
end
@views @. solver.elements.u_t[1, .., :] += grav_scale * (u_euler[1, .., :] - rho0)

delta_stage = delta[stage]
gamma1_stage = gamma1[stage]
Expand Down