18561934460

Committed 16 Oct 2025 12:54PM UTC coverage: 65.961% (-0.03%) from 65.988%

Build # 18561934460

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push

github

Committed by

web-flow

Commit Message

Removed `test_case` and made several dispatches more precise (#104)

* Removed `test_case`.

* Made several dispatches more precise.

* Removed `examples.md` (was comitted by accident).

* Renamed `AbstractVariable` to `AbstractPredictand` and removed some of its subtypes (these are direct subtypes of `Any` now).

* Some simplifications and additional comments in initialize_rays!.

* Corrected a few typos.

* Moved the namelist parameter "model" to AtmosphereNamelist and removed SettingNamelist. Reformatted the code.

Run Details

104 of 119 new or added lines in 44 files covered. (87.39%)

4 existing lines in 4 files now uncovered.

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0.0

/src/Output/read_input!.jl

"""
```julia
read_input!(state::State)
```

Read initial values for all prognostic variables from an HDF5 input file.

# Arguments

  - `state`: Model state.
"""
function read_input! end

function read_input!(state::State)
    (; x_size, y_size) = state.namelists.domain
    (; iin, input_file) = state.namelists.output
    (; model) = state.namelists.atmosphere
    (; wkb_mode) = state.namelists.wkb
    (; comm, nx, ny, nz, io, jo, ko, i0, i1, j0, j1, k0, k1) = state.domain
    (; lref, tref, rhoref, uref, thetaref) = state.constants
    (; rho, rhop, u, v, w, pip, p) = state.variables.predictands
    (; nray_max, nray, rays) = state.wkb
    (; rhobar) = state.atmosphere

    # Determine dimensionality.
    dim = 1
    if x_size > 1
        dim += 1
    end
    if y_size > 1
        dim += 1
    end

    # Define slices.
    dk0 = ko == 0 ? 1 : 0
    (rr, ii, jj, kk, kkr) = (1:nray_max, i0:i1, j0:j1, k0:k1, (k0 - dk0):k1)
    (iid, jjd, kkd, kkrd) = (
        (io + 1):(io + nx),
        (jo + 1):(jo + ny),
        (ko + 1):(ko + nz),
        (ko + 2 - dk0):(ko + nz + 1),
    )

    # Open the file. Note: Fused in-place assignments cannot be used here!
    @ivy time = h5open(input_file, "r", comm) do file

        # Read the time.
        time = file["t"][iin] / tref

        # Read the density fluctuations.
        rhop[ii, jj, kk] = file["rhop"][iid, jjd, kkd, iin] ./ rhoref
        if model != Boussinesq()
            rho[ii, jj, kk] .= rhop[ii, jj, kk]
        end

        # Read the staggered zonal wind.
        u[ii, jj, kk] = file["us"][iid, jjd, kkd, iin] ./ uref

        # Read the staggered meridional wind.
        v[ii, jj, kk] = file["vs"][iid, jjd, kkd, iin] ./ uref

        # Read the staggered transformed vertical wind.
        w[ii, jj, kk] = file["wts"][iid, jjd, kkd, iin] ./ uref

        # Read the Exner-pressure fluctuations.
        pip[ii, jj, kk] = file["pip"][iid, jjd, kkd, iin]

        # Read the mass-weighted potential temperature.
        if model == Compressible()
            p[ii, jj, kk] = file["p"][iid, jjd, kkd, iin] ./ rhoref ./ thetaref
        end

        if !(typeof(state.namelists.tracer.tracer_setup) <: NoTracer)
            for field in fieldnames(TracerPredictands)
                getfield(state.tracer.tracerpredictands, field)[ii, jj, kk] =
                    file[string(field)][iid, jjd, kkd, iin] .*
                    (rhobar[ii, jj, kk] .+ rho[ii, jj, kk])
            end
        end

        # Read ray-volume properties.
        if wkb_mode != NoWKB()
            for (output_name, field_name) in zip(
                ("xr", "yr", "zr", "dxr", "dyr", "dzr"),
                (:x, :y, :z, :dxray, :dyray, :dzray),
            )
                getfield(rays, field_name)[rr, ii, jj, kkr] =
                    file[output_name][rr, iid, jjd, kkrd, iin] ./ lref
            end

            for (output_name, field_name) in zip(
                ("kr", "lr", "mr", "dkr", "dlr", "dmr"),
                (:k, :l, :m, :dkray, :dlray, :dmray),
            )
                getfield(rays, field_name)[rr, ii, jj, kkr] =
                    file[output_name][rr, iid, jjd, kkrd, iin] .* lref
            end

            rays.dens[rr, ii, jj, kkr] =
                file["nr"][rr, iid, jjd, kkrd, iin] ./ rhoref ./ uref .^ 2 ./ tref ./ lref .^ dim

            # Determine nray.
            for k in kkr, j in jj, i in ii
                local_count = 0
                for r in rr
                    if rays.dens[r, i, j, k] == 0
                        continue
                    end
                    local_count += 1
                end
                nray[i, j, k] = local_count
            end
        end

        return time
    end

    return time
end

1	"""
2	```julia
3	read_input!(state::State)
4	```
5
6	Read initial values for all prognostic variables from an HDF5 input file.
7
8	# Arguments
9
10	- `state`: Model state.
11	"""
12	function read_input! end
13
14	function read_input!(state::State)	×
15	(; x_size, y_size) = state.namelists.domain	×
16	(; iin, input_file) = state.namelists.output	×
NEW 17	(; model) = state.namelists.atmosphere	×
NEW 18	(; wkb_mode) = state.namelists.wkb	×
19	(; comm, nx, ny, nz, io, jo, ko, i0, i1, j0, j1, k0, k1) = state.domain	×
20	(; lref, tref, rhoref, uref, thetaref) = state.constants	×
21	(; rho, rhop, u, v, w, pip, p) = state.variables.predictands	×
22	(; nray_max, nray, rays) = state.wkb	×
23	(; rhobar) = state.atmosphere	×
24
25	# Determine dimensionality.
26	dim = 1	×
27	if x_size > 1	×
28	dim += 1	×
29	end
30	if y_size > 1	×
31	dim += 1	×
32	end
33
34	# Define slices.
35	dk0 = ko == 0 ? 1 : 0	×
36	(rr, ii, jj, kk, kkr) = (1:nray_max, i0:i1, j0:j1, k0:k1, (k0 - dk0):k1)	×
37	(iid, jjd, kkd, kkrd) = (	×
38	(io + 1):(io + nx),
39	(jo + 1):(jo + ny),
40	(ko + 1):(ko + nz),
41	(ko + 2 - dk0):(ko + nz + 1),
42	)
43
44	# Open the file. Note: Fused in-place assignments cannot be used here!
45	@ivy time = h5open(input_file, "r", comm) do file	×
46
47	# Read the time.
48	time = file["t"][iin] / tref	×
49
50	# Read the density fluctuations.
51	rhop[ii, jj, kk] = file["rhop"][iid, jjd, kkd, iin] ./ rhoref	×
52	if model != Boussinesq()	×
53	rho[ii, jj, kk] .= rhop[ii, jj, kk]	×
54	end
55
56	# Read the staggered zonal wind.
57	u[ii, jj, kk] = file["us"][iid, jjd, kkd, iin] ./ uref	×
58
59	# Read the staggered meridional wind.
60	v[ii, jj, kk] = file["vs"][iid, jjd, kkd, iin] ./ uref	×
61
62	# Read the staggered transformed vertical wind.
63	w[ii, jj, kk] = file["wts"][iid, jjd, kkd, iin] ./ uref	×
64
65	# Read the Exner-pressure fluctuations.
66	pip[ii, jj, kk] = file["pip"][iid, jjd, kkd, iin]	×
67
68	# Read the mass-weighted potential temperature.
69	if model == Compressible()	×
70	p[ii, jj, kk] = file["p"][iid, jjd, kkd, iin] ./ rhoref ./ thetaref	×
71	end
72
73	if !(typeof(state.namelists.tracer.tracer_setup) <: NoTracer)	×
74	for field in fieldnames(TracerPredictands)	×
75	getfield(state.tracer.tracerpredictands, field)[ii, jj, kk] =	×
76	file[string(field)][iid, jjd, kkd, iin] .*
77	(rhobar[ii, jj, kk] .+ rho[ii, jj, kk])
78	end	×
79	end
80
81	# Read ray-volume properties.
NEW 82	if wkb_mode != NoWKB()	×
83	for (output_name, field_name) in zip(	×
84	("xr", "yr", "zr", "dxr", "dyr", "dzr"),
85	(:x, :y, :z, :dxray, :dyray, :dzray),
86	)
87	getfield(rays, field_name)[rr, ii, jj, kkr] =	×
88	file[output_name][rr, iid, jjd, kkrd, iin] ./ lref
89	end	×
90
91	for (output_name, field_name) in zip(	×
92	("kr", "lr", "mr", "dkr", "dlr", "dmr"),
93	(:k, :l, :m, :dkray, :dlray, :dmray),
94	)
95	getfield(rays, field_name)[rr, ii, jj, kkr] =	×
96	file[output_name][rr, iid, jjd, kkrd, iin] .* lref
97	end	×
98
99	rays.dens[rr, ii, jj, kkr] =	×
100	file["nr"][rr, iid, jjd, kkrd, iin] ./ rhoref ./ uref .^ 2 ./ tref ./ lref .^ dim
101
102	# Determine nray.
103	for k in kkr, j in jj, i in ii	×
104	local_count = 0	×
105	for r in rr	×
106	if rays.dens[r, i, j, k] == 0	×
107	continue	×
108	end
109	local_count += 1	×
110	end	×
111	nray[i, j, k] = local_count	×
112	end	×
113	end
114
115	return time	×
116	end
117
118	return time	×
119	end

Atmospheric-Dynamics-GUF / PinCFlow.jl / 18561934460

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