Merge pull request #19 from sintefmath/parse

Support for parsing and simulating .DATA files

Project.toml

@@ -1,19 +1,22 @@
 name = "JutulDarcy"
 uuid = "82210473-ab04-4dce-b31b-11573c4f8e0a"
 authors = ["Olav Møyner <[email protected]>"]
-version = "0.2.7"
+version = "0.2.8"
 
 [deps]
 AlgebraicMultigrid = "2169fc97-5a83-5252-b627-83903c6c433c"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Jutul = "2b460a1a-8a2b-45b2-b125-b5c536396eb9"
 Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890"
 MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
 MultiComponentFlash = "35e5bd01-9722-4017-9deb-64a5d32478ff"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -23,44 +26,47 @@ TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 Tullio = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc"
 
+[weakdeps]
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771"
+MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
+PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
+
+[extensions]
+JutulDarcyGLMakieExt = "GLMakie"
+JutulDarcyHYPREExt = "HYPRE"
+JutulDarcyPartitionedArraysExt = ["PartitionedArrays", "MPI", "HYPRE"]
+
 [compat]
 AlgebraicMultigrid = "0.5.1"
 DataStructures = "0.18.13"
+DelimitedFiles = "1.9.1"
 ForwardDiff = "0.10.30"
-Jutul = "0.2.10"
+HYPRE = "1.4.0"
+Jutul = "0.2.12"
+Krylov = "0.9.1"
 LoopVectorization = "0.12.115"
 MAT = "0.10.3"
 MultiComponentFlash = "1.1.3"
+OrderedCollections = "1.6.2"
+Parsers = "2.7.1"
+PartitionedArrays = "0.3.2"
 Polyester = "0.6.11, 0.7.3"
 PrecompileTools = "1.0.1"
-PartitionedArrays = "0.3.2"
 StaticArrays = "1.4.4"
 TestItems = "0.1.0"
 TimerOutputs = "0.5.19"
 Tullio = "0.3.4"
-HYPRE = "1.4.0"
 julia = "1.7"
-Krylov = "0.9.1"
 
 [extras]
-TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
-TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771"
-PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
+PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
+TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
 
 [targets]
 test = ["Test", "TestItemRunner", "TestItems", "HYPRE", "MPI", "PartitionedArrays"]
-
-[weakdeps]
-GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
-HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771"
-PartitionedArrays = "5a9dfac6-5c52-46f7-8278-5e2210713be9"
-MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
-
-[extensions]
-JutulDarcyGLMakieExt = "GLMakie"
-JutulDarcyHYPREExt = "HYPRE"
-JutulDarcyPartitionedArraysExt = ["PartitionedArrays", "MPI", "HYPRE"]

ext/JutulDarcyGLMakieExt/well_plots.jl

@@ -100,7 +100,7 @@ function JutulDarcy.plot_well_results(well_data::Vector, time = nothing; start_d
         else
             c_key = :Paired_10
         end
-        cmap = cgrad(c_key, nw, categorical=true)
+        cmap = cgrad(c_key, max(nw, 2), categorical=true)
     end
     wellstr = [String(x) for x in wells]
 

ext/JutulDarcyPartitionedArraysExt/JutulDarcyPartitionedArraysExt.jl

@@ -40,7 +40,7 @@ module JutulDarcyPartitionedArraysExt
     function Jutul.parray_preconditioner_apply!(global_out, main_prec::CPRPreconditioner{<:BoomerAMGPreconditioner, <:Any}, X, preconditioners, simulator, arg...)
         global_cell_vector = simulator.storage.distributed_cell_buffer
         global_buf = simulator.storage.distributed_residual_buffer
-        map(local_values(X), preconditioners, ghost_values(X)) do x, prec, x_g
+        @tic "cpr first stage" map(local_values(X), preconditioners, ghost_values(X)) do x, prec, x_g
             @. x_g = 0.0
             JutulDarcy.apply_cpr_first_stage!(prec, x, arg...)
             nothing
@@ -49,7 +49,7 @@ module JutulDarcyPartitionedArraysExt
         # copy!(global_cell_vector, main_prec.p)
         p_h = main_prec.p
         @assert !isnothing(p_h) "CPR is not properly initialized."
-        map(own_values(global_cell_vector), preconditioners) do ov, prec
+        @tic "hypre GetValues" map(own_values(global_cell_vector), preconditioners) do ov, prec
             helper = prec.pressure_precond.data[:assembly_helper]
             indices = helper.indices
             indices::Vector{HYPRE.HYPRE_BigInt}
@@ -59,29 +59,27 @@ module JutulDarcyPartitionedArraysExt
         # End unsafe shenanigans
 
         # consistent!(global_cell_vector) |> wait
-        map(own_values(global_buf), own_values(global_cell_vector), preconditioners) do dx, dp, prec
+        @tic "set dp" map(own_values(global_buf), own_values(global_cell_vector), preconditioners) do dx, dp, prec
             bz = prec.block_size
             for i in eachindex(dp)
                 JutulDarcy.set_dp!(dx, bz, dp, i)
             end
             nothing
         end
-        if main_prec.full_system_correction
-            mul_ix = nothing
-        else
-            mul_ix = 1
+
+        @tic "correct residual" begin
+            mul!(X, main_prec.A_ps, global_buf, -1.0, true)
+            nothing
         end
-        full_op = Jutul.parray_linear_system_operator(simulator.storage.simulators, global_buf)
-        mul!(X, full_op, global_buf, -1.0, true)
 
-        map(local_values(global_out), local_values(X), preconditioners, local_values(global_cell_vector), ghost_values(X)) do y, x, prec, dp, x_g
+        @tic "increment dp" map(local_values(global_out), local_values(X), preconditioners, local_values(global_cell_vector), ghost_values(X)) do y, x, prec, dp, x_g
             @. x_g = 0.0
             apply!(y, prec.system_precond, x, arg...)
             bz = prec.block_size
             JutulDarcy.increment_pressure!(y, dp, bz)
             nothing
         end
-        consistent!(global_out) |> wait
+        @tic "communication" consistent!(global_out) |> wait
         global_out
     end
 
@@ -90,7 +88,7 @@ module JutulDarcyPartitionedArraysExt
         n = sim.storage.nc_process
         comm = sim.storage.comm
         if sim.storage[:number_of_processes] > 1
-            @assert sim.backend isa Jutul.MPI_PArrayBackend "Cannot use HYPRE with emulated multiple processes."
+            @assert sim.backend isa Jutul.MPI_PArrayBackend "Cannot use HYPRE with emulated multiple processes. Backend was $(sim.backend)"
         end
 
         function create_hypre_vector()
@@ -104,16 +102,25 @@ module JutulDarcyPartitionedArraysExt
             cpr.r_p = create_hypre_vector()
             cpr.p = create_hypre_vector()
             cpr.np = n
+            if cpr.full_system_correction
+                mul_ix = nothing
+            else
+                mul_ix = 1
+            end
+            global_buf = sim.storage.distributed_residual_buffer
+            cpr.A_ps = Jutul.parray_linear_system_operator(sim.storage.simulators, global_buf)
         end
         A_p = cpr.A_p
+        A_ps = cpr.A_ps
         r_p = cpr.r_p
         x_p = cpr.p
 
         map(sim.storage.simulators, preconditioners) do sim, prec
-            sys = sim.storage.LinearizedSystem
-            model = sim.model
-            storage = sim.storage
+            storage = Jutul.get_simulator_storage(sim)
+            model = Jutul.get_simulator_model(sim)
+            sys = storage.LinearizedSystem
             prec.A_p = A_p
+            prec.A_ps = A_ps
             prec.p = x_p
             prec.r_p = r_p
             prec.np = n

src/InputParser/InputParser.jl

@@ -0,0 +1,6 @@
+module InputParser
+    using Parsers, DelimitedFiles, Jutul, OrderedCollections, Dates
+    export parse_data_file
+
+    include("deckinput/parser.jl")
+end

src/InputParser/deckinput/keywords/grid.jl

@@ -0,0 +1,62 @@
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:INIT})
+    data["INIT"] = true
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:COORDSYS})
+    read_record(f)
+    @warn "COORDSYS skipped."
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:COORD})
+    coord = parse_deck_matrix(f, Float64)
+    coord = swap_unit_system!(coord, units, Val(:length))
+    data["COORD"] = coord
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:ZCORN})
+    zcorn = parse_deck_vector(f, Float64)
+    zcorn = swap_unit_system!(zcorn, units, Val(:length))
+    data["ZCORN"] = zcorn
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, v::Union{Val{:PERMX}, Val{:PERMY}, Val{:PERMZ}})
+    k = unpack_val(v)
+    vals = parse_grid_vector(f, get_cartdims(outer_data), Float64)
+    vals = swap_unit_system!(vals, units, Val(:permeability))
+    data["$k"] = vals
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:PORO})
+    data["PORO"] = parse_grid_vector(f, get_cartdims(outer_data), Float64)
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:NTG})
+    data["NTG"] = parse_grid_vector(f, get_cartdims(outer_data), Float64)
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, v::Union{Val{:DX}, Val{:DY}, Val{:DZ}})
+    k = unpack_val(v)
+    data["$k"] = parse_grid_vector(f, get_cartdims(outer_data), Float64)
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:TOPS})
+    tops = parse_deck_vector(f, Float64)
+    data["TOPS"] = swap_unit_system!(tops, units, Val(:length))
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:DIMENS})
+    rec = read_record(f)
+    to_int = x -> Parsers.parse(Int, x)
+    d = to_int.(filter!(x -> length(x) > 0, split(only(rec), DECK_SPLIT_REGEX)))
+    data["DIMENS"] = d
+    set_cartdims!(outer_data, d)
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:SPECGRID})
+    rec = read_record(f)
+    tdims = [1, 1, 1, 1, "F"]
+    data["SPECGRID"] = parse_defaulted_line(rec, tdims)
+    set_cartdims!(outer_data, data["SPECGRID"][1:3])
+end
+

src/InputParser/deckinput/keywords/keywords.jl

@@ -0,0 +1,8 @@
+include("runspec.jl")
+include("grid.jl")
+include("props.jl")
+include("regions.jl")
+include("schedule.jl")
+include("solution.jl")
+include("summary.jl")
+include("special.jl")

src/InputParser/deckinput/keywords/props.jl

@@ -0,0 +1,88 @@
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:RPTPROPS})
+    read_record(f)
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, v::Union{Val{:SWOF}, Val{:SGOF}})
+    k = unpack_val(v)
+    sat_tab = parse_saturation_table(f, outer_data)
+    for tab in sat_tab
+        swap_unit_system_axes!(tab, units, (:identity, :identity, :identity, :pressure))
+    end
+    data["$k"] = sat_tab
+end
+
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:PVDG})
+    pvdg = parse_dead_pvt_table(f, outer_data)
+    for tab in pvdg
+        swap_unit_system_axes!(tab, units, (:pressure, :gas_formation_volume_factor, :viscosity))
+    end
+    data["PVDG"] = pvdg
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:PVTO})
+    pvto = parse_live_pvt_table(f, outer_data)
+    for tab in pvto
+        swap_unit_system_axes!(tab["data"], units, (:pressure, :liquid_formation_volume_factor, :viscosity))
+        swap_unit_system!(tab["key"], units, :u_rs)
+    end
+    data["PVTO"] = pvto
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:PVTW})
+    rec = read_record(f)
+    tdims = [NaN, NaN, NaN, NaN, NaN]
+    utypes = (:pressure, :liquid_formation_volume_factor, :compressibility, :viscosity, :compressibility)
+    nreg = number_of_tables(outer_data, :pvt)
+    out = []
+    for i = 1:nreg
+        t = parse_defaulted_line(rec, tdims)
+        swap_unit_system_axes!(t, units, utypes)
+        @assert all(isfinite, t) "PVTW cannot be defaulted, found defaulted record in region $i"
+        push!(out, t)
+    end
+    data["PVTW"] = out
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:PVCDO})
+    rec = read_record(f)
+    tdims = [NaN, NaN, NaN, NaN, NaN]
+    utypes = (:pressure, :liquid_formation_volume_factor, :compressibility, :viscosity, :compressibility)
+    nreg = number_of_tables(outer_data, :pvt)
+    out = []
+    for i = 1:nreg
+        t = parse_defaulted_line(rec, tdims)
+        swap_unit_system_axes!(t, units, utypes)
+        @assert all(isfinite, t) "PVCDO cannot be defaulted, found defaulted record in region $i"
+        push!(out, t)
+    end
+    data["PVCDO"] = out
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:ROCK})
+    rec = read_record(f)
+    tdims = [NaN, NaN, NaN, NaN, NaN, NaN]
+    utypes = [:pressure, :compressibility, :compressibility, :compressibility, :id, :id]
+    out = []
+    nreg = number_of_tables(outer_data, :pvt)
+    for i = 1:nreg
+        l = parse_defaulted_line(rec, tdims)
+        swap_unit_system_axes!(l, units, utypes)
+        push!(out, l)
+    end
+    data["ROCK"] = out
+end
+
+function parse_keyword!(data, outer_data, units, cfg, f, ::Val{:DENSITY})
+    rec = read_record(f)
+    tdims = [NaN, NaN, NaN]
+    nreg = number_of_tables(outer_data, :pvt)
+    out = []
+    for i = 1:nreg
+        t = parse_defaulted_line(rec, tdims)
+        swap_unit_system!(t, units, :density)
+        push!(out, t)
+    end
+    data["DENSITY"] = out
+end