Merge pull request #138 from milankl/julia14

Julia14

Author: Milan K

.appveyor.yml

@@ -1,7 +1,6 @@
 environment:
   matrix:
-  - julia_version: 1
-  - julia_version: 1.3
+  - julia_version: 1.4
   - julia_version: nightly
 
 platform:

.travis.yml

@@ -4,8 +4,7 @@ os:
   - linux
   - osx
 julia:
-  - 1.0
-  - 1.3
+  - 1.4
   - nightly
 notifications:
   email: false

Manifest.toml

@@ -11,15 +11,9 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[BinDeps]]
 deps = ["Libdl", "Pkg", "SHA", "URIParser", "Unicode"]
-git-tree-sha1 = "66158ad56b4bf6cc8413b37d0b7bc52402682764"
+git-tree-sha1 = "46cf2c1668ad07aba5a9d331bdeea994a1f13856"
 uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee"
-version = "1.0.0"
-
-[[Compat]]
-deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "ed2c4abadf84c53d9e58510b5fc48912c2336fbb"
-uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "2.2.0"
+version = "1.0.1"
 
 [[Conda]]
 deps = ["JSON", "VersionParsing"]
@@ -37,9 +31,10 @@ version = "0.2.0"
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
-[[DelimitedFiles]]
-deps = ["Mmap"]
-uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+[[DiskArrays]]
+git-tree-sha1 = "d89f6d225ea9e107ab1903e8b7881f1b1bd06148"
+uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
+version = "0.2.3"
 
 [[Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
@@ -57,9 +52,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[Interpolations]]
 deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"]
-git-tree-sha1 = "c7579b2617b513d8e6eb9f4b91837eefe7080af8"
+git-tree-sha1 = "3af735234d9b1ff9ff1af89875735cd9549c0c5f"
 uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
-version = "0.12.8"
+version = "0.12.9"
 
 [[JSON]]
 deps = ["Dates", "Mmap", "Parsers", "Unicode"]
@@ -68,6 +63,7 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.0"
 
 [[LibGit2]]
+deps = ["Printf"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
 [[Libdl]]
@@ -88,15 +84,15 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[NetCDF]]
-deps = ["BinDeps", "CondaBinDeps", "Formatting", "Libdl"]
-git-tree-sha1 = "fce0c7962fb14b8cf2f33ea77885f3b7c7e1485e"
+deps = ["BinDeps", "CondaBinDeps", "DiskArrays", "Formatting", "Libdl"]
+git-tree-sha1 = "0c6a63d16e9261bf2fa4eecbab575ae7e7fef11c"
 uuid = "30363a11-5582-574a-97bb-aa9a979735b9"
-version = "0.8.0"
+version = "0.10.2"
 
 [[OffsetArrays]]
-git-tree-sha1 = "707e34562700b81e8aa13548eb6b23b18112e49b"
+git-tree-sha1 = "930db8ef90483570107f2396b1ffc6680f08e8b7"
 uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-version = "1.0.2"
+version = "1.0.4"
 
 [[OrderedCollections]]
 deps = ["Random", "Serialization", "Test"]
@@ -112,12 +108,12 @@ version = "0.12.0"
 
 [[Parsers]]
 deps = ["Dates", "Test"]
-git-tree-sha1 = "d112c19ccca00924d5d3a38b11ae2b4b268dda39"
+git-tree-sha1 = "f8f5d2d4b4b07342e5811d2b6428e45524e241df"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "0.3.11"
+version = "1.0.2"
 
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Test", "UUIDs"]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[Printf]]
@@ -133,10 +129,9 @@ deps = ["Serialization"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[Ratios]]
-deps = ["Compat"]
-git-tree-sha1 = "cdbbe0f350581296f3a2e3e7a91b214121934407"
+git-tree-sha1 = "37d210f612d70f3f7d57d488cb3b6eff56ad4e41"
 uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439"
-version = "0.3.1"
+version = "0.4.0"
 
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
@@ -157,9 +152,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "5a3bcb6233adabde68ebc97be66e95dcb787424c"
+git-tree-sha1 = "4118cba3529e99af61aea9a83f7bfd3cff5ffb28"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "0.12.1"
+version = "0.12.2"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -170,10 +165,10 @@ deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[URIParser]]
-deps = ["Test", "Unicode"]
-git-tree-sha1 = "6ddf8244220dfda2f17539fa8c9de20d6c575b69"
+deps = ["Unicode"]
+git-tree-sha1 = "53a9f49546b8d2dd2e688d216421d050c9a31d0d"
 uuid = "30578b45-9adc-5946-b283-645ec420af67"
-version = "0.4.0"
+version = "0.4.1"
 
 [[UUIDs]]
 deps = ["Random", "SHA"]
@@ -189,6 +184,6 @@ version = "1.2.0"
 
 [[WoodburyMatrices]]
 deps = ["LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "bbb9f7fd6fbdd9582e77c0b698312c543de5eb71"
+git-tree-sha1 = "28ffe06d28b1ba8fdb2f36ec7bb079fac81bac0d"
 uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
-version = "0.5.0"
+version = "0.5.2"

Project.toml

@@ -1,7 +1,7 @@
 name = "ShallowWaters"
 uuid = "56019723-2d87-4a65-81ff-59d5d8913e3c"
 authors = ["Milan Kloewer"]
-version = "0.2.0"
+version = "0.3.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -11,10 +11,10 @@ Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [compat]
-NetCDF = "^0.8"
+Interpolations = "^0.12"
+NetCDF = "^0.10"
 Parameters = "^0.12"
 julia = "1"
-Interpolations = "^0.12"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -15,20 +15,22 @@ ShallowWaters is fully-explicit with an energy and enstrophy conserving advectio
 
 Please feel free to raise an [issue](https://github.com/milankl/ShallowWaters.jl/issues) if you discover bugs or have an idea how to improve ShallowWaters.
 
+Requires: Julia 1.2
+
 ### How to use
 
-`RunModel` initialises the model, preallocates memory and starts the time integration. You find the options and default parameters in `src/DefaultParameters.jl` (or by typing `?Parameter`). 
+`RunModel` initialises the model, preallocates memory and starts the time integration. You find the options and default parameters in `src/DefaultParameters.jl` (or by typing `?Parameter`).
 ```julia
 help?> Parameter
 search: Parameter
 
   Creates a Parameter struct with following options and default values
 
   T::DataType=Float32                 # number format
-  
+
   Tprog::DataType=T                   # number format for prognostic variables
   Tcomm::DataType=Tprog               # number format for ghost-point copies
-  
+
   # DOMAIN RESOLUTION AND RATIO
   nx::Int=100                         # number of grid cells in x-direction
   Lx::Real=2000e3                     # length of the domain in x-direction [m]

src/DefaultParameters.jl

@@ -185,7 +185,7 @@ Creates a Parameter struct with following options and default values
 
     # SURFACE FORCING
     surface_forcing::Bool=false         # yes?
-    ωFη::Real=1.0                       # (annual) frequency [1/year]
+    ωFη::Real=1.0                       # frequency [1/year] for surfance forcing
     A::Real=3e-5                        # Amplitude [m/s]
     ϕk::Real=ϕ                          # Central latitude of Kelvin wave pumping
     wk::Real=10e3                       # width [m] in y of Gaussian used for surface forcing

src/InitialConditions.jl

@@ -53,15 +53,15 @@ function initial_conditions(::Type{T},S::ModelSetup) where {T<:AbstractFloat}
         end
 
         u = ncu.vars["u"][:,:,init_starti]
-        NetCDF.close(ncu)
+        # NetCDF.close(ncu)
 
         ncv = NetCDF.open(joinpath(inirunpath,"v.nc"))
         v = ncv.vars["v"][:,:,init_starti]
-        NetCDF.close(ncv)
+        # NetCDF.close(ncv)
 
         ncη = NetCDF.open(joinpath(inirunpath,"eta.nc"))
         η = ncη.vars["eta"][:,:,init_starti]
-        NetCDF.close(ncη)
+        # NetCDF.close(ncη)
 
         # remove singleton time dimension
         u = reshape(u,size(u)[1:2])
@@ -147,7 +147,7 @@ function initial_conditions(::Type{T},S::ModelSetup) where {T<:AbstractFloat}
     if initial_cond == "ncfile" && sst_initial == "restart"
         ncsst = NetCDF.open(joinpath(inirunpath,"sst.nc"))
         sst = ncsst.vars["sst"][:,:,init_starti]
-        NetCDF.close(ncsst)
+        # NetCDF.close(ncsst)
 
         sst = reshape(sst,size(sst)[1:2])
     end
@@ -164,11 +164,3 @@ function initial_conditions(::Type{T},S::ModelSetup) where {T<:AbstractFloat}
 
     return PrognosticVars{T}(u,v,η,sst)
 end
-
-# if injection_region == "south"
-#     sst_inj_region = sst_south
-# elseif injection_region == "west"
-#     sst_inj_region = sst_west
-# elseif injection_region == "rect"
-#     sst_inj_region = sst_rect
-# end

src/Output.jl

@@ -88,54 +88,45 @@ function output_nc!(i::Int,
         @unpack f_q,ep,dtint = S.grid
 
         # CUT OFF HALOS
-        # @views u = Prog.u[halo+1:end-halo,halo+1:end-halo]
-        # @views v = Prog.v[halo+1:end-halo,halo+1:end-halo]
-        # @views η = Prog.η[haloη+1:end-haloη,haloη+1:end-haloη]
-        # @views sst = Prog.sst[halosstx+1:end-halosstx,halossty+1:end-halossty]
-        # @views ζ = (dvdx[2:end-1,2:end-1]-dudy[2+ep:end-1,2:end-1])./abs.(f_q)
-        # @views du = Diag.Tendencies.du[halo+1:end-halo,halo+1:end-halo]
-        # @views dv = Diag.Tendencies.dv[halo+1:end-halo,halo+1:end-halo]
-        # @views dη = Diag.Tendencies.dη[haloη+1:end-haloη,haloη+1:end-haloη]
-
         # As output is before copyto!(u,u0), take u0,v0,η0
-        @views u = Float32.(Diag.RungeKutta.u0[halo+1:end-halo,halo+1:end-halo])
-        @views v = Float32.(Diag.RungeKutta.v0[halo+1:end-halo,halo+1:end-halo])
-        @views η = Float32.(Diag.RungeKutta.η0[haloη+1:end-haloη,haloη+1:end-haloη])
-        
-        @views sst = Float32.(Prog.sst[halosstx+1:end-halosstx,halossty+1:end-halossty])
-        @views ζ = Float32.((dvdx[2:end-1,2:end-1]-dudy[2+ep:end-1,2:end-1])./abs.(f_q))
-
         # Tendencies calculate from the last time step, du = u_n+1-u_n etc
-        @views du = u-Float32.(Prog.u[halo+1:end-halo,halo+1:end-halo])
-        @views dv = v-Float32.(Prog.v[halo+1:end-halo,halo+1:end-halo])
-        @views dη = η-Float32.(Prog.η[haloη+1:end-haloη,haloη+1:end-haloη])
-
         # WRITING THE VARIABLES
         if ncs.u != nothing
+            @views u = Float32.(Diag.RungeKutta.u0[halo+1:end-halo,halo+1:end-halo])
             NetCDF.putvar(ncs.u,"u",u,start=[1,1,iout],count=[-1,-1,1])
         end
         if ncs.v != nothing
+            @views v = Float32.(Diag.RungeKutta.v0[halo+1:end-halo,halo+1:end-halo])
             NetCDF.putvar(ncs.v,"v",v,start=[1,1,iout],count=[-1,-1,1])
         end
         if ncs.η != nothing
+            @views η = Float32.(Diag.RungeKutta.η0[haloη+1:end-haloη,haloη+1:end-haloη])
             NetCDF.putvar(ncs.η,"eta",η,start=[1,1,iout],count=[-1,-1,1])
         end
         if ncs.sst != nothing
+            @views sst = Float32.(Prog.sst[halosstx+1:end-halosstx,halossty+1:end-halossty])
             NetCDF.putvar(ncs.sst,"sst",sst,start=[1,1,iout],count=[-1,-1,1])
         end
         if ncs.q != nothing
             NetCDF.putvar(ncs.q,"q",q,start=[1,1,iout],count=[-1,-1,1])
         end
         if ncs.ζ != nothing
+            @views ζ = Float32.((dvdx[2:end-1,2:end-1]-dudy[2+ep:end-1,2:end-1])./abs.(f_q))
             NetCDF.putvar(ncs.ζ,"relvort",ζ,start=[1,1,iout],count=[-1,-1,1])
         end
         if ncs.du != nothing
+            @views u = Float32.(Diag.RungeKutta.u0[halo+1:end-halo,halo+1:end-halo])
+            @views du = u-Float32.(Prog.u[halo+1:end-halo,halo+1:end-halo])
             NetCDF.putvar(ncs.du,"du",du,start=[1,1,iout],count=[-1,-1,1])
         end
         if ncs.dv != nothing
+            @views v = Float32.(Diag.RungeKutta.v0[halo+1:end-halo,halo+1:end-halo])
+            @views dv = v-Float32.(Prog.v[halo+1:end-halo,halo+1:end-halo])
             NetCDF.putvar(ncs.dv,"dv",dv,start=[1,1,iout],count=[-1,-1,1])
         end
         if ncs.dη != nothing
+            @views η = Float32.(Diag.RungeKutta.η0[haloη+1:end-haloη,haloη+1:end-haloη])
+            @views dη = η-Float32.(Prog.η[haloη+1:end-haloη,haloη+1:end-haloη])
             NetCDF.putvar(ncs.dη,"deta",dη,start=[1,1,iout],count=[-1,-1,1])
         end
 
@@ -156,11 +147,11 @@ function output_close!(ncs::NcFiles,feedback::Feedback,S::ModelSetup)
     @unpack output = S.parameters
 
     if output
-        for nc in (ncs.u,ncs.v,ncs.η,ncs.sst,ncs.q,ncs.ζ,ncs.du,ncs.dv,ncs.dη)
-            if nc != nothing
-                NetCDF.close(nc)
-            end
-        end
+        # for nc in (ncs.u,ncs.v,ncs.η,ncs.sst,ncs.q,ncs.ζ,ncs.du,ncs.dv,ncs.dη)
+        #     if nc != nothing
+        #         NetCDF.close(nc)
+        #     end
+        # end
         println("All data stored.")
         write(feedback.progress_txt,"All data stored.")
         close(feedback.progress_txt)