Merge pull request #86 from FourierFlows/RemoveGeophysicalFlows

Remove Geophysical Flows Modules

Author: glwagner

.travis.yml

@@ -14,19 +14,16 @@ matrix:
     - julia: 1.0
     - julia: nightly
 
-before_script:
- - julia -e 'using Pkg; Pkg.add("JLD2"); Pkg.add("SpecialFunctions"); Pkg.add("CuArrays");'
- - julia -e 'using Pkg; Pkg.add("Interpolations"); Pkg.add("Requires");'
- - julia -e 'using Pkg; Pkg.add("FFTW");'
-
-# script:
-#   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-#   - julia -e 'using Pkg; Pkg.test("FourierFlows", coverage=true)'
+# before_script:
+#  - julia -e 'using Pkg; Pkg.add("JLD2"); Pkg.add("SpecialFunctions"); Pkg.add("CuArrays");'
+#  - julia -e 'using Pkg; Pkg.add("Interpolations"); Pkg.add("Requires");'
+#  - julia -e 'using Pkg; Pkg.add("FFTW");'
 
 after_success:
   - julia -e 'using Pkg; Pkg.add("Documenter")'
   - julia -e 'using Pkg; Pkg.add("Documenter"); Pkg.dir("FourierFlows"); include(joinpath("docs", "make.jl"))'
   - julia -e 'using Pkg; Pkg.add("Coverage"); Pkg.dir("FourierFlows"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
+  - julia -e 'using Pkg; Pkg.add("Coverage"); Pkg.dir("FourierFlows"); using Coverage; Codecov.submit(Codecov.process_folder())''
 
 notifications:
   email: true

Manifest.toml

@@ -27,27 +27,27 @@ version = "0.8.10"
 
 [[BinaryProvider]]
 deps = ["Libdl", "Pkg", "SHA", "Test"]
-git-tree-sha1 = "b530fbeb6f41ab5a83fbe3db1fcbe879334bcd2d"
+git-tree-sha1 = "38be61810f280c3c478f5c38aaf387f8f9199275"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-version = "0.4.2"
+version = "0.5.1"
 
 [[CUDAapi]]
-deps = ["InteractiveUtils", "Libdl", "Logging", "Pkg", "Test"]
-git-tree-sha1 = "576625a0922ab766ff5d7f685c6907d28dccf52f"
+deps = ["Libdl", "Logging", "Test"]
+git-tree-sha1 = "6684fd39c199e79456a121da40bbbcf370e646d3"
 uuid = "3895d2a7-ec45-59b8-82bb-cfc6a382f9b3"
-version = "0.5.0"
+version = "0.5.2"
 
 [[CUDAdrv]]
-deps = ["CUDAapi", "InteractiveUtils", "Libdl", "Pkg", "Printf", "Test"]
-git-tree-sha1 = "0bbb47620dfda5b90dfc1820f6b44dfd71ad875c"
+deps = ["CUDAapi", "Libdl", "Printf", "Test"]
+git-tree-sha1 = "94a3b9afb137e8d08136b334e51a25375557ca24"
 uuid = "c5f51814-7f29-56b8-a69c-e4d8f6be1fde"
-version = "0.8.5"
+version = "0.8.6"
 
 [[CUDAnative]]
 deps = ["CUDAapi", "CUDAdrv", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Pkg", "Printf", "Statistics", "Test"]
-git-tree-sha1 = "d0f3aebc1fde1eb4822006da6b52854acffa6186"
+git-tree-sha1 = "debfe5af100e335b5df7109184e2e450f616dd1f"
 uuid = "be33ccc6-a3ff-5ff2-a52e-74243cff1e17"
-version = "0.8.10"
+version = "0.9.1"
 
 [[CodecZlib]]
 deps = ["BinaryProvider", "Libdl", "Pkg", "Test", "TranscodingStreams"]
@@ -63,9 +63,9 @@ version = "0.2.0"
 
 [[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 = "ae262fa91da6a74e8937add6b613f58cd56cdad4"
+git-tree-sha1 = "ff2595695fc4f14427358ce2593f867085c45dcb"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "1.1.0"
+version = "1.2.0"
 
 [[ComputationalResources]]
 deps = ["Pkg", "Test"]
@@ -75,9 +75,9 @@ version = "0.3.0"
 
 [[Conda]]
 deps = ["Compat", "JSON", "VersionParsing"]
-git-tree-sha1 = "a47f9a2c7b80095e6a935536795635522fe27f5d"
+git-tree-sha1 = "85b5bf3ffcf4f39abe019dab1dd00a0aead8d882"
 uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-version = "1.0.1"
+version = "1.0.2"
 
 [[Coverage]]
 deps = ["Compat", "HTTP", "JSON", "MbedTLS"]
@@ -92,10 +92,10 @@ uuid = "3a865a2d-5b23-5a0f-bc46-62713ec82fae"
 version = "0.8.0"
 
 [[DataStructures]]
-deps = ["InteractiveUtils", "REPL", "Random", "Serialization", "Test"]
-git-tree-sha1 = "5162c360c52e9265e0bfafb71415c31f746f7e04"
+deps = ["InteractiveUtils", "OrderedCollections", "REPL", "Random", "Serialization", "Test"]
+git-tree-sha1 = "8fc6e166e24fda04b2b648d4260cdad241788c54"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.12.0"
+version = "0.14.0"
 
 [[Dates]]
 deps = ["Printf"]
@@ -141,9 +141,9 @@ version = "0.2.4"
 
 [[FileIO]]
 deps = ["Pkg", "Random", "Test"]
-git-tree-sha1 = "b80161b7e679a1241f9441ebfa60b62d4239cf99"
+git-tree-sha1 = "481e4db939f005db39f7296599d0543c0744fe30"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.0.1"
+version = "1.0.2"
 
 [[FillArrays]]
 deps = ["Compat", "LinearAlgebra", "Random", "SparseArrays"]
@@ -159,15 +159,15 @@ version = "0.9.0"
 
 [[GPUArrays]]
 deps = ["FFTW", "FillArrays", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "StaticArrays", "Test"]
-git-tree-sha1 = "718a68157a867a5883c7715f441190e70245e86e"
+git-tree-sha1 = "0b1a3469e776ae30d198e0e9d1ba8b1dedc352e6"
 uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "0.4.0"
+version = "0.4.2"
 
 [[HTTP]]
 deps = ["Base64", "Dates", "Distributed", "IniFile", "MbedTLS", "Sockets", "Test"]
-git-tree-sha1 = "8a0f75e8b09df01d9f1ba9ad3fbf8b4983595d20"
+git-tree-sha1 = "b881f69331e85642be315c63d05ed65d6fc8a05b"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "0.6.14"
+version = "0.7.1"
 
 [[IniFile]]
 deps = ["Test"]
@@ -181,9 +181,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[Interpolations]]
 deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "Test", "WoodburyMatrices"]
-git-tree-sha1 = "ea6fdc5d2144bd5ee3e465f4c9329a1562744803"
+git-tree-sha1 = "d3328be2a9624d62957607a8bdfcc164d24f1b6d"
 uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
-version = "0.9.0"
+version = "0.10.3"
 
 [[JLD2]]
 deps = ["CodecZlib", "DataStructures", "FileIO", "LinearAlgebra", "Mmap", "Printf", "Random", "Test"]
@@ -198,10 +198,10 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.19.0"
 
 [[LLVM]]
-deps = ["InteractiveUtils", "Printf", "Test", "Unicode"]
-git-tree-sha1 = "ca92c66f3bbea27d7dc755e19719bb571ac773a9"
+deps = ["InteractiveUtils", "Libdl", "Printf", "Test", "Unicode"]
+git-tree-sha1 = "68e13858ba0601d3616e76fecb2d0c472bb9a742"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "0.9.14"
+version = "0.9.15"
 
 [[LibGit2]]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -227,10 +227,10 @@ deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[MbedTLS]]
-deps = ["BinaryProvider", "Compat", "Libdl", "Pkg", "Sockets"]
-git-tree-sha1 = "17d5a81dbb1e682d4ff707c01f0afe5948068fa6"
+deps = ["BinaryProvider", "Libdl", "Pkg", "Random", "Sockets", "Test"]
+git-tree-sha1 = "3775d205b09b624aa06d39012a8920ba99cb3b8b"
 uuid = "739be429-bea8-5141-9913-cc70e7f3736d"
-version = "0.6.0"
+version = "0.6.3"
 
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
@@ -253,6 +253,12 @@ git-tree-sha1 = "f8cd140824f74f2948ff8660bc2292e16d29c1b7"
 uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 version = "0.8.1"
 
+[[OrderedCollections]]
+deps = ["Pkg", "Random", "Serialization", "Test"]
+git-tree-sha1 = "85619a3f3e17bb4761fe1b1fd47f0e979f964d5b"
+uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+version = "1.0.2"
+
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
@@ -305,10 +311,10 @@ deps = ["LinearAlgebra", "Random"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SpecialFunctions]]
-deps = ["BinDeps", "BinaryProvider", "Compat", "Libdl"]
-git-tree-sha1 = "d12f8917be3782f4b800ba16003b8d0d4858c2e5"
+deps = ["BinDeps", "BinaryProvider", "Libdl", "Test"]
+git-tree-sha1 = "c35c9c76008babf4d658060fc64aeb369a41e7bd"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "0.7.0"
+version = "0.7.1"
 
 [[StaticArrays]]
 deps = ["InteractiveUtils", "LinearAlgebra", "Random", "Statistics", "Test"]
@@ -347,7 +353,7 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 deps = ["Compat"]
 git-tree-sha1 = "c9d5aa108588b978bd859554660c8a5c4f2f7669"
 uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
-version = "1.1.2"
+version = "1.1.3"
 
 [[WoodburyMatrices]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "Test"]

README.md

@@ -18,7 +18,7 @@
 
 ## Overview
 
-This software provides solvers for partial differential equations on
+This software provides tools for partial differential equations on
 doubly-periodic domains using Fourier-based pseudospectral methods.
 A central intent of the software's design is also to provide a framework
 for writing new, fast solvers for new physical problems.
@@ -35,88 +35,10 @@ julia> using Pkg
 julia> Pkg.add("FourierFlows")
 ```
 
-## Source code organization
-
-The code is divided along conceptual lines into problem-agnostic and
-problem-specific components. Files that contain problem-agnostic parts
-of the code are stored in `/src`. Files in `/src` define the domain,
-'AbstractTypes' that supertype problem-specific types, and
-time-stepper types and routines. Problem-specific modules are stores in
-`/src/physics`.
-
-Here's an overview of the code structure:
-
-- `/src/`
-    - `FourierFlows.jl`
-        - Defines supertyping AbstractParams, AbstractGrid, etc.
-        - Defines a `Problem` type to organize the grid, vars, params,
-            equation, and timestepper into a single structure.
-        - Includes all sources files and physics files.
-   - `timesteppers.jl`: defines modules and `stepforward!` routines for
-        various time-steppers. Current implemented time-steppers are:
-        - Forward Euler
-        - 3rd-order Adams-Bashforth (AB3)
-        - 4th-order Runge-Kutta (RK4)
-        - 4th-order Runge-Kutta Exponential Time Differencing (ETDRK4)
-        - 4th-order Dual Runge-Kutta (DualRK4)
-        - 4th-order Dual Runge-Kutta Exponential Time Differencing (DualETDRK4)
-
-        For each time-stepper exists also a "filtered" version that filters
-        out high-wavenumber spectral components of the solution. The `Dual`
-        time-steppers evolve a state variable that comprises both of real valued
-        and complex valued fields.
-
-    - `physics/`
-        - `kuramotosivashinsky.jl`: Defines a `KuramotoSivashinsky` module that
-                solves the 1D Kuramoto-Sivashinsky equation.
-        - `twodturb.jl`: Defines a `TwoDTurb` module that provides a
-                solver for the two-dimensional vorticity equation.
-        - `barotropicqg.jl`: Defines a `BarotropicQG` module that provides
-                several solvers for the barotropic QG model that permit beta,
-                topography, beta + topography, and forcing.
-        - `verticallyfourierboussinesq.jl`: Defines a `VerticallyFourierBoussinesq` module that
-                solves the two-mode truncation of the Fourier series thin-layer approximation to the hydrostatic Boussinesq equations.
-        - `verticallycosinerboussinesq.jl`: Defines a `VerticallyCosineBoussinesq` module that
-                solves the two-mode truncation of the Sin/Cos series thin-layer approximation to the hydrostatic Boussinesq equations.
-        - `traceradvdiff.jl`: Defines a `TracerAdvDiff` module that
-                provides a solver for a two-dimensional and periodic tracer
-                field in a given 2D flow (u, w), which can be an arbitrary
-                function of x, z, and t.
-
-
-## Basic Notation
-
-The code solves partial differential equations of the general
-form: `∂u/∂t = L*u + N(u)`, where `u` denotes the solution, which is
-typically an array of complex coefficients for each Fourier mode. In general,
-`L` is an array of coeffients that describe the linear part of the equation
-governing `u`, while `N(u)` is an arbitrary function that may contain terms
-both linear and nonlinear in `u`, as well forcing terms.
-The time-steppers currently implemented only accepted
-diagonal `L` arrays, which means that `L` and `u` have the same size.
-Currently, the ETDRK4 time-stepper is the only time-stepper implemented that
-makes special use of `L`. Both `L` and the function that calculates `N(u)` are
-stored as fields of the type `AbstractEquation`.
-
-
-## Writing fast solvers
-
-The performance-intensive part of the code involves just two functions: the
-timestepping scheme `stepforward!`, and the function `calcN!` that
-calculates the nonlinear part of the given equation's right-hand side.
-Optimization of these two functions for a given problem will produce the
-fastest possible code.
-
-
-## Future work
-
-The code is in the chaotic stage of development. A main goal for the future
-is to permit the use of shared memory parallelism in the compute-intensive
-routines (shared-memory parallelism provided already by FFTW/MKLFFT, but
-is not yet native to Julia for things like element-wise matrix multiplication,
-addition, and assignment). This feature may possibly be enabled by
-Intel Lab's [ParallelAccelerator][] package.
+## Example
 
+For a simple example involving the advection and diffusion of a passive tracer,
+see `examples/tracers_cellularflow.jl`.
 
 # Developers