From fb8f016690d2f0c5e8149137c43d5db7a94e2e7e Mon Sep 17 00:00:00 2001
From: milankl <milankloewer@gmx.de>
Date: Tue, 10 Sep 2019 21:37:51 +0100
Subject: [PATCH] to Pkg

---
 README.md        |   4 +-
 src/Juls.jl      |  33 ++++++++++++++
 src/RunJuls.jl   | 116 +++++++++++++++++++++++++++++++++++++++++++++++
 test/runtests.jl |   6 +++
 4 files changed, 157 insertions(+), 2 deletions(-)
 create mode 100644 src/Juls.jl
 create mode 100644 src/RunJuls.jl
 create mode 100644 test/runtests.jl

diff --git a/README.md b/README.md
index f12f520..8b08249 100644
--- a/README.md
+++ b/README.md
@@ -13,7 +13,7 @@ Juls is fully-explicit with a Smagorinsky-like biharmonic diffusion operator, th
 
 Forcing is either with a wind-stress applied to the momentum equations, or surface/interface relaxation or forcing of the contuinity equation is possible. Boundary conditions are either periodic (only in x direction) or super-slip/free-slip/partial-slip/no-slip for non-periodic BCs. Output of all prognositc and various diagnostic variables & tendencies is done via NetCDF.
 
-Requires Julia either v0.6, v0.7 or v1.x and NetCDF.
+Requires Julia v1.x and NetCDF.
 
 # HOW TO USE
 
@@ -40,6 +40,6 @@ The linear shallow water model equivalent is
           ∂η/∂t = -H*∇⋅u⃗ + γ*(η_ref - η) + Fηt(t)*Fη(x,y)         (3)
           ∂ϕ/∂t = -u⃗⋅∇ϕ                                           (4)
 
-Juls discretises the equation on an equi-distant Arakawa C-grid, with 2nd order finite-difference operators. Boundary conditions are implemented via a ghost-point copy and each variable has a halo of variable size to account for different stencil sizes of various operators. 
+Juls discretises the equation on an equi-distant Arakawa C-grid, with 2nd order finite-difference operators. Boundary conditions are implemented via a ghost-point copy and each variable has a halo of variable size to account for different stencil sizes of various operators.
 
 Juls splits the time steps for various terms: Runge Kutta 4th order scheme for the fast varying terms. The diffusive terms (bottom friction and diffusion) are solved semi-implicitly every n-th time step. The tracer equation is solved with a semi-Lagrangian scheme that uses usually much larger time steps.
diff --git a/src/Juls.jl b/src/Juls.jl
new file mode 100644
index 0000000..00ac0db
--- /dev/null
+++ b/src/Juls.jl
@@ -0,0 +1,33 @@
+module Juls
+
+export RunJuls
+
+using Dates, NetCDF, FileIO, Printf
+
+# GRID
+include("grid.jl")
+include("constants.jl")
+#include("domain_decomposition.jl")
+
+# OPERATORS and everything that is needed for the RHS
+include("gradients.jl")
+include("interpolations.jl")
+include("PV_adv.jl")
+include("bottom_friction.jl")
+include("diffusion.jl")
+include("tracer_adv.jl")
+include("coriolis.jl")
+include("forcing.jl")
+include("bottom_topography.jl")
+include("rhs.jl")
+include("continuity.jl")
+include("time_integration.jl")
+include("ghost_points.jl")
+include("initial_conditions.jl")
+include("preallocate.jl")
+
+# OUTPUT AND FEEDBACK
+include("src/feedback.jl")
+include("src/output.jl")
+
+end
diff --git a/src/RunJuls.jl b/src/RunJuls.jl
new file mode 100644
index 0000000..a894003
--- /dev/null
+++ b/src/RunJuls.jl
@@ -0,0 +1,116 @@
+function RunJuls(::Type{T}=Float32;     # number format
+
+    # DOMAIN RESOLUTION AND RATIO
+    nx::Int=100,                        # number of grid cells in x-direction
+    Lx::Real=1000e3,                    # length of the domain in x-direction [m]
+    L_ratio::Real=1,                    # Domain aspect ratio of Lx/Ly
+
+    # PHYSICAL CONSTANTS
+    gravity::Real=10.,                  # gravitational acceleration [m/s]
+    water_depth::Real=500.,             # layer thickness at rest [m]
+    ρ::Real=1e3,                        # density [kg/m^3]
+    ϕ::Real=15.,                        # central latitue of the domain (for coriolis) [°]
+    ω::Real=2π/(24*3600),               # Earth's angular frequency [s^-1]
+    R::Real=6.371e6,                    # Earth's radius [m]
+
+    # WIND FORCING OPTIONS
+    wind_forcing_x::String="channel",   # "channel", "double_gyre", "shear","constant" or "none"
+    wind_forcing_y::String="none",      # "channel", "double_gyre", "shear","constant" or "none"
+    Fx0::Real=0.12,                     # wind stress strength [Pa] in x-direction
+    Fy0::Real=0.0,                      # wind stress strength [Pa] in y-direction
+
+    # BOTTOM TOPOGRAPHY OPTIONS
+    topography_feature::String="ridge", # "ridge", "seamount", "flat", "ridges", "bathtub"
+    topofeat_height::Real=10.,          # height of seamount [m]
+    topofeat_width::Real=300e3,         # horizontal scale [m] of the seamount
+
+    # SURFACE RELAXATION
+    surface_relax::Bool=false,          # yes?
+    t_relax::Real=100.,                 # time scale of the relaxation [days]
+    η_refh::Real=5.,                    # height difference [m] of the interface relaxation profile
+    η_refw::Real=100e3,                 # width [m] of the tangent used for the interface relaxation
+
+    # SURFACE FORCING
+    surface_forcing::Bool=false,        # yes?
+    ωyr::Real=1.0,                      # (annual) frequency [1/year]
+    A₀::Real=3e-5,                      # Amplitude [m/s]
+
+    # TIME STEPPING OPTIONS
+    RKo::Int=4,                         # Order of the RK time stepping scheme (3 or 4)
+    cfl::Real=1.0,                      # CFL number (1.0 recommended for RK4, 0.6 for RK3)
+    Ndays::Real=100.0,                  # number of days to integrate for
+    nstep_diff::Int=1,                  # diffusive part every nstep_diff time steps.
+    nstep_advcor::Int=0,                # advection and coriolis update every nstep_advcor time steps.
+                                        # 0 means it is included in every RK4 substep
+
+    # BOUNDARY CONDITION OPTIONS
+    bc_x::String="periodic",            # "periodic" or anything else for nonperiodic
+    lbc::Real=2.,                       # lateral boundary condition parameter
+                                        # 0 free-slip, 0<lbc<2 partial-slip, 2 no-slip
+
+    # MOMENTUM ADVECTION OPTIONS
+    adv_scheme::String="ArakawaHsu",    # "Sadourny" or "ArakawaHsu"
+    dynamics::String="nonlinear",       # "linear" or "nonlinear"
+
+    # BOTTOM FRICTION OPTIONS
+    bottom_friction::String="quadratic",# "linear", "quadratic" or "none"
+    drag::Real=1e-5,                    # bottom drag coefficient [dimensionless] for quadratic
+    τdrag::Real=300.,                   # bottom drag coefficient [days] for linear
+
+    # DIFFUSION OPTIONS
+    diffusion::String="Smagorinsky",    # "Smagorinsky" or "Constant", biharmonic in both cases
+    ν_const::Real=500.0,                # [m^2/s] scaling constant for Constant biharmonic diffusion
+    c_smag::Real=0.15,                  # Smagorinsky coefficient [dimensionless]
+
+    # TRACER ADVECTION
+    tracer_advection::Bool=true,        # yes?
+    tracer_relaxation::Bool=false,      # yes?
+    tracer_consumption::Bool=false,     # yes?
+    tracer_pumping::Bool=false,         # yes?
+    injection_region::String="west",    # "west", "south", "rect" or flat
+    sst_initial::String="flat",         # same here
+    sstrestart::Bool=true,              # start from previous sst file
+    Uadv::Real=0.15,                    # Velocity scale [m/s] for tracer advection
+    SSTmax::Real=1.,                    # tracer (sea surface temperature) max for restoring
+    SSTmin::Real=0.,                    # tracer (sea surface temperature) min for restoring
+    τSST::Real=500.,                    # tracer restoring time scale [days]
+    jSST::Real=50*365.,                 # tracer consumption [days]
+    SST_λ0::Real=222e3,                 # [m] transition position of relaxation timescale
+    SST_λs::Real=111e3,                 # [m] transition width of relaxation timescale
+    SST_γ0::Real=8.35,                  # [days] injection time scale
+    SSTw::Real=1000e3,                  # width [m] of the tangent used for the IC and interface relaxation
+    SSTϕ::Real=0.5,                     # latitude/longitude fraction ∈ [0,1] of sst edge
+
+    # OUTPUT OPTIONS
+    output::Bool=true,                  # for nc output
+    output_tend::Bool=false,            # ouput for tendencies as well?
+    output_diagn::Bool=false,           # output diagnostic variables as well?
+
+                                        # which prognostic variables to output?
+    output_progn_vars::Array{String,1}=["u","v","eta","sst"],
+                                        # which tendencies to output?
+    output_tend_vars::Array{String,1}=["du","dv","deta","Bu","Bv","LLu1","LLu2","LLv1","LLv2",
+                                "qhv","qhu","dpdx","dpdy","dUdx","dVdy"],
+                                        # which diagnostic variables to output?
+    output_diagn_vars::Array{String,1}=["q","p","dudx","dvdy","dudy","dvdx","Lu",
+                                "Lv","xd","yd"],
+
+    output_dt::Real=6,                  # output time step [hours]
+    outpath::String="data/",            # path to output folder
+
+    # INITIAL CONDITIONS
+    initial_cond::String="rest",        # "rest" or "ncfile" for restart from file
+    initpath::String="data/",           # folder where to pick the restart files from
+    init_run_id::Int=0,                 # run id for restart from run number
+
+    ) where {T<:AbstractFloat}
+
+    G = grid()
+    C = constants()
+    Prog = initial_cond()
+    Diag = preallocate()
+    S = state(G,C,Prog,Diag)
+    time_integration(S)
+
+    return Prog
+end
diff --git a/test/runtests.jl b/test/runtests.jl
new file mode 100644
index 0000000..3999d8a
--- /dev/null
+++ b/test/runtests.jl
@@ -0,0 +1,6 @@
+using Juls
+using Test
+
+@testset "Test1"
+    @test false
+end