Merge branch 'sm/3d'

.gitignore

@@ -1,2 +1,3 @@
+.github/workflows/CI.yml
 docs/build/
 plotnodes.py

problems/equations/CompEuler/wave1d_lag/user_inputs.jl

@@ -32,16 +32,14 @@ function user_inputs()
         # Mesh paramters and files:
         #---------------------------------------------------------------------------
         :lread_gmsh          => false, #If false, a 1D problem will be enforced
-        #:gmsh_filename       => "./meshes/gmsh_grids/2d-grid.msh", 
-        #:gmsh_filename       => "./meshes/gmsh_grids/hexa_TFI_25x25.msh",
-        #:gmsh_filename       => "./meshes/gmsh_grids/circle_TFI.msh",
-        #:gmsh_filename        => "./meshes/gmsh_grids/hexa_TFI_10x10_periodic.msh",
         #---------------------------------------------------------------------------
         # Output formats: "png" -> plots to png file. "ascii" -> data to npoin file
         #---------------------------------------------------------------------------
-        :outformat     => "png", #choice: "png", "ascii" (default is ascii)
-        :plot_vlines   => [-2.5,2.5],
-        :plot_axis     => [-0.05,0.55, -0.35,0.35],
+        :outformat         => "png", #choice: "png", "ascii" (default is ascii)
+        :loverwrite_output => true,
+        :output_dir        => "./CI-runs", #this is in github 
+        :plot_vlines       => [-2.5,2.5],
+        :plot_axis         => [-0.05,0.55, -0.35,0.35],
         #---------------------------------------------------------------------------
         # 1D (lread_gmsh => faluse): the grid is built by jexpresso
         #---------------------------------------------------------------------------

test/CI-ref/CompEuler/theta/user_inputs.jl

@@ -0,0 +1,56 @@
+function user_inputs()
+    inputs = Dict(
+        #---------------------------------------------------------------------------
+        # User define your inputs below: the order doesn't matter
+        #---------------------------------------------------------------------------
+        :ode_solver           => SSPRK54(), #ORK256(),#SSPRK33(), #SSPRK33(), #SSPRK54(),
+        :Δt                   => 0.4,
+        :tinit                => 0.0,
+        :tend                 => 1000.0,
+        #:tinit                => 100.0,
+        #:tend                 => 1000.0,
+        #:lrestart             => true,
+        :restart_input_file_path => "./output/CompEuler/theta/output-19Nov2023-115126",
+        :ndiagnostics_outputs => 2,
+        #:case                 => "rtb",
+        :lsource              => true, 
+        #---------------------------------------------------------------------------
+        #Integration and quadrature properties
+        #---------------------------------------------------------------------------
+        :interpolation_nodes =>"lgl",
+        :nop                 => 4,      # Polynomial order
+        #---------------------------------------------------------------------------
+        # Physical parameters/constants:
+        #---------------------------------------------------------------------------
+        :lvisc                => true, #false by default NOTICE: works only for Inexact
+        :ivisc_equations      => (1, 2, 3, 4),
+        :μ                   => (0.0, 20.0, 20.0, 60.0), #horizontal viscosity constant for momentum
+        #---------------------------------------------------------------------------
+        # Mesh paramters and files:
+        #---------------------------------------------------------------------------
+        :lread_gmsh          => true, #If false, a 1D problem will be enforced
+        #:gmsh_filename       => "./meshes/gmsh_grids/hexa_circle.msh",
+        :gmsh_filename       => "./meshes/gmsh_grids/hexa_TFI_RTB20x20.msh", #for nop=4
+        #---------------------------------------------------------------------------
+        # Filter parameters
+        #---------------------------------------------------------------------------
+        #:lfilter             => true,
+        #:mu_x                => 0.01,
+        #:mu_y                => 0.01,
+        #:filter_type         => "erf",
+        #---------------------------------------------------------------------------
+        # Plotting parameters
+        #---------------------------------------------------------------------------
+        :outformat           => "vtk",
+        :loverwrite_output   => true,
+        :output_dir          => "./output/",
+        :loutput_pert        => true,  #this is only implemented for VTK for now
+        #---------------------------------------------------------------------------
+    ) #Dict
+    #---------------------------------------------------------------------------
+    # END User define your inputs below: the order doesn't matter
+    #---------------------------------------------------------------------------
+
+    return inputs
+
+end

test/CI-ref/CompEuler/wave1d_lag/user_inputs.jl

@@ -0,0 +1,55 @@
+function user_inputs()
+    inputs = Dict(
+        #---------------------------------------------------------------------------
+        #
+        # User define your inputs below: the order doesn't matter
+        # IMPORTANT NOTICE: DO NOT FORGET the "," at the end of each entry!!!
+        #---------------------------------------------------------------------------
+        :ode_solver          => SSPRK33(),
+        :tend                 => 9.0,
+        :Δt                   => 1.0e-3,
+        :ndiagnostics_outputs => 30, #these are steps, not seconds
+        :output_dir          => "./output/",
+        #---------------------------------------------------------------------------
+        #Integration and quadrature properties
+        #---------------------------------------------------------------------------
+        :interpolation_nodes => "lgl", # Choice: "lgl", "cg", "cgl"
+        :nop                 => 6,     # Polynomial order
+        :nop_laguerre        => 50,
+        :lexact_integration  => false,
+        :lsource             => true,
+        :llaguerre_1d_right  => true,
+        :llaguerre_1d_left   => true,
+        :laguerre_beta       => 1.0,
+        :yfac_laguerre       => 0.05,
+        #---------------------------------------------------------------------------
+        # Physical parameters/constants:
+        #---------------------------------------------------------------------------
+        :lvisc                => false,
+        :νx                   => 0.01, #kinematic viscosity constant
+        :νy                   => 0.01, #kinematic viscosity constant
+        #---------------------------------------------------------------------------
+        # Mesh paramters and files:
+        #---------------------------------------------------------------------------
+        :lread_gmsh          => false, #If false, a 1D problem will be enforced
+        #---------------------------------------------------------------------------
+        # Output formats: "png" -> plots to png file. "ascii" -> data to npoin file
+        #---------------------------------------------------------------------------
+        :outformat         => "hdf5", #choice: "png", "ascii" (default is ascii)
+        :loverwrite_output => true,
+        :plot_vlines       => [-2.5,2.5],
+        :plot_axis         => [-0.05,0.55, -0.35,0.35],
+        #---------------------------------------------------------------------------
+        # 1D (lread_gmsh => faluse): the grid is built by jexpresso
+        #---------------------------------------------------------------------------
+        :xmin          =>   -2.5,
+        :xmax          =>   2.5,
+        :nelx          =>   50,
+    ) #Dict
+    #---------------------------------------------------------------------------
+    # END User define your inputs below: the order doesn't matter
+    #---------------------------------------------------------------------------
+
+    return inputs
+
+end

test/CI-runs/CompEuler/runtests.jl

@@ -3,5 +3,7 @@ module CompEulerTests
 using Test
 
 @testset "theta" begin include("theta/thetaTests.jl") end
+@testset "thetaTracers" begin include("thetaTracers/thetaTests.jl") end
+@testset "wave1d_lag" begin include("wave1d_lag/Tests.jl") end
 
 end # module

test/CI-runs/CompEuler/theta/user_inputs.jl

@@ -43,7 +43,6 @@ function user_inputs()
         #---------------------------------------------------------------------------
         :outformat           => "hdf5",
         :loverwrite_output   => true,
-        # :output_dir          => "./test/CI-runs",
         :output_dir          => "./CI-runs", #this is in github
         :loutput_pert        => true,  #this is only implemented for VTK for now
         #---------------------------------------------------------------------------

test/CI-runs/CompEuler/thetaTracers/thetaTests.jl

@@ -0,0 +1,10 @@
+module CompEulerthetaTests
+
+project_root = dirname(Base.current_project())
+include(joinpath(project_root, "test", "solnCompare.jl"))
+
+using .solnCompare
+using Test
+
+@testset "JEXPRESSO Examples" begin run_example("CompEuler", "thetaTracers") end
+end # module

test/CI-runs/CompEuler/thetaTracers/user_inputs.jl

@@ -30,7 +30,6 @@ function user_inputs()
         #---------------------------------------------------------------------------
         :outformat           => "hdf5",
         :loverwrite_output   => true,
-        #:output_dir          => "./test/CI-runs",
         :output_dir          => "./CI-runs",
         :loutput_pert        => true,  #this is only implemented for VTK for now
         #---------------------------------------------------------------------------

test/CI-runs/CompEuler/wave1d_lag/Tests.jl

@@ -0,0 +1,10 @@
+module CompEulerthetaTests
+
+project_root = dirname(Base.current_project())
+include(joinpath(project_root, "test", "solnCompare.jl"))
+
+using .solnCompare
+using Test
+
+@testset "JEXPRESSO Examples" begin run_example("CompEuler", "wave1d_lag") end
+end # module

test/CI-runs/CompEuler/wave1d_lag/initialize.jl

@@ -0,0 +1,40 @@
+function initialize(SD, PT, mesh::St_mesh, inputs::Dict, OUTPUT_DIR::String, TFloat)
+    """
+
+    """
+    @info " Initialize fields for 1D adv diff ........................ "
+
+    #---------------------------------------------------------------------------------
+    # Solution variables:
+    #
+    # NOTICE: while these names can be arbitrary, the length of this tuple
+    # defines neqs, which is used to allocate all necessary equation-dependent arrays
+    # 
+    #---------------------------------------------------------------------------------
+    qvars = ("u", "v")
+    q = define_q(SD, mesh.nelem, mesh.npoin, mesh.ngl, qvars, TFloat; neqs=length(qvars))
+    #---------------------------------------------------------------------------------
+
+    σ = Float64(0.15)
+    σ2= σ*σ
+    for ip=1:mesh.npoin        
+            x = mesh.x[ip]
+
+            ex = -(x - 0.0)^2/σ2
+            q.qn[ip,1] = 2^ex
+            q.qn[ip,2] = 0.0
+
+            #Store initial background state for plotting and analysis of pertuebations
+            q.qe[ip,1] = 0.0
+            q.qe[ip,2] = 0.0
+
+    end
+
+    for ivar=1:length(qvars)
+        plot_initial(SD, mesh.x, q.qn[:,ivar], ivar, OUTPUT_DIR)
+    end
+
+    @info " Initialize fields for 1D adv diff ........................ DONE "
+
+    return q
+end

test/CI-runs/CompEuler/wave1d_lag/user_bc.jl

@@ -0,0 +1,41 @@
+"""
+    qibdy is an Array{Floats} of size `nvars`
+
+    src/equations/EQUATIONS_NAME/user_bc.jl contains a set of user-defined boundary conditions functions
+    that can be modified as needed.
+
+    The function defined in src/equations/EQUATIONS_NAME/user_bc.jl 
+    are called by the b.c. functions defined in src/kernel/custom_bcs.jl
+    within a boundary-edge loop that detects the "tag" string defined in the user-generated *.msh file.
+
+    For example:
+    If some domain boundaries of gmsh file mymesh.msh are tagged as "inflow" and "no_slip", then the user
+    creating the functions in user_bc.jl must define the behavior of the unknown or its derivatives
+    on those boundaries.
+
+    ```math
+    if (tag === "inflow")
+        qibdy[1] = 3.0
+    elseif (tag === "fix_temperature")
+        qibdy[2] = 300.0
+    end
+    return qibdy
+    ```
+    where  `qibdy[i=1:nvar]` is the value unknown `i`
+    
+"""
+function user_bc_dirichlet!(q::SubArray{Float64}, x::AbstractFloat, t::AbstractFloat, tag::String,qbdy::AbstractArray,qe::SubArray{Float64},::TOTAL)
+
+   nothing
+end
+
+function user_bc_dirichlet!(q::SubArray{Float64}, x::AbstractFloat, t::AbstractFloat, tag::String,qbdy::AbstractArray,qe::SubArray{Float64},::PERT)
+
+   nothing
+end
+
+function user_bc_neumann(q::AbstractArray, gradq::AbstractArray, x::AbstractFloat, t::AbstractFloat, inputs::Dict)
+
+    flux = zeros(size(q,2),1)
+    return flux
+end

test/CI-runs/CompEuler/wave1d_lag/user_flux.jl

@@ -0,0 +1,10 @@
+function user_flux!(F::SubArray{Float64}, G::SubArray{Float64}, SD::NSD_1D,
+                    q::SubArray{Float64},
+                    qe::SubArray{Float64},
+                    mesh::St_mesh,
+                    ::CL, ::TOTAL; neqs=4, ip=1)
+
+    F[1] = q[2]
+    F[2] = q[1]
+
+end

test/CI-runs/CompEuler/wave1d_lag/user_inputs.jl

@@ -0,0 +1,56 @@
+function user_inputs()
+    inputs = Dict(
+        #---------------------------------------------------------------------------
+        #
+        # User define your inputs below: the order doesn't matter
+        # IMPORTANT NOTICE: DO NOT FORGET the "," at the end of each entry!!!
+        #---------------------------------------------------------------------------
+        :ode_solver          => SSPRK33(),
+        :tend                 => 9.0,
+        :Δt                   => 1.0e-3,
+        :ndiagnostics_outputs => 30, #these are steps, not seconds
+        :output_dir          => "./output/",
+        #---------------------------------------------------------------------------
+        #Integration and quadrature properties
+        #---------------------------------------------------------------------------
+        :interpolation_nodes => "lgl", # Choice: "lgl", "cg", "cgl"
+        :nop                 => 6,     # Polynomial order
+        :nop_laguerre        => 50,
+        :lexact_integration  => false,
+        :lsource             => true,
+        :llaguerre_1d_right  => true,
+        :llaguerre_1d_left   => true,
+        :laguerre_beta       => 1.0,
+        :yfac_laguerre       => 0.05,
+        #---------------------------------------------------------------------------
+        # Physical parameters/constants:
+        #---------------------------------------------------------------------------
+        :lvisc                => false,
+        :νx                   => 0.01, #kinematic viscosity constant
+        :νy                   => 0.01, #kinematic viscosity constant
+        #---------------------------------------------------------------------------
+        # Mesh paramters and files:
+        #---------------------------------------------------------------------------
+        :lread_gmsh          => false, #If false, a 1D problem will be enforced
+        #---------------------------------------------------------------------------
+        # Output formats: "png" -> plots to png file. "ascii" -> data to npoin file
+        #---------------------------------------------------------------------------
+        :outformat         => "hdf5", #choice: "png", "ascii" (default is ascii)
+        :loverwrite_output => true,
+        :output_dir        => "./CI-runs", #this is in github 
+        :plot_vlines       => [-2.5,2.5],
+        :plot_axis         => [-0.05,0.55, -0.35,0.35],
+        #---------------------------------------------------------------------------
+        # 1D (lread_gmsh => faluse): the grid is built by jexpresso
+        #---------------------------------------------------------------------------
+        :xmin          =>   -2.5,
+        :xmax          =>   2.5,
+        :nelx          =>   50,
+    ) #Dict
+    #---------------------------------------------------------------------------
+    # END User define your inputs below: the order doesn't matter
+    #---------------------------------------------------------------------------
+
+    return inputs
+
+end

test/CI-runs/CompEuler/wave1d_lag/user_source.jl

@@ -0,0 +1,35 @@
+function user_source!(S::SubArray{Float64}, q::SubArray{Float64}, qe::SubArray{Float64}, npoin, ::CL,::TOTAL; neqs=1,x=0.0, y=0.0, ymin=0.0, ymax=30000.0, ngl=5, nely=10,xmin = -120000, xmax =120000)
+
+    PhysConst = PhysicalConst{Float64}()
+
+    #
+    # S(q(x)) = -ρg
+    #
+
+    if (x >= 2.49)#nsponge_points * dsy) #&& dbl >= 0.0)
+        sponge_coe = 2.0/(1+exp((0.3*(xmax-2.5)-x+2.5)/((xmax)/18)))
+    elseif (x <=-2.49)
+        sponge_coe = 2.0/(1+exp(-(0.3*(xmin+2.5)-x-2.5)/((xmax)/18)))
+    else
+        sponge_coe = 0.0
+    end
+    #@info xmin,xmax,x,sponge_coe
+    zt = xmax
+    zd = 5000.0
+    z = max(x-zd,0.0)
+    dgamma  =0.00005
+    alpha = 0.85
+    sigma = zt/18.0
+    fac1 = (alpha*zt-x)/sigma
+    #=if (x >=60.0)
+      cs = dgamma/(1+exp(fac1))
+    else
+     cs = 0.0
+    end=#
+    #cs = 1.0*sinpi(0.5*z/(zt-zd))^2
+    cs = min(sponge_coe,1)
+    #@info "β x: " ctop,cxr,cxl,cs, zs, y, x, ymin, ymax, dsy, dbl
+    S[1] = -(cs)*(q[1])
+    S[2] = -(cs)*(q[2])
+    return  S
+end

test/solnCompare.jl

@@ -81,8 +81,9 @@ function run_example(parsed_equations::String, parsed_equations_case_name::Strin
         end
 
     finally
+        nothing
         # Ensure we navigate back to the initial directory
-        cd(project_root)
+#        cd(project_root)
     end
 end