tadd function to set BCs and add tests of BC functionality - Granular.jl - Julia package for granular dynamics simulation
(HTM) git clone git://src.adamsgaard.dk/Granular.jl
(DIR) Log
(DIR) Files
(DIR) Refs
(DIR) README
(DIR) LICENSE
---
(DIR) commit 4947424934abc67010b9a1e184b5464373f1f94a
(DIR) parent 0c238ad9a3d7510cd2b9b285d482bf0607083dba
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Fri, 3 Nov 2017 14:13:40 -0400
add function to set BCs and add tests of BC functionality
Diffstat:
M src/atmosphere.jl | 4 ++--
M src/datatypes.jl | 36 +++++++++++++++++--------------
M src/grid.jl | 115 +++++++++++++++++++++++++++++++
M src/ocean.jl | 6 +++---
A test/periodic-boundaries.jl | 104 +++++++++++++++++++++++++++++++
M test/runtests.jl | 1 +
6 files changed, 245 insertions(+), 21 deletions(-)
---
(DIR) diff --git a/src/atmosphere.jl b/src/atmosphere.jl
t@@ -17,7 +17,7 @@ function createEmptyAtmosphere()
Array{Vector{Int}}(1, 1),
- 0, 0, 0, 0,
+ 1, 1, 1, 1,
false)
end
t@@ -129,7 +129,7 @@ function createRegularAtmosphereGrid(n::Vector{Int},
zl,
u, v,
Array{Array{Int, 1}}(size(xh, 1), size(xh, 2)),
- 0, 0, 0, 0,
+ 1, 1, 1, 1,
false)
end
(DIR) diff --git a/src/datatypes.jl b/src/datatypes.jl
t@@ -166,17 +166,17 @@ h-points. During read, the velocities are interpolated to the cell corners
* `grain_list::Array{Float64, Int}`: indexes of grains contained in the
ocean grid cells.
* `bc_west::Integer`: Boundary condition type for the west edge of the grid.
- 0: inactive,
- 1: periodic
+ 1: inactive,
+ 2: periodic
* `bc_south::Integer`: Boundary condition type for the south edge of the grid.
- 0: inactive,
- 1: periodic
+ 1: inactive,
+ 2: periodic
* `bc_east::Integer`: Boundary condition type for the east edge of the grid.
- 0: inactive,
- 1: periodic
+ 1: inactive,
+ 2: periodic
* `bc_north::Integer`: Boundary condition type for the north edge of the grid.
- 0: inactive,
- 1: periodic
+ 1: inactive,
+ 2: periodic
=#
mutable struct Ocean
input_file::Any
t@@ -243,17 +243,17 @@ cell corners (q-points).
* `grain_list::Array{Float64, Int}`: interface height relative to mean sea
level [m], dimensions correspond to placement in `[xh, yh, zi, time]`.
* `bc_west::Integer`: Boundary condition type for the west edge of the grid.
- 0: inactive,
- 1: periodic
+ 1: inactive,
+ 2: periodic
* `bc_south::Integer`: Boundary condition type for the south edge of the grid.
- 0: inactive,
- 1: periodic
+ 1: inactive,
+ 2: periodic
* `bc_east::Integer`: Boundary condition type for the east edge of the grid.
- 0: inactive,
- 1: periodic
+ 1: inactive,
+ 2: periodic
* `bc_north::Integer`: Boundary condition type for the north edge of the grid.
- 0: inactive,
- 1: periodic
+ 1: inactive,
+ 2: periodic
=#
mutable struct Atmosphere
input_file::Any
t@@ -306,3 +306,7 @@ mutable struct Simulation
Nc_max::Int
end
+
+# Mappings between boundary condition keys (Integers) and strings
+const grid_bc_strings = ["inactive", "periodic"]
+const grid_bc_flags = Dict(zip(grid_bc_strings, 1:length(grid_bc_strings)))
(DIR) diff --git a/src/grid.jl b/src/grid.jl
t@@ -617,3 +617,118 @@ function copyGridSortingInfo!(ocean::Ocean, atmosphere::Atmosphere,
atmosphere.grain_list = deepcopy(ocean.grain_list)
nothing
end
+
+export setGridBoundaryConditions!
+"""
+ setGridBoundaryConditions!(grid, grid_face, mode)
+
+Set boundary conditions for the granular phase at the edges of `Ocean` or
+`Atmosphere` grids. The target boundary can be selected through the `grid_face`
+argument, or the same boundary condition can be applied to all grid boundaries
+at once.
+
+When the center coordinate of grains crosses an inactive boundary (`mode =
+"inactive"`), the grain is disabled (`GrainCylindrical.enabled = false`). This
+keeps the grain in memory, but stops it from moving or interacting with other
+grains. *By default, all boundaries are inactive*.
+
+If the center coordinate of a grain crosses a periodic boundary (`mode =
+periodic`), the grain is repositioned to the opposite side of the model domain.
+Grains can interact mechanically across the periodic boundary.
+
+# Arguments
+* `grid::Any`: `Ocean` or `Atmosphere` grid to apply the boundary condition to.
+* `grid_face::String`: Grid face to apply the boundary condition to. Valid
+ values are any combination and sequence of `"west"` (-x), `"south"` (-y),
+ `"east"` (+x), `"north"` (+y). The values may be delimited in any way.
+ Also, and by default, all boundaries can be selected with `"all"` (-x, -y,
+ +x, +y), which overrides any other face selection.
+* `mode::String`: Boundary behavior, accepted values are `"inactive"` and
+ `"periodic"`. You cannot specify more than one mode at a time, so if
+ several modes are desired as boundary conditions for the grid, several calls
+ to this function should be made.
+* `verbose::Bool`: Confirm boundary conditions by reporting values to console.
+
+# Examples
+Set all boundaries for the ocean grid to be periodic:
+
+ setGridBoundaryConditions!(ocean, "periodic", "all")
+
+Set the south-north boundaries to be inactive, but the west-east boundaries to
+be periodic:
+
+ setGridBoundaryConditions!(ocean, "inactive", "south north")
+ setGridBoundaryConditions!(ocean, "periodic", "west east")
+
+"""
+function setGridBoundaryConditions!(grid::Any,
+ mode::String,
+ grid_face::String = "all";
+ verbose::Bool=true)
+
+ something_changed = false
+
+ if length(mode) <= 1
+ error("The mode string is required ('$mode')")
+ end
+
+ if !(mode in grid_bc_strings)
+ error("Mode '$mode' not recognized as a valid boundary condition type")
+ end
+
+ if contains(grid_face, "west")
+ grid.bc_west = grid_bc_flags[mode]
+ something_changed = true
+ end
+
+ if contains(grid_face, "south")
+ grid.bc_south = grid_bc_flags[mode]
+ something_changed = true
+ end
+
+ if contains(grid_face, "east")
+ grid.bc_east = grid_bc_flags[mode]
+ something_changed = true
+ end
+
+ if contains(grid_face, "north")
+ grid.bc_north = grid_bc_flags[mode]
+ something_changed = true
+ end
+
+ if grid_face == "all"
+ grid.bc_west = grid_bc_flags[mode]
+ grid.bc_south = grid_bc_flags[mode]
+ grid.bc_east = grid_bc_flags[mode]
+ grid.bc_north = grid_bc_flags[mode]
+ something_changed = true
+ end
+
+ if !something_changed
+ error("grid_face string '$grid_face' not understood, must be east, " *
+ "west, north, and/or south.")
+ end
+
+ if verbose
+ reportGridBoundaryConditions(grid)
+ end
+ nothing
+end
+
+export reportGridBoundaryConditions
+"""
+ reportGridBoundaryConditions(grid)
+
+Report the boundary conditions for the grid to the console.
+"""
+function reportGridBoundaryConditions(grid::Any)
+ println("West (-x): " * grid_bc_strings[grid.bc_west] *
+ "\t($(grid.bc_west))")
+ println("East (+x): " * grid_bc_strings[grid.bc_east] *
+ "\t($(grid.bc_east))")
+ println("South (-y): " * grid_bc_strings[grid.bc_south] *
+ "\t($(grid.bc_south))")
+ println("North (+y): " * grid_bc_strings[grid.bc_north] *
+ "\t($(grid.bc_north))")
+ nothing
+end
(DIR) diff --git a/src/ocean.jl b/src/ocean.jl
t@@ -18,7 +18,7 @@ function createEmptyOcean()
zeros(1,1,1,1),
zeros(1,1,1,1),
Array{Array{Int, 1}}(1, 1),
- 0, 0, 0, 0)
+ 1, 1, 1, 1)
end
export readOceanNetCDF
t@@ -61,7 +61,7 @@ function readOceanNetCDF(velocity_file::String, grid_file::String)
h,
e,
Array{Array{Int, 1}}(size(xh, 1), size(xh, 2)),
- 0, 0, 0, 0
+ 1, 1, 1, 1
)
return ocean
end
t@@ -242,7 +242,7 @@ function createRegularOceanGrid(n::Array{Int, 1},
zl, zi,
u, v, h, e,
Array{Array{Int, 1}}(size(xh, 1), size(xh, 2)),
- 0, 0, 0, 0)
+ 1, 1, 1, 1)
end
export addOceanDrag!
(DIR) diff --git a/test/periodic-boundaries.jl b/test/periodic-boundaries.jl
t@@ -0,0 +1,104 @@
+#!/usr/bin/env julia
+
+info("#### $(basename(@__FILE__)) ####")
+
+verbose=false
+i = 0
+
+info("Testing assignment and reporting of grid boundary conditions")
+ocean = Granular.createEmptyOcean()
+
+Test.@test ocean.bc_west == 1
+Test.@test ocean.bc_east == 1
+Test.@test ocean.bc_north == 1
+Test.@test ocean.bc_south == 1
+
+const originalSTDOUT = STDOUT
+(out_r, out_w) = redirect_stdout()
+Granular.reportGridBoundaryConditions(ocean)
+close(out_w)
+redirect_stdout(originalSTDOUT)
+output = convert(String, readavailable(out_r))
+Test.@test output == """West (-x): inactive\t(1)
+East (+x): inactive\t(1)
+South (-y): inactive\t(1)
+North (+y): inactive\t(1)
+"""
+
+(out_r, out_w) = redirect_stdout()
+Granular.setGridBoundaryConditions!(ocean, "periodic", "south, west", verbose=true)
+close(out_w)
+redirect_stdout(originalSTDOUT)
+output = convert(String, readavailable(out_r))
+Test.@test output == """West (-x): periodic\t(2)
+East (+x): inactive\t(1)
+South (-y): periodic\t(2)
+North (+y): inactive\t(1)
+"""
+Test.@test ocean.bc_west == 2
+Test.@test ocean.bc_east == 1
+Test.@test ocean.bc_north == 1
+Test.@test ocean.bc_south == 2
+
+(out_r, out_w) = redirect_stdout()
+Granular.setGridBoundaryConditions!(ocean, "inactive", "all", verbose=false)
+close(out_w)
+redirect_stdout(originalSTDOUT)
+output = convert(String, readavailable(out_r))
+Test.@test output == ""
+Test.@test ocean.bc_west == 1
+Test.@test ocean.bc_east == 1
+Test.@test ocean.bc_north == 1
+Test.@test ocean.bc_south == 1
+
+(out_r, out_w) = redirect_stdout()
+Granular.setGridBoundaryConditions!(ocean, "periodic", "all")
+close(out_w)
+output = convert(String, readavailable(out_r))
+redirect_stdout(originalSTDOUT)
+Test.@test output == """West (-x): periodic\t(2)
+East (+x): periodic\t(2)
+South (-y): periodic\t(2)
+North (+y): periodic\t(2)
+"""
+Test.@test ocean.bc_west == 2
+Test.@test ocean.bc_east == 2
+Test.@test ocean.bc_north == 2
+Test.@test ocean.bc_south == 2
+
+(out_r, out_w) = redirect_stdout()
+Granular.setGridBoundaryConditions!(ocean, "inactive")
+close(out_w)
+output = convert(String, readavailable(out_r))
+redirect_stdout(originalSTDOUT)
+Test.@test output == """West (-x): inactive\t(1)
+East (+x): inactive\t(1)
+South (-y): inactive\t(1)
+North (+y): inactive\t(1)
+"""
+Test.@test ocean.bc_west == 1
+Test.@test ocean.bc_east == 1
+Test.@test ocean.bc_north == 1
+Test.@test ocean.bc_south == 1
+
+(out_r, out_w) = redirect_stdout()
+Granular.setGridBoundaryConditions!(ocean, "periodic")
+close(out_w)
+output = convert(String, readavailable(out_r))
+redirect_stdout(originalSTDOUT)
+Test.@test output == """West (-x): periodic\t(2)
+East (+x): periodic\t(2)
+South (-y): periodic\t(2)
+North (+y): periodic\t(2)
+"""
+Test.@test ocean.bc_west == 2
+Test.@test ocean.bc_east == 2
+Test.@test ocean.bc_north == 2
+Test.@test ocean.bc_south == 2
+
+Test.@test_throws ErrorException Granular.setGridBoundaryConditions!(ocean,
+ "periodic",
+ "asdf")
+
+Test.@test_throws ErrorException Granular.setGridBoundaryConditions!(ocean,
+ "asdf")
(DIR) diff --git a/test/runtests.jl b/test/runtests.jl
t@@ -13,6 +13,7 @@ include("netcdf.jl")
include("vtk.jl")
include("jld.jl")
include("grid.jl")
+include("periodic-boundaries.jl")
include("ocean.jl")
include("atmosphere.jl")
include("memory-management.jl")