tAdd data structures and handling of fields associated with regular grids - Granular.jl - Julia package for granular dynamics simulation
(HTM) git clone git://src.adamsgaard.dk/Granular.jl
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---
(DIR) commit ea2796081adee6a056d0df05fba1ec0163ddcf0c
(DIR) parent ba27e7cf2151993e2d59aa43b13401a7aea19e5d
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Wed, 3 Jan 2018 10:42:11 -0500
Add data structures and handling of fields associated with regular grids
Diffstat:
M src/atmosphere.jl | 7 +++++--
M src/datatypes.jl | 16 ++++++++++++++++
M src/grid.jl | 8 ++++++++
M src/ocean.jl | 21 ++++++++++++++-------
M test/memory-management.jl | 2 +-
M test/runtests.jl | 10 +++++-----
6 files changed, 49 insertions(+), 15 deletions(-)
---
(DIR) diff --git a/src/atmosphere.jl b/src/atmosphere.jl
t@@ -21,7 +21,9 @@ function createEmptyAtmosphere()
1, 1, 1, 1,
- false)
+ false,
+
+ false, [1.,1.,1.], [1,1,1], [1.,1.,1.])
end
export interpolateAtmosphereVelocitiesToCorners
t@@ -138,7 +140,8 @@ function createRegularAtmosphereGrid(n::Vector{Int},
u, v,
Array{Array{Int, 1}}(size(xh, 1), size(xh, 2)),
bc_west, bc_south, bc_east, bc_north,
- false)
+ false,
+ true, L, n, dx)
end
export addAtmosphereDrag!
(DIR) diff --git a/src/datatypes.jl b/src/datatypes.jl
t@@ -237,6 +237,14 @@ mutable struct Ocean
bc_south::Integer
bc_east::Integer
bc_north::Integer
+
+ # If the grid is regular, allow for simpler particle sorting
+ regular_grid::Bool
+
+ # Grid size when regular_grid == true
+ L::Vector{Float64} # Grid length
+ n::Vector{Integer} # Cell count
+ dx::Vector{Float64} # Cell size
end
#=
t@@ -313,6 +321,14 @@ mutable struct Atmosphere
# If true the grid positions are identical to the ocean grid
collocated_with_ocean_grid::Bool
+
+ # If the grid is regular, allow for simpler particle sorting
+ regular_grid::Bool
+
+ # Grid size when regular_grid == true
+ L::Vector{Float64} # Grid length
+ n::Vector{Integer} # Cell count
+ dx::Vector{Float64} # Cell size
end
# Top-level simulation type
(DIR) diff --git a/src/grid.jl b/src/grid.jl
t@@ -284,6 +284,14 @@ function isPointInCell(grid::Any, i::Int, j::Int,
nw::Vector{Float64} = Vector{Float64}(2);
method::String="Conformal")
+ #=if grid.regular_grid
+ if [i,j] == Int.(ceil.(point ./ grid.dx[1:2]))
+ return true
+ else
+ return false
+ end
+ end=#
+
@views sw .= grid.xq[ i, j], grid.yq[ i, j]
@views se .= grid.xq[ i+1, j], grid.yq[ i+1, j]
@views ne .= grid.xq[ i+1, j+1], grid.yq[ i+1, j+1]
(DIR) diff --git a/src/ocean.jl b/src/ocean.jl
t@@ -20,7 +20,8 @@ function createEmptyOcean()
zeros(1,1,1,1),
zeros(1,1,1,1),
Array{Array{Int, 1}}(1, 1),
- 1, 1, 1, 1)
+ 1, 1, 1, 1,
+ false, [1.,1.,1.], [1,1,1], [1.,1.,1.])
end
export readOceanNetCDF
t@@ -29,12 +30,15 @@ Read ocean NetCDF files generated by MOM6 from disk and return as `Ocean` data
structure.
# Arguments
-* `velocity_file::String`: Path to NetCDF file containing ocean velocities,
+* `velocity_file::String`: path to NetCDF file containing ocean velocities,
etc., (e.g. `prog__####_###.nc`).
-* `grid_file::String`: Path to NetCDF file containing ocean super-grid
+* `grid_file::String`: path to NetCDF file containing ocean super-grid
information (typically `INPUT/ocean_hgrid.nc`).
+* `regular_grid::Bool=false`: `true` if the grid is regular (all cells
+ equal and grid is Cartesian) or `false` (default).
"""
-function readOceanNetCDF(velocity_file::String, grid_file::String)
+function readOceanNetCDF(velocity_file::String, grid_file::String;
+ regular_grid::Bool=false)
time, u, v, h, e, zl, zi = readOceanStateNetCDF(velocity_file)
xh, yh, xq, yq = readOceanGridNetCDF(grid_file)
t@@ -63,7 +67,9 @@ function readOceanNetCDF(velocity_file::String, grid_file::String)
h,
e,
Array{Array{Int, 1}}(size(xh, 1), size(xh, 2)),
- 1, 1, 1, 1
+ 1, 1, 1, 1,
+
+ false, [1.,1.,1.], [1,1,1], [1.,1.,1.]
)
return ocean
end
t@@ -216,7 +222,7 @@ one 4-th dimension matrix per `time` step. Sea surface will be at `z=0.` with
the ocean spanning `z<0.`. Vertical indexing starts with `k=0` at the sea
surface, and increases downwards.
"""
-function createRegularOceanGrid(n::Array{Int, 1},
+function createRegularOceanGrid(n::Vector{Int},
L::Vector{Float64};
origo::Vector{Float64} = zeros(2),
time::Vector{Float64} = zeros(1),
t@@ -250,7 +256,8 @@ function createRegularOceanGrid(n::Array{Int, 1},
zl, zi,
u, v, h, e,
Array{Array{Int, 1}}(size(xh, 1), size(xh, 2)),
- bc_west, bc_south, bc_east, bc_north)
+ bc_west, bc_south, bc_east, bc_north,
+ true, L, n, dx)
end
export addOceanDrag!
(DIR) diff --git a/test/memory-management.jl b/test/memory-management.jl
t@@ -6,7 +6,7 @@ info("Testing memory footprint of Granular types")
sim = Granular.createSimulation()
empty_sim_size = 104
-empty_sim_size_recursive = 552
+empty_sim_size_recursive = 752
@test sizeof(sim) == empty_sim_size
@test Base.summarysize(sim) == empty_sim_size_recursive
(DIR) diff --git a/test/runtests.jl b/test/runtests.jl
t@@ -1,12 +1,16 @@
using Compat.Test
import Granular
+include("grid.jl")
+include("contact-search-and-geometry.jl")
+include("grid-boundaries.jl")
+include("ocean.jl")
+include("atmosphere.jl")
include("wall.jl")
include("grain.jl")
include("packing.jl")
include("util.jl")
include("temporal.jl")
-include("contact-search-and-geometry.jl")
include("collision-2floes-normal.jl")
include("collision-5floes-normal.jl")
include("collision-2floes-oblique.jl")
t@@ -14,8 +18,4 @@ include("cohesion.jl")
include("netcdf.jl")
include("vtk.jl")
include("jld.jl")
-include("grid.jl")
-include("grid-boundaries.jl")
-include("ocean.jl")
-include("atmosphere.jl")
include("memory-management.jl")