tFix srand calls and print_with_color - 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 2e147d502dba2dd18246f4c0d7f92c40a235631d
(DIR) parent a424c3439fff74481ce41e7d33e29dd7d22d4f81
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Mon, 2 Apr 2018 15:02:49 -0400
Fix srand calls and print_with_color
Diffstat:
M examples/double_gyre.jl | 3 ++-
M examples/image.jl | 5 +++--
M examples/logo.jl | 5 +++--
M examples/strait.jl | 3 ++-
M src/grain.jl | 71 +++++++++++++++----------------
M src/grid.jl | 40 ++++++++++++++++---------------
M src/io.jl | 27 +++++++++++++--------------
M src/ocean.jl | 2 +-
M src/packing.jl | 23 ++++++++++++-----------
M src/simulation.jl | 1 -
M test/jld.jl | 3 ++-
M test/profiling.jl | 13 +++++++------
M test/util.jl | 3 ++-
13 files changed, 103 insertions(+), 96 deletions(-)
---
(DIR) diff --git a/examples/double_gyre.jl b/examples/double_gyre.jl
t@@ -1,6 +1,7 @@
#!/usr/bin/env julia
import Granular
import Compat
+using Compat.Random
sim = Granular.createSimulation(id="double_gyre")
t@@ -59,7 +60,7 @@ Compat.@info "added $(n_walls) fixed ice floes as walls"
# Initialize ice floes everywhere
floe_padding = .5*r
noise_amplitude = .8*floe_padding
-Compat.srand(1)
+srand(1)
for y in (4.*r + noise_amplitude):(2.*r + floe_padding):(L[2] - 4.*r -
noise_amplitude)
(DIR) diff --git a/examples/image.jl b/examples/image.jl
t@@ -4,6 +4,7 @@ import Granular
import FileIO
import Colors
import Compat
+using Compat.Random
const verbose = true
t@@ -89,12 +90,12 @@ if forcing == "gyres"
end
elseif forcing == "down" || forcing == "sandpile"
- Compat.srand(1)
+ srand(1)
sim.ocean.u[:, :, 1, 1] = (rand(nx+1, ny+1) - .5)*.1
sim.ocean.v[:, :, 1, 1] = -Ly/5.
elseif forcing == "convergent"
- Compat.srand(1)
+ srand(1)
sim.ocean.u[:, :, 1, 1] = (rand(nx+1, ny+1) - .5)*.1
for j=1:size(sim.ocean.u, 2)
sim.ocean.v[:, j, 1, 1] = -(j/ny - .5)*10.
(DIR) diff --git a/examples/logo.jl b/examples/logo.jl
t@@ -2,6 +2,7 @@
import Granular
import Compat
+using Compat.Random
const verbose = true
t@@ -119,12 +120,12 @@ if forcing == "gyres"
end
elseif forcing == "down"
- Compat.srand(1)
+ srand(1)
sim.ocean.u[:, :, 1, 1] = (rand(nx+1, ny+1) - .5)*.1
sim.ocean.v[:, :, 1, 1] = -5.
elseif forcing == "convergent"
- Compat.srand(1)
+ srand(1)
sim.ocean.u[:, :, 1, 1] = (rand(nx+1, ny+1) - .5)*.1
for j=1:size(sim.ocean.u, 2)
sim.ocean.v[:, j, 1, 1] = -(j/ny - .5)*10.
(DIR) diff --git a/examples/strait.jl b/examples/strait.jl
t@@ -1,6 +1,7 @@
#!/usr/bin/env julia
import SeaIce
import Compat
+using Compat.Random
sim = SeaIce.createSimulation(id="strait")
n = [10, 10, 2]
t@@ -87,7 +88,7 @@ dy = sqrt((2.*r_walls)^2. - dx^2.)
spacing_to_boundaries = 4.*r
floe_padding = .5*r
noise_amplitude = floe_padding
-Compat.srand(1)
+srand(1)
for y in (L[2] - r - noise_amplitude):(-(2.*r + floe_padding)):((L[2] -
Ly_constriction)/2. + Ly_constriction)
for x in (r + noise_amplitude):(2.*r + floe_padding):(Lx - r -
(DIR) diff --git a/src/grain.jl b/src/grain.jl
t@@ -346,27 +346,27 @@ function convertGrainDataToArrays(simulation::Simulation)
ifarr = GrainArrays(
# Material properties
## density
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
# Geometrical properties
## thickness
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## contact_radius
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## areal_radius
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## circumreference
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## horizontal_surface_area
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## side_surface_area
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## volume
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## mass
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## moment_of_inertia
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
# Linear kinematic degrees of freedom along horiz plane
## lin_pos
t@@ -394,58 +394,58 @@ function convertGrainDataToArrays(simulation::Simulation)
# Kinematic constraint flags
## fixed
- Array{Int}(length(simulation.grains)),
+ Array{Int}(undef, length(simulation.grains)),
## allow_x_acc
- Array{Int}(length(simulation.grains)),
+ Array{Int}(undef, length(simulation.grains)),
## allow_y_acc
- Array{Int}(length(simulation.grains)),
+ Array{Int}(undef, length(simulation.grains)),
## rotating
- Array{Int}(length(simulation.grains)),
+ Array{Int}(undef, length(simulation.grains)),
## enabled
- Array{Int}(length(simulation.grains)),
+ Array{Int}(undef, length(simulation.grains)),
# Rheological parameters
## contact_stiffness_normal
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## contact_stiffness_tangential
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## contact_viscosity_normal
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## contact_viscosity_tangential
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## contact_static_friction
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## contact_dynamic_friction
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## youngs_modulus
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## poissons_ratio
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## tensile_strength
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## shear_strength
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## strength_heal_rate
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## fracture_toughness
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
# Ocean/atmosphere interaction parameters
## ocean_drag_coeff_vert
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## ocean_drag_coeff_horiz
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## atmosphere_drag_coeff_vert
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## atmosphere_drag_coeff_horiz
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
# Interaction
## pressure
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
## n_contacts
- Array{Int}(length(simulation.grains)),
+ Array{Int}(undef, length(simulation.grains)),
## granular_stress
zeros(Float64, 3, length(simulation.grains)),
t@@ -455,11 +455,11 @@ function convertGrainDataToArrays(simulation::Simulation)
zeros(Float64, 3, length(simulation.grains)),
## thermal_energy
- Array{Float64}(length(simulation.grains)),
+ Array{Float64}(undef, length(simulation.grains)),
# Visualization parameters
## color
- Array{Int}(length(simulation.grains)),
+ Array{Int}(undef, length(simulation.grains)),
)
t@@ -607,7 +607,6 @@ function deleteGrainArrays!(ifarr::GrainArrays)
ifarr.thermal_energy = f1
ifarr.color = i1
- gc()
nothing
end
(DIR) diff --git a/src/grid.jl b/src/grid.jl
t@@ -1,5 +1,6 @@
-import Compat
+using Compat
using Compat.LinearAlgebra
+using Compat.Random
"""
bilinearInterpolation(field, x_tilde, y_tilde, i, j, k, it)
t@@ -256,10 +257,10 @@ found the function returns `(0,0)`.
not, can be "Conformal" (default) or "Area".
"""
function findCellContainingPoint(grid::Any, point::Vector{Float64},
- sw = Vector{Float64}(2),
- se = Vector{Float64}(2),
- ne = Vector{Float64}(2),
- nw = Vector{Float64}(2);
+ sw = Vector{Float64}(undef, 2),
+ se = Vector{Float64}(undef, 2),
+ ne = Vector{Float64}(undef, 2),
+ nw = Vector{Float64}(undef, 2);
method::String="Conformal")
for i=1:size(grid.xh, 1)
for j=1:size(grid.yh, 2)
t@@ -300,10 +301,10 @@ more robust. This function returns `true` or `false`.
"""
function isPointInCell(grid::Any, i::Int, j::Int,
point::Vector{Float64},
- sw::Vector{Float64} = Vector{Float64}(2),
- se::Vector{Float64} = Vector{Float64}(2),
- ne::Vector{Float64} = Vector{Float64}(2),
- nw::Vector{Float64} = Vector{Float64}(2);
+ sw::Vector{Float64} = Vector{Float64}(undef, 2),
+ se::Vector{Float64} = Vector{Float64}(undef, 2),
+ ne::Vector{Float64} = Vector{Float64}(undef, 2),
+ nw::Vector{Float64} = Vector{Float64}(undef, 2);
method::String="Conformal")
if grid.regular_grid
t@@ -351,10 +352,10 @@ area-based approach (`method = "Area"`), or a conformal mapping approach
function returns `true` or `false`.
"""
function isPointInGrid(grid::Any, point::Vector{Float64},
- sw::Vector{Float64} = Vector{Float64}(2),
- se::Vector{Float64} = Vector{Float64}(2),
- ne::Vector{Float64} = Vector{Float64}(2),
- nw::Vector{Float64} = Vector{Float64}(2);
+ sw::Vector{Float64} = Vector{Float64}(undef, 2),
+ se::Vector{Float64} = Vector{Float64}(undef, 2),
+ ne::Vector{Float64} = Vector{Float64}(undef, 2),
+ nw::Vector{Float64} = Vector{Float64}(undef, 2);
method::String="Conformal")
#sw, se, ne, nw = getCellCornerCoordinates(grid.xq, grid.yq, i, j)
t@@ -585,7 +586,7 @@ function findEmptyPositionInGridCell(simulation::Simulation,
for i_iter=1:n_iter
overlap_found = false
- Compat.srand(i*j*seed*i_iter)
+ srand(i*j*seed*i_iter)
# generate random candidate position
x_tilde = rand()
y_tilde = rand()
t@@ -625,7 +626,8 @@ function findEmptyPositionInGridCell(simulation::Simulation,
if overlap < 0.
if verbose
- Compat.@info "overlap with $grain_idx in cell $i,$j"
+ Compat.@info "overlap with $grain_idx in " *
+ "cell $i,$j"
end
overlap_found = true
break
t@@ -1048,10 +1050,10 @@ function findPorosity!(sim::Simulation, grid::Any; verbose::Bool=true)
sortGrainsInGrid!(sim, grid, verbose=verbose)
end
- sw = Vector{Float64}(2)
- se = Vector{Float64}(2)
- ne = Vector{Float64}(2)
- nw = Vector{Float64}(2)
+ @compat sw = Vector{Float64}(undef, 2)
+ @compat se = Vector{Float64}(undef, 2)
+ @compat ne = Vector{Float64}(undef, 2)
+ @compat nw = Vector{Float64}(undef, 2)
cell_area = 0.0
p = zeros(2)
r = 0.0
(DIR) diff --git a/src/io.jl b/src/io.jl
t@@ -3,7 +3,7 @@ import Compat
using Compat.LinearAlgebra
hasJLD = false
-if typeof(Pkg.installed("JLD")) == VersionNumber
+if typeof(Compat.Pkg.installed("JLD")) == VersionNumber
import JLD
hasJLD = true
end
t@@ -240,31 +240,31 @@ function status(folder::String=".";
if write_header
println("--------------------------------------" *
"--------------------------------------")
- print_with_color(:default, "simulation folder \t")
- print_with_color(time_color, " time \t")
- print_with_color(percentage_color, " completed ")
- print_with_color(lastfile_color, "last file \n")
+ Compat.printstyled("simulation folder \t", color=:default)
+ Compat.printstyled(" time \t", color=time_color)
+ Compat.printstyled(" completed ", color=percentage_color)
+ Compat.printstyled("last file \n", color=lastfile_color)
println("--------------------------------------" *
"--------------------------------------")
end
for file in status_files
data = readdlm(file)
- id = replace(file, ".status.txt", "")
- id = replace(id, "./", "")
- id = replace(id, r".*/", "")
+ id = Compat.replace(file, ".status.txt" => "")
+ id = Compat.replace(id, "./" => "")
+ id = Compat.replace(id, r".*/" => "")
time_s = @sprintf "%6.2fs" data[1]
time_h = @sprintf "%5.1fh" data[1]/(60. * 60.)
percentage = @sprintf "%3.0f%%" data[2]
lastfile = @sprintf "%5d" data[3]
if data[2] < 99.
- print_with_color(id_color_in_progress, "$id \t")
+ Compat.printstyled("$id \t", color=id_color_in_progress)
else
- print_with_color(id_color_complete, "$id \t")
+ Compat.printstyled("$id \t", color=id_color_complete)
end
- print_with_color(time_color, "$time_s ($time_h) \t")
- print_with_color(percentage_color, "$percentage \t")
- print_with_color(lastfile_color, "$lastfile \n")
+ Compat.printstyled("$time_s ($time_h) \t", color=time_color)
+ Compat.printstyled("$percentage \t", color=percentage_color)
+ Compat.printstyled("$lastfile \n", color=lastfile_color)
if visualize
sim = createSimulation(id)
t@@ -443,7 +443,6 @@ function writeGrainVTK(simulation::Simulation,
deleteGrainArrays!(ifarr)
ifarr = 0
- gc()
outfiles = WriteVTK.vtk_save(vtkfile)
if verbose
(DIR) diff --git a/src/ocean.jl b/src/ocean.jl
t@@ -3,7 +3,7 @@ using Compat.Test
using Compat.LinearAlgebra
hasNetCDF = false
-if typeof(Pkg.installed("NetCDF")) == VersionNumber
+if typeof(Compat.Pkg.installed("NetCDF")) == VersionNumber
import NetCDF
hasNetCDF = true
else
(DIR) diff --git a/src/packing.jl b/src/packing.jl
t@@ -1,6 +1,7 @@
## Functions for creating grain packings
import Compat
using Compat.LinearAlgebra
+using Compat.Random
export regularPacking!
"""
t@@ -44,7 +45,7 @@ function regularPacking!(simulation::Simulation,
r_rand = 0.
pos = zeros(2)
h = .5 # disc tickness
- Compat.srand(seed)
+ srand(seed)
if tiling == "square"
dx = r_max * 2. * (1. + padding_factor) # cell size
t@@ -178,7 +179,7 @@ function irregularPacking!(simulation::Simulation;
seed::Integer=1,
plot_during_packing::Bool=false,
verbose::Bool=true)
- Compat.srand(seed)
+ srand(seed)
active_list = Int[] # list of points to originate search from
i = 0
t@@ -207,9 +208,9 @@ function irregularPacking!(simulation::Simulation;
sortGrainsInGrid!(simulation, grid)
push!(active_list, 1)
else
- for i=1:length(simulation.grains)
- simulation.grains[i].color=1
- push!(active_list, i)
+ for idx=1:length(simulation.grains)
+ simulation.grains[idx].color=1
+ push!(active_list, idx)
end
end
t@@ -366,7 +367,7 @@ function rasterPacking!(sim::Simulation,
h = .5 # disc tickness
dx = r_max * 2. * (1. + padding_factor) # cell size
dx_padding = r_max * 2. * padding_factor
- Compat.srand(seed)
+ srand(seed)
np_init = length(sim.grains)
t@@ -450,15 +451,15 @@ function rasterMap(sim::Simulation, dx::Real)
#i, j = Int.(floor.((grain.lin_pos - origo) ./ dx)) + [1,1]
# Find corner indexes for box spanning the grain
- min_i, min_j = Int.(floor.((grain.lin_pos - origo -
- grain.contact_radius) ./ dx)) + [1,1]
- max_i, max_j = Int.(floor.((grain.lin_pos - origo +
- grain.contact_radius) ./ dx)) + [1,1]
+ min_i, min_j = Int.(floor.((grain.lin_pos - origo .-
+ grain.contact_radius) ./ dx)) .+ [1,1]
+ max_i, max_j = Int.(floor.((grain.lin_pos - origo .+
+ grain.contact_radius) ./ dx)) .+ [1,1]
# For each cell in box, check if the grain is contained
for i = min_i:max_i
for j = min_j:max_j
- cell_mid_point = dx .* Vector{Float64}([i,j]) - 0.5 * dx
+ cell_mid_point = dx .* Vector{Float64}([i,j]) .- 0.5 * dx
if (norm(cell_mid_point - grain.lin_pos) -
grain.contact_radius < dist)
(DIR) diff --git a/src/simulation.jl b/src/simulation.jl
t@@ -201,7 +201,6 @@ function run!(simulation::Simulation;
reportSimulationTimeToStdout(simulation)
println()
end
- gc()
nothing
end
(DIR) diff --git a/test/jld.jl b/test/jld.jl
t@@ -1,9 +1,10 @@
#!/usr/bin/env julia
+import Compat
Compat.@info "#### $(basename(@__FILE__)) ####"
Compat.@info "Determining if JLD is installed"
-if typeof(Pkg.installed("JLD")) == VersionNumber
+if typeof(Compat.Pkg.installed("JLD")) == VersionNumber
Compat.@info "JLD found, proceeding with JLD-specific tests"
Compat.@info "Writing simple simulation to JLD file"
(DIR) diff --git a/test/profiling.jl b/test/profiling.jl
t@@ -48,17 +48,18 @@ function timeSingleStepInDenseSimulation(nx::Int; verbose::Bool=true,
fixed=fixed, verbose=false)
end
end
- print_with_color(:green, "number of grains: $(length(sim.grains))\n")
+ Compat.printstyled("number of grains: $(length(sim.grains))\n",
+ color=:green)
if grid_sorting
if include_atmosphere
- print_with_color(:green, "using cell-based spatial decomposition " *
- " (ocean + atmosphere)\n")
+ Compat.printstyled("using cell-based spatial decomposition " *
+ " (ocean + atmosphere)\n", color=:green)
else
- print_with_color(:green, "using cell-based spatial " *
- "decomposition (ocean)\n")
+ Compat.printstyled("using cell-based spatial " *
+ "decomposition (ocean)\n", color=:green)
end
else
- print_with_color(:green, "using all-to-all contact search\n")
+ Compat.printstyled("using all-to-all contact search\n", color=:green)
end
Granular.setTotalTime!(sim, 1.0)
(DIR) diff --git a/test/util.jl b/test/util.jl
t@@ -1,5 +1,6 @@
#!/usr/bin/env julia
import Compat
+using Compat.Random
Compat.@info "#### $(basename(@__FILE__)) ####"
t@@ -14,7 +15,7 @@ Compat.@info "Testing power-law RNG"
@test 5 == length(Granular.randpower(5))
@test (5,) == size(Granular.randpower(5))
-Compat.srand(1)
+srand(1)
for i=1:10^5
@test 0. <= Granular.randpower() <= 1.
@test 0. <= Granular.randpower(1, 1., 0., 1.) <= 1.