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	tfix various errors during test and wall initialization - Granular.jl - Julia p…
	git clone git://src.adamsgaard.dk/Granular.jl
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	---
	commit ccd9921a7fd354df82bcfcfb115844cc26278beb
	parent a9d41bf6abc198818ed79d3ff76f9be05bd9a80b
	Author: Anders Damsgaard <[email protected]>
	Date: Tue, 14 Nov 2017 14:58:58 -0500

	fix various errors during test and wall initialization

	Diffstat:
	M docs/src/man/getting_started.md \| 4 ++--
	M src/simulation.jl \| 4 ++--
	M src/wall.jl \| 61 +++++++++++++++++++++++++++++…
	M test/memory-management.jl \| 4 ++--
	M test/wall.jl \| 20 ++++++++++++++++++--

	5 files changed, 82 insertions(+), 11 deletions(-)
	---
	diff --git a/docs/src/man/getting_started.md b/docs/src/man/getting_started.md
	t@@ -16,14 +16,14 @@ The relevant functions are all contained in the `Granular`…
	imported with `import Granular`. Note: As per Julia conventions, functions
	that contain an exclamation mark (!) modify the values of the arguments.

	-Any of the functions called below are documented in the source code, and their
	+All of the functions called below are documented in the source code, and their
	documentation can be found in the [Public API Index](@ref main-index) in the
	online documentation, or simply from the Julia shell by typing `?<function
	name>`. An example:

	```julia-repl
	julia> ?Granular.createSimulation
	- createSimulation([id::String="unnamed"])
	+ createSimulation([id])

	Create a simulation object to contain all relevant variables such as tempora…
	parameters, fluid grids, grains, and contacts. The parameter id is used to
	diff --git a/src/simulation.jl b/src/simulation.jl
	t@@ -2,7 +2,7 @@

	export createSimulation
	"""
	- createSimulation([id::String="unnamed"])
	+ createSimulation([id])

	Create a simulation object to contain all relevant variables such as temporal
	parameters, fluid grids, grains, and contacts. The parameter `id` is used to
	t@@ -227,7 +227,7 @@ Add an `wall` to the `simulation` object. If `verbose` is…
	confirmation message will be printed to stdout.
	"""
	function addWall!(simulation::Simulation,
	- grain::WallLinearFrictionless,
	+ wall::WallLinearFrictionless,
	verbose::Bool = false)
	push!(simulation.walls, wall)

	diff --git a/src/wall.jl b/src/wall.jl
	t@@ -87,7 +87,7 @@ function addWallLinearFrictionless!(simulation::Simulation,

	# if not set, set wall mass to equal the mass of all grains.
	if isnan(mass)
	- if length(simulation.grains < 1)
	+ if length(simulation.grains) < 1
	error("If wall mass is not specified, walls should be added " *
	"after grains have been added to the simulation.")
	end
	t@@ -100,13 +100,13 @@ function addWallLinearFrictionless!(simulation::Simulati…

	# if not set, set wall thickness to equal largest grain thickness
	if isnan(thickness)
	- if length(simulation.grains < 1)
	+ if length(simulation.grains) < 1
	error("If wall thickness is not specified, walls should be added "…
	"after grains have been added to the simulation.")
	end
	thickness = -Inf
	for grain in simulation.grains
	- if grain.thickess > thickness
	+ if grain.thickness > thickness
	thickness = grain.thickness
	end
	end
	t@@ -128,3 +128,58 @@ function addWallLinearFrictionless!(simulation::Simulatio…
	nothing
	end

	+export getWallSurfaceArea
	+"""
	+ getWallSurfaceArea(simulation, wall_index)
	+
	+Returns the surface area of the wall given the grid size and its index.
	+
	+# Arguments
	+* `simulation::Simulation`: the simulation object containing the wall.
	+* `wall_index::Integer=1`: the wall number in the simulation object.
	+"""
	+function getWallSurfaceArea(sim::Simulation, wall_index::Integer)
	+
	+ if sim.walls[wall_index].normal ≈ [1., 0.]
	+ return (sim.ocean.yq[end,end] - sim.ocean.yq[1,1]) *
	+ sim.walls[wall_index].thickness
	+ elseif sim.walls[wall_index].normal ≈ [0., 1.]
	+ return (sim.ocean.xq[end,end] - sim.ocean.xq[1,1]) *
	+ sim.walls[wall_index].thickness
	+ else
	+ error("Wall normal not understood")
	+ end
	+ nothing
	+end
	+
	+export getWallNormalStress
	+"""
	+ getWallNormalStress(simulation[, wall_index, stress_type])
	+
	+Returns the current "effective" or "defined" normal stress on the wall with
	+index `wall_index` inside the `simulation` object. The returned value is given
	+in Pascal.
	+
	+# Arguments
	+* `simulation::Simulation`: the simulation object containing the wall.
	+* `wall_index::Integer=1`: the wall number in the simulation object.
	+* `stress_type::String="effective"`: the normal-stress type to return. The
	+ defined value corresponds to the normal stress that the wall is asked to
	+ uphold. The effective value is the actual current normal stress. Usually,
	+ the magnitude of the effective normal stress fluctuates around the defined
	+ normal stress.
	+"""
	+function getWallNormalStress(sim::Simulation;
	+ wall_index::Integer=1,
	+ stress_type::String="effective")
	+ if stress_type == "defined"
	+ return sim.walls[wall_index].normal_stress
	+
	+ elseif stress_type == "effective"
	+ return sim.walls[wall_index].force / getWallSurfaceArea(sim, wall_inde…
	+ sim.ocean)
	+ else
	+ error("stress_type not understood, should be 'effective' or 'defined'"…
	+ " but is '$stress_type'.")
	+ end
	+end
	diff --git a/test/memory-management.jl b/test/memory-management.jl
	t@@ -5,8 +5,8 @@ info("#### $(basename(@__FILE__)) ####")
	info("Testing memory footprint of Granular types")

	sim = Granular.createSimulation()
	-empty_sim_size = 96
	-empty_sim_size_recursive = 544
	+empty_sim_size = 104
	+empty_sim_size_recursive = 552

	@test sizeof(sim) == empty_sim_size
	@test Base.summarysize(sim) == empty_sim_size_recursive
	diff --git a/test/wall.jl b/test/wall.jl
	t@@ -28,6 +28,22 @@ Granular.addGrainCylindrical!(sim, [ 0., 0.], 10., 2., verb…
	sim.grains[1].mass = 1.0
	Granular.addWallLinearFrictionless!(sim, [1., 0.], 1., verbose=true)
	@test length(sim.walls) == 1
	-@test sim.walls.mass ≈ 1.0
	-@test sim.walls.mass ≈ 2.0
	+@test sim.walls[1].mass ≈ 1.0
	+@test sim.walls[1].thickness ≈ 2.0
	+
	+info("Test wall surface area and defined normal stress")
	+sim = Granular.createSimulation(id="test")
	+sim.ocean = Granular.createRegularOceanGrid([1, 1, 1], [10., 20., 1.0])
	+Granular.addGrainCylindrical!(sim, [ 0., 0.], 10., 2., verbose=false)
	+sim.grains[1].mass = 1.0
	+Granular.addWallLinearFrictionless!(sim, [1., 0.], 1., verbose=true)
	+Granular.addWallLinearFrictionless!(sim, [0., 1.], 1., verbose=true)
	+@test length(sim.walls) == 2
	+@test sim.walls[1].mass ≈ 1.0
	+@test sim.walls[1].thickness ≈ 2.0
	+@test sim.walls[2].mass ≈ 1.0
	+@test sim.walls[2].thickness ≈ 2.0
	+@test Granular.getWallSurfaceArea(sim, 1) ≈ 20.0*2.0
	+@test Granular.getWallSurfaceArea(sim, 2) ≈ 10.0*2.0
	+