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	tadding compaction - granular-basin - tectonic deformation experiments with Gra…
	git clone git://src.adamsgaard.dk/granular-basin
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	---
	commit cd32b191b93ebb5d1c54be67aeec99786859a276
	parent 17b81e04e6254eb55cd4bd301b3195443d211114
	Author: esbenpalmstrom <[email protected]>
	Date: Tue, 9 Nov 2021 09:59:43 +0100

	adding compaction

	Diffstat:
	A compaction.jl \| 95 ++++++++++++++++++++++++++++++

	1 file changed, 95 insertions(+), 0 deletions(-)
	---
	diff --git a/compaction.jl b/compaction.jl
	t@@ -0,0 +1,95 @@
	+import Granular
	+import JLD2
	+import PyPlot
	+import Dates
	+
	+sim = Granular.readSimulation("stacked60k.jld2")
	+SimSettings = JLD2.load("SimSettings.jld2")
	+
	+N = 20e3
	+SimSettings["N"] = N
	+
	+JLD2.save("SimSettings.jld2", SimSettings)
	+
	+t_comp = 10.0 #compaction max duration [s]
	+
	+sim.id = "compaction-N$(N)Pa"
	+
	+Granular.zeroKinematics!(sim)
	+
	+y_top = -Inf
	+for grain in sim.grains
	+ grain.contact_viscosity_normal = 0
	+ if y_top < grain.lin_pos[2] + grain.contact_radius
	+ global y_top = grain.lin_pos[2] + grain.contact_radius
	+ end
	+end
	+
	+Granular.addWallLinearFrictionless!(sim, [0., 1.],y_top,
	+ bc="normal stress",
	+ normal_stress=-N,
	+ contact_viscosity_normal=1e3)
	+
	+Granular.fitGridToGrains!(sim,sim.ocean)
	+
	+y_bot = Inf
	+for grain in sim.grains
	+ if y_bot > grain.lin_pos[2] - grain.contact_radius
	+ global y_bot = grain.lin_pos[2] - grain.contact_radius
	+ end
	+end
	+fixed_thickness = 2. * SimSettings["r_max"]
	+for grain in sim.grains
	+ if grain.lin_pos[2] <= fixed_thickness
	+ grain.fixed = true # set x and y acceleration to zero
	+ end
	+end
	+
	+Granular.resetTime!(sim)
	+
	+Granular.setTotalTime!(sim,t_comp)
	+
	+time = Float64[]
	+compaction = Float64[]
	+effective_normal_stress = Float64[]
	+
	+filen = 1
	+t_start = Dates.now()
	+
	+
	+while sim.time < sim.time_total
	+
	+ for i = 1:100 #run for a while before measuring the state of the top wall
	+ Granular.run!(sim, single_step=true)
	+ end
	+
	+ #Granular.writeSimulation(sim,filename = "compaction-N$(N)Pa/comp$(filen).…
	+ filen = filen+1
	+
	+ append!(time, sim.time)
	+ append!(compaction, sim.walls[1].pos)
	+ append!(effective_normal_stress, Granular.getWallNormalStress(sim))
	+
	+ t_now = Dates.now()
	+ dur = Dates.canonicalize(t_now-t_start)
	+ print("Time elapsed: ",dur)
	+end
	+
	+defined_normal_stress = ones(length(effective_normal_stress)) *
	+ Granular.getWallNormalStress(sim, stress_type="effective")
	+
	+PyPlot.subplot(211)
	+PyPlot.subplots_adjust(hspace=0.0)
	+ax1 = PyPlot.gca()
	+PyPlot.setp(ax1[:get_xticklabels](),visible=false) # Disable x tick labels
	+PyPlot.plot(time, compaction)
	+PyPlot.ylabel("Top wall height [m]")
	+PyPlot.subplot(212, sharex=ax1)
	+PyPlot.plot(time, defined_normal_stress)
	+PyPlot.plot(time, effective_normal_stress)
	+PyPlot.xlabel("Time [s]")
	+PyPlot.ylabel("Normal stress [Pa]")
	+PyPlot.savefig(sim.id * "-time_vs_compaction-stress.pdf")
	+PyPlot.clf()
	+
	+Granular.writeSimulation(sim,filename = "comp.jld2")