tfix a few calls in shear example - Granular.jl - Julia package for granular dynamics simulation
  HTML git clone git://src.adamsgaard.dk/Granular.jl
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       ---
   DIR commit 45f3f14973f267dc21f19b4fd84bb7d36f1fc528
   DIR parent ef80fff084cc711ed619362809d7b02b38888954
  HTML Author: Anders Damsgaard <andersd@riseup.net>
       Date:   Wed, 15 Nov 2017 21:14:46 -0500
       
       fix a few calls in shear example
       
       Diffstat:
         M examples/shear.jl                   |      22 ++++++++++++++--------
       
       1 file changed, 14 insertions(+), 8 deletions(-)
       ---
   DIR diff --git a/examples/shear.jl b/examples/shear.jl
       t@@ -80,12 +80,12 @@ Granular.zeroKinematics!(sim)
        # normal of this wall is downwards, and we place it at the top of the granular
        # assemblage
        y_top = -Inf
       -for grain in grains
       +for grain in sim.grains
            if y_top < grain.lin_pos[2] + grain.contact_radius
                y_top = grain.lin_pos[2] + grain.contact_radius
            end
        end
       -Granular.addWallLinearFrictionless!(sim, normal=[0., 1.], pos=y_top,
       +Granular.addWallLinearFrictionless!(sim, [0., 1.], y_top,
                                            bc="normal stress", normal_stress=-N)
        
        # Resize the grid to span the current state
       t@@ -93,13 +93,13 @@ Granular.fitGridToGrains!(sim, sim.ocean)
        
        # Lock the grains at the very bottom so that the lower boundary is rough
        y_bot = Inf
       -for grain in grains
       +for grain in sim.grains
            if y_bot > grain.lin_pos[2] - grain.contact_radius
                y_bot = grain.lin_pos[2] - grain.contact_radius
            end
        end
        const fixed_thickness = 2. * r_max
       -for grain in grains
       +for grain in sim.grains
            if grain.lin_pos[2] <= fixed_thickness
                grain.fixed = true  # set x and y acceleration to zero
            end
       t@@ -140,7 +140,7 @@ sim.id = "$(id_prefix)-shear-N$(N)Pa-vel_shear$(vel_shear)m-s"
        Granular.zeroKinematics!(sim)
        
        # Prescribe the shear velocity to the uppermost grains
       -for grain in grains
       +for grain in sim.grains
            if grain.lin_pos[2] <= fixed_thickness
        
                # do not allow changes in velocity
       t@@ -168,7 +168,7 @@ dilation = Float64[]
        const thickness_initial = sim.walls[1].pos - y_bot
        x_min = +Inf
        x_max = -Inf
       -for grain in grains
       +for grain in sim.grains
            if x_min > grain.lin_pos[1] - grain.contact_radius
                x_min = grain.lin_pos[1] - grain.contact_radius
            end
       t@@ -209,8 +209,11 @@ Granular.writeSimulation(sim)
        
        # Plot time vs. shear stress and dilation
        PyPlot.subplot(211)
       +PyPlot.subplots_adjust(hspace=0.0)
       +ax1 = gca()
       +PyPlot.setp(ax1[:get_xticklabels](),visible=false) # Disable x tick labels
        PyPlot.plot(time, shear_stress)
       -PyPlot.subplot(212)
       +PyPlot.subplot(212, sharex=ax1)
        PyPlot.plot(time, dilation)
        PyPlot.xlabel("Time [s]")
        PyPlot.ylabel("Shear stress [Pa]")
       t@@ -219,8 +222,11 @@ PyPlot.clf()
        
        # Plot shear strain vs. shear stress and dilation
        PyPlot.subplot(211)
       +PyPlot.subplots_adjust(hspace=0.0)
       +ax1 = gca()
       +PyPlot.setp(ax1[:get_xticklabels](),visible=false) # Disable x tick labels
        PyPlot.plot(time, shear_stress)
       -PyPlot.subplot(212)
       +PyPlot.subplot(212, sharex=ax1)
        PyPlot.plot(shear_strain, dilation)
        PyPlot.xlabel("Shear strain [-]")
        PyPlot.ylabel("Shear stress [Pa]")