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	tshearVel as alias of shearVelocity - sphere - GPU-based 3D discrete element me…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 3a0dffe3b2b4ac5ad6ad10473b1fb64f6741769d
	parent 452b1fc5599e039d19dc96986a4c97cc79016887
	Author: Anders Damsgaard <[email protected]>
	Date: Mon, 2 Mar 2015 13:15:16 +0100

	shearVel as alias of shearVelocity

	Diffstat:
	M python/halfshear-darcy-combined.py \| 34 ++++++++++++++++++++++++++---…
	M python/halfshear-darcy-rate-depend… \| 19 ++++++++++++++-----
	M python/sphere.py \| 24 ++++++------------------

	3 files changed, 49 insertions(+), 28 deletions(-)
	---
	diff --git a/python/halfshear-darcy-combined.py b/python/halfshear-darcy-combin…
	t@@ -12,6 +12,7 @@ import numpy
	import sphere
	import matplotlib.pyplot as plt
	import matplotlib.patches
	+import matplotlib.colors

	sid = 'halfshear-darcy-sigma0=80000.0-k_c=3.5e-13-mu=1.04e-07-ss=10000.0-A=700…
	outformat = 'pdf'
	t@@ -56,6 +57,7 @@ phi_bar = numpy.empty_like(t)

	# mean horizontal porosity plot
	poros = numpy.empty((sim.num[2], nsteps))
	+#xvel = numpy.zeros((sim.num[2], nsteps))
	zpos_c = numpy.empty(sim.num[2])
	dz = sim.L[2]/sim.num[2]
	for i in numpy.arange(sim.num[2]):
	t@@ -87,6 +89,21 @@ for i in numpy.arange(nsteps):

	poros[:,i] = numpy.average(numpy.average(sim.phi, axis=0),axis=0)

	+ # calculate mean values of xvel
	+ '''
	+ dz = sim.L[2]/(sim.num[2])
	+ for iz in numpy.arange(sim.num[2]):
	+ z_bot = iz*dz
	+ z_top = (iz+1)*dz
	+ I = numpy.nonzero((sim.x[:,2] >= z_bot) & (sim.x[:,2] < z_top))
	+ if I[0].size > 0:
	+ #print I
	+ #xvel[iz,i] = numpy.mean(sim.vel[I,0])
	+ xvel[iz,i] = numpy.mean(numpy.abs(sim.vel[I,0]))
	+ #print numpy.mean(sim.vel[I,0])
	+ #xvel[iz,i] = numpy.abs(numpy.mean(sim.vel[I,0]))
	+ '''
	+
	if calculateforcechains:
	if i > 0:
	loaded_contacts_prev = numpy.copy(loaded_contacts)
	t@@ -167,6 +184,7 @@ ax2.legend(lns, labs, loc='upper right', ncol=3,
	fancybox=True, framealpha=legend_alpha)
	ax1.set_ylim([-30, 200])
	#ax2.set_ylim(ax1.get_ylim())
	+ax2.set_ylim([-115,115])

	ax1.text(bbox_x, bbox_y, 'a',
	horizontalalignment=horizontalalignment,
	t@@ -239,18 +257,20 @@ ax7.text(bbox_x, bbox_y, 'd',

	## ax9: porosity, ax10: unused
	ax9 = plt.subplot(5, 1, 5, sharex=ax1)
	-#poros_max = numpy.max(poros[0:sim.wall0iz(),:])
	-#poros_min = numpy.min(poros)
	-#poros_max = 0.44
	poros_max = 0.45
	poros_min = 0.37
	cmap = matplotlib.cm.get_cmap('Blues_r')
	+#cmap = matplotlib.cm.get_cmap('afmhot')
	+#im9 = ax9.pcolormesh(t, zpos_c, poros,
	+#zpos_c = zpos_c[:-1]
	+#xvel = xvel[:-1]
	im9 = ax9.pcolormesh(t, zpos_c, poros,
	cmap=cmap,
	#cmap=matplotlib.cm.get_cmap('bwr'),
	#cmap=matplotlib.cm.get_cmap('coolwarm'),
	#vmin=-p_ext, vmax=p_ext,
	vmin=poros_min, vmax=poros_max,
	+ #norm=matplotlib.colors.LogNorm(vmin=1.0e-10, vmax=xvel.max()),
	rasterized=True)
	ax9.set_ylim([zpos_c[0], sim.w_x[0]])
	ax9.set_ylabel('Vertical position [m]')
	t@@ -273,9 +293,13 @@ ax9.add_patch(matplotlib.patches.Rectangle(
	facecolor='white'))

	cb9 = plt.colorbar(im9, cax=cbaxes,
	- ticks=[poros_min, poros_min + 0.5*(poros_max-poros_min), poros_max],
	+ ticks=[poros_min,
	+ poros_min + 0.5*(poros_max-poros_min),
	+ poros_max],
	+ #ticks=[xvel.min(), xvel.min() + 0.5*(xvel.max()-xvel.min()), xvel.max…
	orientation='horizontal',
	- extend='min', cmap=cmap)
	+ extend='min',
	+ cmap=cmap)
	cmap.set_under([8./255., 48./255., 107./255.])
	cb9.set_label('Mean horizontal porosity [-]')
	'''
	diff --git a/python/halfshear-darcy-rate-dependence.py b/python/halfshear-darcy…
	t@@ -126,13 +126,23 @@ for sid in sids:
	#c=shearstrain_nonzero[idxfit], linewidth=0.2,
	#cmap=matplotlib.cm.get_cmap('afmhot'))

	- ax1.plot(friction_fit, strainrate_fit)
	- ax1.plot(friction_fit2, strainrate_fit2)
	+ ## plastic limit
	+ x = [0.3, 0.3]
	+ y = ax1.get_ylim()
	+ limitcolor = '#333333'
	+ ax1.plot(x, y, '--', linewidth=2, color=limitcolor)
	+ ax1.text(x[0]+0.03, 2.0e-4,
	+ 'Yield strength', rotation=90, color=limitcolor,
	+ bbox={'fc':'#ffffff', 'pad':3, 'alpha':0.7})
	+

	+ ## Fit
	+ ax1.plot(friction_fit, strainrate_fit)
	+ #ax1.plot(friction_fit2, strainrate_fit2)
	ax1.annotate('$\\dot{\\gamma} = (\\tau/N)^{6.40}$',
	xy = (friction_fit[40], strainrate_fit[40]),
	- xytext = (0.32, 2.0e-7),
	- arrowprops=dict(facecolor='blue', edgecolor='blue', shrink=0.05,
	+ xytext = (0.32+0.05, 2.0e-9),
	+ arrowprops=dict(facecolor='blue', edgecolor='blue', shrink=0.1,
	width=1, headwidth=4, frac=0.2),)
	#xytext = (friction_fit[50]+0.15, strainrate_fit[50]-1.0e-5))#,
	#arrowprops=dict(facecolor='black', shrink=0.05),)
	t@@ -155,7 +165,6 @@ for sid in sids:
	#ax1.set_ylabel('Shear velocity [m/s]')
	ax1.set_ylabel('Shear strain rate $\\dot{\\gamma}$ [s$^{-1}$]')

	-
	plt.tight_layout()
	filename = sid + '-rate-dependence.' + outformat
	plt.savefig(filename)
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -4411,24 +4411,6 @@ class sim:
	video(self.sid, out_folder, video_format, graphics_folder, \
	graphics_format, fps, qscale, bitrate, verbose)

	- def shearVel(self):
	- '''
	- Calculates and returns the shear velocity (gamma_dot) of the
	- experiment. The shear velocity is the x-axis velocity value of the
	- upper particles.
	-
	- :returns: The shear velocity applied by the upper, fixed particles [m/…
	- :return type: float
	-
	- See also: :func:`shearStrainRate()` and :func:`shearStrain()`
	- '''
	-
	- # Find the fixed particles
	- fixvel = numpy.nonzero(self.fixvel > 0.0)
	-
	- # The shear velocity is the x-axis velocity value of the upper particl…
	- return self.vel[fixvel,0].max()
	-
	def shearDisplacement(self):
	'''
	Calculates and returns the current shear displacement. The displacement
	t@@ -4462,6 +4444,12 @@ class sim:
	fixvel = numpy.nonzero(self.fixvel > 0.0)
	return numpy.max(self.vel[fixvel,0])

	+ def shearVel(self):
	+ '''
	+ Alias of :func:`shearVelocity()`
	+ '''
	+ return self.shearVelocity()
	+
	def shearStrain(self):
	'''
	Calculates and returns the current shear strain (gamma) value of the