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	timprove shearStrainRate function, use shear strain and -rate in plot - sphere …
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 592a2e058eb3eeb3962b12a6604e164f6d9c9fcd
	parent 9f8b77e89f90aa53dc6c0c2cfe65c417e62ef1a6
	Author: Anders Damsgaard <[email protected]>
	Date: Tue, 17 Feb 2015 14:29:30 +0100

	improve shearStrainRate function, use shear strain and -rate in plot

	Diffstat:
	M python/sphere.py \| 42 +++++++++++++++++++++++------…

	1 file changed, 31 insertions(+), 11 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -4221,12 +4221,23 @@ class sim:
	'''
	Calculates the shear strain rate (dot(gamma)) value of the experiment.

	- :returns: The value of $I$
	+ :returns: The value of dot(gamma)
	:return type: float

	See also: :func:`shearStrain()` and :func:`shearVel()`
	'''
	- return self.shearStrain()/self.time_current[1]
	+ #return self.shearStrain()/self.time_current[1]
	+
	+ # Current height
	+ w_x0 = self.w_x[0]
	+
	+ # Displacement of the upper, fixed particles in the shear direction
	+ #xdisp = self.time_current[0] * self.shearVel()
	+ fixvel = numpy.nonzero(self.fixvel > 0.0)
	+ xvel = numpy.max(self.vel[fixvel,0])
	+
	+ # Return shear strain rate
	+ return xvel/w_x0

	def inertiaParameterPlanarShear(self):
	'''
	t@@ -6089,7 +6100,8 @@ class sim:

	tau = numpy.empty(sb.status())
	N = numpy.empty(sb.status())
	- v = numpy.empty(sb.status())
	+ #v = numpy.empty(sb.status())
	+ shearstrainrate = numpy.empty(sb.status())
	shearstrain = numpy.empty(sb.status())
	for i in numpy.arange(sb.status()):
	sb.readstep(i+1, verbose=False)
	t@@ -6097,12 +6109,14 @@ class sim:
	tau[i] = sb.w_tau_x # defined shear stress
	#tau[i] = sb.shearStress()[0] # measured shear stress along x
	N[i] = sb.currentNormalStress() # defined normal stress
	- v[i] = sb.shearVel()
	+ #v[i] = sb.shearVel()
	+ shearstrainrate[i] = sb.shearStrainRate()
	shearstrain[i] = sb.shearStrain()

	# remove nonzero sliding velocities and their associated values
	idx = numpy.nonzero(v)
	- v_nonzero = v[idx]
	+ #v_nonzero = v[idx]
	+ shearstrainrate_nonzero = shearstrainrate[idx]
	tau_nonzero = tau[idx]
	N_nonzero = N[idx]
	shearstrain_nonzero = shearstrain[idx]
	t@@ -6112,21 +6126,27 @@ class sim:
	#ax1.semilogy(tau_nonzero/N_nonzero, v_nonzero, '+k')
	#ax1.plot(tau/N, v, '.')
	friction = tau_nonzero/N_nonzero
	- CS = ax1.scatter(friction, v_nonzero, c=shearstrain_nonzero,
	- linewidth=0)
	+ #CS = ax1.scatter(friction, v_nonzero, c=shearstrain_nonzero,
	+ #linewidth=0)
	+ CS = ax1.scatter(friction, shearstrainrate_nonzero,
	+ c=shearstrain_nonzero, linewidth=0)
	ax1.set_yscale('log')
	x_min = numpy.floor(numpy.min(friction))
	x_max = numpy.ceil(numpy.max(friction))
	ax1.set_xlim([x_min, x_max])
	- y_min = numpy.min(v_nonzero)*0.5
	- y_max = numpy.max(v_nonzero)*2.0
	+ #y_min = numpy.min(v_nonzero)*0.5
	+ #y_max = numpy.max(v_nonzero)*2.0
	+ y_min = numpy.min(shearstrainrate_nonzero)*0.5
	+ y_max = numpy.max(shearstrainrate_nonzero)*2.0
	ax1.set_ylim([y_min, y_max])

	- plt.colorbar(CS)
	+ cb = plt.colorbar(CS)
	+ cb.set_ylabel('Shear strain $\\gamma$ [-]')

	#ax1.set_xlabel('Effective normal stress [kPa]')
	ax1.set_xlabel('Friction $\\tau/N$ [-]')
	- ax1.set_ylabel('Shear velocity [m/s]')
	+ #ax1.set_ylabel('Shear velocity [m/s]')
	+ ax1.set_ylabel('Shear strain rate [s$^{-1}$]')