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	timprove shearStrain function - sphere - GPU-based 3D discrete element method a…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 9f8b77e89f90aa53dc6c0c2cfe65c417e62ef1a6
	parent 4655081fc0453fd7a0e469a1b199e67687920dc4
	Author: Anders Damsgaard <[email protected]>
	Date: Tue, 17 Feb 2015 14:24:06 +0100

	improve shearStrain function

	use current displacement of fixed particles instead of multiplying the current
	velocities

	Diffstat:
	M python/sphere.py \| 21 +++++++++++++++++++--

	1 file changed, 19 insertions(+), 2 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -4210,7 +4210,9 @@ class sim:
	w_x0 = self.w_x[0]

	# Displacement of the upper, fixed particles in the shear direction
	- xdisp = self.time_current[0] * self.shearVel()
	+ #xdisp = self.time_current[0] * self.shearVel()
	+ fixvel = numpy.nonzero(self.fixvel > 0.0)
	+ xdisp = numpy.max(self.xyzsum[fixvel,0])

	# Return shear strain
	return xdisp/w_x0
	t@@ -6088,6 +6090,7 @@ class sim:
	tau = numpy.empty(sb.status())
	N = numpy.empty(sb.status())
	v = numpy.empty(sb.status())
	+ shearstrain = numpy.empty(sb.status())
	for i in numpy.arange(sb.status()):
	sb.readstep(i+1, verbose=False)
	#tau = sb.shearStress()
	t@@ -6095,24 +6098,38 @@ class sim:
	#tau[i] = sb.shearStress()[0] # measured shear stress along x
	N[i] = sb.currentNormalStress() # defined normal stress
	v[i] = sb.shearVel()
	+ shearstrain[i] = sb.shearStrain()

	# remove nonzero sliding velocities and their associated values
	idx = numpy.nonzero(v)
	v_nonzero = v[idx]
	tau_nonzero = tau[idx]
	N_nonzero = N[idx]
	+ shearstrain_nonzero = shearstrain[idx]

	ax1 = plt.subplot(111)
	#ax1.semilogy(N/1000., v)
	#ax1.semilogy(tau_nonzero/N_nonzero, v_nonzero, '+k')
	#ax1.plot(tau/N, v, '.')
	- ax1.scatter(tau_nonzero/N_nonzero, v_nonzero, c=idx)
	+ friction = tau_nonzero/N_nonzero
	+ CS = ax1.scatter(friction, v_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
	+ ax1.set_ylim([y_min, y_max])
	+
	+ plt.colorbar(CS)

	#ax1.set_xlabel('Effective normal stress [kPa]')
	ax1.set_xlabel('Friction $\\tau/N$ [-]')
	ax1.set_ylabel('Shear velocity [m/s]')

	+
	+
	'''
	ax2 = plt.subplot(212)
	ax2.plot(tau/N, v, '.')