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	tadd method to visualize sediment rate dependence - sphere - GPU-based 3D discr…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 418246d1ed3a323dae340566ab6c24e0b1ec4ad9
	parent f8229089d0385e01a20cca9f20fdd4fc4afaef88
	Author: Anders Damsgaard <[email protected]>
	Date: Tue, 17 Feb 2015 13:06:33 +0100

	add method to visualize sediment rate dependence

	Diffstat:
	M python/sphere.py \| 38 +++++++++++++++++++++++++++++…

	1 file changed, 36 insertions(+), 2 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -5472,7 +5472,7 @@ class sim:
	return force/(self.L[0]*self.L[1])


	- def visualize(self, method = 'energy', savefig = True, outformat = 'png',
	+ def visualize(self, method='energy', savefig=True, outformat='png',
	pickle=False, xlim=False):
	'''
	Visualize output from the simulation, where the temporal progress is
	t@@ -5482,7 +5482,7 @@ class sim:

	:param method: The type of plot to render. Possible values are 'energy…
	'walls', 'triaxial', 'mean-fluid-pressure', 'fluid-pressure',
	- 'shear', 'shear-displacement', 'porosity'
	+ 'shear', 'shear-displacement', 'porosity', 'rate-dependence'
	:type method: str
	:param savefig: Save the image instead of showing it on screen
	:type savefig: bool
	t@@ -6083,6 +6083,40 @@ class sim:
	fig.tight_layout()
	plt.subplots_adjust(hspace=0.05)

	+ elif method == 'rate-dependence':
	+
	+ tau = numpy.empty(sb.status())
	+ N = numpy.empty(sb.status())
	+ v = numpy.empty(sb.status())
	+ for i in numpy.arange(sb.status()):
	+ sb.readstep(i+1, verbose=False)
	+ #tau = sb.shearStress()
	+ 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()
	+
	+ # remove nonzero sliding velocities and their associated values
	+ idx = numpy.nonzero(v)
	+ v_nonzero = v[idx]
	+ tau_nonzero = tau[idx]
	+ N_nonzero = N[idx]
	+
	+ ax1 = plt.subplot(111)
	+ #ax1.semilogy(N/1000., v)
	+ ax1.semilogy(tau_nonzero/N_nonzero, v_nonzero, '.')
	+ #ax1.plot(tau/N, v, '.')
	+ #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, '.')
	+ ax1.set_xlabel('Friction $\\tau/N$ [-]')
	+ ax1.set_ylabel('Shear velocity [m/s]')
	+ '''
	+
	elif method == 'mean-fluid-pressure':

	# Read pressure values from simulation binaries