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	tadded function to read a specified time - sphere - GPU-based 3D discrete eleme…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 3f5dbc246a357c9339173ebd483f807b2e27b1eb
	parent 7e337442d9b68f38a76a8f2479de8e216fd19c9c
	Author: Anders Damsgaard <[email protected]>
	Date: Fri, 27 Feb 2015 11:42:32 +0100

	added function to read a specified time

	Diffstat:
	M python/halfshear-darcy-combined.py \| 29 +++++++++++++++++------------
	M python/sphere.py \| 29 +++++++++++++++++++++++++++++

	2 files changed, 46 insertions(+), 12 deletions(-)
	---
	diff --git a/python/halfshear-darcy-combined.py b/python/halfshear-darcy-combin…
	t@@ -21,6 +21,9 @@ calculateforcechains = False
	legend_alpha=0.5
	linewidth=0.5

	+t_DEM_to_t_real = 5.787e-5
	+
	+

	###################
	#### DATA READ ####
	t@@ -128,11 +131,13 @@ horizontalalignment='left'
	fontweight='bold'
	bbox={'facecolor':'white', 'alpha':1.0, 'pad':3}

	+t = t/t_DEM_to_t_real / (60.60.24.)
	+
	fig = plt.figure(figsize=[3.5,8])

	## ax1: N, tau, ax2: p_f
	ax1 = plt.subplot(5, 1, 1)
	-lns0 = ax1.plot(t, sigma_def/1000., '-k', label="$\\sigma_0$",
	+lns0 = ax1.plot(t, sigma_def/1000., '-k', label="$N$",
	linewidth=linewidth)
	#lns1 = ax1.plot(t, sigma_eff/1000., '-k', label="$\\sigma'$")
	#lns2 = ax1.plot(t, tau_def/1000., '-r', label="$\\tau$")
	t@@ -145,10 +150,10 @@ ax2color = 'blue'
	#lns4 = ax2.plot(t, p_f_top/1000.0 + 80.0, '-',
	#color=ax2color,
	#label='$p_\\text{f}^\\text{forcing}$')
	-lns5 = ax2.plot(t, p_f_bar/1000.0 + 80.0, '--',
	+lns5 = ax2.plot(t, p_f_bar/1000.0, '--',
	color=ax2color,
	- label='$\\bar{p}_\\text{f}$', linewidth=linewidth)
	-ax2.set_ylabel('Mean fluid pressure [kPa]')
	+ label='$\\Delta\\bar{p}_\\text{f}$', linewidth=linewidth)
	+ax2.set_ylabel('Mean change in fluid pressure [kPa]')
	ax2.yaxis.label.set_color(ax2color)
	for tl in ax2.get_yticklabels():
	tl.set_color(ax2color)
	t@@ -161,7 +166,7 @@ labs = [l.get_label() for l in lns]
	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(ax1.get_ylim())

	ax1.text(bbox_x, bbox_y, 'a',
	horizontalalignment=horizontalalignment,
	t@@ -219,7 +224,7 @@ ax7.set_ylim([1.0e1, 2.0e4])
	ax8 = ax7.twinx()
	ax8color='green'
	ax8.plot(t, coordinationnumber, color=ax8color, linewidth=linewidth)
	-ax8.set_ylabel('Coordination number [-]')
	+ax8.set_ylabel('Contacts per particle [-]')
	ax8.yaxis.label.set_color(ax8color)
	for tl in ax8.get_yticklabels():
	tl.set_color(ax8color)
	t@@ -249,19 +254,19 @@ im9 = ax9.pcolormesh(t, zpos_c, poros,
	rasterized=True)
	ax9.set_ylim([zpos_c[0], sim.w_x[0]])
	ax9.set_ylabel('Vertical position [m]')
	-#cb9 = plt.colorbar(im9, orientation='horizontal')#, pad=0.20)
	+
	cbaxes = fig.add_axes([0.32, 0.1, 0.4, 0.01]) # x,y,w,h
	-#cb9 = plt.colorbar(im9, orientation='horizontal', shrink=0.7)
	+
	#ax9.add_patch(matplotlib.patches.Rectangle(
	- #(3.0, 0.06), # x,y
	+ #(3.0, 0.04), # x,y
	#15., # dx
	#.15, # dy
	#fill=True,
	#linewidth=1,
	#facecolor='white'))
	ax9.add_patch(matplotlib.patches.Rectangle(
	- (3.0, 0.04), # x,y
	- 15., # dx
	+ (0.6, 0.04), # x,y
	+ 3., # dx
	.15, # dy
	fill=True,
	linewidth=1,
	t@@ -298,7 +303,7 @@ plt.setp(ax5.get_xticklabels(), visible=False)
	plt.setp(ax7.get_xticklabels(), visible=False)
	#plt.setp(ax8.get_xticklabels(), visible=False)

	-ax9.set_xlabel('Time [s]')
	+ax9.set_xlabel('Time [d]')
	fig.tight_layout()
	plt.subplots_adjust(hspace=0.05)

	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -2177,6 +2177,35 @@ class sim:
	fn = "../output/{0}.output{1:0=5}.bin".format(self.sid, lastfile)
	self.readbin(fn, verbose)

	+ def readTime(self, time, verbose=True):
	+ '''
	+ Read the output file most closely corresponding to the time given as an
	+ argument.
	+
	+ :param time: The desired current time [s]
	+ :type time: float
	+
	+ See also :func:`readbin()`, :func:`readfirst()`, :func:`readsecond`, a…
	+ :func:`readstep`.
	+ '''
	+
	+ self.readfirst(verbose=False)
	+ t_first = self.currentTime()
	+ n_first = self.time_step_count[0]
	+
	+ self.readlast(verbose=False)
	+ t_last = self.currentTime()
	+ n_last = self.time_step_count[0]
	+
	+ if time < t_first \| time > t_last:
	+ raise Exception('Error: The specified time {} s is outside the ' +
	+ 'range of output files [{}; {}] s.'.format(time, \
	+ t_first, t_last))
	+
	+ dt_dn = (t_last - t_first)/(n_last - n_first)
	+ step = int((time - t_first)/dt_dn) + n_first
	+ sim.readstep(step, verbose=verbose)
	+
	def generateRadii(self, psd = 'logn',
	mean = 440e-6,
	variance = 8.8e-9,