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	tdo not artificially increase porosity at lower boundary - sphere - GPU-based 3…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 9972531e74fd32ad4882082b820f0723a1e533ea
	parent 7ce8fd9b8809c9db23e0b7774a6060dcee461c6f
	Author: Anders Damsgaard <[email protected]>
	Date: Wed, 8 Apr 2015 11:53:19 +0200

	do not artificially increase porosity at lower boundary

	Diffstat:
	M python/halfshear-darcy-combined.py \| 21 +++++++++++++++++----
	M src/darcy.cuh \| 4 ++++

	2 files changed, 21 insertions(+), 4 deletions(-)
	---
	diff --git a/python/halfshear-darcy-combined.py b/python/halfshear-darcy-combin…
	t@@ -18,7 +18,7 @@ sid = 'halfshear-darcy-sigma0=80000.0-k_c=3.5e-13-mu=1.04e-0…
	outformat = 'pdf'
	fluid = True
	#threshold = 100.0 # [N]
	-calculateforcechains = True
	+calculateforcechains = False
	calculateforcechainhistory = False
	legend_alpha=0.7
	linewidth=0.5
	t@@ -181,6 +181,7 @@ lns0 = ax1.plot(t, sigma_def/1000., '-k', label="$N$",
	lns3 = ax1.plot(t, tau_eff/1000., '-r', label="$\\tau'$", linewidth=linewidth)

	ax1.set_ylabel('Stress [kPa]')
	+
	ax2 = ax1.twinx()
	ax2color = 'blue'
	#lns4 = ax2.plot(t, p_f_top/1000.0 + 80.0, '-',
	t@@ -240,7 +241,8 @@ ax5 = plt.subplot(5, 1, 3, sharex=ax1)
	#ax5.plot(t, xdispint, 'k', linewidth=linewidth)

	# normalized displacement
	-ax5.plot(t, xdisp/xdisp[-1], 'k', linewidth=linewidth)
	+#ax5.plot(t, xdisp/xdisp[-1], 'k', linewidth=linewidth)
	+ax5.plot(t, xdisp/xdisp[4500], 'k', linewidth=linewidth)

	# detrended displacement
	#ax5.plot(t, xdisp - (xdisp[-1] - xdisp[0])*t/t[-1], 'k', linewidth=linewidth)
	t@@ -317,8 +319,8 @@ cbaxes = fig.add_axes([0.32, 0.1, 0.4, 0.01]) # x,y,w,h
	#linewidth=1,
	#facecolor='white'))
	ax9.add_patch(matplotlib.patches.Rectangle(
	- (0.6, 0.04), # x,y
	- 3., # dx
	+ (1.5, 0.04), # x,y
	+ 7., # dx
	.15, # dy
	fill=True,
	linewidth=1,
	t@@ -359,6 +361,17 @@ plt.setp(ax5.get_xticklabels(), visible=False)
	plt.setp(ax7.get_xticklabels(), visible=False)
	#plt.setp(ax8.get_xticklabels(), visible=False)

	+ax1.set_xlim([0,9])
	+ax2.set_xlim([0,9])
	+ax3.set_xlim([0,9])
	+#ax4.set_xlim([0,9])
	+ax5.set_xlim([0,9])
	+ax6.set_xlim([0,9])
	+ax7.set_xlim([0,9])
	+ax8.set_xlim([0,9])
	+ax9.set_xlim([0,9])
	+
	+
	ax9.set_xlabel('Time [d]')
	fig.tight_layout()
	plt.subplots_adjust(hspace=0.05)
	diff --git a/src/darcy.cuh b/src/darcy.cuh
	t@@ -411,6 +411,10 @@ __global__ void findDarcyPorositiesLinear(
	// Index of neighbor cell this iteration is looking at
	targetCell = gridPos + make_int3(x_dim, y_dim, z_dim);

	+ // Do not artifically enhance porosity at lower bounda…
	+ if (targetCell.z == -1)
	+ targetCell.z = 1;
	+
	// Get distance modifier for interparticle
	// vector, if it crosses a periodic boundary
	distmod = MAKE_FLOAT3(0.0, 0.0, 0.0);