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	tnormal boundaries by default. use periodicBoundariesX or periodicBoundariesXY …
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit ad617bec05a87782ca2fc5a55b50c8765bb216ff
	parent e21cfdcd81fcb08ebbad7d66e51bcb8df840524e
	Author: Anders Damsgaard <[email protected]>
	Date: Fri, 20 Jun 2014 21:34:15 +0200

	normal boundaries by default. use periodicBoundariesX or periodicBoundariesXY i…

	Diffstat:
	M python/shortening.py \| 12 +++++++++---
	M python/sphere.py \| 2 +-

	2 files changed, 10 insertions(+), 4 deletions(-)
	---
	diff --git a/python/shortening.py b/python/shortening.py
	t@@ -58,6 +58,10 @@ for z in range(nz):
	cube.x[i,1] + y*dy ]
	sim.addParticle(pos, radius=cube.radius[i], color=grid[z,y])

	+# move to x=0
	+min_x = numpy.min(sim.x[:,0] - sim.radius[:])
	+sim.x[:,0] = sim.x[:,0] - min_x
	+
	# move to y=0
	min_y = numpy.min(sim.x[:,1] - sim.radius[:])
	sim.x[:,1] = sim.x[:,1] - min_y
	t@@ -66,7 +70,8 @@ sim.x[:,1] = sim.x[:,1] - min_y
	min_z = numpy.min(sim.x[:,2] - sim.radius[:])
	sim.x[:,2] = sim.x[:,2] - min_z

	-sim.defineWorldBoundaries(L=[Lx, Lz*3, Ly])
	+#sim.defineWorldBoundaries(L=[Lx, Lz*3, Ly])
	+sim.defineWorldBoundaries(L=[numpy.max(sim.x[:,0] + sim.radius[:]), Lz*3, Ly])
	sim.k_t[0] = 2.0/3.0*sim.k_n[0]

	sim.cleanup()
	t@@ -82,10 +87,11 @@ sim.g[0] = 0
	sim.g[1] = -9.81
	sim.g[2] = 0

	-sim.setDampingNormal(1.0e1)
	+sim.setDampingNormal(5.0e1)
	sim.setDampingTangential(1.0e1)

	-sim.periodicBoundariesX()
	+#sim.periodicBoundariesX()
	+sim.normalBoundariesXY()
	sim.uniaxialStrainRate(wvel = 0.0)

	# Set duration of simulation, automatically determine timestep, etc.
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -76,7 +76,7 @@ class sim:
	self.num = numpy.zeros(self.nd, dtype=numpy.uint32)

	# Whether to treat the lateral boundaries as periodic (1) or not (0)
	- self.periodic = numpy.ones(1, dtype=numpy.uint32)
	+ self.periodic = numpy.zeros(1, dtype=numpy.uint32)

	## Particle data
	# Particle position vectors [m]