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	tfix porosity calculation issues - sphere - GPU-based 3D discrete element metho…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit e0f260ff9f6013a354742bb5dc29b2f8ae828d73
	parent 50d5be318df999c94c24af66b8ccf23b57d3d8e5
	Author: Anders Damsgaard <[email protected]>
	Date: Wed, 5 Nov 2014 15:42:40 +0100

	fix porosity calculation issues

	Diffstat:
	M python/sphere.py \| 37 ++++++++++++++++++-----------…
	M tests/porosity_tests.py \| 2 +-

	2 files changed, 23 insertions(+), 16 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -3627,29 +3627,36 @@ class sim:
	e = (V_t - V_s)/V_s
	return e

	- def bulkPorosity(self):
	+ def bulkPorosity(self, trim=True):
	'''
	- Calculates the bulk porosity in the smallest axis-parallel cube.
	+ Calculates the bulk porosity of the particle assemblage.
	+
	+ :param trim: Trim the total volume to the smallest axis-parallel cube
	+ containing all particles.
	+ :type trim: bool

	:returns: The bulk porosity, in [0:1]
	:return type: float
	'''

	- min_x = numpy.min(self.x[:,0] - self.radius)
	- min_y = numpy.min(self.x[:,1] - self.radius)
	- min_z = numpy.min(self.x[:,2] - self.radius)
	- max_x = numpy.max(self.x[:,0] + self.radius)
	- max_y = numpy.max(self.x[:,1] + self.radius)
	- max_z = numpy.max(self.x[:,2] + self.radius)
	+ V_total = 0.0
	+ if trim:
	+ min_x = numpy.min(self.x[:,0] - self.radius)
	+ min_y = numpy.min(self.x[:,1] - self.radius)
	+ min_z = numpy.min(self.x[:,2] - self.radius)
	+ max_x = numpy.max(self.x[:,0] + self.radius)
	+ max_y = numpy.max(self.x[:,1] + self.radius)
	+ max_z = numpy.max(self.x[:,2] + self.radius)
	+ V_total = (max_x - min_x)(max_y - min_y)(max_z - min_z)

	- #if (self.nw == 0):
	- #V_total = self.L[0] * self.L[1] * self.L[2]
	- #elif (self.nw == 1):
	- #V_total = self.L[0] * self.L[1] * self.w_x[0]
	- #if (V_total <= 0.0):
	- #raise Exception("Could not determine total volume")
	+ else:
	+ if (self.nw == 0):
	+ V_total = self.L[0] * self.L[1] * self.L[2]
	+ elif (self.nw == 1):
	+ V_total = self.L[0] * self.L[1] * self.w_x[0]
	+ if (V_total <= 0.0):
	+ raise Exception("Could not determine total volume")

	- V_total = (max_x - min_x)(max_y - min_y)(max_z - min_z)

	# Find the volume of solids
	V_solid = numpy.sum(V_sphere(self.radius))
	diff --git a/tests/porosity_tests.py b/tests/porosity_tests.py
	t@@ -23,7 +23,7 @@ def testPorosities(sim):
	for slices in slicevals:

	# Find correct value of bulk porosity
	- n_bulk = sim.bulkPorosity()
	+ n_bulk = sim.bulkPorosity(trim=False)
	#print("Bulk: " + str(n_bulk))

	porosity = sim.porosity(slices = slices)[0]