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	thydraulic conductivity added to IO - sphere - GPU-based 3D discrete element me…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 1b27cb6a26bebce2f0f2d81abfa7daf395471e19
	parent 38f36866e2d441843d07a8089b9decb966c7b2c8
	Author: Anders Damsgaard <[email protected]>
	Date: Tue, 29 Oct 2013 14:18:02 +0100

	hydraulic conductivity added to IO

	Diffstat:
	M python/sphere.py \| 58 +++++++++++++++++++++++++++--…
	M src/file_io.cpp \| 5 ++++-

	2 files changed, 55 insertions(+), 8 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -134,6 +134,10 @@ class Spherebin:
	dtype=numpy.float64)
	self.f_rho = numpy.zeros((self.num[0], self.num[1], self.num[2]),
	dtype=numpy.float64)
	+ self.f_phi = numpy.zeros((self.num[0], self.num[1], self.num[2]),
	+ dtype=numpy.float64)
	+ self.f_K = numpy.zeros((self.num[0], self.num[1], self.num[2]),
	+ dtype=numpy.float64)

	def __cmp__(self, other):
	""" Called when to Spherebin objects are compared.
	t@@ -202,7 +206,9 @@ class Spherebin:
	self.bonds_omega_t == other.bonds_omega_t and\
	self.nu == other.nu and\
	(self.f_v == other.f_v).all() and\
	- (self.f_rho == other.f_rho).all()\
	+ (self.f_rho == other.f_rho).all() and\
	+ (self.f_K == other.f_K).all() and\
	+ (self.f_phi == other.f_phi).all()\
	).all() == True):
	return 0 # All equal
	else:
	t@@ -385,6 +391,8 @@ class Spherebin:
	(self.num[0], self.num[1], self.num[2], self.nd),
	dtype=numpy.float64)
	self.f_rho = numpy.empty((self.num[0],self.num[1],self.num…
	+ self.f_phi = numpy.empty((self.num[0],self.num[1],self.num…
	+ self.f_K = numpy.empty((self.num[0],self.num[1],self.num[2…
	for z in range(self.num[2]):
	for y in range(self.num[1]):
	for x in range(self.num[0]):
	t@@ -396,6 +404,10 @@ class Spherebin:
	numpy.fromfile(fh, dtype=numpy.float64, count=…
	self.f_rho[x,y,z] = \
	numpy.fromfile(fh, dtype=numpy.float64, count=…
	+ self.f_phi[x,y,z] = \
	+ numpy.fromfile(fh, dtype=numpy.float64, count=…
	+ self.f_K[x,y,z] = \
	+ numpy.fromfile(fh, dtype=numpy.float64, count=…

	finally:
	if fh is not None:
	t@@ -509,6 +521,8 @@ class Spherebin:
	fh.write(self.f_v[x,y,z,1].astype(numpy.float64))
	fh.write(self.f_v[x,y,z,2].astype(numpy.float64))
	fh.write(self.f_rho[x,y,z].astype(numpy.float64))
	+ fh.write(self.f_phi[x,y,z].astype(numpy.float64))
	+ fh.write(self.f_K[x,y,z].astype(numpy.float64))

	finally:
	if fh is not None:
	t@@ -693,7 +707,7 @@ class Spherebin:
	def writeFluidVTK(self, folder = '../output/', verbose = True):
	'Writes fluid data to a target VTK file'

	- filename = folder + '/' + self.sid + '-fluid.vti' # image grid
	+ filename = folder + '/fluid-' + self.sid + '.vti' # image grid

	# initalize VTK data structure
	grid = vtk.vtkImageData()
	t@@ -703,17 +717,30 @@ class Spherebin:
	grid.SetDimensions(self.num) # no. of points in each direction

	# array of scalars: hydraulic pressures
	- pres = vtk.vtkDoubleArray() # data type
	+ pres = vtk.vtkDoubleArray()
	pres.SetName("Pressure")
	- pres.SetNumberOfComponents(1) # this is 3 for a vector
	+ pres.SetNumberOfComponents(1)
	pres.SetNumberOfTuples(grid.GetNumberOfPoints())

	# array of vectors: hydraulic velocities
	- vel = vtk.vtkDoubleArray() # data type
	+ vel = vtk.vtkDoubleArray()
	vel.SetName("Velocity")
	- vel.SetNumberOfComponents(3) # this is 3 for a vector
	+ vel.SetNumberOfComponents(3)
	vel.SetNumberOfTuples(grid.GetNumberOfPoints())

	+ # array of scalars: porosities
	+ poros = vtk.vtkDoubleArray()
	+ poros.SetName("Porosity change")
	+ poros.SetNumberOfComponents(1)
	+ poros.SetNumberOfTuples(grid.GetNumberOfPoints())
	+
	+ # array of scalars: hydraulic conductivities
	+ cond = vtk.vtkDoubleArray()
	+ cond.SetName("Conductivity")
	+ cond.SetNumberOfComponents(1)
	+ cond.SetNumberOfTuples(grid.GetNumberOfPoints())
	+
	+
	# insert values
	for z in range(self.num[2]):
	for y in range(self.num[1]):
	t@@ -721,11 +748,14 @@ class Spherebin:
	idx = x + self.num[0]y + self.num[0]self.num[1]*z;
	pres.SetValue(idx, self.f_rho[x,y,z])
	vel.SetTuple(idx, self.f_v[x,y,z,:])
	- #vel.SetTuple(idx, [x,y,z])
	+ poros.SetValue(idx, self.f_phi[x,y,z])
	+ cond.SetValue(idx, self.f_K[x,y,z])

	# add pres array to grid
	grid.GetPointData().AddArray(pres)
	grid.GetPointData().AddArray(vel)
	+ grid.GetPointData().AddArray(poros)
	+ grid.GetPointData().AddArray(cond)

	# write VTK XML image data file
	writer = vtk.vtkXMLImageDataWriter()
	t@@ -845,6 +875,8 @@ class Spherebin:
	# Init fluid arrays
	self.f_v = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …
	self.f_rho = numpy.ones((self.num[0],self.num[1],self.num[2]), dtype=n…
	+ self.f_phi = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd)…
	+ self.f_K = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …


	# Particle positions randomly distributed without overlap
	t@@ -893,6 +925,8 @@ class Spherebin:
	# Init fluid arrays
	self.f_v = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …
	self.f_rho = numpy.ones((self.num[0],self.num[1],self.num[2]), dtype=n…
	+ self.f_phi = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd)…
	+ self.f_K = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …


	# Put upper wall at top boundary
	t@@ -938,6 +972,8 @@ class Spherebin:
	# Init fluid arrays
	self.f_v = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …
	self.f_rho = numpy.ones((self.num[0],self.num[1],self.num[2]), dtype=n…
	+ self.f_phi = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd)…
	+ self.f_K = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …


	self.contactmodel[0] = contactmodel
	t@@ -1008,6 +1044,8 @@ class Spherebin:
	# Init fluid arrays
	self.f_v = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …
	self.f_rho = numpy.ones((self.num[0],self.num[1],self.num[2]), dtype=n…
	+ self.f_phi = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd)…
	+ self.f_K = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …

	self.contactmodel[0] = contactmodel

	t@@ -1073,6 +1111,8 @@ class Spherebin:
	# Init fluid arrays
	self.f_v = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …
	self.f_rho = numpy.ones((self.num[0],self.num[1],self.num[2]), dtype=n…
	+ self.f_phi = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd)…
	+ self.f_K = numpy.zeros((self.num[0],self.num[1],self.num[2],self.nd), …

	def createBondPair(self, i, j, spacing=-0.1):
	""" Bond particles i and j. Particle j is moved adjacent to particle i,
	t@@ -1342,6 +1382,10 @@ class Spherebin:
	dtype=numpy.float64)
	self.f_v = numpy.zeros((self.num[0], self.num[1], self.num[2], self.nd…
	dtype=numpy.float64)
	+ self.f_phi = numpy.ones((self.num[0], self.num[1], self.num[2]),
	+ dtype=numpy.float64)
	+ self.f_K = numpy.ones((self.num[0], self.num[1], self.num[2]),
	+ dtype=numpy.float64)


	def defaultParams(self,
	diff --git a/src/file_io.cpp b/src/file_io.cpp
	t@@ -283,6 +283,8 @@ void DEM::readbin(const char *target)
	ifs.read(as_bytes(d.V[i].y), sizeof(Float));
	ifs.read(as_bytes(d.V[i].z), sizeof(Float));
	ifs.read(as_bytes(d.H[i]), sizeof(Float));
	+ ifs.read(as_bytes(d.phi[i]), sizeof(Float));
	+ ifs.read(as_bytes(d.K[i]), sizeof(Float));
	}
	}
	}
	t@@ -470,7 +472,8 @@ void DEM::writebin(const char *target)
	ofs.write(as_bytes(d.V[i].y), sizeof(Float));
	ofs.write(as_bytes(d.V[i].z), sizeof(Float));
	ofs.write(as_bytes(d.H[i]), sizeof(Float));
	- //printf("%d,%d,%d: d.H[%d] = %f\n", x,y,z, i, d.H[i]);
	+ ofs.write(as_bytes(d.phi[i]), sizeof(Float));
	+ ofs.write(as_bytes(d.K[i]), sizeof(Float));
	}
	}
	}