GopherProxy

	tbonds implemented - sphere - GPU-based 3D discrete element method algorithm wi…
	git clone git://src.adamsgaard.dk/sphere
	Log
	Files
	Refs
	LICENSE
	---
	commit 8867571c13d59a247c6d0d25952de35c6c76780e
	parent 5faec4ff3c0ddf053fb718331e0e4de1f6492537
	Author: Anders Damsgaard <[email protected]>
	Date: Fri, 25 Jan 2013 15:32:16 +0100

	bonds implemented

	Diffstat:
	M python/sphere.py \| 48 ++++++++++++++++++++++++-----…

	1 file changed, 37 insertions(+), 11 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -99,6 +99,8 @@ class Spherebin:
	self.w_force = numpy.zeros(self.nw, dtype=numpy.float64)
	self.w_devs = numpy.zeros(self.nw, dtype=numpy.float64)

	+ self.nb0 = numpy.zeros(1, dtype=numpy.uint32)
	+
	def __cmp__(self, other):
	""" Called when to Spherebin objects are compared.
	Returns 0 if the values are identical """
	t@@ -152,7 +154,8 @@ class Spherebin:
	(self.w_force == other.w_force).all() and\
	(self.w_devs == other.w_devs).all() and\
	self.gamma_wn == other.gamma_wn and\
	- self.gamma_wt == other.gamma_wt\
	+ self.gamma_wt == other.gamma_wt and\
	+ self.nb0 == other.nb0\
	).all() == True):
	return 0 # All equal
	else :
	t@@ -174,9 +177,9 @@ class Spherebin:
	self.np = numpy.fromfile(fh, dtype=numpy.uint32, count=1)

	# Read the time variables
	- self.time_dt = numpy.fromfile(fh, dtype=numpy.float64, coun…
	+ self.time_dt = numpy.fromfile(fh, dtype=numpy.float64, cou…
	self.time_current = numpy.fromfile(fh, dtype=numpy.float64, cou…
	- self.time_total = numpy.fromfile(fh, dtype=numpy.float64, c…
	+ self.time_total = numpy.fromfile(fh, dtype=numpy.float64, cou…
	self.time_file_dt = numpy.fromfile(fh, dtype=numpy.float64, cou…
	self.time_step_count = numpy.fromfile(fh, dtype=numpy.uint32, coun…

	t@@ -191,9 +194,9 @@ class Spherebin:
	self.angvel = numpy.zeros(self.np*self.nd, dtype=numpy.float64).r…
	self.torque = numpy.zeros(self.np*self.nd, dtype=numpy.float64).r…
	self.es_dot = numpy.zeros(self.np, dtype=numpy.float64)
	- self.es = numpy.zeros(self.np, dtype=numpy.float64)
	+ self.es = numpy.zeros(self.np, dtype=numpy.float64)
	self.ev_dot = numpy.zeros(self.np, dtype=numpy.float64)
	- self.ev = numpy.zeros(self.np, dtype=numpy.float64)
	+ self.ev = numpy.zeros(self.np, dtype=numpy.float64)
	self.p = numpy.zeros(self.np, dtype=numpy.float64)

	# Read remaining data from binary
	t@@ -267,8 +270,12 @@ class Spherebin:
	self.w_force[i] = numpy.fromfile(fh, dtype=numpy.float64, coun…
	self.w_devs[i] = numpy.fromfile(fh, dtype=numpy.float64, coun…

	-
	- fh.close()
	+ # Inter-particle bonds
	+ self.nb0 = numpy.fromfile(fh, dtype=numpy.uint32, count=1)
	+ self.bonds = numpy.zeros((self.nb0, 2), dtype=numpy.uint32)
	+ for i in range(self.nb0):
	+ self.bonds[i,0] = numpy.fromfile(fh, dtype=numpy.uint32, count…
	+ self.bonds[i,1] = numpy.fromfile(fh, dtype=numpy.uint32, count…

	finally:
	if fh is not None:
	t@@ -359,7 +366,10 @@ class Spherebin:
	fh.write(self.w_force[i].astype(numpy.float64))
	fh.write(self.w_devs[i].astype(numpy.float64))

	- fh.close()
	+ fh.write(self.nb0.astype(numpy.uint32))
	+ for i in range(self.nb0):
	+ fh.write(self.bonds[i,0].astype(numpy.uint32))
	+ fh.write(self.bonds[i,1].astype(numpy.uint32))

	finally:
	if fh is not None:
	t@@ -453,7 +463,6 @@ class Spherebin:
	from the particle boundaries.
	"""

	-
	# Cell configuration
	cellsize_min = 2.1 * numpy.amax(self.radius)
	self.num[0] = numpy.ceil((self.L[0]-self.origo[0])/cellsize_min)
	t@@ -471,7 +480,7 @@ class Spherebin:

	# Generate grid based on particle positions
	def initGridAndWorldsize(self, g = numpy.array([0.0, 0.0, -9.80665]),
	- margin = numpy.array([2.0, 2.0, 2.0]),
	+ margin = 2.0,
	periodic = 1,
	contactmodel = 2):
	""" Initialize grid suitable for the particle positions set previously.
	t@@ -505,6 +514,10 @@ class Spherebin:

	self.contactmodel[0] = contactmodel

	+ # Put upper wall at top boundary
	+ if (self.nw > 0):
	+ self.w_x[0] = self.L[0]
	+

	# Initialize particle positions to regular, grid-like, non-overlapping con…
	def initGridPos(self, g = numpy.array([0.0, 0.0, -9.80665]),
	t@@ -753,7 +766,7 @@ class Spherebin:

	def initTemporal(self, total,
	current = 0.0,
	- file_dt = 0.01,
	+ file_dt = 0.05,
	step_count = 0):
	""" Set temporal parameters for the simulation.
	Particle radii and physical parameters need to be set
	t@@ -854,6 +867,19 @@ class Spherebin:
	# Debonding distance
	self.db[0] = (1.0 + theta/2.0) * self.V_b**(1.0/3.0)

	+
	+ def bond(self, i, j):
	+ """ Create a bond between particles i and j """
	+
	+ if (hasattr(self, 'bonds') == False):
	+ self.bonds = numpy.array([[i,j]], dtype=numpy.uint32)
	+ else :
	+ self.bonds = numpy.vstack((bonds, [i,j]))
	+
	+ # Increment the number of bonds with one
	+ self.nb0 += 1
	+
	+
	def energy(self, method):
	""" Calculate the sum of the energy components of all particles.
	"""