def draw_displacement_wrapper(gf, dt, event_type, a, r0=None, sigma=None):
if ((event_type == EventType.COM_ESCAPE or event_type == EventType.SINGLE_ESCAPE) and sigma == None) or (
event_type == EventType.IV_ESCAPE and sigma != None
):
# Escape through this coordinate. We already know the new r.
# Todo. Let gf handle this.
return a
elif event_type == EventType.IV_REACTION and sigma != None:
# Todo. Let gf handle this.
return sigma
rnd = myrandom.uniform()
if __debug__:
log.debug(" *drawR. " + gf.__class__.__name__)
try:
if r0 == None:
r = gf.drawR(rnd, dt)
else:
r = gf.drawR(rnd, r0, dt)
while r > a or r <= sigma: # redraw; shouldn't happen often
if __debug__:
log.debug(" *drawR: redraw")
rnd = myrandom.uniform()
if r0 == None:
r = gf.drawR(rnd, dt)
else:
r = gf.drawR(rnd, r0, dt)
except Exception, e:
raise Exception("gf.drawR() failed, " "%s, rnd = %g, r0 = %s, dt = %g, %s" % (str(e), rnd, r0, dt, gf.dump()))
def draw_displacement_wrapper(gf, dt, event_type, a, r0=None, sigma=None):
if(((event_type == EventType.COM_ESCAPE or
event_type == EventType.SINGLE_ESCAPE) and sigma == None) or
(event_type == EventType.IV_ESCAPE and sigma != None)):
# Escape through this coordinate. We already know the new r.
# Todo. Let gf handle this.
return a
elif event_type == EventType.IV_REACTION and sigma != None:
# Todo. Let gf handle this.
return sigma
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawR. ' + gf.__class__.__name__)
try:
if r0 == None:
r = gf.drawR(rnd, dt)
else:
r = gf.drawR(rnd, r0, dt)
while r > a or r <= sigma: # redraw; shouldn't happen often
if __debug__:
log.debug(' *drawR: redraw')
rnd = myrandom.uniform()
if r0 == None:
r = gf.drawR(rnd, dt)
else:
r = gf.drawR(rnd, r0, dt)
except Exception, e:
raise Exception('gf.drawR() failed, '
'%s, rnd = %g, r0 = %s, dt = %g, %s' %
(str(e), rnd, r0, dt, gf.dump()))
def random_vector(r):
v = [
myrandom.uniform(-1, 1),
myrandom.uniform(-1, 1),
myrandom.uniform(-1, 1)
]
return _gfrd.normalize(v, r)
def random_vector2D(r):
# Return a random 2D cartesian vector of length r.
v = [myrandom.uniform(-1,1), myrandom.uniform(-1,1)]
# Todo. return _gfrd.normalize(v, r)
v = numpy.array(v)
norm = numpy.linalg.norm(v)
return v * (r / norm)
def random_vector2D(r):
# Return a random 2D cartesian vector of length r.
v = [myrandom.uniform(-1, 1), myrandom.uniform(-1, 1)]
# Todo. return _gfrd.normalize(v, r)
v = numpy.array(v)
norm = numpy.linalg.norm(v)
return v * (r / norm)
def random_position(self):
"""Only uniform if vector_x and vector_y have same length.
"""
return (
self.shape.position
+ myrandom.uniform(-1, 1) * self.shape.unit_x * self.shape.extent[0]
+ myrandom.uniform(-1, 1) * self.shape.unit_y * self.shape.extent[1]
)
def random_position(self):
"""Returns a random position equidistributed within
the region in space defined by negative signed distance.
See also signed_distance_to().
"""
corner = self.shape.position - self.size / 2.
return numpy.array([
myrandom.uniform(corner[0], self.size[0]),
myrandom.uniform(corner[1], self.size[1]),
myrandom.uniform(corner[2], self.size[2])
])
def random_position(self):
"""Returns a random position equidistributed within
the region in space defined by negative signed distance.
See also signed_distance_to().
"""
corner = self.shape.position - self.size / 2.0
return numpy.array(
[
myrandom.uniform(corner[0], self.size[0]),
myrandom.uniform(corner[1], self.size[1]),
myrandom.uniform(corner[2], self.size[2]),
]
)
def draw_r_wrapper(gf, dt, a, sigma=None):
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawR. ' + gf.__class__.__name__)
try:
r = gf.drawR(rnd, dt)
while r > a or r <= sigma: # redraw; shouldn't happen often
if __debug__:
log.debug(' *drawR: redraw')
rnd = myrandom.uniform()
r = gf.drawR(rnd, dt)
except Exception, e:
raise Exception('gf.drawR() failed, '
'%s, rnd = %.16g, dt = %.16g, %s' %
(str(e), rnd, dt, gf.dump()))
def draw_r_wrapper(gf, dt, a, sigma=None):
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawR. ' + gf.__class__.__name__)
try:
r = gf.drawR(rnd, dt)
while r > a or r <= sigma: # redraw; shouldn't happen often
if __debug__:
log.debug(' *drawR: redraw')
rnd = myrandom.uniform()
r = gf.drawR(rnd, dt)
except Exception, e:
raise Exception('gf.drawR() failed, '
'%s, rnd = %.16g, dt = %.16g, %s' %
(str(e), rnd, dt, gf.dump()))
def random_vector2D(r):
# Return a random 2D cartesian vector of length r.
phi = myrandom.uniform(0, Pi2)
v = [math.cos(phi), math.sin(phi)] # sincos
# Todo. return _gfrd.normalize(v, r)
v = numpy.array(v)
norm = numpy.linalg.norm(v)
return v * (r / norm)
def random_vector(r):
# v, s = [0.0, 0.0, 0.0], 2.0
# while s > 1.0:
# v[0] = myrandom.uniform (-1, 1)
# v[1] = myrandom.uniform (-1, 1)
# s = v[0] * v[0] + v[1] * v[1]
# v[2] = -1 + 2 * s
# a = 2 * numpy.sqrt(1 - s)
# v[0] *= a
# v[1] *= a
cos_theta = myrandom.uniform(-1, 1)
sin_theta = numpy.sqrt(1 - cos_theta * cos_theta)
phi = myrandom.uniform(0, Pi2)
sin_phi, cos_phi = math.sin(phi), math.cos(phi) # sincos
v = [sin_theta * cos_phi, sin_theta * sin_phi, cos_theta]
return _gfrd.normalize(v, r)
def random_vector(r):
# v, s = [0.0, 0.0, 0.0], 2.0
# while s > 1.0:
# v[0] = myrandom.uniform (-1, 1)
# v[1] = myrandom.uniform (-1, 1)
# s = v[0] * v[0] + v[1] * v[1]
# v[2] = -1 + 2 * s
# a = 2 * numpy.sqrt(1 - s)
# v[0] *= a
# v[1] *= a
cos_theta = myrandom.uniform(-1, 1)
sin_theta = numpy.sqrt(1 - cos_theta * cos_theta)
phi = myrandom.uniform(0, Pi2)
sin_phi, cos_phi = math.sin(phi), math.cos(phi) # sincos
v = [sin_theta * cos_phi, sin_theta * sin_phi, cos_theta]
return _gfrd.normalize(v, r)
def random_vector2D(r):
# Return a random 2D cartesian vector of length r.
phi = myrandom.uniform(0, Pi2)
v = [math.cos(phi), math.sin(phi)] # sincos
# Todo. return _gfrd.normalize(v, r)
v = numpy.array(v)
norm = numpy.linalg.norm(v)
return v * (r / norm)
def draw_time_wrapper(gf):
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawTime. ' + gf.__class__.__name__)
try:
dt = gf.drawTime(rnd)
except Exception, e:
raise Exception('gf.drawTime() failed, '
'%s, rnd = %.16g, %s' % (str(e), rnd, gf.dump()))
def draw_event_type_wrapper(gf, dt):
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawEventType. ' + gf.__class__.__name__)
try:
event_type = gf.drawEventType(rnd, dt)
except Exception, e:
raise Exception('gf.drawEventType() failed, '
'%s, rnd = %.16g, dt = %.16g, %s' %
(str(e), rnd, dt, gf.dump()))
def draw_event_type_wrapper(gf, dt):
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawEventType. ' + gf.__class__.__name__)
try:
event_type = gf.drawEventType(rnd, dt)
except Exception, e:
raise Exception('gf.drawEventType() failed, '
'%s, rnd = %.16g, dt = %.16g, %s' %
(str(e), rnd, dt, gf.dump()))
def draw_time_wrapper(gf):
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawTime. ' + gf.__class__.__name__)
try:
dt = gf.drawTime(rnd)
except Exception, e:
raise Exception('gf.drawTime() failed, '
'%s, rnd = %.16g, %s' %
(str(e), rnd, gf.dump()))
def draw_eventtype_wrapper(gf, dt, r0):
rnd = myrandom.uniform()
if __debug__:
log.debug(" *drawEventType. " + gf.__class__.__name__)
try:
event_type = gf.drawEventType(rnd, r0, dt)
except Exception, e:
raise Exception(
"gf.drawEventType() failed, " "%s, rnd = %g, r0 = %g, dt = %g, %s" % (str(e), rnd, r0, dt, gf.dump())
)
def drawTime_wrapper(gf, r0=None):
rnd = myrandom.uniform()
if __debug__:
log.debug(" *drawTime. " + gf.__class__.__name__)
try:
if r0 == None:
# Todo. Let gf handle this.
dt = gf.drawTime(rnd)
else:
dt = gf.drawTime(rnd, r0)
except Exception, e:
raise Exception("gf.drawTime() failed, " "%s, rnd = %g, %s" % (str(e), rnd, gf.dump()))
def draw_theta_wrapper(gf, r, dt):
"""Draw theta for the inter-particle vector.
"""
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawTheta. ' + gf.__class__.__name__)
try:
theta = gf.drawTheta(rnd, r, dt)
except Exception, e:
raise Exception('gf.drawTheta() failed, '
'%s, rnd = %.16g, r = %.16g, dt = %.16g' %
(str(e), rnd, r, dt)) #, gf.dump()))
def drawTheta_wrapper(gf, r, r0, dt):
"""Draw theta for the inter-particle vector.
"""
rnd = myrandom.uniform()
if __debug__:
log.debug(" *drawTheta. " + gf.__class__.__name__)
try:
theta = gf.drawTheta(rnd, r, r0, dt)
except Exception, e:
raise Exception(
"gf.drawTheta() failed, " "%s, rnd = %g, r = %g, r0 = %g, dt = %g" % (str(e), rnd, r, r0, dt)
) # , gf.dump()))
def drawTime_wrapper(gf, r0=None):
rnd = myrandom.uniform()
if __debug__:
log.debug(' *drawTime. ' + gf.__class__.__name__)
try:
if r0 == None:
# Todo. Let gf handle this.
dt = gf.drawTime(rnd)
else:
dt = gf.drawTime(rnd, r0)
except Exception, e:
raise Exception('gf.drawTime() failed, '
'%s, rnd = %g, %s' %
(str(e), rnd, gf.dump()))
rr['k'] = '.01'
m.network_rules.add_reaction_rule(rr)
nrw = _gfrd.NetworkRulesWrapper(m.network_rules)
w = _gfrd.World(1., 10)
region = _gfrd._CuboidalRegion("default",
_gfrd.Box((.5, .5, .5), (1., 0., 0.), (0., 1., 0.), (0., 0., 1.), 1., 1., .1))
w.add_surface(region)
for s in [S0, S1, S2]:
w.add_species(_gfrd.SpeciesInfo(s.id, float(s['D']), float(s['radius']), s['surface']))
for i in xrange(0, 300):
w.new_particle([S0, S1][i % 2],
[myrandom.uniform(), myrandom.uniform(), myrandom.uniform()])
wn = vtk.vtkRenderWindow()
int = wn.MakeRenderWindowInteractor()
int.Initialize()
int.SetRenderWindow(wn)
r = vtk.vtkRenderer()
wn.AddRenderer(r)
actors = {}
def create_actor(pp):
s = vtk.vtkSphereSource()
s.SetRadius(pp[1].radius)
s.SetCenter(pp[1].position)
m = vtk.vtkPolyDataMapper()
def random_unit_vector_s():
s = numpy.array([1.0, myrandom.uniform(0, Pi), myrandom.uniform(0, Pi2)])
return s
def rng_uniform():
'''Returns a positive random number
'''
while True:
rng = myrandom.uniform(0.0, 1.0)
if rng > 0.0: return rng
def rng_uniform():
'''Returns a positive random number
'''
while True:
rng = myrandom.uniform(0.0, 1.0)
if rng > 0.0: return rng
def random_position(self):
"""Only uniform if vector_x and vector_y have same length.
"""
return self.shape.position + myrandom.uniform(-1, 1) * self.shape.unit_x * self.shape.extent[0] + \
myrandom.uniform(-1, 1) * self.shape.unit_y * self.shape.extent[1]
w = MyParticleContainer(1.0)
region = _gfrd._CuboidalRegion(
"default",
_gfrd.Box((.5, .5, .5), (1., 0., 0.), (0., 1., 0.), (0., 0., 1.), 1., 1.,
.1))
w.add_surface(region)
for s in [S0, S1, S2]:
w.add_species(
_gfrd.SpeciesInfo(s.id, float(s['D']), float(s['radius']),
s['surface']))
for i in xrange(0, 300):
w.new_particle(
[S0, S1][i % 2],
[myrandom.uniform(),
myrandom.uniform(),
myrandom.uniform()])
wn = vtk.vtkRenderWindow()
int = wn.MakeRenderWindowInteractor()
int.Initialize()
int.SetRenderWindow(wn)
r = vtk.vtkRenderer()
wn.AddRenderer(r)
actors = {}
def create_actor(pp):
s = vtk.vtkSphereSource()
def random_position(self):
return (self.shape.position +
myrandom.uniform(-1, 1) * self.shape.unit_z * self.shape.size)
def random_position(self):
return self.shape.position + myrandom.uniform(-1, 1) * self.shape.unit_z * self.shape.size
def random_vector(r):
v = [myrandom.uniform(-1,1), myrandom.uniform(-1,1), myrandom.uniform(-1,1)]
return _gfrd.normalize(v, r)
def random_unit_vector_s():
s = numpy.array([1.0, myrandom.uniform(0, Pi), myrandom.uniform(0, Pi2)])
return s