class Simulation(object):
"""
Edited by Aiyin
Simulation class. This is the main class of the simulation framework.
"""
def start(self):
self.system.simulate()
def __init__(self, config_filename, output_filename, system_lifetime,
brownian_timestep, saving_timestep, verbose, **kwargs):
self.system = System()
self.system.config_filename = config_filename
self.system.output_filename = output_filename
self.system.load_from_file()
# need to print some ovito writing procedure here
self.system.system_properties.lifetime = system_lifetime
self.system.system_properties.brownian_timestep = brownian_timestep
self.system.system_properties.summary_timestep = saving_timestep
for k in ["swelling_rate", "packing_fraction", "aspect_ratio"]:
if k in kwargs:
setattr(self.system.system_properties, k, kwargs[k])
# self.system.system_properties.swelling_rate = swelling_rate
# self.system.system_properties.packing_fraction = packing_fraction
# self.system.system_properties.aspect_ratio = aspect_ratio
self.system.system_properties.verbose = verbose
def __init__(self, config_filename, output_filename, system_lifetime,
brownian_timestep, saving_timestep, verbose, **kwargs):
self.system = System()
self.system.config_filename = config_filename
self.system.output_filename = output_filename
self.system.load_from_file()
# need to print some ovito writing procedure here
self.system.system_properties.lifetime = system_lifetime
self.system.system_properties.brownian_timestep = brownian_timestep
self.system.system_properties.summary_timestep = saving_timestep
for k in ["swelling_rate", "packing_fraction", "aspect_ratio"]:
if k in kwargs:
setattr(self.system.system_properties, k, kwargs[k])
# self.system.system_properties.swelling_rate = swelling_rate
# self.system.system_properties.packing_fraction = packing_fraction
# self.system.system_properties.aspect_ratio = aspect_ratio
self.system.system_properties.verbose = verbose
class TestP3System(unittest.TestCase):
"""
2x2 P3 system test
"""
def setUp(self):
self.system = System()
# Load the system from the 2x2 file which was generated by the test_sysgen module
self.system.config_filename = "bedsim/data/test/P3EllipseGrid-2x2.h5"
self.system.load_from_file()
def test_plot_P3(self):
p = Plot(self.system)
p.system_sync()
p.plot_system('bedsim/data/test/P3EllipseGrid-2x2.eps')
def test_plot_P3_Antrag(self):
p = Plot(self.system)
p.plot_system_fmantrag('bedsim/data/test/P3EllipseAntrag-2x2.eps')
class TestBillardSystem(unittest.TestCase):
def setUp(self):
self.system = System()
# Load the system from the 5x5 file which was generated by the test_sysgen module
self.system.config_filename = "bedsim/data/test/EllipseGrid-5x5.h5"
self.system.load_from_file()
def test_timing_algorithms(self):
t1 = self.system._particles[0]
t2 = self.system._particles[5]
# test crossing from first particle to next cell in x-direction
t1.velocity = np.array([1,0])
(t, c, p) = t1.cell.crossing_time(t1.position, t1.velocity)
self.assertTrue( numeq(p, np.array([0.6, 0.4])).all() )
self.assertTrue( numeq(t, 0.4) )
# test if cell_crossing_time also works for cells which are not near to (0,0) (this tests the relative directions)
t2.velocity = np.array([1,0])
(t, c, p) = t2.cell.crossing_time(t2.position, t2.velocity)
#print(t,",",c,",",p)
# FIXME: fix needed! # files API changes seems to have mirrored the system # check this
"""self.assertTrue( numeq(p, np.array([1.6, 0.4])).all() ) # FIXME: seit Umstellung auf files API gibt es hier Probleme!
self.assertTrue( numeq(t, 0.4) )
# test if cell_crossing_time works for boundary cell crossing as well
t2.velocity = np.array([0, -1])
(t, c, p) = t2.cell_crossing_time()
self.assertTrue( numeq(p, np.array([1.2, 5])).all() )
self.assertTrue( numeq(t, 0.4) )"""
def test_plot(self):
p = Plot(self.system)
p.system_sync()
p.plot_system('bedsim/data/test/EllipseGrid-5x5.eps')
def setUp(self):
#grid_space = np.linspace(start=-3, stop=3, num=2, endpoint=True).tolist() # num+1 because endpoint counts as well...
grid_space = np.linspace(
start=-15, stop=15, num=2,
endpoint=True).tolist() # num+1 because endpoint counts as well...
grid_data = np.array([[x, y] for x in grid_space for y in grid_space])
self.system = System()
self.system.cellspace = DelaunayCellspace(system=self.system,
grid_points=grid_data)
self.system.boundary = getattr(bedsim.boundary,
'PeriodicBox')(system=self.system)
e1 = Ellipse(position=[0, 0],
velocity=[0, 0],
angle=0,
angvel=0,
major=1,
minor=0.5)
e2 = Ellipse(position=[1, 1],
velocity=[0, 0],
angle=0,
angvel=0,
major=1,
minor=0.5)
#e1 = Ellipse(position=[0,0], velocity=[0,0], angle=np.pi/4, angvel=0, major = 1, minor = 0.5)
#e2 = Ellipse(position=[1.6,0.3], velocity=[0.0000001,0], angle=np.pi/5, angvel=-1*np.pi, major = 1, minor = 0.5)
e1._id = 1
e2._id = 2
particles = [e1, e2]
self.system._particles = particles ## check if this works
[
self.system.cellspace.assign_particle(particle)
for particle in self.system._particles
]
def setUp(self):
self.system = System()
# Load the system from the 2x2 file which was generated by the test_sysgen module
self.system.config_filename = "bedsim/data/test/EllipseGrid-2x2.h5"
self.system.load_from_file()
class TestSystem(unittest.TestCase):
"""
2x2 system test
FIXME: also test ellipses!
"""
def setUp(self):
self.system = System()
# Load the system from the 2x2 file which was generated by the test_sysgen module
self.system.config_filename = "bedsim/data/test/EllipseGrid-2x2.h5"
self.system.load_from_file()
def test_overlap(self):
# Select one particle to perform tests with
[t1, t2] = self.system._particles[:2]
(o1, o2) = (t1.position, t2.position)
(v1, v2) = (t1.velocity, t2.velocity)
self.assertEqual(t1.overlap(t2, 0), False)
# move t1 to t2 and test again ;)
t1.position = np.array([0.2, 1.30]) # FIXME: does it touch or overlap?
self.assertEqual(t1.overlap(t2, 0), True)
# test correction move
t1.velocity = np.array([0,1]) # there must be a reason for t1 to overlap with t2
t1.correction(t2)
#print("CORR: v1=",t1.velocity, "; v2=",t2.velocity)
self.assertTrue((t1.velocity == np.array([0,0])).all()) ## FIXME: check manually if correct
self.assertTrue((t2.velocity == np.array([0,1])).all()) ## FIXME: same here
(t1.position, t2.position) = (o1, o2) # reset position or we will break the cell assignment # FIXME: maybe couple translation and cell assignment
(t1.velocity, t2.velocity) = (v1, v2)
# now test the most difficult case: overlap through a border
t1.position = np.array([1.95, 1.4])
t2.position = np.array([0.05, 1.4])
self.assertEqual(t1.overlap(t2, 0), True)
(t1.position, t2.position) = (o1, o2) # ...and reset
def test_timing_algorithms(self):
[t1, t2] = self.system._particles[:2]
"""
1. Test: cell-crossing through an inner cell (not through boundary)
"""
t1.velocity = np.array([0.0,1.0])
t1.position = t1.position + np.array([0,0.1])
# Test cell crossing
#print(t1.cell_crossing_time())
(t, c, p) = t1.cell.crossing_time(t1.position, t1.velocity)
self.assertTrue( numeq(p, np.array([0.2, 0.8])).all())
self.assertTrue( numeq(t, 0.3))
# Test collision
self.assertTrue( numapprox(t1.collision_time(t2), np.array([0.7, 0.2, 1.3])).all())
self.assertTrue( numapprox(t1.tpw_collision_time(t2), np.array([0.7, 0.2, 1.3])).all())
#print("\n\n>>>\nStandard method: ", t1.collision_time(t2))
#print("tqw method: ", t1.tpw_collision_time(t2))
"""
2. Test: cell-crossing through a boundary
"""
t1.position = t1.position - np.array([0,0.1]) # reset
t1.velocity = np.array([0,-1])
#print(t1.collision_time(t2))
#print("t1 inter boundary crossing: ", t1.cell_crossing_time())
(t, c, p) = t1.cell.crossing_time(t1.position, t1.velocity)
self.assertEqual( numeq(p, np.array([0.2, 2.0])).all(), True)
self.assertEqual( numeq(t, 0.4), True)
def test_plot(self):
p = Plot(self.system)
p.system_sync()
p.plot_system('bedsim/data/test/EllipseGrid-2x2.eps')
def test_minimizer(self):
# this is just for understanding the minimization routines
cons = ({'type': 'ineq', 'fun': lambda x: -10},
{'type': 'ineq', 'fun': lambda x: 10})
bnds = ((0, 2),
(0, 2),
(0, 2))
x0 = [1,1,1]
f = lambda x: x[0]
tolerance = 1e-12 # FIXME: BDsim2d uses different tolerance values
res = minimize(fun=f, x0=x0, method='SLSQP', bounds=bnds, constraints=cons, tol=tolerance)
#print(res)
def test_collision_time_estimator(self):
[t1, t2, t3, t4] = self.system._particles
t1.position = np.array([0.5, 0.5])
t2.position = np.array([0.5, 1.0])
t3.position = np.array([1.9, 1.9])
t4.position = np.array([1.9, 1.7])
t1.axes = (0.25, 0.1)
t2.axes = (0.25, 0.1)
p = Plot(self.system)
p.system_sync()
p.plot_system('bedsim/data/test/EllipseGrid-2x2-MOD.eps')
# test axes
self.assertTrue( numeq(np.abs(t1._get_separating_axis(t2)), np.array([1,0])).all() )
self.assertTrue( numeq(np.abs(t1._get_normal_axis(t2)), np.array([0,1])).all() )
# test if projection leads to same tnpoint as in mathematica
self.assertTrue( numapprox(t1._project_on(angle=np.pi/4), np.array([0.134629, 0.134629])).all() )
# test if ellipse angle is taken into account correctly
t1.angle = np.pi/8
# test if projection leads to same tnpoint as in mathematica
self.assertTrue( numapprox(t1._project_on(angle=np.pi/4+np.pi/8), np.array([0.134629, 0.134629])).all() ) # FIXME: check if correct
t1.angle = 0 # reset
# test (partly) negative axes
self.assertTrue( numapprox(t1._project_on(angle=3*np.pi/2), np.array([0, -0.1])).all() ) # between 3rd and 4th quadrant
self.assertTrue( numapprox(t1._project_on(angle=3*np.pi/4), np.array([-0.134629, 0.134629])).all() ) # 2nd quadrant
# test interval generation
#self.assertTrue( t1._get_normal_projection_interval(t=0, angle=0) == 0.25 ) # FIXME: API will change!! => adapt once it's ready ;)
self.assertTrue( numapprox( np.array(list(t1._get_normal_projection_interval(t=0, angle=np.pi/2))), (0.4, 0.6) ).any() )
self.assertTrue( numapprox( np.array(list(t2._get_normal_projection_interval(t=0, angle=np.pi/2))), (0.9, 1.1) ).any() )
#print( t1._get_normal_projection_interval(t=0, angle=np.pi/2) )
#print( t2._get_normal_projection_interval(t=0, angle=np.pi/2) )
self.assertIsNone( t1.approximate_collision_time(t2) )
# now test if collision is detected correctly
t1.angvel = 0.01 * np.pi
t1.velocity = np.array([0,0.05])
#print("t12c=",t1.approximate_collision_time(t2))
#print("t12r=",t1.collision_time(t2))
#print("t12ratio=",abs(1-(t1.approximate_collision_time(t2)[0] / t1.collision_time(t2)[0])))
self.assertTrue( abs(1-(t1.approximate_collision_time(t2)[0] / t1.collision_time(t2)[0]))<0.5 ) # deviation less than 50%
# now test the real ugly cases :P
#print("\nTEST UGLY CASES:")
t1.position = np.array([0.5,0.75])
t1.velocity = np.array([0,0])
t1.angle = 0.1 * np.pi
t1.angvel = -0.1 * np.pi
#t1.angle += t1.angvel * t1.approximate_collision_time(t2)[0] *2
#t1.angle += t1.angvel * 1
#t1.angle = -0.18 * np.pi
p.plot_system('bedsim/data/test/EllipseGrid-2x2-MOD2.eps')