def test(self):
c = ShapeBasedConstraint()
w = Wall(normal=[-1, 0, 0])
c.shape = w
# Does the shape parameter return the correct lcass
self.assertEqual(c.shape.__class__, Wall)
# Do the sciprt object match
self.assertEqual(c.shape, w)
# Different shape
c.shape = Sphere(radius=1)
# Test class
self.assertEqual(c.shape.__class__, Sphere)
# Test parameter retrieval
self.assertAlmostEqual(c.shape.radius, 1, places=8)
with self.assertRaises(RuntimeError):
c.shape = Wall(thisparameterdoesnotexist=0)
class LBBoundariesBase(object):
system = espressomd.System(box_l=[10.0, 10.0, 10.0])
wall_shape1 = Wall(normal=[1., 0., 0.], dist=2.5)
wall_shape2 = Wall(normal=[-1., 0., 0.], dist=-7.5)
def test_add(self):
boundary = espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1)
self.system.lbboundaries.add(boundary)
self.assertEqual(boundary, self.system.lbboundaries[0])
def test_remove(self):
lbb = self.system.lbboundaries
b1 = lbb.add(
espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1))
b2 = lbb.add(
espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1))
lbb.remove(b1)
self.assertFalse(b1 in lbb)
self.assertTrue(b2 in lbb)
def test_size(self):
lbb = self.system.lbboundaries
self.assertEqual(lbb.size(), 0)
lbb.add(espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1))
self.assertEqual(lbb.size(), 1)
lbb.add(espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1))
self.assertEqual(lbb.size(), 2)
def test_empty(self):
lbb = self.system.lbboundaries
self.assertTrue(lbb.empty())
lbb.add(espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1))
self.assertFalse(lbb.empty())
def test_clear(self):
lbb = self.system.lbboundaries
b1 = lbb.add(
espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1))
b2 = lbb.add(
espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1))
lbb.clear()
self.assertTrue(lbb.empty())
def test_boundary_flags(self):
lbb = self.system.lbboundaries
lbb.add(espressomd.lbboundaries.LBBoundary(shape=self.wall_shape1))
lbb.add(espressomd.lbboundaries.LBBoundary(shape=self.wall_shape2))
rng = range(20)
lbf = self.lbf
for i in product(range(0, 5), rng, rng):
self.assertEqual(lbf[i].boundary, 1)
for i in product(range(5, 15), rng, rng):
self.assertEqual(lbf[i].boundary, 0)
for i in product(range(15, 20), rng, rng):
self.assertEqual(lbf[i].boundary, 2)
lbb.clear()
for i in product(rng, rng, rng):
self.assertEqual(lbf[i].boundary, 0)
system.cell_system.skin = 0.3
system.thermostat.set_langevin(kT=temp, gamma=gamma, seed=42)
# Visualizer
visualizer = visualization_opengl.openGLLive(
system,
camera_position=[-3 * box_l, box_l * 0.5, box_l * 0.5],
camera_right=[0, 0, 1],
drag_force=5 * 298,
background_color=[1, 1, 1],
light_pos=[30, 30, 30],
ext_force_arrows_type_scale=[0.0001],
ext_force_arrows=False)
# Walls
system.constraints.add(shape=Wall(dist=0, normal=[0, 0, 1]),
particle_type=types["Electrode"])
system.constraints.add(shape=Wall(dist=-box_z, normal=[0, 0, -1]),
particle_type=types["Electrode"])
# Place particles
for i in range(int(n_ionpairs)):
p = numpy.random.random(3) * box_l
p[2] += lj_sigmas["Electrode"]
system.part.add(id=len(system.part),
type=types["Cl"],
pos=p,
q=charges["Cl"],
mass=masses["Cl"])
for i in range(int(n_ionpairs)):
p = numpy.random.random(3) * box_l
os.remove(os.path.join(checkpoint.checkpoint_dir, filepath))
LB_implementation = None
if 'LB.CPU' in modes:
LB_implementation = espressomd.lb.LBFluid
elif 'LB.GPU' in modes and espressomd.gpu_available():
LB_implementation = espressomd.lb.LBFluidGPU
if LB_implementation:
lbf = LB_implementation(agrid=0.5, visc=1.3, dens=1.5, tau=0.01)
system.actors.add(lbf)
if 'THERM.LB' in modes:
system.thermostat.set_lb(LB_fluid=lbf, seed=23, gamma=2.0)
if any(has_features(i) for i in ["LB_BOUNDARIES", "LB_BOUNDARIES_GPU"]):
if 'EK.GPU' not in modes:
system.lbboundaries.add(
LBBoundary(shape=Wall(normal=(0, 0, 1), dist=0.5),
velocity=(1e-4, 1e-4, 0)))
EK_implementation = None
if 'EK.GPU' in modes and espressomd.gpu_available(
) and espressomd.has_features('ELECTROKINETICS'):
EK_implementation = espressomd.electrokinetics
ek = EK_implementation.Electrokinetics(agrid=0.5,
lb_density=26.15,
viscosity=1.7,
friction=0.0,
T=1.1,
prefactor=0.88,
stencil="linkcentered")
ek_species = EK_implementation.Species(
density=0.4,
checkpoint_id=idx, checkpoint_path="@CMAKE_CURRENT_BINARY_DIR@")
LB_implementation = None
if 'LB.CPU' in modes:
LB_implementation = espressomd.lb.LBFluid
elif 'LB.GPU' in modes and espressomd.gpu_available():
LB_implementation = espressomd.lb.LBFluidGPU
if LB_implementation:
lbf = LB_implementation(agrid=0.5, visc=1.3, dens=1.5, tau=0.01)
system.actors.add(lbf)
if 'LBTHERM' in modes:
system.thermostat.set_lb(LB_fluid=lbf, seed=23, gamma=2.0)
if espressomd.has_features("LB_BOUNDARIES") or espressomd.has_features("LB_BOUNDARIES_GPU"):
if not 'EK.GPU' in modes:
system.lbboundaries.add(
LBBoundary(shape=Wall(normal=(0, 0, 1), dist=0.5), velocity=(1e-4, 1e-4, 0)))
EK_implementation = None
if 'EK.GPU' in modes and espressomd.gpu_available() and espressomd.has_features('ELECTROKINETICS'):
EK_implementation = espressomd.electrokinetics
ek = EK_implementation.Electrokinetics(
agrid=0.5,
lb_density=26.15,
viscosity=1.7,
friction=0.0,
T=1.1,
prefactor=0.88,
stencil="linkcentered")
ek_species = EK_implementation.Species(
density=0.4,
D=0.02,
# Here we use exactly the same parameters for the geometry of the constraints
# that was used for the LB boundaries. This can be done, since the distance
# function used for the constraints is the same as the one used for the
# LB boundaries.
#
##########################################################################
cylinder = Cylinder(center=0.5 * BOX_L,
axis=[1, 0, 0],
radius=DIAMETER / 2.0,
length=LENGTH,
direction=-1)
system.constraints.add(shape=cylinder, particle_type=1)
# Setup walls
wall = Wall(dist=PADDING, normal=[1, 0, 0])
system.constraints.add(shape=wall, particle_type=1)
wall = Wall(dist=-(LENGTH + PADDING), normal=[-1, 0, 0])
system.constraints.add(shape=wall, particle_type=1)
# Setup cone
IRAD = 4.0
ANGLE = pi / 4.0
ORAD = (DIAMETER - IRAD) / sin(ANGLE)
SHIFT = 0.25 * ORAD * cos(ANGLE)
hollow_cone = HollowCone(
center=[BOX_L[0] / 2.0 + SHIFT, BOX_L[1] / 2.0, BOX_L[2] / 2.0],
axis=[-1, 0, 0],
outer_radius=ORAD,
box_l = (n_ionpairs * sum(masses.values()) / density)**(1. / 3.)
box_z = box_l + 2.0 * (lj_sigmas["Electrode"])
box_volume = box_l * box_l * box_z
elc_gap = box_z * 0.15
system.box_l = [box_l, box_l, box_z + elc_gap]
system.periodicity = [1, 1, 1]
system.time_step = time_step
system.cell_system.skin = 0.3
system.thermostat.set_langevin(kT=temp, gamma=gamma)
# Visualizer
visualizer = openGLLive(system, camera_position=[-3 * box_l, box_l * 0.5, box_l * 0.5], camera_right=[
0, 0, 1], drag_force=5 * 298, background_color=[1, 1, 1], light_pos=[30, 30, 30], ext_force_arrows_scale=[0.0001], ext_force_arrows=False)
# Walls
system.constraints.add(shape=Wall(
dist=0, normal=[0, 0, 1]), particle_type=types["Electrode"])
system.constraints.add(shape=Wall(
dist=-box_z, normal=[0, 0, -1]), particle_type=types["Electrode"])
# Place particles
for i in range(int(n_ionpairs)):
p = numpy.random.random(3) * box_l
p[2] += lj_sigmas["Electrode"]
system.part.add(id=len(system.part),
type=types["Cl"], pos=p, q=charges["Cl"], mass=masses["Cl"])
for i in range(int(n_ionpairs)):
p = numpy.random.random(3) * box_l
p[2] += lj_sigmas["Electrode"]
system.part.add(id=len(system.part),
type=types["Na"], pos=p, q=charges["Na"], mass=masses["Na"])
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(
shape=Cylinder(
center=[length / 2.0, (diameter + 4) / 2.0, (diameter + 4) / 2.0],
axis=[1, 0, 0], radius=diameter / 2.0, length=length, direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
wall = LBBoundary(shape=Wall(dist=2, normal=[1, 0, 0]))
system.lbboundaries.add(wall)
wall = LBBoundary(shape=Wall(dist=-(length - 2), normal=[-1, 0, 0]))
system.lbboundaries.add(wall)
# Setup cone
irad = 4.0
angle = pi / 4.0
orad = (diameter - irad) / sin(angle)
shift = 0.25 * orad * cos(angle)
hollow_cone = LBBoundary(
shape=HollowCone(
center=[length / 2.0 + shift,
# function used for the constraints is the same as the one used for the # LB boundaries. # ########################################################################## ## Exercise 2 ## # Complete the geometry from the LB-based # script. You need to add types to the walls # and cone as well. cylinder = Cylinder(...) system.constraints.add(shape=cylinder, particle_type=1) # Setup walls wall = Wall(...) system.constraints.add(shape=wall, particle_type=1) wall = Wall(...) system.constraints.add(shape=wall, particle_type=1) # Setup cone ... hollow_cone = HollowCone(...) system.constraints.add(shape=hollow_cone, particle_type=1) ########################################################################## # # We set up a WCA (almost-hard) interaction between the particles and the
# function used for the constraints is the same as the one used for the
# LB boundaries.
#
##########################################################################
cylinder = Cylinder(
center=[length / 2.0, (diameter + 4) / 2.0, (diameter + 4) / 2.0],
axis=[1, 0, 0],
radius=diameter / 2.0,
length=length,
direction=-1)
system.constraints.add(shape=cylinder, particle_type=1)
# Setup walls
wall = Wall(dist=2, normal=[1, 0, 0])
system.constraints.add(shape=wall, particle_type=2)
wall = Wall(dist=-(length - 2), normal=[-1, 0, 0])
system.constraints.add(shape=wall, particle_type=3)
# Setup cone
irad = 4.0
angle = pi / 4.0
orad = (diameter - irad) / sin(angle)
shift = 0.25 * orad * cos(angle)
hollow_cone = HollowCone(
center=[length / 2.0 + shift, (diameter + 4) / 2.0, (diameter + 4) / 2.0],
axis=[-1, 0, 0],
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(shape=Cylinder(center=0.5 * BOX_L,
axis=[1, 0, 0],
radius=DIAMETER / 2.0,
length=LENGTH,
direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
wall = LBBoundary(shape=Wall(dist=PADDING, normal=[1, 0, 0]))
system.lbboundaries.add(wall)
wall = LBBoundary(shape=Wall(dist=-(LENGTH + PADDING), normal=[-1, 0, 0]))
system.lbboundaries.add(wall)
# Setup cone
IRAD = 4.0
ANGLE = pi / 4.0
ORAD = (DIAMETER - IRAD) / sin(ANGLE)
SHIFT = 0.25 * ORAD * cos(ANGLE)
hollow_cone = LBBoundary(shape=espressomd.shapes.HollowConicalFrustum(
center=[BOX_L[0] / 2.0 - 1.3 * SHIFT, BOX_L[1] / 2.0, BOX_L[2] / 2.0],
axis=[-1, 0, 0],