class VirtualSitesTracers(ut.TestCase, VirtualSitesTracersCommon):
if espressomd.has_features(required_features):
box_height = 10.
box_lw = 8.
system = espressomd.System(box_l=(box_lw, box_lw, box_height))
system.time_step = 0.05
system.cell_system.skin = 0.1
lbf = lb.LBFluidGPU(agrid=1,
dens=1,
visc=2,
tau=system.time_step,
fric=1)
system.actors.add(lbf)
system.thermostat.set_lb(kT=0, act_on_virtual=False)
# Setup boundaries
walls = [lbboundaries.LBBoundary() for k in range(2)]
walls[0].set_params(shape=shapes.Wall(normal=[0, 0, 1], dist=0.5))
walls[1].set_params(
shape=shapes.Wall(normal=[0, 0, -1], dist=-box_height - 0.5))
for wall in walls:
system.lbboundaries.add(wall)
handle_errors("setup")
def reset_lb(self, ext_force_density=(0, 0, 0)):
box_height = 10
box_lw = 8
self.system.actors.clear()
self.system.lbboundaries.clear()
self.lbf = self.LBClass(kT=0.0,
agrid=1,
dens=1,
visc=1.8,
tau=self.system.time_step,
ext_force_density=ext_force_density)
self.system.actors.add(self.lbf)
self.system.thermostat.set_lb(LB_fluid=self.lbf,
act_on_virtual=False,
gamma=1)
# Setup boundaries
walls = [lbboundaries.LBBoundary() for k in range(2)]
walls[0].set_params(shape=shapes.Wall(normal=[0, 0, 1], dist=0.5))
walls[1].set_params(
shape=shapes.Wall(normal=[0, 0, -1], dist=-box_height - 0.5))
for wall in walls:
self.system.lbboundaries.add(wall)
handle_errors("setup")
def test_stokes(self):
self.system.actors.clear()
self.system.lbboundaries.clear()
self.system.actors.add(self.lbf)
# The temperature is zero.
self.system.thermostat.set_lb(kT=0)
# Setup walls
walls = [None] * 4
walls[0] = lbboundaries.LBBoundary(shape=shapes.Wall(
normal=[-1, 0, 0], dist=-(1 + box_width)), velocity=v)
walls[1] = lbboundaries.LBBoundary(
shape=shapes.Wall(
normal=[
1,
0,
0],
dist=1),
velocity=v)
walls[2] = lbboundaries.LBBoundary(shape=shapes.Wall(
normal=[0, -1, 0], dist=-(1 + box_width)), velocity=v)
walls[3] = lbboundaries.LBBoundary(
shape=shapes.Wall(
normal=[
0,
1,
0],
dist=1),
velocity=v)
for wall in walls:
self.system.lbboundaries.add(wall)
# setup sphere without slip in the middle
sphere = lbboundaries.LBBoundary(shape=shapes.Sphere(
radius=radius, center=[real_width / 2] * 2 + [box_length / 2], direction=1))
self.system.lbboundaries.add(sphere)
def size(vector):
tmp = 0
for k in vector:
tmp += k * k
return np.sqrt(tmp)
self.system.integrator.run(800)
stokes_force = 6 * np.pi * KVISC * radius * size(v)
print("Stokes' Law says: f=%f" % stokes_force)
# get force that is exerted on the sphere
for i in range(4):
self.system.integrator.run(200)
force = sphere.get_force()
print("Measured force: f=%f" % size(force))
self.assertLess(abs(1.0 - size(force) / stokes_force), 0.06)
def test(self):
self.system.actors.clear()
self.system.lbboundaries.clear()
self.system.actors.add(self.lbf)
# Setup walls
for i in range(3):
n = np.zeros(3)
n[i] = 1
self.system.lbboundaries.add(
lbboundaries.LBBoundary(shape=shapes.Wall(
normal=-n, dist=-(self.system.box_l[i] - AGRID))))
self.system.lbboundaries.add(lbboundaries.LBBoundary(
shape=shapes.Wall(
normal=n, dist=AGRID)))
# setup sphere without slip in the middle
sphere = lbboundaries.LBBoundary(shape=shapes.Sphere(
radius=RADIUS, center=self.system.box_l / 2, direction=1))
self.system.lbboundaries.add(sphere)
sphere_volume = 4. / 3. * np.pi * RADIUS**3
# Equilibration
last_force = -999999
self.system.integrator.run(100)
while True:
self.system.integrator.run(10)
force = np.linalg.norm(sphere.get_force())
if np.linalg.norm(force - last_force) < 0.01:
break
last_force = force
# Check force balance
boundary_force = np.zeros(3)
for b in self.system.lbboundaries:
boundary_force += b.get_force()
fluid_nodes = count_fluid_nodes(self.lbf)
fluid_volume = fluid_nodes * AGRID**3
applied_force = fluid_volume * np.array(LB_PARAMS['ext_force_density'])
np.testing.assert_allclose(
boundary_force,
applied_force,
atol=0.08 * np.linalg.norm(applied_force))
# Check buoyancy force on the sphere
expected_force = np.array(
[0, -sphere_volume * DENS * G, 0])
np.testing.assert_allclose(
np.copy(sphere.get_force()), expected_force,
atol=np.linalg.norm(expected_force) * 0.02)
def test_stokes(self):
self.system.actors.clear()
self.system.lbboundaries.clear()
self.system.actors.add(self.lbf)
self.system.thermostat.set_lb(LB_fluid=self.lbf, gamma=1.0)
# Setup walls
walls = [None] * 4
walls[0] = lbboundaries.LBBoundary(shape=shapes.Wall(
normal=[-1, 0, 0], dist=-(1 + box_width)),
velocity=v)
walls[1] = lbboundaries.LBBoundary(shape=shapes.Wall(normal=[1, 0, 0],
dist=1),
velocity=v)
walls[2] = lbboundaries.LBBoundary(shape=shapes.Wall(
normal=[0, -1, 0], dist=-(1 + box_width)),
velocity=v)
walls[3] = lbboundaries.LBBoundary(shape=shapes.Wall(normal=[0, 1, 0],
dist=1),
velocity=v)
for wall in walls:
self.system.lbboundaries.add(wall)
# setup sphere without slip in the middle
sphere = lbboundaries.LBBoundary(
shape=shapes.Sphere(radius=radius,
center=[real_width / 2] * 2 + [box_length / 2],
direction=1))
self.system.lbboundaries.add(sphere)
def size(vector):
tmp = 0
for k in vector:
tmp += k * k
return np.sqrt(tmp)
last_force = -1000.
dynamic_viscosity = self.lbf.viscosity * self.lbf.density
stokes_force = 6 * np.pi * dynamic_viscosity * radius * size(v)
self.system.integrator.run(35)
while True:
self.system.integrator.run(5)
force = np.linalg.norm(sphere.get_force())
if np.abs(last_force - force) < 0.01 * stokes_force:
break
last_force = force
force = np.copy(sphere.get_force())
np.testing.assert_allclose(force, [0, 0, stokes_force],
rtol=0.03,
atol=stokes_force * 0.03)
def test_particle_torques(self):
"""setup shear flow and check if resulting torques match
the formulae in the core
"""
bottom = shapes.Wall(normal=[0, 0, 1],
dist=self.LB_params['agrid'])
top = shapes.Wall(normal=[0, 0, -1],
dist=-self.system.box_l[2] + self.LB_params['agrid'])
self.system.lbboundaries.add(lbboundaries.LBBoundary(shape=bottom))
self.system.lbboundaries.add(
lbboundaries.LBBoundary(shape=top, velocity=[1e-3, 1e-3, 0]))
self.system.integrator.run(100)
#fix the particles so inaccuracies from position updates
#before torque calculation don't matter
self.add_all_types_of_swimmers(fix=True, rotation=True,
put_in_corners=False)
self.system.integrator.run(20)
for swimmer in self.system.part:
director = swimmer.director
dip_len = swimmer.swimming["dipole_length"]
mode_fac = 1. if swimmer.swimming["mode"] == "puller" else -1.
source_pos = swimmer.pos + mode_fac * dip_len * director
v_center = self.lbf.get_interpolated_velocity(swimmer.pos)
v_source = self.lbf.get_interpolated_velocity(source_pos)
diff = v_center - v_source
cross = np.cross(diff, director)
#half-step omega with isotropic rinertia
omega_part = swimmer.omega_lab + 0.5 * self.system.time_step * \
swimmer.torque_lab / swimmer.rinertia[0]
omega_swim = cross / np.linalg.norm(cross) * \
np.linalg.norm(diff) / dip_len
torque = swimmer.swimming["rotational_friction"] * \
(omega_swim - omega_part)
self.system.integrator.run(1, reuse_forces=True)
np.testing.assert_allclose(
swimmer.torque_lab,
torque,
atol=self.tol)
def test_advection(self):
# System setup
system = self.s
system.virtual_sites = VirtualSitesInertialessTracers()
system.time_step = 0.02
system.cell_system.skin = 0.1
box_height = 16.
box_lw = 16
system.box_l = box_lw, box_lw, box_height
lbf = lb.LBFluidGPU(agrid=1,
dens=1,
visc=2,
tau=system.time_step,
fric=1)
system.actors.add(lbf)
system.thermostat.set_lb(kT=0)
# Setup boundaries
walls = [lbboundaries.LBBoundary() for k in range(2)]
walls[0].set_params(shape=shapes.Wall(normal=[0, 0, 1], dist=0.5))
walls[1].set_params(
shape=shapes.Wall(normal=[0, 0, -1], dist=-box_height - 0.5))
for wall in walls:
system.lbboundaries.add(wall)
# Establish steady state flow field
system.part.add(id=0,
pos=(0, 5.5, 5.5),
virtual=0,
ext_force=(10, 0, 0))
for i in range(100):
last_t = system.time
last_x = system.part[0].pos
system.integrator.run(500)
print(system.part[0].v,
(system.part[0].pos - last_x) / (system.time - last_t))
valency=1,
ext_force_density=[0, 0, 1.])
neg = electrokinetics.Species(density=0.05,
D=0.1,
valency=-1,
ext_force_density=[0, 0, -1.])
ek.add_species(pos)
ek.add_species(neg)
system.actors.add(ek)
print(ek.get_params())
print(pos.get_params())
print(neg.get_params())
print(pos[5, 5, 5].density)
ek_wall_left = electrokinetics.EKBoundary(shape=shapes.Wall(dist=1,
normal=[1, 0, 0]),
charge_density=-0.01)
ek_wall_right = electrokinetics.EKBoundary(shape=shapes.Wall(dist=-9,
normal=[-1, 0,
0]),
charge_density=0.01)
system.ekboundaries.add(ek_wall_left)
system.ekboundaries.add(ek_wall_right)
for i in range(1000):
system.integrator.run(100)
sys.stdout.write("\rIntegrating: %03i" % i)
sys.stdout.flush()
pos.print_vtk_density("ek/pos_dens_%i.vtk" % i)
neg.print_vtk_density("ek/neg_dens_%i.vtk" % i)
valency=1,
ext_force_density=[0, 0, 1.])
neg = electrokinetics.Species(density=0.05,
D=0.1,
valency=-1,
ext_force_density=[0, 0, -1.])
ek.add_species(pos)
ek.add_species(neg)
system.actors.add(ek)
print(ek.get_params())
print(pos.get_params())
print(neg.get_params())
print(pos[5, 5, 5].density)
ek_wall_left = ekboundaries.EKBoundary(shape=shapes.Wall(dist=1,
normal=[1, 0, 0]),
charge_density=-0.01)
ek_wall_right = ekboundaries.EKBoundary(shape=shapes.Wall(dist=-9,
normal=[-1, 0, 0]),
charge_density=0.01)
system.ekboundaries.add(ek_wall_left)
system.ekboundaries.add(ek_wall_right)
if not os.path.isdir("ek"):
os.makedirs("ek")
n_int_cycles = 1000
for i in range(n_int_cycles):
system.integrator.run(100)
print("\rIntegrating: %03i" % i, end='', flush=True)
system.cell_system.skin = 0.4
# The temperature is zero.
system.thermostat.set_lb(kT=0)
# LB Parameters
v = [0,0,0.01] # The boundary slip
kinematic_visc = 1.0
# Invoke LB fluid
lbf = lb.LBFluid(visc=kinematic_visc, dens=1, agrid=agrid, tau=system.time_step, fric=1)
system.actors.add(lbf)
# Setup walls
walls = [None] * 4
walls[0] = lbboundaries.LBBoundary(shape=shapes.Wall(normal=[-1,0,0],
dist = -(1+box_width)), velocity=v)
walls[1] = lbboundaries.LBBoundary(shape=shapes.Wall(normal=[1,0,0], dist = 1),
velocity=v)
walls[2] = lbboundaries.LBBoundary(shape=shapes.Wall(normal=[0,-1,0],
dist = -(1+box_width)), velocity=v)
walls[3] = lbboundaries.LBBoundary(shape=shapes.Wall(normal=[0,1,0], dist = 1),
velocity=v)
for wall in walls:
system.lbboundaries.add(wall)
# setup sphere without slip in the middle
sphere = lbboundaries.LBBoundary(shape=shapes.Sphere(radius=radius,
center = [real_width/2] * 2 + [box_length/2],
direction = 1))
system.non_bonded_inter[0, 0].wca.set_params(epsilon=1, sigma=1)
num_part = 30
wall_offset = 0.1
# create random positions in the box sufficiently away from the walls
ran_pos = np.random.uniform(low=1 + wall_offset,
high=box_l - 1 - wall_offset,
size=(num_part, 3))
system.part.add(id=np.arange(num_part),
pos=ran_pos,
type=np.zeros(num_part, dtype=int))
# bottom wall, normal pointing in the +z direction, laid at z=0.1
floor = shapes.Wall(normal=[0, 0, 1], dist=wall_offset)
c1 = system.constraints.add(particle_type=0,
penetrable=False,
only_positive=False,
shape=floor)
# top wall, normal pointing in the -z direction, laid at z=49.9, since the
# normal direction points down, dist is -49.9
ceil = shapes.Wall(normal=[0, 0, -1], dist=-(box_l - wall_offset))
c2 = system.constraints.add(particle_type=0,
penetrable=False,
only_positive=False,
shape=ceil)
# create stiff FENE bonds
fene = interactions.FeneBond(k=30, d_r_max=2)
def test_stokes(self):
# System setup
agrid = 1
radius = 5.5
box_width = 54
real_width = box_width + 2 * agrid
box_length = 54
system = espressomd.System(box_l=[real_width, real_width, box_length])
system.box_l = [real_width, real_width, box_length]
system.time_step = 0.4
system.cell_system.skin = 0.4
# The temperature is zero.
system.thermostat.set_lb(kT=0)
# LB Parameters
v = [0, 0, 0.01] # The boundary slip
kinematic_visc = 5.0
# Invoke LB fluid
lbf = lb.LBFluidGPU(visc=kinematic_visc,
dens=1,
agrid=agrid,
tau=system.time_step,
fric=1)
system.actors.add(lbf)
# Setup walls
walls = [None] * 4
walls[0] = lbboundaries.LBBoundary(shape=shapes.Wall(
normal=[-1, 0, 0], dist=-(1 + box_width)),
velocity=v)
walls[1] = lbboundaries.LBBoundary(shape=shapes.Wall(normal=[1, 0, 0],
dist=1),
velocity=v)
walls[2] = lbboundaries.LBBoundary(shape=shapes.Wall(
normal=[0, -1, 0], dist=-(1 + box_width)),
velocity=v)
walls[3] = lbboundaries.LBBoundary(shape=shapes.Wall(normal=[0, 1, 0],
dist=1),
velocity=v)
for wall in walls:
system.lbboundaries.add(wall)
# setup sphere without slip in the middle
sphere = lbboundaries.LBBoundary(
shape=shapes.Sphere(radius=radius,
center=[real_width / 2] * 2 + [box_length / 2],
direction=1))
system.lbboundaries.add(sphere)
def size(vector):
tmp = 0
for k in vector:
tmp += k * k
return np.sqrt(tmp)
system.integrator.run(800)
stokes_force = 6 * np.pi * kinematic_visc * radius * size(v)
print("Stokes' Law says: f=%f" % stokes_force)
# get force that is exerted on the sphere
for i in range(5):
system.integrator.run(200)
force = sphere.get_force()
print("Measured force: f=%f" % size(force))
self.assertLess(abs(1.0 - size(force) / stokes_force), 0.06)
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=1,
sigma=1,
cutoff=2**(1. / 6),
shift="auto")
num_part = 30
# create random positions in the box sufficiently away from the walls
ran_pos = np.random.uniform(low=1, high=49, size=(num_part, 3))
system.part.add(id=np.arange(num_part),
pos=ran_pos,
type=np.zeros(num_part, dtype=int))
# bottom wall, normal pointing in the +z direction, laid at z=0.1
floor = shapes.Wall(normal=[0, 0, 1], dist=0.1)
c1 = system.constraints.add(particle_type=0,
penetrable=False,
only_positive=False,
shape=floor)
# top wall, normal pointing in the -z direction, laid at z=49.9, since the normal direction points down, dist is -49.9
ceil = shapes.Wall(normal=[0, 0, -1], dist=-49.9)
c2 = system.constraints.add(particle_type=0,
penetrable=False,
only_positive=False,
shape=ceil)
# create_polymer will avoid violating the contraints
fene = interactions.FeneBond(k=30, d_r_max=2)
# the force density on the fluid nodes
force_density = 0.001
lbf = lb.LBFluid_GPU(agrid=1,
dens=1,
visc=1,
tau=0.01,
ext_force=[force_density, 0, 0])
system.actors.add(lbf)
system.thermostat.set_lb(kT=0)
# create the boundary "shape"
upper_wall = shapes.Wall(normal=[0, 1, 0], dist=1.5)
lower_wall = shapes.Wall(normal=[0, -1, 0], dist=-(box_l - 1.5))
# from these shapes, define the LB boundary
upper_bound = lbboundaries.LBBoundary(shape=upper_wall)
lower_bound = lbboundaries.LBBoundary(shape=lower_wall)
system.lbboundaries.add(upper_bound)
system.lbboundaries.add(lower_bound)
# save the center x-velocity in this file
center_output = open("center_velocity.dat", "w")
max_time = 1000
for i in range(max_time):
system.integrator.run(500)
prefactor=bjerrum_length)
# Set up the charged and neutral species
density_counterions = -2.0 * sigma / width
counterions = electrokinetics.Species(
density=density_counterions,
D=D,
valency=valency,
ext_force_density=[ext_force_density, 0, 0])
ek.add_species(counterions)
# Set up the walls confining the fluid
ek_wall_left = espressomd.ekboundaries.EKBoundary(charge_density=sigma / agrid,
shape=shapes.Wall(
normal=[0, 0, 1],
dist=padding))
ek_wall_right = espressomd.ekboundaries.EKBoundary(
charge_density=sigma / agrid,
shape=shapes.Wall(normal=[0, 0, -1], dist=-(padding + width)))
system.ekboundaries.add(ek_wall_left)
system.ekboundaries.add(ek_wall_right)
system.actors.add(ek)
# Integrate the system
for i in range(100):
system.integrator.run(integration_length)
sys.stdout.write("\rintegration: %i%%" % (i + 1))
sys.stdout.flush()
AddVolCons(system, kV)
outputDir = "outputVolParaCUDA"
# Add LB Fluid
lbf = lb.LBFluid(agrid=1,
dens=1,
visc=1,
tau=system.time_step,
ext_force_density=[force, 0, 0])
system.actors.add(lbf)
system.thermostat.set_lb(LB_fluid=lbf, gamma=1.0, act_on_virtual=False)
# Setup boundaries
walls = [lbboundaries.LBBoundary() for k in range(2)]
walls[0].set_params(shape=shapes.Wall(normal=[0, 0, 1], dist=0.5))
walls[1].set_params(shape=shapes.Wall(normal=[0, 0, -1], dist=-boxZ + 0.5))
for wall in walls:
system.lbboundaries.add(wall)
## make directory
from os import mkdir
mkdir(outputDir)
## Perform integration
from writeVTK import WriteVTK
WriteVTK(system, str(outputDir + "/cell_" + str(0) + ".vtk"))
stepSize = 1000
numSteps = 20
LB_plane_axis=1,
LB_vel_scale=1e2,
LB_plane_ngrid=15,
camera_position=[8, 16, 50],
velocity_arrows=True,
velocity_arrows_type_scale=[20.],
velocity_arrows_type_radii=[0.1],
velocity_arrows_type_colors=[[0, 1, 0]])
lbf = lb.LBFluid(kT=0,
agrid=1.0,
dens=1.0,
visc=1.0,
tau=0.1,
ext_force_density=[0, 0.003, 0])
system.actors.add(lbf)
system.thermostat.set_lb(LB_fluid=lbf, gamma=1.5)
# Setup boundaries
walls = [lbboundaries.LBBoundary() for k in range(2)]
walls[0].set_params(shape=shapes.Wall(normal=[1, 0, 0], dist=1.5))
walls[1].set_params(shape=shapes.Wall(normal=[-1, 0, 0], dist=-14.5))
for i in range(100):
system.part.add(pos=np.random.random(3) * system.box_l)
for wall in walls:
system.lbboundaries.add(wall)
visualizer.run(1)
def test(self):
system = self.es
pi = math.pi
box_x = 6
box_y = 6
width = 50
padding = 6
box_z = width + 2 * padding
# Set the electrokinetic parameters
agrid = 1.0
dt = 1.0 / 7.
force = 0.13
sigma = -0.05
viscosity_kinematic = 2.3
friction = 4.3
temperature = 2.9
bjerrum_length = 0.47
temperature_LB = agrid * agrid / (3.0 * dt * dt)
kB_LB = 1.0
cs_squared = (1.0 / 3.0) * (agrid * agrid / (dt * dt))
system.box_l = [box_x, box_y, box_z]
# Set the simulation parameters
system.time_step = dt
system.cell_system.skin = 0.1
system.thermostat.turn_off()
integration_length = 10000
# Output density, velocity, and pressure tensor profiles
output_profiles = 1
# Set up the charged and neutral species
density_water = 26.15
density_counterions = -2.0 * float(sigma) / float(width)
valency = 1.0
# Set up the (LB) electrokinetics fluid
ek = electrokinetics.Electrokinetics(agrid=agrid,
lb_density=density_water,
viscosity=viscosity_kinematic,
friction=friction,
T=temperature,
prefactor=bjerrum_length *
temperature,
stencil="nonlinear")
counterions = electrokinetics.Species(density=density_counterions,
D=0.3,
valency=valency,
ext_force=[force, 0, 0])
ek.add_species(counterions)
# Set up the walls confining the fluid and carrying charge
ek_wall1 = electrokinetics.EKBoundary(
charge_density=sigma / (agrid * padding),
shape=shapes.Wall(normal=[0, 0, 1], dist=padding))
system.ekboundaries.add(ek_wall1)
ek_wall2 = electrokinetics.EKBoundary(
charge_density=sigma / (agrid * padding),
shape=shapes.Wall(normal=[0, 0, -1], dist=-(padding + width)))
system.ekboundaries.add(ek_wall2)
system.actors.add(ek)
# Integrate the system
system.integrator.run(integration_length)
# compare the various quantities to the analytic results
total_velocity_difference = 0.0
total_density_difference = 0.0
total_pressure_difference_xx = 0.0
total_pressure_difference_yy = 0.0
total_pressure_difference_zz = 0.0
total_pressure_difference_xy = 0.0
total_pressure_difference_yz = 0.0
total_pressure_difference_xz = 0.0
# initial parameters for bisection scheme
size = pi / (2.0 * width)
pnt0 = 0.0
pntm = pnt0 + size
pnt1 = pnt0 + 1.9 * size
# the bisection scheme
tol = 1.0e-08
while (size > tol):
val0 = solve(pnt0, width, bjerrum_length, sigma, valency)
val1 = solve(pnt1, width, bjerrum_length, sigma, valency)
valm = solve(pntm, width, bjerrum_length, sigma, valency)
if (val0 < 0.0 and val1 > 0.0):
if (valm < 0.0):
pnt0 = pntm
size = size / 2.0
pntm = pnt0 + size
else:
pnt1 = pntm
size = size / 2.0
pntm = pnt1 - size
elif (val0 > 0.0 and val1 < 0.0):
if (valm < 0.0):
pnt1 = pntm
size = size / 2.0
pntm = pnt1 - size
else:
pnt0 = pntm
size = size / 2.0
pntm = pnt0 + size
else:
sys.exit(
"Bisection method fails:\nTuning of domain boundaries may be required."
)
# obtain the desired xi value
xi = pntm
if (output_profiles):
fp = open("ek_eof_profile.dat", "w")
for i in range(int(box_z / agrid)):
if (i * agrid >= padding and i * agrid < box_z - padding):
xvalue = i * agrid - padding
position = i * agrid - padding - width / 2.0 + agrid / 2.0
# density
measured_density = counterions[int(box_x / (2 * agrid)),
int(box_y / (2 * agrid)),
i].density
calculated_density = density(position, xi, bjerrum_length)
density_difference = abs(measured_density - calculated_density)
total_density_difference = total_density_difference + density_difference
# velocity
measured_velocity = ek[int(box_x / (2 * agrid)),
int(box_y / (2 * agrid)), i].velocity[0]
calculated_velocity = velocity(position, xi, width,
bjerrum_length, force,
viscosity_kinematic,
density_water)
velocity_difference = abs(measured_velocity -
calculated_velocity)
total_velocity_difference = total_velocity_difference + velocity_difference
# diagonal pressure tensor
measured_pressure_xx = ek[int(box_x / (2 * agrid)),
int(box_y / (2 * agrid)),
i].pressure[(0, 0)]
calculated_pressure_xx = hydrostatic_pressure_non_lin(
ek, position, xi, bjerrum_length, (0, 0), box_x, box_y,
box_z, agrid, temperature)
measured_pressure_yy = ek[int(box_x / (2 * agrid)),
int(box_y / (2 * agrid)),
i].pressure[(1, 1)]
calculated_pressure_yy = hydrostatic_pressure_non_lin(
ek, position, xi, bjerrum_length, (1, 1), box_x, box_y,
box_z, agrid, temperature)
measured_pressure_zz = ek[int(box_x / (2 * agrid)),
int(box_y / (2 * agrid)),
i].pressure[(2, 2)]
calculated_pressure_zz = hydrostatic_pressure_non_lin(
ek, position, xi, bjerrum_length, (2, 2), box_x, box_y,
box_z, agrid, temperature)
pressure_difference_xx = abs(measured_pressure_xx -
calculated_pressure_xx)
pressure_difference_yy = abs(measured_pressure_yy -
calculated_pressure_yy)
pressure_difference_zz = abs(measured_pressure_zz -
calculated_pressure_zz)
total_pressure_difference_xx = total_pressure_difference_xx + pressure_difference_xx
total_pressure_difference_yy = total_pressure_difference_yy + pressure_difference_yy
total_pressure_difference_zz = total_pressure_difference_zz + pressure_difference_zz
# xy component pressure tensor
measured_pressure_xy = ek[int(box_x / (2 * agrid)),
int(box_y / (2 * agrid)),
i].pressure[(0, 1)]
calculated_pressure_xy = 0.0
pressure_difference_xy = abs(measured_pressure_xy -
calculated_pressure_xy)
total_pressure_difference_xy = total_pressure_difference_xy + pressure_difference_xy
# yz component pressure tensor
measured_pressure_yz = ek[int(box_x / (2 * agrid)),
int(box_y / (2 * agrid)),
i].pressure[(1, 2)]
calculated_pressure_yz = 0.0
pressure_difference_yz = abs(measured_pressure_yz -
calculated_pressure_yz)
total_pressure_difference_yz = total_pressure_difference_yz + pressure_difference_yz
# xz component pressure tensor
measured_pressure_xz = ek[int(box_x / (2 * agrid)),
int(box_y / (2 * agrid)),
i].pressure[(0, 2)]
calculated_pressure_xz = pressure_tensor_offdiagonal(
position, xi, bjerrum_length, force)
pressure_difference_xz = abs(measured_pressure_xz -
calculated_pressure_xz)
total_pressure_difference_xz = total_pressure_difference_xz + pressure_difference_xz
if (output_profiles):
fp.write(
"{} {} {} {} {} {} {} {} {} {} {} {} {} {} {} {} {}\n".
format(position, measured_density, calculated_density,
measured_velocity, calculated_velocity,
measured_pressure_xy, calculated_pressure_xy,
measured_pressure_yz, calculated_pressure_yz,
measured_pressure_xz, calculated_pressure_xz,
measured_pressure_xx, calculated_pressure_xx,
measured_pressure_yy, calculated_pressure_yy,
measured_pressure_zz, calculated_pressure_zz))
if (output_profiles):
fp.close
total_density_difference = agrid * total_density_difference / width
total_velocity_difference = agrid * total_velocity_difference / width
total_pressure_difference_xx = agrid * total_pressure_difference_xx / width
total_pressure_difference_yy = agrid * total_pressure_difference_yy / width
total_pressure_difference_zz = agrid * total_pressure_difference_zz / width
total_pressure_difference_xy = agrid * total_pressure_difference_xy / width
total_pressure_difference_yz = agrid * total_pressure_difference_yz / width
total_pressure_difference_xz = agrid * total_pressure_difference_xz / width
print("Density deviation: {}".format(total_density_difference))
print("Velocity deviation: {}".format(total_velocity_difference))
print("Pressure deviation xx component: {}".format(
total_pressure_difference_xx))
print("Pressure deviation yy component: {}".format(
total_pressure_difference_yy))
print("Pressure deviation zz component: {}".format(
total_pressure_difference_zz))
print("Pressure deviation xy component: {}".format(
total_pressure_difference_xy))
print("Pressure deviation yz component: {}".format(
total_pressure_difference_yz))
print("Pressure deviation xz component: {}".format(
total_pressure_difference_xz))
self.assertLess(total_density_difference, 8.0e-06,
"Density accuracy not achieved")
self.assertLess(total_velocity_difference, 3.0e-06,
"Velocity accuracy not achieved")
self.assertLess(total_pressure_difference_xx, 6.0e-05,
"Pressure accuracy xx component not achieved")
self.assertLess(total_pressure_difference_yy, 8.0e-05,
"Pressure accuracy yy component not achieved")
self.assertLess(total_pressure_difference_zz, 8.0e-05,
"Pressure accuracy zz component not achieved")
self.assertLess(total_pressure_difference_xy, 1.0e-10,
"Pressure accuracy xy component not achieved")
self.assertLess(total_pressure_difference_yz, 1.0e-10,
"Pressure accuracy yz component not achieved")
self.assertLess(total_pressure_difference_xz, 2.0e-05,
"Pressure accuracy xz component not achieved")
def calc(var):
# AVB: Create an output directory for this to store the output files
outdir = "./Noelle/r01.5kBT4Ads/1000=3.2"
if not os.path.exists(outdir):
os.makedirs(outdir)
# Setup constant
time_step = 0.01
loops = 30
step_per_loop = 100
# AVB: the parameters (that I usually use)
a = 0.05
r0 = 2.0 * a
kBT = 4.0e-6
vwf_type = 0
collagen_type = 1
monomer_mass = 0.01
box_l = 32.0
#print("Shear velocity:")
#shear_velocity = float(input())
#vy = box_l*shear_velocity
vy = var
print(vy)
v = [0, vy, 0]
# System setup
system = 0
system = System(box_l=[box_l, box_l, box_l])
system.set_random_state_PRNG()
np.random.seed(seed=system.seed)
system.cell_system.skin = 0.4
mpc = 20 # The number of monomers has been set to be 20 as default
# Change this value for further simulations
# Fene interaction
fene = interactions.FeneBond(k=0.04, d_r_max=0.3)
system.bonded_inter.add(fene)
# Setup polymer of part_id 0 with fene bond
# AVB: Notice the mode, max_tries and shield parameters for pruned self-avoiding random walk algorithm
polymer.create_polymer(N_P=1,
MPC=mpc,
bond=fene,
bond_length=r0,
start_pos=[29.8, 16.0, 16.0],
mode=2,
max_tries=100,
shield=0.6 * r0)
# AVB: setting the type of particles and changing mass of each monomer to 0.01
system.part[:].type = vwf_type
system.part[:].mass = monomer_mass
# AVB: I suggest to add Lennard-Jones interaction between the monomers
# AVB: to reproduce hydrophobicity
# AVB: parameters for the potential (amplitude and cut-off redius)
amplVwfVwf = 4.0 * kBT # sometimes we change this to 2.0*kBT
rcutVwfVwf = 1.5 * r0
# AVB: the potential
system.non_bonded_inter[vwf_type, vwf_type].lennard_jones.set_params(
epsilon=amplVwfVwf,
sigma=r0 / 1.122,
shift="auto",
cutoff=rcutVwfVwf,
min=r0 * 0.6)
print("Warming up the polymer chain.")
## For longer chains (>100) an extensive
## warmup is neccessary ...
system.time_step = 0.002
system.thermostat.set_langevin(kT=4.0e-6, gamma=1.0)
# AVB: Here the Langevin thermostat is needed, because we have not yet initialized the LB-fluid.
# AVB: And somehow it is necessary so that the polymer adopts the equilibrium conformation of the globule.
# AVB: you may skip this step
for i in range(100):
system.force_cap = float(i) + 1
system.integrator.run(100)
print("Warmup finished.")
system.force_cap = 0
system.integrator.run(100)
system.time_step = time_step
system.integrator.run(500)
# AVB: the following command turns the Langevin thermostat on in line 49
system.thermostat.turn_off()
# AVB: This command sets the velocities of all particles to zero
system.part[:].v = [0, 0, 0]
# AVB: The density was too small here. I have set 1.0 for now.
# AVB: It would be necessary to recalculate, but the density of the liquid should not affect the movements of the polymer (this is how our physical model works).
lbf = espressomd.lb.LBFluid(agrid=1,
dens=1.0,
visc=1.0e2,
tau=time_step,
fric=0.01)
system.actors.add(lbf)
system.thermostat.set_lb(kT=4.0e-6)
# Setup boundaries
walls = [lbboundaries.LBBoundary() for k in range(2)]
walls[0].set_params(shape=shapes.Wall(normal=[1, 0, 0], dist=1.5),
velocity=v)
walls[1].set_params(shape=shapes.Wall(normal=[-1, 0, 0], dist=-30.5))
for wall in walls:
system.lbboundaries.add(wall)
print("Warming up the system with LB fluid.")
system.integrator.run(5000)
print("LB fluid warming finished.")
# AVB: after this you should have a completely collapsed polymer globule
# AVB: If you want to watch the process of globule formation in Paraview, just change 5000 to 0 in line 100
N = 25
x_coord = np.array([30] * N)
y_coord = np.arange(14, 24, 5 / N)
z_coord = np.arange(14, 24, 5 / N)
for i in range(N):
for j in range(N):
system.part.add(id=i * N + j + 100,
pos=np.array([x_coord[i], y_coord[j], z_coord[i]]),
v=np.array([0, 0, 0]),
type=i * N + j + 100)
all_collagen = range(100, (N - 1) * N + (N - 1) + 100)
system.comfixed.types = all_collagen
for i in range(100, (N - 1) * N + (N - 1) + 100):
system.non_bonded_inter[vwf_type,
i].lennard_jones.set_params(epsilon=amplVwfVwf,
sigma=r0 / 1.122,
shift="auto",
cutoff=rcutVwfVwf,
min=r0 * 0.6)
# configure correlators
com_pos = ComPosition(ids=(0, ))
c = Correlator(obs1=com_pos,
tau_lin=16,
tau_max=loops * step_per_loop,
delta_N=1,
corr_operation="square_distance_componentwise",
compress1="discard1")
system.auto_update_accumulators.add(c)
print("Sampling started.")
print("lenth after warmup")
print(
system.analysis.calc_re(chain_start=0,
number_of_chains=1,
chain_length=mpc - 1)[0])
lengths = []
ylengths = []
for i in range(loops):
system.integrator.run(step_per_loop)
system.analysis.append()
lengths.append(
system.analysis.calc_re(chain_start=0,
number_of_chains=1,
chain_length=mpc - 1)[0])
lbf.print_vtk_velocity(outdir + "/" + str(vy) + "%04i.vtk" % i)
system.part.writevtk(outdir + "/" + str(vy) + "vwf_all%04i.vtk" % i,
types=all_collagen)
system.part.writevtk(outdir + "/" + str(vy) + "vwf_poly%04i.vtk" % i,
types=[0])
cor = list(system.part[:].pos)
y = []
for l in cor:
y.append(l[1])
ylengths.append(max(y) - min(y))
sys.stdout.write("\rSampling: %05i" % i)
sys.stdout.flush()
walls[0].set_params(shape=shapes.Wall(normal=[1, 0, 0], dist=1.5))
walls[1].set_params(shape=shapes.Wall(normal=[-1, 0, 0], dist=-30.5))
for i in range(100):
system.integrator.run(step_per_loop)
lengths.append(
system.analysis.calc_re(chain_start=0,
number_of_chains=1,
chain_length=mpc - 1)[0])
system.part.writevtk(outdir + "/" + str(vy) +
"vwf_all[r0=2,kBT=4]intheEND.vtk")
with open(outdir + "/lengths" + str(vy) + ".dat", "a") as datafile:
datafile.write("\n".join(map(str, lengths)))
with open(outdir + "/lengthsY" + str(vy) + ".dat", "a") as datafile:
datafile.write("\n".join(map(str, ylengths)))
mean_vy = [(vy * 10000) / 32, sum(ylengths) / len(ylengths)]
print("mean_vy")
print(mean_vy)
with open(outdir + "/mean_vy" + "2kBT_2r0" + ".dat", "a") as datafile:
datafile.write(" ".join(map(str, mean_vy)))
c.finalize()
corrdata = c.result()
corr = zeros((corrdata.shape[0], 2))
corr[:, 0] = corrdata[:, 0]
corr[:, 1] = (corrdata[:, 2] + corrdata[:, 3] + corrdata[:, 4]) / 3
savetxt(outdir + "/msd_nom" + str(mpc) + ".dat", corr)
with open(outdir + "/rh_out.dat", "a") as datafile:
rh = system.analysis.calc_rh(chain_start=0,
number_of_chains=1,
chain_length=mpc - 1)
datafile.write(str(mpc) + " " + str(rh[0]) + "\n")
pos = electrokinetics.Species(
density=0.05, D=0.1, valency=1, ext_force_density=[0, 0, 1.])
neg = electrokinetics.Species(
density=0.05, D=0.1, valency=-1, ext_force_density=[0, 0, -1.])
ek.add_species(pos)
ek.add_species(neg)
system.actors.add(ek)
print(ek.get_params())
print(pos.get_params())
print(neg.get_params())
print(pos[5, 5, 5].density)
ek_wall_left = ekboundaries.EKBoundary(
shape=shapes.Wall(dist=1, normal=[1, 0, 0]), charge_density=-0.01)
ek_wall_right = ekboundaries.EKBoundary(
shape=shapes.Wall(dist=-9, normal=[-1, 0, 0]), charge_density=0.01)
system.ekboundaries.add(ek_wall_left)
system.ekboundaries.add(ek_wall_right)
if not os.path.isdir("ek"):
os.makedirs("ek")
n_int_cycles = 1000
for i in range(n_int_cycles):
system.integrator.run(100)
print("\rIntegrating: %03i" % i, end='', flush=True)
# Particle types
#===========================
type_counter = 0
type_mono = type_counter
type_counter+=1
type_wall = type_counter
system.non_bonded_inter[type_mono, type_mono].lennard_jones.set_params( epsilon=1.0, sigma=1.0, cutoff=2.**(1.0 / 6.0), shift="auto")
system.non_bonded_inter[type_mono, type_wall].lennard_jones.set_params( epsilon=1.0, sigma=1.0, cutoff=2.**(1.0 / 6.0), shift="auto")
#===========================
# define the particle constraints (two walls)
#===========================
left_constr=system.constraints.add(particle_type=type_wall, penetrable=1, only_positive=0, shape=shapes.Wall(normal=[1,0,0], dist=1.12))
right_constr=system.constraints.add(particle_type=type_wall, penetrable=1, only_positive=0, shape=shapes.Wall(normal=[-1,0,0], dist=-(box_l-0.5)))
for p in range(0,n_mono):
system.part.add(id=p, pos=(np.random.random(3) * system.box_l*0.5)+(box_l*0.25,0,0), type=type_mono )
cap=1
system.non_bonded_inter.set_force_cap(cap)
print( "Warming up... ",)
dist=system.analysis.mindist(p1=[type_mono], p2=[type_mono])
for t in range(4000):
print( "Warming step: {} min_dist={} cap={}\r".format(t, dist, cap))
system.integrator.run(200)
dist=system.analysis.mindist(p1=[type_mono], p2=[type_mono])
cap = cap + 1.
