def test(self):
system = self.es
pi = math.pi
box_z = 4
box_y = 4
width = 32
padding = 6
box_x = width + 2 * padding
# Set the electrokinetic parameters
agrid = 0.5
dt = 1.0 / 5.0
force = 0.13
sigma = -0.03
viscosity_kinematic = 1.0
friction = 1.0
temperature = 2.3
bjerrum_length = 0.7
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 = 1500
# 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 = espressomd.electrokinetics.Electrokinetics(
agrid=agrid,
lb_density=density_water,
viscosity=viscosity_kinematic,
friction=friction,
T=temperature,
prefactor=bjerrum_length * temperature,
stencil="nonlinear")
counterions = espressomd.electrokinetics.Species(
density=density_counterions,
D=0.3,
valency=valency,
ext_force_density=[0, force, 0])
ek.add_species(counterions)
# Set up the walls confining the fluid and carrying charge
ek_wall1 = espressomd.ekboundaries.EKBoundary(
charge_density=sigma / (padding),
shape=espressomd.shapes.Wall(normal=[1, 0, 0], dist=padding))
system.ekboundaries.add(ek_wall1)
ek_wall2 = espressomd.ekboundaries.EKBoundary(
charge_density=sigma / (padding),
shape=espressomd.shapes.Wall(normal=[-1, 0, 0],
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 = ek_common.solve(pnt0, width, bjerrum_length, sigma, valency)
val1 = ek_common.solve(pnt1, width, bjerrum_length, sigma, valency)
valm = ek_common.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
for i in range(int(box_x / agrid)):
if (i * agrid >= padding and i * agrid < box_x - padding):
xvalue = i * agrid - padding
position = i * agrid - padding - width / 2.0 + agrid / 2.0
# density
measured_density = counterions[i,
int(box_y / (2 * agrid)),
int(box_z /
(2 * agrid))].density
calculated_density = ek_common.density(position, xi,
bjerrum_length)
density_difference = abs(measured_density - calculated_density)
total_density_difference = total_density_difference + \
density_difference
# velocity
measured_velocity = ek[i,
int(box_y / (2 * agrid)),
int(box_z / (2 * agrid))].velocity[1]
calculated_velocity = ek_common.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[i,
int(box_y / (2 * agrid)),
int(box_z /
(2 * agrid))].pressure[(0, 0)]
calculated_pressure_xx = ek_common.hydrostatic_pressure_non_lin(
ek, position, xi, bjerrum_length, (0, 0), box_x, box_y,
box_z, agrid, temperature)
measured_pressure_yy = ek[i,
int(box_y / (2 * agrid)),
int(box_z /
(2 * agrid))].pressure[(1, 1)]
calculated_pressure_yy = ek_common.hydrostatic_pressure_non_lin(
ek, position, xi, bjerrum_length, (1, 1), box_x, box_y,
box_z, agrid, temperature)
measured_pressure_zz = ek[i,
int(box_y / (2 * agrid)),
int(box_z /
(2 * agrid))].pressure[(2, 2)]
calculated_pressure_zz = ek_common.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[i,
int(box_y / (2 * agrid)),
int(box_z /
(2 * agrid))].pressure[(0, 1)]
calculated_pressure_xy = ek_common.pressure_tensor_offdiagonal(
position, xi, bjerrum_length, force)
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[i,
int(box_y / (2 * agrid)),
int(box_z /
(2 * agrid))].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[i,
int(box_y / (2 * agrid)),
int(box_z /
(2 * agrid))].pressure[(0, 2)]
calculated_pressure_xz = 0.0
pressure_difference_xz = abs(measured_pressure_xz -
calculated_pressure_xz)
total_pressure_difference_xz = total_pressure_difference_xz + \
pressure_difference_xz
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
self.assertLess(total_density_difference, 1.0e-04,
"Density accuracy not achieved")
self.assertLess(total_velocity_difference, 1.0e-04,
"Velocity accuracy not achieved")
self.assertLess(total_pressure_difference_xx, 1.0e-04,
"Pressure accuracy xx component not achieved")
self.assertLess(total_pressure_difference_yy, 1.0e-04,
"Pressure accuracy yy component not achieved")
self.assertLess(total_pressure_difference_zz, 1.0e-04,
"Pressure accuracy zz component not achieved")
self.assertLess(total_pressure_difference_xy, 1.0e-04,
"Pressure accuracy xy component not achieved")
self.assertLess(total_pressure_difference_yz, 1.0e-04,
"Pressure accuracy yz component not achieved")
self.assertLess(total_pressure_difference_xz, 1.0e-04,
"Pressure accuracy xz component not achieved")
def run_test(self, params):
system = self.system
system.box_l = [params['box_x'], params['box_y'], params['box_z']]
system.time_step = params_base['dt']
system.thermostat.turn_off()
system.cell_system.skin = 0.1
system.thermostat.turn_off()
# Set up the (LB) electrokinetics fluid
ek = espressomd.electrokinetics.Electrokinetics(
agrid=params_base['agrid'],
lb_density=params_base['density_water'],
viscosity=params_base['viscosity_kinematic'],
friction=params_base['friction'],
T=params_base['temperature'],
prefactor=params_base['bjerrum_length'] *
params_base['temperature'],
stencil="linkcentered")
counterions = espressomd.electrokinetics.Species(
density=params_base['density_counterions'],
D=0.3,
valency=params_base['valency'],
ext_force_density=params['ext_force_density'])
ek.add_species(counterions)
# Set up the walls confining the fluid and carrying charge
ek_wall1 = espressomd.ekboundaries.EKBoundary(
charge_density=params_base['sigma'] /
params_base['padding'],
shape=espressomd.shapes.Wall(
normal=params['wall_normal_1'],
dist=params_base['padding']))
ek_wall2 = espressomd.ekboundaries.EKBoundary(
charge_density=params_base['sigma'] /
params_base['padding'],
shape=espressomd.shapes.Wall(
normal=params['wall_normal_2'],
dist=-(params_base['padding'] + params_base['width'])))
system.ekboundaries.add(ek_wall1)
system.ekboundaries.add(ek_wall2)
system.actors.add(ek)
# Integrate the system
system.integrator.run(params_base['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
for i in range(
int(system.box_l[params['non_periodic_dir']] / params_base['agrid'])):
if (i *
params_base['agrid'] >= params_base['padding'] and i *
params_base['agrid'] < system.box_l[params['non_periodic_dir']] -
params_base['padding']):
position = i * params_base['agrid'] - params_base['padding'] - \
params_base['width'] / 2.0 + params_base['agrid'] / 2.0
# density
index = np.array([int(system.box_l[params['periodic_dirs'][0]] /
(2 * params_base['agrid'])),
int(system.box_l[params['periodic_dirs'][1]] /
(2 * params_base['agrid'])), i])
index = np.roll(index, params['n_roll_index'])
measured_density = counterions[index].density
calculated_density = ek_common.density(
position, self.xi, params_base['bjerrum_length'])
density_difference = abs(measured_density - calculated_density)
total_density_difference += density_difference
# velocity
measured_velocity = ek[index].velocity[int(
np.nonzero(params['ext_force_density'])[0])]
calculated_velocity = ek_common.velocity(
position,
self.xi,
params_base['width'],
params_base['bjerrum_length'],
params_base['force'],
params_base['viscosity_kinematic'],
params_base['density_water'])
velocity_difference = abs(
measured_velocity - calculated_velocity)
total_velocity_difference = total_velocity_difference + \
velocity_difference
# diagonal pressure tensor
measured_pressure_xx = ek[index].pressure[(0, 0)]
calculated_pressure_xx = ek_common.hydrostatic_pressure(
ek,
(0, 0),
system.box_l[params['periodic_dirs'][0]],
system.box_l[params['periodic_dirs'][1]],
params['box_z'],
params_base['agrid'])
measured_pressure_yy = ek[index].pressure[(1, 1)]
calculated_pressure_yy = ek_common.hydrostatic_pressure(
ek,
(1, 1),
system.box_l[params['periodic_dirs'][0]],
system.box_l[params['periodic_dirs'][1]],
params['box_z'],
params_base['agrid'])
measured_pressure_zz = ek[index].pressure[(2, 2)]
calculated_pressure_zz = ek_common.hydrostatic_pressure(
ek,
(2, 2),
system.box_l[params['periodic_dirs'][0]],
system.box_l[params['periodic_dirs'][1]],
params['box_z'],
params_base['agrid'])
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
calculated_pressure_offdiagonal = ek_common.pressure_tensor_offdiagonal(
position, self.xi, params_base['bjerrum_length'], params_base['force'])
# xy component pressure tensor
measured_pressure_xy = ek[index].pressure[(0, 1)]
calculated_pressure_xy = 0.0
if 'calculated_pressure_xy' not in params:
calculated_pressure_xy = calculated_pressure_offdiagonal
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[index].pressure[(1, 2)]
calculated_pressure_yz = 0.0
if 'calculated_pressure_yz' not in params:
calculated_pressure_yz = calculated_pressure_offdiagonal
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[index].pressure[(0, 2)]
calculated_pressure_xz = 0.0
if 'calculated_pressure_xz' not in params:
calculated_pressure_xz = calculated_pressure_offdiagonal
pressure_difference_xz = abs(
measured_pressure_xz - calculated_pressure_xz)
total_pressure_difference_xz = total_pressure_difference_xz + \
pressure_difference_xz
scale_factor = params_base['agrid'] / params_base['width']
total_density_difference *= scale_factor
total_velocity_difference *= scale_factor
total_pressure_difference_xx *= scale_factor
total_pressure_difference_yy *= scale_factor
total_pressure_difference_zz *= scale_factor
total_pressure_difference_xy *= scale_factor
total_pressure_difference_yz *= scale_factor
total_pressure_difference_xz *= scale_factor
self.assertLess(total_density_difference, 1.0e-04,
"Density accuracy not achieved")
self.assertLess(total_velocity_difference, 1.0e-04,
"Velocity accuracy not achieved")
self.assertLess(total_pressure_difference_xx, 1.0e-04,
"Pressure accuracy xx component not achieved")
self.assertLess(total_pressure_difference_yy, 1.0e-04,
"Pressure accuracy yy component not achieved")
self.assertLess(total_pressure_difference_zz, 1.0e-04,
"Pressure accuracy zz component not achieved")
self.assertLess(total_pressure_difference_xy, 1.0e-04,
"Pressure accuracy xy component not achieved")
self.assertLess(total_pressure_difference_yz, 1.0e-04,
"Pressure accuracy yz component not achieved")
self.assertLess(total_pressure_difference_xz, 1.0e-04,
"Pressure accuracy xz component not achieved")
def test(self):
# 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
system = self.system
ek = self.ek
counterions = self.counterions
for i in range(
int(system.box_l[params['non_periodic_dir']] / params_base['agrid'])):
if (i *
params_base['agrid'] >= params_base['padding'] and i *
params_base['agrid'] < system.box_l[params['non_periodic_dir']] -
params_base['padding']):
position = i * params_base['agrid'] - params_base['padding'] - \
params_base['width'] / 2.0 + params_base['agrid'] / 2.0
# density
index = np.array([int(system.box_l[params['periodic_dirs'][0]] /
(2 * params_base['agrid'])),
int(system.box_l[params['periodic_dirs'][1]] /
(2 * params_base['agrid'])), i])
index = np.roll(index, params['n_roll_index'])
measured_density = counterions[index].density
calculated_density = ek_common.density(
position, self.xi, params_base['bjerrum_length'])
density_difference = abs(measured_density - calculated_density)
total_density_difference += density_difference
# velocity
measured_velocity = ek[index].velocity[int(
np.nonzero(params['ext_force_density'])[0])]
calculated_velocity = ek_common.velocity(
position,
self.xi,
params_base['width'],
params_base['bjerrum_length'],
params_base['force'],
params_base['viscosity_kinematic'],
params_base['density_water'])
velocity_difference = abs(
measured_velocity - calculated_velocity)
total_velocity_difference = total_velocity_difference + \
velocity_difference
# diagonal pressure tensor
measured_pressure_xx = ek[index].pressure_tensor[(0, 0)]
calculated_pressure_xx = ek_common.hydrostatic_pressure(
ek,
(0, 0),
system.box_l[params['periodic_dirs'][0]],
system.box_l[params['periodic_dirs'][1]],
params['box_z'],
params_base['agrid'])
measured_pressure_yy = ek[index].pressure_tensor[(1, 1)]
calculated_pressure_yy = ek_common.hydrostatic_pressure(
ek,
(1, 1),
system.box_l[params['periodic_dirs'][0]],
system.box_l[params['periodic_dirs'][1]],
params['box_z'],
params_base['agrid'])
measured_pressure_zz = ek[index].pressure_tensor[(2, 2)]
calculated_pressure_zz = ek_common.hydrostatic_pressure(
ek,
(2, 2),
system.box_l[params['periodic_dirs'][0]],
system.box_l[params['periodic_dirs'][1]],
params['box_z'],
params_base['agrid'])
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
calculated_pressure_offdiagonal = ek_common.pressure_tensor_offdiagonal(
position, self.xi, params_base['bjerrum_length'], params_base['force'])
# xy component pressure tensor
measured_pressure_xy = ek[index].pressure_tensor[(0, 1)]
calculated_pressure_xy = 0.0
if 'calculated_pressure_xy' not in params:
calculated_pressure_xy = calculated_pressure_offdiagonal
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[index].pressure_tensor[(1, 2)]
calculated_pressure_yz = 0.0
if 'calculated_pressure_yz' not in params:
calculated_pressure_yz = calculated_pressure_offdiagonal
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[index].pressure_tensor[(0, 2)]
calculated_pressure_xz = 0.0
if 'calculated_pressure_xz' not in params:
calculated_pressure_xz = calculated_pressure_offdiagonal
pressure_difference_xz = abs(
measured_pressure_xz - calculated_pressure_xz)
total_pressure_difference_xz = total_pressure_difference_xz + \
pressure_difference_xz
scale_factor = params_base['agrid'] / params_base['width']
total_density_difference *= scale_factor
total_velocity_difference *= scale_factor
total_pressure_difference_xx *= scale_factor
total_pressure_difference_yy *= scale_factor
total_pressure_difference_zz *= scale_factor
total_pressure_difference_xy *= scale_factor
total_pressure_difference_yz *= scale_factor
total_pressure_difference_xz *= scale_factor
self.assertLess(total_density_difference, 1.0e-04,
"Density accuracy not achieved")
self.assertLess(total_velocity_difference, 1.0e-04,
"Velocity accuracy not achieved")
self.assertLess(total_pressure_difference_xx, 1.0e-04,
"Pressure accuracy xx component not achieved")
self.assertLess(total_pressure_difference_yy, 1.0e-04,
"Pressure accuracy yy component not achieved")
self.assertLess(total_pressure_difference_zz, 1.0e-04,
"Pressure accuracy zz component not achieved")
self.assertLess(total_pressure_difference_xy, 1.0e-04,
"Pressure accuracy xy component not achieved")
self.assertLess(total_pressure_difference_yz, 1.0e-04,
"Pressure accuracy yz component not achieved")
self.assertLess(total_pressure_difference_xz, 1.0e-04,
"Pressure accuracy xz component not achieved")
