"""
This sample sets up an electrokinetics (LB) fluid confined between charged walls.
"""
import espressomd
required_features = ["ELECTROKINETICS", "EK_BOUNDARIES", "EXTERNAL_FORCES"]
espressomd.assert_features(required_features)
from espressomd import System, shapes, electrokinetics
import sys
system = System(box_l=[10, 10, 10])
system.set_random_state_PRNG()
#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
system.cell_system.skin = 0.4
system.time_step = 0.1
ek = electrokinetics.Electrokinetics(lb_density=1,
friction=1,
agrid=1,
viscosity=1,
T=1,
prefactor=1)
pos = electrokinetics.Species(density=0.05,
D=0.1,
valency=1,
ext_force_density=[0, 0, 1.])
neg = electrokinetics.Species(density=0.05,
print("""
Start warmup integration:
At maximum {} times {} steps
Stop if minimal distance is larger than {}
""".strip().format(warm_n_times, warm_steps, min_dist))
# set LJ cap
lj_cap = 20
es.nonBondedInter.setForceCap(lj_cap)
print(es.nonBondedInter[0,0].lennardJones)
# Warmup Integration Loop
i = 0
while (i < warm_n_times and act_min_dist < min_dist):
es.integrate(warm_steps)
# Warmup criterion
# act_min_dist = float(es._espressoHandle.Tcl_Eval('analyze mindist'))
act_min_dist = es.analyze.mindist()
# print("\rrun %d at time=%f (LJ cap=%f) min dist = %f\r" % (i,es.glob.time,lj_cap,act_min_dist), end=' ')
i += 1
# write observables
# puts $obs_file "{ time [setmd time] } [analyze energy]"
# Increase LJ cap
lj_cap = lj_cap + 10
es.nonBondedInter.setForceCap(lj_cap)
# Just to see what else we may get from the c code
print("""
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")
class SwimmerTest():
system = System(box_l=3 * [6])
system.cell_system.skin = 1
system.time_step = 1e-2
LB_params = {'agrid': 1,
'dens': 1.1,
'visc': 1.2,
'kT': 0,
'tau': system.time_step}
gamma = 0.3
lbf = None
def add_all_types_of_swimmers(
self,
fix=False,
rotation=False,
put_in_corners=True):
"""Places all combinations of pusher/puller and f_swim/v_swim
in a box, either in the corners or around the center
"""
system = self.system
plus_x = np.sqrt([.5, 0, .5, 0])
plus_y = np.sqrt([0, 0, .5, .5])
plus_z = np.sqrt([.5, 0, 0, .5])
minus_y = np.sqrt([.5, .5, 0, 0])
pos0 = [2, 0.01, 3] if put_in_corners else [2, 3, 2.5]
pos1 = [5.99, 2, 3] if put_in_corners else [3.1, 2.1, 2.2]
pos2 = [2, 3, 5.99] if put_in_corners else [2.9, 2.5, 3]
pos3 = [1.5, 5.99, 1] if put_in_corners else [2, 2, 2.5]
system.part.add(pos=pos0, quat=minus_y, fix=3 * [fix],
mass=0.9, rinertia=3 * [7], rotation=3 * [rotation],
swimming={"mode": "pusher", "f_swim": 0.10,
"dipole_length": 0.5, "rotational_friction": 0.3})
system.part.add(pos=pos1, quat=plus_x, fix=3 * [fix],
mass=1.9, rinertia=3 * [8], rotation=3 * [rotation],
swimming={"mode": "pusher", "v_swim": 0.02,
"dipole_length": 0.6, "rotational_friction": 0.4})
system.part.add(pos=pos2, quat=plus_z, fix=3 * [fix],
mass=2.9, rinertia=3 * [9], rotation=3 * [rotation],
swimming={"mode": "puller", "f_swim": 0.08,
"dipole_length": 0.7, "rotational_friction": 0.8})
system.part.add(pos=pos3, quat=plus_y, fix=3 * [fix],
mass=3.9, rinertia=3 * [10], rotation=3 * [rotation],
swimming={"mode": "puller", "v_swim": 0.05,
"dipole_length": 0.8, "rotational_friction": 0.3})
def tearDown(self):
self.system.part.clear()
self.system.actors.clear()
self.system.lbboundaries.clear()
self.system.thermostat.turn_off()
self.lbf = None
def test_conflicting_parameters(self):
"""v_swim and f_swim can't be set at the same time
"""
swimmer = self.system.part.add(pos=[3] * 3)
with self.assertRaises(Exception):
swimmer.swimming = {"v_swim": 0.3, "f_swim": 0.6}
def test_momentum_conservation(self):
"""friction as well as 'active' forces apply to particles
and to the fluid, so total momentum is conserved
"""
self.add_all_types_of_swimmers(rotation=False)
self.system.integrator.run(20, reuse_forces=True)
tot_mom = self.system.analysis.linear_momentum(include_particles=True,
include_lbfluid=True)
np.testing.assert_allclose(tot_mom, 3 * [0.], atol=self.tol)
def test_particle_forces(self):
"""run through all swimmers to check expected forces
"""
self.add_all_types_of_swimmers(rotation=False)
self.system.integrator.run(10)
for swimmer in self.system.part:
f_swim = swimmer.swimming['f_swim']
v_swim = swimmer.swimming['v_swim']
director = swimmer.director
#due to dt/2 time-shift between force calculation and LB-update,
#v_swimmer has to be calculated at the half step
v_swimmer = swimmer.v + \
0.5 * self.system.time_step * swimmer.f / swimmer.mass
#for friction coupling, the old fluid at the new position is used
v_fluid = self.lbf.get_interpolated_velocity(
swimmer.pos + self.system.time_step * v_swimmer)
force = -self.gamma * (v_swimmer - v_fluid) + \
f_swim * director + self.gamma * v_swim * director
self.system.integrator.run(1, reuse_forces=True)
np.testing.assert_allclose(swimmer.f, force, atol=self.tol)
def check_fluid_force(self, swimmer):
pass
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
Visualization sample for Poiseuille flow with Lattice Boltzmann.
"""
from espressomd import System, lb, shapes, lbboundaries
import numpy as np
from threading import Thread
import espressomd.visualization_opengl
required_features = ["LB_BOUNDARIES", "EXTERNAL_FORCES"]
espressomd.assert_features(required_features)
# System setup
box_l = 16
system = System(box_l=[box_l] * 3)
system.set_random_state_PRNG()
np.random.seed(seed=system.seed)
system.time_step = 0.01
system.cell_system.skin = 0.2
visualizer = espressomd.visualization_opengl.openGLLive(
system,
LB_draw_boundaries=True,
LB_draw_velocity_plane=True,
LB_plane_dist=8,
LB_plane_axis=1,
LB_vel_scale=1e2,
LB_plane_ngrid=15,
camera_position=[8, 16, 50],
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
Set up an electrokinetics (LB) fluid confined between charged walls.
"""
import espressomd
required_features = ["ELECTROKINETICS", "EK_BOUNDARIES", "EXTERNAL_FORCES"]
espressomd.assert_features(required_features)
from espressomd import System, shapes, electrokinetics, ekboundaries
import os
system = System(box_l=[10, 10, 10])
system.cell_system.skin = 0.4
system.time_step = 0.1
ek = electrokinetics.Electrokinetics(
lb_density=1, friction=1, agrid=1, viscosity=1, T=1, prefactor=1)
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)
class DiamondPolymer(ut.TestCase):
"""
Test the functionality of espressomd.polymer.setup_diamond_polymer()
in terms of
* properties of particles created
* connections via bonds
* the geometry of the polymer network
"""
system = System(box_l=3 * [16])
diamond_params = {
'MPC': 15,
'dist_cM': 3,
'val_cM': -1.3,
'val_nodes': 0.6,
'start_id': 3,
'no_bonds': False,
'type_nodes': 2,
'type_nM': 5,
'type_cM': 7
}
bond_length = system.box_l[0] * \
(0.25 * np.sqrt(3)) / (diamond_params['MPC'] + 1)
def setUp(self):
bond = interactions.HarmonicBond(k=1.5, r_0=self.bond_length, r_cut=3)
self.system.bonded_inter.add(bond)
polymer.setup_diamond_polymer(system=self.system,
bond=bond,
**self.diamond_params)
self.system.time_step = 0.1
self.node_parts = self.system.part.select(
type=self.diamond_params['type_nodes'])
self.charged_mono = self.system.part.select(
type=self.diamond_params['type_cM'])
self.noncharged_mono = self.system.part.select(
type=self.diamond_params['type_nM'])
def tearDown(self):
self.system.part.clear()
@utx.skipIfMissingFeatures(["ELECTROSTATICS"])
def test_particle_properties(self):
"""
checks if the particles created have the right type and charge
"""
# number of particles created
number_non_node = 16 * self.diamond_params['MPC']
self.assertEqual(len(self.system.part), number_non_node + 8)
# number of each type
self.assertEqual(len(self.node_parts), 8)
self.assertEqual(
len(self.charged_mono),
np.rint(number_non_node / self.diamond_params['dist_cM']))
self.assertEqual(
len(self.noncharged_mono),
np.rint(number_non_node *
(1 - 1 / self.diamond_params['dist_cM'])))
# charge
np.testing.assert_allclose(
self.node_parts.q,
len(self.node_parts) * [self.diamond_params['val_nodes']])
np.testing.assert_allclose(self.noncharged_mono.q,
len(self.noncharged_mono) * [0])
np.testing.assert_allclose(
self.charged_mono.q,
len(self.charged_mono) * [self.diamond_params['val_cM']])
# particle id
self.assertGreaterEqual(min(self.system.part[:].id),
self.diamond_params['start_id'])
def test_bonds(self):
"""
test that the right number of bonds is formed on each particle
"""
# 4 bonds on nodes
for part in self.node_parts:
self.assertEqual(len(part.bonds), 4)
# 1 or 0 bonds on chain monomers
n_bonds = [
len(bonds)
for bonds in self.noncharged_mono.bonds + self.charged_mono.bonds
]
self.assertLessEqual(np.max(n_bonds), 1)
# total number of bonds
number_non_node = 16 * self.diamond_params['MPC']
self.assertEqual(np.sum(n_bonds), number_non_node - 16)
@utx.skipIfMissingFeatures(["EXTERNAL_FORCES"])
def test_connected(self):
"""
test that all particles in the polymer are connected by pushing one particle
"""
self.system.part[self.diamond_params['start_id']].ext_force = 3 * [2]
self.system.integrator.run(200)
vels = np.linalg.norm(self.system.part[:].v, axis=1)
self.assertGreater(np.min(vels), 1e-6)
def test_geometry(self):
"""
check if the distance between all monomers is correct,
only nearest neighbouring nodes are connected
and that the nodes have the right position
"""
# Energy calculation checks distance indirectly through
# position of minimum of HarmonicBond
# With formula for self.bond_length this also ensures
# that only nearest neighbours can be reached
E = self.system.analysis.energy()['total']
self.assertAlmostEqual(E, 0., delta=1e-13)
node_pos_scaled = np.array(self.node_parts.pos) / self.system.box_l[0]
node_pos_shouldbe = 0.25 * np.array([[0, 0, 0], [1, 1, 1], [2, 2, 0],
[0, 2, 2], [2, 0, 2], [3, 3, 1],
[1, 3, 3], [3, 1, 3]])
for pos1, pos2 in zip(node_pos_scaled, node_pos_shouldbe):
np.testing.assert_allclose(pos1, pos2)
"""
This sample simulates planar Poiseuille flow in Espresso. A spherical RBC-like
particle is added and advected with and without volume conservation.
"""
import espressomd
required_features = ["LB_BOUNDARIES", "VIRTUAL_SITES_INERTIALESS_TRACERS"]
espressomd.assert_features(required_features)
from espressomd import System, lb, shapes, lbboundaries
import numpy as np
from espressomd.virtual_sites import VirtualSitesInertialessTracers
# System setup
boxZ = 20
system = System(box_l=(20, 20, boxZ))
system.time_step = 1 / 6.
system.cell_system.skin = 0.1
system.virtual_sites = VirtualSitesInertialessTracers()
print("Parallelization: " + str(system.cell_system.node_grid))
force = 0.001
from addSoft import AddSoft
k1 = 0.1
k2 = 1
AddSoft(system, 10, 10, 10, k1, k2)
## case without bending and volCons
#outputDir = "outputPure"
## case with bending
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
Visualize the Poiseuille flow in a lattice-Boltzmann fluid with an
external force applied.
"""
from espressomd import System, lb, shapes, lbboundaries
import numpy as np
import espressomd.visualization_opengl
required_features = ["LB_BOUNDARIES", "EXTERNAL_FORCES"]
espressomd.assert_features(required_features)
# System setup
box_l = 16
system = System(box_l=[box_l] * 3)
np.random.seed(seed=42)
system.time_step = 0.01
system.cell_system.skin = 0.2
visualizer = espressomd.visualization_opengl.openGLLive(
system,
LB_draw_boundaries=True,
LB_draw_velocity_plane=True,
LB_plane_dist=8,
LB_plane_axis=1,
LB_vel_scale=1e2,
LB_plane_ngrid=15,
camera_position=[8, 16, 50],
velocity_arrows=True,
# Setup constant
time_step = 0.01
loops = 20
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
monomer_mass = 0.01
# System setup
box_l = 32.0
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
print("The number of monomers")
mpc = float(input()) # The number of monomers has been set to be 20 as default
# Change this value for further simulations
# Lennard-Jones interaction
#system.non_bonded_inter[0,0].lennard_jones.set_params(
# epsilon=0.01, sigma=1.0,
# shift="auto", cutoff=2.0**(1.0/6.0))
# Fene interaction
fene = interactions.FeneBond(k=0.4, d_r_max=0.3)
os.makedirs(outdir)
# Setup constant
time_step = 0.01
loops = 50
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
monomer_mass = 0.01
# System setup
system = System(box_l=[32.0, 32.0, 32.0])
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,